Characteristics of genes determining the phytopathogenic, phytostimulating and antimicrobial properties of Pseudomonas amygdali pv. lachrymans 8: a causative agent of angular leaf spot of cucumber

This article provides information on the genetic determinants, the products of which underlie both pathoge- nesis and the mechanism of stimulation of plant growth and development by Pseudomonas amygdali pv. lachrymans 8 bacteria. In particular, genes presumably responsible for the manifestation of phytopathogenic properties, encoding the synthesis of lipopolysaccharides, components of secretion systems, enzymes destroying the plant cell wall, flagellar apparatus, and chemotaxis system, were identified within the genome of strain 8. Furthermore, bacteria of strain 8 have genetic determinants whose products of which can positively affect plants. These determinants include genes for the biosynthesis of 1-aminocyclopropane-1-carboxylate deaminase, tryptophan and anthranilate, riboflavin (vitamin B2), as well as genes encoding products that determine the solubilization of inorganic phosphates. In the genome of the strain P. amygdali pv. lachrymans 8, 12 loci responsible for the synthesis of secondary metabolites (nonribosomal peptides, hydrogen cyanide, furan, arylpolyene, N-ace- tylglutaminyl glutaminamide, homoserine lactone and pyoverdine) were identified. These loci have the capacity to impede the effects of other phytopathogenic microorganisms or provide a response to stress effects.

1. Muratova A. A., Akhremchuk A. E., Valentovich L. N. Special aspects of structural and functional organization of the genome of Pseudomonas amygdali pv. lachrymans 8: a causative agent of angular leaf spot of cucumber. Vestsi Natsyyanal’nai akademii navuk Belarusi. Seryya biyalagichnykh navuk = Proceedings of the National Academy of Scien- ces of Belarus. Biological series, 2025, vol. 70, no. 2, pp. 135–145 (in Russian). https://doi.org/10.29235/1029-8940-2025-70-2-135-145

2. Hesse C., Schulz F., Bull C. T., Shaffer B. T., Yan Q., Shapiro N., Hassan K. A., Varghese N., Elbourne L. D. H., Paulsen I. T., Kyrpides N., Woyke T., Loper J. E. Genome-based evolutionary history of Pseudomonas spp. Environmental Microbiology, 2018, vol. 20, no. 6, pp. 2142–2159. https://doi.org/10.1111/1462-2920.14130

3. Yu N. Y., Wagner J. R., Laird M. R., Melli G., Rey S., Lo R., Dao P., Sahinalp S. C., Ester M., Foster L. J., Brinkman F. S. L. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 2010, vol. 26, no. 13, pp. 1608–1615. https://doi.org/10.1093/bioinformatics/btq249

4. Blin K., Shaw S., Augustijn H. E., Reitz Z. L., Biermann F., Alanjary M., Fetter A., Terlouw B. R., Metcalf W. W., Helfrich E. J. N., van Wezel G. P., Medema M. H., Weber T. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Research, 2023, vol. 51, no. W1, pp. W46–W50. https://doi.org/10.1093/nar/gkad344

5. Li L., Yuan L., Shi Y., Xie X., Chai A., Wang Q., Li B. Comparative genomic analysis of Pseudomonas amygdali pv. lachrymans NM002: Insights into its potential virulence genes and putative invasion determinants. Genomics, 2019, vol. 111, no. 6, pp. 1493–1503. https://doi.org/10.1016/j.ygeno.2018.10.004

6. Nikolaichik Y., Damienikan A. U. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PeerJ, 2016, vol. 4, art. e2056. https://doi.org/10.7717/peerj.2056

7. Lam H. N., Chakravarthy S., Wei H.-L., BuiNguyen H., Stodghill P. V., Collmer A., Swingle B. M., Cartinhour S. W. Global Analysis of the HrpL Regulon in the Plant Pathogen Pseudomonas syringae pv. tomato DC3000 Reveals New Regulon Members with Diverse Functions. PLoS One, 2014, vol. 9, no. 8, p. e106115. https://doi.org/10.1371/journal.pone.0106115

8. Chang J. H., Desveaux D., Creason A. L. The ABCs and 123s of bacterial secretion systems in plant pathogenesis. Annual Review of Phytopathology, 2014, vol. 52, pp. 317–345. https://doi.org/10.1146/annurev-phyto-011014-015624

9. van der Hoorn R. A. L., Kamoun S. From Guard to Decoy: A New Model for Perception of Plant Pathogen Effectors. The Plant Cell, 2008, vol. 20, no. 8, pp. 2009–2017. https://doi.org/10.1105/tpc.108.060194

10. Hung N. B., Ramkumar G., Lee Y. H. An effector gene hopA1 influences on virulence, host specificity, and lifestyles of Pseudomonas cichorii JBC1. Res Microbiol, 2014, vol. 165, no. 8, pp. 620–629. https://doi.org/10.1016/j.resmic.2014.08.001

11. Jelenska J., van Hal J. A., Greenberg J. T. Pseudomonas syringae hijacks plant stress chaperone machinery for virulence. Proceedings of the National Academy of Sciences, 2010, vol. 107, no. 29, pp. 13177–13182. https://doi.org/10.1073/pnas.0910943107

12. Jha G., Rajeshwari R., Sonti R. V. Bacterial type two secretion system secreted proteins: double-edged swords for plant pathogens. Molecular Plant-Microbe Interactions, 2005, vol. 18, no. 9, pp. 891–898. https://doi.org/10.1094/mpmi-18-0891

13. Costa T. R. D., Harb L., Khara P., Zeng L., Hu B., Christie P. J. Type IV secretion systems: Advances in structure, function, and activation. Molecular Microbiology, 2021, vol. 115, no. 3, pp. 436–452. https://doi.org/10.1111/mmi.14670

14. Juhas M. Type IV secretion systems and genomic islands-mediated horizontal gene transfer in Pseudomonas and Haemophilus. Microbiological Research, 2015, vol. 170, pp. 10–17. https://doi.org/10.1016/j.micres.2014.06.007

15. Li J., Lee T.-Ch. Bacterial ice nucleation and its potential application in the food industry. Trends in Food Science & Technology, 1995, vol. 6, no. 8, pp. 259–265. https://doi.org/10.1016/s0924-2244(00)89110-4

16. Winsor G. L., Griffiths E. J., Lo R., Dhillon B. K., Shay J. A., Brinkman F. S. L. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Research, 2016, vol. 44, no. D1, pp. D646–653. https://doi.org/10.1093/nar/gkv1227

17. Martorana A. M., Benedet M., Maccagni E. A., Sperandeo P., Villa R., Dehò G., Polissi A. Functional Interaction between the Cytoplasmic ABC Protein LptB and the Inner Membrane LptC Protein, Components of the Lipopolysaccharide Transport Machinery in Escherichia coli. Journal of Bacteriology, 2016, vol. 198, no. 16, pp. 2192–2203. https://doi.org/10.1128/jb.00329-16

18. Panopoulos N. J. Role of Flagellar Motility in the Invasion of Bean Leaves by Pseudomonas phaseolicola. Phytopathology, 1974, vol. 64, no. 11, pp. 1389–1397. https://doi.org/10.1094/phyto-64-1389

19. Hung N. B., Ramkumar G., Bhattacharyya D., Lee Y. H. Elucidation of the functional role of flagella in virulence and ecological traits of Pseudomonas cichorii using flagella absence (ΔfliJ) and deficiency (ΔfliI) mutants. Research in Microbiology, 2016, vol. 167, no. 4, pp. 262–271. https://doi.org/10.1016/j.resmic.2016.01.006

20. Cerna-Vargas J. P., Santamaría-Hernando S., Matilla M. A., Rodríguez-Herva J. J., Daddaoua A., Rodríguez-Palenzuela P., Krell, T., López-Solanilla E. Chemoperception of Specific Amino Acids Controls Phytopathogenicity in Pseudomonas syringae pv. tomato. mBio, 2019, vol. 10, no. 5, p. e01868-19. https://doi.org/10.1128/mBio.01868-19

21. Ichinose Y., Watanabe Y., Tumewu S. A., Matsui H., Yamamoto M., Noutoshi Y., Toyoda K. Requirement of chemotaxis and aerotaxis in host tobacco infection by Pseudomonas syringae pv. tabaci 6605. Physiological and Molecular Plant Pathology, 2023, vol. 124, art. 101970. https://doi.org/10.1016/j.pmpp.2023.101970

22. Gómez-Godínez L. J., Aguirre-Noyola J. L., Martínez-Romero E., Arteaga-Garibay R. I., Ireta-Moreno J., RuvalcabaGómez J. M. A Look at Plant-Growth-Promoting Bacteria. Plants, 2023, vol. 12, no. 8, art. 1668. https://doi.org/10.3390/plants12081668

23. 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. Biotechnology Letters, 2014, vol. 36, no. 5, pp. 889–898. https:// doi.org/10.1007/s10529-014-1458-9

24. 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. Frontiers in Microbiology, 2021, vol. 12, art. 628376. https://doi.org/10.3389/fmicb.2021.628376

25. Deng B., Jin X., Yang Y., Lin Z., Zhang Y. The regulatory role of riboflavin in the drought tolerance of tobacco plants depends on ROS production. Plant Growth Regulation, 2014, vol. 72, no. 3, pp. 269–277. https://doi.org/10.1007/s10725013-9858-8

26. 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 Physiology, 2008, vol. 146, no. 2, pp. 323–324. https://doi.org/10.1104/pp.107.112748

27. Thiemer B., Andreesen J. R., Schräder T. Cloning and characterization of a gene cluster involved in tetrahydrofuran degradation in Pseudonocardia sp. strain K1. Archives of Microbiology, 2003, vol. 179, no. 4, pp. 266–277. https://doi.org/10.1007/s00203-003-0526-7

28. Siddiqui I. A., Shaukat S. Sh., Sheikh I. H., Khan A. Role of cyanide production by Pseudomonas fluorescens CHA0 in the suppression of root-knot nematode, Meloidogyne javanica in tomato. World Journal of Microbiology and Biotechnology, 2006, vol. 22, no. 6, pp. 641–650. https://doi.org/10.1007/s11274-005-9084-2

29. Ramette A., Moënne-Loccoz Y., Défago G. Prevalence of fluorescent pseudomonads producing antifungal phloroglucinols and/or hydrogen cyanide in soils naturally suppressive or conducive to tobacco black root rot. FEMS Microbiology Ecology, 2003, vol. 44, no. 1, pp. 35–43. https://doi.org/10.1111/j.1574-6941.2003.tb01088.x

30. 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, vol. 158, no. 2, pp. 412–421. https://doi.org/10.1016/j.cell.2014.06.034

31. D’Souza-Ault M. R., Smith L. T., Smith G. M. Roles of N-acetylglutaminylglutamine amide and glycine betaine in adaptation of Pseudomonas aeruginosa to osmotic stress. Applied and Environmental Microbiology, 1993, vol. 59, no. 2, pp. 473–478. https://doi.org/10.1128/aem.59.2.473-478.1993

32. Götze S., Herbst-Irmer R., Klapper M., Görls H., Schneider K. R. A., Barnett R., Burks T., Neu U., Stallforth P. Structure, Biosynthesis, and Biological Activity of the Cyclic Lipopeptide Anikasin. ACS Chemical Biology, 2017, vol. 12, no. 10, pp. 2498–2502. https://doi.org/10.1021/acschembio.7b00589

33. Haas D., Défago G. Biological control of soil-borne pathogens by fluorescent pseudomonads. Nature Reviews Microbiology, 2005, vol. 3, no. 4, pp. 307–319. https://doi.org/10.1038/nrmicro1129

34. Liu J., Zhou H., Yang, Zh., Wang X., Chen H., Zhong L., Zheng W., Niu W., Wang S., Ren X., Zhong G., Wang Y., Ding X., Müller R., Zhang Y., Bian X. Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria. Nature Communications, 2021, vol. 12, no. 1, art. 4347. https://doi.org/10.1038/s41467-021-24645-0

35. Shin D., Gorgulla Ch., Boursier M. E., Rexrode N., Brown E. C., Arthanari H., Blackwell H. E., Nagarajan R. N-Acyl Homoserine Lactone Analog Modulators of the Pseudomonas aeruginosa Rhll Quorum Sensing Signal Synthase. ACS Chemical Biology, 2019, vol. 14, no. 10, pp. 2305–2314. https://doi.org/10.1021/acschembio.9b00671

36. Ayoub A. T., Elrefaiy M. A., Arakawa K. Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin. ACS Omega, 2019, vol. 4, no. 2, pp. 4461–4471. https://doi.org/10.1021/acsomega.8b03470

37. Jenul Ch., Sieber S., Daeppen Ch., Mathew A., Lardi M., Pessi G., Hoepfner D., Neuburger M., Linden A., Gade- mann K., Eberl L. Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nature Communications, 2018, vol. 9, no. 1, art. 1297. https://doi.org/10.1038/s41467-018-03690-2

38. Leonard S., Hommais F., Nasser W., Reverchon S. Plant–phytopathogen interactions: bacterial responses to environ- mental and plant stimuli. Environmental Microbiology, 2017, vol. 19, no. 5, pp. 1689–1716. https://doi.org/10.1111/1462-2920.13611