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Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction
Inference of Expanded Lrp-Like Feast/Famine Transcription Factor Targets in a Non-Model Organism Using Protein Structure-Based Prediction
- Source :
- PLoS ONE, PLoS ONE, Vol 9, Iss 9, p e107863 (2014)
- Publication Year :
- 2014
- Publisher :
- Public Library of Science, 2014.
-
Abstract
- © 2014 Ashworth et al. Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of nonmodel organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.
- Subjects :
- Halobacterium salinarum
Operon
Gene regulatory network
lcsh:Medicine
Gene Expression
Protein Structure Prediction
Regulatory Sequences, Nucleic Acid
Genome
Biochemistry
Substrate Specificity
Gene Regulatory Networks
Archaean Biology
lcsh:Science
Genetics
Multidisciplinary
Bacterial Genomics
Archaeal Biochemistry
Genomics
Archaeal Physiology
DNA, Archaeal
Regulatory sequence
Research Article
Protein Binding
Protein Structure
General Science & Technology
Archaeal Proteins
Molecular Sequence Data
Microbial Genomics
Biology
Arginine
Microbiology
DNA-binding proteins
Gene Regulation
Amino Acid Sequence
Gene
Transcription factor
Binding Sites
Biology and life sciences
lcsh:R
Proteins
Computational Biology
Bacteriology
Comparative Genomics
Regulon
Pyrimidines
lcsh:Q
Chromatin immunoprecipitation
Transcription Factors
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 9
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....6d26566c0f9c18672da33f32eab0f320