Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

Abstract

Bacterial wilt of potatoes—also called brown rot—is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by sequencing transcripts from infected tissue avoiding prokaryotic RNA enrichment.

The Entner-Doudoroff and Nonoxidative Pentose Phosphate Pathways Bypass Glycolysis and the Oxidative Pentose Phosphate Pathway in Ralstonia solanacearum

“…In addition, on close examination of the publicly available transcriptome data of R. solanacearum strains GMI1000 and UW551 derived from in planta and rich-medium growth (4), it was found that pfk-1 and gnd gene expression levels were not reported (while several other genes such as those of the ED pathway were expressed), potentially owing to their absence. Similarly, the transcriptome analysis by Puigvert et al has no reports of gnd and pfk-1 genes in homologous gene analysis of R. solanacearum strains whereas ED pathway genes were reported (26). These observations further supported our findings that the gnd and pfk-1 genes are inactive or altogether absent in R. solanacearum and that mainly glucose oxidation bypasses glycolysis and OxPPP in favor of the ED pathway and non-OxPPP.…”

Common and distinctive adaptive traits expressed in Dickeya dianthicola and Dickeya solani pathogens when exploiting potato plant host

“…This hypothesis is also supported by the wider range of metabolized amino acids by Dso3337 revealed by the metabolic assays. Our approach analysing expression on tuber slices contrasts to those reported for A. tumefaciens (González‐Mula et al, ), P. syringae (Yu et al ., ) and R. solanacearum (Jacobs et al ., ; Puigvert et al ., ), in which bacteria were recovered from the colonized plant tissues or symptoms. However, some comparisons remain possible on the resource exploitation strategy: a generalist behavior (copiotrophy) in the case of the Dickeya and Agrobacterium pathogens that both exploit abundant and diversified plant metabolites in macerated tissues and plant tumours respectively; a specialist behavior (oligotrophy) in the case of the P. syringae and R. solanacearum that exploit a more limited variety of metabolites that are present on leaf surface and in leaf or root interior and plant vessels.…”

Characterization of CRISPR‐Cas systems in the Ralstonia solanacearum species complex

“…Therefore, the expression profile of the cas genes from RSSC strains may be different in the natural environment. Previous transcriptomic studies have shown that gene expression profiles of RSSC strains drastically change in plants when compared with growth in a synthetic rich medium (Ailloud et al , ; Jacobs et al , ; Puigvert et al , ).…”