<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with MathML3 v1.3 20210610//EN"  "JATS-archivearticle1-3-mathml3.dtd"><article xmlns:ali="http://www.niso.org/schemas/ali/1.0/" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article" dtd-version="1.3"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic" pub-type="epub">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">105264</article-id><article-id pub-id-type="doi">10.7554/eLife.105264</article-id><article-id pub-id-type="doi" specific-use="version">10.7554/eLife.105264.3</article-id><article-version article-version-type="publication-state">version of record</article-version><article-categories><subj-group subj-group-type="display-channel"><subject>Research Article</subject></subj-group><subj-group subj-group-type="heading"><subject>Cell Biology</subject></subj-group></article-categories><title-group><article-title>A Commander-independent function of COMMD3 in endosomal trafficking</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Squiers</surname><given-names>Galen T</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Wan</surname><given-names>Chun</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Gorder</surname><given-names>James</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author"><name><surname>Puscher</surname><given-names>Harrison</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="fn" rid="pa1">†</xref><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Shen</surname><given-names>Jingshi</given-names></name><contrib-id authenticated="true" contrib-id-type="orcid">https://orcid.org/0000-0001-9595-1148</contrib-id><email>jingshi.shen@colorado.edu</email><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="other" rid="fund1"/><xref ref-type="other" rid="fund2"/><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/></contrib><aff id="aff1"><label>1</label><institution-wrap><institution-id institution-id-type="ror">https://ror.org/02ttsq026</institution-id><institution>Department of Molecular, Cellular and Developmental Biology, University of Colorado</institution></institution-wrap><addr-line><named-content content-type="city">Boulder</named-content></addr-line><country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Yu</surname><given-names>Li</given-names></name><role>Reviewing Editor</role><aff><institution-wrap><institution-id institution-id-type="ror">https://ror.org/03cve4549</institution-id><institution>Tsinghua University</institution></institution-wrap><country>China</country></aff></contrib><contrib contrib-type="senior_editor"><name><surname>Dötsch</surname><given-names>Volker</given-names></name><role>Senior Editor</role><aff><institution-wrap><institution-id institution-id-type="ror">https://ror.org/04cvxnb49</institution-id><institution>Goethe University Frankfurt</institution></institution-wrap><country>Germany</country></aff></contrib></contrib-group><author-notes><fn fn-type="present-address" id="pa1"><label>†</label><p>Department of Biological Sciences, University of Southern California, Los Angeles, United States</p></fn></author-notes><pub-date publication-format="electronic" date-type="publication"><day>21</day><month>08</month><year>2025</year></pub-date><volume>14</volume><elocation-id>RP105264</elocation-id><history><date date-type="sent-for-review" iso-8601-date="2024-12-10"><day>10</day><month>12</month><year>2024</year></date></history><pub-history><event><event-desc>This manuscript was published as a preprint.</event-desc><date date-type="preprint" iso-8601-date="2024-12-17"><day>17</day><month>12</month><year>2024</year></date><self-uri content-type="preprint" xlink:href="https://doi.org/10.1101/2024.12.12.628173"/></event><event><event-desc>This manuscript was published as a reviewed preprint.</event-desc><date date-type="reviewed-preprint" iso-8601-date="2025-02-17"><day>17</day><month>02</month><year>2025</year></date><self-uri content-type="reviewed-preprint" xlink:href="https://doi.org/10.7554/eLife.105264.1"/></event><event><event-desc>The reviewed preprint was revised.</event-desc><date date-type="reviewed-preprint" iso-8601-date="2025-06-06"><day>06</day><month>06</month><year>2025</year></date><self-uri content-type="reviewed-preprint" xlink:href="https://doi.org/10.7554/eLife.105264.2"/></event></pub-history><permissions><copyright-statement>© 2025, Squiers et al</copyright-statement><copyright-year>2025</copyright-year><copyright-holder>Squiers et al</copyright-holder><ali:free_to_read/><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><ali:license_ref>http://creativecommons.org/licenses/by/4.0/</ali:license_ref><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife-105264-v1.pdf"/><self-uri content-type="figures-pdf" xlink:href="elife-105264-figures-v1.pdf"/><abstract><p>Endosomal recycling is a branch of intracellular membrane trafficking that retrieves endocytosed cargo proteins from early and late endosomes to prevent their degradation in lysosomes. A key player in endosomal recycling is the Commander complex, a 16-subunit protein assembly that cooperates with other endosomal factors to recruit cargo proteins and facilitate the formation of tubulo-vesicular carriers. While the crucial role of Commander in endosomal recycling is well established, its molecular mechanism remains poorly understood. Here, we genetically dissected the Commander complex using unbiased genetic screens and comparative targeted mutations. Unexpectedly, our findings revealed a Commander-independent function for COMMD3, a subunit of the Commander complex, in endosomal recycling. COMMD3 regulates a subset of cargo proteins independently of the other Commander subunits. The Commander-independent function of COMMD3 is mediated by its N-terminal domain (NTD), which binds and stabilizes ADP-ribosylation factor 1 (ARF1), a small GTPase regulating endosomal recycling. Mutations disrupting the COMMD3-ARF1 interaction diminish ARF1 expression and impair COMMD3-dependent cargo recycling. These data provide direct evidence that Commander subunits can function outside the holo-complex and raise the intriguing possibility that components of other membrane trafficking complexes may also possess functions beyond their respective complexes.</p></abstract><kwd-group kwd-group-type="author-keywords"><kwd>endosomal recycling</kwd><kwd>membrane trafficking</kwd><kwd>vesicle budding</kwd><kwd>Commander</kwd><kwd>COMMD3</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd>None</kwd></kwd-group><funding-group><award-group id="fund1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health</institution></institution-wrap></funding-source><award-id>GM126960</award-id><principal-award-recipient><name><surname>Shen</surname><given-names>Jingshi</given-names></name></principal-award-recipient></award-group><award-group id="fund2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000002</institution-id><institution>National Institutes of Health</institution></institution-wrap></funding-source><award-id>DK124431</award-id><principal-award-recipient><name><surname>Shen</surname><given-names>Jingshi</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>COMMD3 regulates endosomal trafficking outside the Commander holo-complex, revealing that a trafficking complex subunit can function independently of the entire complex.</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>publishing-route</meta-name><meta-value>prc</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>Proteins embedded in the plasma membrane transduce signals, import nutrients, and sense physical changes, enabling cells to respond to external cues (<xref ref-type="bibr" rid="bib10">Bonifacino and Glick, 2004</xref>; <xref ref-type="bibr" rid="bib58">Rothman, 2014</xref>; <xref ref-type="bibr" rid="bib60">Schekman and Novick, 2004</xref>). The cell has evolved complex and interconnected mechanisms to maintain membrane protein levels on the cell surface and to adjust these levels in response to stimuli (<xref ref-type="bibr" rid="bib10">Bonifacino and Glick, 2004</xref>; <xref ref-type="bibr" rid="bib7">Bausch-Fluck et al., 2018</xref>). Disruption of membrane protein homeostasis underlies many human diseases, including cancer, metabolic disorders, and neurodegeneration (<xref ref-type="bibr" rid="bib17">Dell’Angelica and Bonifacino, 2019</xref>; <xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>). Surface levels of a membrane protein are established through exocytosis, a vesicle fusion event, and internalization via endocytosis, a vesicle budding process (<xref ref-type="bibr" rid="bib10">Bonifacino and Glick, 2004</xref>; <xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>; <xref ref-type="bibr" rid="bib25">Gulbranson et al., 2019</xref>). In addition to exocytosis and endocytosis, another branch of intracellular membrane trafficking – endosomal recycling – also plays a crucial role in maintaining surface protein homeostasis (<xref ref-type="bibr" rid="bib63">Simonetti and Cullen, 2019</xref>; <xref ref-type="bibr" rid="bib14">Cullen and Steinberg, 2018</xref>; <xref ref-type="bibr" rid="bib76">Yong et al., 2023</xref>; <xref ref-type="bibr" rid="bib70">Wang et al., 2018</xref>; <xref ref-type="bibr" rid="bib3">Ambrosio et al., 2022</xref>). Following endocytosis, endocytic vesicles fuse into early endosomes, which then progress into late endosomes (<xref ref-type="bibr" rid="bib14">Cullen and Steinberg, 2018</xref>; <xref ref-type="bibr" rid="bib72">Weeratunga et al., 2020</xref>). Within these endosomes, the cell determines which cargoes proceed to lysosomal degradation and which are rescued from degradation through recycling (<xref ref-type="bibr" rid="bib63">Simonetti and Cullen, 2019</xref>; <xref ref-type="bibr" rid="bib14">Cullen and Steinberg, 2018</xref>; <xref ref-type="bibr" rid="bib76">Yong et al., 2023</xref>; <xref ref-type="bibr" rid="bib70">Wang et al., 2018</xref>). Cargoes retrieved from endosomes are packaged into tubulo-vesicular transport carriers and are either recycled back to the plasma membrane or routed to the <italic>trans</italic>-Golgi network (TGN) for re-entry into the exocytic pathway (<xref ref-type="bibr" rid="bib63">Simonetti and Cullen, 2019</xref>; <xref ref-type="bibr" rid="bib14">Cullen and Steinberg, 2018</xref>; <xref ref-type="bibr" rid="bib76">Yong et al., 2023</xref>; <xref ref-type="bibr" rid="bib70">Wang et al., 2018</xref>).</p><p>Two central players in endosomal retrieval are Retromer and Commander. Retromer, a heterotrimeric complex comprised of VPS35, VPS29, and VPS26, recruits cargo proteins on the endosome and mediates the formation of tubulo-vesicular carriers for retrograde trafficking to the TGN or recycling to the plasma membrane (<xref ref-type="bibr" rid="bib70">Wang et al., 2018</xref>; <xref ref-type="bibr" rid="bib57">Rothman and Stevens, 1986</xref>; <xref ref-type="bibr" rid="bib4">Bankaitis et al., 1986</xref>; <xref ref-type="bibr" rid="bib61">Seaman et al., 1998</xref>). The Commander complex, which primarily sorts cargoes from endosomal compartments to the plasma membrane, is a large protein complex composed of the Retriever subcomplex and the CCC subcomplex (COMMD-CCDC22-CCDC93) (<xref ref-type="fig" rid="fig1">Figure 1A</xref>; <xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>; <xref ref-type="bibr" rid="bib76">Yong et al., 2023</xref>; <xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>; <xref ref-type="bibr" rid="bib35">Leneva and Kovtun, 2024</xref>; <xref ref-type="bibr" rid="bib41">Mallam and Marcotte, 2017</xref>; <xref ref-type="bibr" rid="bib43">McNally et al., 2017</xref>). The Retriever subcomplex is a heterotrimer consisting of VPS35L/C16ORF62, VPS26C/DSCR3, and VPS29 and shares a similar overall configuration with Retromer (<xref ref-type="bibr" rid="bib43">McNally et al., 2017</xref>). The CCC complex includes 10 COMMD proteins (COMMD1-10), which interact through their conserved C-terminal copper metabolism MURR1 domains (COMMDs) (<xref ref-type="bibr" rid="bib64">Singla et al., 2019</xref>; <xref ref-type="bibr" rid="bib68">van De Sluis et al., 2002</xref>; <xref ref-type="bibr" rid="bib11">Burstein et al., 2005</xref>). The COMMD proteins bind CCDC22 and CCDC93 to form the CCC subcomplex, which also contains DENND10 (<xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib35">Leneva and Kovtun, 2024</xref>). The 13-subunit CCC subcomplex combines with the Retriever subcomplex to form the 16-subunit Commander holo-complex (<xref ref-type="fig" rid="fig1">Figure 1A</xref>; <xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>; <xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>). On the endosome, Retromer and Commander cooperate with other factors such as sorting nexins (SNXs), Rab GTPases, actin, and the actin-remodeling WASH complex to capture cargoes and facilitate the formation of tubulo-vesicular carriers (<xref ref-type="bibr" rid="bib63">Simonetti and Cullen, 2019</xref>; <xref ref-type="bibr" rid="bib76">Yong et al., 2023</xref>; <xref ref-type="bibr" rid="bib35">Leneva and Kovtun, 2024</xref>; <xref ref-type="bibr" rid="bib75">Yong et al., 2021</xref>).</p><fig id="fig1" position="float"><label>Figure 1.</label><caption><title>Genetic analysis of genes encoding Retromer and Commander subunits using unbiased genome-wide CRISPR screens.</title><p>(<bold>A</bold>) Cartoon representation of the Retromer and Commander complexes. (<bold>B</bold>) Table listing genes encoding the subunits of the Retromer and Commander complexes. (<bold>C</bold>) Ranking of genes encoding the Retromer and Commander complexes in an unbiased CRISPR screen that was conducted to identify genes required for the surface homeostasis of GLUT-SPR (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). The GLUT-SPR reporter was constructed by inserting a hemagglutinin (HA) epitope into an exoplasmic loop of the glucose transporter GLUT4, with a GFP tag fused to the intracellular C-terminus of GLUT4 (<xref ref-type="bibr" rid="bib24">Gulbranson et al., 2017</xref>; <xref ref-type="bibr" rid="bib30">Klip et al., 2019</xref>; <xref ref-type="bibr" rid="bib8">Blot and McGraw, 2008</xref>). Surface expression (HA staining) of the reporter was normalized to total reporter expression (GFP fluorescence) as a measure of relative surface levels of the reporter. Each dot represents a gene. The dashed line depicts the <italic>P</italic>-value cutoff at 0.05. (<bold>D</bold>) Essentiality scores of genes encoding the Retromer and Commander complexes were calculated by comparing gRNA abundance in a passage cell population (without any selection) with that in the initial CRISPR library. Genes with essentiality scores below the horizontal cutoff line are predicted to be essential to cell survival or growth. Full datasets of the CRISPR screens are included in a previous report (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>).</p><p><supplementary-material id="fig1sdata1"><label>Figure 1—source data 1.</label><caption><title>CRISPR screen data ranked by significance is shown in <xref ref-type="fig" rid="fig1">Figure 1C</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig1-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig1sdata2"><label>Figure 1—source data 2.</label><caption><title>Gene essentiality scores are shown in <xref ref-type="fig" rid="fig1">Figure 1D</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig1-data2-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig1-v1.tif"/></fig><p>The Commander complex is ubiquitously expressed, and its 16 subunits display a stringent equimolar stoichiometry within the holo-complex (<xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>; <xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>; <xref ref-type="bibr" rid="bib67">Uhlén et al., 2015</xref>), supporting the notion that these subunits function collectively in endosomal recycling. However, Commander subunits exhibit distinct tissue-specific expression patterns and can associate with different sets of proteins (<xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>; <xref ref-type="bibr" rid="bib64">Singla et al., 2019</xref>; <xref ref-type="bibr" rid="bib11">Burstein et al., 2005</xref>; <xref ref-type="bibr" rid="bib78">You et al., 2023</xref>). Furthermore, CCC and Retriever also exist as subcomplexes, whereas COMMD proteins are found in pools of homo- and hetero-oligomers independent of the Commander complex (<xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>; <xref ref-type="bibr" rid="bib64">Singla et al., 2019</xref>; <xref ref-type="bibr" rid="bib27">Healy et al., 2018</xref>). These observations have led to the hypothesis that Commander subunits may have functions beyond their role in the Commander holo-complex (<xref ref-type="bibr" rid="bib62">Shirai et al., 2023</xref>; <xref ref-type="bibr" rid="bib48">Nakai et al., 2019</xref>; <xref ref-type="bibr" rid="bib12">Campion et al., 2018</xref>; <xref ref-type="bibr" rid="bib66">Suraweera et al., 2021</xref>). However, direct evidence for this hypothesis is still lacking.</p><p>In this work, we systematically dissected the Commander complex through unbiased genetic screens and comparative targeted mutations. Interestingly, we discovered that COMMD3, a subunit of the Commander complex, functions in endosomal recycling independently of other Commander subunits, in addition to its Commander-dependent activity. Comparative genetic analyses revealed that COMMD3 regulates a group of cargo proteins that do not require the Commander holo-complex. This Commander-independent function is mediated by the N-terminal domain (NTD) of COMMD3, which binds and stabilizes ADP-ribosylation factor 1 (ARF1). Guided by an AlphaFold-predicted structural model, we introduced point mutations into COMMD3 to disrupt its binding to ARF1. We found that these mutations diminish ARF1 expression and impair the Commander-independent function of COMMD3. Together, these findings uncovered a role of COMMD3 in endosomal trafficking independent of the Commander holo-complex, and suggest that other membrane trafficking complexes may also possess functions beyond their canonical roles within their respective complexes.</p></sec><sec id="s2" sec-type="results"><title>Results</title><sec id="s2-1"><title>Genetic analysis of the Retromer and Commander complexes using unbiased genome-wide CRISPR screens</title><p>Unbiased genome-wide genetic screens are a powerful approach to study the functions of membrane trafficking genes in cultured mammalian cells (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>; <xref ref-type="bibr" rid="bib25">Gulbranson et al., 2019</xref>; <xref ref-type="bibr" rid="bib24">Gulbranson et al., 2017</xref>). Previously, we conducted a genome-wide CRISPR screen to identify new regulators of surface protein homeostasis using a surface protein reporter (GLUT-SPR) based on the glucose transporter GLUT4 (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). Mouse preadipocytes expressing the GLUT-SPR reporter were mutagenized using the genome-wide GeCKO v2 CRISPR library (<xref ref-type="bibr" rid="bib55">Ran et al., 2013</xref>). In the genome-wide CRISPR screen, we used fluorescence-activated cell sorting (FACS) to isolate mutant preadipocytes with reduced surface levels of the GLUT-SPR reporter (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). The screen recovered known regulators of cargo exocytosis and enabled us to identify previously uncharacterized exocytic regulators, including Reps1 and Ralbp1 (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). Importantly, the new exocytic regulators identified in this GLUT-SPR-based CRISPR screen broadly regulate the surface proteostasis of membrane proteins (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>).</p><p>To gain new insights into the molecular functions of Retromer and Commander, we re-analyzed the data from the CRISPR screen to examine genes encoding Retromer and Commander subunits. The CRISPR library used in the screen contained guide RNAs (gRNAs) targeting the genes encoding the subunits of the Retromer and Commander complexes (<xref ref-type="fig" rid="fig1">Figure 1A and B</xref>). The GLUT-SPR-based CRISPR screen isolated <italic>Vps35</italic> and <italic>Vps29</italic> (<xref ref-type="fig" rid="fig1">Figure 1C</xref>), which encode subunits of the Retromer complex, consistent with the critical role of Retromer in the endosomal recycling of GLUT4 (<xref ref-type="bibr" rid="bib24">Gulbranson et al., 2017</xref>; <xref ref-type="bibr" rid="bib52">Pan et al., 2017</xref>). Genes encoding Vps26 were not recovered in the screen due to redundancy (<italic>Vps26a</italic> and <italic>Vps26b</italic>). Recovery of the Retromer genes also suggests that the CRISPR screen has the sensitivity and specificity to systematically examine the functional roles of endosomal recycling genes. Genes encoding the unique subunits of the Retriever complex – <italic>Vps35l</italic> and <italic>Vps26c</italic> – were not isolated in the CRISPR screen (<xref ref-type="fig" rid="fig1">Figure 1C</xref>). Similarly, virtually none of the genes encoding the CCC complex were recovered as significant hits in the CRISPR screen, except for <italic>Commd3</italic>, which encodes the COMMD3 subunit of the Commander complex (<xref ref-type="fig" rid="fig1">Figure 1A–C</xref>; <xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>). These data indicate that the Commander complex is dispensable for the endosomal recycling of GLUT-SPR.</p><p>To further characterize the functional roles of Retromer- and Commander-encoding genes in cell physiology, next we examined whether these genes are essential for cell viability or growth by re-analyzing data from an unbiased genome-wide essentiality screen. In the essentiality screen, mouse preadipocytes mutagenized by the CRISPR GeCKO v2 library were continuously passaged for two weeks without any selection (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). The abundance of gRNAs in this cell population was sequenced and compared with that in the original CRISPR gRNA library. If a gene is essential for cell viability or growth, its corresponding gRNAs would be depleted after the two-week cell passage. We found that none of the genes encoding the Retromer and Commander complexes are essential in mouse preadipocytes (<xref ref-type="fig" rid="fig1">Figure 1D</xref>). Thus, the disruption of either the Retromer or Commander-dependent endosomal retrieval pathways does not impair the viability or proliferation of these cells.</p><p>Together, these global genetic analyses suggest that COMMD3 plays an unrecognized role in GLUT-SPR trafficking, independent of its canonical function within the Commander holo-complex.</p></sec><sec id="s2-2"><title>Deletion of COMMD3 disrupts endosomal trafficking</title><p>To validate the role of COMMD3 in the surface homeostasis of GLUT-SPR, we deleted the <italic>Commd3</italic> gene in mouse preadipocytes (<xref ref-type="fig" rid="fig2">Figure 2A</xref>). Indeed, surface levels of GLUT-SPR were strongly reduced in <italic>Commd3</italic> KO preadipocytes, which were either cultured under standard conditions or stimulated with insulin to mimic a physiological fed state (<xref ref-type="fig" rid="fig2">Figure 2B</xref>). These data confirm the findings from the CRISPR screen (<xref ref-type="fig" rid="fig1">Figure 1C</xref>). To examine whether COMMD3 regulates the surface homeostasis of GLUT-SPR in another cell type, the fibroblast-like preadipocytes were differentiated into mature adipocytes, which are morphologically and functionally distinct from preadipocytes (<xref ref-type="bibr" rid="bib2">Ahfeldt et al., 2012</xref>). Using flow cytometry, we observed that surface GLUT-SPR levels were markedly reduced in <italic>Commd3</italic> KO adipocytes (<xref ref-type="fig" rid="fig2">Figure 2C</xref>), indicating that the role of COMMD3 in surface protein homeostasis is not restricted to a single cell type. Similar findings were observed in adipocytes using confocal imaging (<xref ref-type="fig" rid="fig2">Figure 2D</xref>). Surface levels of GLUT-SPR were substantially decreased in <italic>Commd3</italic> KO cells, concomitant with elevated intracellular accumulation of the reporter (<xref ref-type="fig" rid="fig2">Figure 2D</xref>). These results demonstrated a critical role of COMMD3 in the endosomal trafficking of GLUT-SPR.</p><fig id="fig2" position="float"><label>Figure 2.</label><caption><title>Intracellular sequestration of GLUT-SPR in COMMD3-deficient cells.</title><p>(<bold>A</bold>) Representative immunoblots showing the indicated proteins in wild-type (WT) and <italic>Commd3</italic> KO mouse preadipocytes. (<bold>B</bold>) Normalized surface levels of GLUT-SPR measured by flow cytometry in WT and KO preadipocytes. The cells were either untreated or treated with 100 nM insulin for 1 hr before surface GLUT-SPR was labeled using anti-HA antibodies and APC-conjugated secondary antibodies. To calculate surface levels of GLUT-SPR, mean APC values were divided by mean GFP fluorescence. To inhibit insulin signaling, 100 nM wortmannin was added prior to insulin stimulation. In all figures, data normalization was performed by setting the mean value of WT data points as 100 or 1, and all data points including WT ones were normalized to that mean value. Data are presented as mean ± SD of three biological replicates. **p&lt;0.01; *p&lt;0.05 (calculated using Student’s t-test). (<bold>C</bold>) Normalized surface levels of GLUT-SPR in WT and KO adipocytes. Data are presented as mean ± SD of three biological replicates. ***p&lt;0.001; n.s., p&gt;0.05 (calculated using Student’s t-test). (<bold>D</bold>) Representative confocal images showing the localization of GLUT-SPR in unpermeabilized WT and <italic>Commd3</italic> KO adipocytes, which were either untreated or treated with 100 nM insulin for one hour. Surface GLUT-SPR was labeled using anti-HA antibodies and Alexa Fluor 568-conjugated secondary antibodies. Nuclei were stained with Hoechst 33342. Scale bars: 10 µm.</p><p><supplementary-material id="fig2sdata1"><label>Figure 2—source data 1.</label><caption><title>PDF file containing original immunoblots for <xref ref-type="fig" rid="fig2">Figure 2A</xref>, indicating the relevant bands and treatments.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig2-data1-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig2sdata2"><label>Figure 2—source data 2.</label><caption><title>Original files for immunoblot analysis displayed in <xref ref-type="fig" rid="fig2">Figure 2A</xref>.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig2-data2-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig2sdata3"><label>Figure 2—source data 3.</label><caption><title>Flow cytometry data of wild-type (WT) and <italic>Commd3</italic> KO preadipocytes shown in <xref ref-type="fig" rid="fig2">Figure 2B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig2-data3-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig2sdata4"><label>Figure 2—source data 4.</label><caption><title>Flow cytometry data of wild-type (WT) and <italic>Commd3</italic> KO adipocytes shown in <xref ref-type="fig" rid="fig2">Figure 2C</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig2-data4-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig2-v1.tif"/></fig><p>To further characterize the function of COMMD3 in the endosomal trafficking of GLUT-SPR, we stained for EEA1, an early endosome marker (<xref ref-type="bibr" rid="bib46">Mishra et al., 2010</xref>), and examined the morphology of EEA1-positive organelles. We observed that the morphology of EEA1-positive endosomes was significantly altered in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig3">Figure 3A</xref>). The size of the EEA1-positive endosomes markedly increased in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig3">Figure 3A and B</xref>), reminiscent of the endosome enlargement observed in Retromer-deficient cells (<xref ref-type="bibr" rid="bib49">Neuman et al., 2021</xref>). We also observed elevated GLUT-SPR accumulation in EEA1-positive endosomes in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig3">Figure 3C</xref>). Next, we used Structured Illumination Microscopy (SIM) to visualize the localization of GLUT-SPR and Rab5, another marker of the early endosome (<xref ref-type="bibr" rid="bib33">Langemeyer et al., 2018</xref>). We found that a portion of GLUT-SPR resided in Rab5-positive compartments and its co-localization with Rab5 increased in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig3">Figure 3D and E</xref>).</p><fig id="fig3" position="float"><label>Figure 3.</label><caption><title>Abnormal endosomal morphology in COMMD3-deficient cells.</title><p>(<bold>A</bold>) Representative confocal images showing the localization of EEA1 and GLUT-SPR in permeabilized wild-type (WT) and <italic>Commd3</italic> KO adipocytes stimulated with 100 nM insulin for 1 hr (scale bars: 10 µm). Enlarged inset images depict co-localization of EEA1 and GLUT-SPR (scale bars: 5 µm). (<bold>B</bold>) Violin plot showing quantification of EEA1-positive puncta using Fiji threshold analysis. Data of the KO adipocytes were normalized to those of WT cells. Three independent experiments are shown with ten cells analyzed in each experiment. ***p&lt;0.001 (calculated using Student’s t-test). (<bold>C</bold>) Violin plot depicting quantification of GFP mean fluorescence intensity (MFI) in EEA1-positive puncta using Fiji threshold analysis. Data of KO adipocytes were normalized to those of WT cells. Three independent experiments are shown with ten cells analyzed in each experiment. ***p&lt;0.001 (calculated using Student’s t-test). (<bold>D</bold>) Representative Structured Illumination Microscopy (SIM) images showing the subcellular localization of Rab5 and GLUT-SPR in WT and <italic>Commd3</italic> KO preadipocytes (scale bars: 5 µm). (<bold>E</bold>) Quantification of Rab5 and GLUT-SPR co-localization based on SIM images, which were captured as in (<bold>D</bold>) and analyzed using ImageJ. Each dot represents data of a subcellular region of interest. Five cells were analyzed and three regions per cell were quantified. ***p&lt;0.001 (calculated using Student’s t-test).</p><p><supplementary-material id="fig3sdata1"><label>Figure 3—source data 1.</label><caption><title>Quantification of EEA1 + areas in wild-type (WT) and <italic>Commd3</italic> KO cells is shown in <xref ref-type="fig" rid="fig3">Figure 3B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig3-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig3sdata2"><label>Figure 3—source data 2.</label><caption><title>Quantification of GFP in EEA1 + compartments in wild-type (WT) and <italic>Commd3</italic> KO cells is shown in <xref ref-type="fig" rid="fig3">Figure 3C</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig3-data2-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig3sdata3"><label>Figure 3—source data 3.</label><caption><title>Flow cytometry data of wild-type (WT) and <italic>Commd3</italic> KO cells is shown in <xref ref-type="fig" rid="fig3">Figure 3D</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig3-data3-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig3-v1.tif"/></fig><p>Together, these data demonstrate that deletion of <italic>Commd3</italic> leads to the enlargement of early endosomes and accumulation of GLUT-SPR in these compartments, consistent with a trafficking defect occurring at the endosomal recycling step.</p></sec><sec id="s2-3"><title>COMMD3 regulates endosomal trafficking in a Commander-independent manner</title><p>Next, we sought to confirm the Commander-independent function of COMMD3 using comparative targeted mutations. We deleted genes encoding other Commander subunits and compared the phenotypes of the KO cells with that of <italic>Commd3</italic> KO cells. The COMMD proteins are found in three subcomplexes prior to forming the heterodecameric COMMD complex: subcomplex A (COMMD1-4-6-8), subcomplex B (COMMD2-3-4-8), and subcomplex C (COMMD5-7-9-10) (<xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>). Here, we selected COMMD1, COMMD3, and COMMD5 as representative subunits of the three subcomplexes. We measured surface levels of integrin alpha-6 (ITGA6), a known Commander-dependent cargo (<xref ref-type="bibr" rid="bib43">McNally et al., 2017</xref>), in cells lacking one of the COMMD proteins. As expected, surface levels of ITGA6 were downregulated in all these KO cell lines (<xref ref-type="fig" rid="fig4">Figure 4A</xref>), confirming the canonical role of COMMD3 within the Commander holo-complex.</p><fig-group><fig id="fig4" position="float"><label>Figure 4.</label><caption><title>COMMD3 regulates a group of cargo proteins independent of other COMMD proteins.</title><p>(<bold>A–D</bold>) Normalized surface levels of ITGA6 (<bold>A</bold>), GLUT-SPR (<bold>B</bold>), TfR (<bold>C</bold>), and LAMP1 (<bold>D</bold>) measured by flow cytometry in the indicated preadipocyte cell lines. To calculate surface levels of GLUT-SPR, mean APC values were divided by mean GFP fluorescence. Data of all cell samples were normalized to those of wild-type (WT) cells. Data of ITGA6 (n=3), GLUT-SPR (n=6), TfR (n=10), and LAMP1 (n=3) are presented as mean ± SD. **p&lt;0.01; ***p&lt;0.001; n.s., p&gt;0.05 (calculated using one-way ANOVA).</p><p><supplementary-material id="fig4sdata1"><label>Figure 4—source data 1.</label><caption><title>Flow cytometry data of wild-type (WT) and KO cells is shown in <xref ref-type="fig" rid="fig4">Figure 4A</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig4-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig4sdata2"><label>Figure 4—source data 2.</label><caption><title>Flow cytometry data of wild-type (WT) and KO cells is shown in <xref ref-type="fig" rid="fig4">Figure 4B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig4-data2-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig4sdata3"><label>Figure 4—source data 3.</label><caption><title>Flow cytometry data of wild-type (WT) and KO cells is shown in <xref ref-type="fig" rid="fig4">Figure 4C</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig4-data3-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig4sdata4"><label>Figure 4—source data 4.</label><caption><title>Flow cytometry data of wild-type (WT) and KO cells are shown in <xref ref-type="fig" rid="fig4">Figure 4D</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig4-data4-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig4-v1.tif"/></fig><fig id="fig4s1" position="float" specific-use="child-fig"><label>Figure 4—figure supplement 1.</label><caption><title>Quantification of transferrin receptor (TfR) in wild-type (WT) and mutant cell lines.</title><p>(<bold>A</bold>) Quantification of total TfR levels in the indicated preadipocyte cell lines based on protein intensities from immunoblots, analyzed using ImageJ. Data were normalized to WT cells. Data are presented as mean ± SD from three biological replicates. **p&lt;0.01; n.s., p&gt;0.05 (one-way ANOVA). (<bold>B</bold>) Normalized surface-to-total TfR ratio. Surface TfR levels, measured by flow cytometry, were normalized to total protein expression. Data are presented as mean ± SD from three biological replicates. *p&lt;0.05; ***p&lt;0.001; n.s., p&gt;0.05 (one-way ANOVA).</p><p><supplementary-material id="fig4s1sdata1"><label>Figure 4—figure supplement 1—source data 1.</label><caption><title>Flow cytometry data of wild-type (WT) and KO cells is shown in <xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1A</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig4-figsupp1-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig4s1sdata2"><label>Figure 4—figure supplement 1—source data 2.</label><caption><title>Flow cytometry data of wild-type (WT) and KO cells is shown in <xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig4-figsupp1-data2-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig4-figsupp1-v1.tif"/></fig></fig-group><p>Next, we examined the trafficking of other cargo proteins. We found that surface levels of GLUT-SPR were slightly increased in the <italic>Commd1</italic> KO cells, in contrast to the strong reduction observed in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig4">Figure 4B</xref>). Surface levels of GLUT-SPR were only slightly affected in <italic>Commd5</italic> KO cells (<xref ref-type="fig" rid="fig4">Figure 4B</xref>). Surface levels of the transferrin receptor (TfR), a Commander-independent cargo (<xref ref-type="bibr" rid="bib54">Puthenveedu et al., 2010</xref>), were markedly decreased in <italic>Commd3</italic> KO cells but remained intact in <italic>Commd1</italic> or <italic>Commd5</italic> KO populations (<xref ref-type="fig" rid="fig4">Figure 4C</xref>). Total TfR levels also decreased in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>), consistent with the notion that unretrieved cargo is routed to the lysosome for degradation (<xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib63">Simonetti and Cullen, 2019</xref>; <xref ref-type="bibr" rid="bib14">Cullen and Steinberg, 2018</xref>). Surface levels of lysosomal-associated membrane protein 1 (LAMP1) were also strongly decreased in <italic>Commd3</italic> KO cells but were not substantially changed in <italic>Commd1</italic> or <italic>Commd5</italic> KO cells (<xref ref-type="fig" rid="fig4">Figure 4D</xref>). Together, comparative analysis of these diverse membrane proteins clearly demonstrates that COMMD3 regulates a group of cargo proteins independent of the Commander holo-complex, in addition to its canonical function within the Commander complex.</p></sec><sec id="s2-4"><title>Mutations of CCDC93 or Retriever lead to upregulation of COMMD3</title><p>To further characterize the Commander-independent function of COMMD3, we examined the KO phenotypes of other Commander subunits. We observed that the expression of CCDC93 and VPS35L was substantially decreased in <italic>Commd3</italic> KO cells, and VPS35L expression was diminished in <italic>Ccdc93</italic> KO cells. These findings are consistent with the notion that stability of subunits within a protein complex is interdependent (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>; <xref ref-type="bibr" rid="bib25">Gulbranson et al., 2019</xref>). Interestingly, we observed that COMMD3 expression was not reduced but upregulated in <italic>Ccdc93</italic> or <italic>Vps35l</italic> KO cells (<xref ref-type="fig" rid="fig5">Figure 5A</xref>, <xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>). Thus, unlike other Commander subunits, COMMD3 persists when other subunits of the Commander complex are depleted, further supporting the ability of COMMD3 to regulate endosomal trafficking independent of the Commander holo-complex.</p><fig-group><fig id="fig5" position="float"><label>Figure 5.</label><caption><title>Upregulation of COMMD3 in cells deficient in CCDC93 or VPS35L.</title><p>(<bold>A</bold>) Representative immunoblots showing protein expression in the indicated preadipocyte cell lines. (<bold>B–D</bold>) Normalized surface levels of transferrin receptor (TfR) measured by flow cytometry in the indicated preadipocyte cell lines. Data of all cell samples were normalized to those of WT cells. Data are presented as mean ± SD of three biological replicates. **p&lt;0.01; ***p&lt;0.001; n.s., p&gt;0.05 (calculated using one-way ANOVA).</p><p><supplementary-material id="fig5sdata1"><label>Figure 5—source data 1.</label><caption><title>PDF file containing original immunoblots for <xref ref-type="fig" rid="fig5">Figure 5A</xref>, indicating the relevant bands and treatments.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig5-data1-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig5sdata2"><label>Figure 5—source data 2.</label><caption><title>Original files for immunoblot analysis displayed in <xref ref-type="fig" rid="fig5">Figure 5A</xref>.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig5-data2-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig5sdata3"><label>Figure 5—source data 3.</label><caption><title>Flow cytometry data of the indicated cell lines shown in <xref ref-type="fig" rid="fig5">Figure 5B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig5-data3-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig5sdata4"><label>Figure 5—source data 4.</label><caption><title>Flow cytometry data of the indicated cell lines shown in <xref ref-type="fig" rid="fig5">Figure 5C</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig5-data4-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig5sdata5"><label>Figure 5—source data 5.</label><caption><title>Flow cytometry data of the indicated cell lines shown in <xref ref-type="fig" rid="fig5">Figure 5D</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig5-data5-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig5-v1.tif"/></fig><fig id="fig5s1" position="float" specific-use="child-fig"><label>Figure 5—figure supplement 1.</label><caption><title>Quantification of total COMMD3 levels.</title><p>Total COMMD3 levels in the indicated preadipocyte cell lines were quantified based on protein intensities from immunoblots, analyzed using ImageJ. Data were normalized to wild-type (WT) cells. Data are presented as mean ± SD from three biological replicates. ***p&lt;0.001; *p&lt;0.05 (one-way ANOVA).</p><p><supplementary-material id="fig5s1sdata1"><label>Figure 5—figure supplement 1—source data 1.</label><caption><title>Flow cytometry data of the indicated cell lines is shown in <xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig5-figsupp1-data1-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig5-figsupp1-v1.tif"/></fig></fig-group><p>The upregulation of COMMD3 in Commander-deficient cells, which likely reflects a compensatory mechanism, offers another strategy to test the Commander-independent function of COMMD3. We reasoned that if a cargo is dependent on COMMD3 but not on the Commander complex, its surface levels could be increased in cells with elevated COMMD3. Indeed, we observed that surface levels of TfR, a cargo dependent on Commd3 but not on the Commander complex (<xref ref-type="fig" rid="fig4">Figure 4C</xref>; <xref ref-type="bibr" rid="bib54">Puthenveedu et al., 2010</xref>), were markedly increased in <italic>Ccdc93</italic> or <italic>Vps35l</italic> KO cells (<xref ref-type="fig" rid="fig5">Figure 5B</xref>). Conversely, surface TfR levels were diminished in <italic>Commd3</italic> KO cells and were fully restored by expression of a <italic>Commd3</italic> rescue gene (<xref ref-type="fig" rid="fig5">Figure 5B</xref>). Total TfR expression was also reduced in <italic>Commd3</italic> KO cells and was rescued by the <italic>Commd3</italic> rescue gene (Figure 7D, <xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1A</xref>). KO of both <italic>Commd3</italic> and <italic>Ccdc93</italic> resulted in decreased surface levels of TfR (<xref ref-type="fig" rid="fig5">Figure 5C</xref>), confirming that the elevated surface TfR observed in <italic>Ccdc93</italic> KO cells was caused by COMMD3 upregulation. Consistent with this notion, overexpression of <italic>Commd3</italic> in WT cells markedly elevated TfR surface levels (<xref ref-type="fig" rid="fig5">Figure 5D</xref>). Altogether, these results demonstrate that COMMD3 is upregulated in Retriever- or CCDC93-deficient cells and enhances the endosomal retrieval of COMMD3-dependent cargoes, further supporting a Commander-independent role of COMMD3 in endosomal recycling.</p></sec><sec id="s2-5"><title>The NTD of COMMD3 mediates its Commander-independent function and interacts with ARF1</title><p>Next, we sought to determine the molecular mechanism by which COMMD3 regulates endosomal trafficking in a Commander-independent manner. The COMMD3 protein is comprised of two autonomously folded domains – NTD and CTD (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). The C-terminal COMMD domains of COMMD proteins are well-conserved and mediate the formation of the heterodecameric COMMD complex within the Commander holo-complex (<xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>; <xref ref-type="bibr" rid="bib39">Maine and Burstein, 2007</xref>). The NTDs of COMMD proteins share a similar structure but are more divergent in sequence (<xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>; <xref ref-type="bibr" rid="bib27">Healy et al., 2018</xref>). The function of the COMMD NTDs is unknown. Next, we examined whether the Commander-independent function of COMMD3 relies on its NTD. We expressed the COMMD3 NTD in <italic>Commd3</italic> KO cells and examined whether the KO phenotype could be rescued. Indeed, expression of the COMMD3 NTD fully restored the surface levels of TfR in <italic>Commd3</italic> KO cells while the CTD did not (<xref ref-type="fig" rid="fig6">Figure 6B</xref>, <xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>), indicating that the NTD is sufficient for this function.</p><fig-group><fig id="fig6" position="float"><label>Figure 6.</label><caption><title>The Commander-independent function of COMMD3 is mediated by its N-terminal domain (NTD).</title><p>(<bold>A</bold>) Top, diagram depicting the domain organization of COMMD3. Bottom: the structural model of COMMD3 (AlphaFold Protein Structure Database: AF-Q9UBI1-F1) showing the independently folded NTD and C-terminal domain (CTD). (<bold>B</bold>) Normalized surface levels of transferrin receptor (TfR) measured by flow cytometry in the indicated preadipocyte cell lines. Data of all cell samples were normalized to those of wild-type (WT) cells. Data are presented as mean ± SD of three biological replicates. *p&lt;0.05; ***p&lt;0.001 (calculated using one-way ANOVA). (<bold>C</bold>) Diagrams of full-length (FL) and truncated COMMD3 proteins used in proteomic experiments. The proteins were tagged with mCherry (mCh) and 3xFLAG (3xF). (<bold>D</bold>) Procedures of proteomic analysis to determine the interactomes of FL and truncated COMMD3 proteins. (<bold>E</bold>) Venn diagram showing the interactomes of COMMD3 proteins. (<bold>F</bold>) A scatter plot showing the fold change of protein abundance over vector control in the interactomes of FL COMMD3 and the NTD of COMMD3. Selected proteins are labeled. (<bold>G</bold>) Representative immunoblots showing the interactions of ARF1 Q71L with COMMD3-NTD. HA-tagged ARF1 Q71L and 3xFLAG-tagged COMMD3-NTD were co-expressed in 293T cells. COMMD3-NTD and associated proteins were immunoprecipitated using anti-FLAG antibodies and detected using immunoblotting. The ARF Q71L mutant was used here because it adopts a GTP-bound configuration (<xref ref-type="bibr" rid="bib13">Cohen and Donaldson, 2010</xref>; <xref ref-type="bibr" rid="bib79">Zhang et al., 1994</xref>).</p><p><supplementary-material id="fig6sdata1"><label>Figure 6—source data 1.</label><caption><title>Flow cytometry data of the indicated cell lines is shown in <xref ref-type="fig" rid="fig6">Figure 6B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig6-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig6sdata2"><label>Figure 6—source data 2.</label><caption><title>Original data of the plot is shown in <xref ref-type="fig" rid="fig6">Figure 6F</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig6-data2-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig6sdata3"><label>Figure 6—source data 3.</label><caption><title>PDF file containing original immunoblots for <xref ref-type="fig" rid="fig6">Figure 6G</xref>, indicating the relevant bands and treatments.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig6-data3-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig6sdata4"><label>Figure 6—source data 4.</label><caption><title>Original files for immunoblot analysis displayed in <xref ref-type="fig" rid="fig6">Figure 6G</xref>.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig6-data4-v1.zip"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig6-v1.tif"/></fig><fig id="fig6s1" position="float" specific-use="child-fig"><label>Figure 6—figure supplement 1.</label><caption><title>The C-terminal domain (CTD) of COMMD3 is unable to rescue transferrin receptor (TfR) surface levels.</title><p>Normalized surface levels of TfR were measured by flow cytometry in the indicated preadipocyte cell lines. Data were normalized to wild-type (WT) cells. Results are presented as mean ± SD from three biological replicates. ***p&lt;0.001; n.s., p&gt;0.05 (one-way ANOVA).</p><p><supplementary-material id="fig6s1sdata1"><label>Figure 6—figure supplement 1—source data 1.</label><caption><title>Flow cytometry data of the indicated cell lines is shown in <xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig6-figsupp1-data1-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig6-figsupp1-v1.tif"/></fig></fig-group><p>To gain molecular insights into the NTD of COMMD3, we determined the interactomes of full-length (FL) COMMD3, NTD, and C-terminal domain (CTD) (<xref ref-type="fig" rid="fig6">Figure 6C and D</xref>). FL COMMD3, NTD, and CTD were individually expressed and isolated through co-immunoprecipitation (co-IP), and the associated proteins within these samples were identified using mass spectrometry. Through this proteomic analysis, we identified a group of proteins present in the interactomes of FL COMMD3 and NTD but absent from the CTD interactome (<xref ref-type="fig" rid="fig6">Figure 6E</xref>, <xref ref-type="supplementary-material" rid="supp1">Supplementary file 1</xref>). Among these proteins, ARF1 emerged as a strong candidate because it acts as a membrane trafficking regulator known to function on endosomes (<xref ref-type="fig" rid="fig6">Figure 6F</xref>; <xref ref-type="bibr" rid="bib47">Nakai et al., 2013</xref>; <xref ref-type="bibr" rid="bib65">Stockhammer et al., 2024</xref>). The ARF family of proteins is small GTPases involved in the recruitment of coat proteins, activation of membrane lipid-modifying enzymes, and interaction with the cytoskeleton (<xref ref-type="bibr" rid="bib65">Stockhammer et al., 2024</xref>; <xref ref-type="bibr" rid="bib18">D’Souza-Schorey and Chavrier, 2006</xref>). Using co-IP, we observed that the NTD of COMMD3 interacted with ARF1 (<xref ref-type="fig" rid="fig6">Figure 6G</xref>), confirming the results of the proteomic experiments. Together, these data demonstrate that the NTD of COMMD3 mediates its Commander-independent function and interacts with ARF1.</p></sec><sec id="s2-6"><title>COMMD3 regulates the stability of ARF1</title><p>To further characterize the interaction between COMMD3 and ARF1, we used SIM to visualize their subcellular localization. We observed significant co-localization between ARF1 and the NTD of COMMD3 (<xref ref-type="fig" rid="fig7">Figure 7A and B</xref>), consistent with their interactions detected in proteomic and co-IP experiments (<xref ref-type="fig" rid="fig6">Figure 6</xref>). We noted that, in the co-IP assays using 293T cells, ARF1 expression levels were significantly elevated when co-expressed with the NTD of COMMD3 (<xref ref-type="fig" rid="fig6">Figure 6G</xref>). A similar ARF1-stabilizing effect was also observed in HeLa cells (<xref ref-type="fig" rid="fig7">Figure 7C</xref>). These findings raised the possibility that COMMD3 uses its NTD to bind and stabilize ARF1. To test this model, we examined endogenous ARF1 levels in <italic>Commd3</italic> KO cells. Interestingly, we found that ARF1 levels were markedly reduced in <italic>Commd3</italic> KO cells and were fully restored upon introduction of a <italic>COMMD3</italic> rescue gene (<xref ref-type="fig" rid="fig7">Figure 7D</xref>). To further investigate the functional link between COMMD3 and ARF1, we overexpressed ARF1 in <italic>Commd3</italic> KO cells. Strikingly, ARF1 overexpression fully restored the surface levels of TfR in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig7">Figure 7E</xref>). These data demonstrate that COMMD3 regulates endosomal trafficking through binding and stabilizing ARF1.</p><fig id="fig7" position="float"><label>Figure 7.</label><caption><title>The N-terminal domain (NTD) of COMMD3 stabilizes ARF1.</title><p>(<bold>A</bold>) Representative Structured Illumination Microscopy (SIM) images showing the subcellular localization of ARF1 and COMMD3-NTD expressed in HeLa cells. HA-tagged ARF1 and 3xFLAG-tagged COMMD3-NTD were transiently expressed in HeLa cells and stained using anti-HA and anti-FLAG antibodies, respectively (scale bars: 5 µm). (<bold>B</bold>) Quantification of ARF1 and COMMD3-NTD co-localization based on SIM images, which were captured as in (<bold>A</bold>) and analyzed using ImageJ. Each dot represents data of an individual cell. In randomized samples, ARF1 images were rotated 90° clockwise, whereas COMMD3-NTD images were not rotated. ***p&lt;0.001 (calculated using Student’s t-test). (<bold>C</bold>) Representative immunoblots showing the ARF1-stabilizing effects of COMMD3-NTD. HA-tagged ARF1 Q71L and 3xFLAG-tagged COMMD3-NTD were transiently expressed in HeLa cells and their total expression levels were measured using immunoblotting. (<bold>D</bold>) Representative immunoblots showing protein expression in the indicated preadipocyte cell lines. (<bold>E</bold>) Normalized surface levels of TfR measured by flow cytometry in the indicated preadipocyte cell lines. Data of all cell samples were normalized to those of wild-type (WT) preadipocytes. Data are presented as mean ± SD of three biological replicates. ***p&lt;0.001; n.s., p&gt;0.05 (calculated using one-way ANOVA).</p><p><supplementary-material id="fig7sdata1"><label>Figure 7—source data 1.</label><caption><title>Original data of the plot shown in <xref ref-type="fig" rid="fig7">Figure 7B</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig7-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig7sdata2"><label>Figure 7—source data 2.</label><caption><title>PDF file containing original immunoblots for <xref ref-type="fig" rid="fig7">Figure 7C and D</xref>, indicating the relevant bands and treatments.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig7-data2-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig7sdata3"><label>Figure 7—source data 3.</label><caption><title>Original files for immunoblot analysis displayed in <xref ref-type="fig" rid="fig7">Figure 7C and D</xref>.</title></caption><media mimetype="application" mime-subtype="zip" xlink:href="elife-105264-fig7-data3-v1.zip"/></supplementary-material></p><p><supplementary-material id="fig7sdata4"><label>Figure 7—source data 4.</label><caption><title>Flow cytometry data of the indicated cell lines is shown in <xref ref-type="fig" rid="fig7">Figure 7E</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig7-data4-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig7-v1.tif"/></fig></sec><sec id="s2-7"><title>Mutations disrupting the COMMD3-ARF1 interaction impair the Commander-independent function of COMMD3</title><p>Finally, we sought to determine whether ARF1 binding is required for the Commander-independent function of COMMD3. AlphaFold3 predicted a high-confidence structure of the ARF1-GTP:COMMD3-NTD heterodimeric complex (<xref ref-type="fig" rid="fig8">Figure 8A and B</xref>). According to this structural model, the α1 helix of COMMD3-NTD binds to the switch 1 of ARF1, while the α3 and α4 helices of COMMD3-NTD interact with the switch 2 of ARF1 (<xref ref-type="fig" rid="fig8">Figure 8A and B</xref>, <xref ref-type="supplementary-material" rid="sdata1">Source data 1</xref>). The switches 1 and 2 of ARF1 are highly conserved regions that are regulated by GTP binding and interact with effectors involved in endosomal recycling (<xref ref-type="bibr" rid="bib23">Goldberg, 1998</xref>; <xref ref-type="bibr" rid="bib59">Sauvageau et al., 2017</xref>). The binding of COMMD3 to ARF1 is mainly mediated by hydrophobic interactions and hydrogen bonds, including hydrogen bonds formed by K60 and H61 of COMMD3 with Y81 of ARF1, K60 of COMMD3 with R79 and Q83 of ARF1, H63 of COMMD3 with H80 of ARF1 (<xref ref-type="fig" rid="fig8">Figure 8A and B</xref>, <xref ref-type="supplementary-material" rid="sdata1">Source data 1</xref>). AphaFold3 did not predict high-confidence structural models between COMMD3-NTD and ARF1-GDP or apo-ARF1, suggesting that COMMD3 selectively recognizes the GTP-bound form of ARF1. This conclusion is consistent with the observation that COMMD3 strongly stabilizes GTP-bound ARF1 (<xref ref-type="fig" rid="fig6">Figures 6G</xref> and <xref ref-type="fig" rid="fig7">7C</xref>).</p><fig id="fig8" position="float"><label>Figure 8.</label><caption><title>The COMMD3-ARF1 interaction is critical to the Commander-independent function of COMMD3.</title><p>(<bold>A</bold>) Left: the AlphaFold3-predicted structure of the COMMD3:ARF1 heterodimer visualized using ChimeraX1.8. The structural prediction was performed using COMMD3-NTD (a.a. 1–120, purple), ARF1 (pink), and GTP (green) as input. Right: key residues at the COMMD3-ARF1 binding interface. The CIF file of the structural model is included in Supplementary Dataset 1. (<bold>B</bold>) Predicted alignment error (PAE) heatmap of the structural model shown in (<bold>A</bold>). (<bold>C</bold>) Diagrams showing the residues mutated in a COMMD3-NTD mutant (COMMD3-NTD*, only a.a. 56–65 are shown). Mutated residues are shown in red. (<bold>D</bold>) Quantification of COMMD-NTD and NTD* stably expressed in preadipocytes based on Structured Illumination Microscopy (SIM) images, which were captured and analyzed as in <xref ref-type="fig" rid="fig7">Figure 7A–B</xref>. Each dot represents data of an individual cell. MFI, mean fluorescence intensity. n.s., p&gt;0.05 (calculated using Student’s t-test). (<bold>E</bold>) Normalized surface levels of transferrin receptor (TfR) measured by flow cytometry in the indicated preadipocyte cell lines. Data of all cell samples were normalized to those of wild-type (WT) cells. Data are presented as mean ± SD of three biological replicates. ***p&lt;0.001; n.s., p&gt;0.05 (calculated using one-way ANOVA). (<bold>F</bold>) Quantification of endogenous ARF1 in the indicated preadipocyte cell lines based on intensities of proteins on immunoblots quantified using ImageJ. Data of all samples were normalized to those of WT cells. Data are presented as mean ± SD of three biological replicates. *p&lt;0.05; n.s., p&gt;0.05; **p&lt;0.01 (calculated using one-way ANOVA).</p><p><supplementary-material id="fig8sdata1"><label>Figure 8—source data 1.</label><caption><title>Flow cytometry data of the indicated cell lines shown in <xref ref-type="fig" rid="fig8">Figure 8D</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig8-data1-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig8sdata2"><label>Figure 8—source data 2.</label><caption><title>Flow cytometry data of the indicated cell lines shown in <xref ref-type="fig" rid="fig8">Figure 8E</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig8-data2-v1.xlsx"/></supplementary-material></p><p><supplementary-material id="fig8sdata3"><label>Figure 8—source data 3.</label><caption><title>Flow cytometry data of the indicated cell lines shown in <xref ref-type="fig" rid="fig8">Figure 8F</xref>.</title></caption><media mimetype="application" mime-subtype="xlsx" xlink:href="elife-105264-fig8-data3-v1.xlsx"/></supplementary-material></p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig8-v1.tif"/></fig><p>Altogether, these results further support the conclusion that COMMD3 regulates endosomal trafficking through binding and stabilizing ARF1 (<xref ref-type="fig" rid="fig9">Figure 9</xref>).</p><fig id="fig9" position="float"><label>Figure 9.</label><caption><title>Model of the Commander-independent function of COMMD3 in endosomal trafficking.</title><p>For clarity, Retromer and other endosomal recycling regulators are not shown.</p></caption><graphic mimetype="image" mime-subtype="tiff" xlink:href="elife-105264-fig9-v1.tif"/></fig><p>Next, we introduced point mutations into the NTD of COMMD3 based on the structural model, aiming to disrupt its interaction with ARF1 (<xref ref-type="fig" rid="fig8">Figure 8C</xref>). The COMMD3-NTD mutant was expressed at a similar level as the WT protein in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig8">Figure 8D</xref>). We observed that the COMMD3-NTD mutant failed to restore surface levels of TfR, whereas WT COMMD3-NTD fully rescued the KO phenotype (<xref ref-type="fig" rid="fig8">Figure 8E</xref>). In agreement with this finding, WT COMMD3-NTD, but not the mutant, restored ARF1 expression in <italic>Commd3</italic> KO cells (<xref ref-type="fig" rid="fig8">Figure 8F</xref>). Altogether, these results further support the conclusion that COMMD3 regulates endosomal trafficking through binding and stabilizing ARF1.</p></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><p>The genetic evidence for a Commander-independent function of COMMD3 in endosomal trafficking is threefold. First, COMMD3 was the only Commander subunit isolated as a significant hit in a genome-scale genetic screen dissecting the surface homeostasis of GLUT-SPR, revealing a unique role of COMMD3 among Commander subunits in the GLUT-SPR trafficking pathway. Unbiased genetic screens are particularly powerful in dissecting a protein complex because they systematically interrogate the functional roles of all subunits within the complex (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>; <xref ref-type="bibr" rid="bib25">Gulbranson et al., 2019</xref>; <xref ref-type="bibr" rid="bib24">Gulbranson et al., 2017</xref>; <xref ref-type="bibr" rid="bib44">Menasche et al., 2020</xref>; <xref ref-type="bibr" rid="bib15">Davis et al., 2015</xref>). Second, our comparative targeted mutations confirmed that the loss-of-function phenotype of COMMD3 is fundamentally distinct from that of other COMMD proteins. Besides GLUT-SPR, a group of other cargoes including TfR also selectively rely on COMMD3 but not on COMMD1 or COMMD5, further supporting the unique role of COMMD3 in the trafficking of these cargo proteins. It should be noted that our findings of ITGA6 are fully consistent with a canonical function of COMMD3 within the Commander holo-complex in endosomal recycling. Third, while the stability of Commander subunits is generally interdependent, COMMD3 persists when other subunits of the Commander complex are depleted. In fact, COMMD3 is upregulated when CCDC93 or Retriever are mutated, resulting in elevated surface levels of TfR.</p><p>The Commander-independent function of COMMD3 is mediated by its NTD, a domain previously lacking an ascribed function, whereas its C-terminal COMMD domain is required for the canonical role of COMMD3 within the Commander complex (<xref ref-type="bibr" rid="bib28">Healy et al., 2023</xref>; <xref ref-type="bibr" rid="bib9">Boesch et al., 2024</xref>; <xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>). At the molecular level, the NTD of COMMD3 binds and stabilizes ARF1, a member of the ARF small GTPase family playing a key role in endosomal recycling (<xref ref-type="bibr" rid="bib47">Nakai et al., 2013</xref>; <xref ref-type="bibr" rid="bib31">Kondo et al., 2012</xref>). These findings suggest that GTP-ARF1 is intrinsically unstable prior to engaging its effectors and, therefore, requires stabilization by COMMD3. Since COMMD3 binds to the same regions of ARF1 recognized by ARF1 effectors, it must dissociate from ARF1 before the latter can engage its effectors to regulate endosomal recycling (<xref ref-type="bibr" rid="bib65">Stockhammer et al., 2024</xref>). Further research is needed to determine whether COMMD3 is released from ARF1 through direct competition by ARF1 effectors or if a more active mechanism is involved.</p><p>COMMD proteins are known to exist outside the Commander holo-complex. While they are unstable as monomers, COMMD proteins can form homo- or hetero-oligomers independently of other Commander subunits (<xref ref-type="bibr" rid="bib27">Healy et al., 2018</xref>; <xref ref-type="bibr" rid="bib62">Shirai et al., 2023</xref>; <xref ref-type="bibr" rid="bib48">Nakai et al., 2019</xref>; <xref ref-type="bibr" rid="bib36">Li et al., 2015</xref>). Since other COMMD proteins were not identified as significant hits in our GLUT-SPR-based CRISPR screen, COMMD3 likely forms homo-oligomers before associating with ARF1 to regulate cargo trafficking in a Commander-independent manner. The Commander-independent function of COMMD3 offers an additional route of endosomal recycling, alongside the Retromer- and Commander-dependent recycling pathways. By leveraging existing proteins such as COMMD3, the cell expands the repertoire of endosomal recycling routes without increasing gene numbers, which helps meet the formidable challenge of sorting thousands of membrane proteins that are constantly endocytosed into the cell. An important future direction is to determine precisely how COMMD3 interacts with ARF1 and cooperates with other endosomal regulators, such as SNXs, to recognize sorting signals on COMMD3-dependent cargoes during endosomal retrieval.</p><p>Our findings raise the intriguing possibility that other COMMD proteins may also possess additional functions outside the Commander holo-complex. In addition to endosomal recycling, Commander is also implicated in biological pathways including vesicle fusion, cytoskeletal organization, intracellular signaling, protein degradation, and gene expression (<xref ref-type="bibr" rid="bib3">Ambrosio et al., 2022</xref>; <xref ref-type="bibr" rid="bib43">McNally et al., 2017</xref>; <xref ref-type="bibr" rid="bib64">Singla et al., 2019</xref>; <xref ref-type="bibr" rid="bib62">Shirai et al., 2023</xref>; <xref ref-type="bibr" rid="bib48">Nakai et al., 2019</xref>; <xref ref-type="bibr" rid="bib12">Campion et al., 2018</xref>; <xref ref-type="bibr" rid="bib66">Suraweera et al., 2021</xref>; <xref ref-type="bibr" rid="bib36">Li et al., 2015</xref>; <xref ref-type="bibr" rid="bib5">Bartuzi et al., 2013</xref>; <xref ref-type="bibr" rid="bib21">Esposito et al., 2016</xref>; <xref ref-type="bibr" rid="bib51">O’Hara et al., 2014</xref>; <xref ref-type="bibr" rid="bib56">Riera‐Romo, 2018</xref>; <xref ref-type="bibr" rid="bib77">You et al., 2018</xref>; <xref ref-type="bibr" rid="bib42">Mao et al., 2011</xref>; <xref ref-type="bibr" rid="bib16">de Bie et al., 2006</xref>; <xref ref-type="bibr" rid="bib40">Maine et al., 2007</xref>; <xref ref-type="bibr" rid="bib53">Phillips-Krawczak et al., 2015</xref>; <xref ref-type="bibr" rid="bib6">Bartuzi et al., 2016</xref>; <xref ref-type="bibr" rid="bib26">Hancock et al., 2023</xref>; <xref ref-type="bibr" rid="bib38">Liu et al., 2013</xref>; <xref ref-type="bibr" rid="bib73">Weiskirchen and Penning, 2021</xref>; <xref ref-type="bibr" rid="bib29">Jiang et al., 2019</xref>; <xref ref-type="bibr" rid="bib19">Dumoulin et al., 2020</xref>). Although many of these pathways are expected to require the Commander holo-complex, others may be mediated by stable pools of individual COMMD proteins outside the Commander complex. These Commander-dependent functions of COMMD proteins are supported by their evolutionary history. COMMD proteins evolved later than other Commander components, concurrent with the expansion of genes encoding membrane trafficking regulators (<xref ref-type="bibr" rid="bib37">Liebeskind et al., 2019</xref>). It is possible that precursors of COMMD proteins may have been stable and functional prior to joining the more ancient Commander core complex. As the Commander holo-complex emerged, some of the primordial functions of COMMD precursors were likely retained in COMMD proteins. Further evidence supporting Commander-independent functions is the distinct tissue-specific expression patterns of COMMD proteins (<xref ref-type="bibr" rid="bib34">Laulumaa et al., 2024</xref>; <xref ref-type="bibr" rid="bib64">Singla et al., 2019</xref>; <xref ref-type="bibr" rid="bib11">Burstein et al., 2005</xref>; <xref ref-type="bibr" rid="bib78">You et al., 2023</xref>; <xref ref-type="bibr" rid="bib74">Yang et al., 2019</xref>). Given their differential expression, a portion of COMMD proteins inevitably exists outside the Commander holo-complex and may play cell type-specific physiological roles. Besides Commander, other membrane trafficking complexes might also contain subunits functioning outside the homo-complexes. In line with this notion, SEC13, a component of the COPII coat formed on the endoplasmic reticulum (ER), is also implicated in the formation of the nuclear pore complex (NPC) (<xref ref-type="bibr" rid="bib50">Niu et al., 2014</xref>; <xref ref-type="bibr" rid="bib20">Enninga et al., 2003</xref>). We suggest that the genetic strategy described in this study will be instrumental in determining whether and how COMMD proteins and SEC13 regulate cell physiology independently of their respective holo-complexes.</p></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><table-wrap id="keyresource" position="anchor"><label>Key resources table</label><table frame="hsides" rules="groups"><thead><tr><th align="left" valign="top">Reagent type (species) or resource</th><th align="left" valign="top">Designation</th><th align="left" valign="top">Source or reference</th><th align="left" valign="top">Identifiers</th><th align="left" valign="top">Additional information</th></tr></thead><tbody><tr><td align="left" valign="top">Gene (<italic>H. sapiens</italic>)</td><td align="left" valign="top">COMMD3</td><td align="left" valign="top">Uniprot</td><td align="left" valign="top">Q9UBI1</td><td align="left" valign="top">Sequence codon optimized to avoid Cas9 targeting</td></tr><tr><td align="left" valign="top">Gene (<italic>H. sapiens</italic>)</td><td align="left" valign="top">ARF1</td><td align="left" valign="top">Entrez</td><td align="left" valign="top">PVNH8</td><td align="left" valign="top">Cloned from Addgene # <ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:addgene_39554">39554</ext-link></td></tr><tr><td align="left" valign="top">Cell line (<italic>M. musculus</italic>)</td><td align="left" valign="top">Preadipocytes</td><td align="left" valign="top">Dr. Shingo Kajimura</td><td align="left" valign="top">N/A</td><td align="left" valign="top"/></tr><tr><td align="left" valign="top">Cell line (<italic>H. sapiens</italic>)</td><td align="left" valign="top">HeLa</td><td align="left" valign="top">ATCC</td><td align="left" valign="top">CCL-2</td><td align="left" valign="top"/></tr><tr><td align="left" valign="top">Cell line (<italic>H. sapiens</italic>)</td><td align="left" valign="top">HEK 293T</td><td align="left" valign="top">ATCC</td><td align="left" valign="top">CRL-3216</td><td align="left" valign="top"/></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>M. musculus</italic>)</td><td align="left" valign="top">pLenti-CRISPR-v2</td><td align="left" valign="top">Addgene</td><td align="left" valign="top">#52961</td><td align="left" valign="top">Lentiviral construct to infect and express Cas9 and gRNA.</td></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>M. musculus</italic>)</td><td align="left" valign="top">pLentiGuide-Puro vector</td><td align="left" valign="top">Addgene</td><td align="left" valign="top">#52963</td><td align="left" valign="top">Lentiviral construct to infect and express gRNA.</td></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>H. sapiens</italic>, <italic>M. musculus</italic>)</td><td align="left" valign="top">SHC003 GFPD</td><td align="left" valign="top">Addgene</td><td align="left" valign="top">#133301</td><td align="left" valign="top">Mammalian expression plasmid backbone.</td></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>H. sapiens</italic>, <italic>M. musculus</italic>)</td><td align="left" valign="top">SHC003 GFPD-humanCOMMD3-FL-mCherry-3xFLAG</td><td align="left" valign="top">This paper</td><td align="left" valign="top">N/A</td><td align="left" valign="top">Lentiviral construct to infect/transfect cells and express genes.</td></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>H. sapiens</italic>, <italic>M. musculus</italic>)</td><td align="left" valign="top">SHC003 GFPD-humanCOMMD3-NTD-mCherry-3xFLAG</td><td align="left" valign="top">This paper</td><td align="left" valign="top">N/A</td><td align="left" valign="top">Lentiviral construct to infect/transfect cells and express genes.</td></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>H. sapiens</italic>, <italic>M. musculus</italic>)</td><td align="left" valign="top">SHC003 GFPD-mCherry-humanCOMMD3-CTD-3xFLAG</td><td align="left" valign="top">This paper</td><td align="left" valign="top">N/A</td><td align="left" valign="top">Lentiviral construct to infect/transfect cells and express genes.</td></tr><tr><td align="left" valign="top">Recombinant DNA reagent (<italic>H. sapiens</italic>, <italic>M. musculus</italic>)</td><td align="left" valign="top">SHC003 GFPD-humanARF1-HA</td><td align="left" valign="top">This paper</td><td align="left" valign="top">N/A</td><td align="left" valign="top">Lentiviral construct to infect/transfect cells and express genes.</td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">COMMD3 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top">N/A</td><td align="left" valign="top"><named-content content-type="sequence">CTTCGCGCTTCTCCTCCGGG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">COMMD3 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">CTTGAAACAGATCGACCCAG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">COMMD1 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">TCACGGACACTCGGGTGTCA</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Commd1 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">ACTGCTCAAACCAAAAAGCA</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Commd5 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">GTTGTTGAAACTCGTAGTCG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Commd5 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">TGCCAGCGCCAACCTGTCAG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Ccdc93 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">CGAAAGTACCGACGGCAGCG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Ccdc93 CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">GATGACCGCCATGGCAAACG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Vps35l CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">GGATTATGTGAACCGCATAG</named-content></td></tr><tr><td align="left" valign="top">Sequence-based reagents</td><td align="left" valign="top">Vps35l CRISPR guide RNA sequence primers</td><td align="left" valign="top">This paper</td><td align="left" valign="top"/><td align="left" valign="top"><named-content content-type="sequence">GGAGGTTTGCAAGTGCATCA</named-content></td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">anti-HA mouse monoclonal</td><td align="left" valign="top">BioLegend</td><td align="left" valign="top">#901501, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2565006">AB_2565006</ext-link></td><td align="left" valign="top">Flow (1:250), IF (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">APC-conjugated anti-LAMP1 mouse monoclonal</td><td align="left" valign="top">BioLegend</td><td align="left" valign="top">#328619, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_1279055">AB_1279055</ext-link></td><td align="left" valign="top">Flow (1:250)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">anti-ITGA6 rat monoclonal</td><td align="left" valign="top">Invitrogen</td><td align="left" valign="top">#14-0495-82, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_891480">AB_891480</ext-link></td><td align="left" valign="top">Flow (1:250)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">APC-conjugated anti-mouse secondary antibodies rat monoclonal</td><td align="left" valign="top">eBioscience</td><td align="left" valign="top">#17-4015-82, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2573205">AB_2573205</ext-link></td><td align="left" valign="top">Flow (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">APC-conjugated anti-rat antibodies goat polyclonal</td><td align="left" valign="top">Invitrogen</td><td align="left" valign="top">#A10540, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_10562535">AB_10562535</ext-link></td><td align="left" valign="top">Flow (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">APC-conjugated anti-TfR/CD71 antibodies mouse monoclonal</td><td align="left" valign="top">BioLegend</td><td align="left" valign="top">#334108, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_10915138">AB_10915138</ext-link></td><td align="left" valign="top">Flow (1:500)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">anti-FLAG M2 mouse monoclonal</td><td align="left" valign="top">Sigma-Aldrich</td><td align="left" valign="top">#F1804, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_262044">AB_262044</ext-link></td><td align="left" valign="top">IF (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">Alexa Fluor 647-conjugated anti-rabbit IgG goat polyclonal</td><td align="left" valign="top">Invitrogen</td><td align="left" valign="top">#A32733, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2633282">AB_2633282</ext-link></td><td align="left" valign="top">IF (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">Alexa Fluor 568-conjugated anti-mouse IgG goat polyclonal</td><td align="left" valign="top">Thermo Fisher Scientific</td><td align="left" valign="top">#A11004, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2534072">AB_2534072</ext-link></td><td align="left" valign="top">IF (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">Anti-COMMD3 rabbit polyclonal</td><td align="left" valign="top">Bethyl</td><td align="left" valign="top">#A304-092A, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2621341">AB_2621341</ext-link></td><td align="left" valign="top">IB (1:200)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">anti-VPS35L rabbit polyclonal</td><td align="left" valign="top">Invitrogen</td><td align="left" valign="top">#PA5-28553, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2546029">AB_2546029</ext-link></td><td align="left" valign="top">IB (1:500)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">anti-CCDC93 mouse monoclonal</td><td align="left" valign="top">Santa Cruz Biotechnology</td><td align="left" valign="top">#sc-514600</td><td align="left" valign="top">IB (1:100)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">anti-alpha-tubulin mouse monoclonal</td><td align="left" valign="top">DSHB</td><td align="left" valign="top">#12G10, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_1210456">AB_1210456</ext-link></td><td align="left" valign="top">IB (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">HRP-conjugated anti-FLAG M2 mouse monoclonal</td><td align="left" valign="top">Sigma-Aldrich</td><td align="left" valign="top">#A8592, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_439702">AB_439702</ext-link></td><td align="left" valign="top">IB (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">HRP-conjugated anti-HA rat monoclonal</td><td align="left" valign="top">Roche</td><td align="left" valign="top">#12013819001, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_390917">AB_390917</ext-link></td><td align="left" valign="top">IB (1:1000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">HRP-conjugated anti-rabbit IgG goat polyclonal</td><td align="left" valign="top">Sigma-Aldrich</td><td align="left" valign="top">#A6154, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_258284">AB_258284</ext-link></td><td align="left" valign="top">IB (1:2000)</td></tr><tr><td align="left" valign="top">Antibody</td><td align="left" valign="top">HRP-conjugated anti-mouse IgG sheep polyclonal</td><td align="left" valign="top">Sigma-Aldrich</td><td align="left" valign="top">#A6782, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_258315">AB_258315</ext-link></td><td align="left" valign="top">IB (1:2000)</td></tr><tr><td align="left" valign="top">Software, algorithm</td><td align="left" valign="top">AlphaFold3 (AF3)</td><td align="left" valign="top">PMID:<ext-link ext-link-type="uri" xlink:href="https://pubmed.ncbi.nlm.nih.gov/38718835">38718835</ext-link></td><td align="left" valign="top"/><td align="left" valign="top">Used for structural prediction</td></tr></tbody></table></table-wrap><sec id="s4-1"><title>Cell lines and cell culture</title><p>HeLa and 293T cells were obtained from ATCC and had been authenticated by the vendor. Mouse preadipocytes were immortalized cells derived from mouse adipose tissue and were validated using expression markers such as GLUT4, as well as functional assays including differentiation into adipocytes and insulin responsiveness. All cell lines were routinely tested for mycoplasma contamination by the StemTech core facility at the University of Colorado Boulder. The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FB Essence (FBE, VWR, #10803–034) and penicillin/streptomycin (Thermo Scientific, #15140122). The cells were maintained in a humidified incubator at 37 ℃ with 5% CO<sub>2</sub>. To differentiate preadipocytes into mature adipocytes, preadipocytes were grown to ~95% confluence before a differentiation cocktail was added at the following final concentrations: 5 µg/mL insulin (Sigma, #I0516), 1 nM Triiodo-L-thyronine (T3, Sigma, #T2877), 125 µM indomethacin (Sigma, #I-7378), 5 µM dexamethasone (Sigma, #D1756), and 0.5 mM 3-isobutyl-1-methylxanthine (IBMX, Sigma, #I5879). After two days, the cells were switched to DMEM supplemented with 10% FBE, 5 µg/mL insulin, and 1 nM T3. After another two days, fresh DMEM media supplemented with 10% FBE and 1 nM T3 were added to the cells. Differentiated adipocytes were usually analyzed six days after addition of the differentiation cocktail.</p></sec><sec id="s4-2"><title>Gene KO using CRISPR-Cas9</title><p>Genome-wide CRISPR screens of GLUT-SPR surface homeostasis and gene essentiality were described previously (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). To individually ablate a candidate gene, gRNAs targeting the gene were chosen via the CRISPick algorithm (<ext-link ext-link-type="uri" xlink:href="https://portals.broadinstitute.org/gppx/crispick/public">https://portals.broadinstitute.org/gppx/crispick/public</ext-link>) to maximize KO efficiency and minimize off-target effects. The upstream guide was cloned into the pLenti-CRISPR-v2 vector (Addgene, #52961) and the downstream guide was cloned into a modified version of the pLentiGuide-Puro vector (Addgene, #52963), in which the puromycin selection marker was replaced with a hygromycin selection marker.</p><p>Guide sequences targeting the mouse <italic>Commd3</italic> gene are: <named-content content-type="sequence">CTTCGCGCTTCTCCTCCGGG</named-content> and <named-content content-type="sequence">CTTGAAACAGATCGACCCAG</named-content>. Guide sequences targeting the mouse <italic>Commd1</italic> gene are: <named-content content-type="sequence">TCACGGACACTCGGGTGTCA</named-content> and <named-content content-type="sequence">ACTGCTCAAACCAAAAAGCA</named-content>. Guide sequences targeting the mouse <italic>Commd5</italic> gene are: <named-content content-type="sequence">GTTGTTGAAACTCGTAGTCG</named-content> and <named-content content-type="sequence">TGCCAGCGCCAACCTGTCAG</named-content>. Guide sequences targeting the mouse <italic>Ccdc93</italic> gene are: <named-content content-type="sequence">CGAAAGTACCGACGGCAGCG</named-content> and <named-content content-type="sequence">GATGACCGCCATGGCAAACG</named-content>. Guide sequences targeting the mouse <italic>Vps35l</italic> gene are: <named-content content-type="sequence">GGATTATGTGAACCGCATAG</named-content> and <named-content content-type="sequence">GGAGGTTTGCAAGTGCATCA</named-content>. Double KO cells of <italic>Commd3</italic> and <italic>Ccdc93</italic> were generated using one guide per gene: <italic>Commd3</italic> – <named-content content-type="sequence">CTTCGCGCTTCTCCTCCGGG</named-content> and <italic>Ccdc93</italic> – <named-content content-type="sequence">GATGACCGCCATGGCAAACG</named-content>.</p><p>CRISPR plasmids were transfected into HEK 293T cells along with pAdVAntage (Promega, #E1711), pCMV-VSVG (Addgene, #8454), and psPax2 (Addgene, #12260). The 293T cell culture media containing lentiviral particles were harvested daily for four days and centrifuged at 25,000 rpm (113,000 g) for 1.5 hr at 4 °C using a Beckman SW28 rotor. Viral pellets were resuspended in PBS and used to infect target cells. After lentiviral infection, cells were selected using 3.5 µg/mL puromycin (Sigma, #3101118) for 2 days, followed by selection using 500 µg/mL hygromycin B (Thermo, #10687010) for another 2 days. All KO cells used in this work were pooled KO cell populations.</p></sec><sec id="s4-3"><title>Gene expression in mammalian cells</title><p>The codon-optimized human <italic>COMMD3</italic> gene with a 3xFLAG-encoding sequence or an mCherry-3xFlag-encoding sequence was subcloned into the SHC003BSD-GFPD vector (Addgene, #133301). This <italic>COMMD3</italic> gene was not targeted by gRNAs used in the KO experiments. The plasmid expressing the NTD (amino acids 1–124) of human COMMD3 was generated in a similar way. For the IP experiments, DNA fragments encoding FL and truncated human COMMD3 were subcloned into the SHC003BSD-GFPD vector. FL COMMD3 (amino acids 1–195) and NTD were fused to mCherry and 3xFlag tags at their C-termini. The CTD (amino acids 125–195) was fused to an mCherry tag at its N-terminus and a 3xFlag tag at its C-terminus. The human <italic>ARF1</italic> gene was subcloned into the SHC003BSD-GFPD vector with an HA-encoding sequence at the 3’ end. The constructs were transfected into 293T cells to produce lentiviral particles using a similar procedure as CRISPR lentiviral production. The lentiviruses were used to infect target cells, followed by selection using 10 µg/mL blasticidin (Thermo Fisher Scientific, #BP2647).</p></sec><sec id="s4-4"><title>Flow cytometry</title><p>Cells grown on cell culture plates were washed with ice-cold KRH buffer and blocked at 4 °C with KRH buffer supplemented with 5% FBE. Subsequently, the cells were labeled for 1 hr with KRH buffer containing 2% FBE and the following antibodies: anti-HA (BioLegend, #901501, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2565006">AB_2565006</ext-link>), APC-conjugated anti-LAMP1 (BioLegend, #328619, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_1279055">AB_1279055</ext-link>), anti-ITGA6 (Invitrogen, #14-0495-82, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_891480">AB_891480</ext-link>), APC-conjugated anti-mouse secondary antibodies (eBioscience, #17-4015-82, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2573205">AB_2573205</ext-link>), APC-conjugated anti-rat antibodies (Invitrogen, #A10540, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_10562535">AB_10562535</ext-link>), and APC-conjugated anti-TfR/CD71 antibodies (BioLegend, #334108, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_10915138">AB_10915138</ext-link>). Following antibody labeling, cells were washed twice with KRH buffer containing 5% FBE and once with PBS. Cells were dissociated using Accutase before resuspension in PBS buffer containing 5% FBE. Cells were analyzed in triplicate on a CyAN ADP analyzer (Beckman Coulter).</p></sec><sec id="s4-5"><title>Immunostaining and imaging</title><p>Cells grown on glass coverslips were washed with PBS and fixed using 4% PFA in PBS. Cells were then permeabilized using 0.1% Tween-20 and blocked with PBS buffer containing 5% FBE. Permeabilization was omitted when surface proteins were stained. Cells were labeled for 1 hr with 2% FBE in PBS using the following antibodies: anti-HA, anti-FLAG M2 (Sigma-Aldrich, #F1804, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_262044">AB_262044</ext-link>), Alexa Fluor 647-conjugated anti-mouse IgG (Invitrogen, #A32733, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2633282">AB_2633282</ext-link>), and Alexa Fluor 568-conjugated anti-rabbit IgG (Thermo Fisher Scientific, #A11004, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2534072">AB_2534072</ext-link>). Confocal images were acquired on a Nikon A1 laser scanning confocal microscope using a ×100×oil immersion objective. In SIM, images were captured using a 100 x oil immersion objective on a Nikon SIM microscope as previously described (<xref ref-type="bibr" rid="bib69">Wan et al., 2024</xref>).</p></sec><sec id="s4-6"><title>Immunoprecipitation (IP) and immunoblotting</title><p>In IP experiments, cells were lysed in IP buffer (25 mM HEPES [pH 7.4], 138 mM NaCl, 10 mM Na3PO4, 2.7 mM KCl, 0.5% CHAPS, 1 mM DTT, and a protease inhibitor cocktail). After centrifugation, proteins were immunoprecipitated from cell extracts using primary antibodies and protein A/G agarose beads (Thermo Scientific, #WF324079). For immunoblotting, immunoprecipitates or whole cell lysates were resolved on 8% Bis-Tris SDS–polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to PVDF membranes. Proteins were detected using unlabeled primary antibodies and horseradish peroxidase (HRP)-conjugated secondary antibodies, or HRP-conjugated primary antibodies. Primary antibodies used in immunoblotting include anti-COMMD3 (Bethyl, #A304-092A, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2621341">AB_2621341</ext-link>), anti-VPS35L (Invitrogen, #PA5-28553, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_2546029">AB_2546029</ext-link>), anti-CCDC93 (Santa Cruz Biotechnology, #sc-514600), anti-alpha-tubulin (DSHB, #12G10, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_1210456">AB_1210456</ext-link>), HRP-conjugated anti-FLAG M2 (Sigma-Aldrich, #A8592, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_439702">AB_439702</ext-link>), and HRP-conjugated anti-HA (Roche, #12013819001, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_390917">AB_390917</ext-link>). Secondary antibodies used in this work include HRP-conjugated anti-rabbit IgG (Sigma-Aldrich, #A6154, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_258284">AB_258284</ext-link>) and HRP-conjugated anti-mouse IgG (Sigma-Aldrich, #A6782, RRID:<ext-link ext-link-type="uri" xlink:href="https://identifiers.org/RRID:AB_258315">AB_258315</ext-link>). All experiments were run in biological triplicates. Intensities of protein bands on immunoblots were quantified using ImageJ.</p></sec><sec id="s4-7"><title>Mass spectrometry</title><p>Mass spectrometry was carried out as previously described (<xref ref-type="bibr" rid="bib71">Wang et al., 2023</xref>). Immunoprecipitates on protein A/G beads were snap-frozen and stored at –70 °C. Peptides were pre-fractionated using high-pH fractionation and analyzed on the Thermo Ultimate 3000 RSLCnano System via direct injection. Data were processed using MaxQuant/Andromeda (version 1.6.2.10) and compared to Uniprot-annotated protein sequences. False discovery rates were set to 0.01 for protein and peptide assignment with a minimum peptide length of four residues and a minimum peptide number of one.</p></sec><sec id="s4-8"><title>Structural prediction and analysis</title><p>The structural model of the ARF1-GTP:COMMD3-NTD (a.a. 1–120) heterodimer was predicted using AlphaFold3 with default settings (<xref ref-type="bibr" rid="bib1">Abramson et al., 2024</xref>). Five independent structural models were generated for each protein complex, and the quality of the predicted models was assessed through their interface predicted template modeling (ipTM) scores, predicted template modeling (pTM) scores, predicted alignment error (PAE) plots, and predicted local distance difference test (pLDDT) scores (<xref ref-type="bibr" rid="bib1">Abramson et al., 2024</xref>; <xref ref-type="bibr" rid="bib45">Mirdita et al., 2022</xref>). Structural analysis was conducted using UCSF ChimeraX (v1.8) (<xref ref-type="bibr" rid="bib22">Goddard et al., 2018</xref>) and PDBePISA (<xref ref-type="bibr" rid="bib32">Krissinel and Henrick, 2007</xref>).</p></sec><sec id="s4-9"><title>Statistical analysis</title><p>All data shown in the figures are from at least three independent biological replicates. Biological replicates were plated, treated, and analyzed in parallel. Statistical analyses were performed using GraphPad Prism 10. Student’s <italic>t</italic>-tests were used for comparisons between two groups. One-way ANOVA with Dunnett’s multiple comparisons test (comparing all groups to control) or Sidak’s multiple comparisons test (for internal group comparisons) was used when analyzing experiments with more than two groups. Significance is indicated as follows: n.s., not significant; *p&lt;0.05; **p&lt;0.01; ***p&lt;0.001. Additional details on sample size, error bars, and statistical tests are provided in the figure legends.</p></sec></sec></body><back><sec sec-type="additional-information" id="s5"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="COI-statement" id="conf1"><p>No competing interests declared</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing - original draft, Writing – review and editing</p></fn><fn fn-type="con" id="con2"><p>Investigation, Writing – review and editing</p></fn><fn fn-type="con" id="con3"><p>Investigation, Methodology</p></fn><fn fn-type="con" id="con4"><p>Investigation, Writing – review and editing</p></fn><fn fn-type="con" id="con5"><p>Conceptualization, Resources, Supervision, Funding acquisition, Validation, Writing - original draft, Project administration, Writing – review and editing</p></fn></fn-group></sec><sec sec-type="supplementary-material" id="s6"><title>Additional files</title><supplementary-material id="mdar"><label>MDAR checklist</label><media xlink:href="elife-105264-mdarchecklist1-v1.pdf" mimetype="application" mime-subtype="pdf"/></supplementary-material><supplementary-material id="supp1"><label>Supplementary file 1.</label><caption><title>The interactome of COMMD3.</title></caption><media xlink:href="elife-105264-supp1-v1.xlsx" mimetype="application" mime-subtype="xlsx"/></supplementary-material><supplementary-material id="sdata1"><label>Source data 1.</label><caption><title>Original CIF file of the structural model shown in <xref ref-type="fig" rid="fig8">Figure 8A</xref>.</title></caption><media xlink:href="elife-105264-data1-v1.cif" mimetype="chemical" mime-subtype="x-cif"/></supplementary-material></sec><sec sec-type="data-availability" id="s7"><title>Data availability</title><p>All data generated or analysed during this study are included in the manuscript and supporting files. The data generated or analyzed in this study are included in the manuscript and supporting files. Source data files for <xref ref-type="fig" rid="fig1">Figures 1</xref>—<xref ref-type="fig" rid="fig8">8</xref>, <xref ref-type="fig" rid="fig4s1">Figure 4—figure supplement 1</xref>, <xref ref-type="fig" rid="fig5s1">Figure 5—figure supplement 1</xref>, <xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref> are provided, containing numerical datasets and uncropped immunoblots. Materials generated in this study will be made available upon request under material transfer agreements.</p></sec><ack id="ack"><title>Acknowledgements</title><p>We thank Drs. Santiago Di Pietro, Da Jia, Andrea Ambrosio, Greg Odorizzi, Gia Voeltz, and Mitchell Leih for reagents or helpful suggestions. We thank Yan Ouyang, Jingyi Wu, James Orth, and Christopher C Ebmeier for technical assistance. This work was supported by National Institutes of Health grants GM126960 (JS) and DK124431 (JS). 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The authors present <bold>solid</bold> evidence to support their claims, though the addition of certain validation experiments could have further strengthened the conclusions. This work will be of particular interest to cell biologists focused on membrane trafficking.</p></body></sub-article><sub-article article-type="referee-report" id="sa1"><front-stub><article-id pub-id-type="doi">10.7554/eLife.105264.3.sa1</article-id><title-group><article-title>Reviewer #1 (Public review):</article-title></title-group><contrib-group><contrib contrib-type="author"><anonymous/><role specific-use="referee">Reviewer</role></contrib></contrib-group></front-stub><body><p>G. Squiers et al. analyzed a previously reported CRISPR genetic screening dataset of engineered GLUT4 cell-surface presentation and identified the Commander complex subunit COMMD3 as being required for endosomal recycling of specific cargo protein, transferrin receptor (TfR), to the cell surface. Through comparison of COMMD3-KO and other Commander subunit-KO cells, they demonstrated that the role of COMMD3 in mediating TfR recycling is independent of the Commander complex. Structural analysis and co-immunoprecipitation followed by mass spectrometry revealed that TfR recycling by COMMD3 relies on ARF1. COMMD3 interacts with ARF1 through its N-terminal domain (NTD) to stabilize ARF1. A mutation in the NTD of COMMD3 failed to rescue cell surface TfR in COMMD3-KO cells. In conclusion, the authors assert that COMMD3 stabilizes ARF1 in a Commander complex-independent manner, which is essential for recycling specific cargo proteins from endosomes to the plasma membrane.</p><p>The conclusions of this paper are generally supported by data, but some validation experiments should be included to strengthen the study.</p><p>(1) Specific role of ARF1 to COMMD3:</p><p>The authors don't think KO/KD of ARF1 is appropriate to address its specificity to COMMD3 cargo selection, so they focused on the COMMD3 NTD mutant. Though the mutant failed to rescue COMMD3 cargo TfR recycling, they did not examine the Commander cargo ITGA6. In addition, they cannot validate that the mutant interrupts the interaction between NTD and ARF1. These missing results and validation make their claim that ARF1 is specific to the COMMD3's Commander-independent function less convincing.</p></body></sub-article><sub-article article-type="referee-report" id="sa2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.105264.3.sa2</article-id><title-group><article-title>Reviewer #2 (Public review):</article-title></title-group><contrib-group><contrib contrib-type="author"><anonymous/><role specific-use="referee">Reviewer</role></contrib></contrib-group></front-stub><body><p>Summary:</p><p>The Commander complex is a key player in endosomal recycling which recruits cargo proteins and facilitates the formation of tubulo-vesicular carriers. Squiers et al found COMMD3, a subunit of the Commander complex, could interact directly with ARF1 and regulate endosomal recycling.</p><p>Strengths:</p><p>Overall, this is a nice study that provides some interesting knowledge on the function of the Commander complex.</p><p>Comments on revisions:</p><p>The authors have addressed all my previous concerns</p></body></sub-article><sub-article article-type="referee-report" id="sa3"><front-stub><article-id pub-id-type="doi">10.7554/eLife.105264.3.sa3</article-id><title-group><article-title>Reviewer #3 (Public review):</article-title></title-group><contrib-group><contrib contrib-type="author"><anonymous/><role specific-use="referee">Reviewer</role></contrib></contrib-group></front-stub><body><p>Summary:</p><p>The study by Squiers and colleagues reveals a novel, Commander-independent role for COMMD3 in endosomal recycling. Through unbiased genetic screens, the authors identified COMMD3 as a regulator of GLUT4-SPR trafficking and validated its function using knockout experiments, which demonstrated its impact on endosomal morphology and trafficking independent of the Commander complex. Importantly, they mapped the interaction between the N-terminal domain (NTD) of COMMD3 and the GTPase Arf1, and through structure-guided mutagenesis, established that this interaction is essential for COMMD3's Commander-independent activity. The manuscript provides compelling evidence supporting this newly identified function of COMMD3, and I find the authors' interpretations well-justified. This is an excellent and intriguing study.</p><p>Comments on revisions:</p><p>The authors addressed all comments. Congratulations on this exciting work.</p></body></sub-article><sub-article article-type="author-comment" id="sa4"><front-stub><article-id pub-id-type="doi">10.7554/eLife.105264.3.sa4</article-id><title-group><article-title>Author response</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Squiers</surname><given-names>Galen T</given-names></name><role specific-use="author">Author</role><aff><institution>University of Colorado Boulder</institution><addr-line><named-content content-type="city">Boulder</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Wan</surname><given-names>Chun</given-names></name><role specific-use="author">Author</role><aff><institution>University of Colorado Boulder</institution><addr-line><named-content content-type="city">Boulder</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Gorder</surname><given-names>James</given-names></name><role specific-use="author">Author</role><aff><institution>University of Colorado Boulder</institution><addr-line><named-content content-type="city">Boulder</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Puscher</surname><given-names>Harrison</given-names></name><role specific-use="author">Author</role><aff><institution>University of Colorado Boulder</institution><addr-line><named-content content-type="city">Boulder</named-content></addr-line><country>United States</country></aff></contrib><contrib contrib-type="author"><name><surname>Shen</surname><given-names>Jingshi</given-names></name><role specific-use="author">Author</role><aff><institution>University of Colorado Boulder</institution><addr-line><named-content content-type="city">Boulder</named-content></addr-line><country>United States</country></aff></contrib></contrib-group></front-stub><body><p>The following is the authors’ response to the original reviews</p><disp-quote content-type="editor-comment"><p><bold>Reviewer 1 (Public reviews):</bold></p><p>(1) Commander-Independent Role of COMMD3: While the authors provided evidence to support the Commander-independent role of COMMD3-such as the absence of other Commander subunits in the CRISPR screen and not decreased COMMD3 levels in other subunit-KO cells- direct evidence is lacking. The mutation that specifically disrupts the COMMD3-ARF1 interaction could serve as a valuable tool to directly address this question.</p></disp-quote><p>The Reviewer raised an excellent point. We fully agree with the Reviewer that multiple lines of evidence are needed to support the novel Commander-independent function of COMMD3.</p><p>Comparative genetic analyses in Figures 4 and 5 indicate that COMMD3 regulates endosomal retrieval independently of the Commander complex. In Figure 8 of the revised manuscript, we show that point mutations introduced into the COMMD3:ARF1 interface impair this Commander-independent function. Moreover, Figure 6 demonstrates that ARF1 upregulation fully rescues the KO phenotype of <italic>COMMD3</italic>. In addition, Figure S2 further supports that COMMD3 levels, but not those of other Commander subunits, correspond to its Commander-independent function in endosomal trafficking. We have also revised the Discussion section to elaborate on the implications of these findings. We appreciate the Reviewer’s advice.</p><disp-quote content-type="editor-comment"><p>(2) Role of ARF1 in Cargo Selection: The Commander-independent function of COMMD3 appears cargo-dependent and relies on ARF1's role in cargo selection. The authors should investigate whether KO/KD of ARF1 reduces cell surface levels of ITGA6 and TfR.</p></disp-quote><p>The Reviewer correctly pointed out that KO/KD of ARF1 may provide further insights into the Commander-independent function of COMMD3. However, since ARF1 is involved in cargo sorting at both the endosome and the <italic>trans</italic>-Golgi network, its KO would disrupt multiple trafficking routes, making the data difficult to interpret. Instead, we focused on point mutations in the NTD that specifically disrupt ARF1 binding without affecting the function of the Commander complex (Fig. 8). As these mutations impair the Commander-independent function of COMMD3, our data strongly support a direct role for ARF1 in this recycling pathway. We note that the discovery of a novel trafficking pathway inevitably opens many research directions. One such direction is to systematically identify cargoes that rely on COMMD3 but not the Commander complex for endosomal retrieval.</p><disp-quote content-type="editor-comment"><p>(3) Impact on TfR Stability: Figure 7D suggests that TfR protein levels are reduced in COMMD3-KO cells, potentially due to degradation caused by disrupted recycling. This raises the question of whether the observed reduction in cell surface TfR is due to impaired endosomal recycling or decreased total protein levels. The authors should quantify the ratio of cell surface protein to total protein for TfR, GLUT-SPR, and ITGA6 in COMMD3-KO cells.</p></disp-quote><p>Based on the Reviewer's suggestion, we quantified both the total levels and the surface-tototal ratio of TfR, as shown in Figure S1 of the revised manuscript. These new data further support the conclusion that defects in TfR retrieval lead to its lysosomal degradation. The GLUT-SPR data presented in the main figures represent the surface-to-total ratio of the GLUT-SPR reporter. We thank the Reviewer for the important suggestion.</p><disp-quote content-type="editor-comment"><p><bold>Reviewer #1 (Recommendations for the authors):</bold></p><p>(1) Commander-Independent Role of COMMD3: The mutation that specifically disrupts the COMMD3-ARF1 interaction could serve as a valuable tool to directly address this question. The authors should evaluate whether the full-length mutant of COMMD3 can rescue decreased levels of CCDC93 and VPS35L, as well as cell surface ITGA6, TfR, and GLUT4 inCOMMD3-KO cells.</p></disp-quote><p>This is an excellent point. In our mechanistic experiments, we focused on the NTD of COMMD3 because this domain mediates its Commander-independent function and is not involved in forming the Commander holo-complex. This approach allowed us to draw unambiguous conclusions. Nevertheless, we anticipate that full-length COMMD3 carrying these point mutations would also be defective in regulating Commander-independent cargo.</p><disp-quote content-type="editor-comment"><p>(2) Role of ARF1 in Cargo Selection: The authors should investigate whether KO/KD of ARF1 reduces cell surface levels of ITGA6 and TfR. Was ARF1 identified in the initial CRISPR screen? If so, this should be explicitly noted. Alternatively, does ARF1 overexpression rescue ITGA6 levels in COMMD3-KO cells? Furthermore, does ARF1 overexpression rescue TfR levels in COMMD3 and CCDC93 double-KO cells?</p></disp-quote><p>Reinto the Commander-independent function of COMMD3. However, since ARF1 is involved in cargo sorting at both the endosome and the <italic>trans</italic>-Golgi network, its KO would disrupt multiple trafficking routes, making the data difficult to interpret. Instead, we focused on point mutations that specifically disrupt ARF1 binding without affecting the function of the Commander complex (Fig. 8). Since these mutations impair the Commander-independent function of COMMD3, our data strongly support a direct role for ARF1 in this novel recycling pathway. Based on our genetic data, we anticipate that all COMMD3-dependent cargoes will be similarly rescued in ARF1-overexpressing cells. In line with the Reviewer's comment, a key research direction we are currently pursuing is systematically determining how surface protein levels are affected by <italic>COMMD3</italic> KO and ARF1 overexpression using surface proteomics.</p><disp-quote content-type="editor-comment"><p>(3) Inconsistency in COMMD3 Rescue Levels (Figure 5A): Figure 5A shows comparable or higher levels of COMMD3 in rescued cells than in CCDC93-KO and VPS35L-KO cells. However, COMMD3 rescue did not increase cell surface TfR as much as in CCDC93-KO and VPS35L-KO cells. This inconsistency should be discussed or validated.</p></disp-quote><p>To address the Reviewer’s inquiry, we quantified COMMD3 expression levels in these cell lines using multiple independent experiments. The new data are presented in Figure S2 of the revised manuscript. These expanded datasets allowed us to more accurately determine the relationship between COMMD3 expression and our genetic data. Since the Commander complex remains intact in the COMMD3 rescue cells, a significant portion of COMMD3 proteins are expected to be incorporated into the Commander complex, which does not regulate TfR recycling. In contrast, because the Commander complex is disrupted in <italic>Ccdc93</italic> and <italic>Vps35l</italic> KO cells, all COMMD3 proteins are available to regulate TfR recycling in a Commander-independent manner. These findings are fully consistent with the similar surface TfR levels observed in <italic>Ccdc93/Vps35l</italic> KO cells and <italic>COMMD3</italic> overexpressing cells. We thank the Reviewer for this excellent suggestion.</p><disp-quote content-type="editor-comment"><p>(4) Significance of NTD in COMMD3 Function: The conclusion that &quot;the NTD of COMMD3 mediates its Commander-independent function and interacts with ARF1&quot; (Page 12) is not fully supported without a side-by-side comparison of NTD, CTD, and FL COMMD3 in the same experiment (e.g., Figures 6B and 6G). Additional data is needed to strengthen this claim.</p></disp-quote><p>We conducted the experiment suggested by the Reviewer and included the data in Figure S3. Our results indicate that the COMMD3 CTD cannot mediate the Commander-independent function of COMMD3 in endosomal retrieval. We appreciate the Reviewer’s suggestion.</p><disp-quote content-type="editor-comment"><p>(5) ARF1 Stabilization Experiments: To substantiate the claim that COMMD3 binds and stabilizes the GTP-form of ARF1, the authors should include a comparative experiment showing GTP-form, GDPform, and wild-type ARF1 (e.g., Figures 6G and 7C).</p></disp-quote><p>We fully agree with the Reviewer that it would be important to compare how the ARF1:COMMD3 interaction is influenced by the nucleotide-binding state. However, trapping ARF1 in its GDP-bound state remains unfeasible, and nucleotide-free small GTPases are inherently unstable. In addition, WT ARF1 likely exists as a mixture of GTP- and GDP-bound forms, further complicating the analysis. To address the Reviewer’s comment, we used AlphaFold3 predictions. Interestingly, we found that the ipTM score of GTP-ARF1:COMMD3 is significantly higher than that of GDP-ARF1:COMMD3 or apo-ARF1:COMMD3, supporting our conclusion that COMMD3 recognizes and stabilizes the active form of ARF1.</p><disp-quote content-type="editor-comment"><p>(6) Validation of NTD Mutation (Figure 8): Co-immunoprecipitation or cellular co-localization experiments should be performed to confirm that the NTD mutation disrupts the interaction between COMMD3 and ARF1, as depicted in Figure 8.</p></disp-quote><p>This is an important question, and the best approach to address it would be to measure the binding affinity of the WT and mutant proteins using ITC or SPR. However, this is currently unfeasible, as we have not yet obtained pure recombinant COMMD3 and GTP-ARF1 proteins. Co-IP, by nature, is a crude assay that often fails to detect changes in binding affinity. A previous study on other proteins showed that mutations in protein-binding interfaces strongly reduced binding affinity as measured by SPR, but these changes would have been missed by co-IP assays (PMID: 25500532). In agreement with this limitation, our co-IP experiments did not yield conclusive results. Instead, we focused on structure-guided genetic experiments, which unequivocally demonstrated the effects of targeted mutations on the Commander-independent function of COMMD3.</p><disp-quote content-type="editor-comment"><p><bold>Reviewer #2 (Public review):</bold></p><p>(1) All existing data suggest that COMMD3 is a subunit of the Commander complex. Is there any evidence that COMMD3 can exist as a monomer?</p></disp-quote><p>The Reviewer raised an intriguing point. Indeed, COMMD proteins, including COMMD3, can exist outside the Commander holo-complex and form homo- or hetero-oligomers, as monomeric COMMD proteins are likely unstable. These observations align well with the Commander-independent function identified in this study. We have revised the Discussion section of the manuscript to further elaborate on this point and thank the Reviewer for the suggestion.</p><disp-quote content-type="editor-comment"><p>(2) In Figure 9, the author emphasizes COMMD3-dependent cargo and Commander-dependent cargo. Can the authors speculate what distinguishes these two types of cargo? Do they contain sequence-specific motifs?</p></disp-quote><p>This is another important question. Our data clearly demonstrate that COMMD3 has a Commander-independent function in addition to its canonical role within the Commander holocomplex. Since cargo proteins typically possess multiple sorting signals that operate at different stages of the exocytic and endocytic pathways, identifying COMMD3-dependent sorting signals remains a challenge. ARF4 has been shown to specifically recognize the VXPX motif (PMID: 15728366), suggesting that ARF1 may similarly bind cytosolic sorting signals, with COMMD3 stabilizing this interaction. A key future direction is to systematically identify COMMD3-dependent cargo proteins and elucidate the mechanisms underlying their endosomal sorting. We have revised the Discussion section of the manuscript to explicitly address this point and thank the Reviewer for this important suggestion.</p><disp-quote content-type="editor-comment"><p>(3) What could be the possible mechanism underlying the observation that the knockout of COMMD3 results in larger early endosomes? How is the disruption of cargo retrieval related to the increase in endosome size?</p></disp-quote><p>The endosomal retrieval process is critical for recycling membrane proteins and lipids back to the plasma membrane or the <italic>trans</italic>-Golgi network. When this process is disrupted, cargo that should be recycled accumulates within endosomes, leading to their enlargement. For example, defects in retromer function can cause endosomal swelling due to cargo accumulation (PMID: 33380435). We added this citation to the revised manuscript and thank the Reviewer for the advice.</p><disp-quote content-type="editor-comment"><p><bold>Reviewer 3 (Recommendations for the authors):</bold></p><p>(1) Figure 4: How do the authors define Commander-dependent vs. Commander-independent cargos?</p><p>In Figure 4, the surface expression of ITGA6 is reduced to approximately 0.75 across all knockouts. However, there is a similar level of reduction for GLUT4-SPR in the commd5 knockout and for LAMP1 in the commd5 and commd1 knockouts. Are GLUT4-SPR and LAMP1 Commander-dependent or Commander-independent cargos? Additionally, how does COMMD3 specifically identify/distinguish these cargos?</p></disp-quote><p>This is an excellent point. Our data suggest that TfR is a COMMD3-dependent but Commander-independent cargo, whereas ITGA6 is a Commander-dependent cargo that does not involve COMMD3-specific functions. The other two cargoes we examined—GLUT-SPR and LAMP1—primarily rely on COMMD3, with the Commander complex playing a minor role. Together, these observations clearly demonstrate that COMMD3 has a Commander-independent function in addition to its canonical role within the Commander holo-complex. Since cargo proteins typically possess multiple sorting signals that operate at different stages of the exocytic and endocytic pathways, identifying COMMD3-dependent sorting signals remains a challenge. ARF4 has been shown to specifically recognize the VXPX motif (PMID: 15728366), suggesting that ARF1 may similarly bind cytosolic sorting signals, with COMMD3 stabilizing this interaction. A key future direction is to systematically identify COMMD3-dependent cargo proteins and elucidate the mechanisms underlying their endosomal sorting. We have revised the Discussion section of the manuscript to explicitly address this point. We thank the Reviewer for this important suggestion.</p><disp-quote content-type="editor-comment"><p>(2) There is an increase in the surface expression of GLUT4-SPR in the commd1 knockout. Is this increase significant? The figure suggests a significant increase, but the text states it remains unchanged. Clarification is needed.</p></disp-quote><p>We found that surface levels of GLUT-SPR were slightly increased in <italic>Commd1</italic> KO cells, in stark contrast to the strong reduction observed in <italic>Commd3</italic> KO cells (Fig. 4B). This finding is consistent with our conclusion that COMMD3 has a distinct role from other Commander subunits. We have revised the Results section to more clearly describe these data and thank the Reviewer for the advice.</p><disp-quote content-type="editor-comment"><p>(3) Figure 5A: To support the claim that COMMD3 is upregulated in the vps35l KO/Ccdc93 KO, the authors should quantify COMMD3 expression. Also, why is there a Vps35l band present in the Vps35l knockout cells?</p></disp-quote><p>Based on the Reviewer’s suggestion, we quantified the total levels of COMMD3 and included these new data in Figure S2. In this study, gene deletion was achieved through the simultaneous introduction of two independent gRNAs. Based on our previous experience, this strategy typically results in the complete loss of gene expression. We posit that the residual band observed in <italic>Vps35l</italic> KO cells originates from background signals, such as nonspecific staining by the antibody.</p><disp-quote content-type="editor-comment"><p>(4) Figure 7: It is intriguing that COMMD3 stabilizes Arf1-GTP and can compensate for COMMD3 in knockout cells. However, is this stabilization specific to TfR cargo only? The authors should test additional Commander-dependent and Commander-independent cargos to clarify this point.</p></disp-quote><p>Based on our genetic data, we anticipate that all COMMD3-dependent cargoes will be similarly rescued in ARF1-overexpressing cells. In line with the Reviewer's comment, an important direction we are pursuing is the use of surface proteomics to systematically determine how surface protein levels are affected by <italic>COMMD3</italic> KO and ARF1 overexpression.</p><disp-quote content-type="editor-comment"><p>(5) Is Arf1 interaction specific to COMMD3? The authors should investigate the effects of Arf1 knockout on COMMD3 expression and test its role in regulating Commander-dependent and Commander-independent cargos.</p></disp-quote><p>The Reviewer raised an excellent point. Since ARF1 is involved in cargo sorting at both the endosome and the <italic>trans</italic>-Golgi network, its KO would interfere with multiple trafficking routes and the data would be difficult to interpret. Thus, in this work, we focused on the function and mechanism of the COMMD3:ARF1 complex on the endosome. Based on the suggestion of the Reviewer, we used AlphaFold3 to predict ARF1 binding to COMMD proteins. Interestingly, the complex with the highest predicted ipTM score is COMMD3:ARF1, while other COMMD proteins have much lower predicted binding scores. These results are consistent with the results of our unbiased CRISPR screens and targeted gene KO, and further support the conclusion that the COMMD3:ARF1 binding is specific and physiologically important in endosomal trafficking.</p></body></sub-article></article>