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Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay

ABSTRACT: Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay

PROVIDER: PRJEB11480 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1104482_1.fastq.gz	Fastqsanger.gz
	ERR1104482_2.fastq.gz	Fastqsanger.gz

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Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay

Project description:Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay

| PRJEB11480 | ENA

Transcription profiling of canola seedling roots and shoots to study the effects of the bacterial enzyme ACC deaminase

Project description:The purpose of this experiment was to study the effects of the bacterial enzyme ACC deaminase on the transcriptional changes within canola seedlings. Seedlings from seeds treated with the plant growth-promoting bacteria Pseudomonas putida UW4 which expresses a high level of ACC deaminase and its ACC deaminase-minus mutant were compared to untreated seedlings along with a transgenic line of canola expressing the ACC deaminase enzyme in the roots. ACC deaminase breaks down 1-aminocyclopropane-1-carboxylic acid, the biosynthetic precursor to the plant hormone ethylene, lowering ethylene levels and improving plant fitness. Plants treated with the ACC deaminase-containing bacteria and transgenic plants expressing ACC deaminase are more tolerant to a variet of stresses and this expression study helps to illuminate the pathways responsible for the growth promotion provided by the beneficial bacteria and the role of the enzyme itself.

2009-03-30 | E-TABM-582 | biostudies-arrayexpress

Effect of bacterial ACC deaminase on plant gene expression

Project description:Canola plants inoculated with plant growth-promoting bacteria either expressing ACC deaminase or not to determine the effect on plant gene expression using an Arabidopsis microarray.

2011-11-01 | GSE31396 | GEO

Effect of bacterial ACC deaminase on plant gene expression

2011-11-01 | E-GEOD-31396 | biostudies-arrayexpress

Transcription profiling of canola trangenic plants expressing ACC deaminase and growth in the presence of nickel

Project description:The purpose of this experiment was to study the effects of a bacterial ACC deaminase transgene in the roots and its impact on nickel tolerance of canola. ACC deaminase breaks down 1-aminocyclopropane-1-carboxylic acid, the biosynthetic precursor to the plant hormone ethylene, lowering ethylene levels and improving plant tolerance to stress. Ethylene evolved during plant stress is thought to causes senescence and cell death and worsen stress symptoms. Transgenic plants expressing ACC deaminase from the plant growth-promoting bacteria Pseudomonas putida UW4 are more tolerant to heavy metals in the soil and this expression study helps to illuminate the pathways responsible for this tolerance.

2009-04-01 | E-TABM-495 | biostudies-arrayexpress

Proteome dynamics of rice with inoculation of ACC deaminase producing endophytic bacteria

Project description:The data presented here are related to the proteins detected in rice plants inoculated with ACC deaminase producing Methylobacterium oryzae CBMB20 and imposed with salt stress.

2021-07-29 | MSV000087922 | MassIVE

Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay, artificial and natural AccD competition constructs

Project description:A starting natural community of AccD genes, and a wild-type AccD gene was cloned and altered. Each were used in an artificial selection assay and sequenced via a 454 GS FLX Titanium system.

| PRJEB11657 | ENA

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay.

Project description:Metagenomes derived from environmental microbiota encode a vast diversity of protein homologs. How this diversity impacts protein function can be explored through selection assays aimed to optimize function. While artificially generated gene sequence pools are typically used in selection assays, their usage may be limited because of technical or ethical reasons. Here, we investigate an alternative strategy, the use of soil microbial DNA as a starting point. We demonstrate this approach by optimizing the function of a widely occurring soil bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase. We identified a specific ACC deaminase domain region (ACCD-DR) that, when PCR amplified from the soil, produced a variant pool that we could swap into functional plasmids carrying ACC deaminase-encoding genes. Functional clones of ACC deaminase were selected for in a competition assay based on their capacity to provide nitrogen to Escherichia coli in vitro. The most successful ACCD-DR variants were identified after multiple rounds of selection by sequence analysis. We observed that previously identified essential active-site residues were fixed in the original unselected library and that additional residues went to fixation after selection. We identified a divergent essential residue whose presence hints at the possible use of alternative substrates and a cluster of neutral residues that did not influence ACCD performance. Using an artificial ACCD-DR variant library generated by DNA oligomer synthesis, we validated the same fixation patterns. Our study demonstrates that soil metagenomes are useful starting pools of protein-coding-gene diversity that can be utilized for protein optimization and functional characterization when synthetic libraries are not appropriate.

| S-EPMC4751833 | biostudies-literature

Gene Expression Analysis of the response to ACC inhibition

Project description:BACKGROUND & AIMS: Nonalcoholic steatohepatitis (NASH) is a chronic liver disease characterized by hepatic lipid accumulation, inflammation, and progressive fibrosis. Acetyl-CoA carboxylase (ACC) catalyzes the rate-limiting step of de novo lipogenesis and regulates fatty-acid beta-oxidation in hepatocytes. ACC inhibition reduces hepatic fat content and markers of liver injury in NASH patients; however, the effect of ACC inhibition on liver fibrosis has not been reported. METHODS: A direct role for ACC in fibrosis was evaluated by measuring de novo lipogenesis, procollagen production, gene expression, glycolysis, and mitochondrial respiration in hepatic stellate cells (HSCs) in the absence or presence of small-molecule inhibitors of ACC. ACC inhibitors were evaluated in rodent models of liver fibrosis induced by diet or the hepatotoxin, DEN. Fibrosis and hepatic steatosis were evaluated by histological and biochemical assessments. RESULTS: In TGF-beta-stimulated HSCs, ACC inhibition reduced activation and collagen production independent of mitochondrial beta-oxidation by blocking de novo lipogenesis. ACC inhibition prevented a metabolic switch necessary for induction of glycolysis and oxidative phosphorylation during HSC activation. Consistent with this direct anti-fibrotic mechanism in HSCs, ACC inhibition reduced liver fibrosis in a rat CDHFD model and in response to chronic DEN-induced liver injury that lacked hepatic lipid accumulation. CONCLUSIONS: In addition to reducing lipid accumulation in hepatocytes, ACC inhibition also directly impairs the pro-fibrogenic activity of HSCs. Small molecule inhibitors of ACC may reduce liver fibrosis by both reducing lipotoxicity in hepatocytes and directly reducing HSC activation, providing a mechanistic rationale for the treatment of patients with advanced liver fibrosis due to NASH.

2020-04-24 | GSE148849 | GEO

A study of pharmacokinetic analysis of capecitabine and cytidine deaminase activity

Project description:Interventions: Blood samples(10 points) are collected after the first administration of capecitabine for pharmacokinetic analysis and cytidine deaminase activity measurement. Primary outcome(s): To evaluate the correlation AUC of 5-DFUR/AUC of 5-DFCR ratio and cytidine deaminase activity. Study Design: Single arm Non-randomized

| 2634538 | ecrin-mdr-crc

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