Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes

PLoS Genetics

Volumn 10, Issue 5, 2014, Pages

  Grosjean, Henri ^a   Breton, Marc ^b,c   Sirand Pugnet, Pascal ^b,c   Tardy, Florence ^d,e   Thiaucourt, François ^f   Citti, Christine ^g   Barré, Aurélien ^c   Yoshizawa, Satoko ^a   Fourmy, Dominique ^a   de Crécy Lagard, Valérie ^h   Blanchard, Alain ^b,c  

^a CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

^b Univ Bordeaux   (France)

^c UNIVERSITÉ DE BORDEAUX   (France)

^d FRENCH AGENCY FOR FOOD   (France)

^e UNIVERSITÉ DE LYON   (France)

^f CIRAD   (France)

^g UNIVERSITÉ DE TOULOUSE   (France)

^h UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; NUCLEOTIDE; RIBOSOME PROTEIN; RNA 16S; TRANSFER RNA;

AMINOACYLATION; ARTICLE; BACILLUS SUBTILIS; CONTROLLED STUDY; ESCHERICHIA COLI; EVOLUTION; GENE LOSS; GENE TRANSFER; GENETIC CODE; MOLECULAR EVOLUTION; MOLLICUTES; NONHUMAN; PREDICTION; RIBOSOME; RNA DEGRADATION; RNA STRUCTURE; RNA TRANSCRIPTION; RNA TRANSLATION; BACTERIAL GENE; GENETICS; PROTEIN SYNTHESIS;

BIOLOGICAL EVOLUTION; GENES, BACTERIAL; PROTEIN BIOSYNTHESIS; TENERICUTES;

EID: 84901626667     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004363     Document Type: Article

References (154)

1. Weisburg WG, Tully JG, Rose DL, Petzel JP, Oyaizu H, et al. (1989) A phylogenetic analysis of mycoplasmas: basis for their classification. J Bacteriol 171: 6455-6467.
2. Razin S, Yogev D, Naot Y, (1998) Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62: 1094-1156.
3. Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, et al. (2009) Impact of genome reduction on bacterial metabolism and its regulation. Science 326: 1263-1268.
4. Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271.
5. Catrein I, Herrmann R, (2011) The proteome of Mycoplasma pneumoniae, a supposedly "simple" cell. Proteomics 11: 3614-3632.
6. Pielak GJ, Miklos AC, (2012) Crowding and function reunite. Proc Natl Acad Sci U S A 107: 17457-17458.
7. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
8. Sorek R, Serrano L, (2011) Bacterial genomes: from regulatory complexity to engineering. Curr Opin Microbiol 14: 577-578.
9. Forster AC, Church GM, (2006) Towards synthesis of a minimal cell. Mol Syst Biol 2: 45.
10. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329: 52-56.
11. Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, et al. (2009) Proteome organization in a genome-reduced bacterium. Science 326: 1235-1240.
12. Koonin EV, (2000) How many genes can make a cell: the minimal-gene-set concept. Annu Rev Genomics Hum Genet 1: 99-116.
13. Parraga-Nino N, Colome-Calls N, Canals F, Querol E, Ferrer-Navarro M, (2012) A comprehensive proteome of Mycoplasma genitalium. J Proteome Res 11: 3305-3316.
14. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, et al. (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150: 389-401.
15. Mushegian AR, Koonin EV, (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. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, et al. (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103: 425-430.
17. Dybvig K, Lao P, Jordan DS, Simmons WL, (2010) Fewer essential genes in mycoplasmas than previous studies suggest. FEMS Microbiol Lett 311: 51-55.
18. French CT, Lao P, Loraine AE, Matthews BT, Yu H, et al. (2008) Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 69: 67-76.
19. Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, et al. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165-2169.
20. Dybvig K, Zuhua C, Lao P, Jordan DS, French CT, et al. (2008) Genome of Mycoplasma arthritidis. Infect Immun 76: 4000-4008.
21. Yutin N, Puigbo P, Koonin EV, Wolf YI, (2012) Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7: e36972.
22. Koonin EV, (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1: 127-136.
23. Mushegian A, (2008) Gene content of LUCA, the last universal common ancestor. Front Biosci 13: 4657-4666.
24. Fang G, Rocha E, Danchin A, (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. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 39: D583-590.
27. Belda E, Sekowska A, Le Fevre F, Morgat A, Mornico D, et al. (2013) An updated metabolic view of the Bacillus subtilis 168 genome. Microbiology 159: 757-770.
28. Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A, (2012) From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet 29: 273-279.
29. Koonin EV, Wolf YI, (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 6688-6719.
30. Himmelreich R, Plagens H, Hilbert H, Reiner B, Herrmann R, (1997) Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium. Nucleic Acids Res 25: 701-712.
31. Oshima K, Kakizawa S, Nishigawa H, Jung HY, Wei W, et al. (2004) Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat Genet 36: 27-29.
32. Pereyre S, Sirand-Pugnet P, Beven L, Charron A, Renaudin H, 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-Pugnet P, Citti C, Barre A, Blanchard A, (2007) Evolution of mollicutes: down a bumpy road with twists and turns. Res Microbiol 158: 754-766.
34. Sirand-Pugnet P, Lartigue C, Marenda M, Jacob D, Barre A, et al. (2007) Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet 3: e75.
35. Vasconcelos AT, Ferreira HB, Bizarro CV, Bonatto SL, Carvalho MO, 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. Csuros M, (2010) Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26: 1910-1912.
37. Farris JS, (1970) Methods for computing Wagner trees. Syst Zool 19: 83-92.
38. Herr AJ, Nelson CC, Wills NM, Gesteland RF, Atkins JF, (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. Nakagawa S, Niimura Y, Miura K, Gojobori T, (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. Lecompte O, Ripp R, Thierry JC, Moras D, Poch O, (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. Shoji S, Dambacher CM, Shajani Z, Williamson JR, Schultz PG, (2011) Systematic chromosomal deletion of bacterial ribosomal protein genes. J Mol Biol 413: 751-761.
43. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, 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. Bubunenko M, Baker T, Court DL, (2007) Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 189: 2844-2853.
45. Akanuma G, Nanamiya H, Natori Y, Yano K, Suzuki S, 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. Pech M, Karim Z, Yamamoto H, Kitakawa M, Qin Y, 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. Bang H, Pecht A, Raddatz G, Scior T, Solbach W, 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. Vogtherr M, Jacobs DM, Parac TN, Maurer M, Pahl A, 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. Hoffmann A, Becker AH, Zachmann-Brand B, Deuerling E, Bukau B, et al. (2012) Concerted action of the ribosome and the associated chaperone trigger factor confines nascent polypeptide folding. Mol Cell 48: 63-74.
50. Calloni G, Chen T, Schermann SM, Chang HC, Genevaux P, et al. (2012) DnaK functions as a central hub in the E. coli chaperone network. Cell Rep 1: 251-264.
51. Mazel D, Pochet S, Marliere P, (1994) Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J 13: 914-923.
52. Atkinson GC, Tenson T, Hauryliuk V, (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. deLivron MA, Makanji HS, Lane MC, Robinson VL, (2009) A novel domain in translational GTPase BipA mediates interaction with the 70S ribosome and influences GTP hydrolysis. Biochemistry 48: 10533-10541.
54. Inagaki Y, Bessho Y, Osawa S, (1993) Lack of peptide-release activity responding to codon UGA in Mycoplasma capricolum. Nucleic Acids Res 21: 1335-1338.
55. Citti C, Marechal-Drouard L, Saillard C, Weil JH, Bove JM, (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. Andachi Y, Yamao F, Muto A, Osawa S, (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. Yoshizawa S, Bock A, (2009) The many levels of control on bacterial selenoprotein synthesis. Biochim Biophys Acta 1790: 1404-1414.
58. Sheppard K, Yuan J, Hohn MJ, Jester B, Devine KM, et al. (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res 36: 1813-1825.
59. Yadavalli SS, Ibba M, (2012) Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 86: 1-43.
60. O'Donoghue P, Sheppard K, Nureki O, Soll D, (2011) Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proc Natl Acad Sci U S A 108: 20485-20490.
61. Tang SN, Huang JF, (2005) Evolution of different oligomeric glycyl-tRNA synthetases. FEBS Lett 579: 1441-1445.
62. Lin J, Huang JF, (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. Hausmann CD, Ibba M, (2008) Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed. FEMS Microbiol Rev 32: 705-721.
64. Li L, Boniecki MT, Jaffe JD, Imai BS, Yau PM, 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. Yadavalli SS, Ibba M, (2013) Selection of tRNA charging quality control mechanisms that increase mistranslation of the genetic code. Nucleic Acids Res 41: 1104-1112.
66. Yan W, Tan M, Eriani G, Wang ED, (2013) Leucine-specific domain modulates the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase. Nucleic Acids Res 41: 4988-4998.
67. Woese CR, Olsen GJ, Ibba M, Soll D, (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64: 202-236.
68. An S, Musier-Forsyth K, (2005) Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase.YbaK.tRNA ternary complex. J Biol Chem 280: 34465-34472.
69. Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, 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. Drummond DA, Wilke CO, (2009) The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet 10: 715-724.
71. Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M, (2012) Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci U S A 109: 18488-18492.
72. Wydau S, van der Rest G, Aubard C, Plateau P, Blanquet S, (2009) Widespread distribution of cell defense against D-aminoacyl-tRNAs. J Biol Chem 284: 14096-14104.
73. Lowe TM, Eddy SR, (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
74. Alluri RK, Li Z, (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. Deutsch C, El Yacoubi B, de Crecy-Lagard V, Iwata-Reuyl D, (2012) Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 287: 13666-13673.
76. Wan LC, Mao DY, Neculai D, Strecker J, Chiovitti D, et al. (2013) Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res 41: 6332-6346.
77. Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O, (2006) Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure 14: 357-366.
78. Vinella D, Brochier-Armanet C, Loiseau L, Talla E, Barras F, (2009) Iron-sulfur (Fe/S) protein biogenesis: phylogenomic and genetic studies of A-type carriers. PLoS Genet 5: e1000497.
79. Albrecht AG, Peuckert F, Landmann H, Miethke M, Seubert A, 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 Yacoubi B, Bailly M, de Crecy-Lagard V, (2012) Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu Rev Genet 46: 69-95.
81. Yokobori SI, Kitamura A, Grosjean H, Bessho Y, (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. Taniguchi T, Miyauchi K, Nakane D, Miyata M, Muto A, 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. Jones TE, Ribas de Pouplana L, Alexander RW, (2013) Evidence for late resolution of the AUX codon box in evolution. J Biol Chem 288: 19625-19632.
84. Ranaei-Siadat E, Fabret C, Seijo B, Dardel F, Grosjean H, 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. Desmolaize B, Fabret C, Bregeon D, Rose S, Grosjean H, 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. Hansen MA, Kirpekar F, Ritterbusch W, Vester B, (2002) Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA 8: 202-213.
87. Hsuchen CC, Dubin DT, (1980) Methylation patterns of mycoplasma transfer and ribosomal ribonucleic acid. J Bacteriol 144: 991-998.
88. Wilson DN, Nierhaus KH, (2007) The weird and wonderful world of bacterial ribosome regulation. Crit Rev Biochem Mol Biol 42: 187-219.
89. Goto S, Muto A, Himeno H, (2013) GTPases involved in bacterial ribosome maturation. J Biochem 153: 403-414.
90. Shajani Z, Sykes MT, Williamson JR, (2011) Assembly of bacterial ribosomes. Annu Rev Biochem 80: 501-526.
91. Verstraeten N, Fauvart M, Versees W, Michiels J, (2011) The universally conserved prokaryotic GTPases. Microbiol Mol Biol Rev 75: 507-542.
92. Jomaa A, Stewart G, Mears JA, Kireeva I, Brown ED, et al. (2011) Cryo-electron microscopy structure of the 30S subunit in complex with the YjeQ biogenesis factor. RNA 17: 2026-2038.
93. Tu C, Zhou X, Tarasov SG, Tropea JE, Austin BP, 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. Absalon C, Obuchowski M, Madec E, Delattre D, Holland IB, 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. Gulati M, Jain N, Anand B, Prakash B, Britton RA, (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. Anand B, Surana P, Prakash B, (2010) Deciphering the catalytic machinery in 30S ribosome assembly GTPase YqeH. PLoS One 5: e9944.
97. Fischer JJ, Coatham ML, Bear SE, Brandon HE, De Laurentiis EI, et al. (2012) The ribosome modulates the structural dynamics of the conserved GTPase HflX and triggers tight nucleotide binding. Biochimie 94: 1647-1659.
98. Goto S, Kato S, Kimura T, Muto A, Himeno H, (2011) RsgA releases RbfA from 30S ribosome during a late stage of ribosome biosynthesis. EMBO J 30: 104-114.
99. Bunner AE, Nord S, Wikstrom PM, Williamson JR, (2010) The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution. J Mol Biol 398: 1-7.
100. Lopez-Ramirez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Alvarez G, (2011) Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins. J Mol Evol 72: 413-431.
101. Owttrim GW, (2013) RNA helicases: diverse roles in prokaryotic response to abiotic stress. RNA Biol 10: 96-110.
102. Strader MB, Costantino N, Elkins CA, Chen CY, Patel I, 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-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH, (2002) The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 21: 769-778.
104. Peil L, Starosta AL, Virumae K, Atkinson GC, Tenson T, et al. (2012) Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Nat Chem Biol 8: 695-697.
105. Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, et al. (2011) The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-beta-lysine. Nat Chem Biol 7: 667-669.
106. Bandyra KJ, Bouvier M, Carpousis AJ, Luisi BF, (2013) The social fabric of the RNA degradosome. Biochim Biophys Acta 1829: 514-522.
107. Condon C, (2003) RNA processing and degradation in Bacillus subtilis. Microbiol Mol Biol Rev 67: 157-174 table of contents.
108. Kazantsev AV, Pace NR, (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 4: 729-740.
109. Jamalli A, Hebert A, Zig L, Putzer H, (2014) Control of Expression of the RNases J1 and J2 in Bacillus subtilis. J Bacteriol 196: 318-324.
110. Richards J, Liu Q, Pellegrini O, Celesnik H, Yao S, et al. (2011) An RNA pyrophosphohydrolase triggers 5′-exonucleolytic degradation of mRNA in Bacillus subtilis. Mol Cell 43: 940-949.
111. Lehnik-Habrink M, Lewis RJ, Mader U, Stulke J, (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol 84: 1005-1017.
112. Newman JA, Hewitt L, Rodrigues C, Solovyova AS, Harwood CR, 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. Dutta T, Malhotra A, Deutscher MP, (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. Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC, (2013) Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol Cell 49: 427-438.
115. MacRae IJ, Doudna JA, (2007) Ribonuclease revisited: structural insights into ribonuclease III family enzymes. Curr Opin Struct Biol 17: 138-145.
116. Oussenko IA, Sanchez R, Bechhofer DH, (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. Fang M, Zeisberg WM, Condon C, Ogryzko V, Danchin A, et al. (2009) Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis. Nucleic Acids Res 37: 5114-5125.
118. Postic G, Danchin A, Mechold U, (2012) Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA 18: 155-165.
119. Piton J, Larue V, Thillier Y, Dorleans A, Pellegrini O, 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. Dambach M, Irnov I, Winkler WC, (2013) Association of RNAs with Bacillus subtilis Hfq. PLoS One 8: e55156.
121. Park JH, Yamaguchi Y, Inouye M, (2011) Bacillus subtilis MazF-bs (EndoA) is a UACAU-specific mRNA interferase. FEBS Lett 585: 2526-2532.
122. Portnoy V, Schuster G, (2008) Mycoplasma gallisepticum as the first analyzed bacterium in which RNA is not polyadenylated. FEMS Microbiol Lett 283: 97-103.
123. Zheng X, Hu GQ, She ZS, Zhu H, (2011) Leaderless genes in bacteria: clue to the evolution of translation initiation mechanisms in prokaryotes. BMC Genomics 12: 361.
124. Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, 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. Melnikov S, Ben-Shem A, Garreau de Loubresse N, Jenner L, Yusupova G, et al. (2012) One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol 19: 560-567.
126. Maier T, Schmidt A, Guell M, Kuhner S, Gavin AC, et al. (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7: 511.
127. Bakshi S, Siryaporn A, Goulian M, Weisshaar JC, (2012) Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells. Mol Microbiol 85: 21-38.
128. Kube M, Siewert C, Migdoll AM, Duduk B, Holz S, 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. Fares MA, Ruiz-Gonzalez MX, Moya A, Elena SF, Barrio E, (2002) Endosymbiotic bacteria: groEL buffers against deleterious mutations. Nature 417: 398.
130. Pal C, Papp B, Lercher MJ, (2006) An integrated view of protein evolution. Nat Rev Genet 7: 337-348.
131. Khachane AN, Timmis KN, Martins dos Santos VA, (2007) Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes. Mol Biol Evol 24: 449-456.
132. Gruschke S, Ott M, (2010) The polypeptide tunnel exit of the mitochondrial ribosome is tailored to meet the specific requirements of the organelle. Bioessays 32: 1050-1057.
133. Agrawal RK, Sharma MR, (2012) Structural aspects of mitochondrial translational apparatus. Curr Opin Struct Biol 22: 797-803.
134. Reynolds NM, Ling J, Roy H, Banerjee R, Repasky SE, et al. (2010) Cell-specific differences in the requirements for translation quality control. Proc Natl Acad Sci U S A 107: 4063-4068.
135. Smits P, Smeitink JA, van den Heuvel LP, Huynen MA, Ettema TJ, (2007) Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 35: 4686-4703.
136. Georgiades K, Merhej V, El Karkouri K, Raoult D, Pontarotti P, (2011) Gene gain and loss events in Rickettsia and Orientia species. Biol Direct 6: 6.
137. McCutcheon JP, Moran NA, (2012) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10: 13-26.
138. Bennett GM, Moran NA, (2013) Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect. Genome Biol Evol 5: 1675-1688.
139. Gil R, Silva FJ, Pereto J, Moya A, (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68: 518-537 table of contents.
140. Glass JI, (2012) Synthetic genomics and the construction of a synthetic bacterial cell. Perspect Biol Med 55: 473-489.
141. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
142. Gouy M, Guindon S, Gascuel O, (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224.
143. Talavera G, Castresana J, (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56: 564-577.
144. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, 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. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, et al. (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36: W465-469.
146. Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, et al. (2013) MODOMICS: a database of RNA modification pathways-2013 update. Nucleic Acids Res 41: D262-267.
147. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33: 6083-6089.
148. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, 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. Tanabe M, Kanehisa M, (2012) Using the KEGG database resource. Curr Protoc Bioinformatics Chapter 1: Unit1 12.
150. Barre A, de Daruvar A, Blanchard A, (2004) MolliGen, a database dedicated to the comparative genomics of Mollicutes. Nucleic Acids Res 32: D307-310.
151. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, et al. (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-229.
152. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
153. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
154. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, et al. (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 100: 4678-4683.