1
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Zheng C, Liang H, Dai L, Yu J, Long C. Dissecting the CRISPR Cas1-Cas2 Protospacer Binding and Selection Mechanism by Using Molecular Dynamics Simulations. J Phys Chem B 2024; 128:3563-3574. [PMID: 38573978 DOI: 10.1021/acs.jpcb.3c07320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Cas1 and Cas2 are highly conserved proteins among the clustered regularly interspaced short palindromic repeat Cas (CRISPR-Cas) systems and play a crucial role in protospacer selection and integration. According to the double-forked CRISPR Cas1-Cas2 complex, we conducted extensive all-atom molecular dynamics simulations to investigate the protospacer DNA binding and recognition. Our findings revealed that single-point amino acid mutations in Cas1 or in Cas2 had little impact on the binding of the protospacer, both in the binding and precatalytic states. In contrast, multiple-point amino acid mutations, particularly G74A, P80L, and V89A mutations on Cas2 and Cas2' proteins (m-multiple1 system), significantly affected the protospacer binding and selection. Notably, mutations on Cas2 and Cas2' led to an increased number of hydrogen bonds (#HBs) between Cas2&Cas2' and the dsDNA in the m-multiple1 system compared with the wild-type system. And the strong electrostatic interactions between Cas1-Cas2 and the protospacer DNA (psDNA) in the m-multiple1 system again suggested the increase in the binding affinity of protospacer acquisition. Specifically, mutations in Cas2 and Cas2' can remotely make the protospacer adjacent motif complementary (PAMc) sequences better in recognition by the two active sites, while multiple mutations K211E, P202Q, P212L, R138L, V134A, A286T, P282H, and P294H on Cas1a/Cas1b&Cas1a'/Cas1b' (m-multiple2 system) decrease the #HBs and the electrostatic interactions and make the PAMc worse in recognition compared with the wild-type system.
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Affiliation(s)
- Chuanbo Zheng
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Hongqiong Liang
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Liqiang Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California 92697, United States
| | - Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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2
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Wimmer F, Englert F, Wandera KG, Alkhnbashi O, Collins S, Backofen R, Beisel C. Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation. Nucleic Acids Res 2024; 52:769-783. [PMID: 38015466 PMCID: PMC10810201 DOI: 10.1093/nar/gkad1097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023] Open
Abstract
CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host's genomic DNA, leading to lethal self-targeting. While self-targeting can be circumvented through different mechanisms, natural examples remain poorly explored. Here, we investigate extensive self-targeting by two CRISPR-Cas systems encoding 24 self-targeting spacers in the plant pathogen Xanthomonas albilineans. We show that the native I-C and I-F1 systems are actively expressed and that CRISPR RNAs are properly processed. When expressed in Escherichia coli, each Cascade complex binds its PAM-flanked DNA target to block transcription, while the addition of Cas3 paired with genome targeting induces cell killing. While exploring how X. albilineans survives self-targeting, we predicted putative anti-CRISPR proteins (Acrs) encoded within the bacterium's genome. Screening of identified candidates with cell-free transcription-translation systems and in E. coli revealed two Acrs, which we named AcrIC11 and AcrIF12Xal, that inhibit the activity of Cas3 but not Cascade of the respective system. While AcrF12Xal is homologous to AcrIF12, AcrIC11 shares sequence and structural homology with the anti-restriction protein KlcA. These findings help explain tolerance of self-targeting through two CRISPR-Cas systems and expand the known suite of DNA degradation-inhibiting Acrs.
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Affiliation(s)
- Franziska Wimmer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Frank Englert
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Katharina G Wandera
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Omer S Alkhnbashi
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
- Interdisciplinary Research Center for Intelligent Secure Systems (IRC-ISS), King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
| | - Scott P Collins
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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3
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Liu C, Wang R, Li J, Cheng F, Shu X, Zhao H, Xue Q, Yu H, Wu A, Wang L, Hu S, Zhang Y, Yang J, Xiang H, Li M. Widespread RNA-based cas regulation monitors crRNA abundance and anti-CRISPR proteins. Cell Host Microbe 2023; 31:1481-1493.e6. [PMID: 37659410 DOI: 10.1016/j.chom.2023.08.005] [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: 03/23/2023] [Revised: 07/04/2023] [Accepted: 08/09/2023] [Indexed: 09/04/2023]
Abstract
CRISPR RNAs (crRNAs) and Cas proteins work together to provide prokaryotes with adaptive immunity against genetic invaders like bacteriophages and plasmids. However, the coordination of crRNA production and cas expression remains poorly understood. Here, we demonstrate that widespread modulatory mini-CRISPRs encode cas-regulating RNAs (CreRs) that mediate autorepression of type I-B, I-E, and V-A Cas proteins, based on their limited complementarity to cas promoters. This autorepression not only reduces autoimmune risks but also responds to changes in the abundance of canonical crRNAs that compete with CreR for Cas proteins. Furthermore, the CreR-guided autorepression of Cas proteins can be alleviated or even subverted by diverse bacteriophage anti-CRISPR (Acr) proteins that inhibit Cas effectors, which, in turn, promotes the generation of new Cas proteins. Our findings reveal a general RNA-guided autorepression paradigm for diverse Cas effectors, shedding light on the intricate self-coordination of CRISPR-Cas and its transcriptional counterstrategy against Acr proteins.
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Affiliation(s)
- Chao Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feiyue Cheng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xian Shu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Huiwei Zhao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qiong Xue
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Aici Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lingyun Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Sushu Hu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yihan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Hebei University, Baoding, Hebei, China
| | - Jun Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China.
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; College of Life Science, University of Chinese Academy of Sciences, Beijing, China.
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4
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Yosef I, Mahata T, Goren MG, Degany OJ, Ben-Shem A, Qimron U. Highly active CRISPR-adaptation proteins revealed by a robust enrichment technology. Nucleic Acids Res 2023; 51:7552-7562. [PMID: 37326009 PMCID: PMC10415146 DOI: 10.1093/nar/gkad510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Natural prokaryotic defense via the CRISPR-Cas system requires spacer integration into the CRISPR array in a process called adaptation. To search for adaptation proteins with enhanced capabilities, we established a robust perpetual DNA packaging and transfer (PeDPaT) system that uses a strain of T7 phage to package plasmids and transfer them without killing the host, and then uses a different strain of T7 phage to repeat the cycle. We used PeDPaT to identify better adaptation proteins-Cas1 and Cas2-by enriching mutants that provide higher adaptation efficiency. We identified two mutant Cas1 proteins that show up to 10-fold enhanced adaptation in vivo. In vitro, one mutant has higher integration and DNA binding activities, and another has a higher disintegration activity compared to the wild-type Cas1. Lastly, we showed that their specificity for selecting a protospacer adjacent motif is decreased. The PeDPaT technology may be used for many robust screens requiring efficient and effortless DNA transduction.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tridib Mahata
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Or J Degany
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Adam Ben-Shem
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA. Genome expansion by a CRISPR trimmer-integrase. Nature 2023:10.1038/s41586-023-06178-2. [PMID: 37316664 DOI: 10.1038/s41586-023-06178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity1. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1-Cas2 integrase is necessary but not sufficient2-5. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation6,7, but many CRISPR-Cas systems lack Cas48. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1-Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited9,10 exonucleases for faithful acquisition of new CRISPR immune sequences.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Owen T Tuck
- Department of Chemistry, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Gary Li
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Julia Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
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6
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Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
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Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
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7
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Yarra SS, Ashok G, Mohan U. "Toehold Switches; a foothold for Synthetic Biology". Biotechnol Bioeng 2023; 120:932-952. [PMID: 36527224 DOI: 10.1002/bit.28309] [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: 02/18/2022] [Revised: 08/24/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Toehold switches are de novo designed riboregulators that contain two RNA components interacting through linear-linear RNA interactions, regulating the gene expression. These are highly versatile, exhibit excellent orthogonality, wide dynamic range, and are highly programmable, so can be used for various applications in synthetic biology. In this review, we summarized and discussed the design characteristics and benefits of toehold switch riboregulators over conventional riboregulators. We also discussed applications and recent advancements of toehold switch riboregulators in various fields like gene editing, DNA nanotechnology, translational repression, and diagnostics (detection of microRNAs and some pathogens). Toehold switches, therefore, furnished advancement in synthetic biology applications in various fields with their prominent features.
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Affiliation(s)
- Sai Sumanjali Yarra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
| | - Ganapathy Ashok
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
| | - Utpal Mohan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
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8
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Wei W, Jiang X, Zhang L, Yan Y, Yan J, Xu L, Gao CH, Yang M. Regulation of CRISPR-Associated Genes by Rv1776c (CasR) in Mycobacterium tuberculosis. Biomolecules 2023; 13:biom13020400. [PMID: 36830769 PMCID: PMC9953421 DOI: 10.3390/biom13020400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/07/2023] [Accepted: 02/18/2023] [Indexed: 02/23/2023] Open
Abstract
The CRISPR-Cas system is an adaptive immune system for many bacteria and archaea to defend against foreign nucleic acid invasion, and this system is conserved in the genome of M. tuberculosis (Mtb). Although the CRISPR-Cas system-mediated immune defense mechanism has been revealed in Mtb, the regulation of cas gene expression is poorly understood. In this study, we identified a transcription factor, CasR (CRISPR-associated protein repressor, encoded by Rv1776c), and it could bind to the upstream DNA sequence of the CRISPR-Cas gene cluster and regulate the expression of cas genes. EMSA and ChIP assays confirmed that CasR could interact with the upstream sequence of the csm6 promoter, both in vivo and in vitro. Furthermore, DNA footprinting assay revealed that CasR recognized a 20 bp palindromic sequence motif and negatively regulated the expression of csm6. In conclusion, our research elucidates the regulatory effect of CasR on the expression of CRISPR-associated genes in mycobacteria, thus providing insight into gene expression regulation of the CRISPR-Cas system.
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Affiliation(s)
- Wenping Wei
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaofang Jiang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Correspondence: (Y.Y.); (M.Y.)
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chun-Hui Gao
- State Key Laboratory of Agricultural Microbiology, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Correspondence: (Y.Y.); (M.Y.)
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9
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Ben Yacoub T, Wohlschlegel J, Sahel JA, Zeitz C, Audo I. [CRISPR/Cas9: From research to therapeutic application]. J Fr Ophtalmol 2023; 46:398-407. [PMID: 36759244 DOI: 10.1016/j.jfo.2022.10.008] [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: 10/03/2022] [Revised: 10/12/2022] [Accepted: 10/21/2022] [Indexed: 02/10/2023]
Abstract
For several decades, genome engineering has raised interest among many researchers and physicians in the study of genetic disorders and their treatments. Compared to its predecessors, zinc-finger nucleases (ZFN) and transcription activator-like effectors (TALEN), clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) is currently the most efficient molecular tool for genome editing. This system, originally identified as a bacterial adaptive immune system, is capable of cutting and modifying any gene of a large number of living organisms. Numerous trials using this technology are being developed to provide effective treatment for several diseases, such as cancer, cardiovascular and ophthalmic disorders. In research, this technology is increasingly used for genetic disease modelling, providing meaningful models of relevant studies as well as a better understanding of underlying pathological mechanisms. Many molecular tools are now available to put this technique into practice in laboratories, and despite the technical and ethical issues raised by manipulation of the genome, CRIPSR/Cas9 offers a new breath of hope for therapeutic research around the world.
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Affiliation(s)
- T Ben Yacoub
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France.
| | - J Wohlschlegel
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France
| | - J-A Sahel
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France; CHNO des Quinze-Vingts, Inserm-DGOS CIC 1423, 75012 Paris, France; Department of ophthalmology, fondation ophtalmologique Adolphe De Rothschild, 75019 Paris, France; Department of ophthalmology, the university of Pittsburgh School of Medicine, Pittsburgh PA 15213, United States; Académie des sciences, institut de France, 75006 Paris, France
| | - C Zeitz
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France
| | - I Audo
- Sorbonne université, Inserm, CNRS, institut de la Vision, 75012 Paris, France; CHNO des Quinze-Vingts, Inserm-DGOS CIC 1423, 75012 Paris, France; Institute of ophthalmology, university College of London, London EC1V 9EL, United Kingdom
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10
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Vasileva A, Selkova P, Arseniev A, Abramova M, Shcheglova N, Musharova O, Mizgirev I, Artamonova T, Khodorkovskii M, Severinov K, Fedorova I. Characterization of CoCas9 nuclease from Capnocytophaga ochracea. RNA Biol 2023; 20:750-759. [PMID: 37743659 PMCID: PMC10521337 DOI: 10.1080/15476286.2023.2256578] [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] [Accepted: 08/31/2023] [Indexed: 09/26/2023] Open
Abstract
Cas9 nucleases are widely used for genome editing and engineering. Cas9 enzymes encoded by CRISPR-Cas defence systems of various prokaryotic organisms possess different properties such as target site preferences, size, and DNA cleavage efficiency. Here, we biochemically characterized CoCas9 from Capnocytophaga ochracea, a bacterium that inhabits the oral cavity of humans and contributes to plaque formation on teeth. CoCas9 recognizes a novel 5'-NRRWC-3' PAM and efficiently cleaves DNA in vitro. Functional characterization of CoCas9 opens ways for genetic engineering of C. ochracea using its endogenous CRISPR-Cas system. The novel PAM requirement makes CoCas9 potentially useful in genome editing applications.
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Affiliation(s)
- A. Vasileva
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - P. Selkova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - A. Arseniev
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - M. Abramova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - N. Shcheglova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - O. Musharova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - I. Mizgirev
- Laboratory of Carcinogenesis and Aging, N.N. Petrov National Medical Research Center of Oncology, St. Petersburg, Russia
| | - T. Artamonova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - M. Khodorkovskii
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - K. Severinov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia
- Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - I. Fedorova
- Center of Nanobiotechnology, Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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11
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Qiu X, Liu C, Zhu C, Zhu L. MicroRNA Detection with CRISPR/Cas. Methods Mol Biol 2023; 2630:25-45. [PMID: 36689174 DOI: 10.1007/978-1-0716-2982-6_3] [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] [Indexed: 01/24/2023]
Abstract
Low-cost detection of miRNAs has caught broad attention in recent years due to the potential application of these small noncoding RNAs for diagnostics and therapeutic purposes. Their small size and low abundance, however, derive challenges in engineering robust detection tools. To date, multiple detection assays have been developed to achieve highly specific recognition of trace amount of miRNA with state-of-the-art nucleic acid detection and signal amplification techniques. In this chapter we describe how isothermal amplification techniques and CRISPR/Cas-based techniques can be integrated to generate rationally designed miRNA detection systems for specific miRNA.
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Affiliation(s)
- Xinyuan Qiu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China
| | - Chushu Zhu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China.
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12
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Zhao L, Qiu M, Li X, Yang J, Li J. CRISPR-Cas13a system: A novel tool for molecular diagnostics. Front Microbiol 2022; 13:1060947. [PMID: 36569102 PMCID: PMC9772028 DOI: 10.3389/fmicb.2022.1060947] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is a natural adaptive immune system of prokaryotes. The CRISPR-Cas system is currently divided into two classes and six types: types I, III, and IV in class 1 systems and types II, V, and VI in class 2 systems. Among the CRISPR-Cas type VI systems, the CRISPR/Cas13a system has been the most widely characterized for its application in molecular diagnostics, gene therapy, gene editing, and RNA imaging. Moreover, because of the trans-cleavage activity of Cas13a and the high specificity of its CRISPR RNA, the CRISPR/Cas13a system has enormous potential in the field of molecular diagnostics. Herein, we summarize the applications of the CRISPR/Cas13a system in the detection of pathogens, including viruses, bacteria, parasites, chlamydia, and fungus; biomarkers, such as microRNAs, lncRNAs, and circRNAs; and some non-nucleic acid targets, including proteins, ions, and methyl groups. Meanwhile, we highlight the working principles of some novel Cas13a-based detection methods, including the Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) and its improved versions, Cas13a-based nucleic acid amplification-free biosensors, and Cas13a-based biosensors for non-nucleic acid target detection. Finally, we focus on some issues that need to be solved and the development prospects of the CRISPR/Cas13a system.
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Affiliation(s)
- Lixin Zhao
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China,Institute of Immunology, PLA, Army Medical University, Chongqing, China
| | - Minyue Qiu
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China,Institute of Immunology, PLA, Army Medical University, Chongqing, China
| | - Xiaojia Li
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Juanzhen Yang
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Jintao Li
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China,Institute of Immunology, PLA, Army Medical University, Chongqing, China,*Correspondence: Jintao Li,
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Chaudhary M, Sharma P, Mukherjee TK. Applications of CRISPR/Cas technology against drug-resistant lung cancers: an update. Mol Biol Rep 2022; 49:11491-11502. [PMID: 36097111 DOI: 10.1007/s11033-022-07766-7] [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: 03/28/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022]
Abstract
Out of all the cancer types, the most prevalent one is lung cancer. Multiple genes and signaling pathways play role in the progression of lung cancer. Considering the wider prevalence and fatality of lung cancer it has become the focus of current cancer research. Though currently used approaches have shown positive results against lung cancer but success against non-small cell lung cancer (NSCLC) still looms as an enigma for the entire research fraternity. The development of resistance against inhibitors within a short span is one of the reasons responsible for the failure and relapse of lung cancer. Under these prevailing conditions genome/gene-editing technology using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated proteins (Cas), popularly known as CRISPR/Cas technology offers a convenient and flexible method for inducing precise changes within the lung cancer cell. Additionally, CRISPR-barcoding and CRISPR knockout screens at the genome-wide level can help in the functional investigation of specific mutations and identification of novel cancer drivers respectively. Several variants of the CRISPR/Cas system are being developed to limit off-targeting with enhanced precision. The present review article updates the usefulness of CRISPR/Cas technology against various types of lung cancers.
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Affiliation(s)
- Mayank Chaudhary
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Pooja Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Tapan Kumar Mukherjee
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India.
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14
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DNA Motifs and an Accessory CRISPR Factor Determine Cas1 Binding and Integration Activity in Sulfolobus islandicus. Int J Mol Sci 2022; 23:ijms231710178. [PMID: 36077578 PMCID: PMC9456107 DOI: 10.3390/ijms231710178] [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: 08/19/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
CRISPR-Cas systems empower prokaryotes with adaptive immunity against invasive mobile genetic elements. At the first step of CRISPR immunity adaptation, short DNA fragments from the invaders are integrated into CRISPR arrays at the leader-proximal end. To date, the mechanism of recognition of the leader-proximal end remains largely unknown. Here, in the Sulfolobus islandicus subtype I-A system, we show that mutations destroying the proximal region reduce CRISPR adaptation in vivo. We identify that a stem-loop structure is present on the leader-proximal end, and we demonstrate that Cas1 preferentially binds the stem-loop structure in vitro. Moreover, we demonstrate that the integrase activity of Cas1 is modulated by interacting with a CRISPR-associated factor Csa3a. When translocated to the CRISPR array, the Csa3a-Cas1 complex is separated by Csa3a binding to the leader-distal motif and Cas1 binding to the leader-proximal end. Mutation at the leader-distal motif reduces CRISPR adaptation efficiency, further confirming the in vivo function of leader-distal motif. Together, our results suggest a general model for binding of Cas1 protein to a leader motif and modulation of integrase activity by an accessory factor.
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15
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Ilyina TS. Adaptive Immunity Systems of Bacteria: Association with Self-Synthesizing Transposons, Polyfunctionality. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2022. [DOI: 10.3103/s0891416822030065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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16
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Cheng F, Wu A, Liu C, Cao X, Wang R, Shu X, Wang L, Zhang Y, Xiang H, Li M. The toxin-antitoxin RNA guards of CRISPR-Cas evolved high specificity through repeat degeneration. Nucleic Acids Res 2022; 50:9442-9452. [PMID: 36018812 PMCID: PMC9458426 DOI: 10.1093/nar/gkac712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/30/2022] [Accepted: 08/10/2022] [Indexed: 12/24/2022] Open
Abstract
Recent discovery of ectopic repeats (outside CRISPR arrays) provided unprecedented insights into the nondefense roles of CRISPR-Cas. A striking example is the addiction module CreTA (CRISPR-regulated toxin-antitoxins), where one or two (in most cases) ectopic repeats produce CRISPR-resembling antitoxic (CreA) RNAs that direct the CRISPR effector Cascade to transcriptionally repress a toxic RNA (CreT). Here, we demonstrated that CreTA repeats are extensively degenerated in sequence, with the first repeat (ψR1) being more diverged than the second one (ψR2). As a result, such addiction modules become highly specific to their physically-linked CRISPR-Cas loci, and in most cases, CreA could not harness a heterologous CRISPR-Cas to suppress its cognate toxin. We further disclosed that this specificity primarily derives from the degeneration of ψR1, and could generally be altered by modifying this repeat element. We also showed that the degenerated repeats of CreTA were insusceptible to recombination and thus more stable compared to a typical CRISPR array, which could be exploited to develop highly stable CRISPR-based tools. These data illustrated that repeat degeneration (a common feature of ectopic repeats) improves the stability and specificity of CreTA in protecting CRISPR-Cas, which could have contributed to the widespread occurrence and deep diversification of CRISPR systems.
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Affiliation(s)
| | | | | | - Xifeng Cao
- School of life Sciences, Hebei University, Baoding, Hebei, China
| | - Rui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xian Shu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lingyun Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China,College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Yihan Zhang
- School of life Sciences, Hebei University, Baoding, Hebei, China,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- Correspondence may also be addressed to Hua Xiang.
| | - Ming Li
- To whom correspondence should be addressed. Tel: +86 10 64807064; Fax: +86 10 64807064;
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17
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Shu X, Zhang D, Li X, Zheng Q, Cai X, Ding S, Yan Y. Integrating CRISPR-Cas12a with a crRNA-Mediated Catalytic Network for the Development of a Modular and Sensitive Aptasensor. ACS Synth Biol 2022; 11:2829-2836. [PMID: 35946354 DOI: 10.1021/acssynbio.2c00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a, which exhibits excellent target DNA-activated trans-cleavage activity under the guidance of a programmable CRISPR RNA (crRNA), has shown great promise in next-generation biosensing technology. However, current CRISPR-Cas12a-based biosensors usually improve sensitivity by the initial nucleic acid amplification, while the distinct programmability and predictability of the crRNA-guided target binding process has not been fully exploited. Herein, we, for the first time, propose a modular and sensitive CRISPR-Cas12a fluorometric aptasensor by integrating an enzyme-free and robust crRNA-mediated catalytic nucleic acid network, namely, Cas12a-CMCAN, in which crRNA acts as an initiator to actuate cascade toehold-mediated strand displacement reactions (TM-SDRs). As a proof of concept, adenosine triphosphate (ATP) was selected as a model target. Owing to the multiturnover of CRISPR-Cas12a trans-cleavage and the inherent recycling amplification network, this method achieved a limit of detection value of 0.16 μM (20-fold lower than direct Cas12a-based ATP detection) with a linear range from 0.30 to 175 μM. In addition, Cas12a-CMCAN can be successfully employed to detect ATP levels in diluted human serum samples. Considering the simplicity, sensitivity, and easy to tune many targets by changing aptamer sequences, the Cas12a-CMCAN sensing method is expected to offer a heuristic idea for the development of CRISPR-Cas12a-based biosensors and unlock its potential for general and convenient molecule diagnostics.
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Affiliation(s)
- Xiaojia Shu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Decai Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Xingrong Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Qingyuan Zheng
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoying Cai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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18
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Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics. Signal Transduct Target Ther 2022; 7:199. [PMID: 35752612 PMCID: PMC9233671 DOI: 10.1038/s41392-022-01056-1] [Citation(s) in RCA: 241] [Impact Index Per Article: 120.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 06/04/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is a Gram-negative opportunistic pathogen that infects patients with cystic fibrosis, burn wounds, immunodeficiency, chronic obstructive pulmonary disorder (COPD), cancer, and severe infection requiring ventilation, such as COVID-19. P. aeruginosa is also a widely-used model bacterium for all biological areas. In addition to continued, intense efforts in understanding bacterial pathogenesis of P. aeruginosa including virulence factors (LPS, quorum sensing, two-component systems, 6 type secretion systems, outer membrane vesicles (OMVs), CRISPR-Cas and their regulation), rapid progress has been made in further studying host-pathogen interaction, particularly host immune networks involving autophagy, inflammasome, non-coding RNAs, cGAS, etc. Furthermore, numerous technologic advances, such as bioinformatics, metabolomics, scRNA-seq, nanoparticles, drug screening, and phage therapy, have been used to improve our understanding of P. aeruginosa pathogenesis and host defense. Nevertheless, much remains to be uncovered about interactions between P. aeruginosa and host immune responses, including mechanisms of drug resistance by known or unannotated bacterial virulence factors as well as mammalian cell signaling pathways. The widespread use of antibiotics and the slow development of effective antimicrobials present daunting challenges and necessitate new theoretical and practical platforms to screen and develop mechanism-tested novel drugs to treat intractable infections, especially those caused by multi-drug resistance strains. Benefited from has advancing in research tools and technology, dissecting this pathogen's feature has entered into molecular and mechanistic details as well as dynamic and holistic views. Herein, we comprehensively review the progress and discuss the current status of P. aeruginosa biophysical traits, behaviors, virulence factors, invasive regulators, and host defense patterns against its infection, which point out new directions for future investigation and add to the design of novel and/or alternative therapeutics to combat this clinically significant pathogen.
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Hawsawi YM, Shams A, Theyab A, Siddiqui J, Barnawee M, Abdali WA, Marghalani NA, Alshelali NH, Al-Sayed R, Alzahrani O, Alqahtani A, Alsulaiman AM. The State-of-the-Art of Gene Editing and its Application to Viral Infections and Diseases Including COVID-19. Front Cell Infect Microbiol 2022; 12:869889. [PMID: 35782122 PMCID: PMC9241565 DOI: 10.3389/fcimb.2022.869889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Gene therapy delivers a promising hope to cure many diseases and defects. The discovery of gene-editing technology fueled the world with valuable tools that have been employed in various domains of science, medicine, and biotechnology. Multiple means of gene editing have been established, including CRISPR/Cas, ZFNs, and TALENs. These strategies are believed to help understand the biological mechanisms of disease progression. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been designated the causative virus for coronavirus disease 2019 (COVID-19) that emerged at the end of 2019. This viral infection is a highly pathogenic and transmissible disease that caused a public health pandemic. As gene editing tools have shown great success in multiple scientific and medical areas, they could eventually contribute to discovering novel therapeutic and diagnostic strategies to battle the COVID-19 pandemic disease. This review aims to briefly highlight the history and some of the recent advancements of gene editing technologies. After that, we will describe various biological features of the CRISPR-Cas9 system and its diverse implications in treating different infectious diseases, both viral and non-viral. Finally, we will present current and future advancements in combating COVID-19 with a potential contribution of the CRISPR system as an antiviral modality in this battle.
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Affiliation(s)
- Yousef M. Hawsawi
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- *Correspondence: Yousef M. Hawsawi, ; Anwar Shams, ;
| | - Anwar Shams
- Department of Pharmacology, College of Medicine, Taif University, Mecca, Saudi Arabia
- *Correspondence: Yousef M. Hawsawi, ; Anwar Shams, ;
| | - Abdulrahman Theyab
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia
| | - Jumana Siddiqui
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mawada Barnawee
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Wed A. Abdali
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Nada A. Marghalani
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Nada H. Alshelali
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Rawan Al-Sayed
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Othman Alzahrani
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Alanoud Alqahtani
- Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
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20
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Rawashdeh O, Rawashdeh RY, Kebede T, Kapp D, Ralescu A. Bio-informatic analysis of CRISPR protospacer adjacent motifs (PAMs) in T4 genome. BMC Genom Data 2022; 23:40. [PMID: 35655130 PMCID: PMC9161530 DOI: 10.1186/s12863-022-01056-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The existence of protospacer adjacent motifs (PAMs) sequences in bacteriophage genome is critical for the recognition and function of the clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) machinery system. We further elucidate the significance of PAMs and their function, particularly as a part of transcriptional regulatory regions in T4 bacteriophages. METHODS A scripting language was used to analyze a sequence of T4 phage genome, and a list of few selected PAMs. Mann-Whitney Wilcoxon (MWW) test was used to compare the sequence hits for the PAMs versus the hits of all the possible sequences of equal lengths. RESULTS The results of MWW test show that certain PAMs such as: 'NGG' and 'TATA' are preferably located at the core of phage promoters: around -10 position, whereas the position around -35 appears to have no detectable count variation of any of the tested PAMs. Among all tested PAMs, the following three sequences: 5'-GCTV-3', 5'-TTGAAT-3' and 5'-TTGGGT-3' have higher prevalence in essential genes. By analyzing all the possible ways of reading PAM sequences as codons for the corresponding amino acids, it was found that deduced amino acids of some PAMs have a significant tendency to prefer the surface of proteins. CONCLUSION These results provide novel insights into the location and the subsequent identification of the role of PAMs as transcriptional regulatory elements. Also, CRISPR targeting certain PAM sequences is somehow likely to be connected to the hydrophilicity (water solubility) of amino acids translated from PAM's triplets. Therefore, these amino acids are found at the interacting unit at protein-protein interfaces.
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Affiliation(s)
- Omar Rawashdeh
- Department of Electrical Engineering and Computer Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Rabeah Y. Rawashdeh
- Department of Biological Sciences, Yarmouk University, Shafiq Irshidat Street, Irbid, 21163 Jordan
| | | | | | - Anca Ralescu
- Department of Electrical Engineering and Computer Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
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21
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Goyzueta-Mamani LD, Chávez-Fumagalli MA, Alvarez-Fernandez K, Aguilar-Pineda JA, Nieto-Montesinos R, Davila Del-Carpio G, Vera-Lopez KJ, Lino Cardenas CL. Alzheimer's Disease: A Silent Pandemic - A Systematic Review on the Situation and Patent Landscape of the Diagnosis. Recent Pat Biotechnol 2022; 16:355-378. [PMID: 35400333 DOI: 10.2174/1872208316666220408114129] [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: 07/16/2021] [Revised: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is characterized by cognitive impairment, tau protein deposits, and amyloid beta plaques. AD impacted 44 million people in 2016, and it is estimated to affect 100 million people by 2050. AD is disregarded as a pandemic compared with other diseases. To date, there is no effective treatment or diagnosis. OBJECTIVE We aimed to discuss the current tools used to diagnose COVID-19, to point out their potential to be adapted for AD diagnosis, and to review the landscape of existing patents in the AD field and future perspectives for AD diagnosis. METHOD We carried out a scientific screening following a research strategy in PubMed; Web of Science; the Derwent Innovation Index; the KCI-Korean Journal Database; SciELO; the Russian Science Citation index; and the CDerwent, EDerwent, and MDerwent index databases. RESULTS A total of 326 from 6,446 articles about AD and 376 from 4,595 articles about COVID-19 were analyzed. Of these, AD patents were focused on biomarkers and neuroimaging with no accurate, validated diagnostic methods, and only 7% of kit development patents were found. In comparison, COVID-19 patents were 60% about kit development for diagnosis; they are highly accurate and are now commercialized. CONCLUSION AD is still neglected and not recognized as a pandemic that affects the people and economies of all nations. There is a gap in the development of AD diagnostic tools that could be filled if the interest and effort that has been invested to tackle the COVID-19 emergency could also be applied for innovation.
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Affiliation(s)
- Luis Daniel Goyzueta-Mamani
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Miguel Angel Chávez-Fumagalli
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Karla Alvarez-Fernandez
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Jorge A Aguilar-Pineda
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Rita Nieto-Montesinos
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Gonzalo Davila Del-Carpio
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Karin J Vera-Lopez
- Laboratory of Genomics and Neurovascular Diseases, Vicerrectorado de investigacion, Universidad Catolica de Santa Maria, Arequipa, Peru
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
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22
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Horie M, Yamano-Adachi N, Kawabe Y, Kaneoka H, Fujita H, Nagamori E, Iwai R, Sato Y, Kanie K, Ohta S, Somiya M, Ino K. Recent advances in animal cell technologies for industrial and medical applications. J Biosci Bioeng 2022; 133:509-514. [DOI: 10.1016/j.jbiosc.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022]
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23
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Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
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24
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Duan G, Kan B, Li D, Song H. Editorial: The CRISPR/Cas System in Pathogen Resistance, Virulence, Diagnosis and Typing. Front Microbiol 2022; 13:832152. [PMID: 35308373 PMCID: PMC8927726 DOI: 10.3389/fmicb.2022.832152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/04/2022] [Indexed: 11/27/2022] Open
Affiliation(s)
- Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Biao Kan
- National Institute for Communicable Diseases Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongsheng Li
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Hongbin Song
- Center for Disease Control and Prevention of PLA, Beijing, China
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25
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Du K, Gong L, Li M, Yu H, Xiang H. Reprogramming the endogenous type I CRISPR-Cas system for simultaneous gene regulation and editing in Haloarcula hispanica. MLIFE 2022; 1:40-50. [PMID: 38818324 PMCID: PMC10989794 DOI: 10.1002/mlf2.12010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 06/01/2024]
Abstract
The type I system is the most widely distributed CRISPR-Cas system identified so far. Recently, we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in halophilic archaea. Here, we conducted a comprehensive study of the impact of redesigned crRNAs with different spacer lengths on gene regulation with the native type I-B CRISPR system in Haloarcula hispanica. When the spacer targeting the chromosomal gene was shortened from 36 to 28 bp, transformation efficiencies of the spacer-encoding plasmids were improved by over three orders of magnitude, indicating a significant loss of interference. However, by conducting whole-genome sequencing and measuring the growth curves of the hosts, we still detected DNA cleavage and its influence on cell growth. Intriguingly, when the spacer was shortened to 24 bp, the transcription of the target gene was downregulated to 10.80%, while both interference and primed adaptation disappeared. By modifying the lengths of the spacers, the expression of the target gene could be suppressed to varying degrees. Significantly, by designing crRNAs with different spacer lengths and targeting different genes, we achieved simultaneous gene editing (cdc6E) and gene regulation (crtB) for the first time with the endogenous type I CRISPR-Cas system.
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Affiliation(s)
- Kaixin Du
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Luyao Gong
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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26
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Zhang X, Garrett S, Graveley BR, Terns MP. Unique properties of spacer acquisition by the type III-A CRISPR-Cas system. Nucleic Acids Res 2021; 50:1562-1582. [PMID: 34893878 PMCID: PMC8860593 DOI: 10.1093/nar/gkab1193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Type III CRISPR-Cas systems have a unique mode of interference, involving crRNA-guided recognition of nascent RNA and leading to DNA and RNA degradation. How type III systems acquire new CRISPR spacers is currently not well understood. Here, we characterize CRISPR spacer uptake by a type III-A system within its native host, Streptococcus thermophilus. Adaptation by the type II-A system in the same host provided a basis for comparison. Cas1 and Cas2 proteins were critical for type III adaptation but deletion of genes responsible for crRNA biogenesis or interference did not detectably change spacer uptake patterns, except those related to host counter-selection. Unlike the type II-A system, type III spacers are acquired in a PAM- and orientation-independent manner. Interestingly, certain regions of plasmids and the host genome were particularly well-sampled during type III-A, but not type II-A, spacer uptake. These regions included the single-stranded origins of rolling-circle replicating plasmids, rRNA and tRNA encoding gene clusters, promoter regions of expressed genes and 5′ UTR regions involved in transcription attenuation. These features share the potential to form DNA secondary structures, suggesting a preferred substrate for type III adaptation. Lastly, the type III-A system adapted to and protected host cells from lytic phage infection.
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Affiliation(s)
- Xinfu Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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27
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Dixit B, Prakash A, Kumar P, Gogoi P, Kumar M. The core Cas1 protein of CRISPR-Cas I-B in Leptospira shows metal-tunable nuclease activity. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100059. [PMID: 34841349 PMCID: PMC8610301 DOI: 10.1016/j.crmicr.2021.100059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/26/2022] Open
Abstract
Leptospira interrogans serovar Copenhageni strain Fiocruz L1-130 is the causative agent of leptospirosis in animals and humans. This organism carries a functional cas1 gene classified under CRISPR-Cas I-B. In this study, using various nuclease assays and bioinformatics analysis, we report that the recombinant Cas1 (LinCas1) possesses metal-ion dependent DNase activity, which is inhibited upon substitution or chelation of metal-ion and/or interaction with recombinant Cas2 (LinCas2) of L. interrogans. Model of LinCas1 structure shows a shorter N-terminal domain unlike other Cas1 orthologs reported to date. The C-terminal domain of LinCas1 contains conserved divalent-metal binding residues (Glu108, His176, and Glu191) and the mutation of these residues leads to abolition in DNase activity. Immunoassay using anti-LinCas2 demonstrates that LinCas1 interacts with LinCas2 and attains a saturation point. Moreover, the nuclease activity of the LinCas1-Cas2 mixture on ds-DNA displayed a reduction in activity compared to the pure core LinCas proteins under in vitro condition. The DNase activity for LinCas1 is consistent with a role for this protein in the recognition/cleavage of foreign DNA and integration of foreign DNA as spacer into the CRISPR array.
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Affiliation(s)
- Bhuvan Dixit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Aman Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pankaj Kumar
- Division of Livestock and Fisheries Management, ICAR Research Complex for Eastern Region, Patna, Bihar 800014, India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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28
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Wang T, Zhang C, Zhang H, Zhu H. CRISPR/Cas9-Mediated Gene Editing Revolutionizes the Improvement of Horticulture Food Crops. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13260-13269. [PMID: 33734711 DOI: 10.1021/acs.jafc.1c00104] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Horticultural food crops are important sources of nutrients for humans. With the increase of the global population, enhanced horticulture food crop production has become a new challenge, and enriching their nutritional content has also been required. Gene editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), have accelerated crop improvement through the modification of targeted genomes precisely. Here, we review the development of various gene editors and compare their advantages and shortcomings, especially the newly emerging CRISPR/Cas systems, such as base editing and prime editing. We also summarize their practical applications in crop trait improvement, including yield, nutritional quality, and other consumer traits.
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Affiliation(s)
- Tian Wang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, People's Republic of China
| | - Hongyan Zhang
- College of Life Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Hongliang Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People's Republic of China
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29
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Hillary VE, Ignacimuthu S, Ceasar SA. Potential of CRISPR/Cas system in the diagnosis of COVID-19 infection. Expert Rev Mol Diagn 2021; 21:1179-1189. [PMID: 34409907 PMCID: PMC8607542 DOI: 10.1080/14737159.2021.1970535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Emerging novel infectious diseases and persistent pandemics with potential to destabilize normal life remain a public health concern for the whole world. The recent outbreak of pneumonia caused by Coronavirus infectious disease-2019 (COVID-19) resulted in high mortality due to a lack of effective drugs or vaccines. With a constantly increasing number of infections with mutated strains and deaths across the globe, rapid, affordable and specific detections with more accurate diagnosis and improved health treatments are needed to combat the spread of this novel pathogen COVID-19. AREAS COVERED Researchers have started to utilize the recently invented clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR/Cas)-based tools for the rapid detection of novel COVID-19. In this review, we summarize the potential of CRISPR/Cas system for the diagnosis and enablement of efficient control of COVID-19. EXPERT OPINION Multiple groups have demonstrated the potential of utilizing CRISPR-based diagnosis tools for the detection of SARS-CoV-2. In coming months, we expect more novel and rapid CRISPR-based kits for mass detection of COVID-19-infected persons within a fraction of a second. Therefore, we believe science will conquer COVID-19 in the near future.
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Affiliation(s)
- V. Edwin Hillary
- Division of Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | | | - S. Antony Ceasar
- Department of Biosciences, Bharath Institute of Higher Education and Research, Chennai, India
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, India
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30
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Cheng F, Wang R, Yu H, Liu C, Yang J, Xiang H, Li M. Divergent degeneration of creA antitoxin genes from minimal CRISPRs and the convergent strategy of tRNA-sequestering CreT toxins. Nucleic Acids Res 2021; 49:10677-10688. [PMID: 34551428 PMCID: PMC8501985 DOI: 10.1093/nar/gkab821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 11/13/2022] Open
Abstract
Aside from providing adaptive immunity, type I CRISPR-Cas was recently unearthed to employ a noncanonical RNA guide (CreA) to transcriptionally repress an RNA toxin (CreT). Here, we report that, for most archaeal and bacterial CreTA modules, the creA gene actually carries two flanking 'CRISPR repeats', which are, however, highly divergent and degenerated. By deep sequencing, we show that the two repeats give rise to an 8-nt 5' handle and a 22-nt 3' handle, respectively, i.e., the conserved elements of a canonical CRISPR RNA, indicating they both retained critical nucleotides for Cas6 processing during divergent degeneration. We also uncovered a minimal CreT toxin that sequesters the rare transfer RNA for isoleucine, tRNAIleCAU, with a six-codon open reading frame containing two consecutive AUA codons. To fully relieve its toxicity, both tRNAIleCAU overexpression and supply of extra agmatine (modifies the wobble base of tRNAIleCAU to decipher AUA codons) are required. By replacing AUA to AGA/AGG codons, we reprogrammed this toxin to sequester rare arginine tRNAs. These data provide essential information on CreTA origin and for future CreTA prediction, and enrich the knowledge of tRNA-sequestering small RNAs that are employed by CRISPR-Cas to get addictive to the host.
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Affiliation(s)
- Feiyue Cheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Rui Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
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31
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Campa AR, Smith LM, Hampton HG, Sharma S, Jackson SA, Bischler T, Sharma CM, Fineran PC. The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. Nucleic Acids Res 2021; 49:9508-9525. [PMID: 34403463 PMCID: PMC8450108 DOI: 10.1093/nar/gkab704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/29/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against phages and plasmids; however, pathways regulating their activity are not well defined. We recently developed a high-throughput genome-wide method (SorTn-seq) and used this to uncover CRISPR-Cas regulators. Here, we demonstrate that the widespread Rsm/Csr pathway regulates the expression of multiple CRISPR-Cas systems in Serratia (type I-E, I-F and III-A). The main pathway component, RsmA (CsrA), is an RNA-binding post-transcriptional regulator of carbon utilisation, virulence and motility. RsmA binds cas mRNAs and suppresses type I and III CRISPR-Cas interference in addition to adaptation by type I systems. Coregulation of CRISPR-Cas and flagella by the Rsm pathway allows modulation of adaptive immunity when changes in receptor availability would alter susceptibility to flagella-tropic phages. Furthermore, we show that Rsm controls CRISPR-Cas in other genera, suggesting conservation of this regulatory strategy. Finally, we identify genes encoding RsmA homologues in phages, which have the potential to manipulate the physiology of host bacteria and might provide an anti-CRISPR activity.
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Affiliation(s)
- Aroa Rey Campa
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Leah M Smith
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sahil Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Cynthia M Sharma
- Chair of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, 97080 Würzburg, Germany
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
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32
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Perčulija V, Lin J, Zhang B, Ouyang S. Functional Features and Current Applications of the RNA-Targeting Type VI CRISPR-Cas Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004685. [PMID: 34254038 PMCID: PMC8209922 DOI: 10.1002/advs.202004685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/26/2021] [Indexed: 05/14/2023]
Abstract
CRISPR-Cas systems are a form of prokaryotic adaptive immunity that employs RNA-guided endonucleases (Cas effectors) to cleave foreign genetic elements. Due to their simplicity, targeting programmability, and efficiency, single-effector CRISPR-Cas systems have great potential for application in research, biotechnology, and therapeutics. While DNA-targeting Cas effectors such as Cas9 and Cas12a have become indispensable tools for genome editing in the past decade, the more recent discovery of RNA-targeting CRISPR-Cas systems has opened the door for implementation of CRISPR-Cas technology in RNA manipulation. With an increasing number of studies reporting their application in transcriptome engineering, viral interference, nucleic acid detection, and RNA imaging, type VI CRISPR-Cas systems and the associated Cas13 effectors particularly hold promise as RNA-targeting or RNA-binding tools. However, even though previous structural and biochemical characterization provided a firm basis for leveraging type VI CRISPR-Cas systems into such tools, the lack of comprehension of certain mechanisms underlying their functions hinders more sophisticated and conventional use. This review will summarize current knowledge on structural and mechanistic properties of type VI CRISPR-Cas systems, give an overview on the reported applications, and discuss functional features that need further investigation in order to improve performance of Cas13-based tools.
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Affiliation(s)
- Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- International College of Chinese StudiesFujian Normal UniversityFuzhou350117China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)Qingdao266237China
- National Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
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33
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Wheatley MS, Yang Y. Versatile Applications of the CRISPR/Cas Toolkit in Plant Pathology and Disease Management. PHYTOPATHOLOGY 2021; 111:1080-1090. [PMID: 33356427 DOI: 10.1094/phyto-08-20-0322-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
New tools and advanced technologies have played key roles in facilitating basic research in plant pathology and practical approaches for disease management and crop health. Recently, the CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR-associated) system has emerged as a powerful and versatile tool for genome editing and other molecular applications. This review aims to introduce and highlight the CRISPR/Cas toolkit and its current and future impact on plant pathology and disease management. We will cover the rapidly expanding horizon of various CRISPR/Cas applications in the basic study of plant-pathogen interactions, genome engineering of plant disease resistance, and molecular diagnosis of diverse pathogens. Using the citrus greening disease as an example, various CRISPR/Cas-enabled strategies are presented to precisely edit the host genome for disease resistance, to rapidly detect the pathogen for disease management, and to potentially use gene drive for insect population control. At the cutting edge of nucleic acid manipulation and detection, the CRISPR/Cas toolkit will accelerate plant breeding and reshape crop production and disease management as we face the challenges of 21st century agriculture.
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Affiliation(s)
- Matthew S Wheatley
- Department of Plant Pathology and Environmental Microbiology, and the Huck Institute of the Life Sciences, the Pennsylvania State University, University Park, PA 16802
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, and the Huck Institute of the Life Sciences, the Pennsylvania State University, University Park, PA 16802
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34
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Long C, Dai L, E C, Da LT, Yu J. Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA and Cas2. Biophys J 2021; 120:3126-3137. [PMID: 34197800 PMCID: PMC8390960 DOI: 10.1016/j.bpj.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
Cas1 and Cas2 are highly conserved proteins across clustered-regularly-interspaced-short-palindromic-repeat-Cas systems and play a significant role in protospacer acquisition. Based on crystal structure of twofold symmetric Cas1-Cas2 in complex with dual-forked protospacer DNA (psDNA), we conducted all-atom molecular dynamics simulations to study the psDNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence, or PAMc, of Cas1-Cas2. In the simulation, we noticed that two active sites of Cas1 and Cas1’ bind asymmetrically to two identical PAMc on the psDNA captured from the crystal structure. For the modified psDNA containing only one PAMc, as that to be recognized by Cas1-Cas2 in general, our simulations show that the non-PAMc association site of Cas1-Cas2 remains destabilized until after the stably bound PAMc being cleaved at the corresponding association site. Thus, long-range correlation appears to exist upon the PAMc cleavage between the two active sites (∼10 nm apart) on Cas1-Cas2, which can be allosterically mediated by psDNA and Cas2 and Cas2’ in bridging. To substantiate such findings, we conducted repeated runs and further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high frequency in acquisition, respectively. Notably, such intersite correlation becomes even more pronounced for the Cas1-Cas2 in complex with psH but remains low for the Cas1-Cas2 in complex with psL. Hence, our studies demonstrate that PAMc recognition and cleavage at one active site of Cas1-Cas2 may allosterically regulate non-PAMc association or even cleavage at the other site, and such regulation can be mediated by noncatalytic Cas2 and DNA protospacer to possibly support the ensued psDNA acquisition.
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Affiliation(s)
- Chunhong Long
- School of Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Liqiang Dai
- Shenzhen JL Computational Science and Applied Research Institute, Shenzhen, China; Beijing Computational Science Research Center, Beijing, China
| | - Chao E
- Beijing Computational Science Research Center, Beijing, China
| | - Lin-Tai Da
- Shanghai Center for Systems Biomedicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Yu
- Departments of Physics and Astronomy and Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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35
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Genetically modified crop regulations: scope and opportunity using the CRISPR-Cas9 genome editing approach. Mol Biol Rep 2021; 48:4851-4863. [PMID: 34114124 DOI: 10.1007/s11033-021-06477-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Global demand for food is increasing day by day due to an increase in population and shrinkage of the arable land area. To meet this increasing demand, there is a need to develop high-yielding varieties that are nutritionally enriched and tolerant against environmental stresses. Various techniques are developed for improving crop quality such as mutagenesis, intergeneric crosses, and translocation breeding. Later, with the development of genetic engineering, genetically modified crops came up with the transgene insertion approach which helps to withstand adverse conditions. The process or product-focused approaches are used for regulating genetically modified crops with their risk analysis on the environment and public health. However, recent advances in gene-editing technologies have led to a new era of plant breeding by developing techniques including site-directed nucleases, zinc finger nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) that involve precise gene editing without the transfer of foreign genes. But these techniques always remain in debate for their regulation status and public acceptance. The European countries and New Zealand, consider the gene-edited plants under the category of genetically modified organism (GMO) regulation while the USA frees the gene-edited plants from such type of regulations. Considering them under the category of GMO makes a long and complicated approval process to use them, which would decrease their immediate commercial value. There is a need to develop strong regulatory approaches for emerging technologies that expedite crop research and attract people to adopt these new varieties without hesitation.
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36
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Taylor HN, Laderman E, Armbrust M, Hallmark T, Keiser D, Bondy-Denomy J, Jackson RN. Positioning Diverse Type IV Structures and Functions Within Class 1 CRISPR-Cas Systems. Front Microbiol 2021; 12:671522. [PMID: 34093491 PMCID: PMC8175902 DOI: 10.3389/fmicb.2021.671522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022] Open
Abstract
Type IV CRISPR systems encode CRISPR associated (Cas)-like proteins that combine with small RNAs to form multi-subunit ribonucleoprotein complexes. However, the lack of Cas nucleases, integrases, and other genetic features commonly observed in most CRISPR systems has made it difficult to predict type IV mechanisms of action and biological function. Here we summarize recent bioinformatic and experimental advancements that collectively provide the first glimpses into the function of specific type IV subtypes. We also provide a bioinformatic and structural analysis of type IV-specific proteins within the context of multi-subunit (class 1) CRISPR systems, informing future studies aimed at elucidating the function of these cryptic systems.
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Affiliation(s)
- Hannah N. Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Eric Laderman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Matt Armbrust
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Thomson Hallmark
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Dylan Keiser
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States
| | - Ryan N. Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, United States
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Li P, Wang L, Yang J, Di LJ, Li J. Applications of the CRISPR-Cas system for infectious disease diagnostics. Expert Rev Mol Diagn 2021; 21:723-732. [PMID: 33899643 DOI: 10.1080/14737159.2021.1922080] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Rapid and accurate diagnostic approaches are essential for impeding the spread of infectious diseases. This review aims to summarize current progress of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) systems in the applications for diagnostics of infectious diseases including the ongoing COVID-19 epidemic. AREAS COVERED In this review, we discuss class 2 CRISPR-Cas biosensing systems-based diagnostics in various emerging and reemerging infectious diseases, CRISPR-Cas systems have created a new era for early diagnostics of infectious diseases, especially with the discovery of the collateral cleavage activity of Cas12 and Cas13. We mainly focus on different CRISPR-Cas effectors for the detection of pathogenic microorganisms as well as provide a detailed explanation of the pros and cons of CRISPR-Cas biosensing systems. In addition, we also introduce future research perspectives. EXPERT COMMENTARY However, further improvement of newly discovered systems and engineering existing ones should be developed to increase the specificity, sensitivity or stability of the diagnostic tools. It may be a long journey to finish the clinical transition from research use. CRISPR-Cas approaches will emerge as more promising and robust tools for infectious disease diagnosis in the future.
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Affiliation(s)
- Peipei Li
- Kobilka Institute of Innovative Drug Discovery, Faculty of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Junning Yang
- Frontage Laboratories Inc, Exton, Pennsylvania, USA
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Jingjing Li
- Jinming Yu Academician Workstation of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
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Zhao R, Yang Y, Zheng F, Zeng Z, Feng W, Jin X, Wang J, Yang K, Liang YX, She Q, Han W. A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger. Cell Rep 2021; 32:108133. [PMID: 32937129 DOI: 10.1016/j.celrep.2020.108133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/21/2020] [Accepted: 08/20/2020] [Indexed: 12/26/2022] Open
Abstract
Type III CRISPR-Cas systems initiate an intracellular signaling pathway to confer immunity. The signaling pathway includes synthesis of cyclic oligo-adenylate (cOA) and activation of the RNase activity of type III accessory ribonuclease Csm6/Csx1 by cOA. After the immune response, cOA should be cleared on time to avoid constant cellular RNA degradation. In this study, we find a metal-dependent cOA degradation activity in Sulfolobus islandicus. The activity is associated with the cell membrane and able to accelerate cOA clearance at a high cOA level. Further, we show that a metal-dependent and membrane-associated DHH-DHHA1 family nuclease (MAD) rapidly cleaves cOA and deactivates Csx1 ribonuclease. The cOA degradation efficiency of MAD is much higher than the cellular ring nuclease. However, the subcellular organization may prevent it from degrading nascent cOA. Together, the data suggest that MAD acts as the second cOA degrader after the ring nuclease to remove diffused redundant cOA.
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Affiliation(s)
- Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yang Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Fan Zheng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Wenqian Feng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Xuexia Jin
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Jiayi Wang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237 Qingdao, China; Danish Archaea Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen Biocenter, 2200 Copenhagen N, Denmark
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, China.
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Prakash A, Kumar M. Characterizing the transcripts of Leptospira CRISPR I-B array and its processing with endoribonuclease LinCas6. Int J Biol Macromol 2021; 182:785-795. [PMID: 33862076 DOI: 10.1016/j.ijbiomac.2021.04.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/08/2021] [Accepted: 04/10/2021] [Indexed: 12/26/2022]
Abstract
In Leptospira interrogans serovar Copenhageni, the CRISPR-Cas I-B locus possesses a CRISPR array between the two independent cas-operons. Using the reverse transcription-PCR and the in vitro endoribonuclease assay with Cas6 of Leptospira (LinCas6), we account that the CRISPR is transcriptionally active and is conventionally processed. The LinCas6 specifically excises at one site within the synthetic cognate repeat RNA or the repeats of precursor-CRISPR RNA (pre-crRNA) in the sense direction. In contrast, the antisense repeat RNA is cleaved at multiple sites. LinCas6 functions as a single turnover endoribonuclease on its repeat RNA substrate, where substitution of one of predicted active site residues (His38) resulted in reduced activity. This study highlights the comprehensive understanding of the Leptospira CRISPR array transcription and its processing by LinCas6 that is central to RNA-mediated CRISPR-Cas I-B adaptive immunity.
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Affiliation(s)
- Aman Prakash
- 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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40
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Garrett SC. Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array. Front Microbiol 2021; 12:664299. [PMID: 33868219 PMCID: PMC8047081 DOI: 10.3389/fmicb.2021.664299] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/12/2021] [Indexed: 01/22/2023] Open
Abstract
CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes) is a type of prokaryotic immune system that is unique in its ability to provide sequence-specific adaptive protection, which can be updated in response to new threats. CRISPR-Cas does this by storing fragments of DNA from invading genetic elements in an array interspersed with short repeats. The CRISPR array can be continuously updated through integration of new DNA fragments (termed spacers) at one end, but over time existing spacers become obsolete. To optimize immunity, spacer uptake, residency, and loss must be regulated. This mini-review summarizes what is known about how spacers are organized, maintained, and lost from CRISPR arrays.
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Affiliation(s)
- Sandra C Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, United States
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41
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Abstract
CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader’s genome. CRISPR-Cas immune systems adapt to new threats by acquiring new spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition despite variation in spacer content between microbial strains. It has been suggested that such loci may use acquisition machinery from cooccurring CRISPR-Cas systems within the same strain. Here, following infection by a virulent phage with a double-stranded DNA (dsDNA) genome, we observed spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient CRISPR-Cas subtype VI-B system and a complete subtype II-C system. We show that the VI-B locus acquires spacers from both the bacterial and phage genomes, while the newly acquired II-C spacers mainly target the viral genome. Both loci preferably target the terminal end of the phage genome, with priming-like patterns around a preexisting II-C protospacer. Through gene deletion, we show that the RNA-cleaving VI-B system acquires spacers in trans using acquisition machinery from the DNA-cleaving II-C system. Our observations support the concept of cross talk between CRISPR-Cas systems and raise further questions regarding the plasticity of adaptation modules.
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Bhattacharjee G, Gohil N, Lam NL, Singh V. CRISPR-based diagnostics for detection of pathogens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:45-57. [PMID: 34127201 DOI: 10.1016/bs.pmbts.2021.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The improved sensitivity and superior specificity associated with the use of molecular assays has improved the fate of disease diagnosis by bestowing the clinicians with outcomes that are both rapid and precise. In recent years, CRISPR has made considerable progress in in vitro diagnostic platform which has paved its way for developing rapid and sensitive CRISPR-based diagnostic tools. Improved perception and better understanding of diverse CRISPR-Cas systems has broadened the reach of CRISPR applications for not just early detection of pathogens but also for early onset of diseases such as cancer. The inherent allele specificity of CRISPR is the predominant reason for its application in designing a diagnostic-tool that is field-deployable, portable, sensitive, specific and rapid. In this chapter, we highlight various CRISPR-based diagnostic platforms, its applications, challenges and future prospects of the CRISPR-Cas system.
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Affiliation(s)
- Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Navya Lavina Lam
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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Newsom S, Parameshwaran HP, Martin L, Rajan R. The CRISPR-Cas Mechanism for Adaptive Immunity and Alternate Bacterial Functions Fuels Diverse Biotechnologies. Front Cell Infect Microbiol 2021; 10:619763. [PMID: 33585286 PMCID: PMC7876343 DOI: 10.3389/fcimb.2020.619763] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/14/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial and archaeal CRISPR-Cas systems offer adaptive immune protection against foreign mobile genetic elements (MGEs). This function is regulated by sequence specific binding of CRISPR RNA (crRNA) to target DNA/RNA, with an additional requirement of a flanking DNA motif called the protospacer adjacent motif (PAM) in certain CRISPR systems. In this review, we discuss how the same fundamental mechanism of RNA-DNA and/or RNA-RNA complementarity is utilized by bacteria to regulate two distinct functions: to ward off intruding genetic materials and to modulate diverse physiological functions. The best documented examples of alternate functions are bacterial virulence, biofilm formation, adherence, programmed cell death, and quorum sensing. While extensive complementarity between the crRNA and the targeted DNA and/or RNA seems to constitute an efficient phage protection system, partial complementarity seems to be the key for several of the characterized alternate functions. Cas proteins are also involved in sequence-specific and non-specific RNA cleavage and control of transcriptional regulator expression, the mechanisms of which are still elusive. Over the past decade, the mechanisms of RNA-guided targeting and auxiliary functions of several Cas proteins have been transformed into powerful gene editing and biotechnological tools. We provide a synopsis of CRISPR technologies in this review. Even with the abundant mechanistic insights and biotechnology tools that are currently available, the discovery of new and diverse CRISPR types holds promise for future technological innovations, which will pave the way for precision genome medicine.
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Affiliation(s)
- Sydney Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Hari Priya Parameshwaran
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Lindsie Martin
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Structural Biology Center, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, OK, United States
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Nara PL, Sindelar D, Penn MS, Potempa J, Griffin WST. Porphyromonas gingivalis Outer Membrane Vesicles as the Major Driver of and Explanation for Neuropathogenesis, the Cholinergic Hypothesis, Iron Dyshomeostasis, and Salivary Lactoferrin in Alzheimer's Disease. J Alzheimers Dis 2021; 82:1417-1450. [PMID: 34275903 PMCID: PMC8461682 DOI: 10.3233/jad-210448] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/22/2022]
Abstract
Porphyromonas gingivalis (Pg) is a primary oral pathogen in the widespread biofilm-induced "chronic" multi-systems inflammatory disease(s) including Alzheimer's disease (AD). It is possibly the only second identified unique example of a biological extremophile in the human body. Having a better understanding of the key microbiological and genetic mechanisms of its pathogenesis and disease induction are central to its future diagnosis, treatment, and possible prevention. The published literature around the role of Pg in AD highlights the bacteria's direct role within the brain to cause disease. The available evidence, although somewhat adopted, does not fully support this as the major process. There are alternative pathogenic/virulence features associated with Pg that have been overlooked and may better explain the pathogenic processes found in the "infection hypothesis" of AD. A better explanation is offered here for the discrepancy in the relatively low amounts of "Pg bacteria" residing in the brain compared to the rather florid amounts and broad distribution of one or more of its major bacterial protein toxins. Related to this, the "Gingipains Hypothesis", AD-related iron dyshomeostasis, and the early reduced salivary lactoferrin, along with the resurrection of the Cholinergic Hypothesis may now be integrated into one working model. The current paper suggests the highly evolved and developed Type IX secretory cargo system of Pg producing outer membrane vesicles may better explain the observed diseases. Thus it is hoped this paper can provide a unifying model for the sporadic form of AD and guide the direction of research, treatment, and possible prevention.
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Affiliation(s)
| | | | - Marc S. Penn
- Summa Heart Health and Vascular Institute, Akron, OH, USA
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases in the School of Dentistry, University of Louisville, Louisville, KY, USA
| | - W. Sue T. Griffin
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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45
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New Strategies to Overcome Present CRISPR/Cas9 Limitations in Apple and Pear: Efficient Dechimerization and Base Editing. Int J Mol Sci 2020; 22:ijms22010319. [PMID: 33396822 PMCID: PMC7795782 DOI: 10.3390/ijms22010319] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 12/19/2022] Open
Abstract
Despite recent progress, the application of CRISPR/Cas9 in perennial plants still has many obstacles to overcome. Our previous results with CRISPR/Cas9 in apple and pear indicated the frequent production of phenotypic and genotypic chimeras, after editing of the phytoene desaturase (PDS) gene conferring albino phenotype. Therefore, our first objective was to determine if adding an adventitious regeneration step from leaves of the primary transgenic plants (T0) would allow a reduction in chimerism. Among hundreds of adventitious buds regenerated from a variegated T0 line, 89% were homogeneous albino. Furthermore, the analysis of the target zone sequences of twelve of these regenerated lines (RT0 for “regenerated T0” lines) indicated that 99% of the RT0 alleles were predicted to produce a truncated target protein and that 67% of RT0 plants had less heterogeneous editing profiles than the T0. Base editors are CRISPR/Cas9-derived new genome-editing tools that allow precise nucleotide substitutions without double-stranded breaks. Hence, our second goal was to demonstrate the feasibility of CRISPR/Cas9 base editing in apple and pear using two easily scorable genes: acetolactate synthase—ALS (conferring resistance to chlorsulfuron) and PDS. The two guide RNAs under MdU3 and MdU6 promoters were coupled into a cytidine base editor harboring a cytidine deaminase fused to a nickase Cas9. Using this vector; we induced C-to-T DNA substitutions in the target genes; leading to discrete variation in the amino-acid sequence and generating new alleles. By co-editing ALS and PDS genes; we successfully obtained chlorsulfuron resistant and albino lines in pear. Overall; our work indicates that a regeneration step can efficiently reduce the initial chimerism and could be coupled with the application of base editing to create accurate genome edits in perennial plants.
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46
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Pattharaprachayakul N, Lee M, Incharoensakdi A, Woo HM. Current understanding of the cyanobacterial CRISPR-Cas systems and development of the synthetic CRISPR-Cas systems for cyanobacteria. Enzyme Microb Technol 2020; 140:109619. [PMID: 32912679 DOI: 10.1016/j.enzmictec.2020.109619] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/14/2020] [Accepted: 06/05/2020] [Indexed: 11/20/2022]
Abstract
Cyanobacteria are photosynthetic microorganisms that are capable of converting CO2 to value-added chemicals. Engineering of cyanobacteria with synthetic biology tools, including the CRISPR-Cas system, has allowed an opportunity for biological CO2 utilization. Here, we described natural CRISPR-Cas systems for understanding cyanobacterial genomics and synthetic CRISPR-Cas systems for metabolic engineering applications. The natural CRISPR-Cas systems in cyanobacteria have been identified as Class 1, with type I and III, and some Class 2, with type V, as an adaptive immune system against viral invasion. As synthetic tools, CRISPR-Cas9 and -Cas12a have been successfully established in cyanobacteria to delete a target gene without a selection marker. Deactivated Cas9 and Cas12a have also been used to repress genes for metabolic engineering. In addition, a perspective on how advanced CRISPR-Cas systems and a pool of the guide RNAs can be advantageous for precise genome engineering and understanding of unknown functions was discussed for advanced engineering of cyanobacteria.
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Affiliation(s)
- Napisa Pattharaprachayakul
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea; Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330 Thailand; Program in Biotechnology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Mieun Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Aran Incharoensakdi
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330 Thailand
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea; BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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47
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Garrett S, Shiimori M, Watts EA, Clark L, Graveley BR, Terns MP. Primed CRISPR DNA uptake in Pyrococcus furiosus. Nucleic Acids Res 2020; 48:6120-6135. [PMID: 32421777 PMCID: PMC7293040 DOI: 10.1093/nar/gkaa381] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/15/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
CRISPR-Cas adaptive immune systems are used by prokaryotes to defend against invaders like viruses and other mobile genetic elements. Immune memories are stored in the form of 'spacers' which are short DNA sequences that are captured from invaders and added to the CRISPR array during a process called 'adaptation'. Spacers are transcribed and the resulting CRISPR (cr)RNAs assemble with different Cas proteins to form effector complexes that recognize matching nucleic acid and destroy it ('interference'). Adaptation can be 'naïve', i.e. independent of any existing spacer matches, or it can be 'primed', i.e. spurred by the crRNA-mediated detection of a complete or partial match to an invader sequence. Here we show that primed adaptation occurs in Pyrococcus furiosus. Although P. furiosus has three distinct CRISPR-Cas interference systems (I-B, I-A and III-B), only the I-B system and Cas3 were necessary for priming. Cas4, which is important for selection and processing of new spacers in naïve adaptation, was also essential for priming. Loss of either the I-B effector proteins or Cas3 reduced naïve adaptation. However, when Cas3 and all crRNP genes were deleted, uptake of correctly processed spacers was observed, indicating that none of these interference proteins are necessary for naïve adaptation.
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Affiliation(s)
- Sandra Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Masami Shiimori
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth A Watts
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Landon Clark
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Stem Cell Institute, UConn Health, Farmington, CT 06030, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.,Department of Microbiology, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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48
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Ye Q, Zhao X, Liu J, Zeng Z, Zhang Z, Liu T, Li Y, Han W, Peng N. CRISPR-Associated Factor Csa3b Regulates CRISPR Adaptation and Cmr-Mediated RNA Interference in Sulfolobus islandicus. Front Microbiol 2020; 11:2038. [PMID: 32983033 PMCID: PMC7480081 DOI: 10.3389/fmicb.2020.02038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Acquisition of spacers confers the CRISPR–Cas system with the memory to defend against invading mobile genetic elements. We previously reported that the CRISPR-associated factor Csa3a triggers CRISPR adaptation in Sulfolobus islandicus. However, a feedback regulation of CRISPR adaptation remains unclear. Here we show that another CRISPR-associated factor, Csa3b, binds a cyclic oligoadenylate (cOA) analog (5′-CAAAA-3′) and mutation at its CARF domain, which reduces the binding affinity. Csa3b also binds the promoter of adaptation cas genes, and the cOA analog enhances their binding probably by allosteric regulation. Deletion of the csa3b gene triggers spacer acquisition from both plasmid and viral DNAs, indicating that Csa3b acted as a repressor for CRISPR adaptation. Moreover, we also find that Csa3b activates the expression of subtype cmr-α and cmr-β genes according to transcriptome data and demonstrate that Csa3b binds the promoters of cmr genes. The deletion of the csa3b gene reduces Cmr-mediated RNA interference activity, indicating that Csa3b acts as a transcriptional activator for Cmr-mediated RNA interference. In summary, our findings reveal a novel pathway for the regulation of CRISPR adaptation and CRISPR–Cmr RNA interference in S. islandicus. Our results also suggest a feedback repression of CRIPSR adaptation by the Csa3b factor and the cOA signal produced by the Cmr complex at the CRISPR interference stage.
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Affiliation(s)
- Qing Ye
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xueqiao Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jilin Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhufeng Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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49
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Van Orden MJ, Newsom S, Rajan R. CRISPR type II-A subgroups exhibit phylogenetically distinct mechanisms for prespacer insertion. J Biol Chem 2020; 295:10956-10968. [PMID: 32513871 DOI: 10.1074/jbc.ra120.013554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas is an adaptive immune system that protects prokaryotes against foreign nucleic acids. Prokaryotes gain immunity by acquiring short pieces of the invading nucleic acid termed prespacers and inserting them into their CRISPR array. In type II-A systems, Cas1 and Cas2 proteins insert prespacers always at the leader-repeat junction of the CRISPR array. Among type II-A CRISPR systems, three distinct groups (G1, G2, and G3) exist according to the extent of DNA sequence conservation at the 3' end of the leader. However, the mechanisms by which these conserved motifs interact with their cognate Cas1 and Cas2 proteins remain unclear. Here, we performed in vitro integration assays, finding that for G1 and G2, the insertion site is recognized through defined mechanisms, at least in members examined to date, whereas G3 exhibits no sequence-specific insertion. G1 first recognized a 12-bp sequence at the leader-repeat junction and performed leader-side insertion before proceeding to spacer-side insertion. G2 recognized the full repeat sequence and could perform independent leader-side or spacer-side insertions, although the leader-side insertion was faster than spacer-side. The prespacer morphology requirements for Cas1-Cas2 varied, with G1 stringently requiring a 5-nucleotide 3' overhang and G2 being able to insert many forms of prespacers with variable efficiencies. These results highlight the intricacy of protein-DNA sequence interactions within the seemingly similar type II-A integration complexes and provide mechanistic insights into prespacer insertion. These interactions can be fine-tuned to expand the Cas1-Cas2 toolset for inserting small DNAs into diverse DNA targets.
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Affiliation(s)
- Mason J Van Orden
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Sydney Newsom
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
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Histone-like Nucleoid-Structuring Protein (H-NS) Paralogue StpA Activates the Type I-E CRISPR-Cas System against Natural Transformation in Escherichia coli. Appl Environ Microbiol 2020; 86:AEM.00731-20. [PMID: 32385085 DOI: 10.1128/aem.00731-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Working mechanisms of CRISPR-Cas systems have been intensively studied. However, far less is known about how they are regulated. The histone-like nucleoid-structuring protein H-NS binds the promoter of cas genes (P cas ) and suppresses the type I-E CRISPR-Cas system in Escherichia coli Although the H-NS paralogue StpA also binds P cas , its role in regulating the CRISPR-Cas system remains unidentified. Our previous work established that E. coli is able to take up double-stranded DNA during natural transformation. Here, we investigated the function of StpA in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli We first documented that although the activated type I-E CRISPR-Cas system, due to hns deletion, interfered with CRISPR-Cas-targeted plasmid transfer, stpA inactivation restored the level of natural transformation. Second, we showed that inactivating stpA reduced the transcriptional activity of P cas Third, by comparing transcriptional activities of the intact P cas and the P cas with a disrupted H-NS binding site in the hns and hns stpA null deletion mutants, we demonstrated that StpA activated transcription of cas genes by binding to the same site as H-NS in P cas Fourth, by expressing StpA with an arabinose-inducible promoter, we confirmed that StpA expressed at a low level stimulated the activity of P cas Finally, by quantifying the level of mature CRISPR RNA (crRNA), we demonstrated that StpA was able to promote the amount of crRNA. Taken together, our work establishes that StpA serves as a transcriptional activator in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli IMPORTANCE StpA is normally considered a molecular backup of the nucleoid-structuring protein H-NS, which was reported as a transcriptional repressor of the type I-E CRISPR-Cas system in Escherichia coli However, the role of StpA in regulating the type I-E CRISPR-Cas system remains elusive. Our previous work uncovered a new route for double-stranded DNA (dsDNA) entry during natural transformation of E. coli In this study, we show that StpA plays a role opposite to that of its paralogue H-NS in regulating the type I-E CRISPR-Cas system against natural transformation of E. coli Our work not only expands our knowledge on CRISPR-Cas-mediated adaptive immunity against extracellular nucleic acids but also sheds new light on understanding the complex regulation mechanism of the CRISPR-Cas system. Moreover, the finding that paralogues StpA and H-NS share a DNA binding site but play opposite roles in transcriptional regulation indicates that higher-order compaction of bacterial chromatin by histone-like proteins could switch prokaryotic transcriptional modes.
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