Biochemistry and genetics of autotrophy in Methanococcus

Abstract

The project investigated fundamental aspects of carbon metabolism and genetics in the methane-producing archaeon Methanococcus maripaludis. The project yielded 23 peer-reviewed publications and five reviews from 1997-2007. PDFs of the peer-reviewed publications are included in the next section. Some papers of special interest are listed below. The pathway of pyruvate biosynthesis was elucidated by a combination of biochemical and physiological studies. This work characterized the very oxygen sensitive pyruvate oxidoreductase and showed that the enzyme was irreversible under physiological conditions. Evidence for the flow of electrons from the energy coupling hydrogenase b (Ehb) was presented. These results were published in the following papers. Yang, Y.L., J.N. Gluska, and W.B. Whitman (2002) Intracellular pyruvate flux in the methane-producing archaeon Methanococcus maripaludis. Arch. Microbiol. 178: 493-498. Lin, W.C., Y.L. Yang, and W.B. Whitman (2003) The anabolic pyruvate oxidoreductase from Methanococcus maripaludis. Arch. Microbiol. 179: 444-456. Lin, W., and W.B. Whitman (2004) The importance of porE and porF in the anabolic pyruvate oxidoreductase of Methanococcus maripaludis. Arch. Microbiol. 181: 68-73. Porat, I., W. Kim, E.L. Hendrickson, Q. Xia, Y. Zhang, T. Wang, F. Taub, B.C. Moore, I.J. Anderson, M. Hackett, J.A. Leigh, and W.B. Whitman (2006) Disruption of the Ehb hydrogenase operon limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J. Bacteriol. 188: 1373-1380. The presence of a novel pathway of aromatic amino acid biosynthesis was discovered and elucidated as part of these studies. These results were published in the following papers. Tumbula, D. L., Q. Teng, M. G. Bartlett, and W. B. Whitman (1997) Ribose biosynthesis and evidence for an alternative first step in the common aromatic amino acid pathway in Methanococcus maripaludis. J. Bacteriol. 179:6010-6013. Porat, I., B.W. Waters, Q. Teng, and W.B. Whitman (2004) Two biosynthetic pathways for the aromatic amino acids in the archaeon Methanococcus maripaludis. J. Bacteriol. 186: 4940-4950. Porat, I., M. Sieprawska-Lupa, Q. Teng, F.J. Bohanon, R.H. White, and W.B. Whitman. 2006. Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis. Mol. Microbiol. 62: 1117-1132. A variety of computational, biochemical and genetic methods were used to elucidate the amino acyl-tRNA synthetases in methanococci. These were of special interest because genomic sequencing of a related archaeon Methanocaldococcus jannaschii revealed that these organisms were lacking four of the enzymes thought to be universal in all living organisms. Many of these results were published in the following papers. Rother, M., A. Resch, W.L. Gardner, W.B. Whitman, and A. Bock (2001) Heterologous expression of archaeal selenoprotein genes directed by the SECIS element located in the 3' non-translated region. Mol. Microbiol. 40: 900-908. Stathopoulos, C., W. Kim, T. Li, I. Anderson, B. Deutsch, S. Palioura, W. Whitman, and D. Soll. (2001) Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. U.S.A. 98: 14292-14297. Farahi, K., G.D. Pusch, R. Overbeek, and W.B. Whitman (2004) Detection of lateral gene transfer (LGT) events in the prokaryotic tRNA synthetases by the Ratios of Evolutionary Distances method. J. Mol. Evol. 58: 615-631. Sauerwald, A., W. Zhu, T.A. Major, H. Roy, S. Palioura, D. Jahn, W.B. Whitman, J.R. Yates 3rd, M. Ibba, and D. Soll (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307: 1969-1972. Yuan, J., S. Palioura, J.C. Salazar, D. Su, P. O’Donoghue, M.J. Hohn, A.M. Cardoso, W.B. Whitman, and D. Soll (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. USA 103:18923-18927.