期刊论文详细信息
BMC Microbiology
Genetic basis for denitrification in Ensifer meliloti
María J Delgado1  Eulogio J Bedmar1  José J Pueyo2  Teodoro Coba de la Peña2  Maria I Rubia1  Maria J Torres1 
[1] Estación Experimental del Zaidin, Consejo Superior de Investigaciones Científicas (CSIC), P.O. Box 419, 18080 Granada, Spain;Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 115-bis, 28006 Madrid, Spain
关键词: Periplasmic nitrate reductase;    Nitrous oxide reductase;    Nitric oxide reductase;    Nitrate respiration;    Cu-containing nitrite reductase;   
Others  :  1140990
DOI  :  10.1186/1471-2180-14-142
 received in 2014-02-19, accepted in 2014-05-28,  发布年份 2014
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【 摘 要 】

Background

Denitrification is defined as the dissimilatory reduction of nitrate or nitrite to nitric oxide (NO), nitrous oxide (N2O), or dinitrogen gas (N2). N2O is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Legume crops might contribute to N2O production by providing nitrogen-rich residues for decomposition or by associating with rhizobia that are able to denitrify under free-living and symbiotic conditions. However, there are limited direct empirical data concerning N2O production by endosymbiotic bacteria associated with legume crops. Analysis of the Ensifer meliloti 1021 genome sequence revealed the presence of the napEFDABC, nirK, norECBQD and nosRZDFYLX denitrification genes. It was recently reported that this bacterium is able to grow using nitrate respiration when cells are incubated with an initial O2 concentration of 2%; however, these cells were unable to use nitrate respiration when initially incubated anoxically. The involvement of the nap, nirK, nor and nos genes in E. meliloti denitrification has not been reported.

Results

E. meliloti nap, nirK and norC mutant strains exhibited defects in their ability to grow using nitrate as a respiratory substrate. However, E meliloti nosZ was not essential for growth under these conditions. The E. meliloti napA, nirK, norC and nosZ genes encode corresponding nitrate, nitrite, nitric oxide and nitrous oxide reductases, respectively. The NorC component of the E. meliloti nitric oxide reductase has been identified as a c-type cytochrome that is 16 kDa in size. Herein, we also show that maximal expression of the E. meliloti napA, nirK, norC and nosZ genes occurred when cells were initially incubated anoxically with nitrate.

Conclusion

The E. meliloti napA, nirK, norC and nosZ genes are involved in nitrate respiration and in the expression of denitrification enzymes in this bacterium. Our findings expand the short list of rhizobia for which denitrification gene function has been demonstrated. The inability of E. meliloti to grow when cells are initially subjected to anoxic conditions is not attributable to defects in the expression of the napA, nirK, norC and nosZ denitrification genes.

【 授权许可】

   
2014 Torres et al.; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Bates BC, Kundzewicz ZW, Wu S, Palutikof JP: Climate Change and Water.Technical Paper of the Intergovernmental Panel on Climate Change. Geneva, Switzerland: IPCC Secretariat; 2008:210.
  • [2]Gonzalez PJ, Correia C, Moura I, Brondino CD, Moura JJ: Bacterial nitrate reductases: molecular and biological aspects of nitrate reduction. J Inorg Biochem 2006, 100(5–6):1015-1023.
  • [3]Kraft B, Strous M, Tegetmeyer HE: Microbial nitrate respiration–genes, enzymes and environmental distribution. J Biotechnol 2011, 155(1):104-117.
  • [4]Richardson DJ: Redox complexes of the nitrogen cycle. In Nitrogen Cycling in Bacteria. Edited by Moir JWB. Norkfolk, UK: Caister Academic Press; 2011:23-39.
  • [5]Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ: Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 2001, 58(2):165-178.
  • [6]Richardson DJ, van Spanning RJ, Ferguson SJ: The prokaryotic nitrate reductases. In Biology of the Nitrogen Cycle. Edited by Bothe H, Ferguson SJ, Newton WE. The Nerthelands: Elservier; 2007:21-35.
  • [7]Rinaldo S, Arcovito A, Giardina G, Castiglione N, Brunori M, Cutruzzola F: New insights into the activity of Pseudomonas aeruginosa cd1 nitrite reductase. Biochem Soc Trans 2008, 36(Pt 6):1155-1159.
  • [8]Rinaldo S, Cutruzzola F: Nitrite reductases in denitrification. In Biology of the Nitrogen Cycle. Edited by Bothe H, Ferguson SJ, Newton WE. The Netherlands: Elservier; 2007:37-56.
  • [9]van Spanning RJ, Delgado MJ, Richardson DJ: The nitrogen cycle: denitrification and its relationship to N2 fixation. In Nitrogen Fixation in Agriculture, Forestry, Ecology and the Environment. Edited by Werner D, Newton WE. Netherlands: Springer; 2005:277-342.
  • [10]van Spanning RJ, Richardson DJ, Ferguson SJ: Introduction to the biochemistry and molecular biology of denitrification. In Biology of the Nitrogen Cycle.3-20. Edited by Bothe H, Ferguson SJ, Newton WE. Amsterdam: Elsevier Science; 2007.
  • [11]van Spanning RJ: Structure, function, regulation and evolution of the nitrite and nitrous oxide reductase: denitrification enzymes with a b-propeller fold. In Nitrogen Cycling in Bacteria. Edited by Moir JWB. Norkfolk, UK: Caister Academic Press; 2011:135-161.
  • [12]de Vries R, Suharti R, Pouvreau LAM: Nitric oxide reductase: structural variations and catalytic mechanism. In Biology of the Nitrogen Cycle. Edited by Bothe H, Ferguson SJ, Newton WE. The Netherlands: Elsevier; 2007:57-66.
  • [13]Zumft WG, Kroneck PM: Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol 2007, 52:107-227.
  • [14]Thomson AJ, Giannopoulos G, Pretty J, Baggs EM, Richardson DJ: Biological sources and sinks of nitrous oxide and strategies to mitigate emissions. Philos Trans R Soc Lond B Biol Sci 2012, 367(1593):1157-1168.
  • [15]Hartsock A, Shapleigh JP: Identification, functional studies, and genomic comparisons of new members of the NnrR regulon in Rhodobacter sphaeroides. J Bacteriol 2010, 192(4):903-911.
  • [16]Baggs EM, Rees RM, Smith KA, Vinten AJA: Nitrous oxide emission from soils after incorporating crop residues. Soil Use Manag 2000, 16(2):82-87.
  • [17]Bedmar EJ, Robles EF, Delgado MJ: The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum. Biochem Soc Trans 2005, 33(Pt 1):141-144.
  • [18]Garcia-Plazaola JI, Becerril JM, Arrese-Igor C, Hernandez A, Gonzalez-Murua C, Aparicio-Tejo PM: Denitrifying ability of thirteen Rhizobium meliloti strains. Plant Soil 1993, 149:43-50.
  • [19]Sánchez C, Bedmar EJ Delgado MJ: Denitrification in Legume-associated endosymbiotic Bacteria. In Nitrogen cycling in Bacteria. Edited by Moir JWB. Norfolk, UK: Caister Academic Press; 2011:197-210.
  • [20]Delgado MJ, Casella S, Bedmar EJ: Denitrification in rhizobia-legume symbiosis. In Biology of the Nitrogen Cycle. Edited by Bothe H, Ferguson SJ, Newton WE. Amsterdam: Elsevier Science; 2007:83-93.
  • [21]Torres MJ, Rubia MI, Bedmar EJ, Delgado MJ: Denitrification in Sinorhizobium meliloti. Biochem Soc Trans 2011, 39(6):1886-1889.
  • [22]Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F, Bowser L, Capela D, Galibert F, Gouzy J, Gurjal M, Hong A, Huizar L, Hyman RW, Kahn D, Kahn ML, Kalman S, Keating DH, Palm C, Peck MC, Surzycki R, Wells DH, Yeh KC, Davis RW, Federspiel NA, Long SR: Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci U S A 2001, 98(17):9883-9888.
  • [23]Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, de Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Puhler A, Weidner S, Batut J: Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions. Mol Plant Microbe Interact 2004, 17(3):292-303.
  • [24]Bobik C, Meilhoc E, Batut J: FixJ: a major regulator of the oxygen limitation response and late symbiotic functions of Sinorhizobium meliloti. J Bacteriol 2006, 188(13):4890-4902.
  • [25]Meilhoc E, Cam Y, Skapski A, Bruand C: The response to nitric oxide of the nitrogen-fixing symbiont Sinorhizobium meliloti. Mol Plant Microbe Interact 2010, 23(6):748-759.
  • [26]Horchani F, Prevot M, Boscari A, Evangelisti E, Meilhoc E, Bruand C, Raymond P, Boncompagni E, Aschi-Smiti S, Puppo A, Brouquisse R: Both plant and bacterial nitrate reductases contribute to nitric oxide production in Medicago truncatula nitrogen-fixing nodules. Plant Physiol 2011, 155(2):1023-1036.
  • [27]Meade HM, Long SR, Ruvkun GB, Brown SE, Ausubel FM: Physical and genetic characterization of symbiotic and auxotrophic mutants of Rhizobium meliloti induced by transposon Tn5 mutagenesis. J Bacteriol 1982, 149(1):114-122.
  • [28]Casse F, Boucher C, Julliot JS, Michel M, Dénarié J: Identification and Characterization of Large Plasmids in Rhizobium meliloti using Agarose Gel Electrophoresis. J Gen Microbiol 1979, 113(2):229-242.
  • [29]Pobigaylo N, Wetter D, Szymczak S, Schiller U, Kurtz S, Meyer F, Nattkemper TW, Becker A: Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. Appl Environ Microbiol 2006, 72(6):4329-4337.
  • [30]Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Ruberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Puhler A, Goesmann A: A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data. J Biotechnol 2009, 140(1–2):45-50.
  • [31]Torres MJ, Hidalgo-Garcia A, Bedmar EJ, Delgado MJ: Functional analysis of the copy 1 of the fixNOQP operon of Ensifer meliloti under free-living micro-oxic and symbiotic conditions. J Appl Microbiol 2013, 114(6):1772-1781.
  • [32]Delgado MJ, Bonnard N, Tresierra-Ayala A, Bedmar EJ, Muller P: The Bradyrhizobium japonicum napEDABC genes encoding the periplasmic nitrate reductase are essential for nitrate respiration. Microbiology 2003, 149(Pt 12):3395-3403.
  • [33]García-Plazaola JI: Denitrification in lucerne nodules is not involved in nitrite detoxification. Plant Soil 1996, 182:149-155.
  • [34]Bedzyk L, Wang T, Ye RW: The periplasmic nitrate reductase in Pseudomonas sp. strain G-179 catalyzes the first step of denitrification. J Bacteriol 1999, 181(9):2802-2806.
  • [35]Velasco L, Mesa S, Delgado MJ, Bedmar EJ: Characterization of the nirK gene encoding the respiratory, Cu-containing nitrite reductase of Bradyrhizobium japonicum. Biochim Biophys Acta 2001, 1521(1–3):130-134.
  • [36]Mesa S, Velasco L, Manzanera ME, Delgado MJ, Bedmar EJ: Characterization of the norCBQD genes, encoding nitric oxide reductase, in the nitrogen fixing bacterium Bradyrhizobium japonicum. Microbiology 2002, 148(Pt 11):3553-3560.
  • [37]Gomez-Hernandez N, Reyes-Gonzalez A, Sanchez C, Mora Y, Delgado MJ, Girard L: Regulation and symbiotic role of nirK and norC expression in Rhizobium etli. Mol Plant Microbe Interact 2011, 24(2):233-245.
  • [38]Velasco L, Mesa S, Xu CA, Delgado MJ, Bedmar EJ: Molecular characterization of nosRZDFYLX genes coding for denitrifying nitrous oxide reductase of Bradyrhizobium japonicum. Antonie Van Leeuwenhoek 2004, 85(3):229-235.
  • [39]Aida T, Hata S, Kusunoki H: Temporary low oxygen conditions for the formation of nitrate reductase and nitrous oxide reductase by denitrifying Pseudomonas sp. G59. Can J Microbiol 1986, 32(7):543-547.
  • [40]Bergaust L, Shapleigh J, Frostegard A, Bakken L: Transcription and activities of NOx reductases in Agrobacterium tumefaciens: the influence of nitrate, nitrite and oxygen availability. Environ Microbiol 2008, 10(11):3070-3081.
  • [41]Bergaust L, Mao Y, Bakken LR, Frostegard A: Denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal pH on nitrous oxide reductase in Paracoccus denitrificans. Appl Environ Microbiol 2010, 76(19):6387-6396.
  • [42]Nadeem S, Dorsch P, Bakken LR: The significance of early accumulation of nanomolar concentrations of NO as an inducer of denitrification. FEMS Microbiol Ecol 2013, 83(3):672-684.
  • [43]Beringer JE: R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 1974, 84(1):188-198.
  • [44]Robertsen BK, Aman P, Darvill AG, McNeil M, Albersheim P: The structure of acidic extracellular polysaccharides secreted by Rhizobium leguminosarum and Rhizobium trifolii. Plant Physiol 1981, 67(3):389-400.
  • [45]Vargas C, McEwan AG, Downie JA: Detection of c-type cytochromes using enhanced chemiluminescence. Anal Biochem 1993, 209(2):323-326.
  • [46]Nicholas DJD, Nason A: Determination of nitrate and nitrite. In Methods in Enzymology, VOlume III. Edited by Colowick SP, Kaplan NO. London: Academic Press; 1957:974-977.
  • [47]Zhang X, Broderick M: Amperometric detection of nitric oxide. Mod Asp Immunobiol 2000, 1(4):160-165.
  • [48]Sambrook J, Fritsch EF, Maniatics T: Molecular cloning: a laboratory manual. New York: Cold Spring Harbor Laboratory Press; 1989.
  • [49]Glenn SA, Gurich N, Feeney MA, Gonzalez JE: The ExpR/Sin quorum-sensing system controls succinoglycan production in Sinorhizobium meliloti. J Bacteriol 2007, 189(19):7077-7088.
  • [50]Krol E, Becker A: Global transcriptional analysis of the phosphate starvation response in Sinorhizobium meliloti strains 1021 and 2011. Mol Genet Genomics 2004, 272(1):1-17.
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