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

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 an...

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Autores principales: Tsers, Ivan, Gorshkov, Vladimir, Gogoleva, Natalia, Parfirova, Olga, Petrova, Olga, Gogolev, Yuri
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7570247/
https://www.ncbi.nlm.nih.gov/pubmed/32927917
http://dx.doi.org/10.3390/plants9091176
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author Tsers, Ivan
Gorshkov, Vladimir
Gogoleva, Natalia
Parfirova, Olga
Petrova, Olga
Gogolev, Yuri
author_facet Tsers, Ivan
Gorshkov, Vladimir
Gogoleva, Natalia
Parfirova, Olga
Petrova, Olga
Gogolev, Yuri
author_sort Tsers, Ivan
collection PubMed
description 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.
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spelling pubmed-75702472020-10-28 Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling Tsers, Ivan Gorshkov, Vladimir Gogoleva, Natalia Parfirova, Olga Petrova, Olga Gogolev, Yuri Plants (Basel) Article 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. MDPI 2020-09-10 /pmc/articles/PMC7570247/ /pubmed/32927917 http://dx.doi.org/10.3390/plants9091176 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tsers, Ivan
Gorshkov, Vladimir
Gogoleva, Natalia
Parfirova, Olga
Petrova, Olga
Gogolev, Yuri
Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
title Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
title_full Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
title_fullStr Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
title_full_unstemmed Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
title_short Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling
title_sort plant soft rot development and regulation from the viewpoint of transcriptomic profiling
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7570247/
https://www.ncbi.nlm.nih.gov/pubmed/32927917
http://dx.doi.org/10.3390/plants9091176
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