A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

English version České info

Deciphering the architecture of the tRNA pool is a prime challenge in translation research, as tRNAs govern the efficiency and accuracy of the process. Towards this challenge, we created a systematic tRNA deletion library in Saccharomyces cerevisiae, aimed at dissecting the specific contribution of each tRNA gene to the tRNA pool and to the cell's fitness. By harnessing this resource, we observed that the majority of tRNA deletions show no appreciable phenotype in rich medium, yet under more challenging conditions, additional phenotypes were observed. Robustness to tRNA gene deletion was often facilitated through extensive backup compensation within and between tRNA families. Interestingly, we found that within tRNA families, genes carrying identical anti-codons can contribute differently to the cellular fitness, suggesting the importance of the genomic surrounding to tRNA expression. Characterization of the transcriptome response to deletions of tRNA genes exposed two disparate patterns: in single-copy families, deletions elicited a stress response; in deletions of genes from multi-copy families, expression of the translation machinery increased. Our results uncover the complex architecture of the tRNA pool and pave the way towards complete understanding of their role in cell physiology.

Vyšlo v časopise: A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool. PLoS Genet 10(1): e32767. doi:10.1371/journal.pgen.1004084
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004084

Souhrn

Zdroje

1. KozakM (2005) Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361: 13–37 doi:10.1016/j.gene.2005.06.037

2. JacksonRJ, HellenCUT, PestovaTV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nature reviews Molecular cell biology 11: 113–127 doi:10.1038/nrm2838

3. VarenneS, BucJ, LloubesR, LazdunskiC (1984) Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. Journal of molecular biology 180: 549–576.

4. KudlaG, MurrayAW, TollerveyD, PlotkinJB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science (New York, NY) 324: 255–258 doi:10.1126/science.1170160

5. StoletzkiN, Eyre-WalkerA (2007) Synonymous codon usage in Escherichia coli: selection for translational accuracy. Molecular biology and evolution 24: 374–381 doi:10.1093/molbev/msl166

6. PlotkinJB, KudlaG (2011) Synonymous but not the same: the causes and consequences of codon bias. Nature reviews Genetics 12: 32–42 doi:10.1038/nrg2899

7. GingoldH, PilpelY (2011) Determinants of translation efficiency and accuracy. Molecular systems biology 7: 481 doi:10.1038/msb.2011.14

8. DrummondDA, WilkeCOC (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341–352 doi:10.1016/j.cell.2008.05.042

9. Bermudez-SantanaC, AttoliniCS-O, KirstenT, EngelhardtJ, ProhaskaSJ, et al. (2010) Genomic organization of eukaryotic tRNAs. BMC genomics 11: 270 doi:10.1186/1471-2164-11-270

10. GoodenbourJM, PanT (2006) Diversity of tRNA genes in eukaryotes. Nucleic acids research 34: 6137–6146 doi:10.1093/nar/gkl725

11. KanayaS, YamadaY, KinouchiM, KudoY, IkemuraT (2001) Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. Journal of molecular evolution 53: 290–298 doi:10.1007/s002390010219

12. TullerT, CarmiA, VestsigianK, NavonS, DorfanY, et al. (2010) An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141: 344–354 doi:10.1016/j.cell.2010.03.031

13. PercudaniR, PavesiA, OttonelloS (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. Journal of molecular biology 268: 322–330 doi:10.1006/jmbi.1997.0942

14. ManO, PilpelY (2007) Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nature genetics 39: 415–421 doi:10.1038/ng1967

15. PechmannS, FrydmanJ (2012) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nature structural & molecular biology 20: 237–243 doi:10.1038/nsmb.2466

16. DieciG, FiorinoG, CastelnuovoM, TeichmannM, PaganoA (2007) The expanding RNA polymerase III transcriptome. Trends in genetics: TIG 23: 614–622 doi:10.1016/j.tig.2007.09.001

17. CanellaD, PrazV, ReinaJH, CousinP, HernandezN (2010) Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome research 20: 710–721 doi:10.1101/gr.101337.109

18. RobertsDN, StewartAJ, HuffJT, CairnsBR (2003) The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proceedings of the National Academy of Sciences of the United States of America 100: 14695–14700 doi:10.1073/pnas.2435566100

19. MoqtaderiZ, StruhlK (2004) Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Molecular and cellular biology 24: 4118–4127 doi:10.1128/MCB.24.10.4118

20. DittmarKA, GoodenbourJM, PanT (2006) Tissue-specific differences in human transfer RNA expression. PLoS genetics 2: e221 doi:10.1371/journal.pgen.0020221

21. RahaD, WangZ, MoqtaderiZ, WuL, ZhongG, et al. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proceedings of the National Academy of Sciences of the United States of America 107: 3639–3644 doi:10.1073/pnas.0911315106

22. KutterC, BrownGD, GonçalvesA, WilsonMD, WattS, et al. (2011) Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nature genetics 43: 948–955 doi:10.1038/ng.906

23. BrachmannCB, DaviesA, CostGJ, CaputoE, LiJ, et al. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast (Chichester, England) 14: 115–132 doi:;10.1002/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2

24. ChakshusmathiG, KimSDo, RubinsonDA, WolinSL (2003) A La protein requirement for efficient pre-tRNA folding. The EMBO journal 22: 6562–6572 doi:10.1093/emboj/cdg625

25. WeissWA, FriedbergEC (1986) Normal yeast tRNA(CAGGln) can suppress amber codons and is encoded by an essential gene. Journal of molecular biology 192: 725–735.

26. JohanssonMJO, EsbergA, HuangB, BjörkGR, ByströmAS (2008) Eukaryotic wobble uridine modifications promote a functionally redundant decoding system. Molecular and cellular biology 28: 3301–3312 doi:10.1128/MCB.01542-07

27. BreslowDK, CameronDM, CollinsSR, SchuldinerM, Stewart-OrnsteinJ, et al. (2008) A comprehensive strategy enabling high-resolution functional analysis of the yeast genome. Nature methods 5: 711–718 doi:10.1038/nmeth.1234

28. DelneriD, HoyleDC, GkargkasK, CrossEJM, RashB, et al. (2008) Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nature genetics 40: 113–117 doi:10.1038/ng.2007.49

29. CaustonHC, RenB, KohSS, HarbisonCT, KaninE, et al. (2001) Remodeling of Yeast Genome Expression in Response to Environmental Changes. Mol Biol Cell 12: 323–337.

30. GaschAP, SpellmanPT, KaoCM, Carmel-HarelO, EisenMB, et al. (2000) Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Mol Biol Cell 11: 4241–4257.

31. GaschAP, Werner-WashburneM (2002) The genomics of yeast responses to environmental stress and starvation. Functional & integrative genomics 2: 181–192 doi:10.1007/s10142-002-0058-2

32. StoebelDM, DeanAM, DykhuizenDE (2008) The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 178: 1653–1660 doi:10.1534/genetics.107.085399

33. KafriR, Bar-EvenA, PilpelY (2005) Transcription control reprogramming in genetic backup circuits. Nature genetics 37: 295–299 doi:10.1038/ng1523

34. KafriR, LevyM, PilpelY (2006) The regulatory utilization of genetic redundancy through responsive backup circuits. Proceedings of the National Academy of Sciences of the United States of America 103: 11653–11658 doi:10.1073/pnas.0604883103

35. DeLunaA, SpringerM, KirschnerMW, KishonyR (2010) Need-based up-regulation of protein levels in response to deletion of their duplicate genes. PLoS biology 8: e1000347 doi:10.1371/journal.pbio.1000347

36. AgrisPF (2004) Decoding the genome: a modified view. Nucleic acids research 32: 223–238 doi:10.1093/nar/gkh185

37. BegleyU, DyavaiahM, PatilA, RooneyJP, DiRenzoD, et al. (2007) Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Molecular cell 28: 860–870 doi:10.1016/j.molcel.2007.09.021

38. KalhorHR, ClarkeS (2003) Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Molecular and cellular biology 23: 9283–9292.

39. BragliaP, PercudaniR, DieciG (2005) Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. The Journal of biological chemistry 280: 19551–19562 doi:10.1074/jbc.M412238200

40. ZhangG, LukoszekR, Mueller-RoeberB, IgnatovaZ (2011) Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation. Nucleic Acids Research 39: 3331–3339.

41. HernandezN (2001) Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. The Journal of biological chemistry 276: 26733–26736 doi:10.1074/jbc.R100032200

42. GiuliodoriS, PercudaniR, BragliaP, FerrariR, GuffantiE, et al. (2003) A composite upstream sequence motif potentiates tRNA gene transcription in yeast. Journal of molecular biology 333: 1–20.

43. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings/. International Conference on Intelligent Systems for Molecular Biology; ISMB International Conference on Intelligent Systems for Molecular Biology 2: 28–36.

44. TrotterEW, KaoCM-F, BerenfeldL, BotsteinD, PetskoGa, et al. (2002) Misfolded proteins are competent to mediate a subset of the responses to heat shock in Saccharomyces cerevisiae. The Journal of biological chemistry 277: 44817–44825 doi:10.1074/jbc.M204686200

45. TraversKJ, PatilCK, WodickaL, LockhartDJ, WeissmanJS, et al. (2000) Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101: 249–258.

46. MitchellA, RomanoGH, GroismanB, YonaA, DekelE, et al. (2009) Adaptive prediction of environmental changes by microorganisms. Nature 460: 220–224 doi:10.1038/nature08112

47. KaganovichD, KopitoR, FrydmanJ (2008) Misfolded proteins partition between two distinct quality control compartments. Nature 454: 1088–1095 doi:10.1038/nature07195

48. SpokoiniR, MoldavskiO, NahmiasY, EnglandJL, SchuldinerM, et al. (2012) Confinement to organelle-associated inclusion structures mediates asymmetric inheritance of aggregated protein in budding yeast. Cell reports 2: 738–747 doi:10.1016/j.celrep.2012.08.024

49. KanehisaM, GotoS, SatoY, FurumichiM, TanabeM (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic acids research 40: D109–14 doi:10.1093/nar/gkr988

50. KanehisaM, GotoS (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28: 27–30.

51. SubramanianA, TamayoP, MoothaVK, MukherjeeS, EbertBL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 102: 15545–15550 doi:10.1073/pnas.0506580102

52. MoothaVK, LindgrenCM, ErikssonK-F, SubramanianA, SihagS, et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nature genetics 34: 267–273 doi:10.1038/ng1180

53. Bailly-BechetM, BorgsC, BraunsteinA, ChayesJ, DagkessamanskaiaA, et al. (2011) Finding undetected protein associations in cell signaling by belief propagation. Proceedings of the National Academy of Sciences of the United States of America 108: 882–887 doi:10.1073/pnas.1004751108

54. IhmelsJ, CollinsSR, SchuldinerM, KroganNJ, WeissmanJS (2007) Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss. Molecular systems biology 3: 86 doi:10.1038/msb4100127

55. PappB, PálC, HurstLD (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661–664 doi:10.1038/nature02636

56. KafriR, DahanO, LevyJ, PilpelY (2008) Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy. Proceedings of the National Academy of Sciences 105: 1243–1248 doi:10.1073/pnas.0711043105

57. HillenmeyerME, FungE, WildenhainJ, PierceSE, HoonS, et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (New York, NY) 320: 362–365 doi:10.1126/science.1150021

58. GiaeverG, ChuAM, NiL, ConnellyC, RilesL, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387–391 doi:10.1038/nature00935

59. GingoldH, DahanO, PilpelY (2012) Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome. Nucleic acids research 40: 10053–10063 doi:10.1093/nar/gks772

60. MoqtaderiZ, WangJ, RahaD, WhiteRJ, SnyderM, et al. (2010) Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nature structural & molecular biology 17: 635–640 doi:10.1038/nsmb.1794

61. PatilA, ChanCTY, DyavaiahM, RooneyJP, DedonPC, et al. (2012) Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA biology 9: 990–1001 doi:10.4161/rna.20531

62. ParedesJa, CarretoL, SimõesJ, BezerraAR, GomesAC, et al. (2012) Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast. BMC biology 10: 55 doi:10.1186/1741-7007-10-55

63. ShalgiR, HurtJA, KrykbaevaI, TaipaleM, LindquistS, et al. (2012) Widespread Regulation of Translation by Elongation Pausing in Heat Shock. Molecular cell 49: 439–452 doi:10.1016/j.molcel.2012.11.028

64. LiuB, HanY, QianS-B (2013) Cotranslational Response to Proteotoxic Stress by Elongation Pausing of Ribosomes. Molecular cell 49: 453–463 doi:10.1016/j.molcel.2012.12.001

65. KafriR, SpringerM, PilpelY (2009) Genetic redundancy: new tricks for old genes. Cell 136: 389–392 doi:10.1016/j.cell.2009.01.027

66. CostanzoM, BaryshnikovaA, BellayJ, KimY, SpearED, et al. (2010) The genetic landscape of a cell. Science (New York, NY) 327: 425–431 doi:10.1126/science.1180823

67. SchuldinerM, CollinsSR, ThompsonNJ, DenicV, BhamidipatiA, et al. (2005) Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123: 507–519 doi:10.1016/j.cell.2005.08.031

68. ZaborskeJ, PanT (2010) Genome-wide analysis of aminoacylation (charging) levels of tRNA using microarrays. Journal of visualized experiments (4) 2007 doi:10.3791/2007

69. GirstmairH, SaffertP, RodeS, CzechA, HollandG, et al. (2013) Depletion of Cognate Charged Transfer RNA Causes Translational Frameshifting within the Expanded CAG Stretch in Huntingtin. Cell reports 3: 148–159 doi:10.1016/j.celrep.2012.12.019

70. ChanPP, LoweTM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic acids research 37: D93–7 doi:10.1093/nar/gkn787

71. BaudinA, Ozier-KalogeropoulosO, DenouelA, LacrouteF, CullinC (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic acids research 21: 3329–3330.

72. WachA (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast (Chichester, England) 12: 259–265 doi:;10.1002/(SICI)1097-0061(19960315)12:3<259::AID-YEA901>3.0.CO;2-C

73. GoldsteinAL, McCuskerJH (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast (Chichester, England) 15: 1541–1553 doi:;10.1002/(SICI)1097-0061(199910)15:14<1541::AID-YEA476>3.0.CO;2-K