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Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves

By Liang Wang, Jianye Yang, Yue Huang, Qinghua Liu, Yaping Xu, Xue Piao, Michael J. Wise

Posted 10 Feb 2019
bioRxiv DOI: 10.1101/545715 (published DOI: 10.1534/g3.119.400123)

Metabolism of energy reserves is essential for bacterial functions, such as pathogenicity, metabolic adaptation, and environmental persistence, etc. Previous bioinformatics studies have linked gain or loss of energy reserves such as glycogen and polyphosphate (polyP) with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the theoretical distribution patterns of energy reserves across bacterial species provides a shortcut route to look into bacterial lifestyle and physiology. So far, five major energy reserves have been identified in bacteria due to their capacity to support bacterial persistence under nutrient deprivation conditions. These include polyphosphate (polyP), glycogen, wax ester (WE), triacylglycerol (TAG), and polyhydroxyalkanoates (PHAs). Although the enzymes related with metabolism of energy reserves are well understood, there is a lack of systematic investigations into the distribution of bacterial energy reserves from an evolutionary point of view. In this study, we sourced 8282 manually reviewed bacterial reference proteomes from UniProt database and combined a set of hidden Markov sequence models to search homologs of key enzymes related with the metabolism of energy reserves. The distribution patterns were visualized in taxonomy-based phylogenetic trees. This study reveals that specific pathways and enzymes are restricted within certain types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirms that loss of energy reserves is correlated with bacterial genome reduction. Through this analysis, a much clearer picture about the metabolism of energy reserves in bacteria is presented, which could serve as a guide for further theoretical and experimental analyses of bacterial energy metabolism.

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