Department of Bioinformatics, School of Medical Informatics,
Jiangsu Key Lab of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, Jiangsu Province, 221000, China.
G3 (Bethesda). 2019 Aug 8;9(8):2489-2496. doi: 10.1534/g3.119.400123.
Previous bioinformatics studies have linked gain or loss of energy reserves 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 could provide 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 and combined a set of hidden Markov sequence models (HMMs) to search homologs of key enzymes related with the metabolism of energy reserves. Our results revealed that specific pathways like trehalose-related glycogen metabolism and enzymes such as wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) are mainly restricted within specific 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 like polyP metabolism absence in is correlated with bacterial genome reduction. Through this analysis, a 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.
先前的生物信息学研究基于相对较少的细菌基因组或蛋白质组，将能量储备的增加或减少与宿主-病原体相互作用和细菌毒力联系起来。因此，了解能量储备在细菌物种中的理论分布模式可能为研究细菌的生活方式和生理学提供一条捷径。到目前为止，由于它们能够在营养缺乏条件下支持细菌的存活，已经在细菌中鉴定出了五种主要的能量储备，包括多磷酸盐（polyP）、糖原、蜡酯（WE）、三酰基甘油（TAG）和聚羟基烷酸（PHA）。尽管与能量储备代谢相关的酶已得到很好的理解，但从进化的角度来看，对细菌能量储备的分布缺乏系统的研究。在这项研究中，我们从 8282 个经过人工审查的细菌参考蛋白质组中获取了数据，并结合了一组隐藏的 Markov 序列模型（HMMs）来搜索与能量储备代谢相关的关键酶的同源物。我们的研究结果表明，特定的途径，如海藻糖相关的糖原代谢和蜡酯合酶/酰基辅酶 A：二酰基甘油酰基转移酶（WS/DGAT）等酶，主要局限于特定类型的细菌群体内，这为理解它们的起源和功能提供了进化上的见解。此外，该研究还证实，能量储备的丧失，如多磷酸盐代谢的缺失，与细菌基因组的减少有关。通过这种分析，呈现了一幅关于细菌能量储备代谢的更清晰的画面，这可以为进一步的细菌能量代谢理论和实验分析提供指导。
