Bacterial-phage relationships and development of novel genome editing technologies

Bacteria are the most abundant organisms on earth, yet they are outnumbered by a factor of 10-to-1 by their natural predator, the bacteriophage. Under a constant bombardment of phage, bacteria are forced to rapidly evolve ways of evading infection and cell death. Recently, many bacteria and archaea were found to possess an RNA based adaptive immunity consisting of viral DNA integrated into the bacterial genome referred to as CRISPR (clustered regularly interspaced short palindromic repeats). In the broad view, my research interests seek to understand (and exploit) the molecular mechanisms employed by bacteria in defense and the subversions developed by phages in this on-going evolutionary war.

Genome Engineering:

CRISPRs have been adapted for biotech applications as powerful tools used in genome editing. For instance, the CRISPR system from Streptococcus pyogenes encodes the protein Cas9, which has been used to insert new sequences of DNA and replace existing sequences of DNA in a targeted manner. Although these reactions work remarkably well in certain situations, manipulation of the genome on an organism in vivo remains inefficient. Although Cas9 and similar variants have opened the door to potentially curing many devastating genetic disorders, current limitations in our understanding of the underlying molecular processes and ability to control them must be overcome to fully unlock the potential of gene therapy. We use protein design methodologies to create variants of CRISPR proteins such as Cas9 to improve their use as genome editing tools in ways that will hopefully enable more widespread implementation of gene therapies.

Bacteriophage therapy:

Growing bacterial resistance to existing antibiotics that outpaces the discovery of new classes of antibiotics is creating bacterial strains that are resistant to nearly all or in some cases, all known drugs. These ‘superbugs’ are essentially untreatable and threaten to push us back to a medical period not seen since world war 2, before the mass production and use of the first antibiotics such as penicillin. New treatment options must be found and made available for bacterial infections. My lab seeks to identify novel bacteriophages that may be useful as therapeutics for bacterial infections. Though this idea of bacteriophage therapy is nearly 100 years old, new technology has the potential to fully realize the potential of phages for treating infections. Bacteriophages can be found wherever the target bacteria live. Undergraduate students participating in this research sample environments to find candidate bacteriophages. Once found these phages are characterized and genetically engineered to maximize the therapeutic potential.

Selected Publications

• Ma CJ*, Gibb B*, Kwon Y, Sung P, Greene EC. “Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament.” Nucleic Acids Res. 2017 PMID: 27903895. Impact Factor: 10.162 *shared authorship.
• Redding S, Sternberg S, Marshall M, Gibb B, Bhat P, Guegler C, Wiedenheft B, Doudna J, Greene EC, “Surveillance and processing of foreign DNA by the Escherichia coli CRISPR-Cas system.” Accepted at Cell August 2015.
• Qi Z, Redding S, Lee JY, Gibb B, Kwon Y, Niu H, Gaines WA, Sung P, Greene EC., “DNA sequence alignment by microhomology sampling during homologous recombination.” 2014. PMID: 25684365
• Gibb B., Ye L.F., Kwon Y., Niu H., Sung P., Greene E.C., “Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules” Nature Structure & Molecular Biology. 2014. PMID: 25195049
• Gibb B., Silverstein T.S., Greene E.C., DNA Repair. PMID: 24598576
• Deng S., Gibb B., Almeida M.J., Greene E.C., Symington L.S., “RPA antagonizes microhomology-mediated repair of DNA double-strand breaks” Nature Structure & Molecular Biology. 2014. PMID: 24608368
• Gibb B., Ye L.F., Gergoudis S.C., Kwon Y., Niu H., Sung P., Greene E.C., “Concentration-dependent exchange of Replication protein A on single-stranded DNA revealed by single-molecule imaging” PLoS One. 2014. PMID: 24498402.
• Gibb B., Silverstein T.D., Finkelstein I.J., Greene E.C., “Single-Stranded DNA Curtains for Real-Time Single-Molecule Visualization of Protein-Nucleic Acid Interactions” Analytical Chemistry. 2012. PMID: 22950646.
• Gibb B., Gupta K., Ghosh K., Sharp R., Chen J., Van Duyne G.D., “Requirements for catalysis in the Cre recombinase active site” Nucleic Acids Research. 2010. PMID: 20462863