The ability of V. cholerae to prevent phage predation is critical for its evolutionary fitness and epidemic potential. In turn, as obligate bacterial parasites, phages must co-evolve to overcome this resistance or they will face extinction. Our research is aimed at understanding the bacterial immunity and opposing phage immune evasion strategies at play in this dynamic co-evolutionary arms race. We use comparative genomics and complementary molecular approaches to identify and experimentally validate such strategies in disease associated phage and V. cholerae isolates.
A key weapon: a CRISPR–Cas adaptive immune system
CRISPR–Cas (clustered regularly interspaced short palindromic repeats– CRISPR-associated proteins) systems are sophisticated adaptive immune systems traditionally used by bacteria and archaea to protect against invading nucleic acids, including phage. CRISPR loci consist of an array of short direct repeats separated by highly variable spacer sequences corresponding to segments of previously captured invader-derived DNA. The CRISPR array is transcribed and the transcript cleaved into small CRISPR RNAs (crRNAs) that, in conjunction with the Cas proteins, execute an efficient process of immunity in which foreign nucleic acids are recognized by hybridization to crRNAs and cleaved.
ICP1 phages are prevalent phages found with V. cholerae in cholera patient samples from Bangladesh. Some ICP1 isolates harbor a complete and functional CRISPR–Cas system. This system was the first immune system shown to function in bacterial viruses, and it is used by ICP1 to overcome an antiviral system in V. cholerae, designated a PLE (phage inducible chromosomal island-like element). While it is clear how the CRISPR–Cas system functions to benefit the phage, the mechanism of phage interference by V. cholerae PLE is unknown and is an active area of research in our lab.