The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria (original) (raw)
Kramer, G., Boehringer, D., Ban, N. & Bukau, B. The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nature Struct. Mol. Biol.16, 589–597 (2009) ArticleCAS Google Scholar
Plotkin, J. B. & Kudla, G. Synonymous but not the same: the causes and consequences of codon bias. Nature Rev. Genet.12, 32–42 (2011) ArticleCAS 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. Science324, 218–223 (2009) ArticleADSCAS 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. Cell147, 789–802 (2011) ArticleCAS Google Scholar
Oh, E. et al. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo . Cell147, 1295–1308 (2011) ArticleCAS Google Scholar
Shine, J. & Dalgarno, L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl Acad. Sci. USA71, 1342–1346 (1974) ArticleADSCAS Google Scholar
Hui, A. & de Boer, H. A. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli . Proc. Natl Acad. Sci. USA84, 4762–4766 (1987) ArticleADSCAS Google Scholar
Rackham, O. & Chin, J. W. A network of orthogonal ribosomėmRNA pairs. Nature Chem. Biol.1, 159–166 (2005) ArticleCAS Google Scholar
Varenne, S., Buc, J., Lloubes, R. & Lazdunski, C. Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol.180, 549–576 (1984) ArticleCAS Google Scholar
Pedersen, S. Escherichia coli ribosomes translate in vivo with variable rate. EMBO J.3, 2895–2898 (1984) ArticleCAS Google Scholar
Sorensen, M. A., Kurland, C. G. & Pedersen, S. Codon usage determines translation rate in Escherichia coli . J. Mol. Biol.207, 365–377 (1989) ArticleCAS Google Scholar
Andersson, S. G. & Kurland, C. G. Codon preferences in free-living microorganisms. Microbiol. Rev.54, 198–210 (1990) ArticleCAS Google Scholar
Sorensen, M. A. & Pedersen, S. Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J. Mol. Biol.222, 265–280 (1991) ArticleCAS Google Scholar
Gutman, G. A. & Hatfield, G. W. Nonrandom utilization of codon pairs in Escherichia coli . Proc. Natl Acad. Sci. USA86, 3699–3703 (1989) ArticleADSCAS Google Scholar
Nakatogawa, H. & Ito, K. The ribosomal exit tunnel functions as a discriminating gate. Cell108, 629–636 (2002) ArticleCAS Google Scholar
Gong, F. & Yanofsky, C. Instruction of translating ribosome by nascent peptide. Science297, 1864–1867 (2002) ArticleADSCAS Google Scholar
Chiba, S. et al. Recruitment of a species-specific translational arrest module to monitor different cellular processes. Proc. Natl Acad. Sci. USA108, 6073–6078 (2011) ArticleADSCAS Google Scholar
Dong, H., Nilsson, L. & Kurland, C. G. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol.260, 649–663 (1996) ArticleCAS Google Scholar
Pruss, B. M., Nelms, J. M., Park, C. & Wolfe, A. J. Mutations in NADH:ubiquinone oxidoreductase of Escherichia coli affect growth on mixed amino acids. J. Bacteriol.176, 2143–2150 (1994) ArticleCAS Google Scholar
Sezonov, G., Joseleau-Petit, D. & D’Ari, R. Escherichia coli physiology in Luria–Bertani broth. J. Bacteriol.189, 8746–8749 (2007) ArticleCAS Google Scholar
Chen, H., Bjerknes, M., Kumar, R. & Jay, E. Determination of the optimal aligned spacing between the Shine–Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res.22, 4953–4957 (1994) ArticleCAS Google Scholar
Weiss, R. B., Dunn, D. M., Dahlberg, A. E., Atkins, J. F. & Gesteland, R. F. Reading frame switch caused by base-pair formation between the 3′ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli . EMBO J.7, 1503–1507 (1988) ArticleCAS Google Scholar
Larsen, B., Wills, N. M., Gesteland, R. F. & Atkins, J. F. rRNA–mRNA base pairing stimulates a programmed −1 ribosomal frameshift. J. Bacteriol.176, 6842–6851 (1994) ArticleCAS Google Scholar
Wen, J. D. et al. Following translation by single ribosomes one codon at a time. Nature452, 598–603 (2008) ArticleADSCAS Google Scholar
Ikemura, T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E.coli translational system. J. Mol. Biol.151, 389–409 (1981) ArticleCAS Google Scholar
Baranov, P. V., Gesteland, R. F. & Atkins, J. F. Release factor 2 frameshifting sites in different bacteria. EMBO Rep.3, 373–377 (2002) ArticleCAS Google Scholar
Burmann, B. M. et al. A NusE:NusG complex links transcription and translation. Science328, 501–504 (2010) ArticleADSCAS Google Scholar
Proshkin, S., Rahmouni, A. R., Mironov, A. & Nudler, E. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science328, 504–508 (2010) ArticleADSCAS Google Scholar
Kolter, R. & Yanofsky, C. Attenuation in amino acid biosynthetic operons. Annu. Rev. Genet.16, 113–134 (1982) ArticleCAS Google Scholar
Elf, J. & Ehrenberg, M. What makes ribosome-mediated transcriptional attenuation sensitive to amino acid limitation? PLOS Comput. Biol.1, e2 (2005) ArticleADS Google Scholar
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA97, 6640–6645 (2000) ArticleADSCAS Google Scholar
Neidhardt, F. C., Bloch, P. L. & Smith, D. F. Culture medium for enterobacteria. J. Bacteriol.119, 736–747 (1974) ArticleCAS Google Scholar
Kanaya, S., Yamada, Y., Kudo, Y. & Ikemura, T. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene238, 143–155 (1999) ArticleCAS Google Scholar
Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res.36, (suppl. 2)W70–W74 (2008) ArticleCAS Google Scholar
Wu, M. & Eisen, J. A. A simple, fast, and accurate method of phylogenomic inference. Genome Biol.9, R151 (2008) Article Google Scholar
Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol.292, 195–202 (1999) ArticleCAS Google Scholar
Li, W., Jaroszewski, L. & Godzik, A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics17, 282–283 (2001) ArticleCAS Google Scholar