CRISPR-Cas systems are prokaryotic immune systems that provide their hosts with sequence-specific protection from foreign genetic elements like bacteriophages, plasmids, and transposons. CRISPR systems are widespread in the microbial world: they’ve been identified in 40% of bacterial genomes and 90% of archaeal genomes. A CRISPR locus contains an array of short (~30 bp) repeating DNA sequences with unique “spacer” sequences in between. The spacers are of foreign origin and specify the sequences targeted by the CRISPR system. New spacer sequences can be captured from invading genetic elements and integrated into the CRISPR array. To interfere against these elements, the CRISPR array is transcribed and processed into small RNAs called crRNAs, which are loaded into Cas nucleases. Together, Cas nucleases and their crRNAs form surveillance complexes that recognize and destroy nucleic acids complementary to the crRNA. 

Despite sharing a name, CRISPR systems are extremely diverse with respect to the proteins they encode and their mechanisms of action. They have been categorized into 6 types and 33 subtypes (and counting). While many Cas nucleases use their crRNA to recognize and cleave complementary DNA targets, we now know other Cas proteins and their accessory factors harbor diverse biochemical activities in lieu of or in addition to DNA cleavage. Cas protein activities include RNA cleavage, ssDNA cleavage, synthesis of small molecule second messengers, and even transposon integration. In response to the evolutionary pressures imposed by CRISPR immunity, phages often encode small anti-CRISPR proteins that inhibit specific Cas protein activities and permit the phage infection to succeed. 

Our lab is broadly interested in: (1) the mechanisms and consequences of CRISPR immunity in native bacterial hosts; (2) how these systems are regulated by their hosts and subverted by phages; and (3) roles that CRISPR systems play beyond immunity. We use a combination of microbial genetics, high-throughput genetic screens, time-lapse microscopy, and biochemical reconstitution to better understand the diverse roles of CRISPR in the microbial world.