In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB)
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ORIGINAL ARTICLE
In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB) Vikas Sharma1 · Fauzul Mobeen1 · Tulika Prakash1 Received: 26 July 2019 / Accepted: 28 July 2020 © King Abdulaziz City for Science and Technology 2020
Abstract The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB. Keywords Evolution · Horizontal gene transfer · Natural rubber degradation · Phylogeny · Rubber oxygenases · Selective pressure
Introduction Natural rubber (NR) is a biopolymer of cis-1,4-isoprene and has been commercially exploited because of its wide range of domestic and industrial applications. As NR does not accumulate in the environment, NR-degradation must occur. Bioremediation of NR is a potential eco-friendly alternative Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02371-6) contains supplementary material, which is available to authorized users. * Tulika Prakash [email protected] Vikas Sharma [email protected] Fauzul Mobeen [email protected] 1
School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi 175005, Himachal Pradesh, India
strategy to cope with the environmental and health hazards associated with the traditional methods of NR-degradation. Several reports on bacterial biodegradation of NR have been published which have revealed two distinct groups of NRdegrading bacteria, viz., Gram-positive Actinobacteria and Gram-negative Proteobacteria (Jendrossek and Birke 2019). The key enzyme
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