| [1] | Cabiscol E, Tamarit J, Ros J (2000) Oxidative stress in bacteria and protein damage by reactive oxygen species. Int Microbiol 3: 3–8. pmid:10963327
|
| [2] | Kryston TB, Georgiev AB, Pissis P, Georgakilas AG (2011) Role of oxidative stress and DNA damage in human carcinogenesis. Mutat Res 711: 193–201. doi: 10.1016/j.mrfmmm.2010.12.016. pmid:21216256
|
| [3] | Imlay JA (2013) The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium. Nat Rev Microbiol 11: 443–454. doi: 10.1038/nrmicro3032. pmid:23712352
|
| [4] | Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, et al. (2010) Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol 6: 364. doi: 10.1038/msb.2010.18. pmid:20461071
|
| [5] | Lackner DH, Schmidt MW, Wu S, Wolf DA, Bahler J (2012) Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast. Genome Biol 13: R25. doi: 10.1186/gb-2012-13-4-r25. pmid:22512868
|
| [6] | Davies KJ (1999) The broad spectrum of responses to oxidants in proliferating cells: a new paradigm for oxidative stress. IUBMB Life 48: 41–47. pmid:10791914 doi: 10.1080/713803463
|
| [7] | de Nadal E, Ammerer G, Posas F (2011) Controlling gene expression in response to stress. Nat Rev Genet 12: 833–845. doi: 10.1038/nrg3055. pmid:22048664
|
| [8] | Shenton D, Smirnova JB, Selley JN, Carroll K, Hubbard SJ, et al. (2006) Global translational responses to oxidative stress impact upon multiple levels of protein synthesis. J Biol Chem 281: 29011–29021. pmid:16849329 doi: 10.1074/jbc.m601545200
|
| [9] | Thompson DM, Lu C, Green PJ, Parker R (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 2095–2103. doi: 10.1261/rna.1232808. pmid:18719243
|
| [10] | Yamasaki S, Ivanov P, Hu GF, Anderson P (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185: 35–42. doi: 10.1083/jcb.200811106. pmid:19332886
|
| [11] | Fu H, Feng J, Liu Q, Sun F, Tie Y, et al. (2009) Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett 583: 437–442. doi: 10.1016/j.febslet.2008.12.043. pmid:19114040
|
| [12] | Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, et al. (2012) Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem 287: 42708–42725. doi: 10.1074/jbc.M112.371799. pmid:23086926
|
| [13] | Czech A, Wende S, Morl M, Pan T, Ignatova Z (2013) Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet 9: e1003767. doi: 10.1371/journal.pgen.1003767. pmid:24009533
|
| [14] | Lee YS, Shibata Y, Malhotra A, Dutta A (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23: 2639–2649. doi: 10.1101/gad.1837609. pmid:19933153
|
| [15] | Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P (2011) Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 43: 613–623. doi: 10.1016/j.molcel.2011.06.022. pmid:21855800
|
| [16] | Vogel C, Silva GM, Marcotte EM (2011) Protein expression regulation under oxidative stress. Mol Cell Proteomics 10: M111 009217. doi: 10.1074/mcp.m111.009217
|
| [17] | Chan CT, Pang YL, Deng W, Babu IR, Dyavaiah M, et al. (2012) Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 3: 937. doi: 10.1038/ncomms1938. pmid:22760636
|
| [18] | Tomita K, Ogawa T, Uozumi T, Watanabe K, Masaki H (2000) A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. Proc Natl Acad Sci U S A 97: 8278–8283. pmid:10880568 doi: 10.1073/pnas.140213797
|
| [19] | Jiang Y, Meidler R, Amitsur M, Kaufmann G (2001) Specific interaction between anticodon nuclease and the tRNA(Lys) wobble base. J Mol Biol 305: 377–388. pmid:11152597 doi: 10.1006/jmbi.2000.4282
|
| [20] | Meineke B, Shuman S (2012) Determinants of the cytotoxicity of PrrC anticodon nuclease and its amelioration by tRNA repair. RNA 18: 145–154. doi: 10.1261/rna.030171.111. pmid:22101242
|
| [21] | Ling J, Soll D (2010) Severe oxidative stress induces protein mistranslation through impairment of an aminoacyl-tRNA synthetase editing site. Proc Natl Acad Sci U S A 107: 4028–4033. doi: 10.1073/pnas.1000315107. pmid:20160114
|
| [22] | Bessette PH, Aslund F, Beckwith J, Georgiou G (1999) Efficient folding of proteins with multiple disulfide bonds in the Escherichia coli cytoplasm. Proc Natl Acad Sci U S A 96: 13703–13708. pmid:10570136 doi: 10.1073/pnas.96.24.13703
|
| [23] | Sorensen HP, Mortensen KK (2005) Advanced genetic strategies for recombinant protein expression in Escherichia coli. J Biotechnol 115: 113–128. pmid:15607230 doi: 10.1016/j.jbiotec.2004.08.004
|
| [24] | Tang Y, Quail MA, Artymiuk PJ, Guest JR, Green J (2002) Escherichia coli aconitases and oxidative stress: post-transcriptional regulation of sodA expression. Microbiology 148: 1027–1037. pmid:11932448
|
| [25] | Luders S, Fallet C, Franco-Lara E (2009) Proteome analysis of the Escherichia coli heat shock response under steady-state conditions. Proteome Sci 7: 36. doi: 10.1186/1477-5956-7-36. pmid:19772559
|
| [26] | 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. doi: 10.1038/msb.2011.38. pmid:21772259
|
| [27] | Wu J, Jiang Z, Liu M, Gong X, Wu S, et al. (2009) Polynucleotide phosphorylase protects Escherichia coli against oxidative stress. Biochemistry 48: 2012–2020. doi: 10.1021/bi801752p. pmid:19219992
|
| [28] | Mostertz J, Scharf C, Hecker M, Homuth G (2004) Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiology 150: 497–512. pmid:14766928 doi: 10.1099/mic.0.26665-0
|
| [29] | Doherty MK, Hammond DE, Clague MJ, Gaskell SJ, Beynon RJ (2009) Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J Proteome Res 8: 104–112. doi: 10.1021/pr800641v. pmid:18954100
|
| [30] | Westman-Brinkmalm A, Abramsson A, Pannee J, Gang C, Gustavsson MK, et al. (2011) SILAC zebrafish for quantitative analysis of protein turnover and tissue regeneration. J Proteomics 75: 425–434. doi: 10.1016/j.jprot.2011.08.008. pmid:21890006
|
| [31] | Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Kruger M, et al. (2011) Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J Proteome Res 10: 5275–5284. doi: 10.1021/pr101183k. pmid:22050367
|
| [32] | Mann M (2006) Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol 7: 952–958. pmid:17139335 doi: 10.1038/nrm2067
|
| [33] | Hinkson IV, Elias JE (2011) The dynamic state of protein turnover: It's about time. Trends Cell Biol 21: 293–303. doi: 10.1016/j.tcb.2011.02.002. pmid:21474317
|
| [34] | Snijders AP, de Koning B, Wright PC (2005) Perturbation and interpretation of nitrogen isotope distribution patterns in proteomics. J Proteome Res 4: 2185–2191. pmid:16335965 doi: 10.1021/pr050260l
|
| [35] | Martin SF, Munagapati VS, Salvo-Chirnside E, Kerr LE, Le Bihan T (2012) Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry. J Proteome Res 11: 476–486. doi: 10.1021/pr2009302. pmid:22077659
|
| [36] | Xiao CL, Chen XZ, Du YL, Sun X, Zhang G, et al. (2013) Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information. J Proteome Res 12: 328–335. doi: 10.1021/pr300781t. pmid:23163785
|
| [37] | Imlay JA, Linn S (1986) Bimodal pattern of killing of DNA-repair-defective or anoxically grown Escherichia coli by hydrogen peroxide. J Bacteriol 166: 519–527. pmid:3516975
|
| [38] | Imlay JA, Linn S (1987) Mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide. J Bacteriol 169: 2967–2976. pmid:3298208 doi: 10.1242/jcs.1984.supplement_6.19
|
| [39] | Filiou MD, Varadarajulu J, Teplytska L, Reckow S, Maccarrone G, et al. (2012) The 15N isotope effect in Escherichia coli: a neutron can make the difference. Proteomics 12: 3121–3128. doi: 10.1002/pmic.201200209. pmid:22887715
|
| [40] | Fedyunin I, Lehnhardt L, Bohmer N, Kaufmann P, Zhang G, et al. (2012) tRNA concentration fine tunes protein solubility. FEBS Lett 586: 3336–3340. doi: 10.1016/j.febslet.2012.07.012. pmid:22819830
|
| [41] | Tamarit J, Cabiscol E, Ros J (1998) Identification of the major oxidatively damaged proteins in Escherichia coli cells exposed to oxidative stress. J Biol Chem 273: 3027–3032. pmid:9446617 doi: 10.1074/jbc.273.5.3027
|
| [42] | 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. doi: 10.1093/nar/gks1007. pmid:23118484
|
| [43] | Puri P, Wetzel C, Saffert P, Gaston KW, Russell SP, et al. (2014) Systematic identification of tRNAome and its dynamics in Lactococcus lactis. Mol Microbiol. doi: 10.1111/mmi.12710
|
| [44] | Zhang G, Fedyunin I, Miekley O, Valleriani A, Moura A, et al. (2010) Global and local depletion of ternary complex limits translational elongation. Nucleic Acids Res 38: 4778–4787. doi: 10.1093/nar/gkq196. pmid:20360046
|
| [45] | Zhang G, Hubalewska M, Ignatova Z (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat Struct Mol Biol 16: 274–280. doi: 10.1038/nsmb.1554. pmid:19198590
|
| [46] | Goswami M, Mangoli SH, Jawali N (2006) Involvement of reactive oxygen species in the action of ciprofloxacin against Escherichia coli. Antimicrob Agents Chemother 50: 949–954. pmid:16495256 doi: 10.1128/aac.50.3.949-954.2006
|
| [47] | Dwyer DJ, Kohanski MA, Hayete B, Collins JJ (2007) Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol 3: 91. pmid:17353933 doi: 10.1038/msb4100135
|
| [48] | Katz A, Orellana O (2012) Protein Synthesis and the Stress Response. In: Biyani M, editor. Cell-Free Protein Synthesis: InTech. pp. 111–134.
|
| [49] | Moll I, Engelberg-Kulka H (2012) Selective translation during stress in Escherichia coli. Trends Biochem Sci 37: 493–498. doi: 10.1016/j.tibs.2012.07.007. pmid:22939840
|
| [50] | Nakamura T, Cho DH, Lipton SA (2012) Redox regulation of protein misfolding, mitochondrial dysfunction, synaptic damage, and cell death in neurodegenerative diseases. Exp Neurol 238: 12–21. doi: 10.1016/j.expneurol.2012.06.032. pmid:22771760
|
| [51] | Bhattacharya A, Wei R, Hamilton RT, Chaudhuri AR (2014) Neuronal cells but not muscle cells are resistant to oxidative stress mediated protein misfolding and cell death: role of molecular chaperones. Biochem Biophys Res Commun 446: 1250–1254. doi: 10.1016/j.bbrc.2014.03.097. pmid:24685484
|
| [52] | Collins LJ, Biggs PJ (2011) RNA networks in prokaryotes II: tRNA processing and small RNAs. Adv Exp Med Biol 722: 221–230. doi: 10.1007/978-1-4614-0332-6_14. pmid:21915792
|
| [53] | Deutscher MP (1984) Processing of tRNA in prokaryotes and eukaryotes. CRC Crit Rev Biochem 17: 45–71. pmid:6094100
|
| [54] | Durfee T, Hansen AM, Zhi H, Blattner FR, Jin DJ (2008) Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 190: 1084–1096. pmid:18039766 doi: 10.1128/jb.01092-07
|
| [55] | 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. pmid:9023104 doi: 10.1093/nar/25.5.955
|
| [56] | Chan PP, Lowe TM (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 37: D93–97. doi: 10.1093/nar/gkn787. pmid:18984615
|
| [57] | Zhang G, Lukoszek R, Mueller-Roeber B, Ignatova Z (2011) Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation. Nucleic Acids Res 39: 3331–3339. doi: 10.1093/nar/gkq1257. pmid:21138970
|
| [58] | Phizicky EM, Hopper AK (2010) tRNA biology charges to the front. Genes Dev 24: 1832–1860. doi: 10.1101/gad.1956510. pmid:20810645
|
| [59] | Chen P, Jager G, Zheng B (2010) Transfer RNA modifications and genes for modifying enzymes in Arabidopsis thaliana. BMC Plant Biol 10: 201. doi: 10.1186/1471-2229-10-201. pmid:20836892
|
| [60] | Hopper AK, Phizicky EM (2003) tRNA transfers to the limelight. Genes Dev 17: 162–180. pmid:12533506 doi: 10.1101/gad.1049103
|
| [61] | Sneppen K, Dodd IB, Shearwin KE, Palmer AC, Schubert RA, et al. (2005) A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli. J Mol Biol 346: 399–409. pmid:15670592 doi: 10.1016/j.jmb.2004.11.075
|
| [62] | Perez-Ortin JE, Alepuz PM, Moreno J (2007) Genomics and gene transcription kinetics in yeast. Trends Genet 23: 250–257. pmid:17379352 doi: 10.1016/j.tig.2007.03.006
|
| [63] | Jepras RI, Carter J, Pearson SC, Paul FE, Wilkinson MJ (1995) Development of a robust flow cytometric assay for determining numbers of viable bacteria. Appl Environ Microbiol 61: 2696–2701. pmid:16535078
|
| [64] | Rault A, Beal C, Ghorbal S, Ogier JC, Bouix M (2007) Multiparametric flow cytometry allows rapid assessment and comparison of lactic acid bacteria viability after freezing and during frozen storage. Cryobiology 55: 35–43. pmid:17577587 doi: 10.1016/j.cryobiol.2007.04.005
|
| [65] | Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006) In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1: 2856–2860. pmid:17406544 doi: 10.1038/nprot.2006.468
|
| [66] | Sun X, Jia HL, Xiao CL, Yin XF, Yang XY, et al. (2011) Bacterial proteome of streptococcus pneumoniae through multidimensional separations coupled with LC-MS/MS. OMICS 15: 477–482. doi: 10.1089/omi.2010.0113. pmid:21699404
|
| [67] | Bore E, Hebraud M, Chafsey I, Chambon C, Skjaeret C, et al. (2007) Adapted tolerance to benzalkonium chloride in Escherichia coli K-12 studied by transcriptome and proteome analyses. Microbiology 153: 935–946. pmid:17379704 doi: 10.1099/mic.0.29288-0
|
| [68] | Alexandrov A, Chernyakov I, Gu W, Hiley SL, Hughes TR, et al. (2006) Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell 21: 87–96. pmid:16387656 doi: 10.1016/j.molcel.2005.10.036
|
