Chapter 28 : Anaerobiosis

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This chapter on anaerobiosis talks about that can respond to changes in oxygen availability and redox state by changing metabolic direction in favor of anaerobiosis. During anaerobiosis, degradation of arginine occurs via the arginine deiminase pathway rather than the aerobic arginase pathway. Many genes required for antibiotic production are induced by anaerobiosis. Unlike , which is slightly repressed by anaerobiosis, expression of is highly induced by anaerobiosis. All of the ResDE-dependent genes tested show higher expression during anaerobiosis than during aerobiosis. Nitrate respiration of makes sense from an ecological standpoint because soil, a natural habitat for , contains numerous anaerobic microenvironments, especially when water content is high, and also contains an abundant source of nitrate and nitrite. Studies of anaerobiosis offer great promise for potential applications in the biomedical and biotechnology fields. Knowledge of anaerobic metabolism is useful for the fermentation industry to plan strategies for improved product yield and metabolic engineering by redirection of metabolic flows. Anaerobiosis of microorganisms in soil plays a key role in ecosystem homeostasis and affects atmospheric composition through the formation of trace gases.

Citation: Nakano M, Zuber P. 2002. Anaerobiosis, p 393-404. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch28

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Two-Component Signal Transduction Systems
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Fermentation pathways of . The fermentation end products are shown in bold. Genes known to code for the enzymes involved in fermentation are shown in parentheses. Abbreviations: ACK, acetate kinase; ADH, alcohol dehydrogenase; ALDC, α-acetolactate decarboxylase; ALDH, aldehyde dehydrogenase; ALS, α-acetolactate synthase; AR, acetoin reductase; LDH, L-lactate dehydrogenase; PTA, phosphotransacetylase; CoA, coenzyme A.

Citation: Nakano M, Zuber P. 2002. Anaerobiosis, p 393-404. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch28
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Image of FIGURE 2

Regulatory pathways for redox-dependent gene expression in . Genes in boldface represent regulatory genes. Genes dependent on ResDE, FNR, and YwiD (ArfM) are shown in the boxes, although in some cases it is unknown whether these regulators are directly involved in the expression of the target genes. YwfI protein level is not significantly affected by a mutation ( ). Details are described in the text.

Citation: Nakano M, Zuber P. 2002. Anaerobiosis, p 393-404. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch28
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1. Albertini, A. M.,, T. Caramori,, F. Scoffone,, C. Scotti,, and A. Galizzi. 1995. Sequence around the 159 degree region of the Bacillus subtilis genome: the pksX locus spans 33.6 kb. Microbiology 141:299309.
2. Antelmann, H.,, S. Engelmann,, R. Schmid,, and M. Hecker. 1996. General and oxidative stress responses in Bacillus subtilis: cloning, expression, and mutation of the alkyl hydroperoxide reductase operon. J. Bacteriol. 178: 65716578.
3. Antelmann, H.,, S. Engelmann,, R. Schmid,, A. Sorokin,, A. Lapidus,, and M. Hecker. 1997. Expression of a stress-and starvation-induced dpslpexB-homologous gene is controlled by the alternative sigma factor sigmaB in Bacillus subtilis. J. Bacteriol. 179:72517256.
4. Azarkina, N.,, S. Siletsky,, V. Borisov,, C. von Wachenfeldt,, L. Hederstedt,, and A. A. Konstantinov. 1999. A cytochrome bb'-type quinol oxidase in Bacillus subtilis strain 168. J. Biol. Chem. 274:3281032817.
5. Babasaki, K.,, T. Takao,, Y. Shimonishi,, and K. Kurahashi. 1985. Subtilosin A, a new antibiotic peptide produced by Bacillus subtilis 168: isolation, structural analysis, and biogenesis. J. Biochem. 98:585603.
6. Bauer, C. E.,, S. Elsen,, and T. H. Bird. 1999. Mechanisms for redox control of gene expression. Annu. Rev. Microbiol. 53:495523.
7. Blasco, F.,, J.-P. D. 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. 28:435447.
8. Bock, A.,, and G. Sawers,. 1996. Fermentation, p. 262282. In F. C. Neidhardt,, R. Curtis III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, vol. I. ASM Press, Washington, D.C.
9. Boone, D. R.,, Y. Liu,, Z. J. Zhao,, D. L. Balkwill,, G. R. Drake,, T. O. Stevens,, and H. C. Aldrich. 1995. Bacillus infemus sp. nov., an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int. J. Syst. Bacteriol. 45:441448.
10. Broman, K.,, N. Lauwers,, V. Stalon,, and J.-M. Wiame. 1978. Oxygen and nitrate utilization by Bacillus licheniformis of the arginase and arginine deiminase routes of arginine catabolism and other factors affecting their synthesis. J. Bacteriol. 135:920927.
11. Buggy, J.,, and C. E. Bauer. 1995. Cloning and characterization of senC, a gene involved in both aerobic respiration and photosynthesis gene expression in Rhodobacter capsufotus. J. Bacteriol. 177:69586965.
12. Chen, L.,, and J. D. Helmann. 1995. Bacillus subtilis MrgA in a Dps (PexB) homologue: evidence for metalloregulation of an oxidative-stress gene. Mol. Microbiol. 18: 295300.
13. Cole, J. 1996. Nitrate reduction to ammonia by enteric bacteria: redundancy, or a strategy for survival during oxygen starvation? FEMS Microbiol. Lett. 136:111.
14. Conrad, R. 1996. Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol. Rev. 60:609640.
15. Cramm, R.,, R. A. Siddiqui,, and B. Friedrich. 1994. Primary sequence and evidence for a physiological function of the flavohemoprotein of Alcaligenes eutrophus. J. Biol. Chem. 269:73497354.
16. Crawford, M. J.,, and D. E. Goldberg. 1998. Role for Salmonella flavohemoglobin in protection from nitric oxide. J. Biol. Chem. 273:1254312547.
17. Cronan, J., Jr.,, and D. LaPorte,. 1996. Tricarboxylic acid cycle and glyoxylate bypass, p. 206216. In F. C. Neidhardt,, R. Curtis III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, vol. 1. ASM Press, Washington, D.C.
18. Cruz Ramos, H.,, L. Boursier,, I. Moszer,, F. Kunst,, A. Danchin,, and P. Glaser. 1995. Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and -independent regulatory mechanisms. EMBO J. 14:59845994.
19. Cruz Ramos, H.,, T. Hoffmann,, M. Marino,, H. Nedjari,, E. Presecan-Siedel,, O. Dressen,, P. Glaser,, and D. Jahn. 2000. Fermentative metabolism of Bacillus subtilis: physiology and regulation of gene expression. J. Bacteriol. 182: 30723080.
20. Cunningham, L.,, M. J. Gruer,, and J. R. Guest. 1997. Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. Microbiology 143:37953805.
21. Diels, L.,, M. De Smet,, L. Hooyberghs,, and P. Corbisier. 1999. Heavy metals bioremediation of soil. Mol. Biotechnol. 12:149158.
22. Drzewiecki, K.,, C. Eymann,, G. Mittenhuber,, and M. Hecker. 1998. The yvyD gene of Bacillus subtilis is under dual control of σB and σH. J. Bacteriol. 180:66746680.
23. Ebbole, D. J.,, and H. Zalkin. 1987. Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. J. Biol. Chem. 262:82748287.
24. Fabret, C.,, V. A. Feher,, and J. A. Hoch. 1999. Two-corn ponent signal transduction in Bacillus subtilis: how one organism sees its world. J. Bacteriol. 181:19751983.
25. Fotheringham, I. 2000. Engineering biosynthetic pathways: new routes to chiral amino acids. Curr. Opin. Chem. Biol. 4:120124.
26. Fouet, A.,, S. Jin,, G. Raffel,, and A. L. Sonenshein. 1990. Multiple regulatory sites in the Bacillus subtilis citB promoter region. J. Bacteriol. 172:54085415.
27. Fouet, A.,, and A. L. Sonenshein. 1990. A target for carbon source-dependent negative regulation of the ritB promoter of Bacillus subtilis. J. Bacteriol. 172:835844.
28. Gardner, P. R.,, A. M. Gardner,, L. A. Martin,, and A. L. Salzman. 1998. Nitric oxide dioxygenase: an enzymic function for flavohemoglobin. Proc. Natl. Acad. Sci. USA 95:1037810383.
29. Gennis, R. B.,, and V. Stewart,. 1996. Respiration, p. 217261. In F. C. Neidhardt,, R. Curtis III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, vol. I. ASM Press, Washington, D.C.
30. Georgellis, D.,, O. Kwon,, and E. C. C. Lin. 1999. Amplification of signaling activity of the Arc two-component system of Escherichia coli by anaerobic metabolites. J. Biol. Chem. 274:3595035954.
31. Georgellis, F.,, A. S. Lynch,, and E. C. C. Lin. 1997. In vitro phosphorylation study of the Arc two-component signal transduction system of Escherichia coli. J. Bacteriol. 179: 54295435.
32. Glaser, P.,, A. Danchin,, F. Kunst,, P. Zuber, and M. M. Nakano. 1995. Identification and isolation of a gene required for nitrate assimilation and anaerobic growth of Bacillus subtilis. J. Bacteriol. 177:11121115.
33. Gostick, D. O.,, J. Green,, A. S. Irvine,, M. J. Gasson,, and J. R. Guest. 1998. A novel regulatory switch mediated by the FNR-like protein of Lactobacillus casei. Microbiology 144:705717.
34. Gostick, D. O.,, H. G. Griffin,, C. A. Shearman,, C. Scott,, J. Green,, M. J. Gasson,, and J. R. Guest. 1999. Two operons that encode FNR-like proteins in Lactococcus lactis. Mol. Microbiol. 31:15231535.
35. Gruer, M. J.,, A. J. Bradbury,, and J. R. Guest. 1997. Construction and properties of aconitase mutants of Escherichia coli. Microbiology 143:18371846.
36. Hansson, M.,, and L. Hederstedt. 1992. Cloning and characterization of the Bacillus subtilis hemEHY gene cluster, which encodes protoheme IX biosynthetic enzymes. J. Bacteriol. 174:80818093.
37. Hausladen, A.,, A. J. Gow,, and J. S. Stamler. 1998. Nitrosative stress: metabolic pathway involving the flavohemoglobin. Proc. Natl. Acad. Sci. USA 95:1410014105.
38. Hemila, H.,, A. Palva,, L. Paulin,, S. Arvidson,, and I. Palva. 1990. Secretory S complex of Bacillus subtilis: sequence analysis and identity to pyruvate dehydrogenase. J. Bacteriol. 172:50525063.
39. Hippler, B.,, G. Homuth,, T. Hoffman,, C. Hungerer,, W. Schumann,, and D. Jahn. 1997. Characterization of Bacillus subtilis hemN. J. Bacteriol. 179:71817185.
40. Hoffmann, T.,, N. Frankenberg,, M. Marino,, and D. Jahn. 1998. Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J. Bacteriol. 180:186189.
41. Hoffmann, T.,, B. Troup,, A. Szabo,, C. Hungerer,, and D. Jahn. 1995. The anaerobic life of Bacillus subtilis: cloning of the genes encoding the respiratory nitrate reductase system. FEMS Microbiol. Lett. 131:219225.
42. Højberg, O.,, U. Schnider,, H. V. Winteler,, J. Sørensen,, and D. Haas. 1999. Oxygen-sensing reporter strain of Pseudomonas fluorescens for monitoring the distribution of low-oxygen habitats in soil. Appl. Environ. Microbiol. 65: 40854093.
43. Holmberg, C.,, L. Beijer,, B. Rutberg,, and L. Rutberg. 1990. Glycerol catabolism in Bacillus subtilis: nucleotide sequence of the genes encoding glycerol kinase (glpK) and glycerol-3-phosphate dehydrogenase (glpD). J. Gen. Microbiol. 136:23672375.
44. Homuth, G.,, U. Mader,, M. Marino,, D. Jahn,, and M. Hecker. Unpublished results.
45. Homuth, G.,, A. Rompf,, W. Schumann,, and D. Jahn. 1999. Transcriptional control of Bacillus subtilis hemN and hemZ. J. Bacteriol. 181:59225929.
46. Hou, S.,, R. W. Larsen,, D. Boudko,, C. W. Riley,, E. Karatan,, M. Zimmer,, G. W. Ordal,, and M. Alan. 2000. Myoglobin-like aerotaxis transducers in Archaea and Bacteria. Nature 403:540544
47. Hu, Y.,, P. D. Butcher,, J. A. Mangan,, M.-A. Rajandream,, and A. R. M. Coates. 1999. Regulation of hmp gene transcription in Mycobacterium tuberculosis: effects of oxygen limitation and nitrosative and oxidative stress. J. Bacteriol. 181:34863493.
48. Hugenholtz, J.,, and M. Kleerebezem. 1999. Metabolic engineering of lactic acid bacteria: overview of the approaches and results of pathway rerouting involved in food fermentations. Curr. Opin. Biotechnol. 10:492497.
49. Hulett, F. M. 1996. The signal-transduction network for Pho regulation in Bacillus subtilis. Mol. Microbiol. 19:933939.
50. Ishige, K.,, S. Nagasawa,, S. Tokishita,, and T. Mizuno. 1994. A novel device of bacterial signal transducers. EMBO J. 13:51955202.
51. luchi, S. 1993. Phosphorylation/dephosphorylation of the receiver module at the conserved aspartate residue controls transphosphorylation activity of histidine kinase in sensor protein ArcB of Escherichia coli. J. Biol. Chem. 268:2397223980.
52. luchi, S.,, and E. C. C. Lin. 1988. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc. Natl. Acad. Sci. USA 85:18881892.
53. Jourlin-Castelli, C.,, N. Mani,, M. M. Nakano,, and A. L. Sonenshein. 2000. CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. J. Mol. Biol. 295:865878.
54. Keasling, J. D. 1999. Gene-expression tools for the metabolic engineering of bacteria. Trends Biotechnol. 17: 452460.
55. Khoroshilova, N.,, C. Popescu,, E. Munck,, H. Beinert,, and P. J. Kiley. 1997. Iron-sulfur cluster disassembly in the FNR protein of Escherichia coli by O2: [4Fe-4S] to [2Fe-2S] conversion with loss of biological activity. Proc. Natl. Acad. Sci. USA 94:60876092.
56. Kiley, P. J.,, and H. Beinert. 1999. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiol. Rev. 22:341352.
57. Kim, S. O.,, Y. Orii,, D. Lloyd,, M. N. Hughes,, and R. K. Poole. 1999. Anoxic function for the Escherichia coli flavohaemoglobin (Hmp): reversible binding of nitric oxide and reduction to nitrous oxide. FEBS Lett. 445:389394.
58. Klinger, A.,, J. Schirawski,, P. Glaser,, and G. Unden. 1998. The fnr gene of Bacillus licheniformis and the cysteine ligands of the C-terminal FeS cluster. J. Bacteriol. 180:34833485.
59. Kwon, O.,, M. E. S. Hudspeth,, and R. Meganathan. 1996. Anaerobic biosynthesis of enterobactin in Escherichia coli: regulation of entC gene expression and evidence against its involvement in menaquinone (vitamin K2) biosynthesis. J. Bacteriol. 178:32523259.
60. LaCelle, M.,, M. Kumano,, K. Kurita,, K. Yamane,, P. Zuber,, and M. M. Nakano. 1996. Oxygen-controlled regulation of the flavohemoglobin gene in Bacillus subtilis. J. Bacteriol. 178:38033808.
61. Lazazzera, B. A.,, D. M. Bates,, and P. J. Kiley. 1993. The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Genes Dev. 7:19932005.
62. Liu, X.,, and H. W. Taber. 1998. Catabolite regulation of the Bacillus subtilis ctaBCDEF gene cluster. J. Bacteriol. 180:61546163.
63. Lovley, D. R.,, and J. D. Coates. 1997. Bioremediation of metal contamination. Curr. Opin. Biotechnology 8:285289.
64. Lovley, D. R.,, and J. D. Coates. 2000. Novel forms of anaerobic respiration of environmental relevance. Curr. Opin. Microbiol. 3:252256.
65. Lynch, A. S.,, and E. C. C. Lin,. 1996. Responses to molecular oxygen, p. 15261538. In F. C. Neidhardt,, R. Curtis III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, vol. I. ASM Press, Washington, D.C.
66. Maghnouj, A.,, T. F. de Sousa Cabral,, V. Stalon,, and C. Vander Wauven. 1998. The arcABDC gene cluster, encoding the arginine deiminase pathway of Bacillus licheniformis, and its activation by the arginine repressor ArgR. J. Bacteriol. 180:64686475.
67. Maklashina, E.,, D. A. Berthold,, and G. Cecchini. 1998. Anaerobic expression of Escherichia coli succinate dehydrogenase: functional replacement of fumarate reductase in the respiratory chain during anaerobic growth. J. Bacteriol. 180:59895996.
68. Marino, M.,, T. Hoffmann,, R. Schmid,, H. Mobitz,, and D. Jahn. 2000. Changes in protein synthesis during the adaptation of Bacillus subtilis to anaerobic growth conditions. Microbiology 146:97105.
69. Mat-Jan, F.,, K. Y. Alam,, and D. P. Clark. 1989. Mutants of Escherichia coli deficient in the fermentative lactate dehydrogenase. J. Bacteriol. 171:342348.
70. Matsushika, A.,, and T. Mizuno. 1998. A dual-signaling mechanism mediated by the ArcB hybrid sensor kinase containing the histidine-containing phosphotransfer domain in Escherichia coli. J. Bacteriol. 180:39733977.
71. May, S. W. 1999. Applications of oxidoreductases. Curr. Opin. Biotechnol. 10:370375.
72. Membrillo-Hernandez, J.,, M. D. Coopamah,, M. F. Anjum,, T. M. Stevanin,, A. Kelly,, M. N. Hughes,, and R. K. Poole. 1999. The flavohemoglobin of Escherichia coli confers resistance to a nitrosating agent, a “nitric oxide releaser,” and paraquat and is essential for transcriptional responses to oxidative stress. J. Biol. Chem. 274:748754.
73. Mitchell, W. J. 1998. Physiology of carbohydrate to solvent conversion by Clostridia. Adv. Microb. Physiol. 39:31130.
74. Moreno-Vivian, C.,, P. Cabello,, M. Martinez-Luque,, R. Blasco,, and F. Castillo. 1999. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J. Bacteriol. 181: 65736584.
75. Mueller, J. P.,, and H. W. Taber. 1989. Isolation and sequence of ctaA, a gene required for cytochrome aa3 biosynthesis and sporulation in Bacillus subtilis. J. Bacteriol. 171: 49674978.
76. Nakano, M. M. Unpublished results.
77. Nakano, M. M.,, Y. P. Dailly,, P. Zuber,, and D. P. Clark. 1997. Characterization of anaerobic fermentative growth in Bacillus subtilis: identification of fermentation end products and genes required for the growth. J. Bacteriol. 179: 67496755.
78. Nakano, M. M.,, T. Hoffmann,, Y. Zhu,, and D. Jahn. 1998. Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrAandResDE. J. Bacteriol. 180:53445350.
79. Nakano, M. M.,, and F. M. Hulett. 1997. Adaptation of Bacillus subtilis to oxygen limitation. FEMS Microbiol. Lett. 157:17.
80. Nakano, M. M.,, F. Yang,, P. Hardin,, and P. Zuber. 1995. Nitrogen regulation of nasA and the nasB operon, which encode genes required for nitrate assimilation in Bacillus subtilis. J. Bacteriol. 177:573579.
81. Nakano, M. M.,, G. Zheng,, and P. Zuber. 2000. Dual control of sbo-alb operon expression by the Spo0 and ResDE systems of signal transduction under anaerobic conditions in Bacillus subtilis. J. Bacteriol. 182:32743277.
82. Nakano, M. M.,, Y. Zhu,, K. Haga,, H. Yoshikawa,, A. L. Sonenshein,, and P. Zuber. 1999. A mutation in the 3-phosphoglycerate kinase gene bypasses the requirement of ResE kinase for anaerobic growth in Bacillus subtilis. J. Bacteriol. 181:70877097.
83. Nakano, M. M.,, Y. Zhu,, M. LaCelle,, X. Zhang,, and F. M. Hulett. 2000. Interaction of ResD with regulatory regions of anaerobically induced genes in Bacillus subtilis. Mol. Microbiol. 37:11981207.
84. Nakano, M. M.,, and P. Zuber. 1998. Anaerobic growth of a “strict aerobe” (Bacillus subtilis). Annu. Rev. Microbiol. 52:165190.
85. Nakano, M. M.,, P. Zuber,, P. Glaser,, A. Danchin,, and F. M. Hulett. 1996. Two-component regulatory proteins ResD-ResE are required for transcriptional activation of fnr upon oxygen limitation in Bacillus subtilis. J. Bacteriol. 178:37963802.
86. Nakano, M. M.,, P. Zuber,, and A. L. Sonenshein. 1998. Anaerobic regulation of Bacillus subtilis Krebs cycle genes. J. Bacteriol. 180:33043311.
87. Neubauer, H.,, I. Pantel,, and F. Gotz. 1999. Molecular characterization of the nitrite-reducing systems of Staphylococcus carnosus. J. Bacteriol. 181:14811488.
88. O'Gara, J. P.,, J. M. Eraso,, and S. Kaplan. 1998. A redox-responsive pathway for aerobic regulation of photosynthesis gene expression in Rhodobacter sphaeroides 2.4.1. J. Bacteriol. 180:40444050.
89. Ogawa, K.,, E. Akagawa,, K. Yamane,, Z.-W. Sun,, M. LaCelle,, P. Zuber,, and M. M. Nakano. 1995. The nosB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtitis. J. Bacteriol. 177:14091413.
90. Oh, J.-I.,, and S. Kaplan. 1999. The cbb3 terminal oxidase of Rhodobacter sphaeroides 2.4.1: structural and functional implications for the regulation of spectral complex formation. Biochemistry 38:26882696.
91. Oh, J. I.,, and S. Kaplan. 2000. Redox signaling: globalization of gene expression. EMBO J. 19:42374247.
92. Paik, S. H.,, A. Chakicherla,, and J. N. Hansen. 1998. Identification and characterization of the structural and transporter genes for, and the chemical and biological properties of, sublancin 168, a novel lantibiotic produced by Bacillus subtilis 168. J. Biol. Chem. 273:2313423142.
93. Park, S.-J.,, J. McCabe,, J. Turna,, and R. P. Gunsalus. 1994. Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: role of the arcA gene product. J. Bacteriol. 176:50865092.
94. Paul, E. A.,, and F. E. Clark. 1989. Soil Microbiology and Biochemistry. Academic Press, San Diego, Calif.
95. Poole, R. K.,, and M. N. Hughes. 2000. New functions for the ancient globin family: bacterial responses to nitric oxide and nitrosative stress. Mol. Microbiol. 36:775783.
96. Popescu, C. V.,, D. M. Bates,, H. Beinert,, E. Munck,, and P. J. Kiley. 1998. Mossbauer spectroscopy as a tool for the study of activation/inactivation of the transcription regulator FNR in whole cells of Escherichia coli. Proc Natl. Acad. Sci. USA 95:1343113435.
97. Priest, F. G., 1993. Systematics and ecology of Bacillus, p. 316. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D.C.
98. Quinn, C. L.,, B. T. Stephenson,, and R. L. Switzer. 1991. Functional organization and nucleotide sequence of the Bacillus subtilis pyrimidine biosynthetic operon. J. Biol. Chem. 266:91139127.
99. Rajagopalan, K. V. 1997. Biosynthesis and processing of the molybdenum cofactors. Biochem. Soc. Trans. 25:757761.
100. Renna, M. C.,, N. Najimudin,, L. R. Winik,, and S. A. Zahler. 1993. Regulation of the Bacillus subtilis alsS, alsD, and ahR genes involved in post-exponential-phase production of acetoin. J. Bacteriol. 175:38633875.
101. Richardson, D. J. 2000. Bacterial respiration: a flexible process for a changing environment. Microbiology 146: 551571.
102. Roe, B. Unpublished results.
103. Rowland, B. M.,, T. H. Grossman,, M. S. Osburne,, and H. W. Taber. 1996. Sequence and genetic organization of a Bacillus subtilis operon encoding 2,3-dihydroxybenzoate biosynthetic enzymes. Gene 178:119123.
104. Santana, M.,, F. Kunst,, M. F. Hullo,, G. Rapoport,, A. Danchin,, and P. Glaser. 1992. Molecular cloning, sequencing, and physiological characterization of the qpx operon from Bacillus subtilis encoding the aa3-600 quinol oxidase. J. Biol. Chem. 267:1022510231.
105. Sawers, G. 1999. The aerobic/anaerobic interface. Curr. Opin. Microbiol. 2:181187.
106. Schirawski, J.,, T. Hankeln,, and G. Unden. 1998. Expression of the succinate dehydrogenase genes (sdhCAB) from the facultatively anaerobic Paenibacillus macerans during aerobic growth. Arch. Microbiol. 170:304308.
107. Schirawski, J.,, and G. Unden. 1995. Anaerobic respiration of Bacillus macerans with fumarate, TMAO, nitrate and nitrite and regulation of the pathways by oxygen and nitrate. Arch. Miaobiol. 163:148154.
108. Schneider, R.,, and K. Hantke. 1993. Iron-hydroxamate uptake systems in Bacillus subtilis: identification of a lipoprotein as part of a binding protein-dependent transport system. Mol. Microbiol. 8:111121.
109. Schumann, W. 1999. FtsH—a single-chain charonin? FEMS Microbiol. Rev. 23:111.
110. Scotti, C.,, M. Piatti,, A. Cuzzoni,, P. Perani,, A. Tognoni,, G. Grandi,, A. Galizzi,, and A. M. Albertini. 1993. A Bacillus subtilis large ORF coding for a polypeptide highly similar to polyketide synthases. Gene 130:6571.
111. Semenza, G. L. 1999. Perspectives on oxygen sensing. Cell 98:281284.
112. Shariati, P.,, W. J. Mitchell,, A. Boyd,, and F. G. Priest. 1995. Anaerobic metabolism in Bacillus licheniformis NCIB 6346. Microbiology 141:11171124.
113. Sorokin, A.,, E. Zumstein,, V. Azevedo,, S. D. Ehrlich,, and P. Serror. 1993. The organization of the Bacillus subtilis 168 chromosome region between the spoVA and serA genetic loci, based on sequence data. Mol. Microbiol. 10: 385395.
114. Speck, E. L.,, and E. Freese. 1973. Control of metabolite secretion in Bacillus subtilis. J. Gen. Microbiol. 78:261275.
115. Stewart, V. 1993. Nitrate regulation of anaerobic respiratory gene expression in Escherichia coli. Mol. Microbiol. 9: 425434.
116. Strauch, M. A.,, G. B. Spiegelman,, M. Perego,, W. C. Johnson,, D. Burbulys,, and J. A. Hoch. 1989. The transition state transcription regulator abrB of Bacillus subtilis is a DNA binding protein. EMBO J. 8:16151621.
117. Sun, D.,, and P. Setlow. 1991. Cloning, nucleotide sequence, and expression of the Bacillus subtilis ans operon, which codes for L-asparaginase and L-aspartase. J. Bacteriol. 173:38313845.
118. Sun, G.,, S. M. Birkey,, and F. M. Hulett. 1996. Three two-component signal-transduction systems interact for Pho regulation in Bacillus subtilis. Mol. Microbiol. 19:942948.
119. Sun, G.,, E. Sharkova,, R. Chesnut,, S. Birkey,, M. F. Duggan,, A. Sorokin,, P. Pujic,, S. D. Ehrlich,, and F. M. Hulett. 1996. Regulators of aerobic and anaerobic respiration in Bacillus subtilis. J. Bacteriol. 178:13741385.
120. Switzer Blum, J.,, A. Burns Bindi,, J. Buzzelli,, J. F. Stolz,, and R. S. Oremland. 1998. Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloalkaliphiles from Mono Lake, California that respire oxyan-ions of selenium and arsenite. Arch. Microbiol. 171:1930.
121. Taylor, B. L.,, and I. B. Zhulin. 1998. In search of higher energy: metabolism-dependent behaviour in bacteria. Mol. Microbiol. 28:683690.
122. Taylor, B. L.,, I. B. Zhulin,, and M. S. Johnson. 1999. Aerotaxis and other energy-sensing behavior in bacteria. Annu. Rev. Microbiol. 53:103128.
123. Throne-Hoist, M.,, and L. Hederstedt. 2000. The Bacillus subtilis ctaB paralogue, yjdK, can complement the heme A synthesis deficiency of a CtaB-deficient mutant. FEMS Microbiol. Lett. 183:247251.
124. Tobisch, S.,, D. Zuhlke,, J. Bernhardt,, J. Stulke,, and M. Hecker. 1999. Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J. Bacteriol. 181:69967004.
125. Tsuzuki, M.,, K. Ishige,, and T. Mizuno. 1995. Phosphotransfer circuitry of the putative multi-signal transducer, ArcB, of Escherichia coli: in vitro studies with mutants. Mol. Microbiol. 18:953962.
126. Unden, G.,, and J. Schirawski. 1997. The oxygen-responsive transcriptional regulator FNR of Escherichia coli: the search for signals and reactions. Mol. Microbiol. 25: 205210.
127. Vollack, K.-U.,, E. Harting,, H. Korner,, and W. G. Zumft. 1999. Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes. Mol. Microbiol. 31:16811694.
128. Weber, I.,, C. Fritz,, S. Ruttkowski,, A. Kreft,, and F.-C. Bange. 2000. Anaerobic nitrate reductase (narGHJI) activity of Mycobacterium bovis BCG in vitro and its contribution to virulence in immunodeficient mice. Mol. Microbiol. 35:10171025.
129. Williams, S. B.,, and V. Stewart. 1999. Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction. Mol. Microbiol. 33:10931102.
130. Willner, I.,, and E. Katz. 2000. Integration of layered redox proteins and conductive supports for bioelectronic applications. Angew. Chem. Int. Ed. Engl. 39:11801218.
131. Wimpenny, J. W. T.,, and J. P. Coombs. 1983. Penetration of oxygen into bacterial colonies. J. Gen. Microbiol. 129:12391242.
132. Winstedt, L.,, K. Yoshida,, Y. Fujita,, and C. von Wachenfeldt. 1998. Cytochrome bd biosynthesis in Bacillus subtilis: characterization of the cydABCD operon. J. Bacteriol. 180:65716580.
133. Wong, L. S.,, M. S. Johnson,, I. B. Zhulin,, and B. L. Taylor. 1995. Role of methylation in aerotaxis in Bacillus subtilis. J. Bacteriol. 177:39853991.
134. Wray, L. V., Jr.,, A. E. Ferson,, K. Rohrer,, and S. H. Fisher. 1996. TnrA, a transcription factor required for global nitrogen regulation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 93:88418845.
135. Wu, Q.,, G. D. Storrier,, F. Pariente,, Y. Wang,, J. P. Shapleigh,, and H. D. Abruna. 1997. A nitrite biosensor based on a maltose binding protein nitrite reductase fusion immobilized on an electropolymerized film of a pyrrole-derived bipyridinium. Anal. Chem. 69:48564863.
136. Ye, R. W. Unpublished results.
137. Ye, R. W.,, W. Tao,, L. Bedzyk,, T. Young,, M. Chen,, and L. Li. 2000. Global gene expression profiles of Bacillus subtilis grown under anaerobic conditions. J. Bacteriol. 182:44584465.
138. Young, M.,, and S. T. Cole,. 1993. Clostridium, p. 3563. In A. L. Sonenshein,, J. A. Hoch,, and R. Losick (ed.), Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics. American Society for Microbiology, Washington, D. C.
139. Yu, J.,, L. Herderstedt,, and P. J. Piggot. 1995. The cytochrome be complex (menaquinonexytochrome c reductase) in Bacillus subtilis has a nontraditional subunit organization. J. Bacteriol. 177:67516760.
140. Zhang, X.,, and F. M. Hulett. 2000. ResD signal transduction regulator of aerobic respiration in Bacillus subtilis; cta promoter regulation. Mol. Microbiol. 37:12081219.
141. Zheng, G.,, R. Hehn,, and P. Zuber. 2000. Mutational analysis of sbo-alb locus of Bacillus subtilis: identification of genes required for subtilosin production and immunity. J. Bacteriol. 182:32663273.
142. Zheng, G.,, L. Z. Yan,, J. C. Vederas,, and P. Zuber. 1999. Genes of the sbo-alb locus of Bacillus subtilis are required for production of the antilisterial bacteriocin subtilosin. J. Bacteriol. 181:73467355.


Generic image for table

Genes induced or repressed by oxygen limitation

The results of this table are mainly based on DNA micro- and macroarray experiments by Ye et al. ( ) and Homuth et al. ( ).

The expression of genes in aerobic and anaerobic cultures was compared either by fermentative growth or by growth in the presence of nitrate or nitrite. +, induced by anaerobiosis. —, repressed by anaerobiosis; 0, no change.

The result obtained by Ye et al. ( ).

The result obtained by Homuth et al. ( ).

PdhD protein level is higher under anaerobiosis ( ).

The result obtained by Ye ( ).

Expression of the gene is either slightly induced ( ) or repressed ( ) under anaerobic fermentative growth.

Genes whose products have no similarity to known proteins.

Citation: Nakano M, Zuber P. 2002. Anaerobiosis, p 393-404. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch28

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