Comparative Genomics of Carbohydrate Utilization in Bacteria of the Family Sphaerochaetaceae: Evolutionary Origin of the Genes Encoding Galacturonidase and Unsaturated Rhamnogalacturonyl Hydrolase

A comparative analysis of carbohydrate degradation proteins encoded in the currently available genomic sequences of bacteria of the family Sphaerochaetaceae, namely Sphaerochaeta associata GLS2^T, S. globosa Buddy^T, S. pleomorpha Grapes^T, S. halotolerans 4-11^T, S. halotolerans 585, Sphaerochaeta sp. S2, Sphaerochaeta sp. PS, and Parasphaerochaeta coccoides SPN1^T was carried out. The genomes of Sphaerochaeta spp. encode a medium-sized and diverse set of proteins potentially involved in the degradation of different classes of carbohydrates, mainly oligosaccharides. All studied genomes encode glycoside hydrolases of the GH1, GH2, GH3, GH4, GH13, GH20, GH28, GH36, GH43, GH57, GH63, GH77 and GH105 families, as well as carbohydrate esterases of the CE8 and CE9 families. All studied bacteria, with the exception of P. coccoides SPN1^T, have many genes of the GH31 family proteins. The studied members of Sphaerochaetaceae do not have genes coding for endo-β-acetylmuramidase (lysozyme) of the GH23 family, which participates in peptidoglycan turnover. However, the genomes of S. associata, S. globosa, Sphaerochaeta sp. PS, and S. pleomorpha contain exo-β-acetylmuramidase genes (GH171 family). A significant part of the genes encoding carbohydrate degradation enzymes have the closest homologues among representatives of the phyla Bacillota, Bacteroidota, and Pseudomonadota. The genomes of the studied bacteria encode proteins that could potentially be involved in the degradation of pectin. The ability of the Sphaerochaetaceae members to use pectin for growth, as well as the evolutionary origin of the genes encoding potential α-galacturonidase (GH4 family) and unsaturated glucuronyl/rhamnogalacturonyl hydrolase (GH105 family), which participate in the degradation of pectin components, were studied.