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Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.

Todor H, Sharma K, Pittman AM, Schmid AK - Nucleic Acids Res. (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University, Durham, NC 27708, USA and Center for Systems Biology, Institute for Genome Science and Policy, Duke University, Durham, NC 27708, USA.

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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Related in: MedlinePlus

ppsA (A) and pykA (B) do not respond significantly to 5% sucrose in the Δura3 strain (black lines). ppsA and pykA respond to 0.167% glycerol stimulus in the Δura3 strain (gray lines). Gene expression was measured by RT-qPCR and is shown plotted on a logarithmic axis. Asterisks indicate significance of the difference in expression level between the beginning and the end of the time course; * significant at P < 0.05; ** significant at P < 0.01; *** significant at P < 0.001.
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gkt659-F2: ppsA (A) and pykA (B) do not respond significantly to 5% sucrose in the Δura3 strain (black lines). ppsA and pykA respond to 0.167% glycerol stimulus in the Δura3 strain (gray lines). Gene expression was measured by RT-qPCR and is shown plotted on a logarithmic axis. Asterisks indicate significance of the difference in expression level between the beginning and the end of the time course; * significant at P < 0.05; ** significant at P < 0.01; *** significant at P < 0.001.

Mentions: Our previous work demonstrated that TrmB binds the promoter of metabolic enzyme-coding genes throughout the genome in response to carbon source availability (17). However, these studies were conducted at steady state. To investigate the dynamic expression response of TrmB-regulated genes to nutrients (glucose, glycerol and sucrose), we used RT-qPCR to measure repressed (pykA) and activated (ppsA) gene levels in response to nutrients over time (Figures 1 and 2). TrmB is thought to regulate these genes by binding to the promoter either to activate or to repress expression in the absence of glucose. Addition of glucose to the medium results in TrmB dissociation from the promoter and de-activation or de-repression of the target gene (17). Briefly, H. salinarum cells were grown on amino acids as a carbon and energy source to mid-logarithmic phase. Cells were sampled thrice before and seven times after the addition of nutrients (‘Materials and Methods’ section). We considered a change relevant when a 1.5-fold or greater up- or downregulation of the target gene was significant (P < 0.05). As these genes are a key control point in glycolysis (pykA) and gluconeogenesis (ppsA), their levels are highly informative of the regulation of that pathway (31,32).Figure 1.


Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea.

Todor H, Sharma K, Pittman AM, Schmid AK - Nucleic Acids Res. (2013)

ppsA (A) and pykA (B) do not respond significantly to 5% sucrose in the Δura3 strain (black lines). ppsA and pykA respond to 0.167% glycerol stimulus in the Δura3 strain (gray lines). Gene expression was measured by RT-qPCR and is shown plotted on a logarithmic axis. Asterisks indicate significance of the difference in expression level between the beginning and the end of the time course; * significant at P < 0.05; ** significant at P < 0.01; *** significant at P < 0.001.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3794607&req=5

gkt659-F2: ppsA (A) and pykA (B) do not respond significantly to 5% sucrose in the Δura3 strain (black lines). ppsA and pykA respond to 0.167% glycerol stimulus in the Δura3 strain (gray lines). Gene expression was measured by RT-qPCR and is shown plotted on a logarithmic axis. Asterisks indicate significance of the difference in expression level between the beginning and the end of the time course; * significant at P < 0.05; ** significant at P < 0.01; *** significant at P < 0.001.
Mentions: Our previous work demonstrated that TrmB binds the promoter of metabolic enzyme-coding genes throughout the genome in response to carbon source availability (17). However, these studies were conducted at steady state. To investigate the dynamic expression response of TrmB-regulated genes to nutrients (glucose, glycerol and sucrose), we used RT-qPCR to measure repressed (pykA) and activated (ppsA) gene levels in response to nutrients over time (Figures 1 and 2). TrmB is thought to regulate these genes by binding to the promoter either to activate or to repress expression in the absence of glucose. Addition of glucose to the medium results in TrmB dissociation from the promoter and de-activation or de-repression of the target gene (17). Briefly, H. salinarum cells were grown on amino acids as a carbon and energy source to mid-logarithmic phase. Cells were sampled thrice before and seven times after the addition of nutrients (‘Materials and Methods’ section). We considered a change relevant when a 1.5-fold or greater up- or downregulation of the target gene was significant (P < 0.05). As these genes are a key control point in glycolysis (pykA) and gluconeogenesis (ppsA), their levels are highly informative of the regulation of that pathway (31,32).Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University, Durham, NC 27708, USA and Center for Systems Biology, Institute for Genome Science and Policy, Duke University, Durham, NC 27708, USA.

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.

Show MeSH
Related in: MedlinePlus