Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2014 (2014), Article ID 123058, 10 pages
http://dx.doi.org/10.1155/2014/123058
Research Article

Genome Sequencing of a Mung Bean Plant Growth Promoting Strain of P. aeruginosa with Biocontrol Ability

1Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamilnadu 625021, India
2Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
3Department of Cell and Developmental Biology, John Innes Center, Norwich Research Park, Norwich NR4 7UH, UK

Received 17 May 2014; Accepted 15 July 2014; Published 12 August 2014

Academic Editor: Ferenc Olasz

Copyright © 2014 Devaraj Illakkiam et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. B. Lyczak, C. L. Cannon, and G. B. Pier, “Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist,” Microbes and Infection, vol. 2, no. 9, pp. 1051–1060, 2000. View at Publisher · View at Google Scholar · View at Scopus
  2. C. K. Stover, X. Q. Pham, A. L. Erwin et al., “Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen,” Nature, vol. 406, no. 6799, pp. 959–964, 2000. View at Publisher · View at Google Scholar · View at Scopus
  3. S. Buysens, K. Heungens, J. Poppe, and M. Hofte, “Involvement of pyochelin and pyoverdin in suppression of pythium-induced damping-off of tomato by Pseudomonas aeruginosa 7NSK2,” Applied and Environmental Microbiology, vol. 62, no. 3, pp. 865–871, 1996. View at Google Scholar · View at Scopus
  4. V. Anjaiah, P. Cornelis, and N. Koedam, “Effect of genotype and root colonization in biological control of fusarium wilts in pigeonpea and chickpea by Pseudomonas aeruginosa PNA1,” Canadian Journal of Microbiology, vol. 49, no. 2, pp. 85–91, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. N. Bano and J. Musarrat, “Characterization of a new Pseudomonas aeruginosa strain NJ-15 as a potential biocontrol agent,” Current Microbiology, vol. 46, no. 5, pp. 324–328, 2003. View at Publisher · View at Google Scholar · View at Scopus
  6. R. S. Kumar, N. Ayyadurai, P. Pandiaraja et al., “Characterization of antifungal metabolite produced by a new strain Pseudomonas aeruginosa PUPa3 that exhibits broad-spectrum antifungal activity biofertilizing traits,” Journal of Applied Microbiology, vol. 98, no. 1, pp. 145–154, 2005. View at Publisher · View at Google Scholar · View at Scopus
  7. D. Illakkiam, P. Ponraj, M. Shankar, S. Muthusubramanian, J. Rajendhran, and P. Gunasekaran, “Identification and structure elucidation of a novel antifungal compound produced by Pseudomonas aeruginosa PGPR2 against Macrophomina phaseolina,” Applied Biochemistry and Biotechnology, vol. 171, pp. 2176–2185, 2013. View at Google Scholar
  8. B. Chevreux, T. Wetter, and S. Suhai, “Genome sequence assembly using trace signals and additional sequence information. Computer science and biology,” in Proceedings of the German Conference on Bioinformatics, vol. 99, pp. 45–56, 1999.
  9. R. Staden, K. F. Beal, and J. K. Bonfield, “The Staden package, 1998,” Methods in Molecular Biology, vol. 132, pp. 115–130, 2000. View at Google Scholar · View at Scopus
  10. R. K. Aziz, D. Bartels, A. Best et al., “The RAST server: rapid annotations using subsystems technology,” BMC Genomics, vol. 9, article 75, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. K. Lagesen, P. Hallin, E. A. Rødland, H.-H. Stærfeldt, T. Rognes, and D. W. Ussery, “RNAmmer: Consistent and rapid annotation of ribosomal RNA genes,” Nucleic Acids Research, vol. 35, no. 9, pp. 3100–3108, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. T. M. Lowe and S. R. Eddy, “tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence,” Nucleic Acids Research, vol. 25, no. 5, pp. 955–964, 1997. View at Publisher · View at Google Scholar · View at Scopus
  13. A. L. Delcher, D. Harmon, S. Kasif, O. White, and S. L. Salzberg, “Improved microbial gene identification with GLIMMER,” Nucleic Acids Research, vol. 27, no. 23, pp. 4636–4641, 1999. View at Publisher · View at Google Scholar · View at Scopus
  14. A. L. Delcher, A. Phillippy, J. Carlton, and S. L. Salzberg, “Fast algorithms for large-scale genome alignment and comparison,” Nucleic Acids Research, vol. 30, no. 11, pp. 2478–2483, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. A. C. E. Darling, B. Mau, F. R. Blattner, and N. T. Perna, “Mauve: multiple alignment of conserved genomic sequence with rearrangements,” Genome Research, vol. 14, no. 7, pp. 1394–1403, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. E. Quevillon, V. Silventoinen, S. Pillai et al., “InterProScan: protein domains identifier,” Nucleic Acids Research, vol. 33, no. 2, pp. W116–W120, 2005. View at Publisher · View at Google Scholar · View at Scopus
  17. T. J. Carver, K. M. Rutherford, M. Berriman, M. A. Rajandream, B. G. Barrell, and J. Parkhill, “ACT: the artemis comparison tool,” Bioinformatics, vol. 21, no. 16, pp. 3422–3423, 2005. View at Publisher · View at Google Scholar · View at Scopus
  18. T. Carver, N. Thomson, A. Bleasby, M. Berriman, and J. Parkhill, “DNAPlotter: circular and linear interactive genome visualization,” Bioinformatics, vol. 25, no. 1, pp. 119–120, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. I. Grissa, G. Vergnaud, and C. Pourcel, “CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats,” Nucleic Acids Research, vol. 35, no. 2, pp. W52–W57, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. Z. Xu and B. Hao, “CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes,” Nucleic Acids Research, vol. 37, no. 2, pp. W174–W178, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. C. Laing, C. Buchanan, E. N. Taboada et al., “Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions,” BMC Bioinformatics, vol. 11, article 461, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. M. Kanehisa, M. Araki, S. Goto et al., “KEGG for linking genomes to life and the environment,” Nucleic Acids Research, vol. 36, no. 1, pp. D480–D484, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. R. Caspi, T. Altman, K. Dreher et al., “The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases,” Nucleic Acids Research, vol. 40, no. 1, pp. D742–D753, 2012. View at Publisher · View at Google Scholar · View at Scopus
  24. Y. Bashan and L. E. de-Bashan, “Fresh-weight measurements of roots provide inaccurate estimates of the effects of plant growth-promoting bacteria on root growth: a critical examination,” Soil Biology & Biochemistry, vol. 37, no. 10, pp. 1795–1804, 2005. View at Publisher · View at Google Scholar · View at Scopus
  25. D. Illakkiam, N. L. Anuj, P. Ponraj, M. Shankar, J. Rajendhran, and P. Gunasekaran, “Proteolytic enzyme mediated antagonistic potential of Pseudomonas aeruginosa against Macrophomina phaseolina,” Indian Journal of Experimental Biology, vol. 51, pp. 1024–1031, 2013. View at Google Scholar
  26. D. Wu, J. Ye, H. Ou et al., “Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18,” BMC Genomics, vol. 12, article 438, 2011. View at Publisher · View at Google Scholar · View at Scopus
  27. P. Nannipieri, L. Giagnoni, L. Landi, and G. Renella, “Role of phosphatase enzymes in soil,” in Phosphorus in Action, E. K. Bunemann, A. Obreson, and E. Frossard, Eds., pp. 215–243, Springer, Berlin, Germany, 2011. View at Google Scholar
  28. A. E. Richardson, “Soil microorganisms and phosphorous availability,” in Soil Biota: Management in Sustainable Farming Systems, C. E. Pankhurst, B. M. Doube, and V. V. S. R. Gupta, Eds., pp. 50–62, CSIRO, Victoria, Australia, 1994. View at Google Scholar
  29. H. Rodriguez, R. Fraga, T. Gonzalez, and Y. Bashan Y, “Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria,” Plant and Soil, vol. 287, pp. 15–21, 2006. View at Google Scholar
  30. B. L. Lim, “TonB-dependent receptors in nitrogen-fixing nodulating bacteria,” Microbes and Environments, vol. 25, no. 2, pp. 67–74, 2010. View at Publisher · View at Google Scholar · View at Scopus
  31. N. Gottig, B. S. Garavaglia, C. G. Garofalo, E. G. Orellano, and J. Ottado, “A filamentous hemagglutinin -like protein of Xanthomonas axonopodis pv . citri , the phytopathogen responsible for citrus canker, is involved in bacterial virulence,” PLoS ONE, vol. 4, Article ID e4358, 2009. View at Google Scholar
  32. E. J. Lim, J. C. Kim, G. J. Choi et al., “Forest soil metagenome gene cluster involved in antifungal activity expression in Escherichia coli,” Applied and Environmental Microbiology, vol. 74, pp. 723–730, 2008. View at Google Scholar
  33. P. D. Newell, S. Yoshioka, K. L. Hvorecny, R. D. Monds, and G. A. O'Toole, “Systematic analysis of diguanylate cyclases that promote biofilm formation by Pseudomonas fluorescens Pf0-1,” Journal of Bacteriology, vol. 193, no. 18, pp. 4685–4698, 2011. View at Publisher · View at Google Scholar · View at Scopus
  34. N. Ausmees, R. Mayer, H. Weinhouse et al., “Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity,” FEMS Microbiology Letters, vol. 204, no. 1, pp. 163–167, 2001. View at Publisher · View at Google Scholar · View at Scopus
  35. F. Putker, R. Tommassen-van Boxtel, M. Stork, J. J. Rodríguez-Herva, M. Koster, and J. Tommassen, “The type II secretion system (Xcp) of Pseudomonas putida is active and involved in the secretion of phosphatases,” Environmental Microbiology, vol. 15, pp. 2658–2671, 2013. View at Publisher · View at Google Scholar · View at Scopus
  36. G. Mei, X. Yan, A. Turak, Z. Luo, and L. Zhang, “AidH, an alpha/beta-hydrolase fold family member from an ochrobactrum sp. strain, Is a novel N-acylhomoserine lactonase,” Applied and Environmental Microbiology, vol. 76, no. 15, pp. 4933–4942, 2010. View at Publisher · View at Google Scholar · View at Scopus
  37. S. Oku, A. Komatsu, T. Tajima, Y. Nakashimada, and J. Kato, “Identification of chemotaxis sensory proteins for amino acids in Pseudomonas fluorescens Pf0-1 and their involvement in chemotaxis to tomato root exudate and root colonization,” Microbes and Environments, vol. 27, no. 4, pp. 462–469, 2012. View at Publisher · View at Google Scholar · View at Scopus
  38. H. H. Liu, J. Liu, S. L. Fan et al., “Molecular cloning and characterization of a salinity stress-induced gene encoding DEAD-box helicase from the halophyte Apocynum venetum,” Journal of Experimental Botany, vol. 59, no. 3, pp. 633–644, 2008. View at Publisher · View at Google Scholar · View at Scopus
  39. M. D. Lundrigan and R. J. Kadner, “Nucleotide sequence of the gene for the ferrienterochelin receptor FepA in Escherichia coli. Homology among outer membrane receptors that interact with TonB,” The Journal of Biological Chemistry, vol. 261, no. 23, pp. 10797–10801, 1986. View at Google Scholar · View at Scopus
  40. B. R. Glick, “The enhancement of plant growth by free-living bacteria,” Canadian Journal of Microbiology, vol. 41, no. 2, pp. 109–117, 1995. View at Publisher · View at Google Scholar · View at Scopus
  41. C. H. J. Phoebe, J. Combie, F. G. Albert et al., “Extremophilic organisms as an unexplored source of antifungal compounds,” Journal of Antibiotics, vol. 54, no. 1, pp. 56–65, 2001. View at Publisher · View at Google Scholar · View at Scopus
  42. C. L. Patten and B. R. Glick, “Bacterial biosynthesis of indole-3-acetic acid,” Canadian Journal of Microbiology, vol. 42, no. 3, pp. 207–220, 1996. View at Publisher · View at Google Scholar · View at Scopus
  43. E. Khare and N. K. Arora, “Effect of indole-3-acetic acid (IAA) produced by Pseudomonas aeruginosa in suppression of charcoal rot disease of chickpea,” Current Microbiology, vol. 61, no. 1, pp. 64–68, 2010. View at Publisher · View at Google Scholar · View at Scopus
  44. M. J. Paul, L. F. Primavesi, D. Jhurreea, and Y. Zhang, “Trehalose metabolism and signaling,” Annual Review of Plant Biology, vol. 59, pp. 417–441, 2008. View at Publisher · View at Google Scholar · View at Scopus
  45. J. Rodríguez-Salazar, R. Suárez, J. Caballero-Mellado, and G. Iturriaga, “Trehalose accumulation in Azospirillum brasilense improves drought tolerance and biomass in maize plants,” FEMS Microbiology Letters, vol. 296, no. 1, pp. 52–59, 2009. View at Publisher · View at Google Scholar · View at Scopus
  46. K. Blomqvist, M. Nikkola, P. Lehtovaara et al., “Characterization of the genes of the 2,3-butanediol operons from Klebsiella terrigena and Enterobacter aerogenes,” Journal of Bacteriology, vol. 175, no. 5, pp. 1392–1404, 1993. View at Google Scholar · View at Scopus
  47. S. M. Cho, B. R. Kang, S. H. Han et al., “2R,3R-butanediol, a bacterial volatile produced by Pseudomonas chlororaphis O6, is involved in induction of systemic tolerance to drought in Arabidopsis thaliana,” Molecular Plant-Microbe Interactions, vol. 21, no. 8, pp. 1067–1075, 2008. View at Publisher · View at Google Scholar · View at Scopus
  48. S. H. Han, S. J. Lee, J. H. Moon et al., “GacS-dependent production of 2R, 3R-butanediol by Pseudomonas chlororaphis O6 is a major determinant for eliciting systemic resistance against Erwinia carotovora but not against Pseudomonas syringae pv. tabaci in tobacco,” Molecular Plant-Microbe Interactions, vol. 19, no. 8, pp. 924–930, 2006. View at Publisher · View at Google Scholar · View at Scopus
  49. J. Laville, C. Blumer, C. von Schroetter et al., “Characterization of the hcnABC gene cluster encoding hydrogen cyanide synthase and anaerobic regulation by ANR in the strictly aerobic biocontrol agent Pseudomonas fluorescens CHA0,” Journal of Bacteriology, vol. 180, no. 12, pp. 3187–3196, 1998. View at Google Scholar · View at Scopus
  50. C. Lanteigne, V. J. Gadkar, T. Wallon, A. Novinscak, and M. Filion, “Production of DAPG and HCN by Pseudomonas sp. LBUM300 contributes to the biological control of bacterial canker of tomato,” Phytopathology, vol. 102, no. 10, pp. 967–973, 2012. View at Publisher · View at Google Scholar · View at Scopus
  51. A. W. Bakker and B. Schippers, “Microbial cyanide production in the rhizosphere in relation to potato yield reduction and Pseudomonas SPP-mediated plant growth-stimulation,” Soil Biology & Biochemistry, vol. 19, no. 4, pp. 451–457, 1987. View at Publisher · View at Google Scholar · View at Scopus
  52. S. Ramyasmruthi, O. Pallavi, S. Pallavi, K. Tilak, and S. Srividya, “Chitinolytic and secondary metabolite producing Pseudomonas fluorescens isolated from Solanaceae rhizosphere effective against broad spectrum fungal phytopathogens,” Asian Journal of Plant Science Research, vol. 2, no. 1, pp. 16–24, 2012. View at Google Scholar
  53. J. Barriuso, B. R. Solano, and F. J. G. Mañero, “Protection against pathogen and salt stress by four plant growth-promoting rhizobacteria isolated from Pinus sp. on Arabidopsis thaliana,” Phytopathology, vol. 98, no. 6, pp. 666–672, 2008. View at Publisher · View at Google Scholar · View at Scopus
  54. M. Bokhove, P. N. Jimenez, W. J. Quax, and B. W. Dijkstra, “The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 2, pp. 686–691, 2010. View at Publisher · View at Google Scholar · View at Scopus
  55. C. F. Sio, L. G. Otten, R. H. Cool et al., “Quorum quenching by an N-acyl-homoserine lactone acylase from Pseudomonas aeruginosa PAO1,” Infection and Immunity, vol. 74, no. 3, pp. 1673–1682, 2006. View at Publisher · View at Google Scholar · View at Scopus