Lateral Gene Transfer in the Deep Sea of Mariana Trench: Identification of nar Gene Cluster Encoding Membrane-bound Nitrate Reductase from Pseudomonas sp. Strain MT-1

References

• Blasco F., Iobbi G., Giordano G., Chippaux M. and Bonnefoy V. (1989) “Nitrate reductase of Escherichia coli: Completion of the nucleotide sequence of the nar operon and reassesment of the role of the a and b subunits in iron binding and electron transfer”, Molecular and General Genetics 218, 249-256.
   Google Scholar
• Christensen, J.P., Murray, J.W., Devol, A.H. and Codispoti, L.A. (1987) “Denitrification in continental shelf sediments has major impact on the oceanic nitrogen budget”, Global Biogeochemical Cycles 1, 97-116.
   Google Scholar
• Gregory, L.G., Karakas-Sen A., Richardson, D.J. and Spiro S. (2000) “Detection of genes for membrane-bound nitrate reductase in nitrate-respiring bacteria and in community DNA”, FEMS Microbiology Letters 183, 275-279.
   Google Scholar
• Guigliarelli B., Magalon A., Asso M., Bertrand P., Frixon C., Giordano G. and Blasco F. (1996) “Complete coordination of the four Fe-S centers of the b subunit from Escherichia coli nitrate reductase. Physiological, biochemical, and EPR characterization of site-directed mutants lacking the highest or lowest potential [4Fe-4S] clusters”, Biochemistry 35, 4828-4836.
   Google Scholar
• Heiss B., Frunzke K. and Zumft, W.G. (1989) “Formation of the N-N bond from nitric oxide by a membrane-bound cytochrome bc complex of nitrate respiring (denitrifying) Pseudomonas stutzeri”, Journal of Bacteriology 171, 3288-3297.
   Google Scholar
• Hirokawa T., Boon-Chieng S. and Mitaku S. (1998) “SOSUI: classification and secondary structure predictionsystem for membrane proteins”, Bioinfomatics 14, 378-379.
   Google Scholar
• Hartig E., Schiek U., Vollack, K.U. and Zumft, W.G. (1999) “Nitrate and nitrite control of respiratory nitrate reduction in denitrifying Pseudomonas stutzeri by a two-component regulatory system homologues to NarXL of Escherichia coli”, Journal of Bacteriology 181, 3658-3665.
   Google Scholar
• Mogi T., Tsubaki M., Hori H., Miyoshi H., Nakamura H. and Anraku Y. (1998) “Two terminal quinol oxidase families in Escherichia coli: variations on molecular machinery for dioxygen reduction”, Journal of Biochemistry, Molecular Biology and Biophysics 2, 79-110.
   Google Scholar
• Moreno-Vivia´n, C., Cabello P., Mart´?nez-Luque M., Blasko R. and Castillo F. (1999) “Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases”, Journal of Bacteriology 181, 6573-6584.
   Google Scholar
• Philippot L., Mirleau P., Mazurier S., Siblot S., Hartmann A., Lemanceau P. and Germon, J.C. (2001) “Characterization and transcriptional analysis of Pseudomonas fluorescens denitrifying clusters containing the nar, nir, nor and nos genes”, Biochimica et Biophysica Acta 1517, 436-440.
   Google Scholar
• Saitou N. and Nei M. (1987) “The neighbour-joining method: a new method for reconstituting phylogenetic trees”, Molelular Biology and Evolution 4, 406-425.
   Google Scholar
• Sakamoto T., Inoue-Sakamoto K. and Bryant, D.A. (1999) “A novel nitrate/nitrite permease in the marine cyanobacterium Synechococcus sp. strain PCC7002”, Journal of Bacteriology 181, 7363-7372.
   Google Scholar
• Sambrook J., Fritsch, E.F. and Maniatis T. (1989) Molecular Cloning: A laboratory Manual, 2nd Ed. (Cold Spring Harbor Laboratory, New York).
   Google Scholar
• Saraste M. and Castresana J. (1994) “Cytochrome oxidase evolved by tinkering with denitrification enzymes”, FEBS Letters 341, 1-4.
   Google Scholar
• Seitzinger, S.P. and Giblin, A.E. (1996) “Estimating denitrification in North Atlantic continental shelf sediment”, Biogeochemistry 35, 235-260.
   Google Scholar
• Stover, C.K., Pham, X.Q.T., Erwin, A.L., Mizoguchi, S.D., Warrener P., Hickey, M.J., Brinkman, F.S.L., Hufnagle, W.O., Kowalik, D.J., Lagrou M., Garber, R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y., Brody, L.L., Coulter, S.N., Folger, K.R., Kas A., Larbig K., Lim, R.M., Smith, K.A., Spencer, D.H., Wong, G.K.S., Wu Z. and Paulsen, I.T. (2000) “Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen”, Nature 406, 959-964.
   Google Scholar
• Tamegai H., Li L., Masui N. and Kato C. (1997) “A denitrifying bacterium from the deep sea at 11000-m depth”, Extremophiles 1, 207-211.
   Google Scholar
• Tamegai H., Kato C. and Horikoshi K. (2002) “Gene cluster of nitrous oxide reduction in the deep sea of Mariana Trench”, Journal of Biochemistry, Molecular Biology and Biophysics. 6, 221-224.
   Google Scholar
• Vollack, K.U., Hartig E., Korner H. and Zumft, W.G. (1999) “Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes”, Molecular Microbiology 31, 1681-1694.
   Google Scholar
• Wang Q., Li H. and Post, A.F. (2000) “Nitrate assimilation genes of the marine diazotrophic, filamentous cyanobacterium Trichodesmium sp. strain WH9601”, Journal of Bacteriology 182, 1764-1767.
   Google Scholar
• Warnecke-Eberz U. and Friedrich B. (1993) “Three nitrate reductase activities in Alcaligenes eutrophus”, Archives of Microbiology 159, 405-409.
   Google Scholar
• Yamanaka T. and Okunuki K. (1962) “Crystalline Pseudomonas cytochrome oxidase I. enzymic properties with special reference to the biological specificity”, Biochimica et Biophysica Acta 67, 379-393.
   Google Scholar
• Yoshimatsu K., Iwasaki T. and Fujiwara T. (2002) “Sequence and electron paramagnetic resonance analyses of nitrate reductase NarGH from a denitrifying halophilic euryarchaeote Haloar-cula marismortui”, FEBS Letters 516, 145-150.
   Google Scholar
• Zumft, W.G. (1997) “Cell biology and molecular basis of denitrification”, Microbiology and Molecular Biology Reviews 61, 533-616.
   Google Scholar
• Zumft, W.G. and Matsubara T. (1982) “A novel kind of multi-copper protein as terminal oxidoreductase of nitrous oxide respiration in Pseudomonas perfectomarinus”, FEBS Letters 148, 107-112.
   Google Scholar