Development of Proteogenomic Approaches to Analyze the Role of Virus-Microbe Interactions in Shaping Natural Microbial Communities
- Univ. of California, Berkeley, CA (United States)
CRISPRs (clustered regularly interspaced short palindromic repeats) are adaptive immune systems in Bacteria and Archaea. Transcripts of the spacers that separate the repeats confer immunity through sequence identity with a targeted region (proto-spacer) in phage/viral, plasmid, or other foreign DNA. Short sequences immediately flanking the proto-spacer (proto-spacer adjacent motifs—PAMs) are important in both procuring spacers from and providing immunity to targeted sequences. New spacers are incorporated unidirectionally at the leader end of the CRISPR loci, thus recording a timeline of recent viral exposure. In the early phase of our research, we documented extremely rapid diversification of the CRISPR loci in natural populations [Tyson and Banfield, 2008] matched by high levels of sequence variation in natural viral populations [Andersson and Banfield, 2008]. Since then, in a genetically tractable model laboratory system, we have 1) tracked phage mutation and CRISPR diversification, and in a natural model system, we have 2) examined population history via over time, 3) investigated the timescale over which spacers become ineffective and the process by which ineffective spacers are removed, and 4) analyzed viral diversity. In addition to research activities, our group has organized five international CRISPR meetings, the fifth to be held at University of California, Berkeley in June 2012. Most importantly, the project provided the majority of funding support for Christine Sun (Ph.D. 2012).
- Research Organization:
- Univ. of California, Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- FG02-07ER64505
- OSTI ID:
- 1129432
- Report Number(s):
- DOE-UCB-15218
- Country of Publication:
- United States
- Language:
- English
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