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Updated: May 1, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
Structural and functional diversity of metalloproteinases encoded by the Bacteroides fragilis pathogenicity island
Sergey A Shiryaev1, Alexander E Aleshin, Norihito Muranaka
1Sanford-Burnham Medical Research Institute, La Jolla, CA, USA.
Abstract:
Bacteroides fragilis causes the majority of anaerobic infections in humans. The presence of a pathogenicity island in the genome discriminates pathogenic and commensal B. fragilis strains. The island encodes metalloproteinase II (MPII), a potential virulence protein, and one of three homologous fragilysin isozymes (FRA; also termed B. fragilis toxin or BFT). Here, we report biochemical data on the structural-functional characteristics of the B. fragilis pathogenicity island proteases by reporting the crystal structure of MPII at 2.13 Å resolution, combined with detailed characterization of the cleavage preferences of MPII and FRA3 (as a representative of the FRA isoforms), identified using a high-throughput peptide cleavage assay with 18 583 substrate peptides. We suggest that the evolution of the MPII catalytic domain can be traced to human and archaebacterial proteinases, whereas the prodomain fold is a feature specific to MPII and FRA. We conclude that the catalytic domain of both MPII and FRA3 evolved differently relative to the prodomain, and that the prodomain evolved specifically to fit the B. fragilis pathogenicity. Overall, our data provide insights into the evolution of cleavage specificity and activation mechanisms in the virulent metalloproteinases.
Insights
Bacteroides fragilis virulence factors, metalloproteinase II (MPII) and fragilysin (FRA), have distinct evolutionary paths. Their unique prodomain structures are crucial for pathogenicity in B. fragilis infections.
Area of Science:
- Microbiology
- Structural Biology
- Evolutionary Biology
Background:
- Bacteroides fragilis is a major cause of anaerobic infections.
- A pathogenicity island distinguishes virulent B. fragilis strains, encoding metalloproteinase II (MPII) and fragilysin (FRA).
Discussion:
- The crystal structure of MPII was determined at 2.13 Å resolution.
- Cleavage preferences of MPII and FRA3 were characterized using a high-throughput peptide assay.
- MPII's catalytic domain evolution traces to human and archaebacterial proteinases.
- The prodomain fold is specific to MPII and FRA, suggesting adaptation for B. fragilis pathogenicity.
Key Insights:
- MPII and FRA3 catalytic domains evolved distinctly from their shared prodomain.
- The prodomain's evolution is specifically linked to B. fragilis pathogenicity.
- Understanding these proteases offers insights into virulence mechanisms.
Outlook:
- Further research into metalloproteinase evolution and activation mechanisms.
- Potential for novel therapeutic targets against B. fragilis infections.
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