Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

ABSTRACT The peptidoglycan (PG, or murein) is a mesh-like structure, which made of glycan polymers connected by short peptides and surrounds the cell membrane nearly all bacterial species. In contrast, there no PG counterpart that would be universally found in Archaea but rather various are specific to some lineages. Methanopyrales Methanobacteriales two orders Euryarchaeota harbor pseudomurein (PM), structural analog PG. Owing differences between PM biosynthesis, have argued origin both not connected. However, recent studies revealed genomes PM-containing encode homologs genes involved even though neither their functions nor relationships within corresponding inter-domain phylogenies been investigated so far. this work, we devised pangenomic bioinformatic pipeline identify proteins for biosynthesis without prior genetic knowledge. taxonomic distribution evolutionary candidate were studied detail Bacteria through HMM sequence mining phylogenetic inference Mur domain-containing family, ATP-grasp superfamily, MraY-like family. Our results show archaeal muramyl ligases diversified mixture horizontal gene transfers duplications. families, members originate from Bacteria. approach further identified five new potentially synthesis deserve functional characterization. IMPORTANCE Methanobrevibacter smithii an archaea commonly human gut, its presence alongside pathogenic bacteria during infections has led researchers consider it as opportunistic pathogen. Fortunately, endoisopeptidases isolated phages, such PeiW PeiP, can cleave walls M. other pseudomurein-containing archaea. additional research required effective anti-archaeal agents combat these microorganisms. A better understanding wall necessary achieve goal. study sheds light on structures those microorganisms, showing responsible formation origins. This discovery challenges conventional view cell-wall architecture last common ancestor shows distinction “common origin” “convergent evolution” blurred cases.

Language: Английский

Challenges in Assembling the Dated Tree of Life

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(10)

Published: Oct. 1, 2024

Abstract The assembly of a comprehensive and dated Tree Life (ToL) remains one the most formidable challenges in evolutionary biology. complexity life's history, involving both vertical horizontal transmission genetic information, defies its representation by simple bifurcating phylogeny. With advent genome metagenome sequencing, vast amounts data have become available. However, employing this information for phylogeny divergence time inference has introduced significant theoretical computational hurdles. This perspective addresses some key methodological assembling ToL, namely, identification classification homologous genes, accounting gene tree-species tree mismatch due to population-level processes along with duplication, loss, transfer, accurate dating events. Ultimately, success endeavor requires new approaches that integrate knowledge databases optimized phylogenetic algorithms capable managing complex models.

Language: Английский