Impact of NADH on gene expression of Streptococcus pneumoniae and role of Rex as a transcriptional repressor of the Rex regulon
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ABSTRACT:
ORGANISM(S): Streptococcus pneumoniae D39
PROVIDER: GSE94573 | GEO | 2018/06/01
REPOSITORIES: GEO
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Project description:Nicotinamide adenine dinucleotides (NAD(H)) play a vital role in various biological processes, including keeping the cellular redox balance. In this study, we investigate the regulatory responses of Streptococcus pneumoniae D39 to NADH and characterize the role of the Rex protein as a transcriptional repressor of the gapN, fba, pncB, adhB2, gap, and adhE genes. Transcriptomic analysis was used to observe the response of S. pneumoniae D39 to NADH. Our microarray studies revealed elevated expression of various genes/operons involved in transport and biosynthesis of niacin (gapN, fba, pncB, adhB2, gap, and adhE). Promoter lacZ-fusion assays and microarray studies with the rex mutant revealed the role of Rex as a transcriptional repressor of gapN, fba, pncB, adhB2, gap, and adhE involved in niacin uptake and biosynthesis, in the presence of NADH. We predict the operator site (5'-TTGTKAWAAWWTTCACAA-3') of Rex in the regulatory regions of Rex-regulated genes that was subsequently validated by promoter mutational experiments.
| S-EPMC6018154 | biostudies-literature
Project description:Impact of NADH on gene expression of Streptococcus pneumoniae and role of Rex as a transcriptional repressor of the Rex regulon
| PRJNA371481 | ENA
Project description:The objective of this comparison was to identify the impact of rex deletion on the transcriptome of Streptococcus pneumoniae D39. This comparison showed that the transcriptional regulator, Rex acts as a transcriptional repressor of a number of genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in niacin uptake and biosynthesis in the presence of NADH. In this study, we investigated the transcriptomic response of Streptococcus pneumoniae D39 to NADH. Transcriptome comparison of the D39 wild-type grown in chemically-defined medium (CDM) with 0 mg/ml NADH to 0.5 mg/ml NADH revealed elevated expression of various genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in the transport and biosynthesis of niacin. Microarray results were further confirmed by β-galactosidase assays. Promoter-lacZ fusions assays and microarray studies showed that the transcriptional regulator, Rex acts as a transcriptional repressor of a number of genes/operons (adhB1, fba, hemH, rex, gapN, nirC, pncB, gap, adhE, and adhB2) involved in niacin uptake and biosynthesis in the presence of NADH. The putative operator site of Rex in the promoter regions of Rex-regulated genes is predicted and confirmed by promoter mutational experiments.
2018-06-01 | GSE94571 | GEO
Project description:Reversible or phenotypic tolerance to antibiotics within microbial populations has been implicated in treatment failure of chronic infections and development of persister cells. However, the molecular mechanisms regulating phenotypic drug tolerance are largely unknown. In this study, we identified a four-gene operon in Streptococcus pneumoniae that contributes to phenotypic tolerance to vancomycin (ptv). RNA sequencing, quantiative reverse transcriptase PCR, and transcriptional luciferase reporter experiments revealed that transcription of the ptv operon (consisting of ptvR, ptvA, ptvB, and ptvC) is induced by exposure to vancomycin. Further investigation showed that transcription of the ptv operon is repressed by PtvR, a PadR family repressor. Transcriptional induction of the ptv operon by vancomycin was achieved by transcriptional derepression of this locus, which was mediated by PtvR. Importantly, fully derepressing ptvABC by deleting ptvR or overexpressing the ptv operon with an exogenous promoter significantly enhanced vancomycin tolerance. Gene deletion analysis revealed that PtvA, PtvB, and PtvC are all required for the PtvR-regulated phenotypic tolerance to vancomycin. Finally, the results of an electrophoretic mobility shift assay with recombinant PtvR showed that PtvR represses the transcription of the ptv operon by binding to two palindromic sequences within the ptv promoter. Together, the ptv locus represents an inducible system in S. pneumoniae in response to stressful conditions, including those caused by antibiotics.IMPORTANCE Reversible or phenotypic tolerance to antibiotics within microbial populations is associated with treatment failure of bacterial diseases, but the underlying mechanisms regulating phenotypic drug tolerance remain obscure. This study reports our finding of a multigene locus that contributes to inducible tolerance to vancomycin in Streptococcus pneumoniae, an important opportunistic human pathogen. The vancomycin tolerance phenotype depends on the PtvR transcriptional repressor and three predicted membrane-associated proteins encoded by the ptv locus. This represents the first example of a gene locus in S. pneumoniae that is responsible for antibiotic tolerance and has important implications for further understanding bacterial responses and phenotypic tolerance to antibiotic treatment in this and other pathogens.
| S-EPMC5494751 | biostudies-literature
Project description:The maltose regulon (mal regulon) has previously been shown to consist of the mal gene cluster (malMP, malXCD and malAR operons) in Streptococcus pneumoniae. In this study, we have further elucidated the complete mal regulon in S. pneumoniae D39 using microarray analyses and ?-galactosidase assays. In addition to the mal gene cluster, the complete mal regulon of S. pneumoniae D39 consists of a pullulanase (PulA), a glucosidase (DexB), a glucokinase (RokB), a PTS component (PtsG) and an amylase (AmyA2). Our microarray studies and ?-galactosidase assays further showed that the LacI-family transcriptional regulator MalR represses the expression of the mal regulon in the absence of maltose. Furthermore, the role of the pleiotropic transcriptional regulator CcpA in the regulation of the mal regulon in the presence of maltose was explored. Our microarray analysis with a ?ccpA strain showed that CcpA only represses the expression of the malXCD operon and the pulA gene in the presence of maltose. Hence, we extend the mal regulon now consisting of pulA, dexB, rokB, ptsG and amyA2 in addition to malMP, malXCD and malAR operons.
| S-EPMC4451989 | biostudies-literature
Project description:The transcriptional repressor Rex has been implicated in the regulation of energy metabolism and fermentative growth in response to redox potential. Streptococcus mutans, the primary causative agent of human dental caries, possesses a gene that encodes a protein with high similarity to members of the Rex family of proteins. In this study, we showed that Rex-deficiency compromised the ability of S. mutans to cope with oxidative stress and to form biofilms. The Rex-deficient mutant also accumulated less biofilm after 3 days than the wild-type strain, especially when grown in sucrose-containing medium, but produced more extracellular glucans than the parental strain. Rex-deficiency caused substantial alterations in gene transcription, including those involved in heterofermentative metabolism, NAD(+) regeneration and oxidative stress. Among the upregulated genes was gtfC, which encodes glucosyltransferase C, an enzyme primarily responsible for synthesis of water-insoluble glucans. These results reveal that Rex plays an important role in oxidative stress responses and biofilm formation by S. mutans.
| S-EPMC3115380 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-04-23 | E-GEOD-65550 | biostudies-arrayexpress
Project description:The cellular redox state of organisms continues to fluctuate during the metabolism. All organisms have various sensors that help detect and adapt to changes in the redox state. Nicotinamide adenine dinucleotides (NAD+/NADH), which are involved in various cellular metabolic activities as cofactors, have been revealed as the key molecules sensing the intra-cellular redox state. The Rex family members are well conserved transcriptional repressors that regulate the expression of respiratory genes by sensing the redox state according to the intra-cellular NAD+/NADH balance. Herein, we reported crystal structures of apo and NAD+- and NADH-bound forms of Rex from Thermotoga maritima to analyse the structural basis of transcriptional regulation depending on either NAD+ or NADH binding. The different orientation of the reduced nicotinamide group to helix ?9 caused the rearrangement of N-terminal DNA binding domain, thus resulting in closed form of Rex to dissociate from cognate DNA. The structural data of Rex from T. maritima also support the previous redox-sensing mechanism models of Rex homologues.
| S-EPMC6125430 | biostudies-literature
Project description:Rex factors are bacterial transcription factors thought to respond to the cellular NAD(+)/NADH ratio in order to modulate gene expression by differentially binding DNA. To date, Rex factors have been implicated in regulating genes of central metabolism, oxidative stress response, and biofilm formation. The genome of Enterococcus faecalis, a low-GC Gram-positive opportunistic pathogen, encodes EF2638, a putative Rex factor. To study the role of E. faecalis Rex, we purified EF2638 and evaluated its DNA binding activity in vitro. EF2638 was able to bind putative promoter segments of several E. faecalis genes in an NADH-responsive manner, indicating that it represents an authentic Rex factor. Transcriptome analysis of a ΔEF2638 mutant revealed that genes likely to be involved in anaerobic metabolism were upregulated during aerobic growth, and the mutant exhibited an altered NAD(+)/NADH ratio. The ΔEF2638 mutant also exhibited a growth defect when grown with aeration on several carbon sources, suggesting an impaired ability to cope with oxidative stress. Inclusion of catalase in the medium alleviated the growth defect. H(2)O(2) measurements revealed that the mutant accumulates significantly more H(2)O(2) than wild-type E. faecalis. In summary, EF2638 represents an authentic Rex factor in E. faecalis that influences the production or detoxification of H(2)O(2) in addition to its more familiar role as a regulator of anaerobic gene expression.
| S-EPMC3624565 | biostudies-literature
Project description:In many Gram-positive bacteria, the redox-sensing transcriptional repressor Rex controls central carbon and energy metabolism by sensing the intra cellular balance between the reduced and oxidized forms of nicotinamide adenine dinucleotide; the NADH/NAD+ ratio. Here, we report high-resolution crystal structures and characterization of a Rex ortholog (Gbs1167) in the opportunistic pathogen, Streptococcus agalactiae, also known as group B streptococcus (GBS). We present structures of Rex bound to NAD+ and to a DNA operator which are the first structures of a Rex-family member from a pathogenic bacterium. The structures reveal the molecular basis of DNA binding and the conformation alterations between the free NAD+ complex and DNA-bound form of Rex. Transcriptomic analysis revealed that GBS Rex controls not only central metabolism, but also expression of the monocistronic rex gene as well as virulence gene expression. Rex enhances GBS virulence after disseminated infection in mice. Mechanistically, NAD+ stabilizes Rex as a repressor in the absence of NADH. However, GBS Rex is unique compared to Rex regulators previously characterized because of its sensing mechanism: we show that it primarily responds to NAD+ levels (or growth rate) rather than to the NADH/NAD+ ratio. These results indicate that Rex plays a key role in GBS pathogenicity by modulating virulence factor gene expression and carbon metabolism to harvest nutrients from the host.
| S-EPMC8376106 | biostudies-literature