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Protein–DNA binding dynamics predict transcriptional response to nutrients in archaea
- Source :
- Nucleic Acids Research
- Publication Year :
- 2013
- Publisher :
- Oxford University Press, 2013.
-
Abstract
- Organisms across all three domains of life use gene regulatory networks (GRNs) to integrate varied stimuli into coherent transcriptional responses to environmental pressures. However, inferring GRN topology and regulatory causality remains a central challenge in systems biology. Previous work characterized TrmB as a global metabolic transcription factor in archaeal extremophiles. However, it remains unclear how TrmB dynamically regulates its ∼100 metabolic enzyme-coding gene targets. Using a dynamic perturbation approach, we elucidate the topology of the TrmB metabolic GRN in the model archaeon Halobacterium salinarum. Clustering of dynamic gene expression patterns reveals that TrmB functions alone to regulate central metabolic enzyme-coding genes but cooperates with various regulators to control peripheral metabolic pathways. Using a dynamical model, we predict gene expression patterns for some TrmB-dependent promoters and infer secondary regulators for others. Our data suggest feed-forward gene regulatory topology for cobalamin biosynthesis. In contrast, purine biosynthesis appears to require TrmB-independent regulators. We conclude that TrmB is an important component for mediating metabolic modularity, integrating nutrient status and regulating gene expression dynamics alone and in concert with secondary regulators.
- Subjects :
- Halobacterium salinarum
Cobalamin biosynthesis
Transcription, Genetic
Systems biology
Archaeal Proteins
Gene regulatory network
Computational biology
Biology
Gene Regulation, Chromatin and Epigenetics
03 medical and health sciences
Genetics
Gene Regulatory Networks
Promoter Regions, Genetic
Transcription factor
Gene
030304 developmental biology
Regulation of gene expression
0303 health sciences
030306 microbiology
Promoter
Phosphotransferases (Paired Acceptors)
Metabolic pathway
Glucose
Gene Expression Regulation, Archaeal
Transcription Factors
Subjects
Details
- Language :
- English
- ISSN :
- 13624962 and 03051048
- Volume :
- 41
- Issue :
- 18
- Database :
- OpenAIRE
- Journal :
- Nucleic Acids Research
- Accession number :
- edsair.doi.dedup.....c3f6e0dfc0609a74e22e5ea6a4bfdaff