A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii

Abstract

Pantoea beijingensis, a gram-negative pathogenic bacterium, causes soft rot disease in the fungus Pleurotus eryngii in China. However, the taxonomic classification of this pathogen is controversial due to close relationships between bacteria of the genera Pantoea and Erwinia. This study aimed to resolve the identity of P. beijingensis using phylogenomic and systematic analyses of Pantoea and Erwinia by whole-genome sequencing. Single-copy orthologs identified from the Erwinia/Pantoea core genomes were used to delineate Erwinia/Pantoea phylogeny. P. beijingensis LMG27579T clustered within a single Erwinia clade. A whole-genome-based phylogenetic tree and average nucleotide and amino-acid identity values indicate that P. beijingensis LMG27579T should be renamed Erwinia beijingensis. The hrp/hrc genes encoding type III secretion system (T3SS) proteins in Erwinia and Pantoea were divided into five groups according to gene contents and organization. Neighbor-joining-inferred phylogenetic trees based on concatenated HrcU, HrcN, and HrcR in the main hrp/hrc cluster showed that E. beijingensis T3SS proteins are closely related to those in Ewingella americana, implying that E. beijingensis and E. americana have a recent common hrp/hrc gene ancestor. Furthermore, T3SS proteins of Erwinia and Pantoea were clustered in different clades separated by other bacterial T3SS proteins. Thus, T3SS genes in Pantoea and Erwinia strains might have been acquired by horizontal gene transfer. Overall, our findings clarify the taxonomy of the bacterium causing soft rot in P. eryngii, as well as the genetic structure and classification of the hrp/hrc T3SS virulence factor. We propose that T3SS acquisition is important for E. beijingensis emergence and pathogenesis.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  1. 1.

    Walterson AM, Stavrinides J (2015) Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiol Rev 39:968–984

    CAS  Article  Google Scholar 

  2. 2.

    Prakash O, Nimonkar Y, Vaishampayan A, Mishra M, Kumbhare S, Josef N, Shouche YS (2015) Pantoea intestinalis sp. nov., isolated from the human gut. Int J Syst Evol Microbiol 65:3352–3358

    CAS  Article  Google Scholar 

  3. 3.

    Zhang Y, Qiu S (2015) Examining phylogenetic relationships of Erwinia and Pantoea species using whole genome sequence data. Antonie Van Leeuwenhoek 108:1037–1046

    Article  Google Scholar 

  4. 4.

    Young JM, Park DC (2007) Relationships of plant pathogenic enterobacteria based on partial atpD, carA, and recA as individual and concatenated nucleotide and peptide sequences. Syst Appl Microbiol 30:343–354

    CAS  Article  Google Scholar 

  5. 5.

    Brady C, Cleenwerck I, Venter S, Vancanneyt M, Swings J, Coutinho T (2008) Phylogeny and identification of Pantoea species associated with plants, humans and the natural environment based on multilocus sequence analysis (MLSA). Syst Appl Microbiol 31:447–460

    CAS  Article  Google Scholar 

  6. 6.

    Zhang Y, Fan Q, Loria R (2016) A re-evaluation of the taxonomy of phytopathogenic genera Dickeya and Pectobacterium using whole-genome sequencing data. Syst Appl Microbiol 39:252–259

    Article  Google Scholar 

  7. 7.

    Kim MK, Ryu JS, Lee YH, Kim HR (2013) Breeding of a long shelf-life strain for commercial cultivation by mono–mono crossing in Pleurotus eryngii. Sci Hortic 162:265–270

    Article  Google Scholar 

  8. 8.

    Liu Y, Wang SX, Zhang DP, Wei SJ, Zhao S, Chen SF, Xu F (2013) Pantoea beijingensis sp nov., isolated from the fruiting body of Pleurotus eryngii. Antonie Van Leeuwenhoek 104:1039–1047

    CAS  Article  Google Scholar 

  9. 9.

    Ma YW, Liu Y, Wang SX, Zhang DP, Zhao S, Xu F (2014) Occurrence of Pantoea beijingensis on Pleurotus eryngii in China. J Plant Pathol 96:433

    Google Scholar 

  10. 10.

    Ruiying Z, Dandan H, Jinggang G, Xuemei Z, Qingxiu H (2013) Isolation and identification of pathogenic bacteria from Pleurotus eryngii of soft rot fruiting bodies. Acta edulis fungi 20(3):43–49

    Google Scholar 

  11. 11.

    Kuhlen L, Abrusci P, Johnson S, Gault J, Deme J, Caesar J, Dietsche T, Mebrhatu MT, Ganief T, Macek B et al (2018) Structure of the core of the type III secretion system export apparatus. Nat Struct Mol Biol 25:583–590

    CAS  Article  PubMed Central  Google Scholar 

  12. 12.

    Kato J, Dey S, Soto JE, Butan C, Wilkinson MC, De Guzman RN, Galan JE (2018) A protein secreted by the Salmonella type III secretion system controls needle filament assembly. Elife. https://doi.org/10.7554/eLife.35886

    Article  PubMed Central  Google Scholar 

  13. 13.

    Lynch JP, Lesser CF (2018) Host-pathogen interactions: What the EHEC are we learning from host genome-wide Screens? MBio 9:5

    Article  Google Scholar 

  14. 14.

    Hu Y, Huang H, Cheng X, Shu X, White AP, Stavrinides J, Koster W, Zhu G, Zhao Z, Wang Y (2017) A global survey of bacterial type III secretion systems and their effectors. Environ Microbiol 19:3879–3895

    CAS  Article  PubMed Central  Google Scholar 

  15. 15.

    He TT, Zhou Y, Liu YL, Li DY, Nie P, Li AH, Xie HX (2020) Edwardsiella piscicida type III protein EseJ suppresses apoptosis through down regulating type 1 fimbriae, which stimulate the cleavage of caspase-8. Cell Microbiol. https://doi.org/10.1111/cmi.13193

    Article  PubMed Central  Google Scholar 

  16. 16.

    Galan JE, Waksman G (2018) Protein-injection machines in bacteria. Cell 172:1306–1318

    CAS  Article  PubMed Central  Google Scholar 

  17. 17.

    Kirzinger MW, Butz CJ, Stavrinides J (2015) Inheritance of Pantoea type III secretion systems through both vertical and horizontal transfer. Mol Genet Genomics 290:2075–2088

    CAS  Article  PubMed Central  Google Scholar 

  18. 18.

    Buttner D (2016) Behind the lines-actions of bacterial type III effector proteins in plant cells. FEMS Microbiol Rev 40(6):894–937

    Article  PubMed Central  Google Scholar 

  19. 19.

    Lee JH, Zhao Y (2018) Integration of multiple stimuli-sensing systems to regulate HrpS and type III secretion system in Erwinia amylovora. Mol Genet Genomics 293:187–196

    CAS  Article  PubMed Central  Google Scholar 

  20. 20.

    Merighi M, Majerczak DR, Zianni M, Tessanne K, Coplin DL (2006) Molecular characterization of Pantoea stewartii subsp. stewartii HrpY, a conserved response regulator of the Hrp type III secretion system, and its interaction with the hrpS promoter. J Bacteriol 188:5089–5100

    CAS  Article  PubMed Central  Google Scholar 

  21. 21.

    Cui Z, Yuan X, Yang CH, Huntley RB, Sun W, Wang J, Sundin GW, Zeng Q (2018) Development of a method to monitor gene expression in single bacterial cells during the interaction with plants and use to study the expression of the type III secretion system in single cells of Dickeya dadantii in Potato. Front Microbiol 9:1429

    Article  PubMed Central  Google Scholar 

  22. 22.

    White FF, Potnis N, Jones JB, Koebnik R (2009) The type III effectors of Xanthomonas. Mol Plant Pathol 10:749–766

    CAS  Article  PubMed Central  Google Scholar 

  23. 23.

    Xin XF, He SY (2013) Pseudomonas syringae pv. tomato DC3000: a model pathogen for probing disease susceptibility and hormone signaling in plants. Annu Rev Phytopathol 51:473–498

    CAS  Article  Google Scholar 

  24. 24.

    Kim HS, Thammarat P, Lommel SA, Hogan CS, Charkowski AO (2011) Pectobacterium carotovorum elicits plant cell death with DspE/F but the P. carotovorum DspE does not suppress callose or induce expression of plant genes early in plant-microbe interactions. Mol Plant Microbe Interact 24:773–786

    CAS  Article  Google Scholar 

  25. 25.

    Tampakaki AP, Skandalis N, Gazi AD, Bastaki MN, Sarris PF, Charova SN, Kokkinidis M, Panopoulos NJ (2010) Playing the “Harp”: evolution of our understanding of hrp/hrc genes. Annu Rev Phytopathol 48:347–370

    CAS  Article  Google Scholar 

  26. 26.

    Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679

    CAS  Article  PubMed Central  Google Scholar 

  27. 27.

    Xie JB, Du Z, Bai L, Tian C, Zhang Y, Xie JY, Wang T, Liu X, Chen X, Cheng Q et al (2014) Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes. PLoS Genet 10(3):e1004231

    Article  PubMed Central  Google Scholar 

  28. 28.

    Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131

    CAS  Article  PubMed Central  Google Scholar 

  29. 29.

    Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12

    Article  PubMed Central  Google Scholar 

  30. 30.

    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  Article  Google Scholar 

  31. 31.

    Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552

    CAS  Article  Google Scholar 

  32. 32.

    Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

    CAS  Article  Google Scholar 

  33. 33.

    Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    CAS  PubMed Central  Google Scholar 

  34. 34.

    Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–1247

    CAS  Article  Google Scholar 

  35. 35.

    Cleenwerck I, Vandemeulebroecke K, Janssens D, Swings J (2002) Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int J Syst Evol Microb 52:1551–1558

    CAS  Google Scholar 

  36. 36.

    Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  37. 37.

    Medlar AJ, Toronen P, Holm L (2018) AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination. Nucleic Acids Res 46:W479–W485

    CAS  Article  PubMed Central  Google Scholar 

  38. 38.

    Salichos L, Rokas A (2013) Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497:327–331

    CAS  Article  PubMed Central  Google Scholar 

  39. 39.

    Naum M, Brown EW, Mason-Gamer RJ (2009) Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens. Microbiology 155:3187–3199

    CAS  Article  PubMed Central  Google Scholar 

  40. 40.

    Hassan S, Amer S, Mittal C, Sharma R (2012) Ewingella americana: an emerging true pathogen. Case Rep Infect Dis 2012:730720

    PubMed Central  Google Scholar 

  41. 41.

    Ryoo NH, Ha JS, Jeon DS, Kim JR, Kim HC (2005) A case of Pneumonia caused by Ewingella americana in a patient with chronic renal failure. J Korean Med Sci 20:143–145

    Article  PubMed Central  Google Scholar 

  42. 42.

    Lee CJ, Jhune CS, Cheong JC, Yun HS, Cho WD (2009) Occurrence of internal stipe necrosis of cultivated mushrooms (Agaricus bisporus) caused by Ewingella americana in Korea. Mycobiology 37(1):62–66

    Article  PubMed Central  Google Scholar 

Download references

Funding

This work was supported by National Natural Science Foundation of China (NSFC 31701975).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Jianbo Xie or Chengbo Rong.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (xlsx 24 kb)

Supplementary file2 (docx 630 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Xu, F., Yan, H., Liu, Y. et al. A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii. Curr Microbiol (2020). https://doi.org/10.1007/s00284-020-02253-3

Download citation