Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex

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 NADsensing 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. Bacteria can adapt to changes in their environment by utilizing a range of transcription factors that receive an appropriate intra-or extracellular signal and trigger the specific transcriptional response. The Rex regulator is a transcription factor that responds to intracellular redox potential and negatively controls expression of genes involved in energy metabolism and fermentative growth in Gram-positive bacteria, including the actinobacterium Streptomyces coelicolor (4) and various Firmicutes, such as Bacillus subtilis (35), Staphylococcus aureus (25), and Streptococcus mutans (3). NAD plays an important role in different biological processes, including redox cellular balance. During the catabolism of carbohydrates, NAD ϩ is reduced to NADH by glycolytic enzymes. The NADH formed is reoxidized back either by respiratory electron transport chains or by NADH-linked fermentative enzymes. The DNA-binding activity of Rex is modulated by the intracellular ratio of NADH:NAD ϩ . Under the low NADH:NAD ϩ ratio, the Rex protein binds to the target sites and represses transcription of genes involved in NADH reoxidation, while the increase of NADH concentration results in the dissociation of Rex from DNA and derepression of its target genes (4, 25, 35).Rex was initially described in S. coelicolor, where it controls the cytochrome bd terminal oxidase operon cydABCD and the heme biosynthesis genes hemACD, as well as the membrane-bound proton-translocating NADH dehydrogenase operon nuoA-nuoN (4). The Rex-regulated promoters contain a common DNA motif with consensus 5=-TGTGNNCNNNT...

Suitable extracellular oxidoreduction potential inhibit

“…gov/nuccore/NZ_GL877878.1), was blasted with rex in Saccharopolyspora erythraea, Streptomyces coelicolor, and Streptomyces avermitilis by using the BLASTP algorithm with significant sequence similarity (E value < 10 −40 ). The rex gene in the S. spinosa genome sequencing was identified (Additional file 1: Figure S1) [15]. By blasting genes located in the downstream of rex with the genome of Saccharopolyspora erythraea, Streptomyces coelicolor, and Streptomyces avermitilis, we found that genes located in the downstream of rex were cytochrome bd oxidase synthesis gene, cytAB.…”

“…Studies have demonstrated that the rex regulator responds to intracellular NADH/NAD + levels and controls the expression of genes involved in lots of metabolisms in Actinomycetales [15]. The complete genome of S. spinosa ATCC 49460, accession number NZ_GL877878 in the NCBI nucleotide database (http://www.ncbi.nlm.nih.…”

The master regulator PhoP coordinates phosphate and nitrogen metabolism, respiration, cell differentiation and antibiotic biosynthesis: comparison in Streptomyces coelicolor and Streptomyces avermitilis

“…Several of these genes are also regulated by the redox response regulator Rex. 26 Most of the oxidative phosphorylation genes have a profile that indicates that they are repressed by PhoP following phosphate depletion, whereas the nitrate reductase genes are activated. 4,19 These results suggest that depletion of phosphate results in a switch from aerobic respiration to nitrate respiration.…”

“…Moreover, the oxidative phosphorylation genes contain sequences that are recognized by both, PhoP and the Rex regulator. 26 Similarly, in chitin metabolism, a regulatory protein, DasR, binds to promoter regions involved in N-acetylglucosamine metabolism that are also regulated by PhoP. 41 The interaction of regulatory proteins may estabilize the binding of PhoP to weakly conserved PHO boxes and explains why there are so many PhoPbinding regions detected in the DNA by the ChIP-on-chip technique.…”

Metabolic mechanisms and regulation of mixed culture fermentation

“…They regulate the oxidation state of the NAD pool and control product formation by binding to operons upstream of genes which code primarily for hydrogenases and cytochromes when the NADH:NAD+ ratio is low, preventing production of enzymes that oxidize NADH ( Figure 9). Forms of Rex have been found to be highly conserved across many species of bacteria, including aerobes and anaerobes, and span a wide range of distantly related taxonomic groups 104 . In function, it has been found that Rex enzymes are either inhibited by NADH 99 or activated by NAD +102 , though the outcome of down-regulating NADH oxidation is the same.…”