Structural insights into Deinococcus radiodurans BamA: extracellular loop diversity and its evolutionary implications

Diderm bacteria, characterized by an additional lipid membrane layer known as the outer membrane, fold their outer membrane proteins (OMPs) via the β-barrel assembly machinery (BAM) complex. Understanding how the BAM complex, particularly its key component BamA, assists in OMP folding remains crucial in bacterial cell biology. Recent research has focused primarily on the structural and functional characteristics of BamA within the Gracilicutes clade, such as in Escherichia coli (E. coli). However, another major evolutionary branch, Terrabacteria, has received comparatively less attention. An example of a Terrabacteria is Deinococcus radiodurans (D. radiodurans), a Gram-positive bacterium that possesses a distinctive outer membrane structure. In this study, we first demonstrated that the β-barrel domains of BamA are not interchangeable between D. radiodurans and E. coli. The structure of D. radiodurans BamA was subsequently determined at 3.8 Å resolution using cryo-electron microscopy, revealing obviously distinct arrangements of extracellular loop 4 (ECL4) and ECL6 after structural comparison with their counterparts in gracilicutes. Despite the overall similarity in the topology of the β-barrel domain, our results indicate that certain ECLs have evolved into distinct structures between the Terrabacteria and Gracilicutes clades. While BamA and its function are generally conserved across diderm bacterial species, our findings underscore the evolutionary diversity of this core OMP folder among bacteria, offering new insights into bacterial physiology and evolutionary biology.