A structure-guided classification framework reveals the diversity and catalytic architecture of BECR ribonuclease
Microorganisms across all domains of life engage in molecular conflict, deploying toxins to inhibit competitors or respond to biological threats. Among these, ribonuclease toxins are particularly widespread and diverse. A substantial fraction is associated with the BECR fold, a compact /{beta} architecture that supports RNase activity despite extensive divergence. Although several canonical…
Microbial organisms, present in every domain of life, utilize molecular warfare to outcompete others or react to biological threats. Ribonuclease toxins, a prevalent and varied subset, play a significant role in this context. A significant portion of these toxins belong to the BECR fold, a compact {beta} architecture enabling RNase function despite considerable variation.
While several representative members of this class are well understood, many BECR-fold proteins remain challenging to identify due to low sequence similarity, varying catalytic residues, and structural features that complicate evolutionary connections. Recent advancements in high-confidence protein structure predictions offer an opportunity to reevaluate this extensive and varied protein family.
This study utilizes iterative profile-HMM searches, profile-similarity networks, structural analyses, active-site mapping, and genomic context to investigate BECR proteins across the entire evolutionary tree. The investigation reveals a broader BECR-fold landscape encompassing both classic BECR and BECR-like families, refines the arrangement of conventional BECR proteins, and uncovers previously unknown families.
Furthermore, the study confirms BECR-Tox2 as a toxin counteracted by a matching immunity protein and demonstrates that its homologs are found in both Menshen-like anti-phage systems and polymorphic toxin loci. In summary, these discoveries broaden and elucidate the BECR-fold landscape, offering a framework for recognizing and understanding highly divergent proteins of this fold.
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