ArticleNucleic acids research2013
Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- A TrmBL2-like transcription factor mediates the growth phase-dependent expression of halolysin SptA in a concentration-dependent manner inApplied and environmental microbiology · 2024Article
- TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii.Molecular microbiology · 2024Article
- TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.Nucleic acids research · 2024Article
- A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.PLoS genetics · 2024Article
- Article
- Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.Journal of molecular biology · 2019Review
- Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.Emerging topics in life sciences · 2018Article
- GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii.Journal of bacteriology · 2018Article
- A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea.Nucleic acids research · 2017Article
- Detecting differential growth of microbial populations with Gaussian process regression.Genome research · 2017Article
- Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus.BMC genomics · 2016Article
- Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences.PloS one · 2015Article
- A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.PLoS genetics · 2015Article
- The TrmB family: a versatile group of transcriptional regulators in Archaea.Extremophiles : life under extreme conditions · 2014Review
- Salty sisters: The women of halophiles.Frontiers in microbiology · 2014Article
- Article
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4 authors.
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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.
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