Archaeal pseudomurein and bacterial murein cell wall biosynthesis share a common evolutionary ancestry

Abstract

Bacteria near-universally contain a cell wall sacculus of murein (peptidoglycan), the synthesis of which has been intensively studied for over 50 years. In striking contrast, archaeal species possess a variety of other cell wall types, none of them closely resembling murein. Interestingly though, one type of archaeal cell wall termed pseudomurein found in the methanogen orders Methanobacteriales and Methanopyrales is a structural analogue of murein in that it contains a glycan backbone that is cross-linked by a L-amino acid peptide. Here, we present taxonomic distribution, gene cluster and phylogenetic analyses that confirm orthologues of 13 bacterial murein biosynthesis enzymes in pseudomurein-containing methanogens, most of which are distantly related to their bacterial counterparts. We also present the first structure of an archaeal pseudomurein peptide ligase from Methanothermus fervidus DSM1088 (Mfer336) to a resolution of 2.5 Å and show that it possesses a similar overall tertiary three domain structure to bacterial MurC and MurD type murein peptide ligases. Taken together the data strongly indicate that murein and pseudomurein biosynthetic pathways share a common evolutionary history.

Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases

“…We recently reported gene cluster, taxonomic distribution and phylogenetic analyses of (pseudo)murein peptide ligases indicated to be involved in pseudomurein biosynthesis [21]. Thirteen cell wall biosynthesis enzymes were found to be shared between pseudomurein-containing methanogens and bacteria, with most of the enzymes suggested to have been present in the Last Universal Common Ancestor (LUCA).…”

“…Thirteen cell wall biosynthesis enzymes were found to be shared between pseudomurein-containing methanogens and bacteria, with most of the enzymes suggested to have been present in the Last Universal Common Ancestor (LUCA). MurA, MurB, FEM proteins, murein cross-linking transpeptidases and transglycosylases (penicillin-binding proteins (PBPs)), and murein recycling enzymes are not found in pseudomurein-containing methanogens [21]. Another major difference, the gamma-glutamyl-epsilon-lysine cross link in pseudomurein is thought to be catalysed by transglutaminase-like proteins [21,22].…”

“…MurA, MurB, FEM proteins, murein cross-linking transpeptidases and transglycosylases (penicillin-binding proteins (PBPs)), and murein recycling enzymes are not found in pseudomurein-containing methanogens [21]. Another major difference, the gamma-glutamyl-epsilon-lysine cross link in pseudomurein is thought to be catalysed by transglutaminase-like proteins [21,22]. The peptide ligases (pMurC, pMurD1/D2 and pMurE) were found exclusively in pseudomurein-containing methanogens and the genes are almost always found in two clusters.…”

“…Cluster one typically contains pmurD2-pmurD1-pmurC followed by vanA/B and mobA-like genes. Cluster two always contains ddl (encoding a d-Ala-d-Ala ligase orthologue)-mraY-pmurE but can sometimes also contain pmurC and/or pmurD1 as well as two pseudomurein-methanogenspecific conserved genes [21]. This differs largely from (summarised in Subedi et al 2021 [21]) the E. coli dcw gene cluster (mraZ-mraW-ftsL-ftsI-murE-murF-mraY-murD-ftsW-murG-murC-ddl-ftsQ-ftsA-ftsZ with murB being closely associated but separated by more than one intervening gene) and the Bacillus subtilis cluster (mraZ-mraW-ftsL-ftsI-murE-murD-ftsW-murG-murB-ftsQ with ftsA-ftsZ and murC being closely associated but separated by more than one intervening gene), with the two methanogen clusters bearing little if any resemblance to the bacterial clusters [21,23].…”

“Universal” Antimicrobial Combination of Bacitracin and His6-OPH with Lactonase Activity, Acting against Various Bacterial and Yeast Cells

“…Interestingly, despite the differences in the structure of the cell wall of G(+) and G(−) bacterial cells, as well as in pro- and eukaryotic cells of microorganisms (for example, bacteria and yeast), all of them are characterized by the structural presence of NAG: chitin is the main component of the cell wall of fungi, and, in fact, peptidoglycan is the most important part of the bacterial cell wall, as well as pseudopeptidoglycan (also known as pseudomurein) which presents in archaea cells [ 14 ]. Consequently, it can be expected that a violation of the NA molecule transfer process to the assembly site of the corresponding polysaccharides may lead to a slowdown, or even complete inhibition, of the synthesis of the cell wall of these microorganisms.…”