The Emergence of the Slc11 Clade MCbgut: A Parsimonious Hypothesis for the Dawn of Lactobacillales in the Gut of Early Vertebrates

Abstract

The Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g., Bordetella, Achromobacter). Herein, the Slc11 clade MCb is subdivided in sister groups: MCbie and MCbgut. MCbie derives directly from the Slc11 clade MCa, pointing an intermediate stage in the evolution of MCbgut. MCbie predominates in marine Bacillaceae, is more conserved than MCbgut, lacks the structural plasticity that typify MCbgut carriers, and responds differently to identical mutagenesis. Exchanging MCbie/MCbgut amino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCbie and MCbgut templates, and the 3D location of the targeted sites in the carrier structure together suggests that the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCbie and MCbgut. Building on the established phylogeny for Enterococcus revealed that a pair of genes encoding MCbgut was present in the common ancestor of LB, as MCbgu1 and MCbgu2 templates exhibited distinct structural dynamics properties. These data are discussed when examining whether MCbgut+ LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems.