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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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2
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Hussain MS, Anand V, Kumar M. Functional PAM sequence for DNA interference by CRISPR-Cas I-B system of Leptospira interrogans and the role of LinCas11b encoded within lincas8b. Int J Biol Macromol 2023; 237:124086. [PMID: 36940764 DOI: 10.1016/j.ijbiomac.2023.124086] [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: 12/14/2022] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 03/23/2023]
Abstract
Pathogenic species of Leptospira are recalcitrant for genetic manipulation using conventional tools, and therefore there is a need to explore techniques of higher efficiency. Application of endogenous CRISPR-Cas tool is emerging and efficient; nevertheless, it is limited by a poor understanding of interference machinery in the bacterial genome and its associated protospacer adjacent motif (PAM). In this study, interference machinery of CRISPR-Cas subtype I-B (Lin_I-B) from L. interrogans was experimentally validated in E. coli using the various identified PAM (TGA, ATG, ATA). The overexpression of the Lin_I-B interference machinery in E. coli demonstrated that LinCas5, LinCas6, LinCas7, and LinCas8b can self-assemble on cognate CRISPR RNA to form an interference complex (LinCascade). Moreover, a robust interference of target plasmids containing a protospacer with a PAM suggested a functional LinCascade. We also recognized a small open reading frame within lincas8b that independently co-translates LinCas11b. A mutant variant of LinCascade-Cas11b that lacks LinCas11b co-expression erred to mount target plasmid interference. At the same time, LinCas11b complementation in LinCascade-Cas11b rescued target plasmid interference. Thus, the present study establishes Leptospira subtype I-B interference machinery to be functional and, soon, may pave the way for scientists to harness it as a programmable endogenous genetic manipulation tool.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Vineet Anand
- 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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3
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CRISPR-Cas assisted diagnostics: A broad application biosensing approach. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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4
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Kundar R, Gokarn K. CRISPR-Cas System: A Tool to Eliminate Drug-Resistant Gram-Negative Bacteria. Pharmaceuticals (Basel) 2022; 15:ph15121498. [PMID: 36558949 PMCID: PMC9781512 DOI: 10.3390/ph15121498] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
Rapidly emerging drug-resistant superbugs, especially Gram-negative bacteria, pose a serious threat to healthcare systems all over the globe. Newer strategies are being developed to detect and overcome the arsenal of weapons that these bacteria possess. The development of antibiotics is time-consuming and may not provide full proof of action on evolving drug-resistant pathogens. The clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) systems are promising in curbing drug-resistant bacteria. This review focuses on the pathogenesis of Gram-negative bacteria, emergence of antimicrobial drug resistance, and their treatment failures. It also draws attention to the present status of the CRISPR-Cas system in diagnosisand treatment of Gram-negative bacterial infections.
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Affiliation(s)
- Rajeshwari Kundar
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
| | - Karuna Gokarn
- Department of Microbiology, Sir H.N. Medical Research Society, Sir H.N. Reliance Foundation Hospital & Research Centre, Mumbai 400004, Maharashtra, India
- Department of Microbiology, St. Xavier’s College, 5- Mahapalika Marg, Mumbai 400001, Maharashtra, India
- Correspondence: or
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5
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Treatment strategies for HIV infection with emphasis on role of CRISPR/Cas9 gene: Success so far and road ahead. Eur J Pharmacol 2022; 931:175173. [DOI: 10.1016/j.ejphar.2022.175173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/20/2022]
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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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Chaudhuri A, Halder K, Datta A. Classification of CRISPR/Cas system and its application in tomato breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:367-387. [PMID: 34973111 PMCID: PMC8866350 DOI: 10.1007/s00122-021-03984-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/21/2021] [Indexed: 05/03/2023]
Abstract
Remarkable diversity in the domain of genome loci architecture, structure of effector complex, array of protein composition, mechanisms of adaptation along with difference in pre-crRNA processing and interference have led to a vast scope of detailed classification in bacterial and archaeal CRISPR/Cas systems, their intrinsic weapon of adaptive immunity. Two classes: Class 1 and Class 2, several types and subtypes have been identified so far. While the evolution of the effector complexes of Class 2 is assigned solely to mobile genetic elements, the origin of Class 1 effector molecules is still in a haze. Majority of the types target DNA except type VI, which have been found to target RNA exclusively. Cas9, the single effector protein, has been the primary focus of CRISPR-mediated genome editing revolution and is an integral part of Class 2 (type II) system. The present review focuses on the different CRISPR types in depth and the application of CRISPR/Cas9 for epigenome modification, targeted base editing and improving traits such as abiotic and biotic stress tolerance, yield and nutritional aspects of tomato breeding.
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Affiliation(s)
- Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067 India
| | - Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067 India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110 067 India
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Xia P, Dutta A, Gupta K, Batish M, Parashar V. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. J Biol Chem 2022; 298:101591. [PMID: 35038453 PMCID: PMC8844856 DOI: 10.1016/j.jbc.2022.101591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/28/2023] Open
Abstract
RNA interference by type III CRISPR systems results in the synthesis of cyclic oligoadenylate (cOA) second messengers, which are known to bind and regulate various CARF domain-containing nuclease receptors. The CARF domain-containing Csa3 family of transcriptional factors associated with the DNA-targeting type I CRISPR systems regulate expression of various CRISPR and DNA repair genes in many prokaryotes. In this study, we extend the known receptor repertoire of cOA messengers to include transcriptional factors by demonstrating specific binding of cyclic tetra-adenylate (cA4) to Saccharolobus solfataricus Csa3 (Csa3Sso). Our 2.0-Å resolution X-ray crystal structure of cA4-bound full-length Csa3Sso reveals the binding of its CARF domain to an elongated conformation of cA4. Using cA4 binding affinity analyses of Csa3Sso mutants targeting the observed Csa3Sso•cA4 structural interface, we identified a Csa3-specific cA4 binding motif distinct from a more widely conserved cOA-binding CARF motif. Using a rational surface engineering approach, we increased the cA4 binding affinity of Csa3Sso up to ∼145-fold over the wildtype, which has potential applications for future second messenger-driven CRISPR gene expression and editing systems. Our in-solution Csa3Sso structural analysis identified cA4-induced allosteric and asymmetric conformational rearrangement of its C-terminal winged helix-turn-helix effector domains, which could potentially be incompatible to DNA binding. However, specific in vitro binding of the purified Csa3Sso to its putative promoter (PCas4a) was found to be cA4 independent, suggesting a complex mode of Csa3Sso regulation. Overall, our results support cA4-and Csa3-mediated cross talk between type III and type I CRISPR systems.
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Affiliation(s)
- Pengjun Xia
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Anirudha Dutta
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Kushol Gupta
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Vijay Parashar
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA.
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9
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Zhang E, Zhou W, Zhou J, He Z, Zhou Y, Han J, Qu D. CRISPR-Cas systems are present predominantly on chromosome and its relationship with MEGs in Vibrio species. Arch Microbiol 2021; 204:76. [DOI: 10.1007/s00203-021-02656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
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10
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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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11
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Liu Q, Wang S, Long J, Chen Z, Yang B, Lin F. Functional Identification of the Xanthomonas oryzae pv. oryzae Type I-C CRISPR-Cas System and Its Potential in Gene Editing Application. Front Microbiol 2021; 12:686715. [PMID: 34475857 PMCID: PMC8406640 DOI: 10.3389/fmicb.2021.686715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
The type I clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system is one of five adaptive immune systems and exists widely in bacteria and archaea. In this study, we showed that Xanthomonas oryzae pv. oryzae (Xoo) possesses a functional CRISPR system by engineering constructs mimicking its CRISPR cassette. CRISPR array analysis showed that the TTC at the 5'-end of the target sequence is a functional protospacer-adjacent motif (PAM) of CRISPR. Guide RNA (gRNA) deletion analysis identified a minimum of 27-bp spacer that was required to ensure successful self-target killing in PXO99A strain. Mutants with deletion of individual Cas genes were constructed to analyze the effects of Cas proteins on mature CRISPR RNA (crRNA), processing intermediates and DNA interference. Results showed that depleting each of the three genes, cas5d, csd1, and csd2 inactivated the pre-crRNA processing, whereas inactivation of cas3 impaired in processing pre-crRNA. Furthermore, the Xoo CRISPR/Cas system was functional in Pseudomonas syringae pv. tomato. Collectively, our results would contribute to the functional study of CRISPR/Cas system of Xoo, and also provide a new vision on the use of bacterial endogenous systems as a convenient tool for gene editing.
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Affiliation(s)
- Qibing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Siwei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Juying Long
- Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Zhuoyue Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.,Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Fei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources/Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
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12
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Nethery MA, Korvink M, Makarova KS, Wolf YI, Koonin EV, Barrangou R. CRISPRclassify: Repeat-Based Classification of CRISPR Loci. CRISPR J 2021; 4:558-574. [PMID: 34406047 DOI: 10.1089/crispr.2021.0021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Detection and classification of CRISPR-Cas systems in metagenomic data have become increasingly prevalent in recent years due to their potential for diverse applications in genome editing. Traditionally, CRISPR-Cas systems are classified through reference-based identification of proximate cas genes. Here, we present a machine learning approach for the detection and classification of CRISPR loci using repeat sequences in a cas-independent context, enabling identification of unclassified loci missed by traditional cas-based approaches. Using biological attributes of the CRISPR repeat, the core element in CRISPR arrays, and leveraging methods from natural language processing, we developed a machine learning model capable of accurate classification of CRISPR loci in an extensive set of metagenomes, resulting in an F1 measure of 0.82 across all predictions and an F1 measure of 0.97 when limiting to classifications with probabilities >0.85. Furthermore, assessing performance on novel repeats yielded an F1 measure of 0.96. Although the performance of cas-based identification will exceed that of a repeat-based approach in many cases, CRISPRclassify provides an efficient approach to classification of CRISPR loci for cases in which cas gene information is unavailable, such as metagenomes and fragmented genome assemblies.
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Affiliation(s)
- Matthew A Nethery
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, North Carolina, USA; National Library of Medicine, Bethesda, Maryland, USA
| | - Michael Korvink
- ITS Data Science, Premier Inc., Charlotte, North Carolina, USA; and National Library of Medicine, Bethesda, Maryland, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Rodolphe Barrangou
- Genomic Sciences Graduate Program, North Carolina State University, Raleigh, North Carolina, USA; National Library of Medicine, Bethesda, Maryland, USA
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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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14
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Ghorbani A, Hadifar S, Salari R, Izadpanah K, Burmistrz M, Afsharifar A, Eskandari MH, Niazi A, Denes CE, Neely GG. A short overview of CRISPR-Cas technology and its application in viral disease control. Transgenic Res 2021; 30:221-238. [PMID: 33830423 PMCID: PMC8027712 DOI: 10.1007/s11248-021-00247-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/26/2021] [Indexed: 12/19/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) together with CRISPR-associated (Cas) proteins have catalysed a revolution in genetic engineering. Native CRISPR-Cas systems exist in many bacteria and archaea where they provide an adaptive immune response through sequence-specific degradation of an invading pathogen's genome. This system has been reconfigured for use in genome editing, drug development, gene expression regulation, diagnostics, the prevention and treatment of cancers, and the treatment of genetic and infectious diseases. In recent years, CRISPR-Cas systems have been used in the diagnosis and control of viral diseases, for example, CRISPR-Cas12/13 coupled with new amplification techniques to improve the specificity of sequence-specific fluorescent probe detection. Importantly, CRISPR applications are both sensitive and specific and usually only require commonly available lab equipment. Unlike the canonical Cas9 which is guided to double-stranded DNA sites of interest, Cas13 systems target RNA sequences and thus can be employed in strategies directed against RNA viruses or for transcriptional silencing. Many challenges remain for these approach, including issues with specificity and the requirement for better mammalian delivery systems. In this review, we summarize the applications of CRISPR-Cas systems in controlling mammalian viral infections. Following necessary improvements, it is expected that CRISPR-Cas systems will be used effectively for such applications in the future.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran.
| | - Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Roya Salari
- Institute of Biotechnology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Michal Burmistrz
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-089, Warsaw, Poland
| | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher E Denes
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW, 2006, Australia
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW, 2006, Australia
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15
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Adiguzel MC, Goulart DB, Wu Z, Pang J, Cengiz S, Zhang Q, Sahin O. Distribution of CRISPR Types in Fluoroquinolone-Resistant Campylobacter jejuni Isolates. Pathogens 2021; 10:345. [PMID: 33809410 PMCID: PMC8000906 DOI: 10.3390/pathogens10030345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/10/2021] [Accepted: 03/13/2021] [Indexed: 12/20/2022] Open
Abstract
To aid development of phage therapy against Campylobacter, we investigated the distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) systems in fluoroquinolone (FQ)-resistant Campylobacter jejuni. A total of 100 FQ-resistant C. jejuni strains from different sources were analyzed by PCR and DNA sequencing to determine resistance-conferring mutation in the gyrA gene and the presence of various CRISPR systems. All but one isolate harbored 1-5 point mutations in gyrA, and the most common mutation was the Thr86Ile change. Ninety-five isolates were positive with the CRISPR PCR, and spacer sequences were found in 86 of them. Among the 292 spacer sequences identified in this study, 204 shared 93-100% nucleotide homology to Campylobacter phage D10, 44 showed 100% homology to Campylobacter phage CP39, and 3 had 100% homology with Campylobacter phage CJIE4-5. The remaining 41 spacer sequences did not match with any phages in the database. Based on the results, it was inferred that the FQ-resistant C. jejuni isolates analyzed in this study were potentially resistant to Campylobacter phages D10, CP39, and CJIE4-5 as well as some unidentified phages. These phages should be excluded from cocktails of phages that may be utilized to treat FQ-resistant Campylobacter.
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Affiliation(s)
- Mehmet Cemal Adiguzel
- Department of Microbiology, College of Veterinary Medicine, Ataturk University, Erzurum 25240, Turkey; (M.C.A.); (S.C.)
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.B.G.); (Z.W.); (J.P.); (Q.Z.)
| | - Debora Brito Goulart
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.B.G.); (Z.W.); (J.P.); (Q.Z.)
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.B.G.); (Z.W.); (J.P.); (Q.Z.)
| | - Jinji Pang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.B.G.); (Z.W.); (J.P.); (Q.Z.)
| | - Seyda Cengiz
- Department of Microbiology, College of Veterinary Medicine, Ataturk University, Erzurum 25240, Turkey; (M.C.A.); (S.C.)
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (D.B.G.); (Z.W.); (J.P.); (Q.Z.)
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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16
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Manav MC, Van LB, Lin J, Fuglsang A, Peng X, Brodersen DE. Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein. Nat Commun 2020; 11:5993. [PMID: 33239638 PMCID: PMC7689449 DOI: 10.1038/s41467-020-19847-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
A hallmark of type I CRISPR-Cas systems is the presence of Cas3, which contains both the nuclease and helicase activities required for DNA cleavage during interference. In subtype I-D systems, however, the histidine-aspartate (HD) nuclease domain is encoded as part of a Cas10-like large effector complex subunit and the helicase activity in a separate Cas3' subunit, but the functional and mechanistic consequences of this organisation are not currently understood. Here we show that the Sulfolobus islandicus type I-D Cas10d large subunit exhibits an unusual domain architecture consisting of a Cas3-like HD nuclease domain fused to a degenerate polymerase fold and a C-terminal domain structurally similar to Cas11. Crystal structures of Cas10d both in isolation and bound to S. islandicus rod-shaped virus 3 AcrID1 reveal that the anti-CRISPR protein sequesters the large subunit in a non-functional state unable to form a cleavage-competent effector complex. The architecture of Cas10d suggests that the type I-D effector complex is similar to those found in type III CRISPR-Cas systems and that this feature is specifically exploited by phages for anti-CRISPR defence.
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Affiliation(s)
- M Cemre Manav
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Lan B Van
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark
| | - Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Anders Fuglsang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark
| | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, København N, Denmark.
| | - Ditlev E Brodersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000, Aarhus C, Denmark.
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17
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Jolany vangah S, Katalani C, Booneh HA, Hajizade A, Sijercic A, Ahmadian G. CRISPR-Based Diagnosis of Infectious and Noninfectious Diseases. Biol Proced Online 2020; 22:22. [PMID: 32939188 PMCID: PMC7489454 DOI: 10.1186/s12575-020-00135-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022] Open
Abstract
Interest in CRISPR technology, an instrumental component of prokaryotic adaptive immunity which enables prokaryotes to detect any foreign DNA and then destroy it, has gained popularity among members of the scientific community. This is due to CRISPR's remarkable gene editing and cleaving abilities. While the application of CRISPR in human genome editing and diagnosis needs to be researched more fully, and any potential side effects or ambiguities resolved, CRISPR has already shown its capacity in an astonishing variety of applications related to genome editing and genetic engineering. One of its most currently relevant applications is in diagnosis of infectious and non-infectious diseases. Since its initial discovery, 6 types and 22 subtypes of CRISPR systems have been discovered and explored. Diagnostic CRISPR systems are most often derived from types II, V, and VI. Different types of CRISPR-Cas systems which have been identified in different microorganisms can target DNA (e.g. Cas9 and Cas12 enzymes) or RNA (e.g. Cas13 enzyme). Viral, bacterial, and non-infectious diseases such as cancer can all be diagnosed using the cleavage activity of CRISPR enzymes from the aforementioned types. Diagnostic tests using Cas12 and Cas13 enzymes have already been developed for detection of the emerging SARS-CoV-2 virus. Additionally, CRISPR diagnostic tests can be performed using simple reagents and paper-based lateral flow assays, which can potentially reduce laboratory and patient costs significantly. In this review, the classification of CRISPR-Cas systems as well as the basis of the CRISPR/Cas mechanisms of action will be presented. The application of these systems in medical diagnostics with emphasis on the diagnosis of COVID-19 will be discussed.
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Affiliation(s)
- Somayeh Jolany vangah
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, P.O.BOX: 14155-6343 Iran
| | - Camellia Katalani
- Department of Plant Biotechnology and Agricultural Science, Sari Agricultural Science and Natural Resource University, Sari, Iran
| | - Hannah A. Booneh
- Department of Genetics and Bioengineering, International Burch University, Francuske Revolucije bb, Ilidza, 71210 Sarajevo, Bosnia and Herzegovina
| | - Abbas Hajizade
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Adna Sijercic
- Department of Genetics and Bioengineering, International Burch University, Francuske Revolucije bb, Ilidza, 71210 Sarajevo, Bosnia and Herzegovina
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, P.O.BOX: 14155-6343 Iran
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18
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Cañez C, Selle K, Goh YJ, Barrangou R. Outcomes and characterization of chromosomal self-targeting by native CRISPR-Cas systems in Streptococcus thermophilus. FEMS Microbiol Lett 2020; 366:5488433. [PMID: 31077282 DOI: 10.1093/femsle/fnz105] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/09/2019] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas systems provide adaptive immunity against phages in prokaryotes via DNA-encoded, RNA-mediated, nuclease-dependent targeting and cleavage. Due to inefficient and relatively limited DNA repair pathways in bacteria, CRISPR-Cas systems can be repurposed for lethal DNA targeting that selects for sequence variants. In this study, the relative killing efficiencies of endogenous Type I and Type II CRISPR-Cas systems in the model organism Streptococcus thermophilus DGCC7710 were assessed. Additionally, the genetic and phenotypic outcomes of chromosomal targeting by plasmid-programmed Type I-E or Type II-A systems were analyzed. Efficient killing was observed using both systems, in a dose-dependent manner when delivering 0.4-400 ng of plasmid DNA. Targeted PCR screening and genome sequencing were used to determine the genetic basis enabling survival, showing that evasion of Type I-E self-targeting was primarily the result of low-frequency defective plasmids that excised the targeting spacer. The most notable genotype recovered from Type II-A targeting of genomic locus, lacZ, was a 34 kb-deletion derived from homologous recombination (HR) between identical conserved sequences in two separate galE coding regions, resulting in 2% loss of the genome. Collectively, these results suggest that HR contributes to the plasticity and remodeling of bacterial genomes, leading to evasion of genome targeting by CRISPR-Cas systems.
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Affiliation(s)
- Cassandra Cañez
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Kurt Selle
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Functional Genomics Graduate Program, North Carolina State University, Raleigh, NC 27695, USA
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19
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Abstract
CRISPR-Cas, the bacterial and archaeal adaptive immunity systems, encompass a complex machinery that integrates fragments of foreign nucleic acids, mostly from mobile genetic elements (MGE), into CRISPR arrays embedded in microbial genomes. Transcripts of the inserted segments (spacers) are employed by CRISPR-Cas systems as guide (g)RNAs for recognition and inactivation of the cognate targets. The CRISPR-Cas systems consist of distinct adaptation and effector modules whose evolutionary trajectories appear to be at least partially independent. Comparative genome analysis reveals the origin of the adaptation module from casposons, a distinct type of transposons, which employ a homologue of Cas1 protein, the integrase responsible for the spacer incorporation into CRISPR arrays, as the transposase. The origin of the effector module(s) is far less clear. The CRISPR-Cas systems are partitioned into two classes, class 1 with multisubunit effectors, and class 2 in which the effector consists of a single, large protein. The class 2 effectors originate from nucleases encoded by different MGE, whereas the origin of the class 1 effector complexes remains murky. However, the recent discovery of a signalling pathway built into the type III systems of class 1 might offer a clue, suggesting that type III effector modules could have evolved from a signal transduction system involved in stress-induced programmed cell death. The subsequent evolution of the class 1 effector complexes through serial gene duplication and displacement, primarily of genes for proteins containing RNA recognition motif domains, can be hypothetically reconstructed. In addition to the multiple contributions of MGE to the evolution of CRISPR-Cas, the reverse flow of information is notable, namely, recruitment of minimalist variants of CRISPR-Cas systems by MGE for functions that remain to be elucidated. Here, we attempt a synthesis of the diverse threads that shed light on CRISPR-Cas origins and evolution. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine , Bethesda, MD 20894 , USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine , Bethesda, MD 20894 , USA
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20
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Zheng Y, Li J, Wang B, Han J, Hao Y, Wang S, Ma X, Yang S, Ma L, Yi L, Peng W. Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering. Front Bioeng Biotechnol 2020; 8:62. [PMID: 32195227 PMCID: PMC7064716 DOI: 10.3389/fbioe.2020.00062] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2020] [Indexed: 12/18/2022] Open
Abstract
Establishment of production platforms through prokaryotic engineering in microbial organisms would be one of the most efficient means for chemicals, protein, and biofuels production. Despite the fact that CRISPR (clustered regularly interspaced short palindromic repeats)–based technologies have readily emerged as powerful and versatile tools for genetic manipulations, their applications are generally limited in prokaryotes, possibly owing to the large size and severe cytotoxicity of the heterogeneous Cas (CRISPR-associated) effector. Nevertheless, the rich natural occurrence of CRISPR-Cas systems in many bacteria and most archaea holds great potential for endogenous CRISPR-based prokaryotic engineering. The endogenous CRISPR-Cas systems, with type I systems that constitute the most abundant and diverse group, would be repurposed as genetic manipulation tools once they are identified and characterized as functional in their native hosts. This article reviews the major progress made in understanding the mechanisms of invading DNA immunity by type I CRISPR-Cas and summarizes the practical applications of endogenous type I CRISPR-based toolkits for prokaryotic engineering.
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Affiliation(s)
- Yanli Zheng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Baiyang Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Jiamei Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Yile Hao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shengchen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Xiangdong Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Wenfang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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21
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Burmistrz M, Krakowski K, Krawczyk-Balska A. RNA-Targeting CRISPR-Cas Systems and Their Applications. Int J Mol Sci 2020; 21:ijms21031122. [PMID: 32046217 PMCID: PMC7036953 DOI: 10.3390/ijms21031122] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) systems have revolutionized modern molecular biology. Numerous types of these systems have been discovered to date. Many CRISPR-Cas systems have been used as a backbone for the development of potent research tools, with Cas9 being the most widespread. While most of the utilized systems are DNA-targeting, recently more and more attention is being gained by those that target RNA. Their ability to specifically recognize a given RNA sequence in an easily programmable way makes them ideal candidates for developing new research tools. In this review we summarize current knowledge on CRISPR-Cas systems which have been shown to target RNA molecules, that is type III (Csm/Cmr), type VI (Cas13), and type II (Cas9). We also present a list of available technologies based on these systems.
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22
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Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 2019; 18:67-83. [DOI: 10.1038/s41579-019-0299-x] [Citation(s) in RCA: 797] [Impact Index Per Article: 159.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/16/2022]
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23
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Ka D, Jang DM, Han BW, Bae E. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Nucleic Acids Res 2019; 46:9805-9815. [PMID: 30102386 PMCID: PMC6182153 DOI: 10.1093/nar/gky702] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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24
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Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
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Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
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25
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Shabbir MA, Wu Q, Shabbir MZ, Sajid A, Ahmed S, Sattar A, Tang Y, Li J, Maan MK, Hao H, Yuan Z. The CRISPR-cas system promotes antimicrobial resistance in Campylobacter jejuni. Future Microbiol 2018; 13:1757-1774. [PMID: 30526040 DOI: 10.2217/fmb-2018-0234] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AIM The purpose of current study is to find out relationship between cas9 gene and antimicrobial resistance in Campylobacter jejuni NCTC11168. MATERIALS & METHODS The involvement of the cas9 gene in antimicrobial resistance of C. jejuni was determined by assessment of minimum inhibitory concentration, clustered regularly interspaced short palindromic repeats (CRISPR)-cas gene expression in standard strains, in vitro resistance development and transcriptome analysis of a cas9 deletion mutant and wild strains. RESULTS Increased expression of CRISPR-related genes was observed in standard strains. We also observed that Δcas9 mutant strain is more sensitive to antibiotics than its wild strain. Transcriptome analysis revealed that cas9 gene regulate several genes to promote antimicrobial resistance in C. jejuni. CONCLUSION CRISPR-cas system plays role in the enhancement of antimicrobial resistance in C. jejuni.
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Affiliation(s)
- Muhammad Ab Shabbir
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Qin Wu
- National Reference Laboratory of Veterinary Drug Residues & MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad Z Shabbir
- Quality Operation Laboratory at University of Veterinary & Animal Sciences, Lahore, 54600, Pakistan
| | - Abdul Sajid
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China.,College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Saeed Ahmed
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Adeel Sattar
- Department of Pharmacology & Toxicology, University of Veterinary & Animal Sciences, Lahore, 54600, Pakistan
| | - Yanping Tang
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jun Li
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Muhammad K Maan
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Haihong Hao
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China.,National Reference Laboratory of Veterinary Drug Residues & MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zonghui Yuan
- China MOA Laboratory for Risk Assessment of Quality & Safety of Livestock & Poultry Products, Huazhong Agricultural University, Wuhan 430070, PR China.,National Reference Laboratory of Veterinary Drug Residues & MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan 430070, PR China
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26
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Ahmed W, Hafeez MA, Ahmad R, Mahmood S. CRISPR-Cas system in regulation of immunity and virulence of bacterial pathogens. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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27
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Shu M, Fu R, Wang W. A bacteriophage model based on CRISPR/Cas immune system in a chemostat. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2018; 14:1361-1377. [PMID: 29161865 DOI: 10.3934/mbe.2017070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats(CRISPRs) along with Cas proteins are a widespread immune system across bacteria and archaea. In this paper, a mathematical model in a chemostat is proposed to investigate the effect of CRISPR/Cas on the bacteriophage dynamics. It is shown that the introduction of CRISPR/Cas can induce a backward bifurcation and transcritical bifurcation. Numerical simulations reveal the coexistence of a stable infection-free equilibrium with an infection equilibrium, or a stable infection-free equilibrium with a stable periodic solution.
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Affiliation(s)
- Mengshi Shu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing 400715, China
| | - Rui Fu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing 400715, China
| | - Wendi Wang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region, School of Mathematics and Statistics, Southwest University, Chongqing, 400715, China
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Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A. The nuts and bolts of the Haloferax CRISPR-Cas system I-B. RNA Biol 2018; 16:469-480. [PMID: 29649958 PMCID: PMC6546412 DOI: 10.1080/15476286.2018.1460994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Invading genetic elements pose a constant threat to prokaryotic survival, requiring an effective defence. Eleven years ago, the arsenal of known defence mechanisms was expanded by the discovery of the CRISPR-Cas system. Although CRISPR-Cas is present in the majority of archaea, research often focuses on bacterial models. Here, we provide a perspective based on insights gained studying CRISPR-Cas system I-B of the archaeon Haloferax volcanii. The system relies on more than 50 different crRNAs, whose stability and maintenance critically depend on the proteins Cas5 and Cas7, which bind the crRNA and form the Cascade complex. The interference machinery requires a seed sequence and can interact with multiple PAM sequences. H. volcanii stands out as the first example of an organism that can tolerate autoimmunity via the CRISPR-Cas system while maintaining a constitutively active system. In addition, the H. volcanii system was successfully developed into a tool for gene regulation.
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Affiliation(s)
| | | | | | | | | | - Karina A Haas
- a Biology II, Ulm University , Ulm , Germany.,b Microbiology and Biotechnology, Ulm University , Ulm , Germany
| | | | - Omer S Alkhnbashi
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany
| | - Kundan Sharma
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,f Ludwig Institute for Cancer Research, University of Oxford , Oxford , United Kingdom
| | - Henning Urlaub
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,g Institute for Clinical Chemistry, University Medical Center Göttingen , Robert Koch Straße 10, Göttingen , Germany
| | - Rolf Backofen
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany.,d Centre for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg , Germany
| | - Uri Gophna
- h School of Molecular Cell Biology & Biotechnology, George S. Wise, Faculty of Life Sciences, Tel Aviv University , Tel Aviv , Israel
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Uppada V, Gokara M, Rasineni GK. Diagnosis and therapy with CRISPR advanced CRISPR based tools for point of care diagnostics and early therapies. Gene 2018; 656:22-29. [PMID: 29496558 DOI: 10.1016/j.gene.2018.02.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 02/24/2018] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics is of critical importance to public health worldwide. It facilitates not only detection and characterization of diseases, but also monitors drug responses, assists in the identification of genetic modifiers and disease susceptibility. Based upon DNA variation, a wide range of molecular-based tests are available to assess/diagnose diseases. The CRISPR-Cas9 system has recently emerged as a versatile tool for biological and medical research. In this system, a single guide RNA (sgRNA) directs the endonuclease Cas9 to a targeted DNA sequence for site-specific manipulation. As designing CRISPR-guided nucleases can be done easily and relatively fast, the CRISPR/Cas9 system has evolved as widely used DNA editing tool. This technique led to a large number of gene editing studies in variety of organisms. CRISPR/Cas9-mediated diagnosis and therapy has picked up pace due to specificity and accuracy of CRISPR. The aim is not only to identify specific pathogens, especially virus but also to repair disease-causing alleles by changing the DNA sequence at the exact location on the chromosome. At present, PCR-based molecular diagnostic testing predominates; however, alternative technologies aimed at reducing genome complexity without PCR are anticipated to gain momentum in the coming years. Furthermore, development of integrated chip devices should allow point-of-care testing and facilitate genetic readouts from single cells and molecules. Together with molecular based therapy CRISPR based diagnostic testing will be a revolution in modern health care settings. In this review, we emphasize on current developing diagnostic techniques based upon CRISPR Cas approach along with short insights on its therapeutic usage.
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Affiliation(s)
- Vanita Uppada
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Mahesh Gokara
- Department of Biochemistry, University of Hyderabad, Hyderabad 500046, Telangana, India
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30
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Hong S, Ka D, Yoon SJ, Suh N, Jeong M, Suh JY, Bae E. CRISPR RNA and anti-CRISPR protein binding to the Xanthomonas albilineans Csy1-Csy2 heterodimer in the type I-F CRISPR-Cas system. J Biol Chem 2018; 293:2744-2754. [PMID: 29348170 PMCID: PMC5827448 DOI: 10.1074/jbc.ra117.001611] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/12/2018] [Indexed: 01/07/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against bacteriophages. In type I-F CRISPR-Cas systems, multiple Cas proteins (Csy1-4) compose a surveillance complex (Csy complex) with CRISPR RNA (crRNA) for target recognition. Here, we report the biochemical characterization of the Csy1-Csy2 subcomplex from Xanthomonas albilineans, including the analysis of its interaction with crRNA and AcrF2, an anti-CRISPR (Acr) protein from a phage that infects Pseudomonas aeruginosa The X. albilineans Csy1 and Csy2 proteins (XaCsy1 and XaCsy2, respectively) formed a stable heterodimeric complex that specifically bound the 8-nucleotide (nt) 5'-handle of the crRNA. In contrast, the XaCsy1-XaCsy2 heterodimer exhibited reduced affinity for the 28-nt X. albilineans CRISPR repeat RNA containing the 5'-handle sequence. Chromatographic and calorimetric analyses revealed tight binding between the Acr protein from the P. aeruginosa phage and the heterodimeric subunit of the X. albilineans Csy complex, suggesting that AcrF2 recognizes conserved features of Csy1-Csy2 heterodimers. We found that neither XaCsy1 nor XaCsy2 alone forms a stable complex with AcrF2 and the 5'-handle RNA, indicating that XaCsy1-XaCsy2 heterodimerization is required for binding them. We also solved the crystal structure of AcrF2 to a resolution of 1.34 Å, enabling a more detailed structural analysis of the residues involved in the interactions with the Csy1-Csy2 heterodimer. Our results provide information about the order of events during the formation of the multisubunit crRNA-guided surveillance complex and suggest that the Acr protein inactivating type I-F CRISPR-Cas systems has broad specificity.
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Affiliation(s)
- Suji Hong
- From the Departments of Agricultural Biotechnology and
| | - Donghyun Ka
- From the Departments of Agricultural Biotechnology and
| | | | - Nayoung Suh
- Department of Pharmaceutical Engineering, Soon Chun Hyang University, Asan 31538, Korea, and
| | | | - Jeong-Yong Suh
- From the Departments of Agricultural Biotechnology and ,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea, ,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Euiyoung Bae
- From the Departments of Agricultural Biotechnology and ,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea, , To whom correspondence should be addressed:
Dept. of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea. Tel.:
82-2-880-4648; Fax:
82-2-873-3112; E-mail:
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31
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Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System. J Bacteriol 2017; 199:JB.00275-17. [PMID: 28893837 DOI: 10.1128/jb.00275-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/25/2017] [Indexed: 11/20/2022] Open
Abstract
The CRISPR-Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated protein) system is unique to prokaryotes and provides the majority of bacteria and archaea with immunity against nucleic acids of foreign origin. CRISPR RNAs (crRNAs) are the key element of this system, since they are responsible for its selectivity and effectiveness. Typical crRNAs consist of a spacer sequence flanked with 5' and 3' handles originating from repeat sequences that are important for recognition of these small RNAs by the Cas machinery. In this investigation, we studied the type I-C CRISPR-Cas system in Porphyromonas gingivalis, a human pathogen associated with periodontitis, rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. We demonstrated the importance of the 5' handle for crRNA recognition by the effector complex and consequently activity, as well as secondary trimming of the 3' handle, which was not affected by modifications of the repeat sequence.IMPORTANCEPorphyromonas gingivalis, a clinically relevant Gram-negative, anaerobic bacterium, is one of the major etiologic agents of periodontitis and has been linked with the development of other clinical conditions, including rheumatoid arthritis, cardiovascular disease, and aspiration pneumonia. The presented results on the biogenesis and functions of crRNAs expand our understanding of CRISPR-Cas cellular defenses in P. gingivalis and of horizontal gene transfer in bacteria.
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Ka D, Hong S, Jeong U, Jeong M, Suh N, Suh JY, Bae E. Structural and dynamic insights into the role of conformational switching in the nuclease activity of the Xanthomonas albilineans Cas2 in CRISPR-mediated adaptive immunity. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:054701. [PMID: 28612041 PMCID: PMC5438308 DOI: 10.1063/1.4984052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins constitute a microbial, adaptive immune system countering invading nucleic acids. Cas2 is a universal Cas protein found in all types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition into CRISPR loci. In subtype I-C CRISPR-Cas systems, Cas2 proteins are metal-dependent double-stranded DNA (dsDNA) nucleases, and a pH-dependent conformational transition has been proposed as a prerequisite for catalytic action. Here, we report the crystal structure of Xanthomonas albilineans Cas2 (XaCas2) and provide experimental evidence of a pH-dependent conformational change during functional activation. XaCas2 crystallized at an acidic pH represented a catalytically inactive conformational state in which two Asp8 residues were too far apart to coordinate a single catalytic metal ion. Consistently, XaCas2 exhibited dsDNA nuclease activity only under neutral and basic conditions. Despite the overall structural similarity of the two protomers, significant conformational heterogeneity was evident in the putative hinge regions, suggesting that XaCas2 engages in hinge-bending conformational switching. The presence of a Trp residue in the hinge region enabled the investigation of hinge dynamics by fluorescence spectroscopy. The pH dependence of the fluorescence intensity overlapped precisely with that of nuclease activity. Mutational analyses further suggested that conformational activation proceeded via a rigid-body hinge-bending motion as both D8E and hinge mutations significantly reduced nuclease activity. Together, our results reveal strong correlations between the conformational states, catalytic activity, and hinge dynamics of XaCas2, and provide structural and dynamic insights into the conformational activation of the nuclease function of Cas2.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Suji Hong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Ugeene Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Migyeong Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Nayoung Suh
- Department of Pharmaceutical Engineering, Soon Chun Hyang University, Asan 31538, South Korea
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Van Orden MJ, Klein P, Babu K, Najar FZ, Rajan R. Conserved DNA motifs in the type II-A CRISPR leader region. PeerJ 2017; 5:e3161. [PMID: 28392985 PMCID: PMC5382924 DOI: 10.7717/peerj.3161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/07/2017] [Indexed: 12/26/2022] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.
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Affiliation(s)
- Mason J Van Orden
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Peter Klein
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Kesavan Babu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Fares Z Najar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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Stout E, Klaenhammer T, Barrangou R. CRISPR-Cas Technologies and Applications in Food Bacteria. Annu Rev Food Sci Technol 2017; 8:413-437. [DOI: 10.1146/annurev-food-072816-024723] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.
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Affiliation(s)
- Emily Stout
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Todd Klaenhammer
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
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35
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Abstract
Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress. Increasingly, CRISPR-Cas systems, in particular the Type II systems containing the Cas9 endonuclease, have been exploited for their ability to bind desired nucleic acid sequences, as well as direct sequence-specific cleavage of their targets. Cas9-mediated genome engineering is transcending biological research as a versatile and portable platform for manipulating genetic content in myriad systems. Here, we present a systematic overview of CRISPR-Cas history and biology, highlighting the revolutionary tools derived from these systems, which greatly expand the molecular biologists' toolkit.
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Affiliation(s)
- Hannah K Ratner
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - Timothy R Sampson
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - David S Weiss
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329
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36
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Elhadi D, Lv L, Jiang XR, Wu H, Chen GQ. CRISPRi engineering E. coli for morphology diversification. Metab Eng 2016; 38:358-369. [DOI: 10.1016/j.ymben.2016.09.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/21/2016] [Accepted: 09/11/2016] [Indexed: 01/09/2023]
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37
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Shabbir MAB, Hao H, Shabbir MZ, Hussain HI, Iqbal Z, Ahmed S, Sattar A, Iqbal M, Li J, Yuan Z. Survival and Evolution of CRISPR-Cas System in Prokaryotes and Its Applications. Front Immunol 2016; 7:375. [PMID: 27725818 PMCID: PMC5035730 DOI: 10.3389/fimmu.2016.00375] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/07/2016] [Indexed: 12/12/2022] Open
Abstract
Prokaryotes have developed numerous innate immune mechanisms in order to fend off bacteriophage or plasmid attack. One of these immune systems is clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated proteins play a key role in survival of prokaryotes against invaders, as these systems cleave DNA of foreign genetic elements. Beyond providing immunity, these systems have significant impact in altering the bacterial physiology in term of its virulence and pathogenicity, as well as evolution. Also, due to their diverse nature of functionality, cas9 endoribonuclease can be easily reprogrammed with the help of guide RNAs, showing unprecedented potential and significance for gene editing in treating genetic diseases. Here, we also discuss the use of NgAgo–gDNA system in genome editing of human cells.
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Affiliation(s)
- Muhammad Abu Bakr Shabbir
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Muhammad Zubair Shabbir
- Quality Operations Laboratory at University of Veterinary and Animal Sciences Lahore , Pakistan
| | - Hafiz Iftikhar Hussain
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Zahid Iqbal
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Saeed Ahmed
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Adeel Sattar
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China; MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Mujahid Iqbal
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China; MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Jun Li
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Zonghui Yuan
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China; MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
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38
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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Künne T, Kieper SN, Bannenberg JW, Vogel AIM, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJJ. Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation. Mol Cell 2016; 63:852-64. [PMID: 27546790 DOI: 10.1016/j.molcel.2016.07.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/01/2016] [Accepted: 07/15/2016] [Indexed: 11/16/2022]
Abstract
Prokaryotes use a mechanism called priming to update their CRISPR immunological memory to rapidly counter revisiting, mutated viruses, and plasmids. Here we have determined how new spacers are produced and selected for integration into the CRISPR array during priming. We show that Cas3 couples CRISPR interference to adaptation by producing DNA breakdown products that fuel the spacer integration process in a two-step, PAM-associated manner. The helicase-nuclease Cas3 pre-processes target DNA into fragments of about 30-100 nt enriched for thymine-stretches in their 3' ends. The Cas1-2 complex further processes these fragments and integrates them sequence-specifically into CRISPR repeats by coupling of a 3' cytosine of the fragment. Our results highlight that the selection of PAM-compliant spacers during priming is enhanced by the combined sequence specificities of Cas3 and the Cas1-2 complex, leading to an increased propensity of integrating functional CTT-containing spacers.
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Affiliation(s)
- Tim Künne
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Sebastian N Kieper
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Jasper W Bannenberg
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Anne I M Vogel
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Willem R Miellet
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Misha Klein
- Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ, Delft, the Netherlands
| | - Martin Depken
- Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ, Delft, the Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Stan J J Brouns
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, the Netherlands; Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ, Delft, the Netherlands.
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40
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Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science 2016; 353:aad5147. [PMID: 27493190 DOI: 10.1126/science.aad5147] [Citation(s) in RCA: 388] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Adaptive immunity had been long thought of as an exclusive feature of animals. However, the discovery of the CRISPR-Cas defense system, present in almost half of prokaryotic genomes, proves otherwise. Because of the everlasting parasite-host arms race, CRISPR-Cas has rapidly evolved through horizontal transfer of complete loci or individual modules, resulting in extreme structural and functional diversity. CRISPR-Cas systems are divided into two distinct classes that each consist of three types and multiple subtypes. We discuss recent advances in CRISPR-Cas research that reveal elaborate molecular mechanisms and provide for a plausible scenario of CRISPR-Cas evolution. We also briefly describe the latest developments of a wide range of CRISPR-based applications.
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Affiliation(s)
- Prarthana Mohanraju
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, Netherlands.
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41
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Topuzlu E, Lawrence CM. Recognition of a pseudo-symmetric RNA tetranucleotide by Csx3, a new member of the CRISPR associated Rossmann fold superfamily. RNA Biol 2016; 13:254-7. [PMID: 26727591 DOI: 10.1080/15476286.2015.1130209] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The CRISPR/Cas adaptive immune system shows extreme diversity in the number of CRISPR/Cas types and subtypes, and in the multitude of CRISPR associated protein families of which they are composed. Despite this diversity, the roles of many Cas protein families are now defined with regard to spacer acquisition, crRNA biogenesis, and DNA or RNA surveillance and targeting. However, a number of unclassified CRISPR-Cas proteins remain. Such proteins have traditionally been designated as CRISPR subtype x (Csx). Here we revisit the structural analysis of one such protein, Csx3, and show that this homodimeric protein utilizes a Rossmann fold for the recognition of an RNA tetranucleotide. Tertiary and quaternary structural similarities of Csx3 to CRISPR/Cas proteins Csx1 and Csa3 are identified and suggest Csx3 is a new member of the CRISPR Associated Rossmann Fold (CARF) superfamily. The structure of the Csx3/RNA complex illustrates one way CARF domain proteins may recognize pseudo-symmetric polynucleotides.
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Affiliation(s)
- Ece Topuzlu
- a Department of Chemistry and Biochemistry , Montana State University , Bozeman , MT 59717 , USA
| | - C Martin Lawrence
- a Department of Chemistry and Biochemistry , Montana State University , Bozeman , MT 59717 , USA
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Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L. Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 2016; 44:5872-82. [PMID: 27216815 PMCID: PMC4937334 DOI: 10.1093/nar/gkw469] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/13/2016] [Indexed: 12/26/2022] Open
Abstract
Shewanella putrefaciens CN-32 contains a single Type I-Fv CRISPR-Cas system which confers adaptive immunity against bacteriophage infection. Three Cas proteins (Cas6f, Cas7fv, Cas5fv) and mature CRISPR RNAs were shown to be required for the assembly of an interference complex termed Cascade. The Cas protein-CRISPR RNA interaction sites within this complex were identified via mass spectrometry. Additional Cas proteins, commonly described as large and small subunits, that are present in all other investigated Cascade structures, were not detected. We introduced this minimal Type I system in Escherichia coli and show that it provides heterologous protection against lambda phage. The absence of a large subunit suggests that the length of the crRNA might not be fixed and recombinant Cascade complexes with drastically shortened and elongated crRNAs were engineered. Size-exclusion chromatography and small-angle X-ray scattering analyses revealed that the number of Cas7fv backbone subunits is adjusted in these shortened and extended Cascade variants. Larger Cascade complexes can still confer immunity against lambda phage infection in E. coli. Minimized Type I CRISPR-Cas systems expand our understanding of the evolution of Cascade assembly and diversity. Their adjustable crRNA length opens the possibility for customizing target DNA specificity.
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Affiliation(s)
- Daniel Gleditzsch
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Hanna Müller-Esparza
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Kundan Sharma
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany
| | - Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Henning Urlaub
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany
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43
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Friendly Fire: Biological Functions and Consequences of Chromosomal Targeting by CRISPR-Cas Systems. J Bacteriol 2016; 198:1481-6. [PMID: 26929301 DOI: 10.1128/jb.00086-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) systems in bacteria and archaea target foreign elements, such as bacteriophages and conjugative plasmids, through the incorporation of short sequences (termed spacers) from the foreign element into the CRISPR array, thereby allowing sequence-specific targeting of the invader. Thus, CRISPR-Cas systems are typically considered a microbial adaptive immune system. While many of these incorporated spacers match targets on bacteriophages and plasmids, a noticeable number are derived from chromosomal DNA. While usually lethal to the self-targeting bacteria, in certain circumstances, these self-targeting spacers can have profound effects in regard to microbial biology, including functions beyond adaptive immunity. In this minireview, we discuss recent studies that focus on the functions and consequences of CRISPR-Cas self-targeting, including reshaping of the host population, group behavior modification, and the potential applications of CRISPR-Cas self-targeting as a tool in microbial biotechnology. Understanding the effects of CRISPR-Cas self-targeting is vital to fully understanding the spectrum of function of these systems.
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44
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Shao Y, Richter H, Sun S, Sharma K, Urlaub H, Randau L, Li H. A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6. Structure 2016; 24:547-554. [PMID: 26996962 PMCID: PMC4823167 DOI: 10.1016/j.str.2016.02.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 02/05/2016] [Accepted: 02/17/2016] [Indexed: 01/07/2023]
Abstract
A subclass of recently discovered CRISPR repeat RNA in bacteria contains minimally recognizable structural features that facilitate an unknown mechanism of recognition and processing by the Cas6 family of endoribonucleases. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual site binding structure and a cleavage site conformation poised for phosphodiester bond breakage. Two non-interacting MmCas6b bind to two separate AAYAA motifs within the same repeat, one distal and one adjacent to the cleavage site. This bound structure potentially competes with a stable but non-productive RNA structure. At the cleavage site, MmCas6b supplies a base pair mimic to stabilize a short 2 base pair stem immediately upstream of the scissile phosphate. Complementary biochemical analyses support the dual-AAYAA binding model and a critical role of the protein-RNA base pair mimic. Our results reveal a previously unknown method of processing non-stem-loop CRISPR RNA by Cas6.
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Affiliation(s)
- Yaming Shao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hagen Richter
- Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Shengfang Sun
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Kundan Sharma
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany,LOEWE Center for Synthetic Microbiology (Synmikro), 35043 Marburg, Germany
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA,Correspondence should be addressed to H.L. ()
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45
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Wang P, Zhang B, Duan G, Wang Y, Hong L, Wang L, Guo X, Xi Y, Yang H. Bioinformatics analyses of Shigella CRISPR structure and spacer classification. World J Microbiol Biotechnol 2016; 32:38. [PMID: 26867599 DOI: 10.1007/s11274-015-2002-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 12/16/2015] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.
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Affiliation(s)
- Pengfei Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Bing Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China. .,Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, People's Republic of China.
| | - Yingfang Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.,Department of Public Health, College of Medical Sciences, Henan University of Science and Technology, Luoyang, 471023, Henan, People's Republic of China
| | - Lijuan Hong
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Linlin Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Xiangjiao Guo
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Yuanlin Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) is a prokaryotic adaptive immune system that is represented in most archaea and many bacteria. Among the currently known prokaryotic defense systems, the CRISPR-Cas genomic loci show unprecedented complexity and diversity. Classification of CRISPR-Cas variants that would capture their evolutionary relationships to the maximum possible extent is essential for comparative genomic and functional characterization of this theoretically and practically important system of adaptive immunity. To this end, a multipronged approach has been developed that combines phylogenetic analysis of the conserved Cas proteins with comparison of gene repertoires and arrangements in CRISPR-Cas loci. This approach led to the current classification of CRISPR-Cas systems into three distinct types and ten subtypes for each of which signature genes have been identified. Comparative genomic analysis of the CRISPR-Cas systems in new archaeal and bacterial genomes performed over the 3 years elapsed since the development of this classification makes it clear that new types and subtypes of CRISPR-Cas need to be introduced. Moreover, this classification system captures only part of the complexity of CRISPR-Cas organization and evolution, due to the intrinsic modularity and evolutionary mobility of these immunity systems, resulting in numerous recombinant variants. Moreover, most of the cas genes evolve rapidly, complicating the family assignment for many Cas proteins and the use of family profiles for the recognition of CRISPR-Cas subtype signatures. Further progress in the comparative analysis of CRISPR-Cas systems requires integration of the most sensitive sequence comparison tools, protein structure comparison, and refined approaches for comparison of gene neighborhoods.
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47
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Gallo G, Augusto G, Rangel G, Zelanis A, Mori MA, Campos CB, Würtele M. Structural basis for dimer formation of the CRISPR-associated protein Csm2 of Thermotoga maritima. FEBS J 2016; 283:694-703. [PMID: 26663887 DOI: 10.1111/febs.13621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/30/2015] [Accepted: 12/03/2015] [Indexed: 12/26/2022]
Abstract
UNLABELLED The clusters of regularly interspaced short palindromic repeats (CRISPR) and the Cas (CRISPR-associated) proteins form an adaptive immune system in bacteria and archaea that evolved as an RNA-guided interference mechanism to target and degrade foreign genetic elements. In the so-called type IIIA CRISPR-Cas systems, Cas proteins from the Csm family form a complex of RNPs that are involved in surveillance and targeting tasks. In the present study, we report the crystal structure of Thermotoga maritima Csm2. This protein is considered to assemble into the helically shaped Csm RNP complex in a site opposite to the CRISPR RNA binding backbone. Csm2 was solved via cadmium single wavelength anomalous diffraction phasing at 2.4 Å resolution. The structure reveals that Csm2 is composed of a large 42 amino-acid long α-helix flanked by three shorter α-helices. The structure also shows that the protein is capable of forming dimers mainly via an extensive contact surface conferred by its long α-helix. This interaction is further stabilized by the N-terminal helix, which is inserted into the C-terminal helical portion of the adjacent subunit. The dimerization of Csm2 was additionally confirmed by size exclusion chromatography of the pure recombinant protein followed by MS analysis of the eluted fractions. Because of its role in the assembly and functioning of the Csm CRISPR RNP complex, the crystal structure of Csm2 is of great importance for clarifying the mechanism of action of the subtype IIIA CRISPR-Cas system, as well as the similarities and diversities between the different CRISPR-Cas system. DATABASE The structure of Thermotoga maritima Csm2 has been deposited in the Protein Data Bank under accession code 5AN6.
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Affiliation(s)
- Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Gilles Augusto
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Giulliana Rangel
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - André Zelanis
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil.,Applied Toxinology Laboratory - LETA and Center of Toxins, Immune-response and Cell Signaling - CeTICS, Instituto Butantan, São Paulo, Brazil
| | - Marcelo A Mori
- Department of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - Cláudia B Campos
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
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48
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Ka D, Lee H, Jung YD, Kim K, Seok C, Suh N, Bae E. Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System. Structure 2015; 24:70-79. [PMID: 26671707 DOI: 10.1016/j.str.2015.10.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/25/2015] [Accepted: 10/20/2015] [Indexed: 11/27/2022]
Abstract
CRISPRs and Cas proteins constitute an RNA-guided microbial immune system against invading nucleic acids. Cas1 is a universal Cas protein found in all three types of CRISPR-Cas systems, and its role is implicated in new spacer acquisition during CRISPR-mediated adaptive immunity. Here, we report the crystal structure of Streptococcus pyogenes Cas1 (SpCas1) in a type II CRISPR-Cas system and characterize its interaction with S. pyogenes Csn2 (SpCsn2). The SpCas1 structure reveals a unique conformational state distinct from type I Cas1 structures, resulting in a more extensive dimerization interface, a more globular overall structure, and a disruption of potential metal-binding sites for catalysis. We demonstrate that SpCas1 directly interacts with SpCsn2, and identify the binding interface and key residues for Cas complex formation. These results provide structural information for a type II Cas1 protein, and lay a foundation for studying multiprotein Cas complexes functioning in type II CRISPR-Cas systems.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Hasup Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Yi-Deun Jung
- Stem Cell Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea
| | - Kyunggon Kim
- Clinical Proteomics Core Lab, Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea; Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Nayoung Suh
- Stem Cell Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Korea; Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 138-736, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea; Center for Food and Bioconvergence, Seoul National University, Seoul 151-921, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
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49
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Abstract
Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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50
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Dwarakanath S, Brenzinger S, Gleditzsch D, Plagens A, Klingl A, Thormann K, Randau L. Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens. Nucleic Acids Res 2015; 43:8913-23. [PMID: 26350210 PMCID: PMC4605320 DOI: 10.1093/nar/gkv882] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/26/2022] Open
Abstract
Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minimal variant of the Type I-F system was identified in proteobacterial species including Shewanella putrefaciens CN-32. This variant lacks a large subunit (Csy1), Csy2 and Csy3 and contains two unclassified cas genes. The genome of S. putrefaciens CN-32 contains only five Cas proteins (Cas1, Cas3, Cas6f, Cas1821 and Cas1822) and a single CRISPR array with 81 spacers. RNA-Seq analyses revealed the transcription of this array and the maturation of crRNAs (CRISPR RNAs). Interference assays based on plasmid conjugation demonstrated that this CRISPR-Cas system is active in vivo and that activity is dependent on the recognition of the dinucleotide GG PAM (Protospacer Adjacent Motif) sequence and crRNA abundance. The deletion of cas1821 and cas1822 reduced the cellular crRNA pool. Recombinant Cas1821 was shown to form helical filaments bound to RNA molecules, which suggests its role as the Cascade backbone protein. A Cascade complex was isolated which contained multiple Cas1821 copies, Cas1822, Cas6f and mature crRNAs.
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Affiliation(s)
- Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - Susanne Brenzinger
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Hessen D-35392, Germany
| | - Daniel Gleditzsch
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - André Plagens
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I, Biocentre LMU Munich, Großhaderner Str. 2-4, Planegg-Martinsried D-82152, Germany
| | - Kai Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Hessen D-35392, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany LOEWE Center for Synthetic Microbiology (Synmikro), Marburg, Hessen D-35043, Germany
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