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

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

PROVIDER: PRJNA485902 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7691806.fastq.gz	Fastqsanger.gz
	SRR7691807.fastq.gz	Fastqsanger.gz
	SRR7691808.fastq.gz	Fastqsanger.gz
	SRR7691809.fastq.gz	Fastqsanger.gz

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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

Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei.

Project description:Among CO2-fixing metabolic pathways in nature, the linear Wood-Ljungdahl pathway (WLP) in phylogenetically diverse acetate-forming acetogens comprises the most energetically efficient pathway, requires the least number of reactions, and converts CO2 to formate and then into acetyl-CoA. Despite two genes encoding glycine synthase being well-conserved in WLP gene clusters, the functional role of glycine synthase under autotrophic growth conditions has remained uncertain. Here, using the reconstructed genome-scale metabolic model iSL771 based on the completed genome sequence, transcriptomics, 13C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression of the pathway in another acetogen, we discovered that the WLP and the glycine synthase pathway are functionally interconnected to fix CO2, subsequently converting CO2 into acetyl-CoA, acetyl-phosphate, and serine. Moreover, the functional cooperation of the pathways enhances CO2 consumption and cellular growth rates via bypassing reducing power required reactions for cellular metabolism during autotrophic growth of acetogens.

| S-EPMC7132306 | biostudies-literature

Clostridium drakei

Project description:Clostridium drakei overview

| PRJNA454518 | ENA

Clostridium drakei strain:SL1

Project description:Clostridium drakei strain:SL1 Genome sequencing

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Clostridium drakei strain:SL1

Project description:Clostridium drakei strain:SL1 Genome sequencing and assembly

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Aplexone Targets the HMG-CoA Reductase Pathway and Differentially Regulates Arteriovenous Angiogenesis

Project description:Arterial and venous endothelial cells exhibit distinct molecular characteristics at early developmental stages. These lineage-specific molecular programs are instructive to the development of distinct vascular architectures and physiological conditions of arteries and veins, but their roles in angiogenesis remain unexplored. Here, we show that the caudal vein plexus in zebrafish forms by endothelial cell sprouting, migration and anastomosis, providing a venous-specific angiogenesis model. Using this model, we identified a novel compound, aplexone, which effectively suppresses venous, but not arterial, angiogenesis. Multiple lines of evidence indicate that aplexone differentially regulates arteriovenous angiogenesis by targeting the HMG-CoA reductase (HMGCR) pathway. Treatment with aplexone affects the transcription of enzymes in the HMGCR pathway and reduces cellular cholesterol levels. Injecting mevalonate, a metabolic product of HMGCR, reverses the inhibitory effect of aplexone on venous angiogenesis. In addition, aplexone treatment inhibits protein prenylation and blocking the activity of geranylgeranyl transferase induces a venous angiogenesis phenotype resembling that observed in aplexone-treated embryos. Furthermore, endothelial cells of venous origin have higher levels of proteins requiring geranylgeranylation than arterial endothelial cells and inhibiting the activity of Rac or Rho Kinase effectively reduces the migration of venous, but not arterial, endothelial cells. Taken together, our findings indicate that angiogenesis is differentially regulated by the HMGCR pathway via an arteriovenousdependent requirement for protein prenylation in zebrafish and human endothelial cells.

2011-01-11 | E-MTAB-494 | biostudies-arrayexpress

Hepatic reductase null

Project description:Microarray analysis to examine the relationship between hepatic phenotype and changes in gene expression in cytochrome P450 reductase (CPR) null mice. Keywords: ordered

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The Mammalian Cytosolic Thioredoxin Reductase Pathway Acts via a Membrane Protein to Reduce ER-localised Proteins

Project description:Folding of proteins entering the mammalian secretory pathway requires the insertion of the correct disulfide bonds. Disulfide formation involves both an oxidative pathway for their insertion and a reductive pathway to remove incorrectly formed disulfides. Reduction of these disulfides is critical for correct folding and degradation of misfolded proteins. Previously, we showed that the reductive pathway is driven by NADPH generated in the cytosol. Here, by reconstituting the pathway using purified proteins and ER microsomal membranes, we demonstrate that the thioredoxin reductase system provides the minimal cytosolic components required for reducing proteins within the ER lumen. In particular, saturation of the pathway and its protease sensitivity demonstrates the requirement for a membrane protein to shuttle electrons from the cytosol to the ER lumen. These results provide compelling evidence for the critical role of the cytosol in regulating ER redox homeostasis to ensure correct protein folding and to facilitate the degradation of misfolded ER proteins.

2020-04-09 | PXD017923 | Pride

Transcription profiling of Arabidopsis thioredoxin reductase knock-out mutant

Project description:Transcriptomic study of a thioredoxin reductase knock-out mutant. Biological question : Thioredoxins are small redox proteins implicated in crucial pathways of cell life. They are reduced by a conserved flavoprotein named NADPH-dependent thioredoxin reductase (NTR). In order to give an insight into the functions of the NTR/thioredoxin pathway in Arabidopsis, we have used a reverse genetic approch. Both NTR genes (NTRA and NTRB) have been inactivated in the double ntra ntrb mutant. T-DNA lines have been provided by the SALK library. Surprisingly, this mutant shows a limited phenotype suggested that some additional redox pathways are involved in compensating the inactivation of the NTR/thioredoxin pathway. In order to isolate compensatory genes that would be transcriptionally induced in the ntra ntrb mutant, we have performed this CATMA project. Seeds of the wild-type Col-0 ecotype and of the ntra ntrb homozygote double mutant were sowed in soil. Three replicates of lines were made (Col-0 1, 2 and 3 ntra ntrb 1, 2 and 3) : plants were put at different places of the greenhouse and grown at different times. Germination was synchronized by 4 days at 4C and plants were grown during 17 days, until they reached a 6 rosette leaves stage. Entire plants (30 plants per sample) were harvested, frozen in liquid nitrogen and stored at -80C until extraction.

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