Abstract
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.
Highlights
Oomycetes are an important class of eukaryotic pathogens that have severe ecological and economic impact [1], which only recently entered the genomic era [2,3]
1,667 differentially expressed P. infestans genes were selected from NimbleGen microarray data of in vitro growth and in planta growth 2–5 days post inoculation of potato plants [4]
For each gene within the co-expressed cluster we identified orthologs in two related species (P. sojae and P. ramorum) and filtered the upstream regions for remnants of transposable elements
Summary
Oomycetes are an important class of eukaryotic pathogens that have severe ecological and economic impact [1], which only recently entered the genomic era [2,3]. The genome sequence of these pathogens facilitated insights into the large repertoire of proteins involved in the interaction with the host [8]. Proteins containing the amino-acid motifs RXLR and LXLFLAK (Crinkler) belong to two distinct classes of effectors that are targeted to the inside of the plant cell presumably to promote infection of the host [4,9,10]. Present hypotheses on the functions of ELLs are still inconclusive, but some members seem to be associated with the cell wall or the cell membrane [11]. Genes encoding effectors and other proteins that are involved in the host-pathogen interaction require a precise spatial and temporal expression to facilitate the successful colonization of the host
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