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Manav MC, Van LB, Lin J, Fuglsang A, Peng X, Brodersen DE. Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein. Nat Commun 2020; 11:5993. [PMID: 33239638 PMCID: PMC7689449 DOI: 10.1038/s41467-020-19847-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
A hallmark of type I CRISPR-Cas systems is the presence of Cas3, which contains both the nuclease and helicase activities required for DNA cleavage during interference. In subtype I-D systems, however, the histidine-aspartate (HD) nuclease domain is encoded as part of a Cas10-like large effector complex subunit and the helicase activity in a separate Cas3' subunit, but the functional and mechanistic consequences of this organisation are not currently understood. Here we show that the Sulfolobus islandicus type I-D Cas10d large subunit exhibits an unusual domain architecture consisting of a Cas3-like HD nuclease domain fused to a degenerate polymerase fold and a C-terminal domain structurally similar to Cas11. Crystal structures of Cas10d both in isolation and bound to S. islandicus rod-shaped virus 3 AcrID1 reveal that the anti-CRISPR protein sequesters the large subunit in a non-functional state unable to form a cleavage-competent effector complex. The architecture of Cas10d suggests that the type I-D effector complex is similar to those found in type III CRISPR-Cas systems and that this feature is specifically exploited by phages for anti-CRISPR defence.
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Affiliation(s)
- M Cemre Manav
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Lan B Van
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark
| | - Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Anders Fuglsang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark.
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark.
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Hansen BK, Larsen CK, Nielsen JT, Svenningsen EB, Van LB, Jacobsen KM, Bjerring M, Flygaard RK, Jenner LB, Nejsum LN, Brodersen DE, Mulder FA, Tørring T, Poulsen TB. Structure and Function of the Bacterial Protein Toxin Phenomycin. Structure 2020; 28:528-539.e9. [DOI: 10.1016/j.str.2020.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/19/2020] [Accepted: 03/09/2020] [Indexed: 10/24/2022]
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He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X. Publisher Correction: Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 2018; 3:1076. [PMID: 29934592 DOI: 10.1038/s41564-018-0184-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the original version of this Article, molecular weight markers in Figs 1c, 2c,d and 4d were displaced during the production process, so that they were not correctly aligned with the corresponding bands. In addition, in Fig. 4c, molecular masses given for three different elution volumes were displaced so that they appeared to the left of the correct positions. These errors have now been corrected.
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Affiliation(s)
- Fei He
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Lan B Van
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anders L Kjeldsen
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Dedola
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Ditlev E Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X. Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 2018; 3:461-469. [DOI: 10.1038/s41564-018-0120-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/30/2018] [Indexed: 11/09/2022]
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Jonstrup AT, Andersen KR, Van LB, Brodersen DE. The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme. Nucleic Acids Res 2007; 35:3153-64. [PMID: 17452359 PMCID: PMC1888821 DOI: 10.1093/nar/gkm178] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Deadenylation is the first and probably also rate-limiting step of controlled mRNA decay in eukaryotes and therefore central for the overall rate of gene expression. In yeast, the process is maintained by the mega-Dalton Ccr4-Not complex, of which both the Ccr4p and Pop2p subunits are 3′–5′ exonucleases potentially responsible for the deadenylation reaction. Here, we present the crystal structure of the Pop2p subunit from Schizosaccharomyces pombe determined to 1.4 Å resolution and show that the enzyme is a competent ribonuclease with a tunable specificity towards poly-A. In contrast to S. cerevisiae Pop2p, the S. pombe enzyme contains a fully conserved DEDDh active site, and the high resolution allows for a detailed analysis of its configuration, including divalent metal ion binding. Functional data further indicates that the identity of the ions in the active site can modulate both activity and specificity of the enzyme, and finally structural superposition of single nucleotides and poly-A oligonucleotides provide insight into the catalytic cycle of the protein.
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Midtgaard SF, Assenholt J, Jonstrup AT, Van LB, Jensen TH, Brodersen DE. Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proc Natl Acad Sci U S A 2006; 103:11898-903. [PMID: 16882719 PMCID: PMC2131688 DOI: 10.1073/pnas.0604731103] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The multisubunit eukaryotic exosome is an essential RNA processing and degradation machine. In its nuclear form, the exosome associates with the auxiliary factor Rrp6p, which participates in both RNA processing and degradation reactions. The crystal structure of Saccharomyces cerevisiae Rrp6p displays a conserved RNase D core with a flanking HRDC (helicase and RNase D C-terminal) domain in an unusual conformation shown to be important for the processing function of the enzyme. Complexes with AMP and UMP, the products of the RNA degradation process, reveal how the protein specifically recognizes ribonucleotides and their bases. Finally, in vivo mutational studies show the importance of the domain contacts for the processing function of Rrp6p and highlight fundamental differences between the protein and its prokaryotic RNase D counterparts.
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Affiliation(s)
- Søren F. Midtgaard
- *Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark; and
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, bygn. 130, DK-8000 Aarhus C, Denmark
| | - Jannie Assenholt
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, bygn. 130, DK-8000 Aarhus C, Denmark
| | - Anette Thyssen Jonstrup
- *Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark; and
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, bygn. 130, DK-8000 Aarhus C, Denmark
| | - Lan B. Van
- *Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark; and
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, bygn. 130, DK-8000 Aarhus C, Denmark
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, bygn. 130, DK-8000 Aarhus C, Denmark
| | - Ditlev E. Brodersen
- *Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark; and
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, bygn. 130, DK-8000 Aarhus C, Denmark
- To whom correspondence should be addressed. E-mail:
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Van LB, Sicotte KM, Lassiter RR, Jablonski KA, Crean DA, Jeng JC, Jordan MH. Digital photography: enhancing communication between burn therapists and nurses. ACTA ACUST UNITED AC 2004; 25:54-60. [PMID: 14726739 DOI: 10.1097/01.bcr.0000105108.40158.0c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Burn rehabilitation therapists rely on nursing staff to follow through with the positioning and splinting programs. To communicate more effectively, a communication tool that consisted of digital photos and written instructions was created. Microsoft Word and Nikon View software were used to design the communication tool. The purpose of the study was to assess the perceived effectiveness of a communication tool between burn therapists and burn nurses for splinting and positioning. Thirty-two surveys were distributed to burn nursing staff to assess their perception of the communication tool (digital photographs with written instructions) compared with previous methods of instructions (without digital photographs). Seventy-three percent of nurses felt the communication tool with verbal instructions were the best methods of communicating splinting and positioning needs. All respondents felt that the rehabilitation staff should continue to use the communication tool.
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Affiliation(s)
- Lan B Van
- Division of Burn Rehabilitation, Burn Center, Washington Hospital Center, Washington, DC 20010, USA
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Vestergaard B, Van LB, Andersen GR, Nyborg J, Buckingham RH, Kjeldgaard M. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol Cell 2001; 8:1375-82. [PMID: 11779511 DOI: 10.1016/s1097-2765(01)00415-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bacterial release factor RF2 promotes termination of protein synthesis, specifically recognizing stop codons UAA or UGA. The crystal structure of Escherichia coli RF2 has been determined to a resolution of 1.8 A. RF2 is structurally distinct from its eukaryotic counterpart eRF1. The tripeptide SPF motif, thought to confer RF2 stop codon specificity, and the universally conserved GGQ motif, proposed to be involved with the peptidyl transferase center, are exposed in loops only 23 A apart, and the structure suggests that stop signal recognition is more complex than generally believed.
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Affiliation(s)
- B Vestergaard
- Institute of Molecular and Structural Biology, University of Aarhus, DK-8000 Aarhus C, Denmark
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