Abstract
Pseudomonas stutzeri A1501, an associative nitrogen-fixing bacterium, was isolated from the rice paddy rhizosphere. This bacterium fixes nitrogen under microaerobic conditions. In this study, genome-wide DNA microarrays were used to analyze the global transcription profile of A1501 under aerobic and microaerobic conditions. The expression of 135 genes was significantly altered by more than 2-fold in response to oxygen stress. Among these genes, 68 were down-regulated under aerobic conditions; these genes included those responsible for nitrogen fixation and denitrification. Sixty-seven genes were up-regulated under aerobic conditions; these genes included sodC, encoding a copper-zinc superoxide dismutase, PST2179, encoding an NAD(P)-dependent oxidoreductase, PST3584, encoding a 2OG-Fe(II) oxygenase, and PST3602, encoding an NAD(P)H-flavin oxidoreductase. Additionally, seven genes involved in capsular polysaccharide and antigen oligosaccharide biosynthesis together with 17 genes encoding proteins of unknown function were up-regulated under aerobic conditions. The overall analysis suggests that the genes we identified are involved in the protection of the bacterium from oxygen, but the mechanisms of their action remain to be elucidated.
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Krieg N R, Hoffman P S. Microaerophily and oxygen toxicity. Arnu Rev Microbiol, 1986, 40: 107–130
Farr S B, Kogoma T. Oxidative stress responses in Escherichia coli and Salmonella typhimurium. Microbiol Rev, 1991, 55: 561–585
Imlay J A. How oxygen damages microbes: Oxygen tolerance and obligate anaerobiosis. Adv Microb Physiol, 2002, 46: 111–153
Gonzalez-Flecha B, Demple B. Metabolic sources of hydrogen peroxide in aerobically growing Escherichia coli. J Biol Chem, 1995, 270: 13681–13687
Messner K R, Imlay J A. The identification of primary sites of superoxide and hydrogen peroxide formation in the aerobic respiratory chain and sulfite reductase complex of Escherichia coli. J Biol Chem, 1999, 274: 10119–10128
Sabra W, Zeng A P, Lünsdorf H, et al. Effect of oxygen on formation and structure of Azotobacter vinelandii alginate and its role in protectin g nitrogenase. Appl Env Micro, 2000, 66: 4037–4044
Yulia V B, Alexander V B, Vladimir P S. Noncoupled NADH: ubiquinone oxidoredutase of Azotobacter vinelandii is required for diazotrophic growth at high oxygen concentrations. J Bacteriol, 2001, 183(23): 6869–6874
Post E, Kleiner D, Oelze J. Whole cell respiration and nitrogenase activities in Azotobacter vinelandii growing in oxygen controlled continuous culture. Arch Microbiol, 1983, 134: 68–72
Chen L, Keramati L, Helmann J D. Coordinate regulation of Bacillus subtilis peroxide stress genes by hydrogen peroxide and metal ions. Proc Natl Acad Sci USA, 1995, 92: 8190–8194
Lin M, Smalla K, Heuer H, et al. Effect of an Alcaligenes faecalis inoculant strain on bacterial communities in flooded microcosms planted with rice seedlings. Appl Soil Ecol, 2000, 15: 211–225
You C B, Song H X, Wang J P, et al. Association of Alcaligenes faecalis with wetland rice. Plant Soil, 1991, 137: 81–85
Desnoues N, Lin M, Guo X W, et al. Nitrogen fixation genetics and regulation in a Pseudomonas stutzeri strain associated with rice. Microbiology, 2003, 149: 2251–2262
Fay P. Oxygen relations of nitrogen fixation in Cyanobacteria. Microbiol Rev, 1992, 56: 340–373
van Niel E W J, Gottschal J C, Oxygen consumption by Desulfovibrio strains with and without polyglucose, Appl Environ Microbiol, 1998, 64: 1034–1039
Yan Y L, Yang J, Chen L H, et al. Structural and functional analysis of denitrification genes in Pseudomonas stutzeri A1501. Sci China Ser C-Life Sci, 2005, 48: 585–592
Patrick W, Walter G Z. Functional domains of NosR, a novel transmembrane iron-sulfur flavoprotein necessary for nitrous oxide respiration. J Bacteriol, 2005, 187: 1992–2001
Schreiber K, Krieger R, Benkert B, et al. The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration. J Bacteriol, 2007, 189: 4310–4314
Vollack K U, Zumft W G. Nitric oxide signaling and transcriptional control of denitrification genes in Pseudomonas stutzeri. J Bacteriol, 2001, 183: 2516–2526
Körner H, Zumft W G. Expression of denitrification enzymes in response to the dissolved oxygen level and respiratory substrate in continuous culture of Pseudomonas stutzeri. Appl Environ Microbiol, 1989, 55: 1670–1676
Moshiri F, Smith E G, Taormino J P, et al. Transcriptional regulation of cytochrome d in nitrogen-fixing Azotobacter vinelandii. Evidence that up-regulation during N2 fixation is independent of nifA but dependent on ntrA. J Biol Chem, 1991, 266: 23169–23174
Dixon R, Kahn D. Genetic regulation of biological nitrogen fixation. Nat Rev, 2004, 2: 621–631
Kawasaki S, Watamura Y, Ono M, et al. Adaptative response to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum. Appl Env Microbiol, 2005, 71: 8442–8450
Martinez-Argudo I, Little R, Shearer N, et al. Nitrogen fixation: key genetic regulatory mechanisms. Biochem Soc Transact, 2005, 33: 152–115
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Supported by the National Basic Research Program of China (Grant Nos. 2001CB108904 and 2007CB707805) and High-Technology Research Development Program of China (Grant Nos. 2006AA020202 and 2006AA0Z229))
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Dou, Y., Yan, Y., Ping, S. et al. Expression profile analysis of the oxygen response in the nitrogen-fixing Pseudomonas stutzeri A1501 by genome-wide DNA microarray. Chin. Sci. Bull. 53, 1197–1204 (2008). https://doi.org/10.1007/s11434-008-0180-1
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DOI: https://doi.org/10.1007/s11434-008-0180-1