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bioRxiv · 10.1101/391854

Transcriptome and Comparative Genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in Pectobacterium and Dickeya spp

Bellieny-Rabelo, D.·Kipngetich Tanui, C.·Miguel, N.·Kwenda, S.·Yufetar Shyntum, D.·Novungayo Moleleki, L.
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Abstract

Soft-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 datasets, we identified novel genomic and transcriptional associations amongst 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 co-activation during infection might indicate a novel functional association involving T1SS/Ctv. Another bacteriophage-borne genomic region mostly confined in less than 10% of Pectobacterium organisms was found, presumably comprising a novel lineage-specific prophage in the genus. We also detected the transcriptional co-regulation of a previously predicted toxin/immunity pair (WHH and SMI1_KNR4 families) along with type VI secretion system (T6SS) and hcp/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 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.

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Bellieny-Rabelo, D., Kipngetich Tanui, C., Miguel, N., Kwenda, S., Yufetar Shyntum, D., Novungayo Moleleki, L.. 2018-08-16. Transcriptome and Comparative Genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in Pectobacterium and Dickeya spp. https://doi.org/10.1101/391854

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