In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3’ additional stop codons

English version

Autoři: Alexander T. Ho ^aff001; Laurence D. Hurst ^aff001
Působiště autorů: Milner Centre for Evolution, University of Bath, Bath, United Kingdom ^aff001
Vyšlo v časopise: In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3’ additional stop codons. PLoS Genet 15(9): e32767. doi:10.1371/journal.pgen.1008386
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008386

Souhrn

Errors throughout gene expression are likely deleterious, hence genomes are under selection to ameliorate their consequences. Additional stop codons (ASCs) are in-frame nonsense ‘codons’ downstream of the primary stop which may be read by translational machinery should the primary stop have been accidentally read through. Prior evidence in several eukaryotes suggests that ASCs are selected to prevent potentially-deleterious consequences of read-through. We extend this evidence showing that enrichment of ASCs is common but not universal for single cell eukaryotes. By contrast, there is limited evidence as to whether the same is true in other taxa. Here, we provide the first systematic test of the hypothesis that ASCs act as a fail-safe mechanism in eubacteria, a group with high read-through rates. Contra to the predictions of the hypothesis we find: there is paucity, not enrichment, of ASCs downstream; substitutions that degrade stops are more frequent in-frame than out-of-frame in 3’ sequence; highly expressed genes are no more likely to have ASCs than lowly expressed genes; usage of the leakiest primary stop (TGA) in highly expressed genes does not predict ASC enrichment even compared to usage of non-leaky stops (TAA) in lowly expressed genes, beyond downstream codon +1. Any effect at the codon immediately proximal to the primary stop can be accounted for by a preference for a T/U residue immediately following the stop, although if anything, TT- and TC- starting codons are preferred. We conclude that there is no compelling evidence for ASC selection in eubacteria. This presents an unusual case in which the same error could be solved by the same mechanism in eukaryotes and prokaryotes but is not. We discuss two possible explanations: that, owing to the absence of nonsense mediated decay, bacteria may solve read-through via gene truncation and in eukaryotes certain prion states cause raised read-through rates.

Klíčová slova:

Biology and life sciences – Organisms – Eukaryota – Bacteria – Mollicutes – Genetics – Gene expression – Protein translation – Genomics – Comparative genomics – Microbial genetics – Computational biology – Biochemistry – Nucleic acids – RNA – Messenger RNA – Untranslated regions – 3' UTR – Microbiology – Bacteriology – Bacterial genetics – Bacterial genomics – Microbial genomics

Zdroje

1. Warnecke T, Hurst LD. Error prevention and mitigation as forces in the evolution of genes and genomes. Nat Rev Genet. 2011;12(12):875–81. doi: 10.1038/nrg3092 WOS:000297252500013. 22094950

2. Fu Q, Liu CJ, Zhang X, Zhai ZS, Wang YZ, Hu MX, et al. Glucocorticoid receptor regulates expression of microRNA-22 and downstream signaling pathway in apoptosis of pancreatic acinar cells. World Journal of Gastroenterology. 2018;24(45):5120–30. doi: 10.3748/wjg.v24.i45.5120 WOS:000452759500007. 30568389

3. Liu Z, Zhang JZ. Human C-to-U coding RNA editing is largely nonadaptive. Mol Biol Evol. 2018;35(4):963–9. doi: 10.1093/molbev/msy011 WOS:000431889000014. 29385526

4. Liu Z, Zhang JZ. Most m(6)A RNA modifications in protein-coding regions are evolutionarily unconserved and likely nonfunctional. Mol Biol Evol. 2018;35(3):666–75. doi: 10.1093/molbev/msx320 WOS:000427260700013. 29228327

5. Yang JR, Maclean CJ, Park C, Zhao HB, Zhang JZ. Intra and interspecific variations of gene expression levels in yeast are largely neutral: (Nei Lecture, SMBE 2016, Gold Coast). Mol Biol Evol. 2017;34(9):2125–39. doi: 10.1093/molbev/msx171 WOS:000408307400001. 28575451

6. Drummond DA, Wilke CO. The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet. 2009;10(10):715–24. doi: 10.1038/nrg2662 ISI:000269965100014. 19763154

7. Xu C, Park JK, Zhang JZ. Evidence that alternative transcriptional initiation is largely nonadaptive. PLoS Biol. 2019;17(3):e3000197. doi: 10.1371/journal.pbio.3000197 WOS:000462993700035. 30883542

8. Chuan L, Zhang J. Stop-codon read-through arises largely from molecular errors and is generally nonadaptive. PLoS Genet. 2019;15(5):e1008141. doi: 10.1371/journal.pgen.1008141 31120886

9. Abrahams L, Hurst LD. Adenine enrichment at the fourth CDS residue in bacterial genes is consistent with error proofing for +1 frameshifts. Mol Biol Evol. 2017;34(12):3064–80. doi: 10.1093/molbev/msx223 WOS:000416178900003. 28961919

10. Seligmann H, Pollock DD. The ambush hypothesis: Hidden stop codons prevent off-frame gene reading. DNA Cell Biol. 2004;23(10):701–5. doi: 10.1089/dna.2004.23.701 WOS:000225034200012. 15585128

11. Seligmann H. Cost minimization of ribosomal frameshifts. J Theor Biol. 2007;249(1):162–7. doi: 10.1016/j.jtbi.2007.07.007 WOS:000250847700014. 17706680

12. Belinky F, Babenko VN, Rogozin IB, Koonin EV. Purifying and positive selection in the evolution of stop codons. Sci Rep. 2018;8(1):9260. doi: 10.1038/s41598-018-27570-3 WOS:000435448300003. 29915293

13. Korkmaz G, Holm M, Wiens T, Sanyal S. Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance. J Biol Chem. 2014;289(44):30334–42. doi: 10.1074/jbc.M114.606632 WOS:000344549700016. 25217634

14. Wei YL, Wang J, Xia XH. Coevolution between stop codon usage and release factors in bacterial species. Mol Biol Evol. 2016;33(9):2357–67. doi: 10.1093/molbev/msw107 WOS:000381702500016. 27297468

15. Strigini P, Brickman E. Analysis of specific misreading in Escherichia-coli. J Mol Biol. 1973;75(4):659–72. doi: 10.1016/0022-2836(73)90299-4 WOS:A1973P411600007. 4581523

16. Geller AI, Rich A. UGA termination suppression transfer RNAtrp active in rabbit reticulocytes. Nature. 1980;283(5742):41–6. doi: 10.1038/283041a0 WOS:A1980JA27900029. 7350525

17. Parker J. Errors and alternatives in reading the universal genetic-code. Microbiol Rev. 1989;53(3):273–98. WOS:A1989AN47600001. 2677635

18. Jorgensen F, Adamski FM, Tate WP, Kurland CG. Release factor-dependent false stops are infrequent in Escherichia-coli. J Mol Biol. 1993;230(1):41–50. doi: 10.1006/jmbi.1993.1124 WOS:A1993KR93300007. 8450549

19. Meng SY, Hui JO, Haniu M, Tsai LB. Analysis of translational termination of recombinant human methionyl-neurotrophin-3 in Escherichia-coli. Biochem Biophys Res Commun. 1995;211(1):40–8. doi: 10.1006/bbrc.1995.1775 WOS:A1995RB85000007. 7779107

20. Sanchez JC, Padron G, Santana H, Herrera L. Elimination of an HuIFN alpha 2b readthrough species, produced in Escherichia coli, by replacing its natural translational stop signal. J Biotechnol. 1998;63(3):179–86. WOS:000076580900002. 9803532

21. Tate WP, Mansell JB, Mannering SA, Irvine JH, Major LL, Wilson DN. UGA: a dual signal for "stop" and for recoding in protein synthesis. Biochemistry-Moscow. 1999;64(12):1342–53. WOS:000084900100002. 10648957

22. Nichols JL. Nucleotide sequence from polypeptide chain termination region of coat protein cistron in bacteriophage-R17 RNA. Nature. 1970;225(5228):147–51. doi: 10.1038/225147a0 WOS:A1970F007100021. 5409960

23. Doronina VA, Brown JD. When nonsense makes sense and vice versa: Non-canonical decoding events at stop codons in eukaryotes. Mol Biol. 2006;40(4):731–41. WOS:000239572100018.

24. Namy O, Rousset JP. Specification of standard amino acids by stop codons. In: Atkins JF, Gesteland RF, editors. Recoding: Expansion of Decoding Rules Enriches Gene Expression. Nucleic Acids and Molecular Biology. 242010. p. 79–100.

25. Roy B, Leszyk JD, Mangus DA, Jacobson A. Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3. Proc Natl Acad Sci USA. 2015;112(10):3038–43. doi: 10.1073/pnas.1424127112 WOS:000350646500044. 25733896

26. Beznoskova P, Gunisova S, Valasek LS. Rules of UGA-N decoding by near-cognate tRNAs and analysis of readthrough on short uORFs in yeast. RNA. 2016;22(3):456–66. doi: 10.1261/rna.054452.115 WOS:000371365400013. 26759455

27. Jungreis I, Lin MF, Spokony R, Chan CS, Negre N, Victorsen A, et al. Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res. 2011;21(12):2096–113. doi: 10.1101/gr.119974.110 WOS:000297918600011. 21994247

28. Bossi L, Roth JR. The influence of codon context on genetic-code translation. Nature. 1980;286(5769):123–7. doi: 10.1038/286123a0 WOS:A1980JY73500026. 7402305

29. Ryden SM, Isaksson LA. A temperature-sensitive mutant of Escherichia-coli that shows enhanced misreading of UAG/A and increased efficiency for some transfer-RNA nonsense suppressors. Mol Gen Genet. 1984;193(1):38–45. doi: 10.1007/bf00327411 WOS:A1984RY11900006. 6419024

30. Sambrook JF, Fan DP, Brenner S. A strong suppressor specific for UGA. Nature. 1967;214(5087):452–3. doi: 10.1038/214452a0 WOS:A19679255200007. 5340340

31. Roth JR. UGA nonsense mutations in Salmonella-typhimurium. J Bacteriol. 1970;102(2):467–75. WOS:A1970G085800022. 4315894

32. Bossi L. Context effects—translation of UAG codon by suppressor transfer-RNA is affected by the sequence following UAG in the message. J Mol Biol. 1983;164(1):73–87. doi: 10.1016/0022-2836(83)90088-8 WOS:A1983QD31100005. 6188841

33. Miller JH, Albertini AM. Effects of surrounding sequence on the suppression of nonsense codons. J Mol Biol. 1983;164(1):59–71. doi: 10.1016/0022-2836(83)90087-6 WOS:A1983QD31100004. 6188840

34. Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. Elife. 2013;2. doi: 10.7554/eLife.01179 WOS:000328643800002. 24302569

35. Wagner A. Energy constraints on the evolution of gene expression. Mol Biol Evol. 2005;22(6):1365–74. ISI:000229279100001. doi: 10.1093/molbev/msi126 15758206

36. Klauer AA, van Hoof A. Degradation of mRNAs that lack a stop codon: a decade of nonstop progress. WIREs RNA. 2012;3(5):649–60. doi: 10.1002/wrna.1124 WOS:000307731000005. 22740367

37. Ito-Harashima S, Kuroha K, Tatematsu T, Inada T. Translation of the poly(A) tail plays crucial roles in nonstop mRNA surveillance via translation repression and protein destabilization by proteasome in yeast. Genes Dev. 2007;21(5):519–24. doi: 10.1101/gad.1490207 WOS:000244760600003. 17344413

38. Dimitrova LN, Kuroha K, Tatematsu T, Inada T. Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome. J Biol Chem. 2009;284(16):10343–52. doi: 10.1074/jbc.M808840200 WOS:000265104600008. 19204001

39. Liang H, Cavalcanti ARO, Landweber LF. Conservation of tandem stop codons in yeasts. Genome Biol. 2005;6(4):R31. doi: 10.1186/gb-2005-6-4-r31 WOS:000228436000008. 15833118

40. Adachi M, Cavalcanti ARO. Tandem stop codons in ciliates that reassign stop codons. J Mol Evol. 2009;68(4):424–31. doi: 10.1007/s00239-009-9220-y WOS:000265145500011. 19294453

41. Major LL, Edgar TD, Yip PY, Isaksson LA, Tate WP. Tandem termination signals: myth or reality? FEBS Lett. 2002;514(1):84–9. doi: 10.1016/s0014-5793(02)02301-3 WOS:000174640300017. 11904187

42. Wei YL, Xia XH. The role of+4U as an extended translation termination signal in bacteria. Genetics. 2017;205(2):539–49. doi: 10.1534/genetics.116.193961 WOS:000394144900007. 27903612

43. Brown CM, Tate WP. Direct recognition of messenger-RNA stop signals by Escherichia-coli polypeptide-chain release factor-2. J Biol Chem. 1994;269(52):33164–70. WOS:A1994QA63800066. 7806547

44. Poole ES, Major LL, Mannering SA, Tate WP. Translational termination in Escherichia coli: three bases following the stop codon crosslink to release factor 2 and affect the decoding efficiency of UGA-containing signals. Nucleic Acids Res. 1998;26(4):954–60. doi: 10.1093/nar/26.4.954 WOS:000072236300012. 9461453

45. Tate WP, Cridge AG, Brown CM. 'Stop' inprotein synthesis is modulated with exquisite subtlety by an extended RNA translation signal. Biochem Soc Trans. 2018;46:1615–25. doi: 10.1042/BST20180190 WOS:000453394200020. 30420414

46. Capecchi MR. Polypeptide chain termination in vitro—isolation of a release factor. Proc Natl Acad Sci USA. 1967;58(3):1144–51. doi: 10.1073/pnas.58.3.1144 WOS:A19679929200055. 5233840

47. Caskey CT, Tompkins R, Scolnick E, Caryk T, Nirenberg M. Sequential translation of trinucleotide codons for initiation and termination of protein synthesis. Science. 1968;162(3849):135–8. doi: 10.1126/science.162.3849.135 WOS:A1968B850100026. 4877370

48. Scolnick E, Tompkins R, Caskey T, Nirenber M. Release factors differing in specificity for terminator codons. Proc Natl Acad Sci USA. 1968;61(2):768–74. doi: 10.1073/pnas.61.2.768 WOS:A1968C065000064. 4879404

49. Petry S, Brodersen DE, Murphy FV, Dunham CM, Selmer M, Tarry MJ, et al. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell. 2005;123(7):1255–66. doi: 10.1016/j.cell.2005.09.039 WOS:000234584500014. 16377566

50. Freistroffer DV, Pavlov MY, MacDougall J, Buckingham RH, Ehrenberg M. Release factor RF3 in E-coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 1997;16(13):4126–33. doi: 10.1093/emboj/16.13.4126 WOS:A1997XJ99000037. 9233821

51. Milman G, Goldstein J, Scolnick E, Caskey T. Peptide chain termination, 3. Stimulation of in vitro termination. Proc Natl Acad Sci USA. 1969;63(1):183–90. doi: 10.1073/pnas.63.1.183 WOS:A1969D694400031. 4897024

52. Scolnick EM, Caskey CT. Peptide chain termination, 5. Role of release factors in mRNA terminator codon recognition. Proc Natl Acad Sci USA. 1969;64(4):1235–41. doi: 10.1073/pnas.64.4.1235 WOS:A1969F268900015. 4916922

53. Povolotskaya IS, Kondrashov FA, Ledda A, Vlasov PK. Stop codons in bacteria are not selectively equivalent. Biol Direct. 2012;7(1):30. 30 doi: 10.1186/1745-6150-7-30 WOS:000315725200001. 22974057

54. Poole ES, Brown CM, Tate WP. The identity of the base following the stop codon determines the efficiency of in-vivo translational termination in Escherichia-coli. EMBO J. 1995;14(1):151–8. WOS:A1995QB06100017. 7828587

55. Cridge AG, Crowe-McAuliffe C, Mathew SF, Tate WP. Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel. Nucleic Acids Res. 2018;46(4):1927–44. doi: 10.1093/nar/gkx1315 WOS:000426293300033. 29325104

56. Namy O, Hatin I, Rousset JP. Impact of the six nucleotides downstream of the stop codon on translation termination. Embo Reports. 2001;2(9):787–93. doi: 10.1093/embo-reports/kve176 WOS:000171287400013. 11520858

57. Sharp PM, Bulmer M. Selective differences among translation termination codons. Gene. 1988;63(1):141–5. doi: 10.1016/0378-1119(88)90553-7 WOS:A1988M520000014. 3133285

58. Vakhrusheva AA, Kazanov MD, Mironov AA, Bazykin GA. Evolution of prokaryotic genes by shift of stop codons. J Mol Evol. 2011;72(2):138–46. doi: 10.1007/s00239-010-9408-1 WOS:000288808400002. 21082168

59. Lindeboom RGH, Supek F, Lehner B. The rules and impact of nonsense-mediated mRNA decay in human cancers. Nat Genet. 2016;48(10):1112–8. doi: 10.1038/ng.3664 WOS:000384391600006. 27618451

60. Thermann R, Neu-Yilik G, Deters A, Frede U, Wehr K, Hagemeier C, et al. Binary specification of nonsense codons by splicing and cytoplasmic translation. EMBO J. 1998;17(12):3484–94. doi: 10.1093/emboj/17.12.3484 WOS:000074363800026. 9628884

61. Zhang J, Sun XL, Qian YM, LaDuca JP, Maquat LE. At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation. Mol Cell Biol. 1998;18(9):5272–83. doi: 10.1128/mcb.18.9.5272 WOS:000075484300035. 9710612

62. True HL, Lindquist SL. A yeast prion provides a mechanism for genetic variation and phenotypic diversity. Nature. 2000;407(6803):477–83. doi: 10.1038/35035005 WOS:000089727400040. 11028992

63. Wickner RB, Masison DC, Edskes HK. PSI and URE3 as yeast prions. Yeast. 1995;11(16):1671–85. doi: 10.1002/yea.320111609 WOS:A1995TQ24100007. 8720070

64. Harrison PM. Evolutionary behaviour of bacterial prion-like proteins. Plos One. 2019;14(3). doi: 10.1371/journal.pone.0213030 WOS:000460371800018. 30835736

65. Angarica VE, Ventura S, Sancho J. Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains. BMC Genomics. 2013;14. doi: 10.1186/1471-2164-14-316 WOS:000318944100001. 23663289

66. Yuan AH, Hochschild A. A bacterial global regulator forms a prion. Science. 2017;355(6321):198–201. doi: 10.1126/science.aai7776 WOS:000391743700047. 28082594

67. Hershberg R, Petrov DA. Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 2010;6(9):e1001115. e1001115 doi: 10.1371/journal.pgen.1001115 ISI:000282369200053. 20838599

68. Hildebrand F, Meyer A, Eyre-Walker A. Evidence of selection upon genomic GC-content in bacteria. PLoS Genet. 2010;6(9):e1001107. e1001107 doi: 10.1371/journal.pgen.1001107 ISI:000282369200045. 20838593

69. Wu XM, Hurst LD. Why selection might be stronger when populations are small: intron size and density predict within and between-species usage of exonic splice associated cis-motifs. Mol Biol Evol. 2015;32(7):1847–61. doi: 10.1093/molbev/msv069 WOS:000360585900015. 25771198

70. Warnecke T, Huang Y, Przytycka TM, Hurst LD. Unique cost dynamics elucidate the role of frameshifting errors in promoting translational robustness. Genome Biol Evol. 2010;2(1):636–45. doi: 10.1093/gbe/evq049 WOS:000291467300007. 20688751

71. Wang MC, Herrmann CJ, Simonovic M, Szklarczyk D, von Mering C. Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics. 2015;15(18):3163–8. doi: 10.1002/pmic.201400441 WOS:000362503900007. 25656970

72. Jones E, Oliphant T, Peterson P. SciPy: Open source scientific tools for Python 2001. Available from: http://www.scipy.org/.

73. Belinky F, Rogozin IB, Koonin EV. Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions. Sci Rep. 2017;7. doi: 10.1038/s41598-017-12619-6 WOS:000412032000031. 28963504

74. Rogozin IB, Belinky F, Pavlenko V, Shabalina SA, Kristensen DM, Koonin EV. Evolutionary switches between two serine codon sets are driven by selection. Proc Natl Acad Sci USA. 2016;113(46):13109–13. doi: 10.1073/pnas.1615832113 WOS:000388970100068. 27799560

75. Kristensen DM, Wolf YI, Koonin EV. ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. Nucleic Acids Res. 2017;45(D1):D210–D8. doi: 10.1093/nar/gkw934 WOS:000396575500032. 28053163

76. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 2016;44(14):6614–24. doi: 10.1093/nar/gkw569 WOS:000382999900013. 27342282

77. Katoh K, Kuma K-i, Miyata T, Toh H. Improvement in the accuracy of multiple sequence alignment program MAFFT. Genome informatics International Conference on Genome Informatics. 2005;16(1):22–33. MEDLINE:16362903. 16362903