How do bacteria tune translation efficiency?

Current Opinion in Microbiology

Volumn 24, Issue , 2015, Pages 66-71

  Li, Gene Wei ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; SYNTHETIC DNA; BACTERIAL PROTEIN; RECOMBINANT PROTEIN;

DNA LIBRARY; DNA REPAIR; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; NONHUMAN; OPEN READING FRAME; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS; REVIEW; RNA FOLDING; RNA STRUCTURE; RNA TRANSLATION; START CODON; STATISTICAL SIGNIFICANCE; STOICHIOMETRY; THERMOSTABILITY; TRANSLATION EFFICIENCY; BACTERIUM; CONFORMATION; GENETICS; METABOLISM; RIBOSOME;

BACTERIA (MICROORGANISMS);

BACTERIA; BACTERIAL PROTEINS; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RECOMBINANT PROTEINS; RIBOSOMES; RNA, MESSENGER;

EID: 84921745290     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2015.01.001     Document Type: Review

References (45)

1. Jacob F., Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961, 3:318-356.
2. Ohtaka Y., Spiegelman S. Translational control of protein synthesis in a cell-free system directed by a polycistronic viral RNA. Science 1963, 142:493-497.
3. Lodish H.F. Bacteriophage f2 RNA: control of translation and gene order. Nature 1968, 220:345-350.
4. 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 U S A 1974, 71:1342-1346.
5. Steitz J.A., Jakes K. How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci U S A 1975, 72:4734-4738.
6. Nomura M., Gourse R., Baughman G. Regulation of the synthesis of ribosomes and ribosomal components. Annu Rev Biochem 1984, 53:75-117.
7. Baranov P.V., Gesteland R.F., Atkins J.F. Recoding: translational bifurcations in gene expression. Gene 2002, 286:187-201.
8. Ito K., Chiba S., Pogliano K. Divergent stalling sequences sense and control cellular physiology. Biochem Biophys Res Commun 2010, 393:1-5.
9. Winkler W.C., Breaker R.R. Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 2005, 59:487-517.
10. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 2009, 27:946-950.
11. Allert M., Cox J.C., Hellinga H.W. Multifactorial determinants of protein expression in prokaryotic open reading frames. J Mol Biol 2010, 402:905-918.
12. Goodman D.B., Church G.M., Kosuri S. Causes and effects of N-terminal codon bias in bacterial genes. Science 2013, 342:475-479.
13. Kudla G., Murray A.W., Tollervey D., Plotkin J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324:255-258.
14. 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 2009, 324:218-223.
15. de Smit M.H., van Duin J. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc Natl Acad Sci U S A 1990, 87:7668-7672.
16. Hsu W.T., Weiss S.B. Selective translation of T4 template RNA by ribosomes from T4-infected Escherichia coli. Proc Natl Acad Sci U S A 1969, 64:345-351.
17. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 1985, 2:13-34.
18. Pechmann S., Frydman J. Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat Struct Mol Biol 2013, 20:237-243.
19. Xu Y., Ma P., Shah P., et al. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature 2013, 495:116-120.
20. Gingold H., Pilpel Y. Determinants of translation efficiency and accuracy. Mol Syst Biol 2011, 7:481.
21. Plotkin J.B., Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 2011, 12:32-42.
22. 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 1996, 260:649-663.
23. Shah P., Gilchrist M.A. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc Natl Acad Sci U S A 2011, 108:10231-10236.
24. Andersson S.G., Kurland C.G. Codon preferences in free-living microorganisms. Microbiol Rev 1990, 54:198-210.
25. Klumpp S., Dong J., Hwa T. On ribosome load, codon bias and protein abundance. PLoS One 2012, 7:e48542.
26. Shah P., Ding Y., Niemczyk M., et al. Rate-limiting steps in yeast protein translation. Cell 2013, 153:1589-1601.
27. Subramaniam A.R., Zid B.M., O'Shea E.K. An integrated approach reveals regulatory controls on bacterial translation elongation. Cell 2014, 159:1200-1211.
28. Tuller T., Waldman Y.Y., Kupiec M., Ruppin E. Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A 2010, 107:3645-3650.
29. Eyre-Walker A., Bulmer M. Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res 1993, 21:4599-4603.
30. Scharff L.B., Childs L., Walther D., Bock R. Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. PLoS Genet 2011, 7:e1002155.
31. Bentele K., Saffert P., Rauscher R., et al. Efficient translation initiation dictates codon usage at gene start. Mol Syst Biol 2013, 9:675.
32. Kosuri S., Goodman D.B., Cambray G., et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A 2013, 110:14024-14029.
33. Qi L., Haurwitz R.E., Shao W., et al. RNA processing enables predictable programming of gene expression. Nat Biotechnol 2012, 30:1002-1006.
34. Mutalik V.K., Guimaraes J.C., Cambray G., et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 2013, 10:354-360.
35. Li G.W., Burkhardt D., Gross C., Weissman J.S. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 2014, 157:624-635.
36. Oh E., Becker A.H., Sandikci A., et al. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 2011, 147:1295-1308.
37. Deana A., Belasco J.G. Lost in translation: the influence of ribosomes on bacterial mRNA decay. Genes Dev 2005, 19:2526-2533.
38. Dennis P.P., Bremer H. Macromolecular composition during steady-state growth of Escherichia coli B-r. J Bacteriol 1974, 119:270-281.
39. Neidhardt F.C. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology 1987, American Society for Microbiology, Washington, DC.
40. 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 2011, 147:789-802.
41. Li G.W., Oh E., Weissman J.S. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 2012, 484:538-541.
42. Stadler M., Fire A. Wobble base-pairing slows in vivo translation elongation in metazoans. RNA 2011, 17:2063-2073.
43. Zinshteyn B., Gilbert W.V. Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS Genet 2013, 9:e1003675.
44. Charneski C.A., Hurst L.D. Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol 2013, 11:e1001508.
45. Subramaniam A.R., Pan T., Cluzel P. Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria. Proc Natl Acad Sci U S A 2013, 110:2419-2424.