Dataset Information

Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism.

ABSTRACT: Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system Bacillus subtilis using known data. YVRE is assigned the function as a glucono-lactonase using prediction and phylogenetic analysis. A molecular dynamics simulated homology model of YVRE (with calcium) using human senescence marker protein 30 /SMP30 (PDB ID: 3G4E) as template is reported for functional inference. It is observed that the protein possesses bivalent metal binding domain. Molecular docking studies with the substrate glucono-?-lactone show YVRE binding with the substrate. This data was further validated using cloning and sub-cloning in pUC57 and pET22b+ respectively, followed by expression and purification using nickel affinity chromatography. The activity of YVRE using the substrate glucono-?-lactone was calculated. The results show the function of YVRE as a gluconolactonase, with higher preference to zinc than calcium or magnesium. Thus, YVRE is shown to play key role in three metabolic pathways namely, pentose phosphate pathway, ascorbate and aldarate metabolism, and caprolactam degradation.

SUBMITTER: Reshma SV

PROVIDER: S-EPMC5767921 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism.

Reshma S V SV Sathyanarayanan Nitish N Nagendra H G HG

Bioinformation 20171231 12

Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system Bacillus subtilis using known data. YVRE is assigned the function as a glucono-lactonase using prediction and phylogenetic analysis. A molecular dynamics simulated homology model of YVRE (with calcium) ...[more]

PMID: 29379263

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Project description:Bacillus megaterium is a bacterium of great importance as a plant-beneficial bacterium in agricultural applications and in industrial bioproduction of proteins. Understanding intracellular processing of carbohydrates in this species is crucial to predicting natural carbon utilization as well as informing strategies in metabolic engineering. Here, we applied stable isotope-assisted metabolomics profiling and metabolic flux analysis to elucidate, at high resolution, the connections of the different catabolic routes for carbohydrate metabolism immediately following substrate uptake in B. megaterium QM B1551. We performed multiple 13C tracer experiments to obtain both kinetic and long-term 13C profiling of intracellular metabolites. In addition to the direct phosphorylation of glucose to glucose-6-phosphate (G6P) prior to oxidation to 6-phosphogluconate (6P-gluconate), the labeling data also captured glucose catabolism through the gluconate pathway involving glucose oxidation to gluconate followed by phosphorylation to 6P-gluconate. Our data further confirmed the absence of the Entner-Doudoroff pathway in B. megaterium and showed that subsequent catabolism of 6P-gluconate was instead through the oxidative pentose-phosphate (PP) pathway. Quantitative flux analysis of glucose-grown cells showed equal partition of consumed glucose from G6P to the Embden-Meyerhof-Parnas (EMP) pathway and from G6P to the PP pathway through 6P-gluconate. Growth on fructose alone or xylose alone was consistent with the ability of B. megaterium to use each substrate as a sole source of carbon. However, a detailed 13C mapping during simultaneous feeding of B. megaterium on glucose, fructose, and xylose indicated non-uniform intracellular investment of the different carbohydrate substrates. Flux of glucose-derived carbons dominated the gluconate pathway and the PP pathway, whereas carbon flux from both glucose and fructose populated the EMP pathway; there was no assimilatory flux of xylose-derived carbons. Collectively, our findings provide new quantitative insights on the contribution of the different catabolic routes involved in initiating carbohydrate catabolism in B. megaterium and related Bacillus species.

Dataset Information

Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism.

Publications

Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism.

Similar Datasets

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