Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves

Liang Wang,Chunying Wang,Junfeng Hu,Yue Huang,Zhanzhong Liu,Qinghua Liu,Wei Wang,Michael J Wise,Xiang Wu

doi:10.1038/s41598-018-37768-0

Abstract

Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.

Highlights

Temperature tolerance, and other environmental stresses[6]
A recent phylogenetic study revealed that PPK1 and polyphosphate kinase 2 (PPK2) are less common in bacteria and other unknown enzymes may involve in polyP metabolism[7]
It was proposed that enzymes involved in polyP metabolism show structure conservation among bacteria and archaea, only two enzymes PPX and PPK were analysed in archaea through comparative genomics and there is no overview of a complete polyP metabolism in archaea (Fig. 1)[6]

Summary

Introduction

Temperature tolerance, and other environmental stresses[6]. polyP plays important roles for archaeal physiological adaption to environmental changes and stress conditions where archaea reside. We collected as seed sequences all the enzymes directly linked with metabolism of five energy storage compounds in archaea. A set of eight enzymes that are directly involved in polyP metabolism in prokaryotes was scrutinized in archaeal proteomes.

Results

Conclusion