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Staals RHJ, Zhu Y, Taylor DW, Kornfeld JE, Sharma K, Barendregt A, Koehorst JJ, Vlot M, Neupane N, Varossieau K, Sakamoto K, Suzuki T, Dohmae N, Yokoyama S, Schaap PJ, Urlaub H, Heck AJR, Nogales E, Doudna JA, Shinkai A, van der Oost J. RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus. Mol Cell 2014; 56:518-30. [PMID: 25457165 PMCID: PMC4342149 DOI: 10.1016/j.molcel.2014.10.005] [Citation(s) in RCA: 222] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/27/2014] [Accepted: 10/02/2014] [Indexed: 02/07/2023]
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. Here we report the structure and function of the effector complex of the Type III-A CRISPR-Cas system of Thermus thermophilus: the Csm complex (TtCsm). TtCsm is composed of five different protein subunits (Csm1-Csm5) with an uneven stoichiometry and a single crRNA of variable size (35-53 nt). The TtCsm crRNA content is similar to the Type III-B Cmr complex, indicating that crRNAs are shared among different subtypes. A negative stain EM structure of the TtCsm complex exhibits the characteristic architecture of Type I and Type III CRISPR-associated ribonucleoprotein complexes. crRNA-protein crosslinking studies show extensive contacts between the Csm3 backbone and the bound crRNA. We show that, like TtCmr, TtCsm cleaves complementary target RNAs at multiple sites. Unlike Type I complexes, interference by TtCsm does not proceed via initial base pairing by a seed sequence.
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Affiliation(s)
- Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands.
| | - Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - David W Taylor
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Jack E Kornfeld
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Kundan Sharma
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Arjan Barendregt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Nirajan Neupane
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Koen Varossieau
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands
| | | | | | - Naoshi Dohmae
- Global Research Cluster, RIKEN, Saitama 351-0198, Japan
| | | | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, the Netherlands
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, 37075 Göttingen, Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, the Netherlands
| | - Eva Nogales
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Department of Molecular and Cell Biology, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Life Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720-3200, USA
| | - Jennifer A Doudna
- Howard Hughes Medical Institute and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Department of Molecular and Cell Biology, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-3200, USA; Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA 94720-3200, USA
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan; Structural Biology Laboratory, RIKEN, Kanagawa 230-0045, Japan
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, the Netherlands.
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