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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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2
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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3
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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] [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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4
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Anand V, Prabhakaran HS, Prakash A, Hussain MS, Kumar M. Differential processing of CRISPR RNA by LinCas5c and LinCas6 of Leptospira. Biochim Biophys Acta Gen Subj 2023; 1867:130469. [PMID: 37797871 DOI: 10.1016/j.bbagen.2023.130469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023]
Abstract
Leptospira interrogans serovar Copenhageni's genome harbors two CRISPR-Cas systems belonging to subtypes I-B and I-C. However, in L. interrogans, the subtype I-C locus lacks an array component essential for assembling an interference complex. Thus, the reason for sustaining the expense of a cluster of cas genes (I-C) is obscure. Type I-C (previously Dvulg) is the only CRISPR subtype that engages Cas5c, a Cas5 variant, to process precursor CRISPR-RNA (pre-crRNA). In this study, thus, the recombinant Cas5c (rLinCas5c) of L.interrogans and its mutant variants were cloned, expressed, and purified. The purified rLinCas5c is illustrated as metal-independent, sequence, and size-specific cleavage on repeat RNA and pre-crRNA of subtype I-B or orphan CRISPR array. However, the Cas6-bound mature crRNA of subtype I-B fends off from the rLinCas5c activity. In addition, rLinCas5c holds metal and size-dependent DNase activity. The bioinformatics analysis of LinCas5c inferred that it belongs to the subgroup Cas5c-B. Substitution of Phe141 with a more conserved His residue and deletion of unique (β1'-β2') insertions usher a gain of rLinCas5c activity over nucleic acid. Overall, our results uncover the functional diversity of Cas5c ribonucleases and infer an incognito auxiliary role in the absence of a cognate CRISPR array.
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Affiliation(s)
- Vineet Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Harshini Sheeja Prabhakaran
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Aman Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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5
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Wang S, Gabel C, Siddique R, Klose T, Chang L. Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector. Cell 2023; 186:4204-4215.e19. [PMID: 37557170 PMCID: PMC11027886 DOI: 10.1016/j.cell.2023.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/23/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023]
Abstract
Tn7-like transposons have co-opted CRISPR-Cas systems to facilitate the movement of their own DNA. These CRISPR-associated transposons (CASTs) are promising tools for programmable gene knockin. A key feature of CASTs is their ability to recruit Tn7-like transposons to nuclease-deficient CRISPR effectors. However, how Tn7-like transposons are recruited by diverse CRISPR effectors remains poorly understood. Here, we present the cryo-EM structure of a recruitment complex comprising the Cascade complex, TniQ, TnsC, and the target DNA in the type I-B CAST from Peltigera membranacea cyanobiont 210A. Target DNA recognition by Cascade induces conformational changes in Cas6 and primes TniQ recruitment through its C-terminal domain. The N-terminal domain of TniQ is bound to the seam region of the TnsC spiral heptamer. Our findings provide insights into the diverse mechanisms for the recruitment of Tn7-like transposons to CRISPR effectors and will aid in the development of CASTs as gene knockin tools.
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Affiliation(s)
- Shukun Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Clinton Gabel
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Romana Siddique
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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6
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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7
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Kauert DJ, Madariaga-Marcos J, Rutkauskas M, Wulfken A, Songailiene I, Sinkunas T, Siksnys V, Seidel R. The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex. Nat Struct Mol Biol 2023:10.1038/s41594-023-01019-2. [PMID: 37415009 DOI: 10.1038/s41594-023-01019-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have revolutionized gene editing with their ability to target specific genomic loci using CRISPR RNA (crRNA) complementarity. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base pairing between crRNA and the DNA target strand, forming an R-loop structure. Full R-loop extension is a prerequisite for subsequent DNA cleavage. However, the recognition of unintended sequences with multiple mismatches has limited therapeutic applications and is still poorly understood on a mechanistic level. Here we set up ultrafast DNA unwinding experiments on the basis of plasmonic DNA origami nanorotors to study R-loop formation by the Cascade effector complex in real time, close to base-pair resolution. We resolve a weak global downhill bias of the forming R-loop, followed by a steep uphill bias for the final base pairs. We also show that the energy landscape is modulated by base flips and mismatches. These findings suggest that Cascade-mediated R-loop formation occurs on short timescales in submillisecond single base-pair steps, but on longer timescales in six base-pair intermediate steps, in agreement with the structural periodicity of the crRNA-DNA hybrid.
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Affiliation(s)
- Dominik J Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | | | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Alexander Wulfken
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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8
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Paraan M, Nasef M, Chou-Zheng L, Khweis SA, Schoeffler AJ, Hatoum-Aslan A, Stagg SM, Dunkle JA. The structure of a Type III-A CRISPR-Cas effector complex reveals conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems. PLoS One 2023; 18:e0287461. [PMID: 37352230 PMCID: PMC10289348 DOI: 10.1371/journal.pone.0287461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
Type III CRISPR-Cas systems employ multiprotein effector complexes bound to small CRISPR RNAs (crRNAs) to detect foreign RNA transcripts and elicit a complex immune response that leads to the destruction of invading RNA and DNA. Type III systems are among the most widespread in nature, and emerging interest in harnessing these systems for biotechnology applications highlights the need for detailed structural analyses of representatives from diverse organisms. We performed cryo-EM reconstructions of the Type III-A Cas10-Csm effector complex from S. epidermidis bound to an intact, cognate target RNA and identified two oligomeric states, a 276 kDa complex and a 318 kDa complex. 3.1 Å density for the well-ordered 276 kDa complex allowed construction of atomic models for the Csm2, Csm3, Csm4 and Csm5 subunits within the complex along with the crRNA and target RNA. We also collected small-angle X-ray scattering data which was consistent with the 276 kDa Cas10-Csm architecture we identified. Detailed comparisons between the S. epidermidis Cas10-Csm structure and the well-resolved bacterial (S. thermophilus) and archaeal (T. onnurineus) Cas10-Csm structures reveal differences in how the complexes interact with target RNA and crRNA which are likely to have functional ramifications. These structural comparisons shed light on the unique features of Type III-A systems from diverse organisms and will assist in improving biotechnologies derived from Type III-A effector complexes.
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Affiliation(s)
- Mohammadreza Paraan
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States of America
| | - Mohamed Nasef
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL, United States of America
| | - Lucy Chou-Zheng
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL, United States of America
| | - Sarah A. Khweis
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL, United States of America
| | - Allyn J. Schoeffler
- Department of Chemistry and Biochemistry, Loyola University New Orleans, New Orleans, LA, United States of America
| | - Asma Hatoum-Aslan
- Department of Microbiology, University of Illinois, Urbana-Champaign, IL, United States of America
| | - Scott M. Stagg
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States of America
| | - Jack A. Dunkle
- Department of Chemistry and Biochemistry, University of Alabama, Tuscaloosa, AL, United States of America
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9
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Cui N, Zhang JT, Liu Y, Liu Y, Liu XY, Wang C, Huang H, Jia N. Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment. Mol Cell 2023:S1097-2765(23)00420-3. [PMID: 37343553 DOI: 10.1016/j.molcel.2023.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/19/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023]
Abstract
Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic details of their function remain unknown. Here, we provide high-resolution functional snapshots of type IV-A Csf complexes before and after target dsDNA binding, either in the absence or presence of CasDinG, revealing the mechanisms underlying CsfcrRNA complex assembly, "DWN" PAM-dependent dsDNA targeting, R-loop formation, and CasDinG recruitment. Furthermore, we establish that CasDinG, a signature DinG family helicase, harbors ssDNA-stimulated ATPase activity and ATP-dependent 5'-3' DNA helicase activity. In addition, we show that CasDinG unwinds the non-target strand (NTS) and target strand (TS) of target dsDNA from the CsfcrRNA complex. These molecular details advance our mechanistic understanding of type IV-A CRISPR-Csf function and should enable Csf complexes to be harnessed as genome-engineering tools for biotechnological applications.
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Affiliation(s)
- Ning Cui
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jun-Tao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yongrui Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yanhong Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao-Yu Liu
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chongyuan Wang
- Faculty of Pharmaceutical Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China; Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518055, China
| | - Hongda Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Shenzhen Key Laboratory of Cell Microenvironment, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China; Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China.
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10
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Seo PW, Gu DH, Kim JW, Kim JH, Park SY, Kim JS. Structural characterization of the type I-B CRISPR Cas7 from Thermobaculum terrenum. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140900. [PMID: 36682394 DOI: 10.1016/j.bbapap.2023.140900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) in many prokaryotes functions as an adaptive immune system against mobile genetic elements. A heterologous ribonucleoprotein silencing complex composed of CRISPR-associated (Cas) proteins and a CRISPR RNA (crRNA) neutralizes the incoming mobile genetic elements. The type I and III silencing complexes commonly include a protein-helical backbone of several copies of identical subunits, for example, Cas7 in the type I silencing complex. In this study, we structurally characterized type I-B Cas7 (Csh2 from Thermobaculum terrenum; TterCsh2). The revealed crystal structure of TterCsh2 shows a typical glove-like architecture of Cas7, which consists of a palm, a thumb, and a finger domain. Csh2 proteins have 5 conserved sequence motifs that are arranged to form a presumable crRNA-binding site in the TterCsh2 structure. This crRNA binding site of TterCsh2 is structurally and potentially comparable to those observed in helix-forming Cas7 structures in other sub-types. Analysis of the reported Cas7 structures and their sequences suggests that Cas7s can be divided into at least two sub-classes. These data will broaden our understanding on the Cascade complex of CRISPR/Cas systems.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Do-Heon Gu
- Pohang Accelerator Laboratory, Pohang, South Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | | | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea.
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11
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Yin P, Zhang Y, Yang L, Feng Y. Non-canonical inhibition strategies and structural basis of anti-CRISPR proteins targeting type I CRISPR-Cas systems. J Mol Biol 2023; 435:167996. [PMID: 36754343 DOI: 10.1016/j.jmb.2023.167996] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/10/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023]
Abstract
Mobile genetic elements (MGEs) such as bacteriophages and their host prokaryotes are trapped in an eternal battle against each other. To cope with foreign infection, bacteria and archaea have evolved multiple immune strategies, out of which CRISPR-Cas system is up to now the only discovered adaptive system in prokaryotes. Despite the fact that CRISPR-Cas system provides powerful and delicate protection against MGEs, MGEs have also evolved anti-CRISPR proteins (Acrs) to counteract the CRISPR-Cas immune defenses. To date, 46 families of Acrs targeting type I CRISPR-Cas system have been characterized, out of which structure information of 21 families have provided insights on their inhibition strategies. Here, we review the non-canonical inhibition strategies adopted by Acrs targeting type I CRISPR-Cas systems based on their structure information by incorporating the most recent advances in this field, and discuss our current understanding and future perspectives. The delicate interplay between type I CRISPR-Cas systems and their Acrs provides us with important insights into the ongoing fierce arms race between prokaryotic hosts and their predators.
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Affiliation(s)
- Peipei Yin
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, College of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingguang Yang
- Jiangxi Provincial Key Laboratory of Natural Active Pharmaceutical Constituents, College of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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12
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Hsieh SC, Peters JE. Discovery and characterization of novel type I-D CRISPR-guided transposons identified among diverse Tn7-like elements in cyanobacteria. Nucleic Acids Res 2023; 51:765-782. [PMID: 36537206 PMCID: PMC9881144 DOI: 10.1093/nar/gkac1216] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
CRISPR-Cas defense systems have been naturally coopted for guide RNA-directed transposition by Tn7 family bacterial transposons. We find cyanobacterial genomes are rich in Tn7-like elements, including most of the known guide RNA-directed transposons, the type V-K, I-B1, and I-B2 CRISPR-Cas based systems. We discovered and characterized an example of a type I-D CRISPR-Cas system which was naturally coopted for guide RNA-directed transposition. Multiple novel adaptations were found specific to the I-D subtype, including natural inactivation of the Cas10 nuclease. The type I-D CRISPR-Cas transposition system showed flexibility in guide RNA length requirements and could be engineered to function with ribozyme-based self-processing guide RNAs removing the requirement for Cas6 in the heterologous system. The type I-D CRISPR-Cas transposon also has naturally fused transposase proteins that are functional for cut-and-paste transposition. Multiple attributes of the type I-D system offer unique possibilities for future work in gene editing. Our bioinformatic analysis also revealed a broader understanding of the evolution of Tn7-like elements. Extensive swapping of targeting systems was identified among Tn7-like elements in cyanobacteria and multiple examples of convergent evolution, including systems targeting integration into genes required for natural transformation.
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Affiliation(s)
- Shan-Chi Hsieh
- Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
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13
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Wada N, Osakabe K, Osakabe Y. Type I-D CRISPR System-Mediated Genome Editing in Plants. Methods Mol Biol 2023; 2653:21-38. [PMID: 36995617 DOI: 10.1007/978-1-0716-3131-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Genome editing has revolutionized plant research and plant breeding by enabling precise genome manipulation. In particular, the application of type II CRISPR-Cas9 systems to genome editing has proved an important milestone, accelerating genetic engineering and the analysis of gene function. On the other hand, the potential of other types of CRISPR-Cas systems, especially many of the most abundant type I CRISPR-Cas systems, remains unexplored. We recently developed a novel genome editing tool, TiD, based on the type I-D CRISPR-Cas system. In this chapter, we describe a protocol for genome editing of plant cells using TiD. This protocol allows the application of TiD to induce short insertion and deletions (indels) or long-range deletions at target sites with high specificity in tomato cells.
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Affiliation(s)
- Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Yuriko Osakabe
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan.
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14
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A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex. Nat Commun 2022; 13:7460. [PMID: 36460652 PMCID: PMC9718816 DOI: 10.1038/s41467-022-35116-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.
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15
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Watts EA, Garrett SC, Catchpole RJ, Clark LM, Graveley BR, Terns MP. Hyper-stimulation of Pyrococcus furiosus CRISPR DNA uptake by a self-transmissible plasmid. Extremophiles 2022; 26:36. [PMID: 36385310 PMCID: PMC9838737 DOI: 10.1007/s00792-022-01281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Pyrococcus furiosus is a hyperthermophilic archaeon with three effector CRISPR complexes (types I-A, I-B, and III-B) that each employ crRNAs derived from seven CRISPR arrays. Here, we investigate the CRISPR adaptation response to a newly discovered and self-transmissible plasmid, pT33.3. Transconjugant strains of Pyrococcus furiosus exhibited dramatically elevated levels of new spacer integration at CRISPR loci relative to the strain harboring a commonly employed, laboratory-constructed plasmid. High-throughput sequence analysis demonstrated that the vast majority of the newly acquired spacers were preferentially selected from DNA surrounding a particular region of the pT33.3 plasmid and exhibited a bi-directional pattern of strand bias that is a hallmark of primed adaptation by type I systems. We observed that one of the CRISPR arrays of our Pyrococcus furiosus laboratory strain encodes a spacer that closely matches the region of the conjugative plasmid that is targeted for adaptation. The hyper-adaptation phenotype was found to strictly depend both on the presence of this single matching spacer as well as the I-B effector complex, known to mediate primed adaptation. Our results indicate that Pyrococcus furiosus naturally encountered this conjugative plasmid or a related mobile genetic element in the past and responds to reinfection with robust primed adaptation.
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Affiliation(s)
- Elizabeth A Watts
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Sandra C Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA
| | - Ryan J Catchpole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Landon M Clark
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, 06030, USA.
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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16
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Shangguan Q, Graham S, Sundaramoorthy R, White M. Structure and mechanism of the type I-G CRISPR effector. Nucleic Acids Res 2022; 50:11214-11228. [PMID: 36305833 PMCID: PMC9638904 DOI: 10.1093/nar/gkac925] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 08/15/2023] Open
Abstract
Type I CRISPR systems are the most common CRISPR type found in bacteria. They use a multisubunit effector, guided by crRNA, to detect and bind dsDNA targets, forming an R-loop and recruiting the Cas3 enzyme to facilitate target DNA destruction, thus providing immunity against mobile genetic elements. Subtypes have been classified into families A-G, with type I-G being the least well understood. Here, we report the composition, structure and function of the type I-G Cascade CRISPR effector from Thioalkalivibrio sulfidiphilus, revealing key new molecular details. The unique Csb2 subunit processes pre-crRNA, remaining bound to the 3' end of the mature crRNA, and seven Cas7 subunits form the backbone of the effector. Cas3 associates stably with the effector complex via the Cas8g subunit and is important for target DNA recognition. Structural analysis by cryo-Electron Microscopy reveals a strikingly curved backbone conformation with Cas8g spanning the belly of the structure. These biochemical and structural insights shed new light on the diversity of type I systems and open the way to applications in genome engineering.
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Affiliation(s)
- Qilin Shangguan
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | | | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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17
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Ke G, Zhang J, Gao W, Chen J, Liu L, Wang S, Zhang H, Yan G. Application of advanced technology in traditional Chinese medicine for cancer therapy. Front Pharmacol 2022; 13:1038063. [PMID: 36313284 PMCID: PMC9606699 DOI: 10.3389/fphar.2022.1038063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Although cancer has seriously threatened people’s health, it is also identified by the World Health Organization as a controllable, treatable and even curable chronic disease. Traditional Chinese medicine (TCM) has been extensively used to treat cancer due to its multiple targets, minimum side effects and potent therapeutic effects, and thus plays an important role in all stages of tumor therapy. With the continuous progress in cancer treatment, the overall efficacy of cancer therapy has been significantly improved, and the survival time of patients has been dramatically prolonged. In recent years, a series of advanced technologies, including nanotechnology, gene editing technology, real-time cell-based assay (RTCA) technology, and flow cytometry analysis technology, have been developed and applied to study TCM for cancer therapy, which efficiently improve the medicinal value of TCM and accelerate the research progress of TCM in cancer therapy. Therefore, the applications of these advanced technologies in TCM for cancer therapy are summarized in this review. We hope this review will provide a good guidance for TCM in cancer therapy.
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Affiliation(s)
- Gaofeng Ke
- Department of Rehabilitation Medicine, The Affiliated Wenling Hospital of Wenzhou Medical University, Wenling, China
| | - Jia Zhang
- School of Pharmacy, Jiangsu Provincial Engineering Research Center of Traditional Chinese Medicine External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wufeng Gao
- School of Pharmacy, Jiangsu Provincial Engineering Research Center of Traditional Chinese Medicine External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiayi Chen
- School of Life Sciences, Jilin University, Changchun, China
| | - Luotong Liu
- School of Life Sciences, Jilin University, Changchun, China
| | - Simiao Wang
- School of Life Sciences, Jilin University, Changchun, China
| | - Huan Zhang
- School of Life Sciences, Jilin University, Changchun, China
- *Correspondence: Huan Zhang, ; Guojun Yan,
| | - Guojun Yan
- School of Pharmacy, Jiangsu Provincial Engineering Research Center of Traditional Chinese Medicine External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Huan Zhang, ; Guojun Yan,
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18
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Yoshimi K, Takeshita K, Kodera N, Shibumura S, Yamauchi Y, Omatsu M, Umeda K, Kunihiro Y, Yamamoto M, Mashimo T. Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3. Nat Commun 2022; 13:4917. [PMID: 36042215 PMCID: PMC9427990 DOI: 10.1038/s41467-022-32618-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Type I CRISPR-Cas3 uses an RNA-guided multi Cas-protein complex, Cascade, which detects and degrades foreign nucleic acids via the helicase-nuclease Cas3 protein. Despite many studies using cryoEM and smFRET, the precise mechanism of Cas3-mediated cleavage and degradation of target DNA remains elusive. Here we reconstitute the CRISPR-Cas3 system in vitro to show how the Escherichia coli Cas3 (EcoCas3) with EcoCascade exhibits collateral non-specific single-stranded DNA (ssDNA) cleavage and target specific DNA degradation. Partial binding of EcoCascade to target DNA with tolerated mismatches within the spacer sequence, but not the PAM, elicits collateral ssDNA cleavage activity of recruited EcoCas3. Conversely, stable binding with complete R-loop formation drives EcoCas3 to nick the non-target strand (NTS) in the bound DNA. Helicase-dependent unwinding then combines with trans ssDNA cleavage of the target strand and repetitive cis cleavage of the NTS to degrade the target double-stranded DNA (dsDNA) substrate. High-speed atomic force microscopy demonstrates that EcoCas3 bound to EcoCascade repeatedly reels and releases the target DNA, followed by target fragmentation. Together, these results provide a revised model for collateral ssDNA cleavage and target dsDNA degradation by CRISPR-Cas3, furthering understanding of type I CRISPR priming and interference and informing future genome editing tools.
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Affiliation(s)
- Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Kohei Takeshita
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Noriyuki Kodera
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | | | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Mine Omatsu
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Kenichi Umeda
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | | | - Masaki Yamamoto
- Life Science Research Infrastructure Group, Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.,Laboratory of Macromolecular Dynamics and X-ray Crystallography, Department of Life Science, University of Hyogo, Hyogo, 678-1297, Japan
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan. .,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
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19
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Aguion PI, Marchanka A, Carlomagno T. Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy. J Struct Biol X 2022; 6:100072. [PMID: 36090770 PMCID: PMC9449856 DOI: 10.1016/j.yjsbx.2022.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Solid-state NMR (ssNMR) has become a well-established technique to study large and insoluble protein assemblies. However, its application to nucleic acid-protein complexes has remained scarce, mainly due to the challenges presented by overlapping nucleic acid signals. In the past decade, several efforts have led to the first structure determination of an RNA molecule by ssNMR. With the establishment of these tools, it has become possible to address the problem of structure determination of nucleic acid-protein complexes by ssNMR. Here we review first and more recent ssNMR methodologies that study nucleic acid-protein interfaces by means of chemical shift and peak intensity perturbations, direct distance measurements and paramagnetic effects. At the end, we review the first structure of an RNA-protein complex that has been determined from ssNMR-derived intermolecular restraints.
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Affiliation(s)
- Philipp Innig Aguion
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - Alexander Marchanka
- Institute for Organic Chemistry and Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Teresa Carlomagno
- School of Biosciences/College of Life and Enviromental Sciences, Institute of Cancer and Genomic Sciences/College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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20
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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: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [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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21
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Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. Nat Commun 2022; 13:2829. [PMID: 35595728 PMCID: PMC9123187 DOI: 10.1038/s41467-022-30402-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/27/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems. Here, we present the structures of type I-D Cascade bound to both a double-stranded (ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We show that type I-D Cascade is capable of specifically binding ssRNA and reveal how PAM recognition of dsDNA targets initiates long-range structural rearrangements that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA cleavage. These structures allow us to model how binding of the anti-CRISPR protein AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA substrate engagement with the Cas10d active site. This work elucidates the unique mechanisms used by type I-D Cascade for discrimination of single-stranded and double stranded targets. Thus, our data supports a model for the hybrid nature of this complex with features of type III and type I systems. I-D CRISPR-Cascade can target both single-stranded and double-stranded nucleic acids. Here, Schwartz et. al determine these structures and reveal large-scale rearrangements that allow for target discrimination and destruction.
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22
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Hussain MS, Kumar M. Assembly of Cas7 subunits of Leptospira on the mature crRNA of CRISPR-Cas I-B is modulated by divalent ions. Gene X 2022; 818:146244. [PMID: 35074418 DOI: 10.1016/j.gene.2022.146244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/02/2023] Open
Abstract
The spirochete Leptospira interrogans serovar Copenhageni harbors the genetic elements of the CRISPR-Cas type I-B system in its genome. CRISPR-Cas is a CRISPR RNA (crRNA) mediated adaptive immune system in most prokaryotes against mobile genetic elements (MGEs). To eliminate the intruding MGEs, CRISPR-Cas type I systems utilize a Cascade (CRISPR-associated complex for antiviral defense) complex composed of Cas5, Cas6, Cas7, and Cas8 bound with a crRNA. The Cas7 is essentially known to constitute the major component of the Cascade complex. The present study reports the biochemical characterization of the Cas7 (LinCas7) from the CRISPR-Cas type I-B system of L. interrogans serovar Copenhageni. The pure recombinant LinCas7 (rLinCas7) exists as a monomer in the solution by size exclusion chromatography. The rLinCas7 demonstrates an endoDNase activity dependent upon divalent Mg2+ ions, monovalent ions, pH, temperature, and substrate size. Analysis of ribonucleoprotein composite (rLinCas7-crRNA) by electron microscopy and native-PAGE demonstrated that rLinCas7 could oligomerize on the mature CRISPR RNA (crRNA) framework in the presence of Mg2+ ions. The ribonucleoprotein composite attains a helical shape similar to the backbone of the Cascade complex. However, in the absence of Mg2+ ions, rLinCas7 acts as an RNase. The fluorescence spectroscopy disclosed a weak interaction (Kd = 26.81 mM) between rLinCas7 and Mg2+ ions, leading to an overall conformational change in rLinCas7 that modulates the rLinCas7's activity on DNA and RNA substrates. The nuclease activity of LinCas7 characterized in this study aids to the functional divergences among proteins of the Cas7 family from different CRISPR-Cas systems in various organisms.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India.
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23
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McKenzie RE, Keizer EM, Vink JNA, van Lopik J, Büke F, Kalkman V, Fleck C, Tans SJ, Brouns SJJ. Single cell variability of CRISPR-Cas interference and adaptation. Mol Syst Biol 2022; 18:e10680. [PMID: 35467080 PMCID: PMC10561596 DOI: 10.15252/msb.202110680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 12/26/2022] Open
Abstract
While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in individual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell-to-cell variability, which originates from primed CRISPR adaptation. Faster growth and cell division and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cascade binding to the mutated invader DNA, rather than spacer integration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.
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Affiliation(s)
- Rebecca E McKenzie
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Emma M Keizer
- Biometris, Department of Mathematical and Statistical MethodsWageningen UniversityWageningenThe Netherlands
| | - Jochem N A Vink
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Jasper van Lopik
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Ferhat Büke
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Vera Kalkman
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM)Spatial Systems Biology GroupUniversity of FreiburgFreiburgGermany
| | - Sander J Tans
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
- AMOLFAmsterdamThe Netherlands
| | - Stan J J Brouns
- Department of BionanoscienceDelft University of TechnologyDelftThe Netherlands
- Kavli Institute of NanoscienceDelftThe Netherlands
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24
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Wada N, Osakabe K, Osakabe Y. Expanding the plant genome editing toolbox with recently developed CRISPR-Cas systems. PLANT PHYSIOLOGY 2022; 188:1825-1837. [PMID: 35099553 PMCID: PMC8968252 DOI: 10.1093/plphys/kiac027] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/13/2022] [Indexed: 05/15/2023]
Abstract
Since its first appearance, CRISPR-Cas9 has been developed extensively as a programmable genome-editing tool, opening a new era in plant genome engineering. However, CRISPR-Cas9 still has some drawbacks, such as limitations of the protospacer-adjacent motif (PAM) sequence, target specificity, and the large size of the cas9 gene. To combat invading bacterial phages and plasmid DNAs, bacteria and archaea have diverse and unexplored CRISPR-Cas systems, which have the potential to be developed as a useful genome editing tools. Recently, discovery and characterization of additional CRISPR-Cas systems have been reported. Among them, several CRISPR-Cas systems have been applied successfully to plant and human genome editing. For example, several groups have achieved genome editing using CRISPR-Cas type I-D and type I-E systems, which had never been applied for genome editing previously. In addition to higher specificity and recognition of different PAM sequences, recently developed CRISPR-Cas systems often provide unique characteristics that differ from well-known Cas proteins such as Cas9 and Cas12a. For example, type I CRISPR-Cas10 induces small indels and bi-directional long-range deletions ranging up to 7.2 kb in tomatoes (Solanum lycopersicum L.). Type IV CRISPR-Cas13 targets RNA, not double-strand DNA, enabling highly specific knockdown of target genes. In this article, we review the development of CRISPR-Cas systems, focusing especially on their application to plant genome engineering. Recent CRISPR-Cas tools are helping expand our plant genome engineering toolbox.
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Affiliation(s)
- Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
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25
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Yoshimi K, Takeshita K, Yamayoshi S, Shibumura S, Yamauchi Y, Yamamoto M, Yotsuyanagi H, Kawaoka Y, Mashimo T. CRISPR-Cas3-based diagnostics for SARS-CoV-2 and influenza virus. iScience 2022; 25:103830. [PMID: 35128347 PMCID: PMC8801231 DOI: 10.1016/j.isci.2022.103830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/21/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
CRISPR-based diagnostics (CRISPR-dx), including the Cas12-based DETECTR and Cas13-based SHERLOCK Class 2 CRISPRs, have been used to detect the presence of DNA or RNA from pathogens, such as the 2009 pandemic influenza virus A (IAV) and the 2019 novel coronavirus SARS-CoV-2. Here, we describe the collateral single-stranded DNA cleavage with Class 1 type I CRISPR-Cas3 and highlight its potential for development as a Cas3-mediated rapid (within 40 min), low-cost, instrument-free detection method for SARS-CoV-2. This assay, which we call Cas3-Operated Nucleic Acid detectioN (CONAN), not only detects SARS-CoV-2 in clinical samples, but also offers specific detection of single-base-pair mutations in IAV variants. This tool allows rapid and accurate point-of-care testing for patients with suspected SARS-CoV-2 or drug-resistant IAV infections in hospitals. Type I CRISPR-Cas3 shows trans-cleavage activity on nearby nonspecific ssDNA We developed CONAN as a method to easily and accurately detect viral RNA CONAN provides rapid, low-cost, and instrument-free detection of SARS-CoV-2 and IAV CONAN also allows the specific detection of single-base-pair mutations
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Affiliation(s)
- Kazuto Yoshimi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kohei Takeshita
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | | | - Yuko Yamauchi
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Masaki Yamamoto
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases and Applied Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Tomoji Mashimo
- Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Division of Genome Engineering, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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26
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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: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [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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27
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Wimmer F, Mougiakos I, Englert F, Beisel CL. Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons. Mol Cell 2022; 82:1210-1224.e6. [PMID: 35216669 DOI: 10.1016/j.molcel.2022.01.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/30/2021] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
CRISPR-Cas biology and technologies have been largely shaped to date by the characterization and use of single-effector nucleases. By contrast, multi-subunit effectors dominate natural systems, represent emerging technologies, and were recently associated with RNA-guided DNA transposition. This disconnect stems from the challenge of working with multiple protein subunits in vitro and in vivo. Here, we apply cell-free transcription-translation (TXTL) systems to radically accelerate the characterization of multi-subunit CRISPR effectors and transposons. Numerous DNA constructs can be combined in one TXTL reaction, yielding defined biomolecular readouts in hours. Using TXTL, we mined phylogenetically diverse I-E effectors, interrogated extensively self-targeting I-C and I-F systems, and elucidated targeting rules for I-B and I-F CRISPR transposons using only DNA-binding components. We further recapitulated DNA transposition in TXTL, which helped reveal a distinct branch of I-B CRISPR transposons. These capabilities will facilitate the study and exploitation of the broad yet underexplored diversity of CRISPR-Cas systems and transposons.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Ioannis Mougiakos
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany; Medical Faculty, University of Würzburg, 97080 Würzburg, Germany.
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28
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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] [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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29
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Gao F, Zheng K, Li YB, Jiang F, Han CY. A Cas6-based RNA tracking platform functioning in a fluorescence-activation mode. Nucleic Acids Res 2022; 50:e46. [PMID: 35061906 PMCID: PMC9071499 DOI: 10.1093/nar/gkac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 12/09/2021] [Accepted: 01/05/2022] [Indexed: 12/17/2022] Open
Abstract
Given the fact that the localization of RNAs is closely associated with their functions, techniques developed for tracking the distribution of RNAs in live cells have greatly advanced the study of RNA biology. Recently, innovative application of fluorescent protein-labelled Cas9 and Cas13 into live-cell RNA tracking further enriches the toolbox. However, the Cas9/Cas13 platform, as well as the widely-used MS2-MCP technique, failed to solve the problem of high background noise. It was recently reported that CRISPR/Cas6 would exhibit allosteric alteration after interacting with the Cas6 binding site (CBS) on RNAs. Here, we exploited this feature and designed a Cas6-based switch platform for detecting target RNAs in vivo. Conjugating split-Venus fragments to both ends of the endoribonuclease-mutated Escherichia coli Cas6(dEcCas6) allowed ligand (CBS)-activated split-Venus complementation. We name this platform as Cas6 based Fluorescence Complementation (Cas6FC). In living cells, Cas6FC could detect target RNAs with nearly free background noise. Moreover, as minimal as one copy of CBS (29nt) tagged in an RNA of interest was able to turn on Cas6FC fluorescence, which greatly reduced the odds of potential alteration of conformation and localization of target RNAs. Thus, we developed a new RNA tracking platform inherently with high sensitivity and specificity.
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Affiliation(s)
- Feng Gao
- Gene Editing Research Center, Hebei University of Science and Technology, Shijiazhuang, Hebei 050018, China
| | - Ke Zheng
- Gene Editing Research Center, Hebei University of Science and Technology, Shijiazhuang, Hebei 050018, China
| | - You-Bo Li
- School of Basic Medical Sciences, Hebei University, Baoding, Hebei 071000, China
| | - Feng Jiang
- Gene Editing Research Center, Hebei University of Science and Technology, Shijiazhuang, Hebei 050018, China
| | - Chun-Yu Han
- Gene Editing Research Center, Hebei University of Science and Technology, Shijiazhuang, Hebei 050018, China
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30
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Malone LM, Hampton HG, Morgan XC, Fineran PC. Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress. Nucleic Acids Res 2021; 50:160-174. [PMID: 34928385 PMCID: PMC8754663 DOI: 10.1093/nar/gkab1210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
During infection, phages manipulate bacteria to redirect metabolism towards viral proliferation. To counteract phages, some bacteria employ CRISPR-Cas systems that provide adaptive immunity. While CRISPR-Cas mechanisms have been studied extensively, their effects on both the phage and the host during phage infection remains poorly understood. Here, we analysed the infection of Serratia by a siphovirus (JS26) and the transcriptomic response with, or without type I-E or I-F CRISPR-Cas immunity. In non-immune Serratia, phage infection altered bacterial metabolism by upregulating anaerobic respiration and amino acid biosynthesis genes, while flagella production was suppressed. Furthermore, phage proliferation required a late-expressed viral Cas4 homologue, which did not influence CRISPR adaptation. While type I-E and I-F immunity provided robust defence against phage infection, phage development still impacted the bacterial host. Moreover, DNA repair and SOS response pathways were upregulated during type I immunity. We also discovered that the type I-F system is controlled by a positive autoregulatory feedback loop that is activated upon phage targeting during type I-F immunity, leading to a controlled anti-phage response. Overall, our results provide new insight into phage-host dynamics and the impact of CRISPR immunity within the infected cell.
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Affiliation(s)
- Lucia M Malone
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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32
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Kolesnik MV, Fedorova I, Karneyeva KA, Artamonova DN, Severinov KV. Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System. BIOCHEMISTRY. BIOKHIMIIA 2021; 86:1301-1314. [PMID: 34903162 PMCID: PMC8527444 DOI: 10.1134/s0006297921100114] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/24/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022]
Abstract
The emergence and persistence of selfish genetic elements is an intrinsic feature of all living systems. Cellular organisms have evolved a plethora of elaborate defense systems that limit the spread of such genetic parasites. CRISPR-Cas are RNA-guided defense systems used by prokaryotes to recognize and destroy foreign nucleic acids. These systems acquire and store fragments of foreign nucleic acids and utilize the stored sequences as guides to recognize and destroy genetic invaders. CRISPR-Cas systems have been extensively studied, as some of them are used in various genome editing technologies. Although Type III CRISPR-Cas systems are among the most common CRISPR-Cas systems, they are also some of the least investigated ones, mostly due to the complexity of their action compared to other CRISPR-Cas system types. Type III effector complexes specifically recognize and cleave RNA molecules. The recognition of the target RNA activates the effector large subunit - the so-called CRISPR polymerase - which cleaves DNA and produces small cyclic oligonucleotides that act as signaling molecules to activate auxiliary effectors, notably non-specific RNases. In this review, we provide a historical overview of the sometimes meandering pathway of the Type III CRISPR research. We also review the current data on the structures and activities of Type III CRISPR-Cas systems components, their biological roles, and evolutionary history. Finally, using structural modeling with AlphaFold2, we show that the archaeal HRAMP signature protein, which heretofore has had no assigned function, is a degenerate relative of Type III CRISPR-Cas signature protein Cas10, suggesting that HRAMP systems have descended from Type III CRISPR-Cas systems or their ancestors.
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Affiliation(s)
- Matvey V Kolesnik
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Iana Fedorova
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Karyna A Karneyeva
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Daria N Artamonova
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Konstantin V Severinov
- Center of Life Science, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
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33
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Lemak S, Serbanescu MA, Khusnutdinova AN, Ruszkowski M, Beloglazova N, Xu X, Brown G, Cui H, Tan K, Joachimiak A, Cvitkovitch DG, Savchenko A, Yakunin AF. Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans. J Biol Chem 2021; 297:101251. [PMID: 34592310 PMCID: PMC8524198 DOI: 10.1016/j.jbc.2021.101251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 12/01/2022] Open
Abstract
The cariogenic pathogen Streptococcus mutans contains two CRISPR systems (type I-C and type II-A) with the Cas5c protein (SmuCas5c) involved in processing of long CRISPR RNA transcripts (pre-crRNA) containing repeats and spacers to mature crRNA guides. In this study, we determined the crystal structure of SmuCas5c at a resolution of 1.72 Å, which revealed the presence of an N-terminal modified RNA recognition motif and a C-terminal twisted β-sheet domain with four bound sulphate molecules. Analysis of surface charge and residue conservation of the SmuCas5c structure suggested the location of an RNA-binding site in a shallow groove formed by the RNA recognition motif domain with several conserved positively charged residues (Arg39, Lys52, Arg109, Arg127, and Arg134). Purified SmuCas5c exhibited metal-independent ribonuclease activity against single-stranded pre-CRISPR RNAs containing a stem-loop structure with a seven-nucleotide stem and a pentaloop. We found SmuCas5c cleaves substrate RNA within the repeat sequence at a single cleavage site located at the 3'-base of the stem but shows significant tolerance to substrate sequence variations downstream of the cleavage site. Structure-based mutational analysis revealed that the conserved residues Tyr50, Lys120, and His121 comprise the SmuCas5c catalytic residues. In addition, site-directed mutagenesis of positively charged residues Lys52, Arg109, and Arg134 located near the catalytic triad had strong negative effects on the RNase activity of this protein, suggesting that these residues are involved in RNA binding. Taken together, our results reveal functional diversity of Cas5c ribonucleases and provide further insight into the molecular mechanisms of substrate selectivity and activity of these enzymes.
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Affiliation(s)
- Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - M Anca Serbanescu
- Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Anna N Khusnutdinova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, Illinois, USA
| | - Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kemin Tan
- X-Ray Science Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Andrzej Joachimiak
- X-Ray Science Division, Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dennis G Cvitkovitch
- Faculty of Dentistry, Dental Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, UK.
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34
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Guzmán NM, Esquerra-Ruvira B, Mojica FJM. Digging into the lesser-known aspects of CRISPR biology. Int Microbiol 2021; 24:473-498. [PMID: 34487299 PMCID: PMC8616872 DOI: 10.1007/s10123-021-00208-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
A long time has passed since regularly interspaced DNA repeats were discovered in prokaryotes. Today, those enigmatic repetitive elements termed clustered regularly interspaced short palindromic repeats (CRISPR) are acknowledged as an emblematic part of multicomponent CRISPR-Cas (CRISPR associated) systems. These systems are involved in a variety of roles in bacteria and archaea, notably, that of conferring protection against transmissible genetic elements through an adaptive immune-like response. This review summarises the present knowledge on the diversity, molecular mechanisms and biology of CRISPR-Cas. We pay special attention to the most recent findings related to the determinants and consequences of CRISPR-Cas activity. Research on the basic features of these systems illustrates how instrumental the study of prokaryotes is for understanding biology in general, ultimately providing valuable tools for diverse fields and fuelling research beyond the mainstream.
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Affiliation(s)
- Noemí M Guzmán
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Belén Esquerra-Ruvira
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco J M Mojica
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain. .,Instituto Multidisciplinar para el Estudio del Medio, Universidad de Alicante, Alicante, Spain.
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35
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Osakabe K, Wada N, Murakami E, Miyashita N, Osakabe Y. Genome editing in mammalian cells using the CRISPR type I-D nuclease. Nucleic Acids Res 2021; 49:6347-6363. [PMID: 34076237 PMCID: PMC8216271 DOI: 10.1093/nar/gkab348] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 04/15/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
Adoption of CRISPR-Cas systems, such as CRISPR-Cas9 and CRISPR-Cas12a, has revolutionized genome engineering in recent years; however, application of genome editing with CRISPR type I-the most abundant CRISPR system in bacteria-remains less developed. Type I systems, such as type I-E, and I-F, comprise the CRISPR-associated complex for antiviral defense ('Cascade': Cas5, Cas6, Cas7, Cas8 and the small subunit) and Cas3, which degrades the target DNA; in contrast, for the sub-type CRISPR-Cas type I-D, which lacks a typical Cas3 nuclease in its CRISPR locus, the mechanism of target DNA degradation remains unknown. Here, we found that Cas10d is a functional nuclease in the type I-D system, performing the role played by Cas3 in other CRISPR-Cas type I systems. The type I-D system can be used for targeted mutagenesis of genomic DNA in human cells, directing both bi-directional long-range deletions and short insertions/deletions. Our findings suggest the CRISPR-Cas type I-D system as a unique effector pathway in CRISPR that can be repurposed for genome engineering in eukaryotic cells.
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Affiliation(s)
- Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Emi Murakami
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
| | - Naoyuki Miyashita
- Department of Computational Systems Biology, Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Yuriko Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Tokushima 770-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8502, Japan
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36
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. BIOLOGY 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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Taylor HN, Laderman E, Armbrust M, Hallmark T, Keiser D, Bondy-Denomy J, Jackson RN. Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems. Front Microbiol 2021; 12:671522. [PMID: 34093491 PMCID: PMC8175902 DOI: 10.3389/fmicb.2021.671522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022] Open
Abstract
Type IV CRISPR systems encode CRISPR associated (Cas)-like proteins that combine with small RNAs to form multi-subunit ribonucleoprotein complexes. However, the lack of Cas nucleases, integrases, and other genetic features commonly observed in most CRISPR systems has made it difficult to predict type IV mechanisms of action and biological function. Here we summarize recent bioinformatic and experimental advancements that collectively provide the first glimpses into the function of specific type IV subtypes. We also provide a bioinformatic and structural analysis of type IV-specific proteins within the context of multi-subunit (class 1) CRISPR systems, informing future studies aimed at elucidating the function of these cryptic systems.
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Affiliation(s)
- Hannah N. Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Eric Laderman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Matt Armbrust
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Thomson Hallmark
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Dylan Keiser
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Ryan N. Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
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38
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Advancements in macromolecular crystallography: from past to present. Emerg Top Life Sci 2021; 5:127-149. [PMID: 33969867 DOI: 10.1042/etls20200316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/17/2022]
Abstract
Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.
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Zhou Y, Bravo JP, Taylor HN, Steens JA, Jackson RN, Staals RH, Taylor DW. Structure of a type IV CRISPR-Cas ribonucleoprotein complex. iScience 2021; 24:102201. [PMID: 33733066 PMCID: PMC7937560 DOI: 10.1016/j.isci.2021.102201] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/03/2021] [Accepted: 02/12/2021] [Indexed: 12/18/2022] Open
Abstract
We reveal the cryo-electron microscopy structure of a type IV-B CRISPR ribonucleoprotein (RNP) complex (Csf) at 3.9-Å resolution. The complex best resembles the type III-A CRISPR Csm effector complex, consisting of a Cas7-like (Csf2) filament intertwined with a small subunit (Cas11) filament, but the complex lacks subunits for RNA processing and target DNA cleavage. Surprisingly, instead of assembling around a CRISPR-derived RNA (crRNA), the complex assembles upon heterogeneous RNA of a regular length arranged in a pseudo-A-form configuration. These findings provide a high-resolution glimpse into the assembly and function of enigmatic type IV CRISPR systems, expanding our understanding of class I CRISPR-Cas system architecture, and suggesting a function for type IV-B RNPs that may be distinct from other class 1 CRISPR-associated systems.
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Affiliation(s)
- Yi Zhou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jack P.K. Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Hannah N. Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Jurre A. Steens
- Laboratory of Microbiology, Wageningen University and Research, The Netherlands
| | - Ryan N. Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Raymond H.J. Staals
- Laboratory of Microbiology, Wageningen University and Research, The Netherlands
| | - David W. Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, USA
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A Tryptophan 'Gate' in the CRISPR-Cas3 Nuclease Controls ssDNA Entry into the Nuclease Site, That When Removed Results in Nuclease Hyperactivity. Int J Mol Sci 2021; 22:ijms22062848. [PMID: 33799639 PMCID: PMC8001533 DOI: 10.3390/ijms22062848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Cas3 is a ssDNA-targeting nuclease-helicase essential for class 1 prokaryotic CRISPR immunity systems, which has been utilized for genome editing in human cells. Cas3-DNA crystal structures show that ssDNA follows a pathway from helicase domains into a HD-nuclease active site, requiring protein conformational flexibility during DNA translocation. In genetic studies, we had noted that the efficacy of Cas3 in CRISPR immunity was drastically reduced when temperature was increased from 30 °C to 37 °C, caused by an unknown mechanism. Here, using E. coli Cas3 proteins, we show that reduced nuclease activity at higher temperature corresponds with measurable changes in protein structure. This effect of temperature on Cas3 was alleviated by changing a single highly conserved tryptophan residue (Trp-406) into an alanine. This Cas3W406A protein is a hyperactive nuclease that functions independently from temperature and from the interference effector module Cascade. Trp-406 is situated at the interface of Cas3 HD and RecA1 domains that is important for maneuvering DNA into the nuclease active site. Molecular dynamics simulations based on the experimental data showed temperature-induced changes in positioning of Trp-406 that either blocked or cleared the ssDNA pathway. We propose that Trp-406 forms a 'gate' for controlling Cas3 nuclease activity via access of ssDNA to the nuclease active site. The effect of temperature in these experiments may indicate allosteric control of Cas3 nuclease activity caused by changes in protein conformations. The hyperactive Cas3W406A protein may offer improved Cas3-based genetic editing in human cells.
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Ye Z, Moreb EA, Li S, Lebeau J, Menacho-Melgar R, Munson M, Lynch MD. Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability. ACS Synth Biol 2021; 10:29-37. [PMID: 33331764 DOI: 10.1021/acssynbio.0c00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CRISPR-based interference has become common in various applications from genetic circuits to dynamic metabolic control. In E. coli, the native CRISPR Cascade system can be utilized for silencing by deletion of the cas3 nuclease along with expression of guide RNA arrays, where multiple genes can be silenced from a single transcript. We notice the loss of spacer sequences from guide arrays utilized for dynamic silencing. We report that unstable guide arrays are due to expression of the Cas1/2 endonuclease complex. We propose a model wherein basal Cas1/2 endonuclease activity results in the loss of spacers from guide arrays. Subsequently, mutant guide arrays can be amplified through selection. Replacing a constitutive promoter driving Cascade complex expression with a tightly controlled inducible promoter improves guide array stability, while minimizing leaky gene silencing. Additionally, these results demonstrate the potential of Cas1/2 mediated guide deletion as a mechanism to avoid CRISPR based autoimmunity.
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Affiliation(s)
- Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Shuai Li
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Matthew Munson
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
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42
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Petassi MT, Hsieh SC, Peters JE. Guide RNA Categorization Enables Target Site Choice in Tn7-CRISPR-Cas Transposons. Cell 2020; 183:1757-1771.e18. [PMID: 33271061 PMCID: PMC7770071 DOI: 10.1016/j.cell.2020.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/10/2020] [Accepted: 11/03/2020] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas defense systems have been coopted multiple times in nature for guide RNA-directed transposition by Tn7-like elements. Prototypic Tn7 uses dedicated proteins for two targeting pathways: one targeting a neutral and conserved attachment site in the chromosome and a second directing transposition into mobile plasmids facilitating cell-to-cell transfer. We show that Tn7-CRISPR-Cas elements evolved a system of guide RNA categorization to accomplish the same two-pathway lifestyle. Multiple mechanisms allow functionally distinct guide RNAs for transposition: a conventional system capable of acquiring guide RNAs to new plasmid and phage targets and a second providing long-term memory for access to chromosomal sites upon entry into a new host. Guide RNAs are privatized to be recognized only by the transposon-adapted system via sequence specialization, mismatch tolerance, and selective regulation to avoid toxic self-targeting by endogenous CRISPR-Cas defense systems. This information reveals promising avenues to engineer guide RNAs for enhanced CRISPR-Cas functionality for genome modification.
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Affiliation(s)
- Michael T Petassi
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Shan-Chi Hsieh
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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43
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Mejdani M, Pawluk A, Maxwell KL, Davidson AR. Anti-CRISPR AcrIE2 Binds the Type I-E CRISPR-Cas Complex But Does Not Block DNA Binding. J Mol Biol 2020; 433:166759. [PMID: 33338493 DOI: 10.1016/j.jmb.2020.166759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
Anti-CRISPRs are protein inhibitors of CRISPR-Cas systems. They are produced by phages and other mobile genetic elements to evade CRISPR-Cas-mediated destruction. Anti-CRISPRs are remarkably diverse in sequence, structure, and functional mechanism; thus, structural and mechanistic investigations of anti-CRISPRs continue to yield exciting new insights. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AcrIE2, an anti-CRISPR that inhibits the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. Guided by the structure, we used site-directed mutagenesis to identify key residues that are required for AcrIE2 function. Using affinity purification experiments, we found that AcrIE2 binds the type I-E CRISPR-Cas complex (Cascade). In vivo transcriptional assays, in which Cascade was targeted to promoter regions, demonstrated that Cascade still binds to DNA in the presence of AcrIE2. This is the first instance of a type I anti-CRISPR that binds to a CRISPR-Cas complex but does not prevent DNA-binding. Another unusual property of AcrIE2 is that the effect of Cascade:AcrIE2 complex binding to promoter regions varied depending on the position of the binding site. Most surprisingly, Cascade:AcrIE2 binding led to transcriptional activation in some cases rather than repression, which did not occur when Cascade alone bound to the same sites. We conclude that AcrIE2 operates through a distinct mechanism compared to other type I anti-CRISPRs. While AcrIE2 does not prevent Cascade from binding DNA, it likely blocks subsequent recruitment of the Cas3 nuclease to Cascade thereby preventing DNA cleavage.
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Affiliation(s)
- Marios Mejdani
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - April Pawluk
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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Abstract
Prokaryotes have developed numerous defense strategies to combat the constant threat posed by the diverse genetic parasites that endanger them. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas loci guard their hosts with an adaptive immune system against foreign nucleic acids. Protection starts with an immunization phase, in which short pieces of the invader's genome, known as spacers, are captured and integrated into the CRISPR locus after infection. Next, during the targeting phase, spacers are transcribed into CRISPR RNAs (crRNAs) that guide CRISPR-associated (Cas) nucleases to destroy the invader's DNA or RNA. Here we describe the many different molecular mechanisms of CRISPR targeting and how they are interconnected with the immunization phase through a third phase of the CRISPR-Cas immune response: primed spacer acquisition. In this phase, Cas proteins direct the crRNA-guided acquisition of additional spacers to achieve a more rapid and robust immunization of the population.
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Affiliation(s)
- Philip M. Nussenzweig
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Luciano A. Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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45
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O'Brien RE, Santos IC, Wrapp D, Bravo JPK, Schwartz EA, Brodbelt JS, Taylor DW. Structural basis for assembly of non-canonical small subunits into type I-C Cascade. Nat Commun 2020; 11:5931. [PMID: 33230133 PMCID: PMC7684278 DOI: 10.1038/s41467-020-19785-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Bacteria and archaea employ CRISPR (clustered, regularly, interspaced, short palindromic repeats)-Cas (CRISPR-associated) systems as a type of adaptive immunity to target and degrade foreign nucleic acids. While a myriad of CRISPR-Cas systems have been identified to date, type I-C is one of the most commonly found subtypes in nature. Interestingly, the type I-C system employs a minimal Cascade effector complex, which encodes only three unique subunits in its operon. Here, we present a 3.1 Å resolution cryo-EM structure of the Desulfovibrio vulgaris type I-C Cascade, revealing the molecular mechanisms that underlie RNA-directed complex assembly. We demonstrate how this minimal Cascade utilizes previously overlooked, non-canonical small subunits to stabilize R-loop formation. Furthermore, we describe putative PAM and Cas3 binding sites. These findings provide the structural basis for harnessing the type I-C Cascade as a genome-engineering tool.
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Affiliation(s)
- Roisin E O'Brien
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Evan A Schwartz
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - David W Taylor
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.
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46
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Shibata T, Iwasaki W, Hirota K. The intrinsic ability of double-stranded DNA to carry out D-loop and R-loop formation. Comput Struct Biotechnol J 2020; 18:3350-3360. [PMID: 33294131 PMCID: PMC7677664 DOI: 10.1016/j.csbj.2020.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 12/03/2022] Open
Abstract
Double-stranded (ds)DNA, not dsRNA, has an ability to form a homologous complex with single-stranded (ss)DNA or ssRNA of homologous sequence. D-loops and homologous triplexes are homologous complexes formed with ssDNA by RecA/Rad51-family homologous-pairing proteins, and are a key intermediate of homologous (genetic/DNA) recombination. R-loop formation independent of transcription (R-loop formation in trans) was recently found to play roles in gene regulation and development of mammals and plants. In addition, the crRNA-Cas effector complex in CRISPR-Cas systems also relies on R-loop formation to recognize specific target. In homologous complex formation, ssDNA/ssRNA finds a homologous sequence in dsDNA by Watson-Crick base-pairing. crRNA-Cas effector complexes appear to actively melt dsDNA to make its bases available for annealing to crRNA. On the other hand, in D-loop formation and homologous-triplex formation, it is likely that dsDNA recognizes the homologous sequence before the melting of its double helix by using its intrinsic molecular function depending on CH2 at the 2'-position of the deoxyribose, and that the major role of RecA is the extension of ssDNA and the holding dsDNA at a position suitable for homology search. This intrinsic dsDNA function would also play a role in R-loop formation. The dependency of homologous-complex formation on 2'-CH2 of the deoxyribose would explain the absence of homologous complex formation by dsRNA, and dsDNA as sole genome molecule in all cellular organisms.
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Affiliation(s)
- Takehiko Shibata
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Wakana Iwasaki
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi, Yokohama, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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47
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Lin J, Fuglsang A, Kjeldsen AL, Sun K, Bhoobalan-Chitty Y, Peng X. DNA targeting by subtype I-D CRISPR-Cas shows type I and type III features. Nucleic Acids Res 2020; 48:10470-10478. [PMID: 32960267 PMCID: PMC7544194 DOI: 10.1093/nar/gkaa749] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 01/01/2023] Open
Abstract
Prokaryotic CRISPR-Cas immune systems are classified into six types based on their effector complexes which cleave dsDNA specifically (types I, II and V), ssRNA exclusively (type VI) or both ssRNA via a ruler mechanism and ssDNA unspecifically (type III). To date, no specific cleavage of ssDNA target has been reported for CRISPR-Cas. Here, we demonstrate dual dsDNA and ssDNA cleavage activities of a subtype I-D system which carries a type III Cas10-like large subunit, Cas10d. In addition to a specific dsDNA cleavage activity dependent on the HD domain of Cas10d, the helicase Cas3' and a compatible protospacer adjacent motif (PAM), the subtype I-D effector complex can cleave ssDNA that is complementary in sequence to the crRNA. Significantly, the ssDNA cleavage sites occur at 6-nt intervals and the cleavage is catalysed by the backbone subunit Csc2 (Cas7), similar to the periodic cleavage of ssRNA by the backbone subunit of type III effectors. The typical type I cleavage of dsDNA combined with the exceptional 6-nt spaced cleavage of ssDNA and the presence of a type III like large subunit provide strong evidence for the subtype I-D system being an evolutionary intermediate between type I and type III CRISPR-Cas systems.
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Affiliation(s)
- Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Anders Fuglsang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Anders Lynge Kjeldsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kaiyan Sun
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Yuvaraj Bhoobalan-Chitty
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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48
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Fernandez-Garcia L, Pacios O, González-Bardanca M, Blasco L, Bleriot I, Ambroa A, López M, Bou G, Tomás M. Viral Related Tools against SARS-CoV-2. Viruses 2020; 12:E1172. [PMID: 33081350 PMCID: PMC7589879 DOI: 10.3390/v12101172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.
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Affiliation(s)
- Laura Fernandez-Garcia
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Olga Pacios
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Mónica González-Bardanca
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Lucia Blasco
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Inés Bleriot
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Antón Ambroa
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - María López
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - German Bou
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
| | - Maria Tomás
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
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Liu TY, Doudna JA. Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation. J Biol Chem 2020; 295:14473-14487. [PMID: 32817336 PMCID: PMC7573268 DOI: 10.1074/jbc.rev120.007034] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/13/2020] [Indexed: 12/19/2022] Open
Abstract
Among the multiple antiviral defense mechanisms found in prokaryotes, CRISPR-Cas systems stand out as the only known RNA-programmed pathways for detecting and destroying bacteriophages and plasmids. Class 1 CRISPR-Cas systems, the most widespread and diverse of these adaptive immune systems, use an RNA-guided multiprotein complex to find foreign nucleic acids and trigger their destruction. In this review, we describe how these multisubunit complexes target and cleave DNA and RNA and how regulatory molecules control their activities. We also highlight similarities to and differences from Class 2 CRISPR-Cas systems, which use a single-protein effector, as well as other types of bacterial and eukaryotic immune systems. We summarize current applications of the Class 1 CRISPR-Cas systems for DNA/RNA modification, control of gene expression, and nucleic acid detection.
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Affiliation(s)
- Tina Y Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Gladstone Institutes, University of California, San Francisco, California, USA
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Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.00731-20. [PMID: 32385085 DOI: 10.1128/aem.00731-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Working mechanisms of CRISPR-Cas systems have been intensively studied. However, far less is known about how they are regulated. The histone-like nucleoid-structuring protein H-NS binds the promoter of cas genes (P cas ) and suppresses the type I-E CRISPR-Cas system in Escherichia coli Although the H-NS paralogue StpA also binds P cas , its role in regulating the CRISPR-Cas system remains unidentified. Our previous work established that E. coli is able to take up double-stranded DNA during natural transformation. Here, we investigated the function of StpA in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli We first documented that although the activated type I-E CRISPR-Cas system, due to hns deletion, interfered with CRISPR-Cas-targeted plasmid transfer, stpA inactivation restored the level of natural transformation. Second, we showed that inactivating stpA reduced the transcriptional activity of P cas Third, by comparing transcriptional activities of the intact P cas and the P cas with a disrupted H-NS binding site in the hns and hns stpA null deletion mutants, we demonstrated that StpA activated transcription of cas genes by binding to the same site as H-NS in P cas Fourth, by expressing StpA with an arabinose-inducible promoter, we confirmed that StpA expressed at a low level stimulated the activity of P cas Finally, by quantifying the level of mature CRISPR RNA (crRNA), we demonstrated that StpA was able to promote the amount of crRNA. Taken together, our work establishes that StpA serves as a transcriptional activator in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli IMPORTANCE StpA is normally considered a molecular backup of the nucleoid-structuring protein H-NS, which was reported as a transcriptional repressor of the type I-E CRISPR-Cas system in Escherichia coli However, the role of StpA in regulating the type I-E CRISPR-Cas system remains elusive. Our previous work uncovered a new route for double-stranded DNA (dsDNA) entry during natural transformation of E. coli In this study, we show that StpA plays a role opposite to that of its paralogue H-NS in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli Our work not only expands our knowledge on CRISPR-Cas-mediated adaptive immunity against extracellular nucleic acids but also sheds new light on understanding the complex regulation mechanism of the CRISPR-Cas system. Moreover, the finding that paralogues StpA and H-NS share a DNA binding site but play opposite roles in transcriptional regulation indicates that higher-order compaction of bacterial chromatin by histone-like proteins could switch prokaryotic transcriptional modes.
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