Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

Applied and Environmental Microbiology

Volumn 72, Issue 3, 2006, Pages 2050-2063

  Starkenburg, Shawn R ^a   Chain, Patrick S G ^b,c   Sayavedra Soto, Luis A ^a   Hauser, Loren ^d   Land, Miriam L ^d   Larimer, Frank W ^d   Malfatti, Stephanie A ^c   Klotz, Martin G ^e   Bottomley, Peter J ^a   Arp, Daniel J ^a   Hickey, William J ^f  

^a OREGON STATE UNIVERSITY   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF LOUISVILLE   (United States)

^f UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CHROMOSOMES; ENZYMES; GENES; NITRATES; OXIDATION; PROTEINS; SUGARS;

ALPHAPROTEOBACTERIUM; CHEMOLITHOAUTOTROPHIC; CONTROL NITRITE OXIDATION; PHYLOGENETIC IDENTITY;

GENETIC ENGINEERING;

AMINO ACID; ASPARTATE TRANSFER RNA LIGASE; BACTERIUM LIPOPOLYSACCHARIDE; CARBON MONOXIDE DEHYDROGENASE; CARRIER PROTEIN; CATALASE; CHAPERONIN; COENZYME A; COLD SHOCK PROTEIN; CYANOCOBALAMIN; CYTOCHROME C OXIDASE; DNA TOPOISOMERASE (ATP HYDROLYSING); GLUTATHIONE PEROXIDASE; GLUTATHIONE REDUCTASE; GLYOXYLIC ACID; LIPID; LIPID A; NITRATE REDUCTASE; NITRITE; O ANTIGEN; OXIDOREDUCTASE; PEROXIDASE; PYRIDOXINE; RIBULOSEBISPHOSPHATE CARBOXYLASE; RNA POLYMERASE; SUPEROXIDE DISMUTASE; THIAMINE; THIOREDOXIN REDUCTASE; UBIQUINONE; UNINDEXED DRUG;

GENOME;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; CELL DIVISION; CONTROLLED STUDY; DNA SEQUENCE; ELECTRON TRANSPORT; GENETIC TRANSCRIPTION; HETEROTROPHY; NITRIFICATION; NITROBACTER; NITROBACTER WINOGRADSKYI; NITROGEN CYCLING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA TRANSLATION;

BACTERIAL PROTEINS; CARBON DIOXIDE; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; NITRITES; NITROBACTER; OXIDATION-REDUCTION; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM JAPONICUM; NEGIBACTERIA; NITROBACTER; NITROBACTER WINOGRADSKYI; RHODOPSEUDOMONAS PALUSTRIS;

EID: 33644932387     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.72.3.2050-2063.2006     Document Type: Article

References (105)

1. Ahlers, B., W. Konig, and E. Bock. 1990. Nitrite reductase activity in Nitrobacter vulgaris. FEMS Microbiol. Lett. 67:121-126.
2. Aleem, M. I. H., and D. L. Sewell. 1984. Oxidoreductase systems in Nitrobacter agilis, p. 185-210. In W. R. Strohl and O. H. Tuovinen (ed.), Microbial chemoautotrophy. Ohio State University Press, Columbus, Ohio.
3. Andrews, S. C., A. K. Robinson, and F. Rodriguez-Quinones. 2003. Bacterial iron homeostasis. FEMS Microbiol. Rev. 27:215-237.
4. Auran, T. B., and E. L. Schmidt. 1976. Lipids of Nitrobacter and effects of cultural conditions on fatty acid composition. Biochim. Biophys. Acta 431:390-398.
5. Bardin, S. D., R. T. Voegele, and T. M. Finan. 1998. Phosphate assimilation in Rhizobium (Sinorhizobium) meliloti: identification of a pit-like gene. J. Bacteriol. 180:4219-4226.
6. Beaumont, H. J., N. G. Hommes, L. A. Sayavedra-Soto, D. J. Arp, D. M. Arciero, A. B. Hooper, H. V. Westerhoff, and R. J. van Spanning. 2002. Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite. J. Bacteriol. 184:2557-2560.
7. Beaumont, H. J., S. I. Lens, W. N. Reijnders, H. V. Westerhoff, and R. J. van Spanning. 2004. Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor. Mol. Microbiol. 54:148-158.
8. Beaumont, H. J., S. I. Lens, H. V. Westerhoff, and R. J. van Spanning. 2005. Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite. J. Bacteriol. 187:6849-6851.
9. Bendtsen, J., H. Nielsen, D. Widdick, T. Palmer, and S. Brunak. 2005. Prediction of twin-arginine signal peptides. BMC Bioinformatics 6:167-174.
10. Bendtsen, J. D., H. Nielsen, G. von Heijne, and S. Brunak. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340:783-795.
11. Berben, G. 1996. Nitrobacter winogradskyi cytochrome c oxidase genes are organized in a repeated gene cluster. Antonie Van Leeuwenhoek 69:305-315.
12. Bergmann, D. J., J. A. Zahn, A. B. Hooper, and A. A. DiSpirito. 1998. Cytochrome P460 genes from the methanotroph Methylococcus capsulatus Bath. J. Bacteriol. 180:6440-6445.
13. Blasco, F., J. P. Dos Santos, A. Magalon, C. Frixon, B. Guigliarelli, C. L. Santini, and G. Giordano. 1998. NarJ is a specific chaperone required for molybdenum cofactor assembly in nitrate reductase A of Escherichia coli. Mol. Microbiol. 28:435-447.
14. Bock, E. 1976. Growth of Nitrobacter in the presence of organic matter. II. Chemoorganotrophic growth of Nitrobacter agilis. Arch. Microbiol. 108:305-312.
15. Bock, E., H.-P. Koops, H. Harms, and B. Ahlers. 1991. The biochemistry of nitrifying organisms, p. 171-200. In J. M. Shively and L. L. Barton (ed.), Variations in autotrophic life. Academic Press, San Diego, Calif.
16. Bock, E., H. P. Koops, and H. Harm. 1986. Cell biology of nitrifiers, p. 17-38. In J. I. Prosser (ed.), Nitrification, vol. 20. IRL, Washington, D.C.
17. Bock, E., P. A. Wilderer, and A. Freitag. 1988. Growth of Nitrobacter in the absence of dissolved oxygen. Water Res. 22:245-250.
18. Boel, G., I. Mijakovic, A. Maze, S. Poncet, M. K. Taha, M. Larribe, E. Darbon, A. Khemiri, A. Galinier, and J. Deutscher. 2003. Transcription regulators potentially controlled by HPr kinase/phosphorylase in Gram-negative bacteria. J. Mol. Microbiol. Biotechnol. 5:206-215.
19. Bottomley, P. J., A. E. Taylor, S. A. Boyle, S. K. McMahon, J. J. Rich, K. Cromack, Jr., and D. D. Myrold. 2004. Responses of nitrification and ammonia-oxidizing bacteria to reciprocal transfers of soil between adjacent coniferous forest and meadow vegetation in the Cascade Mountains of Oregon. Microb. Ecol. 48:500-508.
20. Braun, V., and C. Herrmann. 1993. Evolutionary relationship of uptake systems for biopolymers in Escherichia coli: cross-complementation between the TonB-ExbB-ExbD and the TolA-TolQ-TolR proteins. Mol. Microbiol. 8:261-268.
21. Bren, A., and M. Eisenbach. 2000. How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation. J. Bacteriol. 182:6865-6873.
22. Cannon, G. C., S. H. Baker, F. Soyer, D. R. Johnson, C. E. Bradburne, J. L. Mehlman, P. S. Davies, Q. L. Jiang, S. Heinhorst, and J. M. Shively. 2003. Organization of carboxysome genes in the Thiobacilli. Curr. Microbiol. 46:115-119.
23. Chain, P., J. Lamerdin, F. Larimer, W. Regala, V. Lao, M. Land, L. Hauser, A. Hooper, M. Klotz, J. Norton, L. Sayavedra-Soto, D. Arciero, N. Hommes, M. Whittaker, and D. Arp. 2003. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. J. Bacteriol. 185:2759-2773.
24. Cheesman, M. R., S. J. Ferguson, J. W. Moir, D. J. Richardson, W. G. Zumft, and A. J. Thomson. 1997. Two enzymes with a common function but different heme ligands in the forms as isolated. Optical and magnetic properties of the heme groups in the oxidized forms of nitrite reductase, cytochrome cd1, from Pseudomonas stutzen and Thiosphaera pantotropha. Biochemistry 36:16267-16276.
25. Chen, R., A. A. Bhagwat, R. Yaklich, and D, L. Keister. 2002. Characterization of ndvD, the third gene involved in the synthesis of cyclic beta-(1→3),(1→6)-D-glucans in Bradyrhizobium japonicum. Can. J. Microbiol. 48:1008-1016.
26. Clegg, S., F. Yu, L. Griffiths, and J. A. Cole. 2002. The roles of the polytopic membrane proteins NarK, NarU and NirC in Escherichia coli K-12: two nitrate and three nitrite transporters. Mol. Microbiol. 44:143-155.
27. Cobley, J. G. 1981. Oxidation of nitrite and formate in Nitrobacter membrane preparations: evidence that both reactions are catalyzed by the same enzyme, p. 169-183. In W. R. Strohl and O. H. Tuovinen (ed.), Microbial chemoautotrophy. Ohio State University Press, Columbus, Ohio.
28. Delwiche, C. C., and M. S. Finstein. 1965. Carbon and energy sources for the nitrifying autotroph Nitrobacter. J. Bacteriol. 60:102-107.
29. de Vries, S., and I. Schroder. 2002. Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases. Biochem. Soc. Trans. 30:662-667.
30. Ditty, J. L., A. C. Grimm, and C. S. Harwood. 1998. Identification of a chemotaxis gene region from Pseudomonas putida. FEMS Microbiol. Lett. 159:267-273.
31. Einsle, O., and P. M. H. Kroneck. 2004. Structural basis of denitrification. Biol. Chem. 385:875-883.
32. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
33. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
34. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F, Tomb, B. A. Dougherty, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
35. Frankenberg, N., J. Moser, and D. Jahn. 2003. Bacterial heme biosynthesis and its biotechnological application. Appl. Microbiol. Biotechnol. 63:115-127.
36. Freitag, A., and E. Bock. 1990. Energy conservation in Nitrobacter. FEMS Microbiol. Lett. 66:157-162.
37. Freitag, A., M. Rudert, and E. Bock. 1987. Growth of Nitrobacter by dissimilatoric nitrate reduction. FEMS Microbiol. Lett. 48:105-109.
38. 2. Gene 322:67-75.
39. Gieseke, A., L. Bjerrum, M. Wagner, and R. Amann. 2003. Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm. Environ. Microbiol. 5:355-369.
40. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202.
41. Hancock, R. E., K. Poole, and R. Benz. 1982. Outer membrane protein P of Pseudomonas aeruginosa: regulation by phosphate deficiency and formation of small anion-specific channels in lipid bilayer membranes. J. Bacteriol. 150:730-738.
42. Hendriks, J., A. Oubrie, J. Castresana, A. Urbani, S. Gemeinhardt, and M. Saraste. 2000. Nitric oxide reductases in bacteria. Biochim. Biophys. Acta 1459:266-273.
43. Hofmann, K., and W. Stoffel. 1993. TMbase-A database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374:166.
44. Holtzendorff, J., D. Hung, P. Brende, A. Reisenauer, P. H. Viollier, H. H. McAdams, and L. Shapiro. 2004. Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Science 304:983-987.
45. Hooper, A. B., D. M. Arciero, D. Bergmann, and M. P. Hendrich. 2005. The oxidation of ammonia as an energy source in bacteria in respiration, vol. 2. Springer, Dordrecht, The Netherlands.
46. Horz, H. P., A. Barbrook, C. B. Field, and B. J. Bohannan. 2004. Ammonia-oxidizing bacteria respond to multifactorial global change. Proc. Natl. Acad. Sci. USA 101:15136-15141.
47. Howell, M. L., E. Alsabbagh, J.-F. Ma, U. A. Ochsner, M. G. Klotz, T. J. Beveridge, K. M. Blumenthal, E. C. Niederhoffer, R. E. Morris, D. Needham, G. E. Dean, M. A. Wani, and D. J. Hassett. 2000. AnkB, a periplasmic ankyrin-like protein in Pseudomonas aeruginosa, is required for optimal catalase B (KatB) activity and resistance to hydrogen peroxide. J. Bacteriol. 182:4545-4556.
48. Jendrossek, D., and R. Handrick. 2002. Microbial degradation of polyhydroxyalkanoates. Annu. Rev. Microbiol. 56:403-432.
49. Kang, B. S., and Y. M. Kim. 1999. Cloning and molecular characterization of the genes for carbon monoxide dehydrogenase and localization of molybdopterin, flavin adenine dinucleotide, and iron-sulfur centers in the enzyme of Hydrogenophaga pseudoflava. J. Bacteriol 181:5581-5590.
50. Kirstein, K., and E. Bock. 1993. Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductases. Arch. Microbiol. 160:447-453.
51. Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543-546.
52. Korshunov, S., and J. A. Imlay. 2001. A potential role for periplasmic superoxide dismutase in blocking the penetration of external superoxide into the cytosol of Gram-negative bacteria. Mol. Microbiol. 43:95-106.
53. Kumar, S., and D. J. D. Nicholas. 1982. Assimilation of Inorganic Nitrogen Compounds by Nitrobacter agilis. J. Gen. Microbiol. 128:1795-1801.
54. Li, L., Y. Jia, Q. Hou, T. C. Charles, E. W. Nester, and S. Q. Pan. 2002. A global pH sensor: Agrobacterium sensor protein ChvG regulates acid-inducible genes on its two chromosomes and Ti plasmid. Proc. Natl. Acad. Sci. USA 99:12369-12374.
55. Lipski, A., E. Spieck, A. Makolla, and K. Altendorf. 2001. Fatty acid profiles of nitrite-oxidizing bacteria reflect their phylogenetic heterogeneity. Syst. Appl. Microbiol. 24:377-384.
56. Liu, P., D. Wood, and E. W. Nester. 2005. Phosphoenolpyruvate carboxykinase is an acid-induced, chromosomally encoded virulence factor in Agrobacterium tumefaciens. J. Bacteriol. 187:6039-6045.
57. Lorite, M. J., J. Tachil, J. Sanjuan, O. Meyer, and E. J. Bedmar. 2000. Carbon monoxide dehydrogenase activity in Bradyrhizobium japonicum. Appl. Environ. Microbiol. 66:1871-1876.
58. Macnab, R. M. 1992. Genetics and biogenesis of bacterial flagella. Annu. Rev. Genet. 26:131-158.
59. McFadden, B. A., and J. M. Shively. 1991. Bacterial assimilation of carbon dioxide by the Calvin cycle, p. 25-49. In J. M. Shively and L. L. Burton (ed.), Variations in autotrophic growth. Harcourt Brace Jovanovich, London, England.
60. Merrick, M. J., and J. R. Coppard. 1989. Mutations in genes downstream of the rpoN gene (encoding sigma 54) of Klebsiella pneumoniae affect expression from sigma 54-dependent promoters. Mol. Microbiol. 3:1765-1775.
61. Meyer, O., K. Frunzke, D. Gadkari, S. Jacobitz, I. Hugendieck, and M. Kraut. 1990. Utilization of carbon-monoxide by aerobes-recent advances. FEMS Microbiol. Rev. 87:253-260.
62. Meyer, O., L. Gremer, R. Ferner, M. Ferner, H. Dobbek, M. Gnida, W. Meyer-Klaucke, and R. Huber. 2000. The role of Se, Mo and Fe in the structure and function of carbon monoxide dehydrogenase. Biol. Chem. 381:865-376.
63. Min, B., J. T. Pelaschier, D. E. Graham, D. Tumbula-Hansen, and D. Soll. 2002. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. USA 99:2678-2683.
64. Moeck, G. S., and J. W. Coulton. 1998. TonB-dependent iron acquisition: mechanisms of siderophore-mediated active transport. Mol. Microbiol. 28:675-681.
65. Mogi, T., K. Saiki, and Y. Anraku. 1994. Biosynthesis and functional-role of heme-o and heme-a. Mol. Microbiol. 14:391-398.
66. Moreno-Vivian, C., and S. J. Ferguson. 1998. Definition and distinction between assimilatory, dissimilatory and respiratory pathways. Mol. Microbiol. 29:661-669.
67. Nomoto, T., Y. Fukumori, and T. Yamanaka. 1993. Membrane-bound cytochrome c is an alternative electron donor for cytochrome aa3 in Nitrobacter winogradskyi. J. Bacteriol. 175:4400-4404.
68. Pao, S. S., I. T. Paulsen, and M. H. Saier, Jr. 1998. Major facilitator superfamily. Microbiol. Mol. Biol. Rev. 62:1-34.
69. Poole, K., and R. E. Hancock. 1986. Phosphate-starvation-induced outer membrane proteins of members of the families Enterobacteriaceae and Pseudomonodaceae: demonstration of immunological cross-reactivity with an antiserum specific for porin protein P of Pseudomonas aeruginosa. J. Bacteriol. 165:987-993.
70. Poole, P., and D. Allaway. 2000. Carbon and nitrogen metabolism in Rhizobium. Adv. Microb. Physiol. 43:117-163.
71. Qi, Z., I. Hamza, and M. R. O'Brian. 1999. Heme is an effector molecule for iron-dependent degradation of the bacterial iron response regulator (Irr) protein. Proc. Natl. Acad. Sci. USA 96:13056-13061.
72. Rao, N. N., and A. Torriani. 1990. Molecular aspects of phosphate transport in Escherichia coli. Mol. Microbiol. 4:1083-1090.
73. Richardson, D. J. 2000. Bacterial respiration: a flexible process for a changing environment. Microbiology 146:551-571.
74. Santiago, B., U. Schubel, C. Egelseer, and O. Meyer. 1999. Sequence analysis, characterization and CO-specific transcription of the cox gene cluster on the megaplasmid pHCG3 of Oligotropha carboxidovorans. Gene 236:115-124.
75. Seaver, L. C., and J. A. Imlay. 2001. Hydrogen peroxide fluxes and compartmentalization inside growing Escherichia coli. J. Bacteriol. 7182-7189.
76. Shively, J. M., G. van Keulen, and W. G. Meijer. 1998. Something from almost nothing: carbon dioxide fixation in chemoautotrophs. Annu. Rev. Microbiol. 52:191-230.
77. Simon, J. 2002. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol. Rev. 26:285-309.
78. Skerker, J. M., and L. Shapiro. 2000. Identification and cell cycle control of a novel pilus system in Caulobacter crescentus. EMBO J. 19:3223-3234.
79. Smith, A. J., and D. S. Hoare. 1968. Acetate assimilation by Nitrobacter agilis in relation to its "obligate autotrophy." J. Bacteriol. 95:844-855.
80. Sockett, H., S. Yamaguchi, M. Kihara, V. M. Irikura, and R. M. Macnab. 1992. Molecular analysis of the flagellar switch protein FliM of Salmonella typhimurium. J. Bacteriol. 174:793-806.
81. Spieck, E., J. Aamand, S. Bartosch, and E. Bock. 1996. Immunocytochemical detection and location of the membrane-bound nitrite oxidoreductase in cells of Nitrobacter and Nitrospira. FEMS Microbiol. Lett. 139:71-76.
82. Spieck, E., S. Muller, A. Engel, E. Mandelkow, H. Patel, and E. Bock. 1996. Two-dimensional structure of membrane-bound nitrite oxidoreductase from Nitrobacter hamburgensis. J. Struct. Biol. 117:117-123.
83. Steinmuller, W., and E. Bock. 1977. Enzymatic studies on autotrophically, mixotrophically and heterotrophically grown Nitrobacter agilis with special reference to nitrite oxidase. Arch. Microbiol. 115:51-54.
84. Steinmuller, W., and E. Bock. 1976. Growth of Nitrobacter in the presence of organic matter. I. Mixotrophic growth. Arch. Microbiol. 108:299-304.
85. Stroud, R. M., D. Savage, L. J. Miercke, J. K. Lee, S. Khademi, and W. Harries. 2003. Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. FEBS Lett. 555:79-84.
86. Svensson, B., and L. Hederstedt. 1994. Bacillus subtilis CTaA is a heme-containing membrane protein involved in heme A biosynthesis. J. Bacteriol. 176:6663-6671.
87. Tanaka, Y., Y. Fukumori, and T. Yamanaka. 1982. The complete amino acid sequence of Nitrobacter agilis cytochrome c-550. Biochim. Biophys. Acta 707:14-20.
88. 1 from Nitrobacter agilis and characterization of nitrite oxidation system of the bacterium. Arch. Microbiol. 135:265-271.
89. Teske, A., E. Alm, J. M. Regan, S. Toze, B. E. Rittmann, and D. A. Stahl. 1994. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J. Bacteriol. 176:6623-6630.
90. Tikhonovich, I. A. 1995. Nitrogen fixation: fundamentals and applications. Proceedings of the 10th International Congress on Nitrogen Fixation. Kluwer Academic Publishers, Boston, Mass.
91. Todd, J. D., M. Wexler, G. Sawers, K. H. Yeoman, P. S. Poole, and A. W. Johnston. 2002. RirA, an iron-responsive regulator in the symbiotic bacterium Rhizobium leguminosarum. Microbiology 148:4059-4071.
92. Vergnes, A., K. Gouffi-Belhabich, F. Blasco, G. Giordano, and A. Magalon. 2004. Involvement of the molybdenum cofactor Biosynthetic machinery in the maturation of the Escherichia coli nitrate reductase A. J. Biol. Chem. 279:41398-41403.
93. Voegele, R. T., S. Bardin, and T. M. Finan. 1997. Characterization of the Rhizobium (Sinorhizobium) meliloti high- and low-affinity phosphate uptake systems. J. Bacteriol. 179:7226-7232.
94. von Heijne, G. 1992. Membrane protein structure prediction, hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225:487-494.
95. Wanner, B. L. 1993. Gene regulation by phosphate in enteric bacteria. J. Cell Biochem. 51:47-54.
96. Watson, S. W., E. Bock, H. Harms, H. P. Koops, and A. B. Hooper. 1989. Genera of nitrite-oxidizing bacteria, p. 1813-1822. In J. T. Staley (ed.), Bergey's manual of systematic bacteriology, vol. 3. Williams and Wilkins, Baltimore, Md.
97. Withers, H., S. Swift, and P. Williams. 2001. Quorum sensing as an intergral component of gene regulatory networks in Gram-negative bacteria. Curr. Opin. Microbiol. 4:186-193.
98. Wood, N. J., T. Alizadeh, D. J. Richardson, S. J. Ferguson, and J. W. B. Moir. 2002. Two domains of a dual-function NarK protein are required for nitrate uptake, the first step of denitrification in Paracoccus pantotrophus. Mol. Microbiol. 44:157-170.
99. Wylie, J. L., and E. A. Worobec. 1995. The OprB porin plays a central role in carbohydrate uptake in Pseudomonas aeruginosa. J. Bacteriol. 177:3021-3026.
100. Yamanaka, T. 1996. Mechanisms of oxidation of inorganic electron donors in autotrophic bacteria. Plant Cell Physiol. 37:569-574.
101. Yamanaka, T., and Y. Fukumori. 1988. The nitrite oxidizing system of Nitrobacter winogradskyi. FEMS Microbiol. Rev. 54:259-270.
102. Yamanaka, T., Y. Tanaka, and Y. Fukumori. 1982. Nitrobacter agilis cytochrome c-550: Isolation, physiochemical and enzymatic properties and primary structure. Plant Cell Physiol. 23:441-449.
103. Yao, S. Y., L. Luo, K. J. Har, A. Becker, S. Ruberg, G. Q. Yu, J. B. Zhu, and H. P. Cheng. 2004. Sinorhizobium meliloti ExoR and ExoS proteins regulate both succinoglycan and flagellum production. J. Bacteriol. 186:6042-6049.
104. Yu, X. C., and W. Margolin. 2000. Deletion of the min operon results in increased thermosensitivity of an ftsZ84 mutant and abnormal FtsZ ring assembly, placement, and disassembly. J. Bacteriol. 182:6203-6213.
105. Zumft, W. G., and H. Korner. 1997. Enzyme diversity and mosaic gene organization in denitrification. Antonie van Leeuwenhoek 71:43-58.