Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.

Plant infection by oomycete pathogens is a complex process. It requires precise expression of a plethora of genes in the pathogen that contribute to a successful interaction with the host. Whereas much effort has been made to uncover the molecular systems underlying this infection process, mechanism...

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Autores principales: Michael F Seidl, Rui-Peng Wang, Guido Van den Ackerveken, Francine Govers, Berend Snel
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Publicado: Public Library of Science (PLoS) 2012
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spelling oai:doaj.org-article:92ea9fa38b8c49babb2a63f340ad788a2021-11-18T08:05:23ZBioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.1932-620310.1371/journal.pone.0051295https://doaj.org/article/92ea9fa38b8c49babb2a63f340ad788a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23251489/?tool=EBIhttps://doaj.org/toc/1932-6203Plant infection by oomycete pathogens is a complex process. It requires precise expression of a plethora of genes in the pathogen that contribute to a successful interaction with the host. Whereas much effort has been made to uncover the molecular systems underlying this infection process, mechanisms of transcriptional regulation of the genes involved remain largely unknown. We performed the first systematic de-novo DNA motif discovery analysis in Phytophthora. To this end, we utilized the genome sequence of the late blight pathogen Phytophthora infestans and two related Phytophthora species (P. ramorum and P. sojae), as well as genome-wide in planta gene expression data to systematically predict 19 conserved DNA motifs. This catalog describes common eukaryotic promoter elements whose functionality is supported by the presence of orthologs of known general transcription factors. Together with strong functional enrichment of the common promoter elements towards effector genes involved in pathogenicity, we obtained a new and expanded picture of the promoter structure in P. infestans. More intriguingly, we identified specific DNA motifs that are either highly abundant or whose presence is significantly correlated with gene expression levels during infection. Several of these motifs are observed upstream of genes encoding transporters, RXLR effectors, but also transcriptional regulators. Motifs that are observed upstream of known pathogenicity-related genes are potentially important binding sites for transcription factors. Our analyses add substantial knowledge to the as of yet virtually unexplored question regarding general and specific gene regulation in this important class of pathogens. We propose hypotheses on the effects of cis-regulatory motifs on the gene regulation of pathogenicity-related genes and pinpoint motifs that are prime targets for further experimental validation.Michael F SeidlRui-Peng WangGuido Van den AckervekenFrancine GoversBerend SnelPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51295 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Michael F Seidl
Rui-Peng Wang
Guido Van den Ackerveken
Francine Govers
Berend Snel
Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.
description Plant infection by oomycete pathogens is a complex process. It requires precise expression of a plethora of genes in the pathogen that contribute to a successful interaction with the host. Whereas much effort has been made to uncover the molecular systems underlying this infection process, mechanisms of transcriptional regulation of the genes involved remain largely unknown. We performed the first systematic de-novo DNA motif discovery analysis in Phytophthora. To this end, we utilized the genome sequence of the late blight pathogen Phytophthora infestans and two related Phytophthora species (P. ramorum and P. sojae), as well as genome-wide in planta gene expression data to systematically predict 19 conserved DNA motifs. This catalog describes common eukaryotic promoter elements whose functionality is supported by the presence of orthologs of known general transcription factors. Together with strong functional enrichment of the common promoter elements towards effector genes involved in pathogenicity, we obtained a new and expanded picture of the promoter structure in P. infestans. More intriguingly, we identified specific DNA motifs that are either highly abundant or whose presence is significantly correlated with gene expression levels during infection. Several of these motifs are observed upstream of genes encoding transporters, RXLR effectors, but also transcriptional regulators. Motifs that are observed upstream of known pathogenicity-related genes are potentially important binding sites for transcription factors. Our analyses add substantial knowledge to the as of yet virtually unexplored question regarding general and specific gene regulation in this important class of pathogens. We propose hypotheses on the effects of cis-regulatory motifs on the gene regulation of pathogenicity-related genes and pinpoint motifs that are prime targets for further experimental validation.
format article
author Michael F Seidl
Rui-Peng Wang
Guido Van den Ackerveken
Francine Govers
Berend Snel
author_facet Michael F Seidl
Rui-Peng Wang
Guido Van den Ackerveken
Francine Govers
Berend Snel
author_sort Michael F Seidl
title Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.
title_short Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.
title_full Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.
title_fullStr Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.
title_full_unstemmed Bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen Phytophthora infestans.
title_sort bioinformatic inference of specific and general transcription factor binding sites in the plant pathogen phytophthora infestans.
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/92ea9fa38b8c49babb2a63f340ad788a
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