Regulation of the multisubunit CCR4-NOT deadenylase in the initiation of mRNA degradation

Garneau, 2007, The highways and byways of mRNA decay, Nat Rev Mol Cell Biol, 8, 113, 10.1038/nrm2104 Wahle, 2013, RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes, Biochim Biophys Acta, 1829, 561, 10.1016/j.bbagrm.2013.01.003 Uchida, 2004, Identification of a human cytoplasmic poly(A) nuclease complex stimulated by poly(A)-binding protein∗, J Biol Chem, 279, 1383, 10.1074/jbc.M309125200 Schäfer, 2019, Molecular basis for poly(A) RNP architecture and recognition by the Pan2-Pan3 deadenylase, Cell, 177, 1619, 10.1016/j.cell.2019.04.013 Yamashita, 2005, Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover, Nat Struct Mol Biol, 12, 1054, 10.1038/nsmb1016 Brown, 1998, Poly(A) tail length control in Saccharomyces cerevisiae occurs by message-specific deadenylation, Mol Cell Biol, 18, 6548, 10.1128/MCB.18.11.6548 Eisen, 2020, The dynamics of cytoplasmic mRNA metabolism, Mol Cell, 77, 786, 10.1016/j.molcel.2019.12.005 Christie, 2013, Structure of the PAN3 pseudokinase reveals the basis for interactions with the PAN2 deadenylase and the GW182 proteins, Mol Cell, 51, 360, 10.1016/j.molcel.2013.07.011 Yi, 2018, PABP cooperates with the CCR4-NOT complex to promote mRNA deadenylation and block precocious decay, Mol Cell, 70, 1081, 10.1016/j.molcel.2018.05.009 Bianchin, 2005, Conservation of the deadenylase activity of proteins of the Caf1 family in human, RNA, 11, 487, 10.1261/rna.7135305 Dlakić, 2000, Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases, Trends Biochem Sci, 25, 272, 10.1016/S0968-0004(00)01582-6 Bawankar, 2013, NOT10 and C2orf29/NOT11 form a conserved module of the CCR4-NOT complex that docks onto the NOT1 N-terminal domain, RNA Biol, 10, 228, 10.4161/rna.23018 Wang, 2010, Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity, EMBO J, 29, 2566, 10.1038/emboj.2010.152 Thore, 2003, X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex, EMBO Rep, 4, 1150, 10.1038/sj.embor.7400020 Jonstrup, 2007, The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme, Nucleic Acids Res, 35, 3153, 10.1093/nar/gkm178 Horiuchi, 2009, Structural basis for the antiproliferative activity of the Tob-hCaf1 complex, J Biol Chem, 284, 13244, 10.1074/jbc.M809250200 Basquin, 2012, Architecture of the nuclease module of the yeast Ccr4-not complex: the Not1-Caf1-Ccr4 interaction, Mol Cell, 48, 207, 10.1016/j.molcel.2012.08.014 Petit, 2012, The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex, Nucleic Acids Res, 40, 11058, 10.1093/nar/gks883 Chen, 2021, Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex, Nucleic Acids Res, 10.1093/nar/gkab414 Zhang, 2021, Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements, Protein Sci Chen, 2014, A DDX6-CNOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing, Mol Cell, 54, 737, 10.1016/j.molcel.2014.03.034 Mathys, 2014, Structural and biochemical insights to the role of the CCR4-NOT complex and DDX6 ATPase in microRNA repression, Mol Cell, 54, 751, 10.1016/j.molcel.2014.03.036 Raisch, 2018, Structural and biochemical analysis of a NOT1 MIF4G-like domain of the CCR4-NOT complex, J Struct Biol, 204, 388, 10.1016/j.jsb.2018.10.009 Boland, 2013, Structure and assembly of the NOT module of the human CCR4–NOT complex, Nat Struct Mol Biol, 20, 1289, 10.1038/nsmb.2681 Bhaskar, 2013, Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex, Nat Struct Mol Biol, 20, 1281, 10.1038/nsmb.2686 Fabian, 2013, Structural basis for the recruitment of the human CCR4-NOT deadenylase complex by tristetraprolin, Nat Struct Mol Biol, 20, 735, 10.1038/nsmb.2572 Nasertorabi, 2011, Insights into the structure of the CCR4-NOT complex by electron microscopy, FEBS Lett, 585, 2182, 10.1016/j.febslet.2011.05.071 Ukleja, 2016, The architecture of the Schizosaccharomyces pombe CCR4-NOT complex, Nat Commun, 7, 1, 10.1038/ncomms10433 Raisch, 2019, Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation, Nat Commun, 10, 3173, 10.1038/s41467-019-11094-z Loh, 2013, The SMG5-SMG7 heterodimer directly recruits the CCR4-NOT deadenylase complex to mRNAs containing nonsense codons via interaction with POP2, Genes Dev, 27, 2125, 10.1101/gad.226951.113 Yamaji, 2017, DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs, Nature, 543, 568, 10.1038/nature21690 Raisch, 2016, Distinct modes of recruitment of the CCR4–NOT complex by Drosophila and vertebrate Nanos, EMBO J, 35, 974, 10.15252/embj.201593634 Bhandari, 2014, Structural basis for the Nanos-mediated recruitment of the CCR4–NOT complex and translational repression, Genes Dev, 28, 888, 10.1101/gad.237289.113 Sgromo, 2017, A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin, Nat Commun, 8, 14307, 10.1038/ncomms14307 Keskeny, 2019, A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4–NOT complex, Genes Dev, 33, 236, 10.1101/gad.320952.118 Bhaskar, 2015, Architecture of the ubiquitylation module of the yeast Ccr4-Not complex, Structure, 23, 921, 10.1016/j.str.2015.03.011 Chicoine, 2007, Bicaudal-C recruits CCR4-NOT deadenylase to target mRNAs and regulates oogenesis, cytoskeletal organization, and its own expression, Dev Cell, 13, 691, 10.1016/j.devcel.2007.10.002 Hanet, 2019, HELZ directly interacts with CCR4–NOT and causes decay of bound mRNAs, Life Sci Alliance, 2, 10.26508/lsa.201900405 Enwerem, 2021, Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome, RNA, 27, 445, 10.1261/rna.078436.120 Sgromo, 2018, Drosophila Bag-of-marbles directly interacts with the CAF40 subunit of the CCR4–NOT complex to elicit repression of mRNA targets, RNA, 24, 381, 10.1261/rna.064584.117 Poetz, 2021, RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation, Nat Commun, 12, 7175, 10.1038/s41467-021-27471-6 Bulbrook, 2018, Tryptophan-mediated interactions between tristetraprolin and the CNOT9 subunit are required for CCR4-NOT deadenylase complex recruitment, J Mol Biol, 430, 722, 10.1016/j.jmb.2017.12.018 Wright, 2015, Intrinsically disordered proteins in cellular signalling and regulation, Nat Rev Mol Cell Biol, 16, 18, 10.1038/nrm3920 Chen, 2020, Tob2 phosphorylation regulates global mRNA turnover to reshape transcriptome and impact cell proliferation, RNA, 26, 1143, 10.1261/rna.073528.119 Stowell, 2016, Reconstitution of targeted deadenylation by the ccr4-not complex and the YTH domain protein Mmi1, Cell Rep, 17, 1978, 10.1016/j.celrep.2016.10.066 Webster, 2017, Analysis of mRNA deadenylation by multi-protein complexes, Methods, 126, 95, 10.1016/j.ymeth.2017.06.009 Pavanello, 2018, The central region of CNOT1 and CNOT9 stimulates deadenylation by the Ccr4-Not nuclease module, Biochem J, 475, 3437, 10.1042/BCJ20180456 Garces, 2007, Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties, Protein Sci, 16, 176, 10.1110/ps.062600507 Webster, 2018, mRNA deadenylation is coupled to translation rates by the differential activities of ccr4-not nucleases, Mol Cell, 70, 1089, 10.1016/j.molcel.2018.05.033 Lima, 2017, Short poly(A) tails are a conserved feature of highly expressed genes, Nat Struct Mol Biol, 24, 1057, 10.1038/nsmb.3499 Ezzeddine, 2007, Human TOB, an antiproliferative transcription factor, is a poly(A)-binding protein-dependent positive regulator of cytoplasmic mRNA deadenylation, Mol Cell Biol, 27, 7791, 10.1128/MCB.01254-07 Webster, 2019, RNA-binding proteins distinguish between similar sequence motifs to promote targeted deadenylation by Ccr4-Not, Elife, 8, 10.7554/eLife.40670 Chang, 2019, A low-complexity region in human XRN1 directly recruits deadenylation and decapping factors in 5’-3' messenger RNA decay, Nucleic Acids Res, 47, 9282, 10.1093/nar/gkz633 Buschauer, 2020, The Ccr4-Not complex monitors the translating ribosome for codon optimality, Science, 368, eaay6912, 10.1126/science.aay6912