Examination of post-transcriptional regulations in prokaryotes by integrative biology

Comptes Rendus - Biologies

Volumn 332, Issue 11, 2009, Pages 958-973

  Picard, Flora ^a,b,c   Dressaire, Clémentine ^a,b,c   Girbal, Laurence ^a,b,c   Cocaign Bousquet, Muriel ^a,b,c  

^a INSA   (France)

^b UMR792 INGÉNIERIE DES SYSTÈMES BIOLOGIQUES ET DES PROCÉDÉS   (France)

^c CNRS   (France)

Author keywords

Integrative biology; mRNA stability; Post transcriptional regulations; Prokaryotes; Protein stability; Translation efficiency

Indexed keywords

ADENOSINE TRIPHOSPHATASE; MESSENGER RNA; PROTEINASE; RIBOSOME RNA; TRANSFER RNA;

BIOLOGY; CELL ORGANELLE; ENVIRONMENTAL CONDITIONS; PROKARYOTE; PROTEIN; RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACILLUS SUBTILIS; BINDING SITE; ENVIRONMENTAL STRESS; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GROWTH PERIOD; INTEGRATIVE MEDICINE; MICROBIAL GROWTH; NONHUMAN; PROKARYOTE; PROTEIN DEGRADATION; PROTEIN PROCESSING; PROTEIN RNA BINDING; PROTEIN STABILITY; PROTEIN SYNTHESIS; RIBOSWITCH; RNA ANALYSIS; RNA SEQUENCE; RNA STABILITY; SHORT SURVEY; START CODON; TRANSCRIPTION REGULATION; TRANSLATION REGULATION;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; LACTOCOCCUS LACTIS; PROKARYOTIC CELLS; PROTEIN BIOSYNTHESIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STABILITY; RIBOSOMES; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; RNA, BACTERIAL; RNA, MESSENGER; RNA, UNTRANSLATED; RNA-BINDING PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; SYSTEMS BIOLOGY; SYSTEMS INTEGRATION;

PROKARYOTA;

EID: 70350712113     PISSN: 16310691     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.crvi.2009.09.005     Document Type: Short Survey

References (107)

1. Rauhut R., and Klug G. mRNA degradation in bacteria. FEMS Microbiol. Rev. 23 (1999) 353-370
2. Deutscher M.P. Degradation of RNA in bacteria: Comparison of mRNA and stable RNA. Nucleic Acids Res. 34 (2006) 659-666
3. Carpousis A.J. The RNA degradosome of Escherichia coli: An mRNA-degrading machine assembled on RNase E. Annu. Rev. Microbiol. 61 (2007) 71-87
4. Feng Y., Vickers T.A., and Cohen S.N. The catalytic domain of RNase E shows inherent 3′ to 5′ directionality in cleavage site selection. Proc. Natl. Acad. Sci. USA 99 (2002) 14746-14751
5. Umitsuki G., Wachi M., Takada A., Hikichi T., and Nagai K. Involvement of RNase G in in vivo mRNA metabolism in Escherichia coli. Genes Cells 6 (2001) 403-410
6. Even S., Pellegrini O., Zig L., Labas V., Vinh J., Brechemmier-Baey D., and Putzer H. Ribonucleases J1 and J2: Two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res. 33 (2005) 2141-2152
7. Condon C. Maturation and degradation of RNA in bacteria. Curr. Opin. Microbiol. 10 (2007) 271-278
8. Drider D., Bolotine A., Renault P., and Prevost H. Functional study of Lactococcus lactis RNase III in Escherichia coli. Plasmid 47 (2002) 246-250
9. Condon C. RNA processing and degradation in Bacillus subtilis. Microbiol. Mol. Biol. Rev. 67 (2003) 157-174 table of contents
10. Santos J.M., Drider D., Marujo P.E., Lopez P., and Arraiano C.M. Determinant role of E. coli RNase III in the decay of both specific and heterologous mRNAs. FEMS Microbiol. Lett. 157 (1997) 31-38
11. Drider D., Garcia-Quintans N., Santos J.M., Arraiano C.M., and Lopez P. A comparative analysis of the citrate permease P mRNA stability in Lactococcus lactis biovar diacetylactis and Escherichia coli. FEMS Microbiol. Lett. 172 (1999) 115-122
12. Zuo Y., and Deutscher M.P. Exoribonuclease superfamilies: Structural analysis and phylogenetic distribution. Nucleic Acids Res. 29 (2001) 1017-1026
13. Ghosh S., and Deutscher M.P. Oligoribonuclease is an essential component of the mRNA decay pathway. Proc. Natl. Acad. Sci. USA 96 (1999) 4372-4377
14. Deana A., Celesnik H., and Belasco J.G. The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451 (2008) 355-358
15. Oussenko I.A., Sanchez R., and Bechhofer D.H. Bacillus subtilis YhaM, a member of a new family of 3′-to-5′ exonucleases in Gram-positive bacteria. J. Bacteriol. 184 (2002) 6250-6259
16. Mathy N., Benard L., Pellegrini O., Daou R., Wen T., and Condon C. 5′-to-3′ exoribonuclease activity in bacteria: Role of RNase J1 in rRNA maturation and 5′ stability of mRNA. Cell 129 (2007) 681-692
17. Arnold T.E., Yu J., and Belasco J.G. mRNA stabilization by the ompA 5′ untranslated region: Two protective elements hinder distinct pathways for mRNA degradation. RNA 4 (1998) 319-330
18. Hambraeus G., Karhumaa K., and Rutberg B. A 5′ stem-loop and ribosome binding but not translation are important for the stability of Bacillus subtilis aprE leader mRNA. Microbiology 148 (2002) 1795-1803
19. Sharp J.S., and Bechhofer D.H. Effect of 5′-proximal elements on decay of a model mRNA in Bacillus subtilis. Mol. Microbiol. 57 (2005) 484-495
20. Redon E., Loubiere P., and Cocaign-Bousquet M. Role of mRNA stability during genome-wide adaptation of Lactococcus lactis to carbon starvation. J. Biol. Chem. 280 (2005) 36380-36385
21. Mohanty B.K., and Kushner S.R. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol. Microbiol. 34 (1999) 1094-1108
22. Mohanty B.K., and Kushner S.R. The majority of Escherichia coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Res. 34 (2006) 5695-5704
23. Campos-Guillen J., Bralley P., Jones G.H., Bechhofer D.H., and Olmedo-Alvarez G. Addition of poly(A) and heteropolymeric 3′ ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J. Bacteriol. 187 (2005) 4698-4706
24. Mohanty B.K., and Kushner S.R. Polyadenylation of Escherichia coli transcripts plays an integral role in regulating intracellular levels of polynucleotide phosphorylase and RNase E. Mol. Microbiol. 45 (2002) 1315-1324
25. Joyce S.A., and Dreyfus M. In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli. J. Mol. Biol. 282 (1998) 241-254
26. Carrier T.A., and Keasling J.D. Mechanistic modeling of prokaryotic mRNA decay. J. Theor. Biol. 189 (1997) 195-209
27. Sharp J.S., and Bechhofer D.H. Effect of translational signals on mRNA decay in Bacillus subtilis. J. Bacteriol. 185 (2003) 5372-5379
28. Bernstein J.A., Khodursky A.B., Lin P.H., Lin-Chao S., and Cohen S.N. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99 (2002) 9697-9702
29. Selinger D.W., Saxena R.M., Cheung K.J., Church G.M., and Rosenow C. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 13 (2003) 216-223
30. Bernstein J.A., Lin P.H., Cohen S.N., and Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc. Natl. Acad. Sci. USA 101 (2004) 2758-2763
31. Hambraeus G., von Wachenfeldt C., and Hederstedt L. Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs. Mol. Genet. Genomics 269 (2003) 706-714
32. Lupas A., Flanagan J.M., Tamura T., and Baumeister W. Self-compartmentalizing proteases. Trends Biochem. Sci. 22 (1997) 399-404
33. Kock H., Gerth U., and Hecker M. The ClpP peptidase is the major determinant of bulk protein turnover in Bacillus subtilis. J. Bacteriol. 186 (2004) 5856-5864
34. Frees D., and Ingmer H. ClpP participates in the degradation of misfolded protein in Lactococcus lactis. Mol. Microbiol. 31 (1999) 79-87
35. Gottesman S. Proteolysis in bacterial regulatory circuits. Annu. Rev. Cell Dev. Biol. 19 (2003) 565-587
36. Wawrzynow A., Wojtkowiak D., Marszalek J., Banecki B., Jonsen M., Graves B., Georgopoulos C., and Zylicz M. The ClpX heat-shock protein of Escherichia coli, the ATP-dependent substrate specificity component of the ClpP-ClpX protease, is a novel molecular chaperone. EMBO J. 14 (1995) 1867-1877
37. Lies M., and Maurizi M.R. Turnover of endogenous SsrA-tagged proteins mediated by ATP-dependent proteases in Escherichia coli. J. Biol. Chem. 283 (2008) 22918-22929
38. Flynn J.M., Neher S.B., Kim Y.I., Sauer R.T., and Baker T.A. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol. Cell 11 (2003) 671-683
39. Zhou Y., Gottesman S., Hoskins J.R., Maurizi M.R., and Wickner S. The RssB response regulator directly targets sigma(S) for degradation by ClpXP. Genes Dev. 15 (2001) 627-637
40. Maglica Z., Striebel F., and Weber-Ban E. An intrinsic degradation tag on the ClpA C-terminus regulates the balance of ClpAP complexes with different substrate specificity. J. Mol. Biol. 384 (2008) 503-511
41. Chandu D., and Nandi D. Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation. Res. Microbiol. 155 (2004) 710-719
42. Tsilibaris V., Maenhaut-Michel G., and Van Melderen L. Biological roles of the Lon ATP-dependent protease. Res. Microbiol. 157 (2006) 701-713
43. Nilsson D., Lauridsen A.A., Tomoyasu T., and Ogura T. A Lactococcus lactis gene encodes a membrane protein with putative ATPase activity that is homologous to the essential Escherichia coli ftsH gene product. Microbiology 140 Pt 10 (1994) 2601-2610
44. Ito K., and Akiyama Y. Cellular functions, mechanism of action, and regulation of FtsH protease. Annu. Rev. Microbiol. 59 (2005) 211-231
45. Varshavsky A. The N-end rule: Functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93 (1996) 12142-12149
46. Mogk A., Schmidt R., and Bukau B. The N-end rule pathway for regulated proteolysis: Prokaryotic and eukaryotic strategies. Trends Cell Biol. 17 (2007) 165-172
47. Erbse A., Schmidt R., Bornemann T., Schneider-Mergener J., Mogk A., Zahn R., Dougan D.A., and Bukau B. ClpS is an essential component of the N-end rule pathway in Escherichia coli. Nature 439 (2006) 753-756
48. Pratt J.M., Petty J., Riba-Garcia I., Robertson D.H., Gaskell S.J., Oliver S.G., and Beynon R.J. Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell. Proteomics 1 (2002) 579-591
49. Belle A., Tanay A., Bitincka L., Shamir R., and O'Shea E.K. Quantification of protein half-lives in the budding yeast proteome. Proc. Natl. Acad. Sci. USA 103 (2006) 13004-13009
50. Osada Y., Saito R., and Tomita M. Analysis of base-pairing potentials between 16S rRNA and 5′ UTR for translation initiation in various prokaryotes. Bioinformatics 15 (1999) 578-581
51. Nie L., Wu G., and Zhang W. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis. Genetics 174 (2006) 2229-2243
52. Rocha E.P., Danchin A., and Viari A. Translation in Bacillus subtilis: Roles and trends of initiation and termination, insights from a genome analysis. Nucleic Acids Res. 27 (1999) 3567-3576
53. van de Guchte M., van der Lende T., Kok J., and Venema G. A possible contribution of mRNA secondary structure to translation initiation efficiency in Lactococcus lactis. FEMS Microbiol. Lett. 65 (1991) 201-208
54. Akashi H., and Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99 (2002) 3695-3700
55. Mitarai N., Sneppen K., and Pedersen S. Ribosome collisions and translation efficiency: Optimization by codon usage and mRNA destabilization. J. Mol. Biol. 382 (2008) 236-245
56. Vitreschak A.G., Rodionov D.A., Mironov A.A., and Gelfand M.S. Riboswitches: The oldest mechanism for the regulation of gene expression?. Trends Genet. 20 (2004) 44-50
57. Coppins R.L., Hall K.B., and Groisman E.A. The intricate world of riboswitches. Curr. Opin. Microbiol. 10 (2007) 176-181
58. Winkler W., Nahvi A., and Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419 (2002) 952-956
59. Brantl S. Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr. Opin. Microbiol. 10 (2007) 102-109
60. Kaberdin V.R., and Blasi U. Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol. Rev. 30 (2006) 967-979
61. Buts L., Lah J., Dao-Thi M.H., Wyns L., and Loris R. Toxin-antitoxin modules as bacterial metabolic stress managers. Trends Biochem. Sci. 30 (2005) 672-679
62. Gerdes K., and Wagner E.G. RNA antitoxins. Curr. Opin. Microbiol. 10 (2007) 117-124
63. Pandey D.P., and Gerdes K. Toxin-antitoxin loci are highly abundant in free-living but lost from host-associated prokaryotes. Nucleic Acids Res. 33 (2005) 966-976
64. Dennis P.P., Ehrenberg M., and Bremer H. Control of rRNA synthesis in Escherichia coli: A systems biology approach. Microbiol. Mol. Biol. Rev. 68 (2004) 639-668
65. Zhang A., Wassarman K.M., Rosenow C., Tjaden B.C., Storz G., and Gottesman S. Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50 (2003) 1111-1124
66. Gottesman S. The small RNA regulators of Escherichia coli: Roles and mechanisms. Annu. Rev. Microbiol. 58 (2004) 303-328
67. Udekwu K.I., Darfeuille F., Vogel J., Reimegard J., Holmqvist E., and Wagner E.G. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. Genes Dev. 19 (2005) 2355-2366
68. Keiler K.C. Biology of trans-translation. Annu. Rev. Microbiol. 62 (2008) 133-151
69. Dulebohn D., Choy J., Sundermeier T., Okan N., and Karzai A.W. Trans-translation: The tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry 46 (2007) 4681-4693
70. Schonhuber W., Le Bourhis G., Tremblay J., Amann R., and Kulakauskas S. Utilization of tmRNA sequences for bacterial identification. BMC Microbiol. 1 (2001) 20
71. Buchan J.R., and Stansfield I. Halting a cellular production line: Responses to ribosomal pausing during translation. Biol. Cell 99 (2007) 475-487
72. Winkler W.C., and Breaker R.R. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59 (2005) 487-517
73. Washburn M.P., Koller A., Oshiro G., Ulaszek R.R., Plouffe D., Deciu C., Winzeler E., and Yates III J.R. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100 (2003) 3107-3112
74. Greenbaum D., Colangelo C., Williams K., and Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4 (2003) 117
75. Beyer A., Hollunder J., Nasheuer H.P., and Wilhelm T. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Proteomics 3 (2004) 1083-1092
76. Wu G., Nie L., and Zhang W. Integrative analyses of posttranscriptional regulation in the yeast Saccharomyces cerevisiae using transcriptomic and proteomic data. Curr. Microbiol. 57 (2008) 18-22
77. Lu P., Vogel C., Wang R., Yao X., and Marcotte E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 25 (2007) 117-124
78. Nie L., Wu G., and Zhang W. Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations. Biochem. Biophys. Res. Commun. 339 (2006) 603-610
79. Arava Y., Wang Y., Storey J.D., Liu C.L., Brown P.O., and Herschlag D. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 100 (2003) 3889-3894
80. Melamed D., and Arava Y. Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Methods Enzymol. 431 (2007) 177-201
81. Lange C., Zaigler A., Hammelmann M., Twellmeyer J., Raddatz G., Schuster S.C., Oesterhelt D., and Soppa J. Genome-wide analysis of growth phase-dependent translational and transcriptional regulation in halophilic archaea. BMC Genomics 8 (2007) 415
82. Zouridis H., and Hatzimanikatis V. A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates. Biophys. J. 92 (2007) 717-730
83. Tenenbaum S.A., Lager P.J., Carson C.C., and Keene J.D. Ribonomics: Identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26 (2002) 191-198
84. Kuzj A.E., Medberry P.S., and Schottel J.L. Stationary phase, amino acid limitation and recovery from stationary phase modulate the stability and translation of chloramphenicol acetyltransferase mRNA and total mRNA in Escherichia coli. Microbiology 144 Pt 3 (1998) 739-750
85. Li X., Yagi M., Morita T., and Aiba H. Cleavage of mRNAs and role of tmRNA system under amino acid starvation in Escherichia coli. Mol. Microbiol. 68 (2008) 462-473
86. Muto A., Fujihara A., Ito K.I., Matsuno J., Ushida C., and Himeno H. Requirement of transfer-messenger RNA for the growth of Bacillus subtilis under stresses. Genes Cells 5 (2000) 627-635
87. Shin J.H., and Price C.W. The SsrA-SmpB ribosome rescue system is important for growth of Bacillus subtilis at low and high temperatures. J. Bacteriol. 189 (2007) 3729-3737
88. Shalem O., Dahan O., Levo M., Martinez M.R., Furman I., Segal E., and Pilpel Y. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol. Syst. Biol. 4 (2008) 223
89. El-Sharoud W.M., and Graumann P.L. Cold shock proteins aid coupling of transcription and translation in bacteria. Sci. Prog. 90 (2007) 15-27
90. Jones P.G., Mitta M., Kim Y., Jiang W., and Inouye M. Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli. Proc. Natl. Acad. Sci. USA 93 (1996) 76-80
91. Xia B., Ke H., Shinde U., and Inouye M. The role of RbfA in 16S rRNA processing and cell growth at low temperature in Escherichia coli. J. Mol. Biol. 332 (2003) 575-584
92. Wassarman K.M. Small RNAs in bacteria: Diverse regulators of gene expression in response to environmental changes. Cell 109 (2002) 141-144
93. Shimoni Y., Friedlander G., Hetzroni G., Niv G., Altuvia S., Biham O., and Margalit H. Regulation of gene expression by small non-coding RNAs: A quantitative view. Mol. Syst. Biol. 3 (2007) 138
94. + protease ClpXP for degradation. Genes Dev. 18 (2004) 2292-2301
95. Poquet I., Saint V., Seznec E., Simoes N., Bolotin A., and Gruss A. HtrA is the unique surface housekeeping protease in Lactococcus lactis and is required for natural protein processing. Mol. Microbiol. 35 (2000) 1042-1051
96. Kim D.Y., and Kim K.K. Structure and function of HtrA family proteins, the key players in protein quality control. J. Biochem. Mol. Biol. 38 (2005) 266-274
97. Yoshida H., Yamamoto H., Uchiumi T., and Wada A. RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel. Genes Cells 9 (2004) 271-278
98. Wada A. Growth phase coupled modulation of Escherichia coli ribosomes. Genes Cells 3 (1998) 203-208
99. Maki Y., Yoshida H., and Wada A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells 5 (2000) 965-974
100. Ueta M., Yoshida H., Wada C., Baba T., Mori H., and Wada A. Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli. Genes Cells 10 (2005) 1103-1112
101. Izutsu K., Wada C., Komine Y., Sako T., Ueguchi C., Nakura S., and Wada A. Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase. J. Bacteriol. 183 (2001) 2765-2773
102. Izutsu K., Wada A., and Wada C. Expression of ribosome modulation factor (RMF) in Escherichia coli requires ppGpp. Genes Cells 6 (2001) 665-676
103. Garay-Arroyo A., Colmenero-Flores J.M., Garciarrubio A., and Covarrubias A.A. Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. J. Biol. Chem. 275 (2000) 5668-5674
104. Niven G.W. Ribosome modulation factor protects Escherichia coli during heat stress, but this may not be dependent on ribosome dimerisation. Arch. Microbiol. 182 (2004) 60-66
105. el-Sharoud W.M., and Niven G.W. The activity of ribosome modulation factor during growth of Escherichia coli under acidic conditions. Arch. Microbiol. 184 (2005) 18-24
106. Even S., Lindley N.D., and Cocaign-Bousquet M. Molecular physiology of sugar catabolism in Lactococcus lactis IL1403. J. Bacteriol. 183 (2001) 3817-3824
107. Even S., Lindley N.D., and Cocaign-Bousquet M. Transcriptional, translational and metabolic regulation of glycolysis in Lactococcus lactis subsp. cremoris MG 1363 grown in continuous acidic cultures. Microbiology 149 (2003) 1935-1944