Leigh Lab : Publications
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J o h n    L e i g h    L a b

University of Washington Department of Microbiology
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Email the Director :
John Leigh, Ph.D.


Publications

Costa, K. C. and J. A. Leigh. 2014. Metabolic versatility in methanogens. Curr. Opin. Biotechnol. 29: 70-75. Abstract
Costa, K. C., T. J. Lie, Q. Xia, and J. A. Leigh. 2013. VhuD facilitates electron flow from H2 or formate to heterodisulfide reductase in Methanococcus maripaludis. J. Bacteriol. 195: 5160-5165. Abstract
Yoon, S. H., S. Turkarslan, D. J. Reiss, M. Pan, J. A. Burn, K. C. Costa, T. J. Lie, J. Slagel, R. L. Moritz, M. Hackett, J. A. Leigh, and N. S. Baliga. 2013. A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res. 23: 1839-1851. Abstract
Lie T. J., K. C. Costa, D. Pak, V. Sakesan, and J. A. Leigh. 2013. Phenotypic evidence that the function of the [Fe]-hydrogenase Hmd in Methanococcus maripaludis requires seven hcg (hmd-cooccuring genes) but not hmdII. FEMS Microbiol. Lett. 343: 156-160. Abstract
Costa, K. C., T. J. Lie, M. A. Jacobs, and J. A. Leigh. 2013. H2-independent growth of the hydrogenotrophic methanogen Methanococcus maripaludis. mBio 4(2):e00062-13. doi: 10.1128/mBio.00062-13. Abstract
Costa, K., S. H. Yoon, M. Pan, J. A. Burn, N. S. Baliga, and J. A. Leigh. 2013. Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. J. Bacteriol 195:1456-1462. Abstract
Lie, T. J., K. C. Costa, B. Lupa, S. Korpole, W. B. Whitman, and J. A. Leigh. 2012. Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. Proc. Natl. Acad. Sci. USA 109:15473-15478. Abstract
Yoon, S. H., D. J. Reiss, J. C. Bare, D. Tenenbaum, M. Pan, J. Slagel, R. L. Moritz, S. Lim, M. Hackett, A. L. Menon, M. W.W. Adams, A. Barnebey, S. M. Yannone, J. A. Leigh, and N. S. Baliga. 2011. Parallel evolution of transcriptome architecture during genome reorganization. Genome Research 21:1892-1904. Abstract
Leigh, J. A., S. V. Albers, H. Atomi, and T. Allers. 2011. Model organisms for genetics in the domain archaea: methanogens, halophiles, thermococcales and sulfolobales. FEMS Microbiol Rev. 35:577-608. Abstract
Wisedchaisri, G., D. M. Dranow, T. J. Lie, J. B. Bonanno, Y. Patskovsky, S. A. Ozyurt, J. M. Sauder, S. C. Almo, S. R. Wasserman, S. K. Burley, J. A. Leigh, and T. Gonen. 2010. Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR. Structure 18:1512-1521. Abstract
Dodsworth, J. A., L. Li, S. Wei, B. P. Hedlund, J. A. Leigh, and P. de Figueiredo. 2010. Interdomain conjugal transfer of DNA from Bacteria to Archaea. Appl. Environ. Microbiol. 76:5644-5647. Abstract
Costa K. C., P. M. Wong, T. Wang, T. J. Lie, J. A. Dodsworth, I. Swanson, J. A. Burn, M. Hackett, and J. A. Leigh. 2010. Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc. Natl. Acad. Sci. USA 107:11050-11055. Abstract
Lie, T. J., E. L. Hendrickson, U. M. Niess, B. C. Moore, A. K. Haydock, and J. A. Leigh. 2010. Overlapping repressor binding sites regulate expression of the Methanococcus maripaludis glnK1 operon. Molecular Microbiol. 75:755-762. Abstract
Xia, Q., T. Wang, E. L. Hendrickson, T. J. Lie, M. Hackett, and J. A. Leigh. 2009. Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis. BMC Microbiol. 9:149. Abstract
Hendrickson, E. L., and J. A. Leigh. 2008. Roles of coenzyme F420-reducing hydrogenases and hydrogen- and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. J. Bacteriol. 190:4818-4821. Abstract
Hendrickson, E. L., Y. Liu, G. Rosas-Sandoval, I. Porat, D. Sll, W. B. Whitman, and J. A. Leigh. 2008. Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J. Bacteriol. 190:2198-2205. Abstract
Dodsworth, J. A., and J. A. Leigh. 2007. NifI inhibits nitrogenase by competing with Fe protein for binding to the MoFe protein. Biochem. Biophys. Res. Commun. 364:378-382. Abstract
Lie, T. J. and J. A. Leigh. 2007. Genetic screen for regulatory mutations in Methanococcus maripaludis and its use in identification of induction-deficient mutants of the euryarchaeal repressor NrpR. Appl. Environ. Microbiol. 73:6595-6600. Abstract
Leigh, J. A. and J. A. Dodsworth. 2007. Nitrogen regulation in Bacteria and Archaea. Annu. Rev. Microbiol. 61:349-377. Abstract
Xia, Q., E. L. Hendrickson, T. Wang, R. J. Lamont, J. A. Leigh, and M. Hackett. 2007. Protein abundance ratios for global studies of prokaryotes. Proteomics 7: 2904-2919. Abstract
Hendrickson, E., A. Haydock, B. Moore, W. Whitman, and J. Leigh. 2007. Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. Proc. Natl. Acad. Sci. USA 104:8930-8934. Abstract
Lie, T. J., J. A. Dodsworth, D. Nickle and J. A. Leigh. 2007. Diverse homologs of the archaeal repressor NrpR function similarly in nitrogen regulation. FEMS Microbiol. Lett. 271:281-288. Abstract
Stolyar, S., S. Van Dien, K. L. Hillesland, N. Pinel, T. J. Lie, J. A. Leigh, and D. A. Stahl. 2007. Metabolic modeling of a mutualistic microbial community. Mol. Syst. Biol. 3:92. Abstract
Hendrickson, E. L., Q. Xia, T. Wang, J. A. Leigh, and M. Hackett. 2006. Comparison of spectral counting and metabolic stable isotope labeling for use with quantitative microbial proteomics. Analyst 131:1335-1341. Abstract
Dodsworth, J. A. and J. A. Leigh. 2006. Regulation of nitrogenase by 2-oxoglutarate-reversible, direct binding of a PII-like nitrogen sensor protein to dinitrogenase. Proc. Natl. Acad. Sci. USA 103:9779-9784. Abstract
Xia, Q., E. L. Hendrickson, Y. Zhang, T. Wang, F. Taub, B. C. Moore, I. Porat , W. B. Whitman, M. Hackett, and J. A. Leigh 2006. Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Molecular and Cellular Proteomics 5:868-881. Abstract
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 operon limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J. Bacteriol. 188:1373-1380. Abstract
Dodsworth, J. A., N. C. Cady, and J. A. Leigh. 2005. 2-oxoglutarate and the PII homologues NifI1 and NifI2 regulate nitrogenase activity in cell extracts of Methanococcus maripaludis. Molecular Microbiol. 56:1527-1538. Abstract
Moore, B.C. and J.A. Leigh. 2005. Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. J. Bacteriol. 187(3):972-9. Abstract
Lie, T.J., Wood, G.E. and J. A. Leigh. 2005. Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators.
     J. Biol. Chem. 280(7):5236-41
Abstract
Hendrickson, E. L., R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J. A. Dodsworth, W. Gillett, D. E. Graham, M. Hackett, A. K. Haydock, A. Kang, M. L. Land, R. Levy, T. J. Lie, T. A. Major, B. C. Moore, I. Porat, A. Palmeiri, G. Rouse, C. Saenphimmachak, D. Sll, S. Van Dien, T. Wang, W. B. Whitman, Q. Xia, Y. Zhang, F. W. Larimer, M. V. Olson, and J. A. Leigh. 2004. Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.
     J. Bacteriol. 186:6956-69
Abstract
Haydock, A. K., I. Porat, W. B. Whitman, J. A. Leigh. 2004. Continuous culture of
     Methanococcus maripaludis under defined nutrient conditions. FEMS Microbiol Lett.
     238(1):85-91
Abstract
Wood, G. E, A. K. Haydock, and J. A. Leigh. 2003. Function and regulation of the
     formate dehydrogenase genes of the methanogenic archaeon Methanococcus
     maripaludis
. J. Bacteriol. 185:2548-2554.
Abstract
Lie, T. J. and J. A. Leigh. 2003. A novel repressor of nif and glnA expression in the
     methanogenic archaeon Methanococcus maripaludis. Molecular Microbiol.
     47:235-246.
Abstract
Lie, T. J. and J. A. Leigh. 2002. Regulatory response of Methanococcus maripaludis to
     alanine, an intermediate nitrogen source. J. Bacteriol. 184:5301-5306.
Abstract
Leigh, J. A. 2002. Evolution of energy metabolism. In: Biodiversity of Microbial Life:
     Foundation of Earth's Biosphere, J. T. Staley and A.-L. Reysenbach, eds.
Abstract Not Available
Kessler, P. S., C. Daniel, and J. A. Leigh. 2001. Ammonia switch-off of nitrogen fixation
     in the methanogenic archaeon Methanococcus maripaludis: mechanistic features and
     requirement for the novel GlnB homologues, NifI1 and NifI2. J. Bacteriol. 183:882-
     889.
Abstract
Leigh, J. A. 2000. Nitrogen fixation in methanogens - the archaeal perspective.
     Curr. Issues Mol. Biol. 2:125-131.
Abstract
Kessler, P. S. and J. A. Leigh. 1999. Genetics of nitrogen regulation in Methanococcus
     maripaludis
. Genetics 152:1343-1351.
Abstract
Cohen-Kupiec, R., M. Kupiec, K. Sandbeck, and J. A. Leigh. 1999. Functional
     conservation between the argininosuccinate lyase of the archaeon Methanococcus
     maripaludis
and the corresponding bacterial and eukaryal genes. FEMS Microbiol.
     Lett. 173:231-238.
Abstract
Leigh, J. A. 1999. Transcriptional regulation in Archaea. Curr. Op. Microbiol. 2:131-134. Abstract
Cohen-Kupiec, R., C. J. Marx, and J. A. Leigh. 1999. Function and regulation of glnA
     in the methanogenic archaeon Methanococcus maripaludis. J. Bacteriol. 181:256-261.
Abstract
Kessler, P. S., C. Blank, and J. A. Leigh. 1998. The nif gene operon of the methanogenic
     archaeon Methanococcus maripaludis. J. Bacteriol. 180:1504-1511.
Abstract
Cohen-Kupiec, R., C. Blank, and J. A. Leigh. 1997. Transcriptional regulation in Archaea:
     In vivo demonstration of a repressor binding site in a methanogen.
     Proc. Natl. Acad. Sci. USA 94:1316-1320.
Abstract

Full Text
Kessler, P. S., J. McLarnan, and J. A. Leigh. 1997. Nitrogenase phylogeny and the
     molybdenum dependence of nitrogen fixation in Methanococcus maripaludis.
     J. Bacteriol. 179:541-543.
Abstract
Argyle, J.L., Tumbula, D.L., and Leigh, J.A. 1996. Neomycin resistance as a selectable
     marker in Methanococcus maripaludis. Appl. Environ. Microbiol. 62:4233-4237.
Abstract
Blank, C.E., Kessler, P.S., and Leigh, J.A. 1995. Genetics in methanogens: Transposon
     insertion mutagenesis of a Methanococcus maripaludis nifH gene. J. Bacteriol.
     177:5773-5777.
Abstract
Sandbeck, K.A. and Leigh, J.A. 1991. Recovery of an integration shuttle vector from
     tandem repeats in Methanococcus maripaludis. Appl. Environ. Microbiol.
     57:2762-2763.
Abstract