Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Abstract

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular “players” in plant–Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by “missed” genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease’s development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.

The Modification of Plant Cell Wall Polysaccharides in Potato Plants during Pectobacterium atrosepticum-Caused Infection

“…Pectin degradation-related genes of potato plants were regulated differentially during the infection: PGA-lyases were all downregulated, while among the genes encoding polygalacturonases and RG-I-lyases, both up- and downregulated ones were revealed ( Table S2 ). Interestingly, a similar expression pattern of pectin degradation-related genes was observed in Pba -infected tobacco plants [ 13 ]. One of the most infection-upregulated tobacco genes, LOC107816998, encoding the RG-I-lyase had the similar gene in potato (PGSC0003DMG400014600) which was also among the most upregulated ones in the course of Pba -caused infection ( Table S4 ).…”

“…In fact, we mentioned that the similar genes of potato (this study) and tobacco [ 13 ] had mostly similar expression patterns during Pba -caused infection compared to non-infected plants ( Table S4 ). This indicates that the transcriptional responses of experimental and natural hosts to Pba -caused infection are similar in general (with some unique features) at least for PCW-related genes.…”

“…Such modification, along with the action of expansins, provides PCW loosening and stretching, e.g., during cell extension growth and fruit ripening [ 41 , 42 ]. In our previous study on tobacco plants, based on RNA-Seq data, we have proposed that the observed upregulation of XTH- and expansin-encoding genes during Pba -caused infection might promote the release of RG-I fragments from the PCW and facilitate PCW degradation by increasing the availability of polymers to the corresponding enzymes [ 13 ]. In Pba -infected potato plants, the infection-upregulated XTH- and expansin-encoding genes were also revealed (this study).…”

“…The release of RG-I occurs even before the bacterial cells invade a vessel and can, thus, be attributed to the action of only plant, but not bacterial, enzymes/proteins. Plant RG-I lyases, XETs, and expansins encoded by plant genes upregulated during Pba -caused infection in tobacco were predicted to be involved in the release of RG-I [ 13 ].…”

The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems

“…Pectobacteria are also known to proliferate stealthily for a while in the vascular tissues before switching to a brute force attack of surrounding tissues via the massive secretion of plant cell wall hydrolases ( Toth and Birch, 2005 ). Our previous work showed that initiation and development of the Pectobacterium -plant pathosystem requires extensive reprogramming of gene expression, both in the pathogen and its host ( Gorshkov et al, 2018 ; Tsers et al, 2020 ). Such transcriptional reprogramming obviously involves multiple transcription factors.…”