Modularity and Hierarchy in CRISPR-Cas Target Recognition

Applied Physics Graduate Program, Rice University (Houston, TX)

M.E. Bonomo & M.W. Deem

Doctoral Research, Spring 2016 – Present

CRISPR – clustered regularly interspaced short palindromic repeats – is an immune system mechanism found in microorganisms, like bacteria.  It consists of an immunological memory stored in the bacteria’s genome with Cas – CRISPR associated – proteins that carry out the adaptation, expression, and interference functions. Viruses attempt to infect a bacteria cell by injecting their DNA into it, however the CRISPR is able to specifically recognize the viral DNA and cut it to stop the infection.

The bacteria’s CRISPR-Cas immune mechanism utilizes three hierarchical modules that recognize and cut the genetic material of invading viruses to protect the bacteria cell from infection. We are deriving a theoretical model of this process to understand the benefit of modularity in helping CRISPR specifically and efficiently find virus targets.

Publications: 

• M.E. Bonomo, “A small PAM optimizes target recognition in the CRISPR-Cas immune system,” Preprint: arXiv:2101.01303, 2021.
• M.E. Bonomo, “Modularity and Hierarchy in CRISPR-Cas Target Recognition,” Rice University Masters Thesis, 2018.
• M.E. Bonomo and M.W. Deem, “The physicist’s guide to one of biotechnology’s hottest new topics: CRISPR-Cas,” Physical Biology, 15 041002, 2018.
• M.E. Bonomo and M.W. Deem, “How the other half lives: CRISPR-Cas’s influence on bacteriophages,” in Evolutionary biology: Self, non-self evolution, species and complex traits; evolution, methods and concepts edited by Pierre Pontarotti, Springer Nature, 2017.

Oral Presentations: