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Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis.
BMC Genomics. 2013 Feb 16; 14:106.BG

Abstract

BACKGROUND

The core promoter is the region flanking the transcription start site (TSS) that directs formation of the pre-initiation complex. Core promoters have been studied intensively in mammals and yeast, but not in more diverse eukaryotes. Here we investigate core promoters in oomycetes, a group within the Stramenopile kingdom that includes important plant and animal pathogens. Prior studies of a small collection of genes proposed that oomycete core promoters contain a 16 to 19 nt motif bearing an Initiator-like sequence (INR) flanked by a novel sequence named FPR, but this has not been extended to whole-genome analysis.

RESULTS

We used expectation maximization to find over-represented motifs near TSSs of Phytophthora infestans, the potato blight pathogen. The motifs corresponded to INR, FPR, and a new element found about 25 nt downstream of the TSS called DPEP. TATA boxes were not detected. Assays of DPEP function by mutagenesis were consistent with its role as a core motif. Genome-wide searches found a well-conserved combined INR+FPR in only about 13% of genes after correcting for false discovery, which contradicted prior reports that INR and FPR are found together in most genes. INR or FPR were found alone near TSSs in 18% and 7% of genes, respectively. Promoters lacking the motifs had pyrimidine-rich regions near the TSS. The combined INR+FPR motif was linked to higher than average mRNA levels, developmentally-regulated transcription, and functions related to plant infection, while DPEP and FPR were over-represented in constitutively-expressed genes. The INR, FPR, and combined INR+FPR motifs were detected in other oomycetes including Hyaloperonospora arabidopsidis, Phytophthora sojae, Pythium ultimum, and Saprolegnia parasitica, while DPEP was found in all but S. parasitica. Only INR seemed present in a non-oomycete stramenopile.

CONCLUSIONS

The absence of a TATA box and presence of novel motifs show that the oomycete core promoter is diverged from that of model systems, and likely explains the lack of activity of non-oomycete promoters in Phytophthora transformants. The association of the INR+FPR motif with developmentally-regulated genes shows that oomycete core elements influence stage-specific transcription in addition to regulating formation of the pre-initiation complex.

Authors+Show Affiliations

Department of Plant Pathology and Microbiology, University of California, 92521, Riverside, CA 92521, USA.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

23414203

Citation

Roy, Sourav, et al. "Novel Core Promoter Elements in the Oomycete Pathogen Phytophthora Infestans and Their Influence On Expression Detected By Genome-wide Analysis." BMC Genomics, vol. 14, 2013, p. 106.
Roy S, Poidevin L, Jiang T, et al. Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis. BMC Genomics. 2013;14:106.
Roy, S., Poidevin, L., Jiang, T., & Judelson, H. S. (2013). Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis. BMC Genomics, 14, 106. https://doi.org/10.1186/1471-2164-14-106
Roy S, et al. Novel Core Promoter Elements in the Oomycete Pathogen Phytophthora Infestans and Their Influence On Expression Detected By Genome-wide Analysis. BMC Genomics. 2013 Feb 16;14:106. PubMed PMID: 23414203.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis. AU - Roy,Sourav, AU - Poidevin,Laetitia, AU - Jiang,Tao, AU - Judelson,Howard S, Y1 - 2013/02/16/ PY - 2012/11/16/received PY - 2013/01/31/accepted PY - 2013/2/19/entrez PY - 2013/2/19/pubmed PY - 2013/7/3/medline SP - 106 EP - 106 JF - BMC genomics JO - BMC Genomics VL - 14 N2 - BACKGROUND: The core promoter is the region flanking the transcription start site (TSS) that directs formation of the pre-initiation complex. Core promoters have been studied intensively in mammals and yeast, but not in more diverse eukaryotes. Here we investigate core promoters in oomycetes, a group within the Stramenopile kingdom that includes important plant and animal pathogens. Prior studies of a small collection of genes proposed that oomycete core promoters contain a 16 to 19 nt motif bearing an Initiator-like sequence (INR) flanked by a novel sequence named FPR, but this has not been extended to whole-genome analysis. RESULTS: We used expectation maximization to find over-represented motifs near TSSs of Phytophthora infestans, the potato blight pathogen. The motifs corresponded to INR, FPR, and a new element found about 25 nt downstream of the TSS called DPEP. TATA boxes were not detected. Assays of DPEP function by mutagenesis were consistent with its role as a core motif. Genome-wide searches found a well-conserved combined INR+FPR in only about 13% of genes after correcting for false discovery, which contradicted prior reports that INR and FPR are found together in most genes. INR or FPR were found alone near TSSs in 18% and 7% of genes, respectively. Promoters lacking the motifs had pyrimidine-rich regions near the TSS. The combined INR+FPR motif was linked to higher than average mRNA levels, developmentally-regulated transcription, and functions related to plant infection, while DPEP and FPR were over-represented in constitutively-expressed genes. The INR, FPR, and combined INR+FPR motifs were detected in other oomycetes including Hyaloperonospora arabidopsidis, Phytophthora sojae, Pythium ultimum, and Saprolegnia parasitica, while DPEP was found in all but S. parasitica. Only INR seemed present in a non-oomycete stramenopile. CONCLUSIONS: The absence of a TATA box and presence of novel motifs show that the oomycete core promoter is diverged from that of model systems, and likely explains the lack of activity of non-oomycete promoters in Phytophthora transformants. The association of the INR+FPR motif with developmentally-regulated genes shows that oomycete core elements influence stage-specific transcription in addition to regulating formation of the pre-initiation complex. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/23414203/Novel_core_promoter_elements_in_the_oomycete_pathogen_Phytophthora_infestans_and_their_influence_on_expression_detected_by_genome_wide_analysis_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-106 DB - PRIME DP - Unbound Medicine ER -