Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events

Article Article scientifique Article Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events eng 2023-02-20 2023-02-20 author Allen George Edward 911276 Département de microbiologie et médecine moléculaire (MIMOL) author Weiss Benjamin 0000-0002-9084-9264 689060 author Panasenko Olesya 0000-0002-0990-7472 629191 Services communs de la faculté de médecine (SCMU) author Huch Susanne author Villanyi Zoltan 766412 author Albert Benjamin 808748 author Dilg Daniel 871519 author Zagatti Marina 885449 author Schaughency Paul author Liao Susan E. 0000-0002-8380-7824 author Corden Jeff author Polte Christine author Shore David M. 0000-0002-9859-143X 102587 Département de biologie moléculaire et cellulaire (MOCEL) author Ignatova Zoya 0000-0002-9478-8825 author Pelechano Vicent author Collart Martine 0000-0001-6955-1773 27009 Département de microbiologie et médecine moléculaire (MIMOL) 30 10.1186/s13059-023-02871-7 36803582 1474-7596 PMC9940351 https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02871-7 Background: The Ccr4-Not complex is mostly known as the major eukaryotic deadenylase. However, several studies have uncovered roles of the complex, in particular of the Not subunits, unrelated to deadenylation and relevant for translation. In particular, the existence of Not condensates that regulate translation elongation dynamics has been reported. Typical studies that evaluate translation efficiency rely on soluble extracts obtained after the disruption of cells and ribosome profiling. Yet cellular mRNAs in condensates can be actively translated and may not be present in such extracts. Results: In this work, by analyzing soluble and insoluble mRNA decay intermediates in yeast, we determine that insoluble mRNAs are enriched for ribosomes dwelling at non-optimal codons compared to soluble mRNAs. mRNA decay is higher for soluble RNAs, but the proportion of co-translational degradation relative to the overall mRNA decay is higher for insoluble mRNAs. We show that depletion of Not1 and Not4 inversely impacts mRNA solubilities and, for soluble mRNAs, ribosome dwelling according to codon optimality. Depletion of Not4 solubilizes mRNAs with lower non-optimal codon content and higher expression that are rendered insoluble by Not1 depletion. By contrast, depletion of Not1 solubilizes mitochondrial mRNAs, which are rendered insoluble upon Not4 depletion. Conclusions: Our results reveal that mRNA solubility defines the dynamics of co-translation events and is oppositely regulated by Not1 and Not4, a mechanism that we additionally determine may already be set by Not1 promoter association in the nucleus. Co-translational mRNA decay Codon optimality Condensation Not1 Not4 Translation elongation dynamics mRNA solubility mRNA stability Dewey 616 Dewey 590 Dewey 570 Swiss National Science Foundation Genetic and biochemical analysis of the regulation of gene expression by the Ccr4-Not complex in the yeast S.cerevisiae 172999 CH Projects Swiss National Science Foundation Regulation of translation elongation dynamics and mRNA solubility by Not proteins in the yeast S.cerevisiae 207420 CH Projects Hungarian National Research GINOP-2.3.2–15-2016–00020 Hungarian National Research UNKP-21-5-595-SZTE Ragnar Söderberg Foundation, Wallenberg Academy Fellowship KAW 2016.0123 Deutsche Forschungsgemeinschaft FOR1805 Swedish Research Council VR 2020–01480 Swedish Research Council 2021–06112 VINNOVA 2020-03620 54 Département de microbiologie et médecine moléculaire 21B 23 Institut de génétique et de génomique 0DH 7daed2ee-1311-4824-9df9-2e51260a966a Département de biologie moléculaire et cellulaire 16484 false 58 Caractérisation génétique et biochimique du complexe Ccr4-Not conservé. 81 813 Groupe Shore https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190658 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE193912 https://github.com/georgeallenunige/NotTranslation https://doi.org/10.5281/zenodo.5150443 Genome biology 24 1 cad71086-b777-4241-800c-3681463d6fe9 Article (Published version) Public Article-scientifique-from-crossref.pdf 4376307 application/pdf CC BY-4.0 387c04f6b7537d8f88779edc2c12c089279aa2ad905721301b03085705ceecb9 94568a28-1c1e-4519-b1e8-c573b53f6e10 Appendix Public 13059_2023_2871_MOESM1_ESM.pdf 1323994 application/pdf Additional figures and figure legends in a single pdf file 24f294f36cadaa6cfcc379e8fbf2ce07f0b2d858e1df3f41d7cc7db29b67622c b05e2499-5065-4d71-a7ab-039b47003b0e Supplemental data Public 13059_2023_2871_MOESM2_ESM.xlsx 3797674 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Table S1 a7bda46ec8bc5dc4fbefbd4b77d84dd41bab7260fc308eeeb9b814ebd78507fd 09b1f951-ad07-46ce-9edf-fdbb5a13394b Supplemental data Public 13059_2023_2871_MOESM3_ESM.xlsx 351241 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Table S2 3d389e73ec8eec82e2afc63e39ec83d2631793c5c1f7b0cd9033045f450ba51f 282b6b1c-a5b1-47da-b09d-4e912a9ff30d Supplemental data Public 13059_2023_2871_MOESM4_ESM.xlsx 349699 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Table S3 3b2859829e613b7eed2751e4c55f049b4d7d23d75fbbcb5999b298dc859b949a c87297c5-3186-4481-acff-2697601144aa Supplemental data Public 13059_2023_2871_MOESM5_ESM.xlsx 239961 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Table S4 019f16a72a9f7465bc94e6cb3a737a714fce024de6029a3e122611d7927cd8ed 37aeb7e8-e1b4-46d3-8505-14bb9a9f6b77 Appendix Public 13059_2023_2871_MOESM6_ESM.pdf 282247 application/pdf Uncropped blots. Related to Figure S2A d1d6c833923a67bb84fe70e11e49becb877974e717686a452ac13641120f745b openAccess Faculté de médecine / Section de médecine fondamentale / Département de microbiologie et médecine moléculaire Centres et instituts / Institut de génétique et de génomique Faculté des sciences / Section de biologie / Département de biologie moléculaire et cellulaire

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Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events	Genome biology			2023	365	315

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