germ warfare in a microbial mat community crisprs provide insights into the co-evolution of host and viral genomes细菌战的微生物垫社区crisprs提供洞察宿主和病毒基因组的进化.pdfVIP

Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes 1 1 2 3 John F. Heidelberg *, William C. Nelson , Thomas Schoenfeld , Devaki Bhaya 1 Department of Biological Sciences, Marine Environmental Biology Division, Wrigley Institute for Environmental Studies, University of Southern California, Avalon, California, United States of America, 2 Lucigen Corporation, Middleton, Wisconsin, United States of America, 3 Department of Plant Biology, Carnegie Institution for Science, Stanford, California, United States of America Abstract CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B9) as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B9 genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B9, but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as ‘‘viritopes’’ to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene i