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| Status |
Public on Jul 03, 2024 |
| Title |
Binding specificities of transcription factors of the oomycete Phytophthorainfestans reflect conserved and divergent evolutionary patterns and function |
| Platform organism |
synthetic construct |
| Sample organism |
Phytophthora infestans |
| Experiment type |
Other
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| Summary |
Identifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a group of microbes that includes many important plant and animal pathogens. Here we describe the use of protein-binding oligonucleotide microarrays (PBMs) to define the DNA-binding preferences of 14 families of TFs from the oomycete Phytophthora infestans, which causes late blight of potato and tomato. DNA motifs obtained from the PBMs for representatives of each major TF family were validated by electrophoretic mobility shift assays (EMSA) or ChIP-seq. Consistent with the large evolutionary distance of oomycetes from traditional models, only some of the P. infestans DNA-binding preferences resembled those of TFs from human and plants. Some families from P. infestans included clusters with canonical targets and others with novel targets. Paralogs having similar binding preferences often displayed distinct patterns of expression, suggesting functional divergence. Many TFs were predicted to either drive stage-specific expression or serve as general activators based on the representation of their binding sites within developmentally-regulated promoters. One such prediction was confirmed using a reporter gene assay. Our data thus provide a basis for understanding transcriptional regulation in P. infestans by linking TFs with their targets on a genome-wide level.
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| Overall design |
Protein binding microarray (PBM) experiments were performed for Phytophthora infestans proteins. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.
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| Contributor(s) |
Vo NN, Yang A, Leesutthiphonchai W, Liu Y, Hughes TR, Judelson HS |
| Citation missing |
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| BioProject |
PRJNA1069773 |
| |
| Submission date |
Jun 20, 2024 |
| Last update date |
Jul 04, 2024 |
| Contact name |
Howard Judelson |
| E-mail(s) |
howard.judelson@ucr.edu
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| Organization name |
University of California-Riverside
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| Department |
Microbiology and Plant Pathology
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| Street address |
Genomics Building
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| City |
Riverside |
| State/province |
CA |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platforms (1) |
| GPL11260 |
Agilent custom ME and HK design array [8mer] |
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| Samples (146)
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