Transcriptomics

Dataset Information

43

Halobacterium NRC-1 VNG1451C deletion mutant growth in defined medium with and without glucose


ABSTRACT: Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in defined medium during growth with and without glucose to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant in response to this sugar. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complete defined medium (CDM; 20 amino acids at concentrations defined by Shand and Perez, 1999. NaCl 250g/L, MgSO4 20 g/L, KCl 1 g/L, NaH2PO4 0.167mM, Biotin 0.02mM, Thiamin 0.015mM, Folic acid 0.0113 mM, MnSO4 0.01mM, FeSO4, 0.01mM, glucose added at 10% w/v where indicated in sample files) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, and stationary phase to measure genome-wide transcription.

ORGANISM(S): Halobacterium salinarum NRC-1  

SUBMITTER: Tie Koide  Min Pan   Amy Schmid   Nitin S Baliga   Amy K Schmid    

PROVIDER: E-GEOD-13529 | ArrayExpress| 2014-05-01

SECONDARY ACCESSION(S): GSE13529PRJNA110143

REPOSITORIES: GEO, ArrayExpress

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Publications

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.

Schmid Amy K AK   Reiss David J DJ   Pan Min M   Koide Tie T   Baliga Nitin S NS  

Molecular systems biology 20090616


During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to acclimate to nutrient fluctuations in a competitive environment. Here, we demonstrate that a single TrmB family transcription factor in Halobacterium salinarum NRC-1 globally coordinates functionally linked enzymes of diverse phylogeny in respons  ...[more]

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