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Krzyżanowska DM, Ossowicki A, Rajewska M, et al. When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens. Front Microbiol. 2016;7:782doi: 10.3389/fmicb.2016.00782.
Krzyżanowska, D. M., Ossowicki, A., Rajewska, M., Maciąg, T., Jabłońska, M., Obuchowski, M., Heeb, S., & Jafra, S. (2016). When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens. Frontiers in microbiology, 7782. https://doi.org/10.3389/fmicb.2016.00782
Krzyżanowska, Dorota M, et al. "When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens." Frontiers in microbiology vol. 7 (2016): 782. doi: https://doi.org/10.3389/fmicb.2016.00782
Krzyżanowska DM, Ossowicki A, Rajewska M, Maciąg T, Jabłońska M, Obuchowski M, Heeb S, Jafra S. When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens. Front Microbiol. 2016 May 26;7:782. doi: 10.3389/fmicb.2016.00782. eCollection 2016. PMID: 27303376; PMCID: PMC4880745.
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Front Microbiol. 2016 May 26;7:782. doi: 10.3389/fmicb.2016.00782. eCollection 2016.

When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens.

Frontiers in microbiology

Dorota M Krzyżanowska, Adam Ossowicki, Magdalena Rajewska, Tomasz Maciąg, Magdalena Jabłońska, Michał Obuchowski, Stephan Heeb, Sylwia Jafra

Affiliations

  1. Laboratory of Biological Plant Protection, Department of Biotechnology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland.
  2. Laboratory of Molecular Bacteriology, Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Medical University of Gdansk Gdansk, Poland.
  3. School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham Nottingham, UK.

PMID: 27303376 PMCID: PMC4880745 DOI: 10.3389/fmicb.2016.00782

Abstract

Dickeya solani and Pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. Pseudomonas sp. strain P482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. In this study, we determined the genetic background of the antibacterial activity of P482, and established the phylogenetic position of this strain. Pseudomonas sp. P482 was classified as Pseudomonas donghuensis. Genome mining revealed that the P482 genome does not contain genes determining the synthesis of known antimicrobials. However, the ClusterFinder algorithm, designed to detect atypical or novel classes of secondary metabolite gene clusters, predicted 18 such clusters in the genome. Screening of a Tn5 mutant library yielded an antimicrobial negative transposon mutant. The transposon insertion was located in a gene encoding an HpcH/HpaI aldolase/citrate lyase family protein. This gene is located in a hypothetical cluster predicted by the ClusterFinder, together with the downstream homologs of four nfs genes, that confer production of a non-fluorescent siderophore by P. donghuensis HYS(T). Site-directed inactivation of the HpcH/HpaI aldolase gene, the adjacent short chain dehydrogenase gene, as well as a homolog of an essential nfs cluster gene, all abolished the antimicrobial activity of the P482, suggesting their involvement in a common biosynthesis pathway. However, none of the mutants showed a decreased siderophore yield, neither was the antimicrobial activity of the wild type P482 compromised by high iron bioavailability. A genomic region comprising the nfs cluster and three upstream genes is involved in the antibacterial activity of P. donghuensis P482 against D. solani and P. carotovorum subsp. brasiliense. The genes studied are unique to the two known P. donghuensis strains. This study illustrates that mining of microbial genomes is a powerful approach for predictingthe presence of novel secondary-metabolite encoding genes especially when coupled with transposon mutagenesis.

Keywords: Dickeya; Pectobacterium; antiSMASH; genome mining; nfs; secondary metabolites

References

  1. Arch Microbiol. 2000 Mar;173(3):170-7 - PubMed
  2. PLoS Genet. 2012 Jul;8(7):e1002784 - PubMed
  3. Am J Respir Crit Care Med. 2005 Jun 1;171(11):1209-23 - PubMed
  4. Mol Syst Biol. 2011 Oct 11;7:539 - PubMed
  5. Annu Rev Phytopathol. 2012;50:403-24 - PubMed
  6. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W347-52 - PubMed
  7. Genome Announc. 2015 Jan 29;3(1):null - PubMed
  8. Nucleic Acids Res. 2000 Jan 1;28(1):27-30 - PubMed
  9. Syst Appl Microbiol. 2011 May;34(3):180-8 - PubMed
  10. Genome Announc. 2014 Jun 26;2(3):null - PubMed
  11. PLoS Pathog. 2011 Jul;7(7):e1002132 - PubMed
  12. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W339-46 - PubMed
  13. Comput Struct Biotechnol J. 2015 Mar 24;13:192-203 - PubMed
  14. J Bacteriol. 2014 Sep;196(18):3259-70 - PubMed
  15. Anal Biochem. 1987 Jan;160(1):47-56 - PubMed
  16. Gene. 1981 Dec;16(1-3):237-47 - PubMed
  17. Nucleic Acids Res. 2010 Jan;38(Database issue):D366-70 - PubMed
  18. Nat Prod Rep. 2009 Nov;26(11):1408-46 - PubMed
  19. Microb Ecol. 2011 Nov;62(4):941-7 - PubMed
  20. J Gen Microbiol. 1955 Dec;13(3):572-81 - PubMed
  21. J Mol Biol. 1997 Jun 27;269(5):719-31 - PubMed
  22. Infect Immun. 1990 Jan;58(1):55-60 - PubMed
  23. J Bacteriol. 1999 Mar;181(5):1415-28 - PubMed
  24. FEBS J. 2005 Oct;272(20):5101-9 - PubMed
  25. PLoS One. 2013 May 17;8(5):e62946 - PubMed
  26. Chem Biol. 2007 Jan;14(1):53-63 - PubMed
  27. Nat Biotechnol. 2005 Jul;23(7):873-8 - PubMed
  28. J Appl Microbiol. 2004;96(3):535-45 - PubMed
  29. Arch Microbiol. 2002 Sep;178(3):193-201 - PubMed
  30. Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91 - PubMed
  31. Appl Microbiol Biotechnol. 2009 Nov;85(1):1-12 - PubMed
  32. BMC Genomics. 2015 Dec 24;16:1103 - PubMed
  33. Int J Syst Bacteriol. 1997 Jul;47(3):846-52 - PubMed
  34. Nucleic Acids Res. 2015 Jul 1;43(W1):W104-8 - PubMed
  35. Front Microbiol. 2015 Mar 18;6:214 - PubMed
  36. J Nat Prod. 2012 Mar 23;75(3):311-35 - PubMed
  37. Genome Biol. 2007;8(1):R10 - PubMed
  38. Nucleic Acids Res. 2015 Jan;43(Database issue):D222-6 - PubMed
  39. Int J Syst Evol Microbiol. 2006 Nov;56(Pt 11):2657-63 - PubMed
  40. Nat Rev Microbiol. 2005 Apr;3(4):307-19 - PubMed
  41. Mol Biol Evol. 2013 Dec;30(12):2725-9 - PubMed
  42. Front Microbiol. 2015 Nov 03;6:1212 - PubMed
  43. Appl Microbiol Biotechnol. 2010 May;86(6):1659-70 - PubMed
  44. J Bacteriol. 1998 Feb;180(3):647-54 - PubMed
  45. Microbiol Mol Biol Rev. 2014 Mar;78(1):1-39 - PubMed
  46. Acc Chem Res. 2012 Mar 20;45(3):463-72 - PubMed
  47. Front Microbiol. 2011 May 02;2:94 - PubMed
  48. Phytopathology. 2007 Feb;97(2):250-6 - PubMed
  49. Cell. 2014 Jul 17;158(2):412-21 - PubMed
  50. PLoS One. 2014 Apr 02;9(4):e93683 - PubMed
  51. J Bacteriol. 2004 Sep;186(17):5649-60 - PubMed
  52. Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18921-6 - PubMed
  53. Antonie Van Leeuwenhoek. 2015 Jan;107(1):83-94 - PubMed
  54. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W160-5 - PubMed
  55. Genome Announc. 2015 Oct 01;3(5):null - PubMed
  56. J Gen Appl Microbiol. 2001 Oct;47(5):247-261 - PubMed
  57. BMC Bioinformatics. 2008 Aug 05;9:329 - PubMed
  58. Microb Biotechnol. 2015 Jul;8(4):716-25 - PubMed
  59. Infect Immun. 2006 Dec;74(12):6949-56 - PubMed
  60. Biotechniques. 1999 May;26(5):824-6, 828 - PubMed
  61. J Antibiot (Tokyo). 2010 Aug;63(8):423-30 - PubMed
  62. Structure. 2001 Jan 10;9(1):R3-9 - PubMed
  63. J Bacteriol. 2012 Aug;194(15):4121 - PubMed
  64. Phytopathology. 2007 Sep;97(9):1150-63 - PubMed
  65. Appl Environ Microbiol. 2008 May;74(10 ):3085-93 - PubMed
  66. J Ind Microbiol. 1995 Sep;15(3):162-8 - PubMed
  67. BMC Bioinformatics. 2009 May 20;10:154 - PubMed
  68. J Bacteriol. 2012 Oct;194(19):5477-8 - PubMed
  69. FEMS Microbiol Rev. 2011 Jul;35(4):652-80 - PubMed
  70. FEMS Microbiol Rev. 2011 Mar;35(2):299-323 - PubMed
  71. Mol Microbiol. 1994 Oct;14(2):347-56 - PubMed
  72. Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31 - PubMed
  73. Mol Plant Microbe Interact. 2006 Jul;19(7):699-710 - PubMed
  74. Syst Appl Microbiol. 2012 May;35(3):145-9 - PubMed
  75. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72 - PubMed
  76. J Appl Microbiol. 2012 Oct;113(4):904-13 - PubMed
  77. J Bacteriol. 2005 Oct;187(20):6962-71 - PubMed
  78. FEMS Microbiol Rev. 2010 Nov;34(6):1037-62 - PubMed
  79. Comput Chem. 2001 Dec;26(1):51-6 - PubMed
  80. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W204-12 - PubMed
  81. PLoS One. 2014 Nov 04;9(11):e110038 - PubMed
  82. FEMS Microbiol Lett. 2009 May;294(2):127-32 - PubMed
  83. Environ Microbiol. 2002 Dec;4(12):787-98 - PubMed
  84. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 - PubMed
  85. FEMS Microbiol Rev. 2008 Jan;32(1):38-55 - PubMed
  86. Appl Environ Microbiol. 2015 Oct 23;82(1):268-78 - PubMed
  87. Proc Natl Acad Sci U S A. 2005 Aug 9;102(32):11414-9 - PubMed
  88. Trends Microbiol. 2007 Jan;15(1):22-30 - PubMed
  89. Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):768-74 - PubMed
  90. Nat Rev Microbiol. 2012 Sep;10(9):599-606 - PubMed

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