Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria
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Products of numerous genes (phaC, phaA, phaB, phaP, phaR, and phaZ) are involved in the synthesis and degradation processes of the ubiquitous prokaryotic polyhydroxyalkanoate (PHA) intracellular reserve storage system. In this study, we performed a bioinformatics analysis to identify PHA-related genes and proteins in the genome of 66 selected organisms (class: Betaproteobacteria) that occur in various habitats; besides, evolutionary trajectories of the PHA system are reported here. The identified PHA-related genes were organized into clusters, and the gene arrangement was highly diverse. The occurrence and distribution of PHA-related clusters revealed that a single cluster was primarily segmented into small gene groups among various genomes, which were further reorganized as novel clusters based on various functional genes. The individual phylogenies of gene and protein sequences supported that the clusters were assembled through the relocation of native orthologous genes that underwent insertion, deletion, and elongation events. Furthermore, the neighboring genes provided valuable evolutionary and functional cues regarding the conservation and maintenance of PHA-related genes in the genome. Overall, the aforementioned results strongly indicate the influence of horizontal gene transfer on the organization of PHA-related gene clusters. Therefore, our results reveal new insights into the organization, evolutionary history, and cluster conservation of the PHA-related gene inventories among Betaproteobacterial organisms.
KeywordsBurkholderiaceae Cupriavidus necator H16 Phylogeny Flanking gene Gene relocation Horizontal gene transfer
The authors express gratitude to Consejo Nacional de Ciencia y Tecnología (CB-2014-01; 236285 and Fronteras de la Ciencia 2015-1: 016) for financial support. The authors thank Miguel Angel Martínez Roque (UPIBI-IPN) for his assistance with data collection and artwork of this study. We are very grateful to Joel Alba Flores (Biotechnology and Bioengineering, CINVESTAV) and Ravi-Kumar Narayanasamy (Central University of Tamil Nadu) for fruitful discussions and valuable suggestions. We thank the editor and anonymous reviewer for their insightful comments, which helped us to improve the manuscript.
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