Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation

Pelletier, J. & Sonenberg, N. The organizing principles of eukaryotic ribosome recruitment. Annu. Rev. Biochem. 88, 307–335 (2019).

CAS  PubMed  Google Scholar 

Hinnebusch, A. G. Structural insights into the mechanism of scanning and start codon recognition in eukaryotic translation initiation. Trends Biochem. Sci. 42, 589–611 (2017).

CAS  PubMed  Google Scholar 

Atkins, J. F. & Bjork, G. R. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol. Mol. Biol. Rev. 73, 178–210 (2009).

CAS  PubMed  PubMed Central  Google Scholar 

Dinman, J. D. Mechanisms and implications of programmed translational frameshifting. Wiley Interdiscip. Rev. RNA 3, 661–673 (2012).

CAS  PubMed  PubMed Central  Google Scholar 

Orr, M. W., Mao, Y., Storz, G. & Qian, S. B. Alternative ORFs and small ORFs: shedding light on the dark proteome. Nucleic Acids Res. 48, 1029–1042 (2020).

CAS  PubMed  Google Scholar 

Kearse, M. G. & Wilusz, J. E. Non-AUG translation: a new start for protein synthesis in eukaryotes. Genes Dev. 31, 1717–1731 (2017).

CAS  PubMed  PubMed Central  Google Scholar 

Pestova, T. V. et al. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403, 332–335 (2000).

CAS  PubMed  Google Scholar 

Wang, J. et al. eIF5B gates the transition from translation initiation to elongation. Nature 573, 605–608 (2019).

CAS  PubMed  PubMed Central  Google Scholar 

Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).

CAS  PubMed  PubMed Central  Google Scholar 

Brar, G. A. & Weissman, J. S. Ribosome profiling reveals the what, when, where and how of protein synthesis. Nat. Rev. Mol. Cell Biol. 16, 651–664 (2015).

CAS  PubMed  PubMed Central  Google Scholar 

Ingolia, N. T., Lareau, L. F. & Weissman, J. S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789–802 (2011).

CAS  PubMed  PubMed Central  Google Scholar 

Gao, X. et al. Quantitative profiling of initiating ribosomes in vivo. Nat. Methods 12, 147–153 (2015).

CAS  PubMed  Google Scholar 

Griss, J. et al. Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nat. Methods 13, 651–656 (2016).

CAS  PubMed  PubMed Central  Google Scholar 

Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550 (2012).

CAS  PubMed  PubMed Central  Google Scholar 

Hafner, M. et al. RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries. RNA 17, 1697–1712 (2011).

CAS  PubMed  PubMed Central  Google Scholar 

Lee, S., Liu, B., Huang, S. X., Shen, B. & Qian, S. B. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl Acad. Sci. USA 109, E2424–E2432 (2012).

CAS  PubMed  PubMed Central  Google Scholar 

Hecht, A. et al. Measurements of translation initiation from all 64 codons in E. coli. Nucleic Acids Res. 45, 3615–3626 (2017).

CAS  PubMed  PubMed Central  Google Scholar 

Kozak, M. Pushing the limits of the scanning mechanism for initiation of translation. Gene 299, 1–34 (2002).

CAS  PubMed  PubMed Central  Google Scholar 

Tuller, T. et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141, 344–354 (2010).

CAS  PubMed  Google Scholar 

Dersh, D., Yewdell, J. W. & Wei, J. A SIINFEKL-based system to measure MHC class I antigen presentation efficiency and kinetics. Methods Mol. Biol. 1988, 109–122 (2019).

CAS  PubMed  PubMed Central  Google Scholar 

Jia, L. et al. Decoding mRNA translatability and stability from the 5′ UTR. Nat. Struct. Mol. Biol. 27, 814–821 (2020).

CAS  PubMed  Google Scholar 

Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).

CAS  PubMed  Google Scholar 

Xiao, Q., Zhang, F., Nacev, B. A., Liu, J. O. & Pei, D. Protein N-terminal processing: substrate specificity of Escherichia coli and human methionine aminopeptidases. Biochemistry 49, 5588–5599 (2010).

CAS  PubMed  Google Scholar 

Aksnes, H., Hole, K. & Arnesen, T. Molecular, cellular, and physiological significance of N-terminal acetylation. Int. Rev. Cell Mol. Biol. 316, 267–305 (2015).

CAS  PubMed  Google Scholar 

An, H., Ordureau, A., Korner, M., Paulo, J. A. & Harper, J. W. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature 583, 303–309 (2020).

CAS  PubMed  PubMed Central  Google Scholar 

Na, C. H. et al. Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini. Genome Res 28, 25–36 (2018).

CAS  PubMed  PubMed Central  Google Scholar 

Hinnebusch, A. G. The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779–812 (2014).

CAS  PubMed  Google Scholar 

Thakur, A. & Hinnebusch, A. G. eIF1 Loop 2 interactions with Met-tRNAi control the accuracy of start codon selection by the scanning preinitiation complex. Proc. Natl Acad. Sci. USA 115, E4159–E4168 (2018).

CAS  PubMed  PubMed Central  Google Scholar 

Tang, L. et al. Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide. Nucleic Acids Res. 45, 11941–11953 (2017).

CAS  PubMed  PubMed Central  Google Scholar 

Nag, N. et al. eIF1A/eIF5B interaction network and its functions in translation initiation complex assembly and remodeling. Nucleic Acids Res. 44, 7441–7456 (2016).

CAS  PubMed  PubMed Central  Google Scholar 

Dixon, A. S. et al. NanoLuc complementation reporter optimized for accurate measurement of protein interactions in cells. ACS Chem. Biol. 11, 400–408 (2016).

CAS  PubMed  Google Scholar 

Wang, J. et al. Structural basis for the transition from translation initiation to elongation by an 80S–eIF5B complex. Nat. Commun. 11, 5003 (2020).

CAS  PubMed  PubMed Central  Google Scholar 

Suraweera, A., Munch, C., Hanssum, A. & Bertolotti, A. Failure of amino acid homeostasis causes cell death following proteasome inhibition. Mol. Cell 48, 242–253 (2012).

CAS  PubMed  PubMed Central  Google Scholar 

Kilberg, M. S., Shan, J. & Su, N. ATF4-dependent transcription mediates signaling of amino acid limitation. Trends Endocrinol. Metab. 20, 436–443 (2009).

CAS  PubMed  PubMed Central  Google Scholar 

Lee, S. et al. Upregulation of eIF5B controls cell-cycle arrest and specific developmental stages. Proc. Natl Acad. Sci. USA 111, E4315–E4322 (2014).

CAS  PubMed  PubMed Central  Google Scholar 

Chukka, P. A. R., Wetmore, S. D. & Thakor, N. Established and emerging regulatory roles of eukaryotic translation initiation factor 5B (eIF5B). Front Genet 12, 737433 (2021).

CAS  PubMed  PubMed Central  Google Scholar 

Shu, X. E., Swanda, R. V. & Qian, S. B. Nutrient control of mRNA translation. Annu. Rev. Nutr. 40, 51–75 (2020).

CAS  PubMed  Google Scholar 

Wyant, G. A. et al. NUFIP1 is a ribosome receptor for starvation-induced ribophagy. Science 360, 751–758 (2018).

CAS  PubMed  PubMed Central  Google Scholar 

Adelman, K. & Lis, J. T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 13, 720–731 (2012).

CAS  PubMed  PubMed Central  Google Scholar 

Netzer, N. et al. Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature 462, 522–526 (2009).

CAS  PubMed  PubMed Central  Google Scholar 

Consortium, T. R. RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 47, D221–D229 (2019).

Google Scholar 

Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 10–12 (2011).

Comments (0)

No login
gif