Affinage

MARCHF9

E3 ubiquitin-protein ligase MARCHF9 · UniProt Q86YJ5

Length
346 aa
Mass
37.8 kDa
Annotated
2026-06-10
21 papers in source corpus 17 papers cited in narrative 16 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

MARCHF9 (MARCH9) is a membrane-anchored RING-CH E3 ubiquitin ligase that down-regulates a broad panel of cell-surface and intracellular membrane proteins by ubiquitinating lysines in their cytoplasmic tails, controlling antigen presentation, innate immune signaling, and organelle homeostasis (PMID:19457934, PMID:20870941). Substrate recognition is governed by its two transmembrane domains: a single serine in TM1 is essential for activity, and solution NMR localizes the functional region to residues near the extracellular face of TM1 and TM2, while the RING and C-terminal domains are additionally required for substrate down-regulation (PMID:30554144, PMID:31488575). Specificity among related substrates is dictated by residues at the transmembrane/cytosol interface of the target, as shown for its preference for HLA-DQ over HLA-DR, with the acceptor lysine acting optimally at its natural distance from the bilayer (PMID:22761441, PMID:22247549). Functionally, MARCH9 routes MHC-I from the secretory pathway into Syntaxin 6-positive trans-Golgi-network endosomal compartments and drives proteasomal degradation of MHC-I/HLA-A via K48-linked ubiquitination, a mechanism co-opted in cancer immune evasion downstream of Tim-3 and LILRB2 signaling (PMID:28559542, PMID:34025669, PMID:38656573). Beyond antigen presentation, MARCH9 ubiquitinates ATG9A in a K63-linked manner to promote heat-stress-induced Golgi fragmentation through loss of GRASP55 oligomerization (PMID:35977480, PMID:36198086), and degrades innate-immune and metabolic targets including NOX2 and NLRP3 to restrain ROS-driven inflammasome activation and pyroptosis (PMID:37378901, PMID:41055760), and Mfn2 to impair mitochondrial fusion (PMID:41114773). The catalytic linkage type is substrate- and context-specific, spanning K48-, K63-, and K33-linked chains that route substrates to proteasomal, lysosomal, or selective-autophagy fates (PMID:35977480, PMID:36198086, PMID:41055760, PMID:42229174).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2009 High

    Established MARCH9 as a transmembrane RING-CH E3 ligase with a broad surface-protein substrate repertoire, defining its core cellular role as a regulator of plasma membrane protein abundance.

    Evidence SILAC quantitative plasma membrane proteomics in a MARCH9-expressing B cell line with flow cytometry confirmation

    PMID:19457934

    Open questions at the time
    • Does not distinguish direct ubiquitination substrates from indirect effects
    • No ubiquitin-linkage type or degradation route defined
  2. 2010 High

    Showed that MARCH9 directly engages substrate cytoplasmic-tail lysines and that the interaction is regulable, linking it to immune ligand control.

    Evidence Co-IP, acceptor-lysine mutagenesis, and heat-shock-induced dissociation of Mult1 from MARCH9 with flow cytometry

    PMID:20870941

    Open questions at the time
    • Mechanism of heat-shock-induced dissociation not resolved
    • Shared activity with MARCH4 not deconvolved
  3. 2012 Medium

    Defined the molecular determinants of substrate selectivity, showing recognition resides at the substrate transmembrane/cytosol interface and that lysine position relative to the bilayer matters.

    Evidence Mutagenesis and chimeric HLA-DR/DQ and HLA-DM constructs with flow cytometry readout

    PMID:22247549 PMID:22761441

    Open questions at the time
    • Single-lab structural model of the ligase-substrate interface absent
    • Discrimination from MARCH8 not structurally explained
  4. 2017 High

    Revealed that MARCH9 acts at the TGN to reroute MHC-I into endosomal compartments, establishing a sorting (not merely degradative) function in antigen presentation.

    Evidence Ubiquitination assay, Syntaxin 6 co-localization microscopy, and DC microbial-pattern stimulation

    PMID:28559542

    Open questions at the time
    • Signal coupling MARCH9 expression to microbial sensing undefined
    • Fate of rerouted MHC-I (recycling vs degradation) not fully traced
  5. 2018 High

    Identified the TM1 serine as catalytically essential and mapped the functional region to the extracellular TM termini, providing a structural basis for substrate regulation.

    Evidence TM-domain site-directed mutagenesis with flow cytometry plus solution NMR of the two-TM fragment

    PMID:30554144

    Open questions at the time
    • No full-length structure including the RING domain
    • Role of the TM1 serine in substrate contact vs ligase conformation unresolved
  6. 2018 Medium

    Extended the substrate range to ICAM-1 with a corresponding cancer cell-migration phenotype, connecting ligase activity to a tumor-relevant outcome.

    Evidence Co-IP, overexpression in lung adenocarcinoma lines, and migration/invasion assays

    PMID:30278450

    Open questions at the time
    • Direct ubiquitination of ICAM-1 not demonstrated by linkage assay
    • Endogenous-level relevance not established
  7. 2021 Medium

    Placed MARCH9 in a defined signaling axis, showing Tim-3 induces MARCH9 to drive K48-linked proteasomal degradation of MHC-I in macrophages.

    Evidence K48-linkage-specific ubiquitination assay, Co-IP, and in vivo Tim-3 antibody/macrophage depletion

    PMID:34025669

    Open questions at the time
    • Tim-3→MARCH9→MHC-I axis not independently replicated
    • Transcriptional vs post-translational induction of MARCH9 unclear
  8. 2022 High

    Demonstrated a non-immune organelle role, with MARCH9 K63-ubiquitinating ATG9A to disperse it from the Golgi and drive heat-stress Golgi fragmentation.

    Evidence Reciprocal Co-IP, K63-specific ubiquitination assay, MARCH9 knockout, and Golgi morphology imaging under heat stress (two papers, same group)

    PMID:35977480 PMID:36198086

    Open questions at the time
    • Upstream stress sensor activating MARCH9 unknown
    • Whether ATG9A dispersal affects autophagy flux not resolved
  9. 2022 Low

    Linked MARCH9 to NF-kB-driven colorectal cancer growth via downregulation of the deubiquitinase CYLD.

    Evidence MARCH9 knockdown/overexpression, western blot, apoptosis/cell-cycle flow cytometry, and xenograft model

    PMID:36185211

    Open questions at the time
    • No direct ubiquitination assay of CYLD by MARCH9
    • Mechanism connecting MARCH9 to CYLD loss undefined
  10. 2023 Medium

    Showed MARCH9 degrades NOX2 to limit ROS and NLRP3 inflammasome activation, defining an anti-pyroptotic role in acute pancreatitis.

    Evidence NOX2 ubiquitination assay, ROS flow cytometry, and cerulein-induced rat model with in vitro overexpression

    PMID:37378901

    Open questions at the time
    • Ubiquitin-linkage type on NOX2 not determined
    • Direct vs ROS-mediated NLRP3 effects not separated
  11. 2024 Medium

    Established LILRB2 as a recruiter promoting MARCH9-mediated K48 degradation of HLA-A, providing a cancer immune-evasion mechanism.

    Evidence Co-IP, histidine-pulldown ubiquitination assay, and syngeneic mouse tumor model

    PMID:38656573

    Open questions at the time
    • How LILRB2 enhances the MARCH9-HLA-A interaction structurally unknown
    • Single-lab finding
  12. 2025 Medium

    Extended degradative regulation to innate-immune and mitochondrial substrates, with MARCH9 K48-ubiquitinating NLRP3 and K63-ubiquitinating Mfn2 under transcriptional control of ETV4.

    Evidence Linkage-specific ubiquitination assays, lysosomal-inhibitor block, ETV4 silencing/rescue, and in vivo MI/R model

    PMID:41055760 PMID:41114773

    Open questions at the time
    • Whether NLRP3 regulation generalizes beyond ischemia-reperfusion untested
    • Mfn2 work limited to in vitro ovarian cancer cells
  13. 2026 Medium

    Demonstrated antiviral function, with RBM10 recruiting MARCHF9 to K33-ubiquitinate a viral protein for p62-mediated selective autophagy, broadening both substrate scope and chain-type repertoire.

    Evidence LC-MS/MS interaction screen, K33-linkage ubiquitination assay, autophagic-flux blockade, and p62 knockdown epistasis

    PMID:42229174

    Open questions at the time
    • Viral (PEDV Nsp3) substrate differs from canonical mammalian targets
    • Single lab, not independently confirmed

Open questions

Synthesis pass · forward-looking unresolved questions
  • How MARCH9 selects among K48-, K63-, and K33-linked chain outputs and routes substrates to proteasomal, lysosomal, or autophagic fates in a context-dependent manner remains unresolved.
  • No structural model of the full-length ligase-substrate-E2 complex
  • Determinants selecting linkage type and degradative route unknown
  • Adaptors/recruiters governing substrate access only partially identified

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0016874 ligase activity 3
Localization
GO:0005794 Golgi apparatus 2 GO:0005886 plasma membrane 2
Pathway
R-HSA-168256 Immune System 4 R-HSA-392499 Metabolism of proteins 3 R-HSA-1852241 Organelle biogenesis and maintenance 2

Evidence

Reading pass · 16 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 MARCH9 is a RING-CH transmembrane E3 ubiquitin ligase that down-regulates multiple plasma membrane proteins in lymphoid cells, including CD4, MHC-I, ICAM-1, PTPRJ/CD148, CD32B, HLA-DQ, CD150, and CD155, as identified by SILAC-based quantitative plasma membrane proteomics combined with flow cytometry confirmation. SILAC quantitative mass spectrometry of plasma membrane proteome in MARCH9-expressing B cell line, confirmed by flow cytometry Molecular & cellular proteomics : MCP High 19457934
2010 MARCH9 (and MARCH4) ubiquitinates the NKG2D ligand Mult1, suppressing its cell-surface expression; lysines in the cytoplasmic tail of Mult1 are essential for this repression. Heat-shock treatment dissociates Mult1 from MARCH9, reversing down-regulation and increasing Mult1 at the cell surface. Co-immunoprecipitation, flow cytometry, lysine mutant analysis, heat-shock functional assay Journal of immunology High 20870941
2012 MARCH9 ubiquitinates HLA-DM via a single lysine in the cytoplasmic tail of the DMα chain, inducing loss of DM from the cell surface by a mechanism involving both direct ubiquitin-chain attachment to DMα and a functional tyrosine-based signal on DMβ. Transfection/overexpression, flow cytometry, mutational analysis of acceptor lysine and tyrosine-based signal The Journal of biological chemistry Medium 22247549
2012 MARCH9 substrate specificity for HLA-DQ (versus MARCH8 preference for HLA-DR) is determined by residues at the interface of the transmembrane domain and cytosol of the HLA β-chain; the acceptor lysine functions optimally at its natural position relative to the bilayer. Mutagenesis and chimeric construct analysis of HLA-DR/DQ transmembrane and cytoplasmic tail residues, flow cytometry readout The Journal of biological chemistry Medium 22761441
2017 MARCH9 ubiquitinates the cytoplasmic tail lysine residues of MHC-I, redirecting MHC-I from the default secretory pathway to Syntaxin 6-positive endosomal compartments at the trans-Golgi network, thereby regulating MHC-I export from the TGN. MARCH9 also targets CD1a. MARCH9 expression is modulated by microbial pattern exposure in dendritic cells. Overexpression/knockdown of MARCH9, co-localization with Syntaxin 6 by microscopy, MHC-I ubiquitination assay, flow cytometry, stimulation of dendritic cells with microbial patterns Immunology and cell biology High 28559542
2018 A single serine-to-alanine substitution in the first transmembrane domain (TM1) of human MARCH9 completely abolishes its ability to down-regulate HLA-A2 and CD4, identifying this serine as critical for substrate regulation. Solution NMR of the MARCH9 two-TM fragment shows that residues closest to the extracellular face of TM1 and TM2 define the key functional region. Site-directed mutagenesis of MARCH9 TM domains, flow cytometry functional assay, solution NMR of TM domain fragment The Journal of biological chemistry High 30554144
2018 MARCH9 interacts with ICAM-1 and overexpression of MARCH9 down-regulates ICAM-1 protein, attenuating migration and invasion of lung adenocarcinoma cells. Co-immunoprecipitation, overexpression in A549 and H1299 cells, flow cytometry/western blot, migration/invasion assays Cellular physiology and biochemistry Medium 30278450
2019 MARCH9 (along with MARCH2, MARCH4, and an isoform of MARCH3) down-regulates the IL-6 receptor alpha chain (IL6Rα) at the cell surface; functional RING domain, transmembrane domains, and C-terminal domains are all required for substrate recognition and down-regulation. cDNA expression library screen, overexpression in M1 cells, domain deletion/mutagenesis constructs, flow cytometry The Biochemical journal Medium 31488575
2021 Tim-3 signaling in macrophages promotes MARCH9 expression, which in turn mediates K48-linked ubiquitination of MHC-I (HLA class I), leading to its proteasome-dependent degradation and reduced surface MHC-I presentation. Western blot, co-immunoprecipitation, ubiquitination assay (K48-linkage specific), Tim-3 antibody treatment and macrophage depletion in vivo Frontiers in immunology Medium 34025669
2022 Under heat stress, MARCH9 promotes K63-linked ubiquitination of ATG9A at the TGN, causing ubiquitinated ATG9A to disperse from the Golgi to the cytoplasm, inhibiting GRASP55 oligomerization and resulting in Golgi fragmentation. Knockout of MARCH9 prevents heat-stress-induced Golgi fragmentation. Co-immunoprecipitation, K63-specific ubiquitination assay, MARCH9 knockout cells, Golgi morphology imaging under heat stress Cell reports High 35977480 36198086
2022 MARCH9 (MARCHF9) promotes colorectal cancer cell proliferation and migration by downregulating the deubiquitinase CYLD and activating NF-κB (p65); knockdown of MARCH9 induces apoptosis and cell-cycle arrest, and suppresses xenograft tumor growth. MARCH9 knockdown/overexpression, western blot for CYLD and p65, apoptosis/cell cycle flow cytometry, xenograft in vivo model Frontiers in oncology Low 36185211
2023 MARCH9 mediates ubiquitination and degradation of NADPH oxidase-2 (NOX2), reducing ROS accumulation and NLRP3 inflammasome activation, thereby suppressing pancreatic cell pyroptosis in acute pancreatitis. MARCH9 overexpression in AR42J cells and cerulein-induced rat model, flow cytometry for ROS, western blot for NLRP3/caspase-1/GSDMD, ubiquitination assay for NOX2 Pancreas Medium 37378901
2024 LILRB2 promotes MARCH9–HLA-A (HLA-A ubiquitin ligase) interaction, facilitating ubiquitination and proteasomal degradation of HLA-A, thereby enabling breast cancer immune evasion by reducing surface MHC-I presentation to CD8+ T cells. Co-immunoprecipitation, histidine pulldown ubiquitination assay, western blot, syngeneic mouse tumor model Cellular oncology Medium 38656573
2025 MARCH9 interacts with NLRP3 and promotes its K48-linked polyubiquitination, leading to proteasomal degradation of NLRP3, thereby inhibiting inflammasome activation and pyroptosis during myocardial ischemia-reperfusion injury. Co-immunoprecipitation, K48-linkage-specific ubiquitination assay, western blot, mouse MI/R in vivo model, H9C2 and HEK293 cell in vitro studies Cellular and molecular life sciences : CMLS Medium 41055760
2025 ETV4 transcriptionally upregulates MARCH9, which then mediates K63-linked ubiquitination of the mitochondrial fusion protein Mfn2, targeting it for lysosomal degradation and impairing mitochondrial fusion in ovarian cancer cells. ETV4 silencing, MARCH9 overexpression rescue, western blot for Mfn2, lysosomal inhibitor (chloroquine) block, K63-ubiquitination assay Cell biology and toxicology Medium 41114773
2026 RBM10 recruits MARCHF9 to catalyze K33-linked ubiquitination of PEDV nonstructural protein 3 (Nsp3); the ubiquitinated Nsp3 is then recognized by the selective autophagy receptor p62 and delivered to autophagosomes for degradation, restricting viral replication. LC-MS/MS interaction screen, functional knockdown/overexpression assays, autophagic flux blockade, p62 knockdown, K33-linkage ubiquitination assay Veterinary microbiology Medium 42229174

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2022 Tegument protein UL21 of alpha-herpesvirus inhibits the innate immunity by triggering CGAS degradation through TOLLIP-mediated selective autophagy. Autophagy 76 36343628
2018 Computational Characterization of Suppressive Immune Microenvironments in Glioblastoma. Cancer research 60 29921698
2009 Stable isotope labeling by amino acids in cell culture and differential plasma membrane proteome quantitation identify new substrates for the MARCH9 transmembrane E3 ligase. Molecular & cellular proteomics : MCP 49 19457934
2010 Stress-regulated targeting of the NKG2D ligand Mult1 by a membrane-associated RING-CH family E3 ligase. Journal of immunology (Baltimore, Md. : 1950) 38 20870941
2017 MARCH9-mediated ubiquitination regulates MHC I export from the TGN. Immunology and cell biology 36 28559542
2012 Ubiquitination of human leukocyte antigen (HLA)-DM by different membrane-associated RING-CH (MARCH) protein family E3 ligases targets different endocytic pathways. The Journal of biological chemistry 27 22247549
2022 Nondegradable ubiquitinated ATG9A organizes Golgi integrity and dynamics upon stresses. Cell reports 25 35977480
2012 Structural requirements for recognition of major histocompatibility complex class II by membrane-associated RING-CH (MARCH) protein E3 ligases. The Journal of biological chemistry 24 22761441
2019 Membrane-associated RING-CH (MARCH) proteins down-regulate cell surface expression of the interleukin-6 receptor alpha chain (IL6Rα). The Biochemical journal 14 31488575
2022 The mediating effect of DNA methylation in the association between maternal sleep during pregnancy and offspring adiposity status: a prospective cohort study. Clinical epigenetics 13 35596190
2021 Peripheral Injection of Tim-3 Antibody Attenuates VSV Encephalitis by Enhancing MHC-I Presentation. Frontiers in immunology 12 34025669
2018 A serine in the first transmembrane domain of the human E3 ubiquitin ligase MARCH9 is critical for down-regulation of its protein substrates. The Journal of biological chemistry 11 30554144
2024 LILRB2 promotes immune escape in breast cancer cells via enhanced HLA-A degradation. Cellular oncology (Dordrecht, Netherlands) 10 38656573
2018 MARCH9 Suppresses Lung Adenocarcinoma Progression by Downregulating ICAM-1. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 8 30278450
2023 MARCH9 Mediates NOX2 Ubiquitination to Alleviate NLRP3 Inflammasome-Dependent Pancreatic Cell Pyroptosis in Acute Pancreatitis. Pancreas 7 37378901
2022 A noncanonical autophagy function of ATG9A for Golgi integrity and dynamics. Autophagy 7 36198086
2019 Monitoring MHC Ubiquitination by MARCH Ubiquitin Ligases. Methods in molecular biology (Clifton, N.J.) 4 31147945
2022 The role of MARCH9 in colorectal cancer progression. Frontiers in oncology 3 36185211
2025 The E3 ubiquitin ligase MARCH9 alleviates pyroptosis by regulating NLPR3 ubiquitination following myocardial ischemia reperfusion. Cellular and molecular life sciences : CMLS 1 41055760
2025 ETV4 promotes ovarian cancer growth by regulating mitochondrial function through Mfn2 ubiquitination mediated by the E3 ubiquitin ligase MARCH9. Cell biology and toxicology 1 41114773
2026 RBM10 suppresses porcine epidemic diarrhea virus replication by degrading nonstructural protein 3 through selective autophagy. Veterinary microbiology 0 42229174

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