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Functional Specificity of the nifA Gene Product within the Group of Root Nodule Bacteria

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Abstract

The functional activity of different phylogenetic variants of the transcriptional activator of nitrogen fixation genes in the cells of root nodule bacteria (rhizobia) of different taxa was analyzed. For this purpose, recombinant strains of root nodule bacteria of the genera Mesorhizobium, Ensifer (Sinorhizobium), and Rhizobium were created using genetic engineering constructs based on the plasmid pJN105. This plasmid contains different phylogenetic variants of the nifA gene typical for bacteria of the genera Mesorhizobium, Ensifer, and Rhizobium under the control of the ParaBAD bacterial promoter. It was shown that in free-living recombinant cells of all three bacterial genera, the introduction of an additional active copy of the nifA gene to their genome resulted in emergence of detectable nitrogenase activity. The level of nitrogenase activity was not directly related to the phylogeny of the introduced nifA gene, which is most likely explained by the universality of the product of this gene within the studied group of bacteria. The data obtained indicate the possibility of combinatorial processes in the evolution of nitrogen fixation genes.

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REFERENCES

  1. An, Q., Dong, Y., Wang, W., Li, Y., and Li, J., Constitutive expression of the nifA gene activates associative nitrogen fixation of Enterobacter gergoviae 57-7, an opportunistic endophytic diazotroph, J. Appl. Microbiol., 2007, vol. 103, pp. 613–620. https://doi.org/10.1111/j.1365-2672.2007.03289.x

    Article  CAS  PubMed  Google Scholar 

  2. Baymiev, An.K., Gumenko, R.S., Vladimirova, A.A., Akimova, E.S., Vershinina, Z.R., and Baymiev, Al.K., Artificial activation of nif gene expression in nodule bacteria ex planta, Ecol. Genet., 2019, vol. 17, no. 2, pp. 35–42.

    Article  Google Scholar 

  3. Baymiev, An.Kh., Ptitsyn, K.G., Muldashev, A.A., and Baymiev, Al.Kh., Genetic characterization of root nodule bacteria from Lathyrus legumes growing at the territory of the Bashkortostan Republic, Ekol. Genet., 2011, vol. 9, no. 2, pp. 3–8.

    Google Scholar 

  4. Buchanan-Wollaston, V., Cannon, M.C., Beynon, J.L., and Cannon, F.C., Role of the nifA gene product in the regulation of nif expression in Klebsiella pneumonia, Nature, 1981, vol. 294, pp. 776–778. https://doi.org/10.1038/294776a0

    Article  CAS  PubMed  Google Scholar 

  5. Bush, M. and Dixon, R., The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription, Microbiol. Mol. Biol. Rev., 2012, vol. 76, pp. 497–529. https://doi.org/10.1128/MMBR.00006-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Dai, Z., Guo, X., Yin, H., Liang, Y., Cong, J., and Liu, X., Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage, PLoS One, 2014, vol. 9, p. e87976. https://doi.org/10.1371/journal.pone.0087976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dixon, R.A. and Postgate, J.R., Genetic transfer of nitrogen fixation from Klebsiella pneumoniae to Escherichia coli, Nature, 1972, vol. 237, pp. 102–103.

    Article  CAS  Google Scholar 

  8. Dixon, R. and Kahn, D., Genetic regulation of biological nitrogen fixation, Nat. Rev. Microbiol., 2004, vol. 2, pp. 621–631. https://doi.org/10.1038/nrmicro954

    Article  CAS  PubMed  Google Scholar 

  9. Fischer, H.M., Environmental regulation of rhizobial symbiotic nitrogen fixation genes, Trends Microbiol., 1996, vol. 4, pp. 317–320. https://doi.org/10.1016/0966-842x(96)10049-4

    Article  CAS  PubMed  Google Scholar 

  10. Han, Y., Lu, N., Chen, Q., Zhan, Y., Liu, W., Lu, W., and Yan, Y., Interspecies transfer and regulation of Pseudomonas stutzeri A1501 nitrogen fixation island in Escherichia coli, J. Microbiol. Biotechnol., 2015, vol. 25, pp. 1339–1348. https://doi.org/10.4014/jmb.1502.02027

    Article  CAS  PubMed  Google Scholar 

  11. Kennedy, C. and Robson, R.L., Activation of nif gene expression in Azotobacter by the nifA gene product of Klebsiella pneumonia, Nature, 1983, vol. 301, pp. 626–628. https://doi.org/10.1038/301626a0

    Article  CAS  PubMed  Google Scholar 

  12. Laranjo, M., Alexandre, A., and Oliveira, S., Legume growth-promoting rhizobia: an overview on the Mesorhizobium genus, Microbiol. Res., 2014, vol. 169, pp. 2–17. https://doi.org/10.1016/j.micres.2013.09.012

    Article  PubMed  Google Scholar 

  13. Li, X.X., Liu, Q., Liu, X.M., Shi, H.W., and Chen, S.F., Using synthetic biology to increase nitrogenase activity, Microb. Cell Factor, 2016, vol. 15, no. 43, pp. 1–11. https://doi.org/10.1186/s12934-016-0442-6

    Article  CAS  Google Scholar 

  14. Mongiardini, E.J., Ausmees, N., Pérez-Giménez, J., Julia Althabegoiti, M., Ignacio Quelas, J., López-García, S.L., and Lodeiro, A.R., The rhizobial adhesion protein RapA1 is involved in adsorption of rhizobia to plant roots but not in nodulation, FEMS Microbiol. Ecol., 2008, vol. 65, pp. 279–288. https://doi.org/10.1111/j.1574-6941.2008.00467.x

    Article  CAS  PubMed  Google Scholar 

  15. Newman, J.R. and Fuqua, C., Broad-host-range expression vectors that carry the L-arabinose-inducible Escherichia coli araBAD promoter and the araC regulator, Gene, 1999, vol. 227, pp. 197–203. https://doi.org/10.1016/s0378-1119(98)00601-5

    Article  CAS  PubMed  Google Scholar 

  16. Norel, F. and Elmerich, C., Nucleotide sequence and functional analysis of the two nifH copies of Rhizobium ORS571, Microbiology (SGM), 1987, vol. 133, pp. 1563–1576. https://doi.org/10.1099/00221287-133-6-1563

    Article  CAS  Google Scholar 

  17. Sambrook, J. and Russell, D.W., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Lab., 2001, 3 ed.

    Google Scholar 

  18. Setten, L., Soto, G., Mozzicafreddo, M., Fox, A.R., Lisi, C., Cuccioloni, M., and Ayub, N.D., Engineering Pseudomonas protegens Pf-5 for nitrogen fixation and its application to improve plant growth under nitrogen-deficient conditions, PLoS One, 2013, vol. 8, pp. e63666. https://doi.org/10.1371/journal.pone.0063666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Smanski, M.J., Bhatia, S., Zhao, D., Park, Y., Woodruff, L.B., Giannoukos, G., Ciulla, D., Busby, M., Calderon, J., Nicol, R., Gordon, D.B., Densmore, D., and Voigt, C.A., Functional optimization of gene clusters by combinatorial design and assembly, Nature Biotechnol., 2014, vol. 32, pp. 1241–1249. https://doi.org/10.1038/nbt.3063

    Article  CAS  Google Scholar 

  20. Sullivan, J.T., Brown, S.D., and Ronson, C.W., The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator, PLoS One, 2013, vol. 8, pp. e53762. https://doi.org/10.1371/journal.pone.0053762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Towbin, H., Staehelin, T., and Gordon, J., Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications, Proc. Natl. Acad. Sci. U. S. A., 1979, vol. 76, pp. 4350–4354. https://doi.org/10.1073/pnas.76.9.4350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Umarov, M.M., Assotsiativnaya azotfiksatsiya (Associative Nitrogen Fixation), Moscow: Mos. Gos. Univ., 1989.

  23. Wang, L., Zhang, L., Liu, Z., Zhao, D., Liu, X., Zhang, B., and Dixon, R., A minimal nitrogen fixation gene cluster from Paenibacillus sp. WLY78 enables expression of active nitrogenase in Escherichia coli, PLoS Genet., 2013, vol. 9, p. e1003865. https://doi.org/10.1371/journal.pgen.1003865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Wongdee, J., Boonkerd, N., Teaumroong, N., Tittabutr, P., and Giraud, E., Regulation of nitrogen fixation in Bradyrhizobium sp. strain DOA9 involves two distinct NifA regulatory proteins that are functionally redundant during symbiosis but not during free-living growth, Front. Microbiol., 2018, vol. 9, p. 1644. https://doi.org/10.3389/fmicb.2018.01644

    Article  PubMed  PubMed Central  Google Scholar 

  25. Xu, H., Gu, B., Nixon, B.T., and Hoover, T.R., Purification and characterization of the AAA+ domain of Sinorhizobium meliloti DctD, a σ54-dependent transcriptional activator, J. Bacteriol., 2004, vol. 186, pp. 3499–3507. https://doi.org/10.1128/JB.186.11.3499-3507.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Yang, J., Xie, X., Wang, X., Dixon, R., and Wang, Y.P., Reconstruction and minimal gene requirements for the alternative iron-only nitrogenase in Escherichia coli, Proc. Natl. Acad. Sci. U. S. A., 2014, vol. 111, pp. 3718–3725. https://doi.org/10.1073/pnas.1411185111                                                  

    Article  CAS  Google Scholar 

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ACKNOWLEDGMENTS

The work was carried out using the equipment of the RCCU “Agidel” and USI “KODINK.”

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Authors and Affiliations

  1. Institute of Biochemistry and Genetics, Ufa Research Center, Russian Academy of Sciences, 450054, Ufa, Russia

    A. A. Vladimirova, R. S. Gumenko, E. S. Akimova, Al. Kh. Baymiev & An. Kh. Baymiev

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  1. A. A. Vladimirova
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  2. R. S. Gumenko
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  3. E. S. Akimova
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  4. Al. Kh. Baymiev
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  5. An. Kh. Baymiev
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Correspondence to A. A. Vladimirova.

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The authors declare that they have no conflict of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by P. Sigalevich

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Vladimirova, A.A., Gumenko, R.S., Akimova, E.S. et al. Functional Specificity of the nifA Gene Product within the Group of Root Nodule Bacteria. Microbiology 90, 481–488 (2021). https://doi.org/10.1134/S0026261721040160

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