Proteome analysis of thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth

Journal of Proteomics

Volumn 74, Issue 10, 2011, Pages 1926-1933

  Yun, Sung Ho ^a   Kwon, Sang Oh ^a,b   Park, Gun Wook ^a   Kim, Jin Young ^a   Kang, Sung Gyun ^c   Lee, Jung Hyun ^c   Chung, Young Ho ^a   Kim, Soohyun ^a   Choi, Jong Soon ^a,b   Kim, Seung Il ^a  

^a Korea Basic Science Institute (KBSI)   (South Korea)

^b Chungnam National University   (South Korea)

^c Korea Research Institute of Ships and Ocean Engineering   (South Korea)

Author keywords

Carboxydotrophic growth; SDS PAGE LC MS MS; Thermococcus onnurineus NA1

Indexed keywords

CARBON MONOXIDE; HEAT SHOCK COGNATE PROTEIN 70; HYDROGENASE; METAGLIDASEN; PROTEOME;

ARCHAEBACTERIUM; ARTICLE; CELL CULTURE; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE MAPPING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; OPEN READING FRAME; ORGANISMS BY ELECTRON DONOR; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; THERMOCOCCUS; THERMOCOCCUS ONNURINEUS; YEAST;

ARCHAEAL PROTEINS; CARBON MONOXIDE; HYDROGEN; HYDROGENASE; MULTIGENE FAMILY; PROTEOME; THERMOCOCCUS;

ARCHAEA; THERMOCOCCUS;

EID: 80052025184     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2011.05.010     Document Type: Article

References (39)

1. Holden J.F., Takai K., Summit M., Bolton S., Zyskowski J., Baross J.A. Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean. FEMS Microbiol Ecol 2001, 36:51-60.
2. Bae S.S., Kim Y.J., Yang S.H., Lim J.K., Jeon J.H., Lee H.S., et al. Thermoccoccus onnurineus sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent area at the PACMANUS field. J Microbiol Biotechnol 2006, 16:1826-1831.
3. Lee H.S., Kang S.G., Bae S.S., Lim J.K., Cho Y., Kim Y.J., et al. The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism. J Bacteriol 2008, 190:7491-7499.
4. Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 2005, 15:352-363.
5. Zivanovic Y., Armengaud J., Lagorce A., Leplat C., Guerin P., Dutertre M., et al. Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol 2009, 10:R70.
6. Sokolova T.G., Jeanthon C., Kostrikina N.A., Chernyh N.A., Lebedinsky A.V., Stackebrandt E., et al. The first evidence of anaerobic CO oxidation coupled with H2 production by a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Extremophiles 2004, 8:317-323.
7. Lim J.K., Kang S.G., Lebedinsky A.V., Lee J.H., Lee H.S. Identification of a novel class of membrane-bound [NiFe]-hydrogenases in Thermococcus onnurineus NA1 by in silico analysis. Appl Environ Microbiol 2010, 76:6286-6289.
8. Kim Y.J., Lee H.S., Kim E.S., Bae S.S., Lim J.K., Matsumi R., et al. Formate-driven growth coupled with H(2) production. Nature 2010, 467:352-355.
9. Kwon S.O., Kang S.G., Park S.H., Kim Y.H., Choi J.S., Lee J.H., et al. Proteomic characterization of the sulfur-reducing hyperthermophilic archaeon Thermococcus onnurineus NA1 by 2-DE/MS-MS. Extremophiles 2009, 13:379-387.
10. Archaea: a laboratory manual 1995, Cold Spring Harbor Laboratory, Cold Spring Harbor. F.T. Robb, A.R. Place, K.R. Sowers, H.J. Schreier, S. DasSarma, E.M. Fleischmann (Eds.).
11. Jolivet E., L'Haridon S., Corre E., Forterre P., Prieur D. Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation. Int J Syst Evol Microbiol 2003, 53:847-851.
12. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976, 72:248-254.
13. Wang J., Xue Y., Feng X., Li X., Wang H., Li W., et al. An analysis of the proteomic profile for Thermoanaerobacter tengcongensis under optimal culture conditions. Proteomics 2004, 4:136-150.
14. Kim J.Y., Lee J.H., Park G.W., Cho K., Kwon K.H., Park Y.M., et al. Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis. Proteomics 2005, 5:3376-3385.
15. Kall L., Canterbury J.D., Weston J., Noble W.S., MacCoss M.J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 2007, 4:923-925.
16. Brosch M., Yu L., Hubbard T., Choudhary J. Accurate and sensitive peptide identification with Mascot Percolator. J Proteome Res 2009, 8:3176-3181.
17. Ishihama Y., Oda Y., Tabata T., Sato T., Nagasu T., Rappsilber J., et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4:1265-1272.
18. Choi J.S., Cho Y.K., Yoon S.H., Kwon S.O., Koo D.B., Yu K. Proteomic analysis of porcine pancreas development. BMB Rep 2009, 42:661-666.
19. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001, 19:242-247.
20. Lee A.M., Sevinsky J.R., Bundy J.L., Grunden A.M., Stephenson J.L. Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods. J Proteome Res 2009, 8:3844-3851.
21. Kirkland P.A., Humbard M.A., Daniels C.J., Maupin-Furlow J.A. Shotgun proteomics of the haloarchaeon Haloferax volcanii. J Proteome Res 2008, 7:5033-5039.
22. Assiddiq B.F., Snijders A.P., Chong P.K., Wright P.C., Dickman M.J. Identification and characterization of Sulfolobus solfataricus P2 proteome using multidimensional liquid phase protein separations. J Proteome Res 2008, 7:2253-2261.
23. Moura I., Tavares P., Ravi N. Characterization of three proteins containing multiple iron sites: rubrerythrin, desulfoferrodoxin, and a protein containing a six-iron cluster. Methods Enzymol 1994, 243:216-240.
24. Das A., Coulter E.D., Kurtz D.M., Ljungdahl L.G. Five-gene cluster in Clostridium thermoaceticum consisting of two divergent operons encoding rubredoxin oxidoreductase-rubredoxin and rubrerythrin-type A flavoprotein-high-molecular-weight rubredoxin. J Bacteriol 2001, 183:1560-1567.
25. Sztukowska M., Bugno M., Potempa J., Travis J., Kurtz D.M. Role of rubrerythrin in the oxidative stress response of Porphyromonas gingivalis. Mol Microbiol 2002, 44:479-488.
26. Weinberg M.V., Jenney F.E., Cui X., Adams M.W. Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase. J Bacteriol 2004, 186:7888-7895.
27. Aivaliotis M., Macek B., Gnad F., Reichelt P., Mann M., Oesterhelt D. Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum-a representative of the third domain of life. PLoS One 2009, 4:e4777.
28. Verhees C.H., Kengen S.W., Tuininga J.E., Schut G.J., Adams M.W., De Vos W.M., et al. The unique features of glycolytic pathways in Archaea. Biochem J 2003, 375:231-246.
29. Orita I., Sato T., Yurimoto H., Kato N., Atomi H., Imanaka T., et al. The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J Bacteriol 2006, 188:4698-4704.
30. Hansen T., Reichstein B., Schmid R., Schonheit P. The first archaeal ATP-dependent glucokinase, from the hyperthermophilic crenarchaeon Aeropyrum pernix, represents a monomeric, extremely thermophilic ROK glucokinase with broad hexose specificity. J Bacteriol 2002, 184:5955-5965.
31. Soderberg T. Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in Archaea: a phylogenetic analysis of archaeal genomes. Archaea 2005, 1:347-352.
32. Fukuda W., Fukui T., Atomi H., Imanaka T. First characterization of an archaeal GTP-dependent phosphoenolpyruvate carboxykinase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 2004, 186:4620-4627.
33. Sato T., Atomi H., Imanaka T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 2007, 315:1003-1006.
34. Yoshida S., Atomi H., Imanaka T. Engineering of a type III RubisCO from a hyperthermophilic archaeon in order to enhance catalytic performance in mesophilic host cells. Appl Environ Microbiol 2007, 73:6254-6261.
35. Finn M.W., Tabita F.R. Synthesis of catalytically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in Archaea. J Bacteriol 2003, 185:3049-3059.
36. Dobbek H., Svetlitchnyi V., Gremer L., Huber R., Meyer O. Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster. Science 2001, 293:1281-1285.
37. Maness P.C., Huang J., Smolinski S., Tek V., Vanzin G. Energy generation from the CO oxidation-hydrogen production pathway in Rubrivivax gelatinosus. Appl Environ Microbiol 2005, 71:2870-2874.
38. Maness P.C., Weaver P.F. Evidence for three distinct hydrogenase activities in Rhodospirillum rubrum. Appl Microbiol Biotechnol 2001, 57:751-756.
39. Symonds R.B., Rose W.I., Bluth G.J.S., Gerlach T.M. Volcanic-gas studies; methods, results, and applications. Rev Miner Geochem 1994, 30:1-66.