Siphoviridae phage tails co-enrich with ex vivo amyloids

Abstract

Amyloid fibrils extracted from patient tissue are enriched by physicochemical fractionation methods and enzymatic tissue digestion with collagenase, resulting in a mixture of sedimented complexes. Reprocessing of an ex vivo lysozyme amyloid dataset revealed non-amyloid tubular assemblies, which we reconstructed to 3.5 angstrom. Sequence-agnostic model building with CryoAtom and fold search with FoldSeek identified a phage tail tube fold. Testing the crude Clostridium histolyticum collagenase used for tissue digestion, negative-stain TEM and LC-MS/MS showed proteins of an F-type tailocin, allowing us to assign the helical reconstruction to a major tail tube protein (TTP) of C. histolyticum. We also observed tailocin contamination in cardiac light-chain amyloid extracts, following the same collagenase treatment. Overall, we identify tailocins as recurrent reagent-borne contaminants in collagenase-treated ex vivo amyloid preparations and propose strategies to detect and avoid such artefacts in single-particle cryo-EM by optimizing the experimental design and data annotation towards a database of common contaminants.