Talk abstracts
Talk on Tuesday 04:30-04:45pm submitted by Anthony Rish
Machine-learning based characterization of a novel bacterial anti-phage system
Anthony Rish (Ohio State Biochemistry Program), Elizabeth Fosuah (Ohio State Biochemistry Program), Tianmin Fu (Comprehensive Cancer Center)
Abstract:
The constant arms race between viruses and their hosts led to the evolution of antiviral defenses. Recent studies have revealed that bacteria developed diverse anti-phage defense systems such as restriction-modification (R-M), CRISPR-Cas, and abortive infection systems. Mechanistic characterization of these systems has revolutionized biomedical research with R-M becoming an essential tool for molecular cloning and CRISPR-Cas having completely changed the genome editing field. Here, we have structurally and functionally characterized a novel bacterial defense system, HerA_Duf, with unknown mechanisms via cryogenic electron microscopy and machine-learning guided biochemical and cellular assays. We have multiple cryo-EM density maps that identify HerA, a classical ATPase DNA helicase homolog, as a cyclic ring-like hexamer, bound to a larger 12-mer Duf assembly. Duf4297 consists of two previously uncharacterized domains, that we have attributed to an N-terminal nuclease domain and a C-terminal unidentified fold oligomerization (UFO) domain. The UFO domain is responsible for extensive interactions with both HerA and other Duf UFO domains. When in complex with HerA, Duf has non-sequence specific nuclease activity for supercoiled and linear dsDNA substrates with lengths above 300 base pairs. Interestingly, HerA has increased ATPase activity when bound to Duf and at physiological concentrations, ATP inhibits the nuclease activity of Duf. There is a distinct decoupling of inhibition by nucleotide binding to HerA and NTP hydrolysis since non-hydrolyzable analogs of ATP are sufficient for nuclease inhibition. Paired with the fact that this HerA homolog has no detectable strand displacement helicase activity, it is likely that HerA acts as a sensor for changes in NTP concentrations within the cell. Upon phage infection, and initial propagation within the cell, local NTP concentrations may drop enough that HerA can no longer efficiently bind any NTPs, allowing for Duf to digest both host and viral nucleic acids, leading to abortive infection of the cell to contain the spread of phages.
Keywords: Cryo-EM, Phage defense, Immunology