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Harrington LB, Ma E, Chen JS, Witte IP, Gertz D, Paez-Espino D, Al-Shayeb B, Kyrpides NC, Burstein D, Banfield JF, Doudna JA. A scoutRNA Is Required for Some Type V CRISPR-Cas Systems. Mol Cell 2020; 79:416-424.e5. [PMID: 32645367 PMCID: PMC8196889 DOI: 10.1016/j.molcel.2020.06.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/02/2020] [Accepted: 06/12/2020] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas12c/d proteins share limited homology with Cas12a and Cas9 bacterial CRISPR RNA (crRNA)-guided nucleases used widely for genome editing and DNA detection. However, Cas12c (C2c3)- and Cas12d (CasY)-catalyzed DNA cleavage and genome editing activities have not been directly observed. We show here that a short-complementarity untranslated RNA (scoutRNA), together with crRNA, is required for Cas12d-catalyzed DNA cutting. The scoutRNA differs in secondary structure from previously described tracrRNAs used by CRISPR-Cas9 and some Cas12 enzymes, and in Cas12d-containing systems, scoutRNA includes a conserved five-nucleotide sequence that is essential for activity. In addition to supporting crRNA-directed DNA recognition, biochemical and cell-based experiments establish scoutRNA as an essential cofactor for Cas12c-catalyzed pre-crRNA maturation. These results define scoutRNA as a third type of transcript encoded by a subset of CRISPR-Cas genomic loci and explain how Cas12c/d systems avoid requirements for host factors including ribonuclease III for bacterial RNA-mediated adaptive immunity.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/immunology
- Bacteria/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Escherichia coli/genetics
- Escherichia coli/immunology
- Escherichia coli/metabolism
- Genome, Bacterial/immunology
- Nucleic Acid Conformation
- Phylogeny
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- Sequence Alignment
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Lucas B Harrington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Janice S Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Isaac P Witte
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dov Gertz
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - David Paez-Espino
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nikos C Kyrpides
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94114, USA.
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Delaney JF, Gertz D, Shreiner DP. Usefulness of brain scans in metastatic carcinoma of the lung. J Nucl Med 1976; 17:406-7. [PMID: 1262948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The usefulness of brain scans for detecting unsuspected cerebral metastasis in patients with carcinoma of the lung was studied in a group of 35 such patients who had had routine brain scans as part of the initial evaluation. Seven (20%) had scans that were positive for tumor, but six of these seven had neurologic deficits corresponding to the brain-scan abnormality. Routine brain scans for evaluation of carcinoma of the lung are not justified if neurologic examination is normal.
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