Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of
In all cells, proteins are synthesized from the message encoded by mRNA using complex machineries involving many proteins and RNAs. In this process, named translation, the ribosome plays a central role. The elements involved in both ribosome biogenesis and its function are extremely conserved in all organisms from the simplest bacteria to mammalian cells. Most of the 260 known proteins involved in translation have been identified and studied in the bacteria Escherichia coli and Bacillus subtilis, two common cellular models in biology. However, comparative genomics has shown that the translation protein set can be much smaller. This is true for bacteria belonging to the class Mollicutes that are characterized by reduced genomes and hence considered as models for minimal cells. Using homology inference approach and expert analyses, we identified the translation apparatus proteins for 39 of these organisms. Although striking variations were found from one group of species to another, some Mollicutes species require half as many proteins as E. coli or B. subtilis. This analysis allowed us to determine a set of proteins necessary for translation in Mollicutes and define the translation apparatus that would be required in a cellular chassis mimicking a minimal bacterial cell.
Vyšlo v časopise:
Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of. PLoS Genet 10(5): e32767. doi:10.1371/journal.pgen.1004363
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Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004363
Souhrn
In all cells, proteins are synthesized from the message encoded by mRNA using complex machineries involving many proteins and RNAs. In this process, named translation, the ribosome plays a central role. The elements involved in both ribosome biogenesis and its function are extremely conserved in all organisms from the simplest bacteria to mammalian cells. Most of the 260 known proteins involved in translation have been identified and studied in the bacteria Escherichia coli and Bacillus subtilis, two common cellular models in biology. However, comparative genomics has shown that the translation protein set can be much smaller. This is true for bacteria belonging to the class Mollicutes that are characterized by reduced genomes and hence considered as models for minimal cells. Using homology inference approach and expert analyses, we identified the translation apparatus proteins for 39 of these organisms. Although striking variations were found from one group of species to another, some Mollicutes species require half as many proteins as E. coli or B. subtilis. This analysis allowed us to determine a set of proteins necessary for translation in Mollicutes and define the translation apparatus that would be required in a cellular chassis mimicking a minimal bacterial cell.
Zdroje
1. WeisburgWG, TullyJG, RoseDL, PetzelJP, OyaizuH, et al. (1989) A phylogenetic analysis of mycoplasmas: basis for their classification. J Bacteriol 171: 6455–6467.
2. RazinS, YogevD, NaotY (1998) Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62: 1094–1156.
3. YusE, MaierT, MichalodimitrakisK, van NoortV, YamadaT, et al. (2009) Impact of genome reduction on bacterial metabolism and its regulation. Science 326: 1263–1268.
4. GuellM, van NoortV, YusE, ChenWH, Leigh-BellJ, et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268–1271.
5. CatreinI, HerrmannR (2011) The proteome of Mycoplasma pneumoniae, a supposedly “simple” cell. Proteomics 11: 3614–3632.
6. PielakGJ, MiklosAC (2012) Crowding and function reunite. Proc Natl Acad Sci U S A 107: 17457–17458.
7. CiccarelliFD, DoerksT, von MeringC, CreeveyCJ, SnelB, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283–1287.
8. SorekR, SerranoL (2011) Bacterial genomes: from regulatory complexity to engineering. Curr Opin Microbiol 14: 577–578.
9. ForsterAC, ChurchGM (2006) Towards synthesis of a minimal cell. Mol Syst Biol 2: 45.
10. GibsonDG, GlassJI, LartigueC, NoskovVN, ChuangRY, et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329: 52–56.
11. KuhnerS, van NoortV, BettsMJ, Leo-MaciasA, BatisseC, et al. (2009) Proteome organization in a genome-reduced bacterium. Science 326: 1235–1240.
12. KooninEV (2000) How many genes can make a cell: the minimal-gene-set concept. Annu Rev Genomics Hum Genet 1: 99–116.
13. Parraga-NinoN, Colome-CallsN, CanalsF, QuerolE, Ferrer-NavarroM (2012) A comprehensive proteome of Mycoplasma genitalium. J Proteome Res 11: 3305–3316.
14. KarrJR, SanghviJC, MacklinDN, GutschowMV, JacobsJM, et al. (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150: 389–401.
15. MushegianAR, KooninEV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93: 10268–10273.
16. GlassJI, Assad-GarciaN, AlperovichN, YoosephS, LewisMR, et al. (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103: 425–430.
17. DybvigK, LaoP, JordanDS, SimmonsWL (2010) Fewer essential genes in mycoplasmas than previous studies suggest. FEMS Microbiol Lett 311: 51–55.
18. FrenchCT, LaoP, LoraineAE, MatthewsBT, YuH, et al. (2008) Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 69: 67–76.
19. HutchisonCA, PetersonSN, GillSR, ClineRT, WhiteO, et al. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165–2169.
20. DybvigK, ZuhuaC, LaoP, JordanDS, FrenchCT, et al. (2008) Genome of Mycoplasma arthritidis. Infect Immun 76: 4000–4008.
21. YutinN, PuigboP, KooninEV, WolfYI (2012) Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7: e36972.
22. KooninEV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1: 127–136.
23. MushegianA (2008) Gene content of LUCA, the last universal common ancestor. Front Biosci 13: 4657–4666.
24. FangG, RochaE, DanchinA (2005) How essential are nonessential genes? Mol Biol Evol 22: 2147–2156.
25. Johansson KE, Pettersson B (2002) Taxonomy of Mollicutes. In: Razin S, Herrmann R, editors. Molecular Biology and Pathogenicity of Mycoplasmas. New York: Kluwer Academic/Plenum Publishers. pp. 1–29.
26. KeselerIM, Collado-VidesJ, Santos-ZavaletaA, Peralta-GilM, Gama-CastroS, et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 39: D583–590.
27. BeldaE, SekowskaA, Le FevreF, MorgatA, MornicoD, et al. (2013) An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 159: 757–770.
28. Acevedo-RochaCG, FangG, SchmidtM, UsseryDW, DanchinA (2012) From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 29: 273–279.
29. KooninEV, WolfYI (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 6688–6719.
30. HimmelreichR, PlagensH, HilbertH, ReinerB, HerrmannR (1997) Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res 25: 701–712.
31. OshimaK, KakizawaS, NishigawaH, JungHY, WeiW, et al. (2004) Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 36: 27–29.
32. PereyreS, Sirand-PugnetP, BevenL, CharronA, RenaudinH, et al. (2009) Life on arginine for Mycoplasma hominis: clues from its minimal genome and comparison with other human urogenital mycoplasmas. PLoS Genet 5: e1000677.
33. Sirand-PugnetP, CittiC, BarreA, BlanchardA (2007) Evolution of mollicutes: down a bumpy road with twists and turns. Res Microbiol 158: 754–766.
34. Sirand-PugnetP, LartigueC, MarendaM, JacobD, BarreA, et al. (2007) Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet 3: e75.
35. VasconcelosAT, FerreiraHB, BizarroCV, BonattoSL, CarvalhoMO, et al. (2005) Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol 187: 5568–5577.
36. CsurosM (2010) Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26: 1910–1912.
37. FarrisJS (1970) Methods for computing Wagner trees. Syst Zool 19: 83–92.
38. HerrAJ, NelsonCC, WillsNM, GestelandRF, AtkinsJF (2001) Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA. J Mol Biol 309: 1029–1048.
39. NakagawaS, NiimuraY, MiuraK, GojoboriT (2010) Dynamic evolution of translation initiation mechanisms in prokaryotes. Proc Natl Acad Sci U S A 107: 6382–6387.
40. Byrgazov K, Vesper O, Moll I (2013) Ribosome heterogeneity: another level of complexity in bacterial translation regulation. Curr Opin Microbiol: 133–139.
41. LecompteO, RippR, ThierryJC, MorasD, PochO (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 30: 5382–5390.
42. ShojiS, DambacherCM, ShajaniZ, WilliamsonJR, SchultzPG (2011) Systematic chromosomal deletion of bacterial ribosomal protein genes. J Mol Biol 413: 751–761.
43. BabaT, AraT, HasegawaM, TakaiY, OkumuraY, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
44. BubunenkoM, BakerT, CourtDL (2007) Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 189: 2844–2853.
45. AkanumaG, NanamiyaH, NatoriY, YanoK, SuzukiS, et al. (2012) Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation. J Bacteriol 194: 6282–6291.
46. PechM, KarimZ, YamamotoH, KitakawaM, QinY, et al. (2011) Elongation factor 4 (EF4/LepA) accelerates protein synthesis at increased Mg2+ concentrations. Proc Natl Acad Sci U S A 108: 3199–3203.
47. BangH, PechtA, RaddatzG, SciorT, SolbachW, et al. (2000) Prolyl isomerases in a minimal cell. Catalysis of protein folding by trigger factor from Mycoplasma genitalium. Eur J Biochem 267: 3270–3280.
48. VogtherrM, JacobsDM, ParacTN, MaurerM, PahlA, et al. (2002) NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from Mycoplasma genitalium compared to FK506-binding protein. J Mol Biol 318: 1097–1115.
49. HoffmannA, BeckerAH, Zachmann-BrandB, DeuerlingE, BukauB, et al. (2012) Concerted action of the ribosome and the associated chaperone trigger factor confines nascent polypeptide folding. Mol Cell 48: 63–74.
50. CalloniG, ChenT, SchermannSM, ChangHC, GenevauxP, et al. (2012) DnaK functions as a central hub in the E. coli chaperone network. Cell Rep 1: 251–264.
51. MazelD, PochetS, MarliereP (1994) Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J 13: 914–923.
52. AtkinsonGC, TensonT, HauryliukV (2011) The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS One 6: e23479.
53. deLivronMA, MakanjiHS, LaneMC, RobinsonVL (2009) A novel domain in translational GTPase BipA mediates interaction with the 70S ribosome and influences GTP hydrolysis. Biochemistry 48: 10533–10541.
54. InagakiY, BesshoY, OsawaS (1993) Lack of peptide-release activity responding to codon UGA in Mycoplasma capricolum. Nucleic Acids Res 21: 1335–1338.
55. CittiC, Marechal-DrouardL, SaillardC, WeilJH, BoveJM (1992) Spiroplasma citri UGG and UGA tryptophan codons: sequence of the two tryptophanyl-tRNAs and organization of the corresponding genes. J Bacteriol 174: 6471–6478.
56. AndachiY, YamaoF, MutoA, OsawaS (1989) Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. J Mol Biol 209: 37–54.
57. YoshizawaS, BockA (2009) The many levels of control on bacterial selenoprotein synthesis. Biochim Biophys Acta 1790: 1404–1414.
58. SheppardK, YuanJ, HohnMJ, JesterB, DevineKM, et al. (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res 36: 1813–1825.
59. YadavalliSS, IbbaM (2012) Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 86: 1–43.
60. O'DonoghueP, SheppardK, NurekiO, SollD (2011) Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proc Natl Acad Sci U S A 108: 20485–20490.
61. TangSN, HuangJF (2005) Evolution of different oligomeric glycyl-tRNA synthetases. FEBS Lett 579: 1441–1445.
62. LinJ, HuangJF (2003) Evolution of phenylalanyl-tRNA synthetase by domain losing. Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35: 1061–1065.
63. HausmannCD, IbbaM (2008) Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed. FEMS Microbiol Rev 32: 705–721.
64. LiL, BonieckiMT, JaffeJD, ImaiBS, YauPM, et al. (2011) Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites. Proc Natl Acad Sci U S A 108: 9378–9383.
65. YadavalliSS, IbbaM (2013) Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code. Nucleic Acids Res 41: 1104–1112.
66. YanW, TanM, ErianiG, WangED (2013) Leucine-specific domain modulates the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase. Nucleic Acids Res 41: 4988–4998.
67. WoeseCR, OlsenGJ, IbbaM, SollD (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64: 202–236.
68. AnS, Musier-ForsythK (2005) Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex. J Biol Chem 280: 34465–34472.
69. DelaneyNF, BalengerS, BonneaudC, MarxCJ, HillGE, et al. (2012) Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum. PLoS Genet 8: e1002511.
70. DrummondDA, WilkeCO (2009) The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 10: 715–724.
71. SungW, AckermanMS, MillerSF, DoakTG, LynchM (2012) Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci U S A 109: 18488–18492.
72. WydauS, van der RestG, AubardC, PlateauP, BlanquetS (2009) Widespread distribution of cell defense against D-aminoacyl-tRNAs. J Biol Chem 284: 14096–14104.
73. LoweTM, EddySR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964.
74. AlluriRK, LiZ (2012) Novel one-step mechanism for tRNA 3′-end maturation by the exoribonuclease RNase R of Mycoplasma genitalium. J Biol Chem 287: 23427–23433.
75. DeutschC, El YacoubiB, de Crecy-LagardV, Iwata-ReuylD (2012) Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 287: 13666–13673.
76. WanLC, MaoDY, NeculaiD, StreckerJ, ChiovittiD, et al. (2013) Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res 41: 6332–6346.
77. NumataT, FukaiS, IkeuchiY, SuzukiT, NurekiO (2006) Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure 14: 357–366.
78. VinellaD, Brochier-ArmanetC, LoiseauL, TallaE, BarrasF (2009) Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers. PLoS Genet 5: e1000497.
79. AlbrechtAG, PeuckertF, LandmannH, MiethkeM, SeubertA, et al. (2011) Mechanistic characterization of sulfur transfer from cysteine desulfurase SufS to the iron-sulfur scaffold SufU in Bacillus subtilis. FEBS Lett 585: 465–470.
80. El YacoubiB, BaillyM, de Crecy-LagardV (2012) Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu Rev Genet 46: 69–95.
81. YokoboriSI, KitamuraA, GrosjeanH, BesshoY (2013) Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes. Nucleic Acids Res 41: 6531–6543.
82. TaniguchiT, MiyauchiK, NakaneD, MiyataM, MutoA, et al. (2013) Decoding system for the AUA codon by tRNAIle with the UAU anticodon in Mycoplasma mobile. Nucleic Acids Res 41: 2621–2631.
83. JonesTE, Ribas de PouplanaL, AlexanderRW (2013) Evidence for late resolution of the AUX codon box in evolution. J Biol Chem 288: 19625–19632.
84. Ranaei-SiadatE, FabretC, SeijoB, DardelF, GrosjeanH, et al. (2013) RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C (5) -methylation of uridine in both tmRNA and tRNA. RNA Biol 10: 572–578.
85. DesmolaizeB, FabretC, BregeonD, RoseS, GrosjeanH, et al. (2011) A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA. Nucleic Acids Res 39: 9368–9375.
86. HansenMA, KirpekarF, RitterbuschW, VesterB (2002) Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA 8: 202–213.
87. HsuchenCC, DubinDT (1980) Methylation patterns of mycoplasma transfer and ribosomal ribonucleic acid. J Bacteriol 144: 991–998.
88. WilsonDN, NierhausKH (2007) The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 42: 187–219.
89. GotoS, MutoA, HimenoH (2013) GTPases involved in bacterial ribosome maturation. J Biochem 153: 403–414.
90. ShajaniZ, SykesMT, WilliamsonJR (2011) Assembly of bacterial ribosomes. Annu Rev Biochem 80: 501–526.
91. VerstraetenN, FauvartM, VerseesW, MichielsJ (2011) The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev 75: 507–542.
92. JomaaA, StewartG, MearsJA, KireevaI, BrownED, et al. (2011) Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor. RNA 17: 2026–2038.
93. TuC, ZhouX, TarasovSG, TropeaJE, AustinBP, et al. (2011) The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3′ end of 16S rRNA. Proc Natl Acad Sci U S A 108: 10156–10161.
94. AbsalonC, ObuchowskiM, MadecE, DelattreD, HollandIB, et al. (2009) CpgA, EF-Tu and the stressosome protein YezB are substrates of the Ser/Thr kinase/phosphatase couple, PrkC/PrpC, in Bacillus subtilis. Microbiology 155: 932–943.
95. GulatiM, JainN, AnandB, PrakashB, BrittonRA (2013) Mutational analysis of the ribosome assembly GTPase RbgA provides insight into ribosome interaction and ribosome-stimulated GTPase activation. Nucleic Acids Res 41: 3217–3227.
96. AnandB, SuranaP, PrakashB (2010) Deciphering the catalytic machinery in 30S ribosome assembly GTPase YqeH. PLoS One 5: e9944.
97. FischerJJ, CoathamML, BearSE, BrandonHE, De LaurentiisEI, et al. (2012) The ribosome modulates the structural dynamics of the conserved GTPase HflX and triggers tight nucleotide binding. Biochimie 94: 1647–1659.
98. GotoS, KatoS, KimuraT, MutoA, HimenoH (2011) RsgA releases RbfA from 30S ribosome during a late stage of ribosome biosynthesis. EMBO J 30: 104–114.
99. BunnerAE, NordS, WikstromPM, WilliamsonJR (2010) The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution. J Mol Biol 398: 1–7.
100. Lopez-RamirezV, AlcarazLD, Moreno-HagelsiebG, Olmedo-AlvarezG (2011) Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins. J Mol Evol 72: 413–431.
101. OwttrimGW (2013) RNA helicases: diverse roles in prokaryotic response to abiotic stress. RNA Biol 10: 96–110.
102. StraderMB, CostantinoN, ElkinsCA, ChenCY, PatelI, et al. (2011) A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol Cell Proteomics 10: M110.005199.
103. Heurgue-HamardV, ChampS, EngstromA, EhrenbergM, BuckinghamRH (2002) The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 21: 769–778.
104. PeilL, StarostaAL, VirumaeK, AtkinsonGC, TensonT, et al. (2012) Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Nat Chem Biol 8: 695–697.
105. RoyH, ZouSB, BullwinkleTJ, WolfeBS, GilreathMS, et al. (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-beta-lysine. Nat Chem Biol 7: 667–669.
106. BandyraKJ, BouvierM, CarpousisAJ, LuisiBF (2013) The social fabric of the RNA degradosome. Biochim Biophys Acta 1829: 514–522.
107. CondonC (2003) RNA processing and degradation in Bacillus subtilis. Microbiol Mol Biol Rev 67: 157–174 table of contents.
108. KazantsevAV, PaceNR (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 4: 729–740.
109. JamalliA, HebertA, ZigL, PutzerH (2014) Control of Expression of the RNases J1 and J2 in Bacillus subtilis. J Bacteriol 196: 318–324.
110. RichardsJ, LiuQ, PellegriniO, CelesnikH, YaoS, et al. (2011) An RNA pyrophosphohydrolase triggers 5′-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol Cell 43: 940–949.
111. Lehnik-HabrinkM, LewisRJ, MaderU, StulkeJ (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol 84: 1005–1017.
112. NewmanJA, HewittL, RodriguesC, SolovyovaAS, HarwoodCR, et al. (2012) Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. J Mol Biol 416: 121–136.
113. DuttaT, MalhotraA, DeutscherMP (2013) How a CCA sequence protects mature tRNAs and tRNA precursors from action of the processing enzyme RNase BN/RNase Z. J Biol Chem 288: 30636–30644.
114. JacobAI, KohrerC, DaviesBW, RajBhandaryUL, WalkerGC (2013) Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell 49: 427–438.
115. MacRaeIJ, DoudnaJA (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol 17: 138–145.
116. OussenkoIA, SanchezR, BechhoferDH (2002) Bacillus subtilis YhaM, a member of a new family of 3′-to-5′ exonucleases in gram-positive bacteria. J Bacteriol 184: 6250–6259.
117. FangM, ZeisbergWM, CondonC, OgryzkoV, DanchinA, et al. (2009) Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis. Nucleic Acids Res 37: 5114–5125.
118. PosticG, DanchinA, MecholdU (2012) Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA 18: 155–165.
119. PitonJ, LarueV, ThillierY, DorleansA, PellegriniO, et al. (2013) Bacillus subtilis RNA deprotection enzyme RppH recognizes guanosine in the second position of its substrates. Proc Natl Acad Sci U S A 110: 8858–8863.
120. DambachM, IrnovI, WinklerWC (2013) Association of RNAs with Bacillus subtilis Hfq. PLoS One 8: e55156.
121. ParkJH, YamaguchiY, InouyeM (2011) Bacillus subtilis MazF-bs (EndoA) is a UACAU-specific mRNA interferase. FEBS Lett 585: 2526–2532.
122. PortnoyV, SchusterG (2008) Mycoplasma gallisepticum as the first analyzed bacterium in which RNA is not polyadenylated. FEMS Microbiol Lett 283: 97–103.
123. ZhengX, HuGQ, SheZS, ZhuH (2011) Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics 12: 361.
124. CannoneJJ, SubramanianS, SchnareMN, CollettJR, D'SouzaLM, et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
125. MelnikovS, Ben-ShemA, Garreau de LoubresseN, JennerL, YusupovaG, et al. (2012) One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol 19: 560–567.
126. MaierT, SchmidtA, GuellM, KuhnerS, GavinAC, et al. (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7: 511.
127. BakshiS, SiryapornA, GoulianM, WeisshaarJC (2012) Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells. Mol Microbiol 85: 21–38.
128. KubeM, SiewertC, MigdollAM, DudukB, HolzS, et al. (2013) Analysis of the complete genomes of Acholeplasma brassicae , A. palmae and A. laidlawii and their comparison to the obligate parasites from ‘Candidatus Phytoplasma’. J Mol Microbiol Biotechnol 24: 19–36.
129. FaresMA, Ruiz-GonzalezMX, MoyaA, ElenaSF, BarrioE (2002) Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature 417: 398.
130. PalC, PappB, LercherMJ (2006) An integrated view of protein evolution. Nat Rev Genet 7: 337–348.
131. KhachaneAN, TimmisKN, Martins dos SantosVA (2007) Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes. Mol Biol Evol 24: 449–456.
132. GruschkeS, OttM (2010) The polypeptide tunnel exit of the mitochondrial ribosome is tailored to meet the specific requirements of the organelle. Bioessays 32: 1050–1057.
133. AgrawalRK, SharmaMR (2012) Structural aspects of mitochondrial translational apparatus. Curr Opin Struct Biol 22: 797–803.
134. ReynoldsNM, LingJ, RoyH, BanerjeeR, RepaskySE, et al. (2010) Cell-specific differences in the requirements for translation quality control. Proc Natl Acad Sci U S A 107: 4063–4068.
135. SmitsP, SmeitinkJA, van den HeuvelLP, HuynenMA, EttemaTJ (2007) Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 35: 4686–4703.
136. GeorgiadesK, MerhejV, El KarkouriK, RaoultD, PontarottiP (2011) Gene gain and loss events in Rickettsia and Orientia species. Biol Direct 6: 6.
137. McCutcheonJP, MoranNA (2012) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10: 13–26.
138. BennettGM, MoranNA (2013) Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect. Genome Biol Evol 5: 1675–1688.
139. GilR, SilvaFJ, PeretoJ, MoyaA (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68: 518–537 table of contents.
140. GlassJI (2012) Synthetic genomics and the construction of a synthetic bacterial cell. Perspect Biol Med 55: 473–489.
141. EdgarRC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797.
142. GouyM, GuindonS, GascuelO (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221–224.
143. TalaveraG, CastresanaJ (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564–577.
144. GuindonS, DufayardJF, LefortV, AnisimovaM, HordijkW, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307–321.
145. DereeperA, GuignonV, BlancG, AudicS, BuffetS, et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: W465–469.
146. MachnickaMA, MilanowskaK, Osman OglouO, PurtaE, KurkowskaM, et al. (2013) MODOMICS: a database of RNA modification pathways–2013 update. Nucleic Acids Res 41: D262–267.
147. KarpPD, OuzounisCA, Moore-KochlacsC, GoldovskyL, KaipaP, et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33: 6083–6089.
148. OverbeekR, BegleyT, ButlerRM, ChoudhuriJV, ChuangHY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691–5702.
149. TanabeM, KanehisaM (2012) Using the KEGG database resource. Curr Protoc Bioinformatics Chapter 1: Unit1 12.
150. BarreA, de DaruvarA, BlanchardA (2004) MolliGen, a database dedicated to the comparative genomics of Mollicutes. Nucleic Acids Res 32: D307–310.
151. Marchler-BauerA, LuS, AndersonJB, ChitsazF, DerbyshireMK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225–229.
152. LarkinMA, BlackshieldsG, BrownNP, ChennaR, McGettiganPA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.
153. TamuraK, PetersonD, PetersonN, StecherG, NeiM, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
154. KobayashiK, EhrlichSD, AlbertiniA, AmatiG, AndersenKK, et al. (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100: 4678–4683.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2014 Číslo 5
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