DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure

Journal of Industrial Microbiology and Biotechnology

Volumn 33, Issue 9, 2006, Pages 784-790

  Zhang, Weiwen ^a   Culley, David E ^a   Nie, Lei ^b   Brockman, Fred J ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b GEORGETOWN UNIVERSITY   (United States)

Author keywords

Methanosarcina barkeri; Microarray; Stress

Indexed keywords

CATALASE; CELLULOSE; CHAPERONE; CHAPERONIN; HEAT SHOCK PROTEIN 60; HEAT SHOCK PROTEIN 70; METHANE; PEROXIDASE; POLYSACCHARIDE; PROTEIN DNAJ; PROTEIN DNAK; REACTIVE OXYGEN METABOLITE; SUPEROXIDE DISMUTASE; THIOREDOXIN REDUCTASE; TRANSPOSASE;

ANAEROBIC BACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL SURVIVAL; BIOGENESIS; DNA MICROARRAY; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; ENERGY CONVERSION; ENERGY YIELD; GENE EXPRESSION; HEAT SHOCK; HEAT STRESS; METHANOSARCINA BARKERI; NONHUMAN; PROTEIN METABOLISM; STRESS; TRANSCRIPTOMICS; UPREGULATION;

AIR; ANAEROBIOSIS; BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; HEAT-SHOCK RESPONSE; METHANOSARCINA BARKERI; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

ARCHAEA; METHANOSARCINA BARKERI;

EID: 33746317296     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-006-0114-3     Document Type: Article

References (39)

1. Brioukhanov A, Netrusov A, Sordel M, Thauer RK, Shima S (2000) Protection of Methanosarcina barkeri against oxidative stress: identification and characterization of an iron superoxide dismutase. Arch Microbiol 174:213-216
2. Carmel-Harel O, Storz G (2000) Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and Saccharomyces cerevisiae responses to oxidative stress. Ann Rev Microbiol 54:439-461
3. Capy P, Gasperi G, Biemont C, Bazin C (2000) Stress and transposable elements: co-evolution or useful parasites? Heredity 85:101-106
4. Chien YT, Auerbuch V, Brabban AD, Zinder SH (2000) Analysis of genes encoding an alternative nitrogenase in the archaeon Methanosarcina barkeri 227. J Bacteriol 182:3247-3253
5. Clarens M, Macario AJL, Conway de Macario E (1995) The archaeal dnaK-dnaJ gene cluster: organization and expression in the methanogen Methanosarcina mazei. J Mol Biol 250:191-201
6. Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, Bruggemann H, Lienard T, Christmann A, Bomeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453-461
7. Eichenbaum Z, Livneh Z (1998) UV light induces IS10 transposition in Escherichia coli. Genetics 149:1173-1181
8. Fetzer S, Bak F, Conra R (1993) Sensitivity of methanogenic bacteria from paddy soil to oxygen and desiccation FEMS. Microbiol Ecol 12:107-115
9. Fournier M, Zhang Y, Wildschut JD, Dolla A, Voordouw JK, Schriemer DC, Voordouw G (2003) Function of oxygen resistance proteins in the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris hildenborough. J Bacteriol 185:71-79
10. Furutani M, Ideno A, Iida T, Maruyama T (2000) FK506 binding protein from a thermophilic archaeon, Methanococcus thermolithotrophicus has chaperone-like activity in vitro. Biochemistry 39:453-462
11. Goff SA, Casson LP, Goldberg AL (1984) Heat shock regulatory gene htpR influences rates of protein degradation and expression of the lon gene in Escherichia coli (USA). Proc Natl Acad Sci 81:6647-6651
12. Iida T, Furutani M, Nishida F, Maruyama T (1998) FKBP-type peptidyl-prolyl cis-trans isomerase from a sulfur-dependent hyperthermophilic archaeon, Thermococcus sp KS-1. Gene 222:249-255
13. Ilves H, Horak R, Kivisaar M (2001) Involvement of sigma(S) in starvation-induced transposition of Pseudomonas putida transposon Tn4652. J Bacteriol 183:5445-5548
14. Iyer LM, Leipe DD, Koonin EV, Aravind L (2004) Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol 146:11-31
15. Klunker D, Haas B, Hirtreiter A, Figueiredo L, Naylor DJ, Pfeifer G, Muller V, Deppenmeier U, Gottschalk G, Hartl FU, Hayer-Hartl M (2003) Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei. J Biol Chem 278:33256-33267
16. Lamrani S, Ranquet C, Gama MJ, Nakai H, Shapiro JA Toussaint A, Maenhaut-Michel G (1999) Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol Microbiol 32:327-343
17. Lang K, Schmid FX, Fischer G (1987) Catalysis of protein folding by prolyl isomerase (London). Nature 329:268-270
18. Lange M, Macario AJL, Ahring BK, Conway de Macario E (1997) Heat-shock response in Methanosarcina mazei S-6. Curr Microbiol 35:116-121
19. Lovley DR, Klug MJ (1982) Intermediary metabolism of organic matter in the sediments of a eutrophic lake. Appl Environ Microbiol 43:552-560
20. Lumppio HL, Shenvi NV, Summers AO, Voordouw G, Kurtz DM Jr (2001) Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system. J Bacteriol 183:101-108
21. Macario AJL, Lange M, Ahring BK, Conway de Macario E (1999) Stress genes and proteins in the archaea. Microbiol. Mol Biol Rev 63:923-967
22. Mascher T, Margulis NG, Wang T, Ye RW, Helmann JD (2003) Cell wall stress responses in Bacillus subtilis: the regulatory network of the bacitracin stimulon. Mol Microbiol 50:1591-1604
23. Netzer WJ, Hartl FU (1998) Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem Sci 23:68-73
24. Nies DH (1992) CzcR and CzcD, gene products affecting regulation of resistance to cobalt, zinc, and cadmium (czc system) in Alcaligenes eutrophus. J Bacteriol 174:8102-8110
25. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, McCormick M, Norton J, Pollock T, Sumwalt T, Butcher L, Porter D, Molla M, Hall C, Blattner F, Sussman MR, Wallace RL, Cerrina F, Green RD (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12:1749-1755
26. Pfeifer F, Blaseio U (1990) Transposition burst of the ISH27 insertion element family in Halobacterium halobium. Nucleic Acids Res 18:6921-6925
27. Raivio TL, Silhavy TJ (2001) Periplasmic stress and ECF sigma factors. Ann Rev Microbiol 55:591-624
28. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol 5:R90
29. Rohlin L, Trent JD, Salmon K, Kim U, Gunsalus RP, Liao JC (2005) Heat shock response of Archaeoglobus fulgidus. J Bacteriol 187:6046-6057
30. Scharf C, Riethdorf S, Ernst H, Engelmann S, Volker U, Hecker M (1998) Thioredoxin is an essential protein induced by multiple stresses in Bacillus subtilis. J Bacteriol 180:1869-1877
31. Shima S, Netrusov A, Sordel M, Wicke M, Hartmann GC, Thauer RK (1999) Purification, characterization, and primary structure of a monofunctional catalase from Methanosarcina barkeri. Arch Microbiol 171:317-323
32. Smalley D, Rocha ER, Smith CJ (2002) Aerobic-type ribonucleotide reductase in the anaerobe Bacteroides fragilis. J Bacteriol 184:895-903
33. Smith PH, Mah RA (1966) Kinetics of acetate metabolism during sludge digestion. Appl Microbiol 14:368-371
34. Stroman P, Muller CC, Sorensen KI (2003) Heat shock treatment increases the frequency of loss of an erythromycin resistance-encoding transposable element from the chromosome of Lactobacillus crispatus CHCC3692. Appl Environ Microbiol 69:7173-7180
35. Ueki T, Inouye S (2002) Transcriptional activation of a heat-shock gene, lonD, of Myxococcus xanthus by a two component histidine-aspartate phosphorelay system. J Biol Chem 277:6170-6177
36. Uziel O, Borovok I, Schreiber R, Cohen G, Aharonowitz Y (2004) Transcriptional regulation of the Staphylococcus aureus thioredoxin and thioredoxin reductase genes in response to oxygen and disulfide stress. J Bacteriol 186:326-334
37. Voordouw JK, Voordouw G (1998) Deletion of the rbo gene increases the oxygen sensitivity of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 64:2882-2887
38. Zhilina TN (1972) Death of Methanosarcina in the air. Mikrobiologia 41:1105-1106
39. Zhong S, Khodursky A, Dykhuizen DE, Dean AM (2004) Evolutionary genomics of ecological specialization (USA). Proc Natl Acad Sci 101:11719-11724