Functional annotation of an ecologically important protein from Chloroflexus aurantiacus involved in polyhydroxyalkanoat
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Functional annotation of an ecologically important protein from Chloroflexus aurantiacus involved in polyhydroxyalkanoates (PHA) biosynthetic pathway Atikur Rahman1 · Tasmina Ferdous Susmi1 · Farzana Yasmin1 · Md. Ekramul Karim2 · Mohammad Uzzal Hossain3 Received: 4 July 2020 / Accepted: 28 September 2020 © Springer Nature Switzerland AG 2020
Abstract Chloroflexus aurantiacus J-10-fI strain is a thermophilic gram-negative bacterium that possesses many proteins in its genome; some are considered as hypothetical proteins. The use of bioinformatics tools can assist in understanding this organism through structural and functional annotation. Our study aimed to assign structure and function to an ecologically important hypothetical protein present in the bacterial genome. To analyze the hypothetical protein (WP_012259469.1), we used an in silico approach to find out various properties like physiochemical characteristics, subcellular localization, 3D structure, protein–protein interaction and functional annotation. Protein–protein interactions were obtained from the STRING database. In silico analysis revealed that the protein is a soluble protein with predominantly alpha-helices in its secondary structure. The 3D model of the protein has been found to be novel and possessed expected quality as assessed by several quality assessment tools. Functional annotation indicated that the protein acted like a (R)-specific enoyl-CoA hydratase which is linked with PHA synthesis. Protein–protein interactions also showed with high confidence that the protein interacted with a protein synthesizer of enoyl-CoA hydratase involved in PHA biosynthesis. Polyhydroxyalkanoate (PHA) is a novel polyester used as a biodegradable thermoplastic and plays a crucial role in environmental biodegradability and biocompatibility. An extensive variety of microorganisms produces PHA for intracellular carbon and energy storage purposes. In the present investigation, we bioinformatically confirmed that the WP_012259469.1 is associated with the PHA biosynthesis pathway. From our anaylses, we also predict that polyhydroxyalkanoate (PHAs) has the potential to become an alternative source of renewable and biodegradable polyesters. Keywords Chloroflexus aurantiacus · Hypothetical protein · Homology modeling · Functional annotation · Protein– protein interaction · PHA synthesis
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s42452-020-03598-x) contains supplementary material, which is available to authorized users. * Mohammad Uzzal Hossain, [email protected]; Atikur Rahman, [email protected]; Tasmina Ferdous Susmi, [email protected]; Farzana Yasmin, [email protected]; Md. Ekramul Karim, [email protected] | 1Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh. 2Department of Microbiology, Faculty of Life and Earth Sciences, Jagannath University, Dhaka 1100, Bangladesh. 3Bioinformat
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