Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex
- 30 December 2011
- journal article
- research article
- Published by American Society for Microbiology in Journal of Bacteriology
- Vol. 194 (5), 1145-1157
- https://doi.org/10.1128/JB.06412-11
Abstract
Redox-sensing repressor Rex was previously implicated in the control of anaerobic respiration in response to the cellular NADH/NAD+ levels in Gram-positive bacteria. We utilized the comparative genomics approach to infer candidate Rex-binding DNA motifs and assess the Rex regulon content in 119 genomes from 11 taxonomic groups. Both DNA-binding and NAD-sensing domains are broadly conserved in Rex orthologs identified in the phyla Firmicutes, Thermotogales, Actinobacteria, Chloroflexi, Deinococcus-Thermus, and Proteobacteria. The identified DNA-binding motifs showed significant conservation in these species, with the only exception detected in Clostridia, where the Rex motif deviates in two positions from the generalized consensus, TTGTGAANNNNTTCACAA. Comparative analysis of candidate Rex sites revealed remarkable variations in functional repertoires of candidate Rex-regulated genes in various microorganisms. Most of the reconstructed regulatory interactions are lineage specific, suggesting frequent events of gain and loss of regulator binding sites in the evolution of Rex regulons. We identified more than 50 novel Rex-regulated operons encoding functions that are essential for resumption of the NADH:NAD+ balance. The novel functional role of Rex in the control of the central carbon metabolism and hydrogen production genes was validated by in vitro DNA binding assays using the TM0169 protein in the hydrogen-producing bacterium Thermotoga maritima.Keywords
This publication has 41 references indexed in Scilit:
- Control of Proteobacterial Central Carbon Metabolism by the HexR Transcriptional Regulator: A CASE STUDY IN SHEWANELLA ONEIDENSIS*Journal of Biological Chemistry, 2011
- Genetically Encoded Fluorescent Sensors for Intracellular NADH DetectionCell Metabolism, 2011
- Imaging Cytosolic NADH-NAD+ Redox State with a Genetically Encoded Fluorescent BiosensorCell Metabolism, 2011
- MicrobesOnline: an integrated portal for comparative and functional genomicsNucleic Acids Research, 2009
- RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotesNucleic Acids Research, 2009
- On the chimeric nature, thermophilic origin, and phylogenetic placement of the ThermotogalesProceedings of the National Academy of Sciences of the United States of America, 2009
- Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulatorsNucleic Acids Research, 2008
- Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulonNucleic Acids Research, 2008
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997