Comparative analysis of adhesin-like proteins from Methanobacteriales species

Methanogenic archaea are key syntrophic partners in animal and human guts. However, the molecular basis of physical and functional interactions of methanogens with other cells remains poorly understood. Adhesin-like proteins (ALPs) are abundant, unusually large, and repeat-rich surface proteins and are potential prime candidates for mediating cell-cell interactions, however, due to poor characterization, ALPs often remain neglected in annotations of genomes and large-scale datasets. Here, we combined structure-guided analysis with comparative genomics to map ALP domain architectures across Methanobacteriales species, with emphasis on intestinal and rumen lineages. We curated predicted ALP structures and manually delineated domain boundaries to build a reference set encompassing ABD, RBH, membrane-anchoring domains (MAD), and miscellaneous accessory domains. Leveraging on a novel approach for ALP domain annotations, we generate ALP annotations and domain architectures for 17 Methanobacteriales species without reliance on primary-sequence homology. Applying this approach to strains of Methanobrevibacter smithii and Methanobrevibacter intestini, we assembled species-level "adhesiomes" and assessed conservation patterns of ALPs. Network analysis indicated that ALPs are more commonly shared among strains within a species than between species, suggesting species-specific adhesin repertoires. While total ALP counts differed significantly between M. smithii and M. intestini (Wilcoxon rank-sum p = 0.00295), median ALP lengths did not (p = 0.606). Our results provide a comprehensive overview of the ALP domain architectures in Methanobacteriales species and reveals species-specific adhesiomes that likely contribute to niche adaptation and syntrophic partnerships in gut ecosystems.