TY - JOUR
T1 - Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
AU - Burstein, David
AU - Sun, Christine L.
AU - Brown, Christopher T.
AU - Sharon, Itai
AU - Anantharaman, Karthik
AU - Probst, Alexander J.
AU - Thomas, Brian C.
AU - Banfield, Jillian F.
N1 - Funding Information:
We thank Andrea Singh for assistance with data management. This research was supported by the US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research under award number DE-AC02–05CH11231 (Sustainable Systems Scientific Focus Area; Lawrence Berkley National Laboratory operated by the University of California) and award number DE-SC0004918 (Systems Biology Knowledge Base Focus Area). Sequencing was performed at the US DOE Joint Genome Institute, a DOE Office of Science User Facility, supported under contract DE-AC02–05CH11231. DB was supported by a long-term EMBO fellowship.
PY - 2016/2/3
Y1 - 2016/2/3
N2 - Current understanding of microorganism-virus interactions, which shape the evolution and functioning of Earth's ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.
AB - Current understanding of microorganism-virus interactions, which shape the evolution and functioning of Earth's ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.
UR - http://www.scopus.com/inward/record.url?scp=84957535039&partnerID=8YFLogxK
U2 - 10.1038/ncomms10613
DO - 10.1038/ncomms10613
M3 - Article
C2 - 26837824
AN - SCOPUS:84957535039
SN - 2041-1723
VL - 7
JO - Nature Communications
JF - Nature Communications
M1 - 10613
ER -