1
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Hu C, Myers MT, Zhou X, Hou Z, Lozen ML, Nam KH, Zhang Y, Ke A. Exploiting activation and inactivation mechanisms in type I-C CRISPR-Cas3 for genome-editing applications. Mol Cell 2024; 84:463-475.e5. [PMID: 38242128 PMCID: PMC10857747 DOI: 10.1016/j.molcel.2023.12.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/20/2023] [Revised: 10/26/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Type I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets and the nuclease-helicase Cas3 to degrade them. Among the seven subtypes, type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here, we use four cryoelectron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9 that strongly inhibit Neisseria lactamica I-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through allosteric inhibition, whereas AcrIC9 achieves so through direct competition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for type I CRISPR eukaryotic genome engineering.
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Affiliation(s)
- Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA; Department of Biological Sciences, Faculty of Science; Department of Biochemistry, Precision Medicine Translational Research Programme (TRP), Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Mason T Myers
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xufei Zhou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Macy L Lozen
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ki Hyun Nam
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
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2
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Hu C, Myers MT, Zhou X, Hou Z, Lozen ML, Zhang Y, Ke A. Exploiting Activation and Inactivation Mechanisms in Type I-C CRISPR-Cas3 for Genome Editing Applications. bioRxiv 2023:2023.08.05.552134. [PMID: 37577534 PMCID: PMC10418205 DOI: 10.1101/2023.08.05.552134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Type I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets, and the nuclease-helicase Cas3 to degrade them. Among seven subtypes, Type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here we use four cryo-electron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling efficient NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9, that strongly inhibit N. lactamica I-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through direct competition, whereas AcrIC9 achieves so through allosteric inhibition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for controllable Type I CRISPR genome engineering.
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3
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Park JU, Petassi MT, Hsieh SC, Mehrotra E, Schuler G, Budhathoki J, Truong VH, Thyme SB, Ke A, Kellogg EH, Peters JE. Multiple adaptations underly co-option of a CRISPR surveillance complex for RNA-guided DNA transposition. Mol Cell 2023; 83:1827-1838.e6. [PMID: 37267904 PMCID: PMC10693918 DOI: 10.1016/j.molcel.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/11/2022] [Revised: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
CRISPR-associated transposons (CASTs) are natural RNA-directed transposition systems. We demonstrate that transposon protein TniQ plays a central role in promoting R-loop formation by RNA-guided DNA-targeting modules. TniQ residues, proximal to CRISPR RNA (crRNA), are required for recognizing different crRNA categories, revealing an unappreciated role of TniQ to direct transposition into different classes of crRNA targets. To investigate adaptations allowing CAST elements to utilize attachment sites inaccessible to CRISPR-Cas surveillance complexes, we compared and contrasted PAM sequence requirements in both I-F3b CAST and I-F1 CRISPR-Cas systems. We identify specific amino acids that enable a wider range of PAM sequences to be accommodated in I-F3b CAST elements compared with I-F1 CRISPR-Cas, enabling CAST elements to access attachment sites as sequences drift and evade host surveillance. Together, this evidence points to the central role of TniQ in facilitating the acquisition of CRISPR effector complexes for RNA-guided DNA transposition.
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Affiliation(s)
- Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael T Petassi
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Shan-Chi Hsieh
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Eshan Mehrotra
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Gabriel Schuler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jagat Budhathoki
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Vinh H Truong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Summer B Thyme
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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4
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Hu C, van Beljouw SPB, Nam KH, Schuler G, Ding F, Cui Y, Rodríguez-Molina A, Haagsma AC, Valk M, Pabst M, Brouns SJ, Ke A. Craspase is a CRISPR RNA-guided, RNA-activated protease. Science 2022; 377:1278-1285. [PMID: 36007061 PMCID: PMC10041820 DOI: 10.1126/science.add5064] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo-electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5' region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain-binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA-activated protease with self-regulatory capacity.
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Affiliation(s)
- Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Sam P. B. van Beljouw
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Gabriel Schuler
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Fran Ding
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Yanru Cui
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Alicia Rodríguez-Molina
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Anna C Haagsma
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Menno Valk
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Martin Pabst
- Department of Environmental Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
| | - Stan J.J. Brouns
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft, Netherlands
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
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5
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Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A. Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Mol Cell 2022; 82:2754-2768.e5. [PMID: 35835111 PMCID: PMC9357151 DOI: 10.1016/j.molcel.2022.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/31/2022] [Revised: 04/08/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022]
Abstract
Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degradation. Contrary to this model, here, we show that type I-A Cascade and Cas3 function as an integral effector complex. We provide four cryoelectron microscopy (cryo-EM) snapshots of the Pyrococcus furiosus (Pfu) type I-A effector complex in different stages of DNA recognition and degradation. The HD nuclease of Cas3 is autoinhibited inside the effector complex. It is only allosterically activated upon full R-loop formation, when the entire targeted region has been validated by the RNA guide. The mechanistic insights inspired us to convert Pfu Cascade-Cas3 into a high-sensitivity, low-background, and temperature-activated nucleic acid detection tool. Moreover, Pfu CRISPR-Cas3 shows robust bi-directional deletion-editing activity in human cells, which could find usage in allele-specific inactivation of disease-causing mutations.
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Affiliation(s)
- Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Institute of Physics, Faculty of Basic Sciences, Swiss Federal Institute of Technology (EPFL), Cubotron, Route de la Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Biology, Faculty of Biology and Medicine, University of Lausanne (UNIL), 1011 Lausanne, Switzerland
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Sonali Majumdar
- Department of Biochemistry and Molecular Biology, Department of Genetics, and Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Justin McLean
- Department of Biochemistry and Molecular Biology, Department of Genetics, and Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, Faculty of Basic Sciences, Swiss Federal Institute of Technology (EPFL), Cubotron, Route de la Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Biology, Faculty of Biology and Medicine, University of Lausanne (UNIL), 1011 Lausanne, Switzerland
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, Department of Genetics, and Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
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6
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Abstract
Class 2 CRISPR effectors Cas9 and Cas12 may have evolved from nucleases in IS200/IS605 transposons. IscB is about two-fifths the size of Cas9 but shares a similar domain organization. The associated ωRNA plays the combined role of CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA) to guide double-stranded DNA (dsDNA) cleavage. Here we report a 2.78-angstrom cryo-electron microscopy structure of IscB-ωRNA bound to a dsDNA target, revealing the architectural and mechanistic similarities between IscB and Cas9 ribonucleoproteins. Target-adjacent motif recognition, R-loop formation, and DNA cleavage mechanisms are explained at high resolution. ωRNA plays the equivalent function of REC domains in Cas9 and contacts the RNA-DNA heteroduplex. The IscB-specific PLMP domain is dispensable for RNA-guided DNA cleavage. The transition from ancestral IscB to Cas9 involved dwarfing the ωRNA and introducing protein domain replacements.
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Affiliation(s)
- Gabriel Schuler
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
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7
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Tan R, Krueger RK, Gramelspacher MJ, Zhou X, Xiao Y, Ke A, Hou Z, Zhang Y. Cas11 enables genome engineering in human cells with compact CRISPR-Cas3 systems. Mol Cell 2022; 82:852-867.e5. [PMID: 35051351 PMCID: PMC8964063 DOI: 10.1016/j.molcel.2021.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/09/2021] [Accepted: 12/21/2021] [Indexed: 11/28/2022]
Abstract
Leading CRISPR-Cas technologies employ Cas9 and Cas12 enzymes that generate RNA-guided dsDNA breaks. Yet, the most abundant microbial adaptive immune systems, Type I CRISPRs, are under-exploited for eukaryotic applications. Here, we report the adoption of a minimal CRISPR-Cas3 from Neisseria lactamica (Nla) type I-C system to create targeted large deletions in the human genome. RNP delivery of its processive Cas3 nuclease and target recognition complex Cascade can confer ∼95% editing efficiency. Unexpectedly, NlaCascade assembly in bacteria requires internal translation of a hidden component Cas11 from within the cas8 gene. Furthermore, expressing a separately encoded NlaCas11 is the key to enable plasmid- and mRNA-based editing in human cells. Finally, we demonstrate that supplying cas11 is a universal strategy to systematically implement divergent I-C, I-D, and I-B CRISPR-Cas3 editors with compact sizes, distinct PAM preferences, and guide orthogonality. These findings greatly expand our ability to engineer long-range genome edits.
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Affiliation(s)
- Renke Tan
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA,These authors contributed equally
| | - Ryan K Krueger
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA,These authors contributed equally
| | - Max J Gramelspacher
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xufei Zhou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Yibei Xiao
- State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing, China
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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8
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Kellogg E, Park JU, Tsai A, Mehrotra E, Petassi M, Hsieh SC, Ke A, Peterson JE. Structural basis of target-site selection in RNA-guided DNA transposition systems. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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9
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Park JU, Tsai AWL, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH. Structural basis for target site selection in RNA-guided DNA transposition systems. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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10
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Hou Z, Hu C, Ke A, Zhang Y. Introducing Large Genomic Deletions in Human Pluripotent Stem Cells Using CRISPR-Cas3. Curr Protoc 2022; 2:e361. [PMID: 35129865 PMCID: PMC8843033 DOI: 10.1002/cpz1.361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
CRISPR-Cas systems provide researchers with eukaryotic genome editing tools and therapeutic platforms that make it possible to target disease mutations in somatic organs. Most of these tools employ Type II (e.g., Cas9) or Type V (e.g., Cas12a) CRISPR enzymes to create RNA-guided precise double-strand breaks in the genome. However, such technologies are limited in their capacity to make targeted large deletions. Recently, the Type I CRISPR system, which is prevalent in microbes and displays unique enzymatic features, has been harnessed to effectively create large chromosomal deletions in human cells. Type I CRISPR first uses a multisubunit ribonucleoprotein (RNP) complex called Cascade to find its guide-complementary target site, and then recruits a helicase-nuclease enzyme, Cas3, to travel along and shred the target DNA over a long distance with high processivity. When introduced into human cells as purified RNPs, the CRISPR-Cas3 complex can efficiently induce large genomic deletions of varying lengths (1-100 kb) from the CRISPR-targeted site. Because of this unique editing outcome, CRISPR-Cas3 holds great promise for tasks such as the removal of integrated viral genomes and the interrogation of structural variants affecting gene function and human disease. Here, we provide detailed protocols for introducing large deletions using CRISPR-Cas3. We describe step-by-step procedures for purifying the Type I-E CRISPR proteins Cascade and Cas3 from Thermobifida fusca, electroporating RNPs into human cells, and characterizing DNA deletions using PCR and sequencing. We focus here on human pluripotent stem cells due to their clinical potential, but these protocols will be broadly useful for other cell lines and model organisms for applications including large genomic deletion, full-gene or -chromosome removal, and CRISPR screening for noncoding elements, among others. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Expression and purification of Tfu Cascade RNP Support Protocol 1: Expression and purification of TfuCas3 protein Support Protocol 2: Culture of human pluripotent stem cells Basic Protocol 2: Introduction of Tfu Cascade RNP and Cas3 protein into hPSCs via electroporation Basic Protocol 3: Characterization of genomic DNA lesions using long-range PCR, TOPO cloning, and Sanger sequencing Alternate Protocol: Comprehensive analysis of genomic lesions by Tn5-based next-generation sequencing Support Protocol 3: Single-cell clonal isolation.
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Affiliation(s)
- Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.,These authors contributed equally to the work
| | - Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.,These authors contributed equally to the work
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA., Correspondence: (A.K.), (Y.Z.)
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA., Correspondence: (A.K.), (Y.Z.)
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11
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Hu C, Ke A. Reconstitution and biochemical characterization of the RNA-guided helicase-nuclease protein Cas3 from type I-A CRISPR–Cas system. Methods Enzymol 2022; 673:405-424. [DOI: 10.1016/bs.mie.2022.03.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Park JU, Tsai AWL, Mehrotra E, Petassi MT, Hsieh SC, Ke A, Peters JE, Kellogg EH. Structural basis for target site selection in RNA-guided DNA transposition systems. Science 2021; 373:768-774. [PMID: 34385391 DOI: 10.1126/science.abi8976] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/07/2021] [Indexed: 12/31/2022]
Abstract
CRISPR-associated transposition systems allow guide RNA-directed integration of a single DNA cargo in one orientation at a fixed distance from a programmable target sequence. We used cryo-electron microscopy (cryo-EM) to define the mechanism that underlies this process by characterizing the transposition regulator, TnsC, from a type V-K CRISPR-transposase system. In this scenario, polymerization of adenosine triphosphate-bound TnsC helical filaments could explain how polarity information is passed to the transposase. TniQ caps the TnsC filament, representing a universal mechanism for target information transfer in Tn7/Tn7-like elements. Transposase-driven disassembly establishes delivery of the element only to unused protospacers. Finally, TnsC transitions to define the fixed point of insertion, as revealed by structures with the transition state mimic ADP•AlF3 These mechanistic findings provide the underpinnings for engineering CRISPR-associated transposition systems for research and therapeutic applications.
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Affiliation(s)
- Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amy Wei-Lun Tsai
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eshan Mehrotra
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael T Petassi
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Shan-Chi Hsieh
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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13
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Marchi R, Duarte L, P S, D R, Ke A, Hl B, E S, P H, M B, Al E. A PHASE 1/2 OPEN LABEL EXTENSION STUDY OF GIVOSIRAN, AN INVESTIGATIONAL RNAI THERAPEUTIC, IN PATIENTS WITH ACUTE INTERMITTENT PORPHYRIA. Hematol Transfus Cell Ther 2020. [DOI: 10.1016/j.htct.2020.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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14
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Cai R, Price IR, Ding F, Wu F, Chen T, Zhang Y, Liu G, Jardine PJ, Lu C, Ke A. ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor. Nucleic Acids Res 2019; 47:9818-9828. [PMID: 31396619 PMCID: PMC6765105 DOI: 10.1093/nar/gkz692] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 11/19/2022] Open
Abstract
Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA–gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a ‘Z’-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.
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Affiliation(s)
- Rujie Cai
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Ian R Price
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Fang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Feifei Wu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Ting Chen
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Yunlong Zhang
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Paul J Jardine
- Department of Diagnostic and Biological Sciences, and Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Changrui Lu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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15
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Battaglia RA, Grigg JC, Ke A. Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nat Struct Mol Biol 2019; 26:1106-1113. [PMID: 31740853 PMCID: PMC6953718 DOI: 10.1038/s41594-019-0327-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/07/2019] [Indexed: 01/31/2023]
Abstract
T-box riboregulators are a class of cis-regulatory RNAs that govern the bacterial response to amino acid starvation by binding, decoding and reading the aminoacylation status of specific transfer RNAs. Here we provide a high-resolution crystal structure of a full-length T-box from Mycobacterium tuberculosis that explains tRNA decoding and aminoacylation sensing by this riboregulator. Overall, the T-box consists of decoding and aminoacylation sensing modules bridged by a rigid pseudoknot structure formed by the mid-region domains. Stem-I and the Stem-II S-turn assemble a claw-like decoding module, while the antiterminator, Stem-III, and the adjacent linker form a tightly interwoven aminoacylation sensing module. The uncharged tRNA is selectively recognized by an unexpected set of favorable contacts from the linker region in the aminoacylation sensing module. A complex structure with a charged tRNA mimic shows that the extra moiety dislodges the linker, which is indicative of the possible chain of events that lead to alternative base-pairing and altered expression output.
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Affiliation(s)
| | - Jason C Grigg
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Ithaca, NY, USA.
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16
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Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG. Local-to-global signal transduction at the core of a Mn 2+ sensing riboswitch. Nat Commun 2019; 10:4304. [PMID: 31541094 PMCID: PMC6754395 DOI: 10.1038/s41467-019-12230-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 04/30/2019] [Accepted: 08/28/2019] [Indexed: 01/01/2023] Open
Abstract
The widespread Mn2+-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn2+ homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 Å resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 µs of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg2+. Only upon adding sub-millimolar Mn2+, however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn2+ in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.
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Affiliation(s)
- Krishna C Suddala
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ian R Price
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Shiba S Dandpat
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michal Janeček
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno, 612 65, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic
| | - Petra Kührová
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno, 612 65, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, Brno, 612 65, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, Olomouc, 771 46, Czech Republic
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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17
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Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y. Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas. Mol Cell 2019; 74:936-950.e5. [PMID: 30975459 PMCID: PMC6555677 DOI: 10.1016/j.molcel.2019.03.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [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: 11/05/2018] [Revised: 02/04/2019] [Accepted: 03/13/2019] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas systems enable microbial adaptive immunity and provide eukaryotic genome editing tools. These tools employ a single effector enzyme of type II or V CRISPR to generate RNA-guided, precise genome breaks. Here we demonstrate the feasibility of using type I CRISPR-Cas to effectively introduce a spectrum of long-range chromosomal deletions with a single RNA guide in human embryonic stem cells and HAP1 cells. Type I CRISPR systems rely on the multi-subunit ribonucleoprotein (RNP) complex Cascade to identify DNA targets and on the helicase-nuclease enzyme Cas3 to degrade DNA processively. With RNP delivery of T. fusca Cascade and Cas3, we obtained 13%-60% editing efficiency. Long-range PCR-based and high-throughput-sequencing-based lesion analyses reveal that a variety of deletions, ranging from a few hundred base pairs to 100 kilobases, are created upstream of the target site. These results highlight the potential utility of type I CRISPR-Cas for long-range genome manipulations and deletion screens in eukaryotes.
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Affiliation(s)
- Adam E Dolan
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Zhonggang Hou
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA; State Key Laboratory of Natural Medicines, Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Max J Gramelspacher
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jaewon Heo
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Sara E Howden
- Murdoch Children's Research Institute, Flemington Rd., Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI 48109, USA.
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18
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Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex. Cell 2018; 175:934-946.e15. [PMID: 30343903 DOI: 10.1016/j.cell.2018.09.039] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/20/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022]
Abstract
CRISPR-Cas systems confer an adaptive immunity against viruses. Following viral injection, Cas1-Cas2 integrates segments of the viral genome (spacers) into the CRISPR locus. In type I CRISPR-Cas systems, efficient "primed" spacer acquisition and viral degradation (interference) require both the Cascade complex and the Cas3 helicase/nuclease. Here, we present single-molecule characterization of the Thermobifida fusca (Tfu) primed acquisition complex (PAC). We show that TfuCascade rapidly samples non-specific DNA via facilitated one-dimensional diffusion. Cas3 loads at target-bound Cascade and the Cascade/Cas3 complex translocates via a looped DNA intermediate. Cascade/Cas3 complexes stall at diverse protein roadblocks, resulting in a double strand break at the stall site. In contrast, Cas1-Cas2 samples DNA transiently via 3D collisions. Moreover, Cas1-Cas2 associates with Cascade and translocates with Cascade/Cas3, forming the PAC. PACs can displace different protein roadblocks, suggesting a mechanism for long-range spacer acquisition. This work provides a molecular basis for the coordinated steps in CRISPR-based adaptive immunity.
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Affiliation(s)
- Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Maxwell W Brown
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Adam Dolan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Erik Hernandez
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel D Dahlhauser
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan R Myler
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Eric V Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA.
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19
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Leeds JM, Derr K, Ke A, Rowland Yeo K, Bandman O, Gretler DD, Vinh N, Conley PB. P2290Physiologically-based pharmacokinetic (PBPK) model predicted versus observed effect of Child Pugh mild and moderate hepatic impairment on betrixaban pharmacokinetics. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p2290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J M Leeds
- Portola Pharmaceuticals, Inc., South San Francisco, United States of America
| | - K Derr
- Portola Pharmaceuticals, Inc., South San Francisco, United States of America
| | - A Ke
- SimCyp LTD, Sheffield, United Kingdom
| | | | - O Bandman
- Portola Pharmaceuticals, Inc., South San Francisco, United States of America
| | - D D Gretler
- Clinical Research Consultant, San Francisco, United States of America
| | - N Vinh
- Portola Pharmaceuticals, Inc., South San Francisco, United States of America
| | - P B Conley
- Portola Pharmaceuticals, Inc., South San Francisco, United States of America
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20
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21
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Abstract
Type I CRISPR-Cas system features a sequential target-searching and degradation process on double-stranded DNA by the RNA-guided Cascade (CRISPR associated complex for antiviral defense) complex and the nuclease-helicase fusion enzyme Cas3, respectively. Here, we present a 3.7-angstrom-resolution cryo-electron microscopy (cryo-EM) structure of the Type I-E Cascade/R-loop/Cas3 complex, poised to initiate DNA degradation. Cas3 distinguishes Cascade conformations and only captures the R-loop-forming Cascade, to avoid cleaving partially complementary targets. Its nuclease domain recruits the nontarget strand (NTS) DNA at a bulged region for the nicking of single-stranded DNA. An additional 4.7-angstrom-resolution cryo-EM structure captures the postnicking state, in which the severed NTS retracts to the helicase entrance, to be threaded for adenosine 5'-triphosphate-dependent processive degradation. These snapshots form the basis for understanding RNA-guided DNA degradation in Type I-E CRISPR-Cas systems.
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Affiliation(s)
- Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Min Luo
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA
| | - Adam E Dolan
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA.
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
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22
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Battaglia RA, Ke A. Guanidine-sensing riboswitches: How do they work and what do they regulate? WIREs RNA 2018; 9:e1482. [DOI: 10.1002/wrna.1482] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Robert A. Battaglia
- Department of Molecular Biology and Genetics; Cornell University; Ithaca New York
| | - Ailong Ke
- Department of Molecular Biology and Genetics; Cornell University; Ithaca New York
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23
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Battaglia RA, Ke A. Acting in tandem. eLife 2018; 7:36489. [PMID: 29683426 PMCID: PMC5912904 DOI: 10.7554/elife.36489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 11/13/2022] Open
Abstract
RNA structures called tandem riboswitches allow bacteria to employ complex logical operations in response to nutrient starvation.
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Affiliation(s)
- Robert A Battaglia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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24
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Jung C, Hawkins JA, Jones SK, Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Cell 2017; 170:35-47.e13. [PMID: 28666121 DOI: 10.1016/j.cell.2017.05.044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 04/23/2017] [Accepted: 05/26/2017] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas nucleoproteins target foreign DNA via base pairing with a crRNA. However, a quantitative description of protein binding and nuclease activation at off-target DNA sequences remains elusive. Here, we describe a chip-hybridized association-mapping platform (CHAMP) that repurposes next-generation sequencing chips to simultaneously measure the interactions between proteins and ∼107 unique DNA sequences. Using CHAMP, we provide the first comprehensive survey of DNA recognition by a type I-E CRISPR-Cas (Cascade) complex and Cas3 nuclease. Analysis of mutated target sequences and human genomic DNA reveal that Cascade recognizes an extended protospacer adjacent motif (PAM). Cascade recognizes DNA with a surprising 3-nt periodicity. The identity of the PAM and the PAM-proximal nucleotides control Cas3 recruitment by releasing the Cse1 subunit. These findings are used to develop a model for the biophysical constraints governing off-target DNA binding. CHAMP provides a framework for high-throughput, quantitative analysis of protein-DNA interactions on synthetic and genomic DNA. PAPERCLIP.
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Affiliation(s)
- Cheulhee Jung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - John A Hawkins
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen K Jones
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - James R Rybarski
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kaylee E Dillard
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey Hussmann
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Cagri A Savran
- School of Mechanical Engineering, Birck Nanotechnology Center, Purdue University, 1205 West State Street, West Lafayette, IN 47907, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - William H Press
- Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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25
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Xiao Y, Luo M, Hayes RP, Kim J, Ng S, Ding F, Liao M, Ke A. Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System. Cell 2017; 170:48-60.e11. [PMID: 28666122 DOI: 10.1016/j.cell.2017.06.012] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [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: 12/22/2016] [Revised: 04/27/2017] [Accepted: 06/08/2017] [Indexed: 01/06/2023]
Abstract
Type I CRISPR systems feature a sequential dsDNA target searching and degradation process, by crRNA-displaying Cascade and nuclease-helicase fusion enzyme Cas3, respectively. Here we present two cryo-EM snapshots of the Thermobifida fusca type I-E Cascade: (1) unwinding 11 bp of dsDNA at the seed-sequence region to scout for sequence complementarity, and (2) further unwinding of the entire protospacer to form a full R-loop. These structures provide the much-needed temporal and spatial resolution to resolve key mechanistic steps leading to Cas3 recruitment. In the early steps, PAM recognition causes severe DNA bending, leading to spontaneous DNA unwinding to form a seed-bubble. The full R-loop formation triggers conformational changes in Cascade, licensing Cas3 to bind. The same process also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage. The combination of both negative and positive checkpoints ensures stringent yet efficient target degradation in type I CRISPR-Cas systems.
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Affiliation(s)
- Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Min Luo
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA
| | - Robert P Hayes
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Jonathan Kim
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Sherwin Ng
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Fang Ding
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, SGM 509, Boston, MA 02115, USA.
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
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26
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Battaglia RA, Price IR, Ke A. Structural basis for guanidine sensing by the ykkC family of riboswitches. RNA 2017; 23:578-585. [PMID: 28096518 PMCID: PMC5340920 DOI: 10.1261/rna.060186.116] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/09/2017] [Indexed: 05/20/2023]
Abstract
Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation-π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification-a previously unappreciated aspect of bacterial physiology.
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Affiliation(s)
- Robert A Battaglia
- Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA
| | - Ian R Price
- Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Ithaca, New York 14853, USA
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27
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Abstract
piRNA guides the action of PIWI proteins to silence deleterious transposons in animal reproductive tissues. Biogenesis of piRNA-induced silencing complex (piRISC) involves a multi-step process. In this issue, Matsumoto et al. report the first crystal structure of a PIWI-clade protein displaying a guide RNA, ready for action.
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Affiliation(s)
- Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, 251 Biotechnology Building, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 251 Biotechnology Building, Ithaca, NY 14853, USA.
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28
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Ke A, Barter Z, Rowland-Yeo K, Almond L. Towards a Best Practice Approach in PBPK Modeling: Case Example of Developing a Unified Efavirenz Model Accounting for Induction of CYPs 3A4 and 2B6. CPT Pharmacometrics Syst Pharmacol 2016; 5:367-76. [PMID: 27435752 PMCID: PMC4961080 DOI: 10.1002/psp4.12088] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022]
Abstract
In this study, we present efavirenz physiologically based pharmacokinetic (PBPK) model development as an example of our best practice approach that uses a stepwise approach to verify the different components of the model. First, a PBPK model for efavirenz incorporating in vitro and clinical pharmacokinetic (PK) data was developed to predict exposure following multiple dosing (600 mg q.d.). Alfentanil i.v. and p.o. drug‐drug interaction (DDI) studies were utilized to evaluate and refine the CYP3A4 induction component in the liver and gut. Next, independent DDI studies with substrates of CYP3A4 (maraviroc, atazanavir, and clarithromycin) and CYP2B6 (bupropion) verified the induction components of the model (area under the curve [AUC] ratios within 1.0–1.7‐fold of observed). Finally, the model was refined to incorporate the fractional contribution of enzymes, including CYP2B6, propagating autoinduction into the model (Racc 1.7 vs. 1.7 observed). This validated mechanistic model can now be applied in clinical pharmacology studies to prospectively assess both the victim and perpetrator DDI potential of efavirenz.
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Affiliation(s)
- A Ke
- Simcyp Limited (a Certara Company), Sheffield, UK
| | - Z Barter
- Simcyp Limited (a Certara Company), Sheffield, UK
| | | | - L Almond
- Simcyp Limited (a Certara Company), Sheffield, UK
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29
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Mizrachi D, Chen Y, Liu J, Peng HM, Ke A, Pollack L, Turner RJ, Auchus RJ, DeLisa MP. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy. Nat Commun 2015; 6:6826. [PMID: 25851941 PMCID: PMC4403311 DOI: 10.1038/ncomms7826] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/03/2015] [Indexed: 11/30/2022] Open
Abstract
Integral membrane proteins (IMPs) play crucial roles in all cells and represent attractive pharmacological targets. However, functional and structural studies of IMPs are hindered by their hydrophobic nature and the fact that they are generally unstable following extraction from their native membrane environment using detergents. Here we devise a general strategy for in vivo solubilization of IMPs in structurally relevant conformations without the need for detergents or mutations to the IMP itself, as an alternative to extraction and in vitro solubilization. This technique, called SIMPLEx (solubilization of IMPs with high levels of expression), allows the direct expression of soluble products in living cells by simply fusing an IMP target with truncated apolipoprotein A-I, which serves as an amphipathic proteic ‘shield' that sequesters the IMP from water and promotes its solubilization. The study of integral membrane proteins (IMPs) is hampered by yields and the difficulty in retaining activity once they have been solubilized. Here Mizrachi et al. develop a strategy for in vivo expression and solubilization of IMPs in functionally relevant states by fusing them to truncated apolipoprotein A-I.
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Affiliation(s)
- Dario Mizrachi
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Jiayan Liu
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hwei-Ming Peng
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Richard J Auchus
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
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Hayes RP, Ke A. One more piece down to solve the III-A CRISPR puzzle. J Mol Biol 2015; 427:228-30. [PMID: 25451600 DOI: 10.1016/j.jmb.2014.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Robert P Hayes
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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31
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Nam KH, DeLisa MP, Ke A. Characterizing Metal-Dependent Nucleases of CRISPR-Cas Prokaryotic Adaptive Immunity Systems. Methods Mol Biol 2015; 1311:265-276. [PMID: 25981479 DOI: 10.1007/978-1-4939-2687-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
CRISPRs (clustered regularly interspaced short palindromic repeats), together with the nearby CRISPR-associated (cas) operon, constitute a prokaryotic RNA-based adaptive immune system against exogenous genetic elements. Here, we describe nuclease assays that are useful for characterizing the substrate-specific function of CRISPR-associated protein Cas2. We also provide methods for characterizing the stoichiometry and affinity between Cas2 and divalent metal ions using isothermal titration calorimetry (ITC).
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Affiliation(s)
- Ki H Nam
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
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Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nat Struct Mol Biol 2014. [PMID: 25132177 DOI: 10.1038/nsmb.2875.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
CRISPR drives prokaryotic adaptation to invasive nucleic acids such as phages and plasmids, using an RNA-mediated interference mechanism. Interference in type I CRISPR-Cas systems requires a targeting Cascade complex and a degradation machine, Cas3, which contains both nuclease and helicase activities. Here we report the crystal structures of Thermobifida fusca Cas3 bound to single-stranded (ss) DNA substrate and show that it is an obligate 3'-to-5' ssDNase that preferentially accepts substrate directly from the helicase moiety. Conserved residues in the HD-type nuclease coordinate two irons for ssDNA cleavage. We demonstrate ATP coordination and conformational flexibility of the SF2-type helicase domain. Cas3 is specifically guided toward Cascade-bound target DNA by a PAM sequence, through physical interactions with both the nontarget substrate strand and the CasA protein. The sequence of recognition events ensures well-controlled DNA targeting and degradation of foreign DNA by Cascade and Cas3.
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Affiliation(s)
- Yanwu Huo
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2]
| | - Ki Hyun Nam
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2] [3]
| | - Fang Ding
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2]
| | - Heejin Lee
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2]
| | - Lijie Wu
- Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - M Daniel Farchione
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Sharleen Zhou
- Howard Hughes Medical Institute, Mass Spectrometry Laboratory, University of California, Berkeley, Berkeley, California, USA
| | - Kanagalaghatta Rajashankar
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, USA
| | - Igor Kurinov
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, USA
| | | | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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34
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Huo Y, Nam KH, Ding F, Lee H, Wu L, Xiao Y, Farchione MD, Zhou S, Rajashankar K, Kurinov I, Zhang R, Ke A. Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation. Nat Struct Mol Biol 2014; 21:771-7. [PMID: 25132177 PMCID: PMC4156918 DOI: 10.1038/nsmb.2875] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/18/2014] [Indexed: 12/19/2022]
Abstract
CRISPR drives prokaryotic adaptation to invasive nucleic acids such as phages and plasmids using an RNA-mediated interference mechanism. Interference in Type I CRISPR-Cas systems requires a targeting Cascade complex and a degradation machine Cas3, which contains both nuclease and helicase activities. Here we report the crystal structures of Cas3 bound to ss-DNA substrate and show that it is an obligated 3′-to-5′ ss-DNase preferentially accepting substrate directly from the helicase moiety. Conserved residues in the HD-type nuclease coordinate two irons for ss-DNA cleavage. ATP coordination and conformational flexibility are revealed for the SF2-type helicase moiety. Cas3 is specifically guided towards Cascade-bound target DNA with a correct PAM sequence, through physical interactions to both the non-target substrate strand and the CasA protein. The cascade of recognition events ensures a well-controlled DNA targeting and degradation of alien DNA by Cascade and Cas3.
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Affiliation(s)
- Yanwu Huo
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2]
| | - Ki Hyun Nam
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2] [3]
| | - Fang Ding
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2]
| | - Heejin Lee
- 1] Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA. [2]
| | - Lijie Wu
- Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yibei Xiao
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - M Daniel Farchione
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Sharleen Zhou
- Howard Hughes Medical Institute, Mass Spectrometry Laboratory, University of California, Berkeley, Berkeley, California, USA
| | - Kanagalaghatta Rajashankar
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, USA
| | - Igor Kurinov
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, Illinois, USA
| | | | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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35
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Price IR, Grigg JC, Ke A. Common themes and differences in SAM recognition among SAM riboswitches. Biochim Biophys Acta 2014; 1839:931-938. [PMID: 24863160 DOI: 10.1016/j.bbagrm.2014.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 12/19/2022]
Abstract
The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-l-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Ian R Price
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jason C Grigg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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36
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Liu JJ, Bratkowski MA, Liu X, Niu CY, Ke A, Wang HW. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM. Nat Struct Mol Biol 2013; 21:95-102. [PMID: 24336220 PMCID: PMC3976988 DOI: 10.1038/nsmb.2736] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 11/06/2013] [Indexed: 12/25/2022]
Abstract
The eukaryotic exosome is a multi-subunit complex typically composed of a catalytically inactive core and the Rrp44 protein, which contains 3’ to 5’ exo- and endo-ribonuclease activities. RNA substrates have been shown to be recruited through the core to reach Rrp44's exoribonuclease (EXO) site. Using single particle electron microscopy and biochemical analysis, we provide visual evidence that two distinct substrate recruitment pathways exist. In the through-core route, channeling of the single stranded substrates from the core to Rrp44 induces a characteristic conformational change in Rrp44. In the alternative direct-access route, this conformational change does not take place and the RNA substrate is visualized to avoid the core and enter Rrp44's EXO site directly. Our results provide mechanistic explanations for several RNA processing scenarios by the eukaryotic exosome and indicate substrate specific modes of degradation by this complex.
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Affiliation(s)
- Jun-Jie Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Joint Graduate Program of Peking-Tsinghua-NBIS, Tsinghua University, Beijing 100084, China
| | - Matthew A Bratkowski
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Xueqi Liu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chu-Ya Niu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Joint Graduate Program of Peking-Tsinghua-NBIS, Tsinghua University, Beijing 100084, China
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37
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Grigg JC, Ke A. Structural determinants for geometry and information decoding of tRNA by T box leader RNA. Structure 2013; 21:2025-32. [PMID: 24095061 PMCID: PMC3879790 DOI: 10.1016/j.str.2013.09.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/01/2013] [Accepted: 09/03/2013] [Indexed: 01/07/2023]
Abstract
T box riboswitches are cis-acting RNA elements that bind to tRNA and sense its aminoacylation state to influence gene expression. Here, we present the 3.2 Å resolution X-ray crystal structures of the T box Stem I-tRNA complex and tRNA, in isolation. T box Stem I forms an arched conformation with extensive intermolecular contacts to two key points of tRNA, the anticodon and D/T-loops. Free and complexed tRNA exist in significantly different conformations, with the contacts stabilizing flexible D/T-loops and a rearrangement of the D-loop. Using a designed T box RNA/tRNA system, we demonstrate that the T box riboswitch monitors the length and orientation of two essential contacts. Length or orientation mismatches engineered into the T box riboswitch and tRNA disrupt the complex, whereas simultaneous insertion of full helical turns realigns the interfaces and restores interaction between artificially elongated T box riboswitch and tRNA molecules.
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Affiliation(s)
- Jason C. Grigg
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14850, USA,Correspondence:
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38
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Abstract
The term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mRNA. They are typically comprised of separate ligand binding and regulatory domains. The T box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, tRNA. It senses the aminoacylation state of tRNA to regulate genes involved in a variety of functions relating to amino acid metabolism and tRNA aminoacylation. T box riboswitches performs an intuitively simple process using a complex structured RNA element and, until recently, the underlying mechanisms were poorly understood. Only two sequence-specific contacts had been previously identified: (1) between the specifier sequence (codon) and the tRNA anticodon and (2) between an anti-terminator stem loop and the tRNA acceptor arm CCA tail. tRNA aminoacylation blocks the latter interaction and therefore serves as the switch between termination and anti-termination. Outside of these two contacts, the structure and functions of T box riboswitches have come to light in some recent studies. We recently described the X-ray crystal structure of the highly conserved T box riboswitch distal Stem I region and demonstrated that this region interacts with the tRNA elbow to anchor it to the riboswitch. Independently, Lehmann et al. used sequence homology search to arrive at a similar model for Stem I-tRNA interactions. The model was further supported by two recent structures of the Stem I-tRNA complex, determined independently by our group and by Zhang and Ferré-D'Amaré. This article highlights some of these contributions to synthesize an updated model for tRNA recognition by the T box riboswitch.
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Affiliation(s)
- Jason C Grigg
- The Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA
| | - Ailong Ke
- The Department of Molecular Biology and Genetics; Cornell University; Ithaca, NY USA
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39
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Affiliation(s)
- Jason C Grigg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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40
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Chen Y, Hyun Nam K, Ke A, Pollack L. A SAXS Study of the CRISPR Associated Gene (Cas) Csn2 in the Presence and Absence of Calcium Ions. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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41
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Nam KH, Huang Q, Ke A. Nucleic acid binding surface and dimer interface revealed by CRISPR-associated CasB protein structures. FEBS Lett 2012; 586:3956-61. [PMID: 23079036 DOI: 10.1016/j.febslet.2012.09.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 09/26/2012] [Accepted: 09/26/2012] [Indexed: 11/26/2022]
Abstract
The CRISPR system is an adaptive RNA-based microbial immune system against invasive genetic elements. CasB is an essential protein component in Type I-E Cascade. Here, we characterize CasB proteins from three different organisms as non-specific nucleic acid binding proteins. The Thermobifida fusca CasB crystal structure reveals conserved positive surface charges, which we show are important for its nucleic acid binding function. EM docking reveals that CasB dimerization aligns individual nucleic acid binding surfaces into a curved, elongated binding surface inside Type I-E Cascade, consistent with the putative functions of CasB in ds-DNA recruitment and crRNA-DNA duplex formation steps.
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Affiliation(s)
- Ki Hyun Nam
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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Abstract
Rrp44 (Dis3) is a key catalytic subunit of the yeast exosome complex and can processively digest structured RNA one nucleotide at a time in the 3' to 5' direction. Its motor function is powered by the energy released from the hydrolytic nuclease reaction instead of adenosine triphosphate hydrolysis as in conventional helicases. Single-molecule fluorescence analysis revealed that instead of unwinding RNA in single base pair steps, Rrp44 accumulates the energy released by multiple single nucleotide step hydrolysis reactions until about four base pairs are unwound in a burst. Kinetic analyses showed that RNA unwinding, not cleavage or strand release, determines the overall RNA degradation rate and that the unwinding step size is determined by the nonlinear elasticity of the Rrp44/RNA complex, but not by duplex stability.
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Affiliation(s)
- Gwangrog Lee
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
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43
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Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 2012. [PMID: 22841292 DOI: 10.1016/j.str.2012.06.016.cas5d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3' single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing, Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.
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Affiliation(s)
- Ki Hyun Nam
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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44
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Nam KH, Ding F, Haitjema C, Huang Q, DeLisa MP, Ke A. Double-stranded endonuclease activity in Bacillus halodurans clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas2 protein. J Biol Chem 2012; 287:35943-52. [PMID: 22942283 DOI: 10.1074/jbc.m112.382598] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.
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Affiliation(s)
- Ki Hyun Nam
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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45
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Nam KH, Haitjema C, Liu X, Ding F, Wang H, DeLisa MP, Ke A. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system. Structure 2012; 20:1574-84. [PMID: 22841292 DOI: 10.1016/j.str.2012.06.016] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 05/30/2012] [Accepted: 06/20/2012] [Indexed: 10/28/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs), together with an operon of CRISPR-associated (Cas) proteins, form an RNA-based prokaryotic immune system against exogenous genetic elements. Cas5 family proteins are found in several type I CRISPR-Cas systems. Here, we report the molecular function of subtype I-C/Dvulg Cas5d from Bacillus halodurans. We show that Cas5d cleaves pre-crRNA into unit length by recognizing both the hairpin structure and the 3' single stranded sequence in the CRISPR repeat region. Cas5d structure reveals a ferredoxin domain-based architecture and a catalytic triad formed by Y46, K116, and H117 residues. We further show that after pre-crRNA processing, Cas5d assembles with crRNA, Csd1, and Csd2 proteins to form a multi-sub-unit interference complex similar to Escherichia coli Cascade (CRISPR-associated complex for antiviral defense) in architecture. Our results suggest that formation of a crRNA-presenting Cascade-like complex is likely a common theme among type I CRISPR subtypes.
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Affiliation(s)
- Ki Hyun Nam
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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46
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Karlsson AJ, Lim HK, Xu H, Rocco MA, Bratkowski MA, Ke A, DeLisa MP. Engineering antibody fitness and function using membrane-anchored display of correctly folded proteins. J Mol Biol 2011; 416:94-107. [PMID: 22197376 DOI: 10.1016/j.jmb.2011.12.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
Abstract
A hallmark of the bacterial twin-arginine translocation (Tat) pathway is its ability to export folded proteins. Here, we discovered that overexpressed Tat substrate proteins form two distinct, long-lived translocation intermediates that are readily detected by immunolabeling methods. Formation of the early translocation intermediate Ti-1, which exposes the N- and C-termini to the cytoplasm, did not require an intact Tat translocase, a functional Tat signal peptide, or a correctly folded substrate. In contrast, formation of the later translocation intermediate, Ti-2, which exhibits a bitopic topology with the N-terminus in the cytoplasm and C-terminus in the periplasm, was much more particular, requiring an intact translocase, a functional signal peptide, and a correctly folded substrate protein. The ability to directly detect Ti-2 intermediates was subsequently exploited for a new protein engineering technology called MAD-TRAP (membrane-anchored display for Tat-based recognition of associating proteins). Through the use of just two rounds of mutagenesis and screening with MAD-TRAP, the intracellular folding and antigen-binding activity of a human single-chain antibody fragment were simultaneously improved. This approach has several advantages for library screening, including the unique involvement of the Tat folding quality control mechanism that ensures only native-like proteins are displayed, thus eliminating poorly folded sequences from the screening process.
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Affiliation(s)
- Amy J Karlsson
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
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47
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Nam KH, Kurinov I, Ke A. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity. J Biol Chem 2011; 286:30759-30768. [PMID: 21697083 DOI: 10.1074/jbc.m111.256263] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.
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Affiliation(s)
- Ki Hyun Nam
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850
| | - Igor Kurinov
- Northeastern Collaborative Access Team (NE-CAT), Department of Chemistry and Chemical Biology, Cornell University, Argonne, Illinois 60439
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850.
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48
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Lu C, Smith AM, Ding F, Chowdhury A, Henkin TM, Ke A. Variable sequences outside the SAM-binding core critically influence the conformational dynamics of the SAM-III/SMK box riboswitch. J Mol Biol 2011; 409:786-99. [PMID: 21549712 DOI: 10.1016/j.jmb.2011.04.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 04/12/2011] [Accepted: 04/13/2011] [Indexed: 12/13/2022]
Abstract
The S(MK) box (SAM-III) translational riboswitches were identified in S-adenosyl-l-methionine (SAM) synthetase metK genes in members of Lactobacillales. This riboswitch switches between two alternative conformations in response to intracellular SAM concentration and controls metK expression at the level of translation initiation. We previously reported the crystal structure of the SAM-bound S(MK) box riboswitch. In this study, we combined selective 2'-hydroxyl acylation analyzed by primer extension chemical probing with mutagenesis to probe the ligand-induced conformational switching mechanism. We revealed that while the majority of the apo S(MK) box RNA molecules exist in an alternatively base-paired (ON) conformation, a subset of them pre-organize into a SAM-bound-like (READY) conformation, which, upon SAM exposure, is selectively stabilized into the SAM-bound (OFF) conformation through an induced-fit mechanism. Mutagenesis showed that the ON state is only slightly more stable than the READY state, as several single-nucleotide substitutions in a hypervariable region outside the SAM-binding core can alter the folding landscape to favor the READY state. Such S(MK) variants display a "constitutively OFF" behavior both in vitro and in vivo. Time-resolved and temperature-dependent selective 2'-hydroxyl acylation analyzed by primer extension analyses revealed adaptation of the S(MK) box RNA to its mesothermal working environment. The latter analysis revealed that the SAM-bound S(MK) box RNA follows a two-step folding/unfolding process.
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Affiliation(s)
- Changrui Lu
- Department of Molecular Biology and Genetics, 251 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
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49
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Ataide SF, Schmitz N, Shen K, Ke A, Shan SO, Doudna JA, Ban N. The crystal structure of the signal recognition particle in complex with its receptor. Science 2011; 331:881-6. [PMID: 21330537 DOI: 10.1126/science.1196473] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Cotranslational targeting of membrane and secretory proteins is mediated by the universally conserved signal recognition particle (SRP). Together with its receptor (SR), SRP mediates the guanine triphosphate (GTP)-dependent delivery of translating ribosomes bearing signal sequences to translocons on the target membrane. Here, we present the crystal structure of the SRP:SR complex at 3.9 angstrom resolution and biochemical data revealing that the activated SRP:SR guanine triphosphatase (GTPase) complex binds the distal end of the SRP hairpin RNA where GTP hydrolysis is stimulated. Combined with previous findings, these results suggest that the SRP:SR GTPase complex initially assembles at the tetraloop end of the SRP RNA and then relocalizes to the opposite end of the RNA. This rearrangement provides a mechanism for coupling GTP hydrolysis to the handover of cargo to the translocon.
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Affiliation(s)
- Sandro F Ataide
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zurich (ETH Zurich), Zurich, Switzerland
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50
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Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP. Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. Mol Microbiol 2011; 79:584-99. [PMID: 21255106 PMCID: PMC3040579 DOI: 10.1111/j.1365-2958.2010.07482.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A widespread feature in the genomes of most bacteria and archaea is an array of clustered, regularly interspaced short palindromic repeats (CRISPRs) that, together with a group of CRISPR-associated (Cas) proteins, mediate immunity against invasive nucleic acids such as plasmids and viruses. Here, the CRISPR-Cas system was activated in cells expressing a plasmid-encoded protein that was targeted to the twin-arginine translocation (Tat) pathway. Expression of this Tat substrate resulted in upregulation of the Cas enzymes and subsequent silencing of the encoding plasmid in a manner that required the BaeSR two-component regulatory system, which is known to respond to extracytoplasmic stress. Furthermore, we confirm that the CasCDE enzymes form a stable ternary complex and appear to function as the catalytic core of the Cas system to process CRISPR RNA into its mature form. Taken together, our results indicate that the CRISPR-Cas system targets DNA directly as part of a defence mechanism in bacteria that is overlapping with but not limited to phage infection.
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Affiliation(s)
| | - Charles Haitjema
- Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Qingqiu Huang
- Macromolecular Diffraction Facility at CHESS, Cornell University, Ithaca, NY, 14853 USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Ki Hyun Nam
- Macromolecular Diffraction Facility at CHESS, Cornell University, Ithaca, NY, 14853 USA
| | - Sarah Bernardis
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Matthew P. DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853 USA
- Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853 USA
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