TY - JOUR
T1 - CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog
AU - Soto-Perez, Paola
AU - Bisanz, Jordan E.
AU - Berry, Joel D.
AU - Lam, Kathy N.
AU - Bondy-Denomy, Joseph
AU - Turnbaugh, Peter J.
N1 - Funding Information:
We are grateful to Stephen Nayfach for providing the E. lenta -enriched metagenomes, Elizabeth Bess for providing RNA sequencing data, Chris Brown and Peter Fineran for including HuVirDB as a database for CRISPRTarget, and all of the members of the Turnbaugh and Bondy-Denomy labs for helpful discussion. This work was supported by the National Institutes of Health ( R01HL122593 ), the Searle Scholars Program ( SSP-2016-1352 ), and the UCSF Program for Breakthrough Biomedical Research (partially funded by the Sandler Foundation ). P.J.T. holds an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund , is a Chan Zuckerberg Biohub investigator, and is Nadia’s Gift Foundation Innovator supported, in part, by the Damon Runyon Cancer Research Foundation ( DRR-42-16 ). Fellowship support was provided by the Canadian Institutes of Health Research (K.N.L.), the Natural Sciences and Engineering Research Council (J.E.B.), and the UCSF Discovery Fellows (P.S.-P.). J.B.-D. was supported by an NIH Office of the Director Early Independence Award ( DP5-OD021344 ).
Funding Information:
We are grateful to Stephen Nayfach for providing the E. lenta-enriched metagenomes, Elizabeth Bess for providing RNA sequencing data, Chris Brown and Peter Fineran for including HuVirDB as a database for CRISPRTarget, and all of the members of the Turnbaugh and Bondy-Denomy labs for helpful discussion. This work was supported by the National Institutes of Health (R01HL122593), the Searle Scholars Program (SSP-2016-1352), and the UCSF Program for Breakthrough Biomedical Research (partially funded by the Sandler Foundation). P.J.T. holds an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund, is a Chan Zuckerberg Biohub investigator, and is Nadia's Gift Foundation Innovator supported, in part, by the Damon Runyon Cancer Research Foundation (DRR-42-16). Fellowship support was provided by the Canadian Institutes of Health Research (K.N.L.), the Natural Sciences and Engineering Research Council (J.E.B.), and the UCSF Discovery Fellows (P.S.-P.). J.B.-D. was supported by an NIH Office of the Director Early Independence Award (DP5-OD021344). Conceptualization, P.S.-P. J.E.B. J.B.-D. and P.J.T.; Methodology, P.S.-P. J.E.B. J.D.B. and K.N.L.; Software, J.E.B.; Investigation, P.S.-P. J.E.B. J.D.B. and K.N.L.; Resources, J.B.-D. and P.J.T.; Writing ? Original Draft, P.S.-P. and J.E.B.; Writing ? Review & Editing, P.S.-P. J.E.B. K.N.L. J.B.-D. and P.J.T.; Supervision, J.B.-D. and P.J.T.; Funding Acquisition, J.B.-D. and P.J.T. P.J.T. is on the scientific advisory board for Kaleido, Seres, SNIPRbiome, uBiome, and WholeBiome, and J.B.-D. is on the scientific advisory board for SNIPRbiome and Excision Biotherapeutics and is a co-founder of Acrigen Biosciences; there is no direct overlap between the current study and these consulting duties.
Publisher Copyright:
© 2019 Elsevier Inc.
PY - 2019/9/11
Y1 - 2019/9/11
N2 - Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered “hyper-targeted” phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.
AB - Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered “hyper-targeted” phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.
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UR - http://www.scopus.com/inward/citedby.url?scp=85071769307&partnerID=8YFLogxK
U2 - 10.1016/j.chom.2019.08.008
DO - 10.1016/j.chom.2019.08.008
M3 - Article
C2 - 31492655
AN - SCOPUS:85071769307
SN - 1931-3128
VL - 26
SP - 325-335.e5
JO - Cell Host and Microbe
JF - Cell Host and Microbe
IS - 3
ER -