메뉴 건너뛰기




Volumn 9, Issue 1, 2014, Pages

Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of Deinococcus radiodurans R1

Author keywords

[No Author keywords available]

Indexed keywords

ANTIOXIDANT; CAROTENOID; COMPLEMENTARY RNA; PHYTOENE SYNTHASE; TRANSFER RNA; UNTRANSLATED RNA;

EID: 84899894462     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085649     Document Type: Article
Times cited : (40)

References (44)
  • 1
    • 79952424488 scopus 로고    scopus 로고
    • Oxidative stress resistance in Deinococcus radiodurans
    • Slade D, Radman M (2011) Oxidative stress resistance in Deinococcus radiodurans. Microbiol Mol Biol Rev 75: 133-191.
    • (2011) Microbiol Mol Biol Rev , vol.75 , pp. 133-191
    • Slade, D.1    Radman, M.2
  • 2
    • 0028223921 scopus 로고
    • Mechanisms of induction and repair of DNA double-strand breaks by ionizing radiation: Some contradictions
    • Hagen U (1994) Mechanisms of induction and repair of DNA double-strand breaks by ionizing radiation: some contradictions. Radiat Environ Biophys 33: 45-61.
    • (1994) Radiat Environ Biophys , vol.33 , pp. 45-61
    • Hagen, U.1
  • 4
    • 28144449309 scopus 로고    scopus 로고
    • Deinococcus radiodurans - The consummate survivor
    • DOI 10.1038/nrmicro1264, PII N1264
    • Cox MM, Battista JR (2005) Deinococcus radiodurans - the consummate survivor. Nat Rev Microbiol 3: 882-892. (Pubitemid 41693183)
    • (2005) Nature Reviews Microbiology , vol.3 , Issue.11 , pp. 882-892
    • Cox, M.M.1    Battista, J.R.2
  • 5
    • 0025753927 scopus 로고
    • Kinetics and mechanism of methanol and formaldehyde interconversion and formaldehyde oxidation catalyzed by liver alcohol dehydrogenase
    • Pocker Y, Li H (1991) Kinetics and mechanism of methanol and formaldehyde interconversion and formaldehyde oxidation catalyzed by liver alcohol dehydrogenase. Adv Exp Med Biol 284: 315-325.
    • (1991) Adv Exp Med Biol , vol.284 , pp. 315-325
    • Pocker, Y.1    Li, H.2
  • 7
    • 0034152767 scopus 로고    scopus 로고
    • Oxidative stress in bacteria and protein damage by reactive oxygen species
    • Cabiscol E, Tamarit J, Ros J (2000) Oxidative stress in bacteria and protein damage by reactive oxygen species. Int Microbiol 3: 3-8.
    • (2000) Int Microbiol , vol.3 , pp. 3-8
    • Cabiscol, E.1    Tamarit, J.2    Ros, J.3
  • 8
    • 0038799736 scopus 로고    scopus 로고
    • Oxidative DNA damage: Mechanisms, mutation, and disease
    • DOI 10.1096/fj.02-0752rev
    • Cooke MS, Evans MD, Dizdaroglu M, Lunec J (2003) Oxidative DNA damage: mechanisms, mutation, and disease. FASEB J 17: 1195-1214. (Pubitemid 36775767)
    • (2003) FASEB Journal , vol.17 , Issue.10 , pp. 1195-1214
    • Cooke, M.S.1    Evans, M.D.2    Dizdaroglu, M.3    Lunec, J.4
  • 11
    • 13044313472 scopus 로고    scopus 로고
    • Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1
    • White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, et al. (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286: 1571-1577.
    • (1999) Science , vol.286 , pp. 1571-1577
    • White, O.1    Eisen, J.A.2    Heidelberg, J.F.3    Hickey, E.K.4    Peterson, J.D.5
  • 12
    • 27744595408 scopus 로고    scopus 로고
    • Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: Divergent routes of adaptation to thermophily and radiation resistance
    • Omelchenko MV, Wolf YI, Gaidamakova EK, Matrosova VY, Vasilenko A, et al. (2005) Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol Biol 5: 57.
    • (2005) BMC Evol Biol , vol.5 , pp. 57
    • Omelchenko, M.V.1    Wolf, Y.I.2    Gaidamakova, E.K.3    Matrosova, V.Y.4    Vasilenko, A.5
  • 13
    • 20844463020 scopus 로고    scopus 로고
    • Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans
    • DOI 10.1021/pr049815n
    • Schmid AK, Lipton MS, Mottaz H, Monroe ME, Smith RD, et al. (2005) Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans. J Proteome Res 4: 709-718. (Pubitemid 40863259)
    • (2005) Journal of Proteome Research , vol.4 , Issue.3 , pp. 709-718
    • Schmid, A.K.1    Lipton, M.S.2    Mottaz, H.3    Monroe, M.E.4    Smith, R.D.5    Lidstrom, M.E.6
  • 14
    • 79954490670 scopus 로고    scopus 로고
    • Genome-wide transcriptome and proteome analysis of Escherichia coli expressing IrrE, a global regulator of Deinococcus radiodurans
    • Zhou Z, Zhang W, Chen M, Pan J, Lu W, et al. (2011) Genome-wide transcriptome and proteome analysis of Escherichia coli expressing IrrE, a global regulator of Deinococcus radiodurans. Mol Biosyst 7: 1613-1620.
    • (2011) Mol Biosyst , vol.7 , pp. 1613-1620
    • Zhou, Z.1    Zhang, W.2    Chen, M.3    Pan, J.4    Lu, W.5
  • 16
    • 70349761225 scopus 로고    scopus 로고
    • A model of interactions between radiationinduced oxidative stress, protein and DNA damage in Deinococcus radiodurans
    • Shuryak I, Brenner DJ (2009) A model of interactions between radiationinduced oxidative stress, protein and DNA damage in Deinococcus radiodurans. J Theor Biol 261: 305-317.
    • (2009) J Theor Biol , vol.261 , pp. 305-317
    • Shuryak, I.1    Brenner, D.J.2
  • 17
    • 34548660834 scopus 로고    scopus 로고
    • Knockout of crtB or crtI gene blocks the carotenoid biosynthetic pathway in Deinococcus radiodurans R1 and influences its resistance to oxidative DNA-damaging agents due to change of free radicals scavenging ability
    • DOI 10.1007/s00203-007-0262-5
    • Zhang L, Yang Q, Luo X, Fang C, Zhang Q, et al. (2007) Knockout of crtB or crtI gene blocks the carotenoid biosynthetic pathway in Deinococcus radiodurans R1 and influences its resistance to oxidative DNA-damaging agents due to change of free radicals scavenging ability. Arch Microbiol 188: 411-419. (Pubitemid 47415698)
    • (2007) Archives of Microbiology , vol.188 , Issue.4 , pp. 411-419
    • Zhang, L.1    Yang, Q.2    Luo, X.3    Fang, C.4    Zhang, Q.5    Tang, Y.6
  • 18
    • 0036154793 scopus 로고    scopus 로고
    • Genetic evidence that the uvsE gene product of Deinococcus radiodurans R1 is a UV damage endonuclease
    • DOI 10.1128/jb.184.4.1003-1009.2002
    • Earl AM, Rankin SK, Kim KP, Lamendola ON, Battista JR (2002) Genetic evidence that the uvsE gene product of Deinococcus radiodurans R1 is a UV damage endonuclease. J Bacteriol 184: 1003-1009. (Pubitemid 34113368)
    • (2002) Journal of Bacteriology , vol.184 , Issue.4 , pp. 1003-1009
    • Earl, A.M.1    Rankin, S.K.2    Kim, K.-P.3    Lamendola, O.N.4    Battista, J.R.5
  • 19
    • 0023876708 scopus 로고
    • Duplication insertion of drug resistance determinants in the radioresistant bacterium Deinococcus radiodurans
    • Smith MD, Lennon E, McNeil LB, Minton KW (1988) Duplication insertion of drug resistance determinants in the radioresistant bacterium Deinococcus radiodurans. J Bacteriol 170: 2126-2135.
    • (1988) J Bacteriol , vol.170 , pp. 2126-2135
    • Smith, M.D.1    Lennon, E.2    McNeil, L.B.3    Minton, K.W.4
  • 20
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.W.4    Yiu, S.M.5
  • 21
    • 84872033704 scopus 로고    scopus 로고
    • Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
    • Wagner GP, Kin K, Lynch VJ (2012) Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci 131: 281-285.
    • (2012) Theory Biosci , vol.131 , pp. 281-285
    • Wagner, G.P.1    Kin, K.2    Lynch, V.J.3
  • 22
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
    • (2010) Genome Biol , vol.11
    • Anders, S.1    Huber, W.2
  • 23
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • DOI 10.1093/bioinformatics/bth456
    • Boyle EI, Weng S, Gollub J, Jin H, Botstein D, et al. (2004) GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715. (Pubitemid 40136825)
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 24
    • 79955551567 scopus 로고    scopus 로고
    • Determination of carotenoids by liquid chromatography/mass spectrometry: Effect of several dopants
    • Rivera S, Vilaro F, Canela R (2011) Determination of carotenoids by liquid chromatography/mass spectrometry: effect of several dopants. Anal Bioanal Chem 400: 1339-1346.
    • (2011) Anal Bioanal Chem , vol.400 , pp. 1339-1346
    • Rivera, S.1    Vilaro, F.2    Canela, R.3
  • 25
    • 32444446805 scopus 로고    scopus 로고
    • XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
    • DOI 10.1021/ac051437y
    • Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78: 779-787. (Pubitemid 43228585)
    • (2006) Analytical Chemistry , vol.78 , Issue.3 , pp. 779-787
    • Smith, C.A.1    Want, E.J.2    O'Maille, G.3    Abagyan, R.4    Siuzdak, G.5
  • 26
    • 80051682403 scopus 로고    scopus 로고
    • Advances in metabolite identification
    • Wishart DS (2011) Advances in metabolite identification. Bioanalysis 3: 1769-1782.
    • (2011) Bioanalysis , vol.3 , pp. 1769-1782
    • Wishart, D.S.1
  • 28
    • 84871776673 scopus 로고    scopus 로고
    • Sbacillithiolation protects conserved and essential proteins against hypochlorite stress in Firmicutes bacteria
    • Chi BK, Roberts AA, Huyen TTT, Bäsell K, Becher D, et al. (2013) Sbacillithiolation protects conserved and essential proteins against hypochlorite stress in Firmicutes bacteria. Antioxidants & Redox Signaling 18: 1273-1295.
    • (2013) Antioxidants & Redox Signaling , vol.18 , pp. 1273-1295
    • Chi, B.K.1    Roberts, A.A.2    Huyen, T.T.T.3    Bäsell, K.4    Becher, D.5
  • 29
    • 63049112423 scopus 로고    scopus 로고
    • Deinococcus radiodurans PprI switches on DNA damage response and cellular survival networks after radiation damage
    • Lu H, Gao G, Xu G, Fan L, Yin L, et al. (2009) Deinococcus radiodurans PprI switches on DNA damage response and cellular survival networks after radiation damage. Mol Cell Proteomics 8: 481-494.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 481-494
    • Lu, H.1    Gao, G.2    Xu, G.3    Fan, L.4    Yin, L.5
  • 31
    • 76649085822 scopus 로고    scopus 로고
    • Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons
    • Baudet M, Ortet P, Gaillard JC, Fernandez B, Guerin P, et al. (2010) Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics 9: 415-426.
    • (2010) Mol Cell Proteomics , vol.9 , pp. 415-426
    • Baudet, M.1    Ortet, P.2    Gaillard, J.C.3    Fernandez, B.4    Guerin, P.5
  • 32
    • 60849129141 scopus 로고    scopus 로고
    • Proteomic analysis of ionizing radiation-induced proteins at the subcellular level
    • Lin RX, Zhao HB, Li CR, Sun YN, Qian XH, et al. (2009) Proteomic analysis of ionizing radiation-induced proteins at the subcellular level. J Proteome Res 8: 390-399.
    • (2009) J Proteome Res , vol.8 , pp. 390-399
    • Lin, R.X.1    Zhao, H.B.2    Li, C.R.3    Sun, Y.N.4    Qian, X.H.5
  • 33
    • 0024319460 scopus 로고
    • Alp, a suppressor of lon protease mutants in Escherichia coli
    • Trempy JE, Gottesman S (1989) Alp, a suppressor of lon protease mutants in Escherichia coli. J Bacteriol 171: 3348-3353. (Pubitemid 19145692)
    • (1989) Journal of Bacteriology , vol.171 , Issue.6 , pp. 3348-3353
    • Trempy, J.E.1    Gottesman, S.2
  • 35
    • 76749109918 scopus 로고    scopus 로고
    • A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans
    • Bentchikou E, Servant P, Coste G, Sommer S (2010) A major role of the RecFOR pathway in DNA double-strand-break repair through ESDSA in Deinococcus radiodurans. PLoS Genet 6: e1000774.
    • (2010) PLoS Genet , vol.6
    • Bentchikou, E.1    Servant, P.2    Coste, G.3    Sommer, S.4
  • 36
    • 33744508935 scopus 로고    scopus 로고
    • The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response
    • DOI 10.1093/nar/gkl238
    • Salsbury Jr FR, Clodfelter JE, Gentry MB, Hollis T, Scarpinato KD (2006) The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response. Nucleic Acids Res 34: 2173-2185. (Pubitemid 43985656)
    • (2006) Nucleic Acids Research , vol.34 , Issue.8 , pp. 2173-2185
    • Salsbury Jr., F.R.1    Clodfelter, J.E.2    Gentry, M.B.3    Hollis, T.4    Scarpinato, K.D.5
  • 38
    • 77950868171 scopus 로고    scopus 로고
    • Biosynthesis and functions of bacillithiol, a major low-molecular-weight thiol in Bacilli
    • Gaballa A, Newton GL, Antelmann H, Parsonage D, Upton H, et al. (2010) Biosynthesis and functions of bacillithiol, a major low-molecular-weight thiol in Bacilli. Proc Natl Acad Sci U S A 107: 6482-6486.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 6482-6486
    • Gaballa, A.1    Newton, G.L.2    Antelmann, H.3    Parsonage, D.4    Upton, H.5
  • 39
    • 70449467556 scopus 로고    scopus 로고
    • Effects of carotenoids from Deinococcus radiodurans on protein oxidation
    • Tian B, Sun Z, Shen S, Wang H, Jiao J, et al. (2009) Effects of carotenoids from Deinococcus radiodurans on protein oxidation. Lett Appl Microbiol 49: 689-694.
    • (2009) Lett Appl Microbiol , vol.49 , pp. 689-694
    • Tian, B.1    Sun, Z.2    Shen, S.3    Wang, H.4    Jiao, J.5
  • 40
    • 84899841937 scopus 로고
    • Effect of gamma-Irradiation on the Biosynthesis of Carotenoids in the Tomato Fruit
    • Villegas CN, Chichester CO, Raymundo LC, Simpson KL (1972) Effect of gamma-Irradiation on the Biosynthesis of Carotenoids in the Tomato Fruit. Plant Physiol 50: 694-697.
    • (1972) Plant Physiol , vol.50 , pp. 694-697
    • Villegas, C.N.1    Chichester, C.O.2    Raymundo, L.C.3    Simpson, K.L.4
  • 41
    • 52949145277 scopus 로고    scopus 로고
    • tRNA cleavage is a conserved response to oxidative stress in eukaryotes
    • Thompson DM, Lu C, Green PJ, Parker R (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 2095-2103.
    • (2008) RNA , vol.14 , pp. 2095-2103
    • Thompson, D.M.1    Lu, C.2    Green, P.J.3    Parker, R.4
  • 44
    • 65649119296 scopus 로고    scopus 로고
    • Antioxidants used by Deinococcus radiodurans and implications for antioxidant drug discovery
    • Zhang HY, Li XJ, Gao N, Chen LL (2009) Antioxidants used by Deinococcus radiodurans and implications for antioxidant drug discovery. Nature Reviews Microbiology 7: 476.
    • (2009) Nature Reviews Microbiology , vol.7 , pp. 476
    • Zhang, H.Y.1    Li, X.J.2    Gao, N.3    Chen, L.L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.