Differences in hydrogenase Gene expression between methanosarcina acetivorans and methanosarcina barkeri

Journal of Bacteriology

Volumn 191, Issue 8, 2009, Pages 2826-2833

  Guss, Adam M ^a,b   Kulkarni, Gargi ^a   Metcalf, William W ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGENASE; BETA GLUCOSIDASE;

ARTICLE; BACTERIAL STRAIN; DNA SEQUENCE; GENE EXPRESSION; GENE FUSION; GENETIC TRANSCRIPTION; METHANOSARCINA BARKERI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA TRANSLATION; BACTERIAL GENE; BIOSYNTHESIS; COMPARATIVE STUDY; ENZYMOLOGY; GENE EXPRESSION PROFILING; GENE ORDER; GENETICS; METABOLISM; METHANOSARCINA; NUCLEOTIDE SEQUENCE; PHYLOGENY; REPORTER GENE; SEQUENCE ALIGNMENT;

METHANOSARCINA; METHANOSARCINA ACETIVORANS; METHANOSARCINA BARKERI; METHANOSARCINA MAZEI;

ARTIFICIAL GENE FUSION; BETA-GLUCOSIDASE; CONSERVED SEQUENCE; GENE EXPRESSION PROFILING; GENE ORDER; GENES, BACTERIAL; GENES, REPORTER; HYDROGENASE; METHANOSARCINA; METHANOSARCINA BARKERI; PHYLOGENY; PROMOTER REGIONS, GENETIC; SEQUENCE ALIGNMENT;

EID: 65249098873     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00563-08     Document Type: Article

References (51)

1. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1992. Current protocols in molecular biology. John Wiley & Sons, New York, NY.
2. Berks, B. C. 1996. A common export pathway for proteins binding complex redox cofactors? Mol. Microbiol. 22:393-404.
3. Blokesch, M., A. Paschos, E. Theodoratou, A. Bauer, M. Hube, S. Huth, and A. Bock. 2002. Metal insertion into NiFe-hydrogenases. Biochem. Soc. Trans. 30:674-680.
4. Boccazzi, P., J. K. Zhang, and W. W. Metcalf. 2000. Generation of dominant selectable markers for resistance to pseudomonic acid by cloning and mu- tagenesis of the ileS gene from the archaeon Methanosarcina barkeri Fusaro. J. Bacteriol. 182:2611-2618.
5. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
6. Deppenmeier, U. 1995. Different structure and expression of the operons encoding the membrane-bound hydrogenases from Methanosarcina mazei Go1. Arch. Microbiol. 164:370-376.
7. Deppenmeier, U., M. Blaut, S. Lentes, C. Herzberg, and G. Gottschalk. 1995. Analysis of the vhoGAC and vhtGAC operons from Methanosarcina mazei strain G61, both encoding a membrane-bound hydrogenase and a cytochrome b. Eur. J. Biochem. 227:261-269.
8. Deppenmeier, U., A. Johann, T. Hartsch, R. Merkl, R. A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Baumer, C. Jacobi, H. Bruggemann, T. Lienard, A. Christmann, M. Bomeke, S. Steckel, A. Bhattacharyya, A. Lykidis, R. Overbeek, H. P. Klenk, R. P. Gunsalus, H. J. Fritz, and G. Gottschalk. 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4:453-461.
9. Elberson, M. A., and K. R. Sowers. 1997. Isolation of an aceticlastic strain of Methanosarcina siciliae from marine canyon sediments and emendation of the species description for Methanosarcina siciliae. Int. J. Syst. Bacteriol. 47:1258-1261.
10. Erkel, C., M. Kube, R. Reinhardt, and W. Liesack. 2006. Genome of rice cluster I archaea-the key methane producers in the rice rhizosphere. Science 313:370-372.
11. Fiebig, K., and B. Friedrich. 1989. Purification of the F420-reducing hydrogenase from Methanosarcina barkeri (strain Fusaro). Eur. J. Biochem. 184: 79-88.
12. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R. D. Barber, I. Cann, D. E. Graham, D. A. Grahame, A. M. Guss, R. Hedderich, C. Ingram-Smith, H. C. Kuettner, J. A. Krzycki, J. A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J. N. Reeve, K. Smith, T. A. Springer, L. A. Umayam, O. White,R.H.White,E. ConwaydeMacario,J.G.Ferry,K.F.Jarrell,H.Jing, A. J. Macario, I. Paulsen, M. Pritchett, K. R. Sowers, R. V. Swanson, S. H. Zinder, E. Lander, W. W. Metcalf, and B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542.
13. Guss, A. M., B. Mukhopadhyay, J. K. Zhang, and W. W. Metcalf. 2005. Genetic analysis of mch mutants in two Methanosarcina species demonstrates multiple roles for the methanopterin-dependent C-1 oxidation/reduction pathway and differences in H(2) metabolism between closely related species. Mol. Microbiol. 55:1671-1680.
14. Guss, A. M., M. Rother, J. K. Zhang, G. Kulkarni, and W. W. Metcalf. 2008. New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species. Archaea 2:193-203.
15. Haldimann, A., and B. L. Wanner. 2001. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J. Bacteriol. 183:6384-6393.
16. Hedderich, R., and L. Forzi. 2005. Energy-converting [NiFe] hydrogenases: more than just H2 activation. J. Mol. Microbiol. Biotechnol. 10:92-104.
17. Jablonski, P. E., A. A. DiMarco, T. A. Bobik, M. C. Cabell, and J. G. Ferry. 1990. Protein content and enzyme activities in methanol- and acetate-grown Methanosarcina thermophila. J. Bacteriol. 172:1271-1275.
18. Jarvis, G. N., C. Strompl, D. M. Burgess, L. C. Skillman, E. R. Moore, and K. N. Joblin. 2000. Isolation and identification of ruminal methanogens from grazing cattle. Curr. Microbiol. 40:327-332.
19. Jussofie, A., F. Mayer, and G. Gottschalk. 1986. Methane formation from methanol and molecular-hydrogen by protoplasts of new methanogenic isolates and inhibition by dicyclohexylcarbodiimide Arch. Microbiol. 146:245-249.
20. Kandler, O., and H. Hippe. 1977. Lack of peptidoglycan in the cell walls of Methanosarcina barkeri. Arch. Microbiol. 113:57-60.
21. Klenk, H. P., R. A. Clayton, J. F. Tomb, O. White, K. E. Nelson, K. A. Ketchum, R. J. Dodson, M. Gwinn, E. K. Hickey, J. D. Peterson, D. L. Richardson, A. R. Kerlavage, D. E. Graham, N. C. Kyrpides, R. D. Fleis- chmann, J. Quackenbush, N. H. Lee, G. G. Sutton, S. Gill, E. F. Kirkness, B. A. Dougherty, K. McKenney, M. D. Adams, B. Loftus, S. Peterson, C. I. Reich, L. K. McNeil, J. H. Badger, A. Glodek, L. Zhou, R. Overbeek, J. D. Gocayne, J. F. Weidman, L. McDonald, T. Utterback, M. D. Cotton, T. Spriggs, P. Artiach, B. P. Kaine, S. M. Sykes, P. W. Sadow, K. P. D'Andrea, C. Bowman, C. Fujii, S. A. Garland, T. M. Mason, G. J. Olsen, C. M. Fraser, H. O. Smith, C. R. Woese, and J. C. Venter. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370.
22. Künkel, A., J. A. Vorholt, R. K. Thauer, and R. Hedderich. 1998. An Esch- erichia coli hydrogenase-3-type hydrogenase in methanogenic archaea. Eur. J. Biochem. 252:467-476.
23. Lai, M. C., and C. J. Shih. 2001. Characterization of Methanococcus voltaei strain P2F9701a: a new methanogen isolated from estuarine environment. Curr. Microbiol. 42:432-437.
24. Lai, M. C., C. M. Shu, M. S. Chiou, T. Y. Hong, M. J. Chuang, and J. J. Hua. 1999. Characterization of Methanosarcina mazei N2M9705 isolated from an aquaculture fishpond. Curr. Microbiol. 39:79-84.
25. Lessner, D. J., L. Li, Q. Li, T. Rejtar, V. P. Andreev, M. Reichlen, K. Hill, J. J. Moran, B. L. Karger, and J. G. Ferry. 2006. An unconventional pathway for reduction of CO2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. Proc. Natl. Acad. Sci. USA 103:17921-17926.
26. Li, L., Q. Li, L. Rohlin, U. Kim, K. Salmon, T. Rejtar, R. P. Gunsalus, B. L. Karger, and J. G. Ferry. 2007. Quantitative proteomic and microarray analysis of the archaeon Methanosarcina acetivorans grown with acetate versus methanol. J. Proteome Res. 6:759-771.
27. Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. 2005. Proteome of Methanosarcina acetivorans. Part I. An expanded view of the biology of the cell. J. Proteome Res. 4:112-128.
28. Li, Q., L. Li, T. Rejtar, B. L. Karger, and J. G. Ferry. 2005. Proteome of Methanosarcina acetivorans. Part II. Comparison of protein levels in acetate- and methanol-grown cells. J. Proteome Res. 4:129-135.
29. Liu, Y., D. R. Boone, R. Sleat, and R. A. Mah. 1985. Methanosarcina mazei LYC, a new methanogenic isolate which produces a disaggregating enzyme. Appl. Environ. Microbiol. 49:608-613.
30. Lyimo, T. J., A. Pol, H. J. Op den Camp, H. R. Harhangi, and G. D. Vogels. 2000. Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. Int. J. Syst. Evol. Microbiol. 50:171-178.
31. Maeder, D. L., I. Anderson, T. S. Brettin, D. C. Bruce, P. Gilna, C. S. Han, A. Lapidus, W. W. Metcalf, E. Saunders, R. Tapia, and K. R. Sowers. 2006. The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J. Bacteriol. 188:7922-7931.
32. Mah, R. A., M. R. Smith, and L. Baresi. 1978. Studies on an acetate-fermenting strain of Methanosarcina. Appl. Environ. Microbiol. 35:1174-1184.
33. Metcalf, W. W., J. K. Zhang, E. Apolinario, K. R. Sowers, and R. S. Wolfe. 1997. A genetic system for Archaea of the genus Methanosarcina: liposome- mediated transformation and construction of shuttle vectors. Proc. Natl. Acad. Sci. USA 94:2626-2631.
34. Metcalf, W. W., J. K. Zhang, X. Shi, and R. S. Wolfe. 1996. Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro. J. Bacteriol. 178:5797-5802.
35. Meuer, J., S. Bartoschek, J. Koch, A. Kunkel, and R. Hedderich. 1999. Purification and catalytic properties of Ech hydrogenase from Methanosarcina barkeri. Eur. J. Biochem. 265:325-335.
36. Meuer, J., H. C. Kuettner, J. K. Zhang, R. Hedderich, and W. W. Metcalf. 2002. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc. Natl. Acad. Sci. USA 99:5632-5637.
37. Nelson, M. J., and J. G. Ferry. 1984. Carbon monoxide-dependent methyl coenzyme M methylreductase in acetotrophic Methanosarcina spp. J. Bacteriol. 160:526-532.
38. Ni, S., C. R. Woese, H. C. Aldrich, and D. R. Boone. 1994. Transfer of Methanolobus siciliae to the genus Methanosarcina, naming it Methanosarcina siciliae, and emendation of the genus Methanosarcina. Int. J. Syst. Bacteriol. 44:357-359.
39. Ni, S. S., and D. R. Boone. 1991. Isolation and characterization of a dimethyl sulfide-degrading methanogen, Methanolobus siciliae HI350, from an oil well, characterization of M. siciliae T4/MT, and emendation of M. siciliae. Int. J. Syst. Bacteriol. 41:410-416.
40. Possot, O., P. Gernhardt, A. Klein, and L. Sibold. 1988. Analysis of drug resistance in the archaebacterium Methanococcus voltae with respect to potential use in genetic engineering. Appl. Environ. Microbiol. 54:734-740.
41. Pritchett, M. A., J. K. Zhang, and W. W. Metcalf. 2004. Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea. Appl. Environ. Microbiol. 70:1425-1433.
42. Rother, M., P. Boccazzi, A. Bose, M. A. Pritchett, and W. W. Metcalf. 2005. Methanol-dependent gene expression demonstrates that methyl-coenzyme M reductase is essential in Methanosarcina acetivorans C2A and allows isolation of mutants with defects in regulation of the methanol utilization pathway. J. Bacteriol. 187:5552-5559.
43. Rother, M., and W. W. Metcalf. 2005. Genetic technologies for Archaea. Curr. Opin. Microbiol. 8:745-751.
44. Simankova, M. V., S. N. Parshina, T. P. Tourova, T. V. Kolganova, A. J. Zehnder, and A. N. Nozhevnikova. 2001. Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments. Syst. Appl. Microbiol. 24:362-367.
45. Singh, N., M. M. Kendall, Y. Liu, and D. R. Boone. 2005. Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. Int. J. Syst. Evol. Microbiol. 55:2531-2538.
46. Sowers, K. R., J. E. Boone, and R. P. Gunsalus. 1993. Disaggregation of Methanosarcina spp. and growth as single cells at elevated osmolarity. Appl. Environ. Microbiol. 59:3832-3839.
47. Stojanowic, A., and R. Hedderich. 2004. CO2 reduction to the level of formylmethanofuran in Methanosarcina barkeri is non-energy driven when CO is the electron donor. FEMS Microbiol. Lett. 235:163-167.
48. Tietze, M., A. Beuchle, I. Lamla, N. Orth, M. Dehler, G. Greiner, and U. Beifuss. 2003. Redox potentials of methanophenazine and CoB-S-S-CoM, factors involved in electron transport in methanogenic archaea. Chembio- chem 4:333-335.
49. Vaupel, M., and R. K. Thauer. 1998. Two F420-reducing hydrogenases in Methanosarcina barken. Arch. Microbiol. 169:201-205.
50. Vignais, P. M., B. Billoud, and J. Meyer. 2001. Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25:455-501.
51. von Klein, D., H. Arab, H. Volker, and M. Thomm. 2002. Methanosarcina baltica, sp. nov., a novel methanogen isolated from the Gotland Deep of the Baltic Sea. Extremophiles 6:103-110.