Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves

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.

Domain-centric dissection and classification of prokaryotic poly(3-hydroxyalkanoate) synthases

“…Previous bioinformatics analysis showed the complete metabolism pathway of PHA in archaea by focusing on enzymes including PhaA, PhaB, PhaC, PhaE, PhaP, and PhaZ, according to which it was confirmed that PHA accumulation is tightly related to halophilic archaea with larger proteome size and higher GC contents [3]. In this study, we are only interested in PHA synthases (PhaCs and its subunits) and explored their distribution patterns in archaea.…”

“…There are three types of PHAs according to their side chains, short-chain length (SCL) PHA (PHA SCL ), medium-chain length (MCL) PHA (PHA MCL ), and the mixture of both SCL and MCL PHAs (PHA SCL-MCL ) [2]. Previous studies confirm that there are three enzymes involved in PHA synthesis, which include Acetyl-CoA acetyltransferase (PhaA), Acetoacetyl-CoA reductase (PhaB), and Poly(3-hydroxyalkanoate) polymerase subunit PhaC (PhaC) [3]. There are another two subunits, PhaE and PhaR, for Poly(3-hydroxyalkanoate) polymerase, which integrate with subunit PhaC to form active PHA synthase, respectively [4].…”

“…A novel type of Class III PhaC was widely identified with an elongated C terminus in halophilic archaea, which is indispensable for enzymatic activity [10]. Another study systematically investigated the distribution patterns of PHA synthesis pathway (PhaA, PhaB, and PhaC) and degradation pathway (PhaZ) in archaeal species, according to which PHA accumulation is skewedly associated with halophilic archaeal species [3].…”

Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves

“…Glycogen metabolism in bacteria has multiple pathways, which include the classical pathway (GlgC, GlgA, GlgB, GlgP and GlgX) [4], trehalose pathway (TreS, Pep2, GlgE, and GlgB), and the novel Rv3032 pathway [29]. Rv3032 is an alternative enzyme for the elongation of α-1,4-glucan, which was compared for distribution patterns with GlgA.…”

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation inMethanosarcina mazei

“…Despite this, a focussed study of archaeal polyP metabolism has yet to be carried out, and so our understanding of the enzymology, gene regulation and environmental triggers for polyP metabolism in the Archaea lags behind that of the Bacteria. 4 Wang et al 22 have previously analysed 427 Archaeal reference proteomes for the pathways of polyP metabolism and identified PPK1, PPK2 and PPX within the genera Methanolobus, Methanoregula, and Methanosarcina. In this paper we interrogate the RefSeq database which, at the time of examination (November 2018), consisted of sequences from 1,126 Archaea to further investigate the distribution of polyP metabolism proteins across the Archaeal domain.…”