The Plant Pathology Journal

The Korean Society of Plant Pathology (한국식물병리학회)
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Genome-Wide Analysis of Type VI System Clusters and Effectors in Burkholderia Species

  • Nguyen, Thao Thi (Department of Microbiology, Pusan National University) ;
  • Lee, Hyun-Hee (Department of Microbiology, Pusan National University) ;
  • Park, Inmyoung (Department of Microbiology, Pusan National University) ;
  • Seo, Young-Su (Department of Microbiology, Pusan National University)
  • Received : 2017.11.09
  • Accepted : 2017.12.04
  • Published : 2018.02.01
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Abstract

Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.

Keywords

References

  1. Abby, S. S., Cury, J., Guglielmini, J., Neron, B., Touchon, M. and Rocha, E. P. C. 2016. Identification of protein secretion systems in bacterial genomes. Sci. Rep. 6:23080. https://doi.org/10.1038/srep23080
  2. Abby, S. S. and Rocha, E. P. C. 2017. Identification of protein secretion systems in bacterial genomes using MacSyFinder. Methods Mol. Biol:1615:1-21.
  3. Alfano, J. R. and Collmer, A. 2004. Type III secretion system effector proteins: double agents in bacterial disease and plant defense. Annu. Rev. Phytopathol. 42:385-414. https://doi.org/10.1146/annurev.phyto.42.040103.110731
  4. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  5. Barret, M., Egan, F., Fargier, E., Morrissey, J. P. and O'Gara, F. 2011. Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered. Microbiology 157:1726-1739. https://doi.org/10.1099/mic.0.048645-0
  6. Bendtsen, J. D., Jensen, L. J., Blom, N., Von Heijne, G. and Brunak, S. 2004. Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng. Des. Sel. 17:349-356. https://doi.org/10.1093/protein/gzh037
  7. Bernal, P., Allsopp, L. P., Filloux, A. and Llamas, M. A. 2017a. The Pseudomonas putida T6SS is a plant warden against phytopathogens. ISME J. 11:972-987. https://doi.org/10.1038/ismej.2016.169
  8. Bernal, P., Llamas, M. A. and Filloux, A. 2017b. Type VI secretion systems in plant-associated bacteria. Environ. Microbiol. doi: 10.1111/1462-2920.13956 (in press).
  9. Bernard, C. S., Brunet, Y. R., Gueguen, E. and Cascales, E. 2010. Nooks and crannies in Type VI secretion regulation. J. Bacteriol. 192:3850-3860. https://doi.org/10.1128/JB.00370-10
  10. Bingle, L. E., Bailey, C. M. and Pallen, M. J. 2008. Type VI secretion: a beginner's guide. Curr. Opin. Microbiol. 11:3-8. https://doi.org/10.1016/j.mib.2008.01.006
  11. Bladergroen, M. R., Badelt, K. and Spaink, H. P. 2003. Infectionblocking genes of a symbiotic Rhizobium leguminosarum strain that are involved in temperature-dependent protein secretion. Mol. Plant-Microbe Interact. 16:53-64. https://doi.org/10.1094/MPMI.2003.16.1.53
  12. Broms, J. E., Meyer, L., Sun, K., Lavander, M. and Sjostedt, A. 2012. Unique substrates secreted by the type VI secretion system of Francisella tularensis during intramacrophage infection. PLoS One 7:20.
  13. Burtnick, M. N., Brett, P. J., Harding, S. V., Ngugi, S. A., Ribot, W. J., Chantratita, N., Scorpio, A., Milne, T. S., Dean, R. E., Fritz, D. L., Peacock, S. J., Prior, J. L., Atkins, T. P. and De-Shazer, D. 2011. The cluster 1 Type VI secretion system is a major virulence determinant in Burkholderia pseudomallei. Infect. Immun. 79:1512-1525. https://doi.org/10.1128/IAI.01218-10
  14. Cascales, E. and Cambillau, C. 2012. Structural biology of type VI secretion systems. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367:1102-1111. https://doi.org/10.1098/rstb.2011.0209
  15. Cianfanelli, F. R., Monlezun, L. and Coulthurst, S. J. 2016. Aim, load, fire: the type VI secretion system, a bacterial nanoweapon. Trends Microbiol. 24:51-62. https://doi.org/10.1016/j.tim.2015.10.005
  16. Coenye, T. and Vandamme, P. 2003. Diversity and significance of Burkholderia species occupying diverse ecological niches. Environ. Microbiol. 5:719-729. https://doi.org/10.1046/j.1462-2920.2003.00471.x
  17. Compant, S., Nowak, J., Coenye, T., Clement, C. and Ait Barka, E. 2008. Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol. Rev. 32:607-626. https://doi.org/10.1111/j.1574-6976.2008.00113.x
  18. de Bruin, O. M., Duplantis, B. N., Ludu, J. S., Hare, R. F., Nix, E. B., Schmerk, C. L., Robb, C. S., Boraston, A. B., Hueffer, K. and Nano, F. E. 2011. The biochemical properties of the Francisella pathogenicity island (FPI)-encoded proteins IglA, IglB, IglC, PdpB and DotU suggest roles in type VI secretion. Microbiology 157:3483-3491. https://doi.org/10.1099/mic.0.052308-0
  19. De Maayer, P., Venter, S. N., Kamber, T., Duffy, B., Coutinho, T. A. and Smits, T. H. M. 2011. Comparative genomics of the type VI secretion systems of Pantoea and Erwinia species reveals the presence of putative effector islands that may be translocated by the VgrG and Hcp proteins. BMC Genomics 12:576-576. https://doi.org/10.1186/1471-2164-12-576
  20. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797. https://doi.org/10.1093/nar/gkh340
  21. Estrada-de los Santos, P., Vinuesa, P., Martinez-Aguilar, L., Hirsch, A. M. and Caballero-Mellado, J. 2013. Phylogenetic analysis of burkholderia species by multilocus sequence analysis. Curr. Microbiol. 67:51-60. https://doi.org/10.1007/s00284-013-0330-9
  22. Filloux, A., Hachani, A. and Bleves, S. 2008. The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology 154:1570-1583. https://doi.org/10.1099/mic.0.2008/016840-0
  23. Finn, R. D., Clements, J. and Eddy, S. R. 2011. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39:W29-W37. https://doi.org/10.1093/nar/gkr367
  24. Flaugnatti, N., Le, T. T., Canaan, S., Aschtgen, M. S., Nguyen, V. S., Blangy, S., Kellenberger, C., Roussel, A., Cambillau, C., Cascales, E. and Journet, L. 2016. A phospholipase A1 antibacterial Type VI secretion effector interacts directly with the C-terminal domain of the VgrG spike protein for delivery. Mol. Microbiol. 99:1099-1118. https://doi.org/10.1111/mmi.13292
  25. Hachani, A., Wood, T. E. and Filloux, A. 2016. Type VI secretion and anti-host effectors. Curr. Opin. Microbiol. 29:81-93. https://doi.org/10.1016/j.mib.2015.11.006
  26. Ham, J. H., Melanson, R. A. and Rush, M. C. 2011. Burkholderia glumae: next major pathogen of rice? Mol. Plant Pathol. 12:329-339. https://doi.org/10.1111/j.1364-3703.2010.00676.x
  27. Jeong, Y., Kim, J., Kim, S., Kang, Y., Nagamatsu, T. and Hwang, I. 2003. Toxoflavin produced by Burkholderia glumae causing rice grain rot is responsible for inducing bacterial wilt in many field crops. Plant Dis. 87:890-895. https://doi.org/10.1094/PDIS.2003.87.8.890
  28. Jiang, F., Waterfield, N., Yang, J., Yang, G. and Jin, Q. 2014. A Pseudomonas aeruginosa type VI secretion phospholipase D effector targets both prokaryotic and eukaryotic cells. Cell Host Microbe 15:600-610. https://doi.org/10.1016/j.chom.2014.04.010
  29. Jones, D. T., Taylor, W. R. and Thornton, J. M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
  30. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E. L. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580. https://doi.org/10.1006/jmbi.2000.4315
  31. Li, J., Yao, Y., Xu, H. H., Hao, L., Deng, Z., Rajakumar, K. and Ou, H.-Y. 2015. SecReT6: a web-based resource for type VI secretion systems found in bacteria. Environ. Microbiol. 17:2196-2202. https://doi.org/10.1111/1462-2920.12794
  32. Ma, J., Sun, M., Bao, Y., Pan, Z., Zhang, W., Lu, C. and Yao, H. 2013. Genetic diversity and features analysis of type VI secretion systems loci in avian pathogenic Escherichia coli by wide genomic scanning. Infect. Genet. Evol. 20:454-464. https://doi.org/10.1016/j.meegid.2013.09.031
  33. Marchler-Bauer, A., Lu, S., Anderson, J. B., Chitsaz, F., Derbyshire, M. K., DeWeese-Scott, C., Fong, J. H., Geer, L. Y., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Jackson, J. D., Ke, Z., Lanczycki, C. J., Lu, F., Marchler, G. H., Mullokandov, M., Omelchenko, M. V., Robertson, C. L., Song, J. S., Thanki, N., Yamashita, R. A., Zhang, D., Zhang, N., Zheng, C. and Bryant, S. H. 2011. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 39:D225-D229. https://doi.org/10.1093/nar/gkq1189
  34. Mitter, B., Petric, A., Shin, M. W., Chain, P. S., Hauberg-Lotte, L., Reinhold-Hurek, B., Nowak, J. and Sessitsch, A. 2013. Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front. Plant Sci. 4:120.
  35. Mougous, J. D., Cuff, M. E., Raunser, S., Shen, A., Zhou, M., Gifford, C. A., Goodman, A. L., Joachimiak, G., Ordonez, C. L., Lory, S., Walz, T., Joachimiak, A. and Mekalanos, J. J. 2006. A virulence locus of Pseudomonas aeruginosa encodes a protein secretion apparatus. Science 312:1526-1530. https://doi.org/10.1126/science.1128393
  36. Petersen, T. N., Brunak, S., von Heijne, G. and Nielsen, H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8:785-786. https://doi.org/10.1038/nmeth.1701
  37. Pukatzki, S., Ma, A. T., Sturtevant, D., Krastins, B., Sarracino, D., Nelson, W. C., Heidelberg, J. F. and Mekalanos, J. J. 2006. Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system. Proc. Natl. Acad. Sci. U.S.A. 103:1528-1533. https://doi.org/10.1073/pnas.0510322103
  38. Rao, P. S., Yamada, Y., Tan, Y. P. and Leung, K. Y. 2004. Use of proteomics to identify novel virulence determinants that are required for Edwardsiella tarda pathogenesis. Mol Microbiol. 53:573-586. https://doi.org/10.1111/j.1365-2958.2004.04123.x
  39. Russell, A. B., LeRoux, M., Hathazi, K., Agnello, D. M., Ishikawa, T., Wiggins, P. A., Wai, S. N. and Mougous, J. D. 2013. Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors. Nature 496:508-512. https://doi.org/10.1038/nature12074
  40. Russell, A. B., Peterson, S. B. and Mougous, J. D. 2014a. Type VI secretion system effectors: poisons with a purpose. Nat. Rev. Microbiol. 12:137-148. https://doi.org/10.1038/nrmicro3185
  41. Russell, A. B., Singh, P., Brittnacher, M., Bui, N. K., Hood, R. D., Carl, M. A., Agnello, D. M., Schwarz, S., Goodlett, D. R., Vollmer, W. and Mougous, J. D. 2012. A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach. Cell Host Microbe 11:538-549. https://doi.org/10.1016/j.chom.2012.04.007
  42. Russell, A. B., Wexler, A. G., Harding, B. N., Whitney, J. C., Bohn, A. J., Goo, Y. A., Tran, B. Q., Barry, N. A., Zheng, H., Peterson, S. B., Chou, S., Gonen, T., Goodlett, D. R., Goodman, A. L. and Mougous, J. D. 2014b. A type VI secretionrelated pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe 16:227-236. https://doi.org/10.1016/j.chom.2014.07.007
  43. Ryu, C.-M. 2015. Against friend and foe: type 6 effectors in plant-associated bacteria. J. Microbiol. 53:201-208. https://doi.org/10.1007/s12275-015-5055-y
  44. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  45. Salomon, D., Kinch, L. N., Trudgian, D. C., Guo, X., Klimko, J. A., Grishin, N. V., Mirzaei, H. and Orth, K. 2014. Marker for type VI secretion system effectors. Proc. Natl. Acad. Sci. U.S.A. 111:9271-9276. https://doi.org/10.1073/pnas.1406110111
  46. Schell, M. A., Ulrich, R. L., Ribot, W. J., Brueggemann, E. E., Hines, H. B., Chen, D., Lipscomb, L., Kim, H. S., Mrazek, J., Nierman, W. C. and Deshazer, D. 2007. Type VI secretion is a major virulence determinant in Burkholderia mallei. Mol. Microbiol. 64:1466-1485. https://doi.org/10.1111/j.1365-2958.2007.05734.x
  47. Schwarz, S., West, T. E., Boyer, F., Chiang, W.-C., Carl, M. A., Hood, R. D., Rohmer, L., Tolker-Nielsen, T., Skerrett, S. J. and Mougous, J. D. 2010. Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions. PLoS Pathog. 6:e1001068. https://doi.org/10.1371/journal.ppat.1001068
  48. Silverman, J. M., Austin, L. S., Hsu, F., Hicks, K. G., Hood, R. D. and Mougous, J. D. 2011. Separate inputs modulate phosphorylation-dependent and -independent type VI secretion activation. Mol. Microbiol. 82:1277-1290. https://doi.org/10.1111/j.1365-2958.2011.07889.x
  49. Solis, R., Bertani, I., Degrassi, G., Devescovi, G. and Venturi, V. 2006. Involvement of quorum sensing and RpoS in rice seedling blight caused by Burkholderia plantarii. FEMS Microbiol. Lett. 259:106-112. https://doi.org/10.1111/j.1574-6968.2006.00254.x
  50. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30:2725-2729. https://doi.org/10.1093/molbev/mst197
  51. Thompson, J. D., Higgins, D. G. and Gibson, T. J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. https://doi.org/10.1093/nar/22.22.4673
  52. Tseng, T.-T., Tyler, B. M. and Setubal, J. C. 2009. Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol. 9:S2. https://doi.org/10.1186/1471-2180-9-S1-S2
  53. Ura, H., Furuya, N., Iiyama, K., Hidaka, M., Tsuchiya, K. and Matsuyama, N. 2006. Burkholderia gladioli associated with symptoms of bacterial grain rot and leaf-sheath browning of rice plants. J. Gen. Plant Pathol. 72:98-103. https://doi.org/10.1007/s10327-005-0256-6
  54. Veluchamy, A., Mary, S., Acharya, V., Mehta, P., Deva, T. and Krishnaswamy, S. 2009. HNHDb: a database on pattern based classification of HNH domains reveals functional relevance of sequence patterns and domain associations. Bioinformation 4:80-83. https://doi.org/10.6026/97320630004080