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Showing CNOT9 — CAF40 is a alias.

CNOT9

CCR4-NOT transcription complex subunit 9 · UniProt Q92600

Length
299 aa
Mass
33.6 kDa
Annotated
2026-06-09
31 papers in source corpus 11 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CNOT9 (CAF40/RCD1/RQCD1) is an armadillo-repeat subunit of the CCR4-NOT deadenylase complex that serves as a docking platform linking sequence-specific mRNA regulatory proteins to the complex's enzymatic machinery (PMID:24768540, PMID:30309886). It binds the DUF3819 domain of the CNOT1 scaffold, and the resulting CNOT9-CNOT1 module presents tandem tryptophan-binding pockets that are engaged by tryptophan- or GW-motif-containing partners including GW182/TNRC6 and TTP, thereby coupling miRNA- and AU-rich-element-directed target recognition to translational repression and deadenylation (PMID:24768540, PMID:29291391). A conserved concave surface of the crescent-shaped armadillo fold provides a mutually exclusive binding site recognized by short α-helical CAF40-binding motifs (CBMs) in Roquin, Bam, and NOT4, each of which uses this interface to recruit CCR4-NOT and drive decay or translational repression of their target mRNAs (PMID:28165457, PMID:29255063, PMID:30692204). Within a reconstituted CNOT9-CNOT1 (MIF4G + DUF3819) module joined to the BTG2-Caf1-Ccr4 nuclease, CNOT9 and the CNOT1 central region stimulate the deadenylation activity of the catalytic module (PMID:30309886). Beyond its role in mRNA decay, CNOT9 has nuclear functions as a transcriptional cofactor that complexes with retinoic acid receptor, ATF-2, and c-Myb to modulate differentiation and target-gene activation (PMID:12356739, PMID:15209511), and it participates in EGFR-Akt signaling through reciprocal complexes with GIGYF1/2, Grb10, EGFR, and Akt (PMID:19724902, PMID:20878056).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2002 Medium

    Established the first functional role for CNOT9, showing it acts in the nucleus as a transcriptional cofactor required for a developmental differentiation decision.

    Evidence Co-IP with retinoic acid receptor and ATF-2 plus antisense knockdown with differentiation readout in F9 cells and lung explants

    PMID:12356739

    Open questions at the time
    • No structural basis for transcription-factor binding
    • Relationship to its cytoplasmic deadenylase role unresolved
    • Single lab, no reconstitution
  2. 2004 Medium

    Extended the transcriptional-cofactor model by identifying c-Myb as a direct partner whose activity CNOT9 represses, and confirmed predominantly nuclear localization.

    Evidence Yeast two-hybrid, in vitro binding, co-IP, promoter reporter assays, and immunostaining in murine cells

    PMID:15209511

    Open questions at the time
    • Mechanism of repression not defined
    • No structural interface mapped
    • Does not connect to CCR4-NOT complex
  3. 2006 High

    Defined the molecular architecture of CNOT9 as an armadillo-repeat protein with a positively charged cleft capable of binding nucleic acids in vitro.

    Evidence 2.2 Å X-ray crystal structure with site-directed mutagenesis and in vitro oligonucleotide binding assays

    PMID:17189474

    Open questions at the time
    • In vivo relevance of direct nucleic acid binding not established
    • Did not place CNOT9 within CCR4-NOT
    • Functional consequence of cleft binding unknown
  4. 2009 Medium

    Linked CNOT9 to growth signaling by showing it associates with GIGYF1/2 and is required for proliferation and Akt phosphorylation in cancer cells.

    Evidence Co-IP, siRNA knockdown, pAkt Western blot, and proliferation/overexpression assays in breast cancer and HEK293 cells

    PMID:19724902

    Open questions at the time
    • Direct vs indirect Akt regulation unclear
    • No structural detail of GIGYF interaction
    • Single lab
  5. 2010 Medium

    Placed CNOT9 within an EGF-responsive signaling complex, mapping its GIGYF1/2 interaction regions and showing it promotes Grb10-GIGYF assembly.

    Evidence Co-IP, domain mapping, siRNA knockdown, and EGF-stimulated pAkt assays

    PMID:20878056

    Open questions at the time
    • Molecular basis of complex assembly unresolved
    • Connection to CCR4-NOT deadenylation not addressed
    • Single lab follow-up
  6. 2014 High

    Resolved how CNOT9 integrates into CCR4-NOT and recognizes miRNA effectors, establishing it as a CNOT1-anchored adaptor presenting tryptophan-binding pockets for GW182/TNRC6.

    Evidence Crystal structure of the CNOT9-CNOT1 DUF3819 complex with co-IP and in vitro GW-motif binding assays; parallel CNOT1 MIF4G-DDX6 structure

    PMID:24768540

    Open questions at the time
    • Did not test deadenylation stimulation directly
    • Scope of W-pocket partners not yet enumerated
    • In vivo target spectrum unaddressed
  7. 2017 High

    Generalized the CNOT9 surface as a recruitment hub by showing Roquin and Bam use short α-helical CAF40-binding motifs to engage its concave face and drive target mRNA repression.

    Evidence Crystal structures of Roquin and Bam CBMs bound to CAF40 with recombinant pulldowns and reporter decay/repression assays

    PMID:28165457 PMID:29255063

    Open questions at the time
    • Cellular target repertoires of each CBM partner incomplete
    • Competition among partners in vivo not quantified
  8. 2018 High

    Demonstrated a catalytic contribution, showing CNOT9 together with the CNOT1 central region stimulates the nuclease module's deadenylation activity in a reconstituted complex.

    Evidence In vitro reconstitution of human CCR4-NOT sub-complexes with biochemical deadenylation assays, including a melanoma-associated P131L variant

    PMID:30309886

    Open questions at the time
    • Mechanism of stimulation not structurally defined
    • P131L variant showed no activity defect, leaving its pathogenic relevance open
  9. 2019 High

    Showed the CNOT9 concave surface is a shared, mutually exclusive docking site by mapping a NOT4 CBM that competes with Roquin and Bam for the same interface.

    Evidence Crystal structure of the NOT4 CBM-CAF40 complex with pulldowns, structure-guided mutagenesis, tethered reporter decay, and CAF40 knockdown

    PMID:30692204

    Open questions at the time
    • Regulation of partner exchange at the shared site unknown
    • Physiological balance among competing CBM proteins unresolved
  10. 2024 Low

    Proposed new biological contexts—centrosomal translational control via Unkempt and germline differentiation via Bam-mediated recruitment—extending CNOT9's reach.

    Evidence Immunofluorescence localization and Unkempt interaction (preprint); Drosophila genetic epistasis of Bam/bgcn with how knockdown (preprint)

    Open questions at the time
    • Preprints without functional validation of CNOT9 at centrosomes
    • Direct deadenylation of how mRNA not demonstrated
    • Awaits peer review and reconstitution

Open questions

Synthesis pass · forward-looking unresolved questions
  • How CNOT9's distinct nuclear transcriptional roles and EGFR-Akt signaling functions mechanistically relate to its cytoplasmic CCR4-NOT adaptor role remains unresolved.
  • No structural model of CNOT9 in transcription-factor complexes
  • Unclear whether signaling roles depend on CCR4-NOT membership
  • Endogenous target mRNA spectrum not defined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 5 GO:0140110 transcription regulator activity 2 GO:0003723 RNA binding 1
Localization
GO:0005634 nucleus 2 GO:0005829 cytosol 2
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-162582 Signal Transduction 2 R-HSA-74160 Gene expression (Transcription) 2
Partners
BAMCNOT1GIGYF2GRB10NOT4ROQUINTNRC6TTP
Complex memberships
CCR4-NOT

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2014 CNOT9 attaches to the DUF3819 domain of the CNOT1 scaffold, and the resulting CNOT9-CNOT1 complex provides tandem tryptophan (W)-binding pockets in CNOT9 that serve as binding sites for TNRC6/GW182 proteins, linking miRNA target recognition to translational repression and deadenylation. Crystal structure of CNOT9-CNOT1 DUF3819 complex; co-immunoprecipitation; in vitro binding assays with GW182 tryptophan motifs Molecular Cell High 24768540
2014 The CNOT1 MIF4G domain interacts with the C-terminal RecA domain of DDX6 (a translational repressor and decapping activator), with the crystal structure revealing striking similarity to the eIF4G-eIF4A complex, providing a physical link between CCR4-NOT and translational repression/decapping. Crystal structure of CNOT1 MIF4G-DDX6 RecA complex Molecular Cell High 24768540
2006 Human RCD1 (CNOT9) has an armadillo-repeat structure forming a positively charged cleft, and can bind single- and double-stranded oligonucleotides in vitro; mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. 2.2 Å X-ray crystal structure; in vitro nucleic acid binding assays; site-directed mutagenesis of active-site arginine Protein Science High 17189474
2017 Drosophila Roquin contains a CAF40-binding motif (CBM) that directly interacts with the CAF40 (CNOT9) subunit of CCR4-NOT; crystal structure reveals the CBM adopts an α-helical conformation upon binding to a conserved concave surface of CAF40, mediating mRNA target repression. Crystal structure of Dm Roquin CBM bound to CAF40; pulldown with purified recombinant proteins; reporter mRNA decay assays Nature Communications High 28165457
2017 Drosophila Bag-of-marbles (Bam) binds directly to the CAF40 (CNOT9) subunit of the CCR4-NOT complex via a conserved N-terminal CAF40-binding motif (CBM); crystal structure shows the CBM adopts an α-helical conformation binding the concave surface of the crescent-shaped CAF40; Bam-mediated mRNA decay and translational repression depend entirely on this CAF40 interaction. Crystal structure of Bam CBM bound to CAF40; pulldown with purified recombinant proteins; mRNA reporter decay and translational repression assays in cells RNA High 29255063
2019 Metazoan NOT4 contains a conserved CAF40-binding motif (CBM) in its C-terminal region that directly binds the CAF40 (CNOT9) subunit of CCR4-NOT; crystal structures reveal a mutually exclusive binding surface shared with Roquin and Bam CBMs; CAF40 depletion or structure-guided mutagenesis of the NOT4-CAF40 interface impairs NOT4-mediated decay of tethered reporter mRNAs. Crystal structure of NOT4 CBM-CAF40 complex; in vitro pulldown with purified proteins; tethered reporter mRNA decay assays; CAF40 knockdown Genes & Development High 30692204
2017 TTP (tristetraprolin) interacts with CNOT9 through conserved tryptophan residues in both TTP N- and C-terminal domains that engage the two tryptophan-binding pockets of CNOT9; this interaction is required for recruitment of the CCR4-NOT complex and TTP-directed decay of AU-rich element-containing mRNAs. SPOT peptide array; site-directed mutagenesis; bio-layer interferometry; mRNA decay reporter assays Journal of Molecular Biology High 29291391
2018 Reconstituted pentameric complex containing CNOT9, the central CNOT1 region (MIF4G + DUF3819 domains), and a BTG2-Caf1-Ccr4 nuclease module shows that CNOT1-CNOT9 components stimulate deadenylation activity of the nuclease module; the melanoma-associated CNOT9 P131L variant supports deadenylation similarly to wild-type in this reconstituted complex. In vitro reconstitution of human CCR4-NOT sub-complexes; biochemical deadenylation assays comparing pentameric vs. nuclease-only complexes Biochemical Journal High 30309886
2002 Mammalian Rcd1 (CNOT9) acts as a transcriptional cofactor that forms complexes with retinoic acid receptor and ATF-2; antisense knockdown of Rcd1 blocks the commitment step in retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells. Co-immunoprecipitation; antisense oligonucleotide knockdown with differentiation phenotype readout; embryonic lung explant treatment The EMBO Journal Medium 12356739
2004 Murine Rcd1 (CNOT9) interacts with c-Myb both in vitro and in vivo, and represses c-Myb-dependent activation of the myeloid mim-1 promoter as well as AP-1 target gene activation; Rcd1 is localized mainly in the nucleus. Yeast two-hybrid; in vitro binding; co-immunoprecipitation; promoter reporter (transactivation) assays; subcellular localization by immunostaining Biochemistry Medium 15209511
2009 RQCD1 (CNOT9) co-immunoprecipitates with GIGYF1 and GIGYF2 in breast cancer cells; siRNA knockdown of RQCD1 suppresses cell proliferation and reduces Akt phosphorylation at Ser473; overexpression of RQCD1 in HEK293 cells enhances cell growth. Co-immunoprecipitation; siRNA knockdown; Western blot for pAkt; cell proliferation assays; overexpression International Journal of Oncology Medium 19724902
2010 RQCD1 (CNOT9) is required for EGF-induced Akt phosphorylation; RQCD1 forms a complex with Akt, EGFR, GIGYF1, GIGYF2, and Grb10; the region 620–665 aa of GIGYF1 and 667–712 aa of GIGYF2 interact with RQCD1; RQCD1 enhances the interaction between Grb10 and GIGYF1/2. Co-immunoprecipitation; siRNA knockdown; Western blot for pAkt after EGF stimulation; domain mapping International Journal of Oncology Medium 20878056
2024 CNOT9, a component of the translational inhibitory CCR4-NOT complex, localizes to centrosomes during Plk4-induced centriole overduplication, coinciding with a transient centrosomal downregulation of translation; CNOT9 was identified as an interactor of the RNA-binding protein Unkempt in this context. Localization by immunofluorescence/imaging; protein interaction with Unkempt identified in the context of centrosome biology bioRxivpreprint Low
2024 In the Drosophila male germ cell lineage, Bam acts as an adapter to recruit the CCR4-NOT deadenylation complex via its CAF40 (CNOT9) subunit to repress how RNA, promoting the switch from spermatogonial proliferation to differentiation. Genetic epistasis (bam and bgcn mutants); knockdown of how in germ cells; forced expression of How; biochemical interaction previously established bioRxivpreprint Low

Source papers

Stage 0 corpus · 31 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Molecular cell 237 24768540
2009 Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. The Plant journal : for cell and molecular biology 133 19548978
2017 A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin. Nature communications 73 28165457
2001 Calcium channel blocker D-cis-diltiazem does not slow retinal degeneration in the PDE6B mutant rcd1 canine model of retinitis pigmentosa. Molecular vision 58 11239245
1994 Cosegregation of codon 807 mutation of the canine rod cGMP phosphodiesterase beta gene and rcd1. Investigative ophthalmology & visual science 55 8002249
1993 Confirmation of the rod cGMP phosphodiesterase beta subunit (PDE beta) nonsense mutation in affected rcd-1 Irish setters in the UK and development of a diagnostic test. Current eye research 53 8261797
2006 Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties. Protein science : a publication of the Protein Society 52 17189474
2017 Tryptophan-Mediated Interactions between Tristetraprolin and the CNOT9 Subunit Are Required for CCR4-NOT Deadenylase Complex Recruitment. Journal of molecular biology 44 29291391
2009 Involvement of RQCD1 overexpression, a novel cancer-testis antigen, in the Akt pathway in breast cancer cells. International journal of oncology 43 19724902
2017 Drosophila Bag-of-marbles directly interacts with the CAF40 subunit of the CCR4-NOT complex to elicit repression of mRNA targets. RNA (New York, N.Y.) 42 29255063
2002 Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation. The EMBO journal 37 12356739
2005 CNTF induces dose-dependent alterations in retinal morphology in normal and rcd-1 canine retina. Experimental eye research 36 16143329
2019 A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4-NOT complex. Genes & development 35 30692204
2019 Programmed Cell Death in Neurospora crassa Is Controlled by the Allorecognition Determinant rcd-1. Genetics 32 31636083
2010 The transcription factor interacting protein RCD1 contains a novel conserved domain. Plant signaling & behavior 32 20592818
2019 Overexpression of miR-361-5p in triple-negative breast cancer (TNBC) inhibits migration and invasion by targeting RQCD1 and inhibiting the EGFR/PI3K/Akt pathway. Bosnian journal of basic medical sciences 29 29924958
2015 Whole exome sequencing identifies a recurrent RQCD1 P131L mutation in cutaneous melanoma. Oncotarget 25 25544760
2018 The central region of CNOT1 and CNOT9 stimulates deadenylation by the Ccr4-Not nuclease module. The Biochemical journal 21 30309886
2010 Critical involvement of RQCD1 in the EGFR-Akt pathway in mammary carcinogenesis. International journal of oncology 18 20878056
2004 c-Myb protein interacts with Rcd-1, a component of the CCR4 transcription mediator complex. Biochemistry 18 15209511
1995 Molecular diagnostic tests for ascertainment of genotype at the rod cone dysplasia 1 (rcd1) locus in Irish setters. Current eye research 17 7796608
2023 Poly(ADP-ribose)-binding protein RCD1 is a plant PARylation reader regulated by Photoregulatory Protein Kinases. Communications biology 12 37076532
1996 An improved diagnostic test for rod cone dysplasia 1 (rcd1) using allele-specific polymerase chain reaction. Current eye research 11 8670760
2016 Reversible Chemical Dimerization by rCD1. Methods in enzymology 8 28063490
2017 1H, 13C and 15N NMR chemical shift assignments of A. thaliana RCD1 RST. Biomolecular NMR assignments 7 28593560
2006 Molecular cloning and characterization of an Rcd1-like protein in excretory-secretory products of Trichinella pseudospiralis. Parasitology 4 16899141
2025 Mechanisms of RCD-1 pore formation and membrane bending. Nature communications 3 39856083
2022 Downregulation of CHCHD2 may Contribute to Parkinson's Disease by Reducing Expression of NFE2L2 and RQCD1. Current neurovascular research 3 35388756
2026 Phase separation of the redox sensor RCD1 mediates differential ROS signals to regulate plant growth and stress responses. Molecular plant 2 41668375
2023 De novo variants in CNOT9 cause a neurodevelopmental disorder with or without epilepsy. Genetics in medicine : official journal of the American College of Medical Genetics 1 37092538
2003 Familial non-rcd1 generalised retinal degeneration in Irish setters. The Journal of small animal practice 1 12653325

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