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Biochemical and structural characterization of a tail-spike protein with depolymerase activity identified in a marine
Serena Sirigu1, Thomas Roret2, Pierre Yves Mocaër3
1Synchrotron SOLEIL, L'Orme des Merisiers, Départementale 128, 91190 Saint-Aubin, France.
Abstract:
Marine phages are, through the infection of their bacterial hosts, key regulators of microbiome and carbon fluxes in the ocean. Despite their important role, the specific molecular mechanisms that underlie infection are so far understudied. Previously, the podovirus Cobetia marina virus 1 (Carin-1), which infects the marine γ-proteobacterium C. marina, was shown to display exopolysaccharide depolymerase activity. This activity is likely to mediate degradation of the host capsule to facilitate access to the bacterial membrane receptor, but no corresponding gene could be annotated in the genome of Carin-1 by comparative genomics. Biochemical characterization enabled assignment of this activity to Dpo31, a protein sharing less than 10% sequence identity with any characterized protein. Here, we report the structural domain organization and biochemical characterization of Dpo31, revealing an overall structure that is analogous to podovirus tail-spike proteins, allowing us to locate the depolymerase activity to the D3 domain and to identify original structural features that explain the absence of detectable similarity at the primary-sequence level.
Insights
Marine phages regulate ocean ecosystems. Researchers identified a novel depolymerase enzyme, Dpo31, in Cobetia marina virus 1 (Carin-1) responsible for degrading bacterial capsules, crucial for understanding viral infection mechanisms.
Area of Science:
- Marine microbiology
- Virology
- Biochemistry
Background:
- Marine phages are crucial regulators of ocean microbial communities and carbon cycling.
- Molecular mechanisms of marine phage infections remain understudied.
- Cobetia marina virus 1 (Carin-1) exhibits exopolysaccharide depolymerase activity, likely for host cell entry.
Purpose of the Study:
- To characterize the structure and function of the depolymerase enzyme Dpo31 from Carin-1.
- To elucidate the molecular basis for the depolymerase activity and its evolutionary novelty.
Main Methods:
- Protein purification and biochemical characterization of Dpo31.
- Structural analysis of Dpo31.
- Comparative genomics and sequence analysis.
Main Results:
- The depolymerase activity was assigned to the Dpo31 protein.
- Dpo31 shares structural homology with podovirus tail-spike proteins but has <10% sequence identity to known proteins.
- Depolymerase activity is localized to the D3 domain of Dpo31, which possesses unique structural features.
Conclusions:
- Dpo31 represents a novel class of depolymerase enzymes in marine viruses.
- Its unique structure explains the lack of sequence similarity to characterized proteins.
- Understanding Dpo31 provides insights into phage-host interactions and viral infection strategies in marine environments.
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