The Peptidoglycan Biosynthesis Gene murC in Frankia: Actinorhizal vs. Plant Type

Abstract

Nitrogen-fixing Actinobacteria of the genus Frankia can be subdivided into four phylogenetically distinct clades; members of clusters one to three engage in nitrogen-fixing root nodule symbioses with actinorhizal plants. Mur enzymes are responsible for the biosynthesis of the peptidoglycan layer of bacteria. The four Mur ligases, MurC, MurD, MurE, and MurF, catalyse the addition of a short polypeptide to UDP-N-acetylmuramic acid. Frankia strains of cluster-2 and cluster-3 contain two copies of murC, while the strains of cluster-1 and cluster-4 contain only one. Phylogenetically, the protein encoded by the murC gene shared only by cluster-2 and cluster-3, termed MurC1, groups with MurC proteins of other Actinobacteria. The protein encoded by the murC gene found in all Frankia strains, MurC2, shows a higher similarity to the MurC proteins of plants than of Actinobacteria. MurC2 could have been either acquired via horizontal gene transfer or via gene duplication and convergent evolution, while murC1 was subsequently lost in the cluster-1 and cluster-4 strains. In the nodules induced by the cluster-2 strains, the expression levels of murC2 were significantly higher than those of murC1. Thus, there is clear sequence divergence between both types of Frankia MurC, and Frankia murC1 is in the process of being replaced by murC2, indicating selection in favour of murC2. Nevertheless, protein modelling showed no major structural differences between the MurCs from any phylogenetic group examined.

Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae

“…Another important distinctive gene is murC , related to peptidoglycan biosynthesis. Different copies in the genomes of the four different clusters were found ( Berckx et al, 2020 ). Two copies, mur C1 and mur C2, are present in clusters 2 and 3, which differ in their orientation with the presence of an open reading frame (ORF) encoding a nitroreductase family deazaflavin-dependent oxidoreductase in cluster 3.…”

Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives

“…BMG5.1) cluster-2 forms the earliest branching and deep-rooted evolutionary group that nodulates the actinorhizal plants from Cucurbitales, Datiscaceae, Coriariaceae, Rosaceae, and Rhamnaceae [4,36,68,78,79]. In contrast, a study on Mur ligase genes (MurC, MurD, MurE, and MurF) that are involved in catalyzing the biosynthesis of bacterial peptidoglycan layer, have revealed sharing of two copies of murC among cluster-2 and cluster-3, while cluster-1 and cluster-4 shared one copy [80]. However, a higher similarity with that of Actinobacteria proteins indicated that murC might have got acquired in all Frankia strains either from a horizontal gene movement or a convergent evolution.…”