Transcriptome and comparative genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in Pectobacterium and Dickeya spp.

dc.contributor.authorBellieny-Rabelo, Daniel
dc.contributor.authorTanui, Collins Kipngetich
dc.contributor.authorMiguel, Nikki
dc.contributor.authorKwenda, Stanford
dc.contributor.authorShyntum, Divine Yufetar
dc.contributor.authorMoleleki, Lucy Novungayo
dc.contributor.emaillucy.moleleki@up.ac.zaen_ZA
dc.date.accessioned2020-04-12T09:51:01Z
dc.date.available2020-04-12T09:51:01Z
dc.date.issued2019-01
dc.descriptionSupplemental file 1: Overall synteny among strains (Fig. S1); gene conservation (Fig. S2); representativeness of serotype-specific block sizes within GFC region in SRE genomes (Fig. S3); sequence alignment (Fig. S4).en_ZA
dc.descriptionSupplemental file 2: Differential expression summaries of Pcb1692 and D. dadantii during in planta infection (Table S1).en_ZA
dc.descriptionSupplemental file 3: Gene neighborhood screenings and differential expression summary of T6SS elements in Pcb1692 (Table S2).en_ZA
dc.descriptionSupplemental file 4: Identification, gene neighborhood screening, and differential expression of carotovoricin in SRE (Table S3).en_ZA
dc.descriptionSupplemental file 5: Conservation and differential expression of PcbPr1 bacteriophage in Pcb1692 (Table S4).en_ZA
dc.descriptionSupplemental file 6: Differential expression of R. solanacearum Rasop1 and -2 prophages during infection (Table S5).en_ZA
dc.descriptionSupplemental file 7: Conservation, annotation, and gene-neighborhood screenings of GFC regions in SRE (Table S6).en_ZA
dc.descriptionSupplemental file 8 : Species abbreviations and genome build accessions (Table S7).en_ZA
dc.description.abstractSoft-rot Enterobacteriaceae (SRE), typified by Pectobacterium and Dickeya genera, are phytopathogenic bacteria inflicting soft-rot disease in crops worldwide. By combining genomic information from 100 SRE with whole-transcriptome data sets, we identified novel genomic and transcriptional associations among key pathogenicity themes in this group. Comparative genomics revealed solid linkage between the type I secretion system (T1SS) and the carotovoricin bacteriophage (Ctv) conserved in 96.7% of Pectobacterium genomes. Moreover, their coactivation during infection indicates a novel functional association involving T1SS and Ctv. Another bacteriophage-borne genomic region, mostly confined to less than 10% of Pectobacterium strains, was found, presumably comprising a novel lineage-specific prophage in the genus. We also detected the transcriptional coregulation of a previously predicted toxin/immunity pair (WHH and SMI1_KNR4 families), along with the type VI secretion system (T6SS), which includes hcp and/or vgrG genes, suggesting a role in disease development as T6SS-dependent effectors. Further, we showed that another predicted T6SS-dependent endonuclease (AHH family) exhibited toxicity in ectopic expression assays, indicating antibacterial activity. Additionally, we report the striking conservation of the group 4 capsule (GFC) cluster in 100 SRE strains which consistently features adjacently conserved serotype-specific gene arrays comprising a previously unknown organization in GFC clusters. Also, extensive sequence variations found in gfcA orthologs suggest a serotype-specific role in the GfcABCD machinery.en_ZA
dc.description.departmentBiochemistryen_ZA
dc.description.departmentForestry and Agricultural Biotechnology Institute (FABI)en_ZA
dc.description.departmentGeneticsen_ZA
dc.description.departmentMicrobiology and Plant Pathologyen_ZA
dc.description.librarianhj2020en_ZA
dc.description.sponsorshipThe National Research Foundation (NRF), South Africa, through Competitive Funding for Rated Researchers (CFRR 98993), NRF Bioin-formatics and Functional Genomics (BFG 93685), and the NRF Research Technology and Transfer Fund (RTF 98654). D.Y.S. received an NRF BFG postdoctoral fellowship. D.B.-R. received a University of Pretoria postdoctoral fellowship. N.M. was funded by NRF Freestanding, PSA, and University of Pretoria Postgraduate bursaries. C.K.T. was funded by a University of Pretoria bursary.en_ZA
dc.description.urihttp://aem.asm.orgen_ZA
dc.identifier.citationBellieny-Rabelo D, Tanui CK, Miguel N, Kwenda S, Shyntum DY, Moleleki LN. 2019. Transcriptome and comparative genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in Pectobacterium and Dickeya spp. Applied and Environmental Microbiology 85:e02050-18. https://doi.org/10.1128/AEM.02050-18.en_ZA
dc.identifier.issn0099-2240 (print)
dc.identifier.issn1098-5336 (online)
dc.identifier.other10.1128/AEM.02050-18
dc.identifier.urihttp://hdl.handle.net/2263/74126
dc.language.isoenen_ZA
dc.publisherAmerican Society for Microbiologyen_ZA
dc.rights© 2019 American Society for Microbiology. All Rights Reserved.en_ZA
dc.subjectSoft-rot Enterobacteriaceae (SRE)en_ZA
dc.subjectType I secretion system (T1SS)en_ZA
dc.subjectCarotovoricin bacteriophage (Ctv)en_ZA
dc.subjectPectobacteriumen_ZA
dc.subjectDickeyaen_ZA
dc.subjectBacterial capsulesen_ZA
dc.subjectBacteriophagesen_ZA
dc.subjectGenomicsen_ZA
dc.subjectTranscriptome analysisen_ZA
dc.subjectType VI secretion system (T6SS)en_ZA
dc.titleTranscriptome and comparative genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in Pectobacterium and Dickeya spp.en_ZA
dc.typePostprint Articleen_ZA

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