GENOME ANALYSIS OF Pseudomonas brassicacearum S-1 – AN ANTAGONIST OF CROP PATHOGENS A. A. Muratova, A. E. Akhremchuk, L. N. Valentovich

Details: Hits: 704

ISSN 2410-7751 (Print)
ISSN 2410-776X (Online)

Biotechnologia Acta V. 14, No 2, 2021
Р. 47-58, Bibliography 37, English
Universal Decimal Classification:
https://doi.org/10.15407/biotech14.02.047

GENOME ANALYSIS OF Pseudomonas brassicacearum S-1 – AN ANTAGONIST OF CROP PATHOGENS

A. A. Muratova, A. E. Akhremchuk, L. N. Valentovich

Institute of Microbiology of the National Academy of Sciences of Belarus, Minsk

The strain Pseudomonas brassicacearum S-1 is the basis of the biopesticide “Ecogreen”, which is used to control pathogens infecting vegetable and green spicy crops in small-scale hydroponics.

Aim. The purpose of this work was to sequence and analyze the nucleotide sequence of the genome of strain P. brassicacearum S-1 (GenBank accession number CP045701).

Methods. Whole-genome sequencing was performed by both MiSeq (Illuminа) and MinION (Oxford Nanopore). Analysis of the genome sequence was performed with a number of bioinformatics programs.

Results. The genome of the P. brassicacearum S-1 strain comprising a single circular 6 577 561-bp chromosome with GC content of 60.8 %. Genome analysis revealed genes that constitute valuable biotechnological potential of the S-1 strain and determine synthesis of a wide range of secondary metabolites. Moreover, mobile genetic elements, prophages and short repetitive sequences were identified in the S-1 genome.

Conclusions. Detected genetic determinants, which are responsible for the synthesis of practically valuable compounds, indicate a significant potential of the P. brassicacearum S-1 strain as a biocontrol agent.

Key words: genome, sequencing, Pseudomonas brassicacearum, secondary metabolites, biocontrol.

References

1. Moraes Bazioli J., Belinato J. R., Costa J. H., Akiyama D. Y., Pontes J. G. M., Kupper K. C., Augusto F., de Carvalho J. E., Fill T. P. Biological Control of Citrus Postharvest Phytopathogens. J. Toxins. 2019, 11 (8), 460. https://doi.org/10.3390/toxins11080460

2. Nelkner J, Tejerizo G. T., Hassa J., Lin T. W., Witte J., Verwaaijen B., Winkler A., Bunk B., Spr?er C., Overmann J., Grosch R., P?hler A., Schl?ter A. A. Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics. Genes. 2019, 10 (8), 601. https://doi.org/10.3390/genes10080601

3. Stockwell V. O., Stack J. P. Using Pseudomonas spp. for Integrated Biological Control. Phytopathology. 2007, 97 (2), 244-249. https://doi.org/10.1094/PHYTO-97-2-0244

4. Kolomiets E. I., Kuptsov V. N., Sverchkova N. V., Evsegneeva N. V., Mandryk-Litvinkovich M. N., Mishin L. T., Voitka D. V., Rapoport A. I., Khrustaly G. M. Bacteria Pseudomonas aurantiaca BIM B-446 - the basis of biopesticide ecogreen intended for control of vegetable and green crop pathogens in low-scale hydroponics. Collection of scientific papers "Microbial Biotechnology: Fundamental and Applied Aspects". 2012, V. 4, P. 98-107. (In Russian).

5. Bertels F., Rainey P. B. Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria. PLOS Genet. 2011, 7 (6), P. e1002132. https://doi.org/10.1371/journal.pgen.1002132

6. Decoin V., Barbey C., Bergeau D., Latour X., Feuilloley M. G., Orange N., Merieau A. A type VI secretion system is involved in Pseudomonas fluorescens bacterial competition. PloS One. 2014, 9 (2), P. e89411. https://doi.org/10.1371/journal.pone.0089411

7. Lee S., Kang M., Bae J. H., Sohn J. H., Sung B. H. Bacterial Valorization of Lignin: Strains, Enzymes, Conversion Pathways, Biosensors, and Perspectives. Front. Bioeng. Biotechnol. 2019, V. 7, P. 209. https://doi.org/10.3389/fbioe.2019.00209

8. Gontia-Mishra I., Sasidharan S., Tiwari S. Recent developments in use of 1-aminocyclopropane-1-carboxylate (ACC) deaminase for conferring tolerance to biotic and abiotic stress. Biotechnol. Lett. 2014, 36 (5), 889-898. https://doi.org/10.1007/s10529-014-1458-9

9. De Werra P., Pйchy-Tarr M., Keel C., Maurhofer M. Role of gluconic acid production in the regulation of biocontrol traits of Pseudomonas fluorescens CHA0. Appl. Environ. Microbiol. 2009, 75 (12), 4162-4174. https://doi.org/10.1128/AEM.00295-09

10. Choi O., Kim J., Kim J. G., Jeong Y., Moon J. S., Park C. S., Hwang I. Pyrroloquinoline Quinone Is a Plant Growth Promotion Factor Produced by Pseudomonas fluorescens B16. Plant Physiol. 2008, 146 (2), 657-668. https://doi.org/10.1104/pp.107.112748

11. Guo Y. B., Li J., Li L., Chen F., Wu W., Wang J., Wang H. Mutations that disrupt either the pqq or the gdh gene of Rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall. Appl. Environ. Microbiol. 2009, 75 (21), 6792-6803. https://doi.org/10.1128/AEM.00902-09

12. Singh P., Singh R. K., Guo D. J., Sharma A., Singh R. N., Li D. P., Malviya M. K., Song X. P., Lakshmanan P., Yang L. T., Li Y. R. Whole Genome Analysis of Sugarcane Root-Associated Endophyte Pseudomonas aeruginosa B18-A Plant Growth-Promoting Bacterium With Antagonistic Potential Against Sporisorium scitamineum. Front. Microbiol. 2021, V. 12, P. 628376. https://doi.org/10.3389/fmicb.2021.628376

13. Mann E. E., Wozniak D. J. Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol. Rev. 2012, 36 (4), 893-916. https://doi.org/10.1111/j.1574-6976.2011.00322.x

14. Ertesvеg H., Sletta H., Senneset M., Sun Y. Q., Klinkenberg G., Konradsen T. A., Ellingsen T. E., Valla S. Identification of genes affecting alginate biosynthesis in Pseudomonas fluorescens by screening a transposon insertion library. BMC Genomics. 2017, 18 (1), 11. https://doi.org/10.1186/s12864-016-3467-7

15. Lammens W., Le Roy K., Schroeven L., Van Laere A., Rabijns A., Van den Ende W. Structural insights into glycoside hydrolase family 32 and 68 enzymes: functional implications. J. Exp. Bot. 2009, 60 (3), 727-740. https://doi.org/10.1093/jxb/ern333

16. Malanovic N., Lohner K. Gram-positive bacterial cell envelopes: The impact on the activity of antimicrobial peptides. Biochim. Biophys. Acta. 2016, 1858 (5), 936-946. https://doi.org/10.1016/j.bbamem.2015.11.004

17. Ye L., Hildebrand F., Dingemans J., Ballet S., Laus G., Matthijs S., Berendsen R., Cornelis P. Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens. PloS One. 2014, 9 (11), e110038. https://doi.org/10.1371/journal.pone.0110038

18. Anand A., Chinchilla D., Tan C., Mиne-Saffranй L., L'Haridon F., Weisskopf L. Contribution of Hydrogen Cyanide to the Antagonistic Activity of Pseudomonas Strains Against Phytophthora infestans. Microorganisms. 2020, 8 (8), 1144. https://doi.org/10.3390/microorganisms8081144

19. Mandryk-Litvinkovich M. N., Muratova A. A., Nosonova T. L., Evdokimova O. V., Valentovich L. N., Titok M. A., Kolomiets E. I. Molecular genetic analysis of determinants defining synthesis of 2,4-diacetylphloroglucinol by Pseudomonas brassicacearum BIM B-446 bacteria. Appl. Biochem. Microbiol. 2017, V. 53, P. 31-39. https://doi.org/10.1134/S0003683817010124

20. Jenul C., Sieber S., Daeppen C., Mathew A., Lardi M., Pessi G., Hoepfner D., Neuburger M., Linden A., Gademann K., Eberl L. Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nat. Commun. 2018, 9 (1), 1297. https://doi.org/10.1038/s41467-018-03690-2

21. Cimermancic P., Medema M. H., Claesen J., Kurita K., Wieland Brown L. C., Mavrommatis K., Pati A., Godfrey P. A., Koehrsen M., Clardy J., Birren B. W., Takano E., Sali A., Linington R. G., Fischbach M. A. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014, 158 (2), 412-421. https://doi.org/10.1016/j.cell.2014.06.034

22. Sagot B., Gaysinski M., Mehiri M., Guigonis J. M., Le Rudulier D., Alloing G. Osmotically induced synthesis of the dipeptide N-acetylglutaminylglutamine amide is mediated by a new pathway conserved among bacteria. Proc. Natl. Acad. Sci. U. S. A. 2010, 107 (28), 12652-12657. https://doi.org/10.1073/pnas.1003063107

23. Chen X. H., Koumoutsi A., Scholz R., Eisenreich A., Schneider K., Heinemeyer I., Morgenstern B., Voss B., Hess W. R., Reva O., Junge H., Voigt B., Jungblut P. R., Vater J., Sьssmuth R., Liesegang H., Strittmatter A., Gottschalk G., Borriss R. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat. Biotechnol. 2007, 25 (9), 1007-1014. https://doi.org/10.1038/nbt1325

24. Kreutzer M. F., Kage H., Nett M. Structure and biosynthetic assembly of cupriachelin, a photoreactive siderophore from the bioplastic producer Cupriavidus necator H16. J. Am. Chem. Soc. 2012, 134 (11), 5415-5422. https://doi.org/10.1021/ja300620z

25. Connolly J. A., Wilson A., Macioszek M., Song Z., Wang L., Mohammad H. H., Yadav M., di Martino M., Miller C. E. Hothersall J., Haines A. S., Stephens E. R., Crump M. P., Willis C. L., Simpson T. J., Winn P. J., Thomas C. M. Defining the genes for the final steps in biosynthesis of the complex polyketide antibiotic mupirocin by Pseudomonas fluorescens NCIMB10586. Sci. Rep. 2019, 9 (1), 1542. https://doi.org/10.1038/s41598-018-38038-9

26. Breil B., Borneman J., Triplett E. W. A newly discovered gene, tfuA, involved in the production of the ribosomally synthesized peptide antibiotic trifolitoxin. J. Bacteriol. 1996, 178 (14), 4150-4156. https://doi.org/10.1128/jb.178.14.4150-4156.1996

27. Michelsen C. F., Watrous J., Glaring M. A., Kersten R., Koyama N., Dorrestein P. C., Stougaard P. Nonribosomal Peptides, Key Biocontrol Components for Pseudomonas fluorescens In5, Isolated from a Greenlandic Suppressive Soil. mBio. 2015, 6 (2), e00079. https://doi.org/10.1128/mBio.00079-15