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A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens

ABSTRACT: A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens

PROVIDER: PRJNA428323 | ENA |

REPOSITORIES: ENA

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A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens

Project description:Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood–Ljungdahl pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterization of acetogen metabolism has recently improved, key transcriptional features such as promoter motifs and transcriptional regulators are still unknown in acetogens. Here, we use differential RNA-sequencing to identify a previously undescribed promoter motif associated with essential genes for autotrophic growth of the model-acetogen Clostridium autoethanogenum. RNA polymerase was shown to bind to the new promoter motif using a DNA-binding protein assay and proteomics enabled the discovery of four candidates to potentially function directly in control of transcription of the WLP and other key genes of C1 fixation metabolism. Next, in vivo experiments showed that a TetR-family transcriptional regulator (CAETHG_0459) and the housekeeping sigma factor (sA) activate expression of a reporter protein (GFP) in-frame with the new promoter motif from a fusion vector in Escherichia coli. Lastly, a protein–protein interaction assay with the RNA polymerase (RNAP) shows that CAETHG_0459 directly binds to the RNAP. Together, the data presented here advance the fundamental understanding of transcriptional regulation of C1 fixation in acetogens and provide a strategy for improving the performance of gas-fermenting bacteria by genetic engineering.

2019-10-28 | GSE108700 | GEO

A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens

Project description:Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood-Ljungdahl pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterisation of acetogen metabolism has recently improved, key transcriptional features such as promoter motifs and transcriptional regulators are still unknown in acetogens. Here, we use differential RNA-sequencing to identify a previously undescribed promoter motif associated with essential genes for autotrophic growth of the model-acetogen Clostridium autoethanogenum. RNA polymerase was shown to bind to the new promoter motif using a DNA-binding protein assay and proteomics enabled the discovery of four candidates to potentially function directly in control of transcription of the WLP and other key genes of C1 fixation metabolism. Next, in vivo experiments showed that a TetR-family transcriptional regulator (CAETHG_0459) and the housekeeping sigma factor (σA) activate expression of a reporter protein (GFP) in-frame with the new promoter motif from a fusion vector in E. coli. Lastly, a protein-protein interaction assay with the RNA polymerase (RNAP) shows that CAETHG_0459 directly binds to the RNAP. Together, the data presented here advance the fundamental understanding of transcriptional regulation of C1 fixation in acetogens and provide a strategy for improving the performance of gas-fermenting bacteria by genetic engineering.

2019-11-20 | PXD014421 | Pride

A TetR-Family Protein (CAETHG_0459) Activates Transcription From a New Promoter Motif Associated With Essential Genes for Autotrophic Growth in Acetogens.

Project description: Not available

| S-EPMC6873888 | biostudies-literature

Functional cooperation of glycine synthase-reductase pathway with Wood-Ljungdahl pathway for autotrophic growth of Clostridium drakei

Project description:The Wood-Ljungdahl pathway in acetogens converts C1 compounds, such as CO2 and CO, into acetyl-CoA. Similarly, the glycine synthase pathway assimilates C1 compounds into glycine. Partial glycine synthase genes are widely conserved in the Wood-Ljungdahl pathway gene cluster but functional relationship between the pathways in autotrophic condition remains unknown. To comprehend, we assembled Clostridium drakei genome (5.7-Mbp) with intact glycine synthase pathway and constructed a genome-scale metabolic model, iSL836, predicting increased metabolic flux rates of the Wood-Ljungdahl pathway and the glycine synthase-reductase associated reactions under autotrophic conditions. Along with the observation of significant transcriptional activation of genes in the pathways, surprisingly, 13C-labeling experiments and enzyme activity assays confirmed the strain synthesizes glycine and converts into acetyl-phosphate. This study suggests the Wood-Ljungdahl and the glycine synthase-reductase pathways convert CO2 into acetyl-CoA and acetyl-phosphate, respectively. In our knowledge, this is the first report on co-utilization of the pathways under autotrophic growth in acetogen.

2019-08-01 | GSE118519 | GEO

Effect of TetR family regulator SAOUHSC_02897 deletion in S. aureus NCTC8325

2013-12-18 | GSE53432 | GEO

Effect of TetR family regulator SAOUHSC_02897 deletion in S. aureus NCTC8325

Project description:To analyze function of TetR family regulator SAOUHSC_02897, we have employed whole genome microarray expression profiling to identify genes transcription changed in respective mutant strains. Target SAOUHSC_02897 was replaced by ermB gene. Bacteria grown in the wells of biofilm formation at 12 hours, and the RNA level of wild type NCTC8325 and SAOUHSC-02897 mutant were compared.

2013-12-18 | E-GEOD-53432 | biostudies-arrayexpress

Functional characterization of TetR-like transcriptional regulator PA3973 from Pseudomonas aeruginosa [RNA-seq]

Project description:Pseudomonas aeruginosa, a human opportunistic pathogen, is a common cause of nosocomial infections. Its ability to survive under different conditions relies on a complex regulatory network engaging transcriptional regulators controlling metabolic pathways and capabilities to efficiently use the available resources. P. aeruginosa PA3973 encodes a putative TetR family transcriptional regulator, with a helix-turn-helix motif involved in DNA binding. We applied transcriptome profiling (RNA-seq), and genome-wide identification of binding sites using ChIP-seq to unravel the biological role of PA3973.

2022-11-22 | GSE211771 | GEO

A novel TetR-like transcriptional regulator is induced in acid-nitrosative stress and controls expression of an efflux pump in mycobacteria

Project description:Mycobacterium tuberculosis has the ability to survive inside macrophages under acid-nitrosative stress. M. tuberculosis Rv1685c and its orthologue in M. smegmatis, MSMEG_3765, are induced on exposure to acid-nitrosative stress. Both genes are annotated as TetR transcriptional regulators, a family of proteins that regulate a wide range of cellular activities, including multidrug resistance, carbon catabolism and virulence. Here we demonstrate that MSMEG_3765 is co-transcribed with the upstream genes MSMEG_3762 and MSMEG_3763, encoding efflux pump components. RTq-PCR and GFP-reporter assays showed that the MSMEG_3762/63/65 gene cluster, and the orthologous region in M. tuberculosis (Rv1687c/86c/85c), was up-regulated in a MSMEG_3765 null mutant, suggesting that MSMEG_3765 acts as a repressor, typical of this family of regulators. We further defined the MSMEG_3765 regulon using genome-wide transcriptional profiling and confirmed that the MSMEG_3762/63/65 promoter is induced under acid-nitrosative stress. A putative 36 bp regulatory motif was identified upstream of the gene clusters in both M. smegmatis and M. tuberculosis and purified recombinant MSMEG_3765 protein was found to bind to DNA fragments containing this motif from both M. smegmatis and M. tuberculosis upstream regulatory regions. These results suggest that the TetR repressor MSMEG_3765/Rv1685c controls expression of an efflux pump with an, as yet, undefined role in the mycobacterial response to acid-nitrosative stress.

2017-10-24 | E-MTAB-5869 | biostudies-arrayexpress

Catma1-bou-bou mutant characterisation: Autotrophic growth acquisition in the ABOUTDESOUFFLE (bou) mutant

Project description:rs07-09_bou - catma1-bou - Autotrophic growth acquisition is abolished in the bou mutant in Arabidopsis thaliana. BOU encodes a putative mitochondrial acyl carnitine carrier. bou mutant is blocked at the cotyledon stage. Autotrophic growth of the bou mutant can be achieved with addition of sugar in the medium or in darkness. Moreover, BOU gene expression is activated by light and depends on plant developmental stage. We wish to determine what are the consequences of bou gene mutation at the transcriptome level. We wish to understand whether bou growth arrest is due to the modification of specific genes expression or to a general effect on metabolism at the transition from heterotrophic to autotrophic growth. - Seeds from a heterozygous plants were grown for either 5 or 8 days after germination on synthetic medium (MS/2) without sugar under continuous light. We harvested cotyledon-stage blocked plants (bou phenotype) from three independent Petri dishes and also green seedlings with true leaves and fully developed root (heterozygotes with a wild-type phenotype) . We also grew independently Col-O plants for 5 and 8 days to compare them with the bou mutants. Keywords: gene knock in (transgenic),normal vs disease comparison,time course

2009-02-05 | GSE10399 | GEO

soil autotrophic archaea

Project description:soil autotrophic archaea Raw sequence reads

| PRJNA599557 | ENA