[논문]Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing

Jee, Samnyu; Kang, In-Jeong; Bak, Gyeryeong; Kang, Sera; Lee, Jeongtae; Heu, Sunggi; Hwang, Ingyu

doi:10.5423/ppj.ft.09.2021.0147

Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing 원문보기

The plant pathology journal, v.38 no.1, 2022년, pp.12 - 24

Jee, Samnyu (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration) , Kang, In-Jeong (Department of Agricultural Biotechnology, Seoul National University) , Bak, Gyeryeong (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration) , Kang, Sera (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration) , Lee, Jeongtae (Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration) , Heu, Sunggi (Department of Plant Science, College of Agriculture and Life Science, Seoul National University) , Hwang, Ingyu (Department of Agricultural Biotechnology, Seoul National University)

Abstract ▼ AI-Helper

In this study, we conducted whole-genome sequencing with six species of Pectobacterium composed of seven strains, JR1.1, BP201601.1, JK2.1, HNP201719, MYP201603, PZ1, and HC, for the analysis of pathogenic factors associated with the genome of Pectobacterium. The genome sizes ranged from 4,724,337 bp to 5,208,618 bp, with the GC content ranging from 50.4% to 52.3%. The average nucleotide identity was 98% among the two Pectobacterium species and ranged from 88% to 96% among the remaining six species. A similar distribution was observed in the carbohydrate-active enzymes (CAZymes) class and extracellular plant cell wall degrading enzymes (PCWDEs). HC showed the highest number of enzymes in CAZymes and the lowest number in the extracellular PCWDEs. Six strains showed four subsets, and HC demonstrated three subsets, except hasDEF, in type I secretion system, while the type II secretion system of the seven strains was conserved. Components of human pathogens, such as Salmonella pathogenicity island 1 type type III secretion system (T3SS) and effectors, were identified in PZ1; T3SSa was not identified in HC. Two putative effectors, including hrpK, were identified in seven strains along with dspEF. We also identified 13 structural genes, six regulator genes, and five accessory genes in the type VI secretion system (T6SS) gene cluster of six Pectobacterium species, along with the loss of T6SS in PZ1. HC had two subsets, and JK2.1 had three subsets of T6SS. With the GxSxG motif, the phospholipase A gene did locate among tssID and duf4123 genes in the T6SSa cluster of all strains. Important domains were identified in the vgrG/paar islands, including duf4123, duf2235, vrr-nuc, and duf3396.

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표/그림 (9)

표 Table 1. Genomic data of seven Pectobacterium strains identified in South Korean collection
그림 Fig. 1. Comparison of whole-genome sequences of seven Pectobacterium strains by progressive Mauve alignment. Same local collinear blocks denote conserved parts between genomes. In the genome of a strain, white segments indicate low-similarity or unique regions compare with other genomes. Under boxes of the central line indicate inverted regions. Ppa, Pectobacterium parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, P. carotovorum; Pve, P. versatile.
그림 Fig. 2. Analysis of average nucleotide identity (ANI) values, in silico DNA-DNA hybridization (isDDH) values, and phylogeny of the seven isolated strains. (A) Yellow indicates isDDH, and red indicates ANI. Two values were calculated as percentages among 20 strains. (B) Phylogenetic tree was constructed with 20 strains including 13 reference strains using binary pan-matrix. Isolated strains are indicated in bold. Pod, Pectobacterium odoriferum; Pca, P. carotovorum; Pve, P. versatile; Pbr, P. brasiliense; Ppo, P. polaris; Ppv, P. parvum; Par, P. aroidearum; Ppu, P. punjabense; Ppa, P. parmentieri; Pwa, P. wasabiae; Pat, P. atrosepticum; Dfa, Dickeya fangzhongdai; Dda, D. dadantii.
그림 Fig. 3. Comparison of coding sequences using cluster of orthologous group classification with seven strains. Ppa, Pectobacterium parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, P. carotovorum; Pve, P. versatile.
그림 Fig. 4. Distribution of carbohydrate-active enzymes (CAZymes) in Pectobacterium species. (A) The average of CAZymes was calculated as percentages among the seven strains. (B) Each CAZymes distribution was compared among the seven Pectobacterium strains. AA, auxiliary activities; CBM, carbohydrate-binding module; CE, carbohydrate esterase; GH, glycoside hydrolase; GT, glycosyltransferase; PL, polysaccharide lyase; Ppa, Pectobacterium parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, P. carotovorum; Pve, P. versatile.
그림 Fig. 5. Physical map of type I secretion system (T1SS) and type II secretion system (T2SS) in Pectobacterium strains. (A) a-d represent different gene clusters of T1SS. (B) T2SS was compared among seven strains. Ppa, Pectobacterium parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, P. carotovorum; Pve, P. versatile.
그림 Fig. 6. Open reading frame maps of structural gene clusters and effector genes of type III secretion system (T3SS) in South Korean Pectobacterium collection. The double-slash indicates long-distance in the genome. (A) Different gene clusters in a genome sequence are indicated as a-c. (B) dspEF, effector-chaperone pair of Pectobacterium, putative effectors including hrpK, and effectors of animal pathogen, yopJ and nleE/ospZ, were identified. Ppa, Pectobacterium parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, P. carotovorum; Pve, P. versatile.
그림 Fig. 7. Open reading frame maps of type VI secretion system (T6SS) and motif of putative effector in South Korean Pectobacterium collection. Structural genes included baseplate complex, membrane complex, and tail tube/sheath complex in T6SS. Accessory genes included chaperons and immune genes. Double slash refers to long distances in the genome. (A) a-d represent different gene clusters of the T6SS. (B) Putative effector, pla, had the typical motif of phospholipase A. Ppa, Pectobacterium parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, P. carotovorum; Pve, P. versatile; sel1, sel1-like repeat; ank, ankyrin repeat domain; sh3, bacterial src homology 3 domain; pppA, serine-threonine phosphatase; pknl, a serine/threonine-protein kinase; prp, pentapeptide repeat; tsp, transposase.
그림 Fig. 8. Distribution of hcp/vgrG/paar islands in the genome of seven Pectobacterium strains. The blue box indicates the basic component of hcp/vgrG/paar island; yellow box, putative chaperon domain; red box, putative effector domain; green box, putative immune domain. Ppa, P. parmentieri; Ppv, P. parvum; Pod, P. odoriferum; Pbr, P. brasiliense; Pca, Pectobacterium carotovorum; Pve, P. versatile.

참고문헌 (37)

Arizala D Arif M 2019 Genome-wide analyses revealed remarkable heterogeneity in pathogenicity determinants, antimicrobial compounds, and CRISPR-Cas systems of complex phytopathogenic genus Pectobacterium Pathogens 8 247

상세보기
Bailey TL Johnson J Grant CE Noble WS 2015 The MEME suite Nucleic Acids Res 43 W39 W49 25953851

상세보기
Bernal P Llamas MA Filloux A 2018 Type VI secretion systems in plant-associated bacteria Environ Microbiol 20 1 15 29027348
Cascales E Cambillau C 2012 Structural biology of type VI secretion systems Philos Trans R Soc Lond B Biol Sci 367 1102 1111 22411981
Coulthurst S 2019 The Type VI secretion system: a versatile bacterial weapon Microbiology 165 503 515 30893029
Darling ACE Mau B Blattner FR Perna NT 2004 Mauve: multiple alignment of conserved genomic sequence with rearrangements Genome Res 14 1394 1403 15231754

상세보기
Figaj D Ambroziak P Przepiora T Skorko-Glonek J 2019 The role of proteases in the virulence of plant pathogenic bacteria Int J Mol Sci 20 672
Green ER Mecsas J 2016 Bacterial secretion systems: an overview Microbiol Spectr 4 10.1128/microbiolspec VMBF-0012–2015

상세보기
Haft DH DiCuccio M Badretdin A Brover V Chetvernin V O’Neill K Li W Chitsaz F Derbyshire MK Gonzales NR Gwadz M Lu F Marchler GH Song JS Thanki N Yamashita RA Zheng C Thibaud-Nissen F Geer LY Marchler-Bauer A Pruitt KD 2018 Ref-Seq: an update on prokaryotic genome annotation and curation Nucleic Acids Res 46 D851 D860 29112715

상세보기
He X Lu T Zhou X 2021 Whole genome sequencing and comparative genomics analysis of Pectobacterium carotovorum identifies key pathogenic genes Mol Phylogenet Evol 162 107114 33744402

상세보기
Jana B Salomon D 2019 Type VI secretion system: a modular toolkit for bacterial dominance Future Microbiol 14 1451 1463 31718312

상세보기
Jee S Choi J-G Lee Y-G Kwon M Hwang I Heu S 2020 Distribution of Pectobacterium species isolated in South Korea and comparison of temperature effects on pathogenicity Plant Pathol J 36 346 354 32788893
Lee DH Kim J-B Lim J-A Han S-W Heu S 2014 Genetic diversity of Pectobacterium carotovorum subsp. brasiliensis isolated in Korea Plant Pathol J 30 117 124 25288994
Lee DH Lim J-A Koh Y-J Heu S Roh E 2017 The draft genome sequence of Pectobacterium carotovorum subsp. actinidiae KKH3 that infects kiwi plant and potential bioconversion applications Korean J Microbiol 53 323 325

원문보기 상세보기
Li L Yuan L Shi Y Xie X Chai A Wang Q Li B 2019 Comparative genomic analysis of Pectobacterium carotovorum subsp. brasiliense SX309 provides novel insights into its genetic and phenotypic features BMC Genomics 20 486 31195968

상세보기
Li W O’Neill KR Haft DH DiCuccio M Chetvernin V Badretdin A Coulouris G Chitsaz F Derbyshire MK Durkin AS Gonzales NR Gwadz M Lanczycki CJ Song JS Thanki N Wang J Yamashita RA Yang M Zheng C Marchler-Bauer A Thibaud-Nissen F 2021 RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation Nucleic Acids Res 49 D1020 D1028 33270901

상세보기
Li X Ma Y Liang S Tian Y Yin S Xie S Xie H 2018 Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle BMC Genomics 19 889 30526490

상세보기
Lou L Zhang P Piao R Wang Y 2019 Salmonella pathogenicity island 1 (SPI-1) and its complex regulatory network Front Cell Infect Microbiol 9 270 31428589

상세보기
Ma S Dong Y Wang N Liu J Lu C Liu Y 2020 Identification of a new effector-immunity pair of Aeromonas hydrophila type VI secretion system Vet Res 51 71 32448355

상세보기
Ma W Dong FFT Stavrinides J Guttman DS 2006 Type III effector diversification via both pathoadaptation and horizontal transfer in response to a coevolutionary arms race PLoS Genet 2 e209 17194219

상세보기
Mattinen L Nissinen R Riipi T Kalkkinen N Pirhonen M 2007 Host-extract induced changes in the secretome of the plant pathogenic bacterium Pectobacterium atrosepticum Proteomics 7 3527 3537 17726675

상세보기
Meier-Kolthoff JP Carbasse JS Peinado-Olarte RL Göker M 2021 TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes Nucleic Acids Res 50 D801 D807
Moussa HB Pédron J Bertrand C Hecquet A Barny M-A 2021 Pectobacterium quasiaquaticum sp. nov., isolated from waterways Int J Syst Evol Microbiol 71 005042
Nguyen TTH Myrold DD Mueller RS 2019 Distributions of extracellular peptidases across prokaryotic genomes reflect phylogeny and habitat Front Microbiol 10 413 30891022

상세보기
Nykyri J Niemi O Koskinen P Nokso-Koivisto J Pasanen M Broberg M Plyusnin I Törönen P Holm L Pirhonen M Palva ET 2012 Revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen Pectobacterium wasabiae SCC3193 PLoS Pathog 8 e1003013 23133391

상세보기
Pallen MJ Beatson SA Bailey CM 2005 Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perpective FEMS Microbiol Rev 29 201 229 15808742

상세보기
Park DH Kim JS Lee HG Hahm YI Lim CK 1999 Black leg of potato plants by Erwinia carotovora subsp. atroseptica Plant Dis Agric 5 64 66
Park T-H Choi B-S Choi A-Y Choi I-Y Heu S Park B-S 2012 Genome sequence of Pectobacterium carotovorum subsp. carotovorum strain PCC21, a pathogen causing soft rot in Chinese cabbage J Bacteriol 194 6345 6346 23105077

상세보기
Pasanen M Waleron M Schott T Cleenwerck I Misztak A Waleron K Pritchard L Bakr R Degefu Y van der Wolf J Vandamme P Pirhonen M 2020 Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like type III secretion system and low virulence Int J Syst Evol Microbiol 70 2440 2448 32100697

상세보기
Portier P Pédron J Taghouti G Dutrieux C Barny MA 2020 Updated taxonomy of Pectobacterium genus in the CIRM-CFBP bacterial collection: when newly described species reveal “Old” endemic population Microorganisms 8 1441

상세보기
Powell S Forslund K Szklarczyk D Trachana K Roth A Huerta-Cepas J Gabaldón T Rattei T Creevey C Kuhn M Jensen LJ von Mering C Bork P 2014 eggNOG v4.0: nested orthology inference across 3686 organisms Nucleic Acids Res 42 D231 D239 24297252

상세보기
Russell AB LeRoux M Hathazi K Agnello DM Ishikawa T Wiggins PA Wai SN Mougous JD 2013 Diverse type VI secretion phospholipases are functionally plastic antibacterial effectors Nature 496 508 512 23552891

상세보기
Tatusova T DiCuccio M Badretdin A Chetvernin V Nawrocki EP Zaslavsky L Lomsadze A Pruitt KD Borodovsky M Ostell J 2016 NCBI prokaryotic genome annotation pipeline Nucleic Acids Res 44 6614 6624 27342282

상세보기
Visnovsky SB Panda P Taylor R Pitman AR 2017 Draft genome sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, two strains isolated from Actinidia chinensis with symptoms of summer canker in South Korea Genome Announc 5 e00104 e00117 28385839
Wang S Geng Z Zhang H She Z Dong Y 2021 The Pseudomonas aeruginosa PAAR2 cluster encodes a putative VRR-NUC domain-containing effector FEBS J 288 5755 5767 33838074

상세보기
Xu P Wang H Qin C Li Z Lin C Liu W Miao W 2021 Analysis of the taxonomy and pathogenic factors of Pectobacterium aroidearum L6 using whole-genome sequencing and comparative genomics Front Microbiol 12 679102 34276610

상세보기
Zhang H Yohe T Huang L Entwistle S Wu P Yang Z Busk PK Xu Y Yin Y 2018 dbCAN2: a meta server for automated carbohydrate-active enzyme annotation Nucleic Acids Res 46 W95 W101 29771380

상세보기

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