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Jaybhaye SG, Chavhan RL, Hinge VR, Deshmukh AS, Kadam US. CRISPR-Cas assisted diagnostics of plant viruses and challenges. Virology 2024; 597:110160. [PMID: 38955083 DOI: 10.1016/j.virol.2024.110160] [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: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges.
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Affiliation(s)
- Siddhant G Jaybhaye
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Rahul L Chavhan
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Vidya R Hinge
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Abhijit S Deshmukh
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Ulhas S Kadam
- Plant Molecular Biology and Biotechnology Research Centre (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Gyeongsangnam-do, South Korea.
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2
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Hajizadeh Y, Badmasti F, Oloomi M. Inhibition of the bla OXA-48 gene expression in Klebsiella pneumoniae by a plasmid carrying CRISPRi-Cas9 system. Gene 2024; 910:148332. [PMID: 38431235 DOI: 10.1016/j.gene.2024.148332] [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: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Antibiotic resistance is an increasing concern that threatens the effectiveness of treating bacterial infections. The spread of carbapenem resistant Klebsiella pneumoniae poses a significant threat to global public health. To combat this issue, the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system is being developed. This system includes a single guide RNA (sgRNA) and a nuclease dead Cas9 (dCas9), which work together to downregulate gene expression. Our project involved the use of the CRISPRi system to reduce gene expression of the beta-lactamase oxacillin-48 (blaOXA-48) gene in K. pneumoniae. We designed a sgRNA and cloned it into pJMP1363 plasmid harboring the CRISPRi system. The pJMP1363-sgRNA construct was transformed in K. pneumoniae harboring the blaOXA-48 gene. The MIC test was used to evaluate the antimicrobial resistance, and quantitative real-time RT-PCR was used to confirm the inhibition of the OXA-48 producing K. pneumoniae harboring the pJMP1363-sgRNA construct expression. The Galleria mellonella larvae model was also utilized for in vivo assay. Following the transformation, the MIC test indicated a 4-fold reduction in meropenem resistance, and qRT-PCR analysis revealed a 60-fold decrease in the mRNA OXA-48 harboring the pJMP1363-sgRNA construct expression. Additionally, G. mellonella larvae infected with OXA-48 producing K. pneumoniae harboring the pJMP1363-sgRNA showed higher survival rates. Based on the findings, it can be concluded that the CRISPR interference technique has successfully reduced antibiotic resistance and virulence in the K. pneumoniae harboring the blaOXA-48 gene.
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Affiliation(s)
- Yeganeh Hajizadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Mana Oloomi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, Iran.
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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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Asmamaw Mengstie M, Teshome Azezew M, Asmamaw Dejenie T, Teshome AA, Tadele Admasu F, Behaile Teklemariam A, Tilahun Mulu A, Mekonnen Agidew M, Adugna DG, Geremew H, Abebe EC. Recent Advancements in Reducing the Off-Target Effect of CRISPR-Cas9 Genome Editing. Biologics 2024; 18:21-28. [PMID: 38260716 PMCID: PMC10802171 DOI: 10.2147/btt.s429411] [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: 07/07/2023] [Accepted: 01/16/2024] [Indexed: 01/24/2024]
Abstract
The CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)) and the associated protein (Cas9) system, a young but well-studied genome-editing tool, holds plausible solutions to a wide range of genetic disorders. The single-guide RNA (sgRNA) with a 20-base user-defined spacer sequence and the Cas9 endonuclease form the core of the CRISPR-Cas9 system. This sgRNA can direct the Cas9 nuclease to any genomic region that includes a protospacer adjacent motif (PAM) just downstream and matches the spacer sequence. The current challenge in the clinical applications of CRISPR-Cas9 genome-editing technology is the potential off-target effects that can cause DNA cleavage at the incorrect sites. Off-target genome editing confuses and diminishes the therapeutic potential of CRISPR-Cas9 in addition to potentially casting doubt on scientific findings regarding the activities of genes. In this review, we summarize the recent technological advancements in reducing the off-target effect of CRISPR-Cas9 genome editing.
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Affiliation(s)
- Misganaw Asmamaw Mengstie
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Muluken Teshome Azezew
- Department of Physiology, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Assefa Agegnehu Teshome
- Department of Anatomy, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Fitalew Tadele Admasu
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Awgichew Behaile Teklemariam
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Anemut Tilahun Mulu
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Melaku Mekonnen Agidew
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Dagnew Getnet Adugna
- Department of Anatomy, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Habtamu Geremew
- College of Health Sciences, Oda Bultum University, Chiro, Ethiopia
| | - Endeshaw Chekol Abebe
- Department of Biochemistry, College of Medicine and Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
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Aquino-Jarquin G. Genome and transcriptome engineering by compact and versatile CRISPR-Cas systems. Drug Discov Today 2023; 28:103793. [PMID: 37797813 DOI: 10.1016/j.drudis.2023.103793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/08/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Comparative genomics has enabled the discovery of tiny clustered regularly interspaced short palindromic repeat (CRISPR) bacterial immune system effectors with enormous potential for manipulating eukaryotic genomes. Recently, smaller Cas proteins, including miniature Cas9, Cas12, and Cas13 proteins, have been identified and validated as efficient genome editing and base editing tools in human cells. The compact size of these novel CRISPR effectors is highly desirable for generating CRISPR-based therapeutic approaches, mainly to overcome in vivo delivery constraints, providing a promising opportunity for editing pathogenic mutations of clinical relevance and knocking down RNAs in human cells without inducing chromosomal insertions or genome alterations. Thus, these tiny CRISPR-Cas systems represent new and highly programmable, specific, and efficient platforms, which expand the CRISPR toolkit for potential therapeutic opportunities.
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Affiliation(s)
- Guillermo Aquino-Jarquin
- RNA Biology and Genome Editing Section. Research on Genomics, Genetics, and Bioinformatics Laboratory. Hemato-Oncology Building, 4th Floor, Section 2. Children's Hospital of Mexico, Federico Gómez, Mexico City, Mexico.
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Liu L, Helal SE, Peng N. CRISPR-Cas-Based Engineering of Probiotics. BIODESIGN RESEARCH 2023; 5:0017. [PMID: 37849462 PMCID: PMC10541000 DOI: 10.34133/bdr.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Probiotics are the treasure of the microbiology fields. They have been widely used in the food industry, clinical treatment, and other fields. The equivocal health-promoting effects and the unknown action mechanism were the largest obstacles for further probiotic's developed applications. In recent years, various genome editing techniques have been developed and applied to explore the mechanisms and functional modifications of probiotics. As important genome editing tools, CRISPR-Cas systems that have opened new improvements in genome editing dedicated to probiotics. The high efficiency, flexibility, and specificity are the advantages of using CRISPR-Cas systems. Here, we summarize the classification and distribution of CRISPR-Cas systems in probiotics, as well as the editing tools developed on the basis of them. Then, we discuss the genome editing of probiotics based on CRISPR-Cas systems and the applications of the engineered probiotics through CRISPR-Cas systems. Finally, we proposed a design route for CRISPR systems that related to the genetically engineered probiotics.
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Affiliation(s)
- Ling Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, China
| | - Shimaa Elsayed Helal
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Seo PW, Gu DH, Kim JW, Kim JH, Park SY, Kim JS. Structural characterization of the type I-B CRISPR Cas7 from Thermobaculum terrenum. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140900. [PMID: 36682394 DOI: 10.1016/j.bbapap.2023.140900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) in many prokaryotes functions as an adaptive immune system against mobile genetic elements. A heterologous ribonucleoprotein silencing complex composed of CRISPR-associated (Cas) proteins and a CRISPR RNA (crRNA) neutralizes the incoming mobile genetic elements. The type I and III silencing complexes commonly include a protein-helical backbone of several copies of identical subunits, for example, Cas7 in the type I silencing complex. In this study, we structurally characterized type I-B Cas7 (Csh2 from Thermobaculum terrenum; TterCsh2). The revealed crystal structure of TterCsh2 shows a typical glove-like architecture of Cas7, which consists of a palm, a thumb, and a finger domain. Csh2 proteins have 5 conserved sequence motifs that are arranged to form a presumable crRNA-binding site in the TterCsh2 structure. This crRNA binding site of TterCsh2 is structurally and potentially comparable to those observed in helix-forming Cas7 structures in other sub-types. Analysis of the reported Cas7 structures and their sequences suggests that Cas7s can be divided into at least two sub-classes. These data will broaden our understanding on the Cascade complex of CRISPR/Cas systems.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Do-Heon Gu
- Pohang Accelerator Laboratory, Pohang, South Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | | | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea.
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8
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Rajan A, Shrivastava S, Janhawi, Kumar A, Singh AK, Arora PK. CRISPR-Cas system: from diagnostic tool to potential antiviral treatment. Appl Microbiol Biotechnol 2022; 106:5863-5877. [PMID: 36008567 PMCID: PMC9411046 DOI: 10.1007/s00253-022-12135-2] [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: 05/29/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/27/2022]
Abstract
This mini review focuses on the diagnosis and treatment of virus diseases using Crisper-Cas technology. The present paper describes various strategies involved in diagnosing diseases using Crispr-Cas-based assays. Additionally, CRISPR-Cas systems offer great potential as new therapeutic tools for treating viral infections including HIV, Influenza, and SARS-CoV-2. There are several major challenges to be overcome before this technology can be applied routinely in clinical settings, such as finding a suitable delivery tool, toxicity, and immunogenicity, as well as off-target effects. This review also discusses ways to deal with the challenges associated with Crisper-Cas technology. KEY POINTS: • Crisper technology is being applied to diagnose infectious and non-infectious diseases. • A new generation of CRISPR-Cas-based assays has been developed which detect pathogens within minutes, providing rapid diagnosis of diseases. • Crispr-Cas tools can be used to combat viral infections, specifically HIV, influenza, and SARS-CoV-2.
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Affiliation(s)
- Aishwarya Rajan
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Stuti Shrivastava
- Electronics and Communication, Jaypee Institute of Information Technology, Noida, India
| | - Janhawi
- Department of Zoology, Kalindi College, University of Delhi, Delhi, India
| | - Akhilesh Kumar
- Department of Botany, Banaras Hindu University, Varanasi, India.
| | - Alok Kumar Singh
- Department of Biochemistry, Shaheed Rajguru College of Applied Sciences for Women, University of Delhi, Delhi, India.
| | - Pankaj Kumar Arora
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, India.
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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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Tao S, Chen H, Li N, Liang W. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infect Drug Resist 2022; 15:4155-4168. [PMID: 35942309 PMCID: PMC9356603 DOI: 10.2147/idr.s370869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.
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Affiliation(s)
- Shuan Tao
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
| | - Huimin Chen
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, Anhui Province, 233030, People’s Republic of China
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
- Correspondence: Wei Liang, Lianyungang Clinical College of Jiangsu University, No. 161. Xingfu Road, Haizhou District, Lianyungang, Jiangsu Province, 222023, People’s Republic of China, Tel/Fax +86-51885213100; Tel/Fax +86 15351883016, Email
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Nazir R, Mandal S, Mitra S, Ghorai M, Das N, Jha NK, Majumder M, Pandey DK, Dey A. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genome-editing toolkit to enhance salt stress tolerance in rice and wheat. PHYSIOLOGIA PLANTARUM 2022; 174:e13642. [PMID: 35099818 DOI: 10.1111/ppl.13642] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/02/2022] [Accepted: 01/27/2022] [Indexed: 05/14/2023]
Abstract
The rice and wheat agricultural system is the primary source of food for billions across the world. However, the productivity and long-term sustainability of rice and wheat are threatened by a large number of abiotic stresses, especially salinity stress. Salinity has a significant impact on plant development and productivity and is one of the leading causes of crop yield losses in agricultural soils worldwide. Over the last few decades, several attempts have been undertaken to enhance salinity stress tolerance, most of which have relied on traditional or molecular breeding approaches. These approaches have so far been insufficient in addressing the issues of abiotic stress. However, due to the availability of genome sequences for cereal crops like rice and wheat and the development of genome editing techniques like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9), it is now possible to "edit" genes and influence key traits. Here, we review the application of the CRISPR/Cas9 system in both rice (Oryza sativa L.) and wheat (Triticum aestivum L.) to develop salinity tolerant cultivars. The CRISPR/Cas genome editing toolkit holds great promise of producing cereal crops tolerant to salt stress to increase agriculture resilience with a strong impact on the environment and public health.
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Affiliation(s)
- Romaan Nazir
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sicon Mitra
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
| | - Mimosa Ghorai
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Neela Das
- Department of Botany, Rishi Bankim Chandra College, Naihati, West Bengal, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
| | | | - Devendra Kumar Pandey
- Department of Biotechnology, Lovely Professional University, Phagwara, Punjab, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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Wentz TG, Tremblay BJM, Bradshaw M, Doxey AC, Sharma SK, Sauer JD, Pellett S. Endogenous CRISPR-Cas Systems in Group I Clostridium botulinum and Clostridium sporogenes Do Not Directly Target the Botulinum Neurotoxin Gene Cluster. Front Microbiol 2022; 12:787726. [PMID: 35222299 PMCID: PMC8865420 DOI: 10.3389/fmicb.2021.787726] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/27/2021] [Indexed: 12/28/2022] Open
Abstract
Most strains of proteolytic group I Clostridium botulinum (G1 C. botulinum) and some strains of Clostridium sporogenes possess genes encoding botulinum neurotoxin (BoNT), a potent neuroparalytic agent. Within G1 C. botulinum, conserved bont gene clusters of three major toxin serotypes (bont/A/B/F) can be found on conjugative plasmids and/or within chromosomal pathogenicity islands. CRISPR-Cas systems enable site-specific targeting of previously encountered mobile genetic elements (MGE) such as plasmids and bacteriophage through the creation of a spacer library complementary to protospacers within the MGEs. To examine whether endogenous CRISPR-Cas systems restrict the transfer of bont gene clusters across strains we conducted a bioinformatic analysis profiling endogenous CRISPR-Cas systems from 241 G1 C. botulinum and C. sporogenes strains. Approximately 6,200 CRISPR spacers were identified across the strains and Type I-B, III-A/B/D cas genes and CRISPR array features were identified in 83% of the strains. Mapping the predicted spacers against the masked strain and RefSeq plasmid dataset identified 56,000 spacer-protospacer matches. While spacers mapped heavily to targets within bont(+) plasmids, no protospacers were identified within the bont gene clusters. These results indicate the toxin is not a direct target of CRISPR-Cas but the plasmids predominantly responsible for its mobilization are. Finally, while the presence of a CRISPR-Cas system did not reliably indicate the presence or absence of a bont gene cluster, comparative genomics across strains indicates they often occupy the same hypervariable loci common to both species, potentially suggesting similar mechanisms are involved in the acquisition and curation of both genomic features.
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Affiliation(s)
- Travis G. Wentz
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, United States,Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States,Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | | | - Marite Bradshaw
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Andrew C. Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Shashi K. Sharma
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, Madison, WI, United States
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States,*Correspondence: Sabine Pellett,
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Abstract
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Clustered regularly interspaced short palindromic repeats along with CRISPR-associated protein
mechanisms preserve the memory of previous experiences with DNA invaders, in particular spacers
that are embedded in CRISPR arrays between coordinate repeats. There has been a fast progression in
the comprehension of this immune system and its implementations; however, there are numerous points
of view that anticipate explanations to make the field an energetic research zone. The efficiency of
CRISPR-Cas depends upon well-considered single guide RNA; for this purpose, many bioinformatics
methods and tools are created to support the design of greatly active and precise single guide RNA. Insilico
single guide RNA architecture is a crucial point for effective gene editing by means of the
CRISPR technique. Persistent attempts have been made to improve in-silico single guide RNA formulation
having great on-target effectiveness and decreased off-target effects. This review offers a summary
of the CRISPR computational tools to help different researchers pick a specific tool for their work according
to pros and cons, along with new thoughts to make new computational tools to overcome all existing
limitations.
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Affiliation(s)
- Mohsin Ali Nasir
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Samia Nawaz
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave,
West Hi-Tech Zone, Chengdu 611731, China
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14
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Lucas-Elío P, Molina-Quintero LR, Xu H, Sánchez-Amat A. A histidine kinase and a response regulator provide phage resistance to Marinomonas mediterranea via CRISPR-Cas regulation. Sci Rep 2021; 11:20564. [PMID: 34663886 PMCID: PMC8523701 DOI: 10.1038/s41598-021-99740-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022] Open
Abstract
CRISPR-Cas systems are used by many prokaryotes to defend against invading genetic elements. In many cases, more than one CRISPR-Cas system co-exist in the same cell. Marinomonas mediterranea MMB-1 possesses two CRISPR-Cas systems, of type I-F and III-B respectively, which collaborate in phage resistance raising questions on how their expression is regulated. This study shows that the expression of both systems is controlled by the histidine kinase PpoS and a response regulator, PpoR, identified and cloned in this study. These proteins show similarity to the global regulators BarA/UvrY. In addition, homologues to the sRNAs CsrB and CsrC and the gene coding for the post-transcriptional repressor CsrA have been also identified indicating the conservation of the elements of the BarA/UvrY regulatory cascade in M. mediterranea. RNA-Seq analyses have revealed that all these genetics elements are regulated by PpoS/R supporting their participation in the regulatory cascade. The regulation by PpoS and PpoR of the CRISPR-Cas systems plays a role in phage defense since mutants in these proteins show an increase in phage sensitivity.
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Affiliation(s)
- Patricia Lucas-Elío
- Department of Genetics and Microbiology, University of Murcia, 30100, Murcia, Spain
| | | | - Hengyi Xu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Antonio Sánchez-Amat
- Department of Genetics and Microbiology, University of Murcia, 30100, Murcia, Spain.
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15
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Lewis AM, Recalde A, Bräsen C, Counts JA, Nussbaum P, Bost J, Schocke L, Shen L, Willard DJ, Quax TEF, Peeters E, Siebers B, Albers SV, Kelly RM. The biology of thermoacidophilic archaea from the order Sulfolobales. FEMS Microbiol Rev 2021; 45:fuaa063. [PMID: 33476388 PMCID: PMC8557808 DOI: 10.1093/femsre/fuaa063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
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Affiliation(s)
- April M Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Alejandra Recalde
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Christopher Bräsen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - James A Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Phillip Nussbaum
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Jan Bost
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Larissa Schocke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lu Shen
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
| | - Tessa E F Quax
- Archaeal Virus–Host Interactions, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sonja-Verena Albers
- Institute for Biology, Molecular Biology of Archaea, University of Freiburg, 79104 Freiburg, Germany
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University. Raleigh, NC 27695, USA
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16
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Zhang Y, Marchisio MA. Type II anti-CRISPR proteins as a new tool for synthetic biology. RNA Biol 2021; 18:1085-1098. [PMID: 32991234 PMCID: PMC8244766 DOI: 10.1080/15476286.2020.1827803] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/03/2020] [Accepted: 09/20/2020] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) system represents, in prokaryotes, an adaptive and inheritable immune response against invading DNA. The discovery of anti-CRISPR proteins (Acrs), which are inhibitors of CRISPR-Cas, mainly encoded by phages and prophages, showed a co-evolution history between prokaryotes and phages. In the past decade, the CRISPR-Cas systems together with the corresponding Acrs have been turned into a genetic-engineering tool. Among the six types of CRISPR-Cas characterized so far, type II CRISPR-Cas system is the most popular in biotechnology. Here, we discuss about the discovery, the reported inhibitory mechanisms, and the applications in both gene editing and gene transcriptional regulation of type II Acrs. Moreover, we provide insights into future potential research and feasible applications.
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Affiliation(s)
- Yadan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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17
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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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18
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A Tryptophan 'Gate' in the CRISPR-Cas3 Nuclease Controls ssDNA Entry into the Nuclease Site, That When Removed Results in Nuclease Hyperactivity. Int J Mol Sci 2021; 22:ijms22062848. [PMID: 33799639 PMCID: PMC8001533 DOI: 10.3390/ijms22062848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Cas3 is a ssDNA-targeting nuclease-helicase essential for class 1 prokaryotic CRISPR immunity systems, which has been utilized for genome editing in human cells. Cas3-DNA crystal structures show that ssDNA follows a pathway from helicase domains into a HD-nuclease active site, requiring protein conformational flexibility during DNA translocation. In genetic studies, we had noted that the efficacy of Cas3 in CRISPR immunity was drastically reduced when temperature was increased from 30 °C to 37 °C, caused by an unknown mechanism. Here, using E. coli Cas3 proteins, we show that reduced nuclease activity at higher temperature corresponds with measurable changes in protein structure. This effect of temperature on Cas3 was alleviated by changing a single highly conserved tryptophan residue (Trp-406) into an alanine. This Cas3W406A protein is a hyperactive nuclease that functions independently from temperature and from the interference effector module Cascade. Trp-406 is situated at the interface of Cas3 HD and RecA1 domains that is important for maneuvering DNA into the nuclease active site. Molecular dynamics simulations based on the experimental data showed temperature-induced changes in positioning of Trp-406 that either blocked or cleared the ssDNA pathway. We propose that Trp-406 forms a 'gate' for controlling Cas3 nuclease activity via access of ssDNA to the nuclease active site. The effect of temperature in these experiments may indicate allosteric control of Cas3 nuclease activity caused by changes in protein conformations. The hyperactive Cas3W406A protein may offer improved Cas3-based genetic editing in human cells.
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19
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Mitrofanov A, Alkhnbashi OS, Shmakov SA, Makarova K, Koonin E, Backofen R. CRISPRidentify: identification of CRISPR arrays using machine learning approach. Nucleic Acids Res 2021; 49:e20. [PMID: 33290505 PMCID: PMC7913763 DOI: 10.1093/nar/gkaa1158] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 02/02/2023] Open
Abstract
CRISPR–Cas are adaptive immune systems that degrade foreign genetic elements in archaea and bacteria. In carrying out their immune functions, CRISPR–Cas systems heavily rely on RNA components. These CRISPR (cr) RNAs are repeat-spacer units that are produced by processing of pre-crRNA, the transcript of CRISPR arrays, and guide Cas protein(s) to the cognate invading nucleic acids, enabling their destruction. Several bioinformatics tools have been developed to detect CRISPR arrays based solely on DNA sequences, but all these tools employ the same strategy of looking for repetitive patterns, which might correspond to CRISPR array repeats. The identified patterns are evaluated using a fixed, built-in scoring function, and arrays exceeding a cut-off value are reported. Here, we instead introduce a data-driven approach that uses machine learning to detect and differentiate true CRISPR arrays from false ones based on several features. Our CRISPR detection tool, CRISPRidentify, performs three steps: detection, feature extraction and classification based on manually curated sets of positive and negative examples of CRISPR arrays. The identified CRISPR arrays are then reported to the user accompanied by detailed annotation. We demonstrate that our approach identifies not only previously detected CRISPR arrays, but also CRISPR array candidates not detected by other tools. Compared to other methods, our tool has a drastically reduced false positive rate. In contrast to the existing tools, our approach not only provides the user with the basic statistics on the identified CRISPR arrays but also produces a certainty score as a practical measure of the likelihood that a given genomic region is a CRISPR array.
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Affiliation(s)
| | | | - Sergey A Shmakov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rolf Backofen
- To whom correspondence should be addressed. Tel: +49 761/203 7461; Fax: +49 761/203 7462;
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20
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Workman RE, Pammi T, Nguyen BTK, Graeff LW, Smith E, Sebald SM, Stoltzfus MJ, Euler CW, Modell JW. A natural single-guide RNA repurposes Cas9 to autoregulate CRISPR-Cas expression. Cell 2021; 184:675-688.e19. [PMID: 33421369 DOI: 10.1016/j.cell.2020.12.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/24/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas systems provide prokaryotes with acquired immunity against viruses and plasmids, but how these systems are regulated to prevent autoimmunity is poorly understood. Here, we show that in the S. pyogenes CRISPR-Cas system, a long-form transactivating CRISPR RNA (tracr-L) folds into a natural single guide that directs Cas9 to transcriptionally repress its own promoter (Pcas). Further, we demonstrate that Pcas serves as a critical regulatory node. De-repression causes a dramatic 3,000-fold increase in immunization rates against viruses; however, heightened immunity comes at the cost of increased autoimmune toxicity. Using bioinformatic analyses, we provide evidence that tracrRNA-mediated autoregulation is widespread in type II-A CRISPR-Cas systems. Collectively, we unveil a new paradigm for the intrinsic regulation of CRISPR-Cas systems by natural single guides, which may facilitate the frequent horizontal transfer of these systems into new hosts that have not yet evolved their own regulatory strategies.
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Affiliation(s)
- Rachael E Workman
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Teja Pammi
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Binh T K Nguyen
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leonardo W Graeff
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Erika Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Suzanne M Sebald
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Marie J Stoltzfus
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chad W Euler
- Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, NY 10065, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua W Modell
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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21
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Comparative Genomic Analysis of Mycobacteriaceae Reveals Horizontal Gene Transfer-Mediated Evolution of the CRISPR-Cas System in the Mycobacterium tuberculosis Complex. mSystems 2021; 6:6/1/e00934-20. [PMID: 33468705 PMCID: PMC7820667 DOI: 10.1128/msystems.00934-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are conserved genetic elements in many prokaryotes, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Although knowledge of CRISPR locus variability has been utilized in M. tuberculosis strain genotyping, its evolutionary path in Mycobacteriaceae is not well understood. In this study, we have performed a comparative analysis of 141 mycobacterial genomes and identified the exclusive presence of the CRISPR-Cas type III-A system in M. tuberculosis complex (MTBC). Our global phylogenetic analysis of CRISPR repeats and Cas10 proteins offers evidence of horizontal gene transfer (HGT) of the CRISPR-Cas module in the last common ancestor of MTBC and Mycobacterium canettii from a Streptococcus-like environmental bacterium. Additionally, our results show that the variation of CRISPR-Cas organization in M. tuberculosis lineages, especially in the Beijing sublineage of lineage 2, is due to the transposition of insertion sequence IS6110 The direct repeat (DR) region of the CRISPR-Cas locus acts as a hot spot for IS6110 insertion. We show in M. tuberculosis H37Rv that the repeat at the 5' end of CRISPR1 of the forward strand is an atypical repeat made up partly of IS-terminal inverted repeat and partly CRISPR DR. By tracing an undetectable spacer sequence in the DR region, the two CRISPR loci could theoretically be joined to reconstruct the ancestral single CRISPR-Cas locus organization, as seen in M. canettii This study retracing the evolutionary events of HGT and IS6110-driven genomic deletions helps us to better understand the strain-specific variations in M. tuberculosis lineages.IMPORTANCE Comparative genomic analysis of prokaryotes has led to a better understanding of the biology of several pathogenic microorganisms. One such clinically important pathogen is M. tuberculosis, the leading cause of bacterial infection worldwide. Recent evidence on the functionality of the CRISPR-Cas system in M. tuberculosis has brought back focus on these conserved genetic elements, present in many prokaryotes. Our study advances understanding of mycobacterial CRISPR-Cas origin and its diversity among the different species. We provide phylogenetic evidence of acquisition of CRISPR-Cas type III-A in the last common ancestor shared between MTBC and M. canettii, by HGT-mediated events. The most likely source of HGT was an environmental Firmicutes bacterium. Genomic mapping of the CRISPR loci showed the IS6110 transposition-driven variations in M. tuberculosis strains. Thus, this study offers insights into events related to the evolution of CRISPR-Cas in M. tuberculosis lineages.
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22
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McBride TM, Schwartz EA, Kumar A, Taylor DW, Fineran PC, Fagerlund RD. Diverse CRISPR-Cas Complexes Require Independent Translation of Small and Large Subunits from a Single Gene. Mol Cell 2020; 80:971-979.e7. [PMID: 33248026 DOI: 10.1016/j.molcel.2020.11.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas adaptive immune systems provide prokaryotes with defense against viruses by degradation of specific invading nucleic acids. Despite advances in the biotechnological exploitation of select systems, multiple CRISPR-Cas types remain uncharacterized. Here, we investigated the previously uncharacterized type I-D interference complex and revealed that it is a genetic and structural hybrid with similarity to both type I and type III systems. Surprisingly, formation of the functional complex required internal in-frame translation of small subunits from within the large subunit gene. We further show that internal translation to generate small subunits is widespread across diverse type I-D, I-B, and I-C systems, which account for roughly one quarter of CRISPR-Cas systems. Our work reveals the unexpected expansion of protein coding potential from within single cas genes, which has important implications for understanding CRISPR-Cas function and evolution.
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Affiliation(s)
- Tess M McBride
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Evan A Schwartz
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1597, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1597, USA
| | - Abhishek Kumar
- Centre for Protein Research, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1597, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1597, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1597, USA; LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX 78712-1597, USA
| | - 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
| | - Robert D Fagerlund
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand; Genetics Otago, University of Otago, Dunedin, New Zealand.
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23
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Liu Z, Sun M, Liu J, Liu T, Ye Q, Li Y, Peng N. A CRISPR-associated factor Csa3a regulates DNA damage repair in Crenarchaeon Sulfolobus islandicus. Nucleic Acids Res 2020; 48:9681-9693. [PMID: 32833023 PMCID: PMC7515695 DOI: 10.1093/nar/gkaa694] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 02/05/2023] Open
Abstract
CRISPR−Cas system provides acquired immunity against invasive genetic elements in prokaryotes. In both bacteria and archaea, transcriptional factors play important roles in regulation of CRISPR adaptation and interference. In the model Crenarchaeon Sulfolobus islandicus, a CRISPR-associated factor Csa3a triggers CRISPR adaptation and activates CRISPR RNA transcription for the immunity. However, regulation of DNA repair systems for repairing the genomic DNA damages caused by the CRISPR self-immunity is less understood. Here, according to the transcriptome and reporter gene data, we found that deletion of the csa3a gene down-regulated the DNA damage response (DDR) genes, including the ups and ced genes. Furthermore, in vitro analyses demonstrated that Csa3a specifically bound the DDR gene promoters. Microscopic analysis showed that deletion of csa3a significantly inhibited DNA damage-induced cell aggregation. Moreover, the flow cytometry study and survival rate analysis revealed that the csa3a deletion strain was more sensitive to the DNA-damaging reagent. Importantly, CRISPR self-targeting and DNA transfer experiments revealed that Csa3a was involved in regulating Ups- and Ced-mediated repair of CRISPR-damaged host genomic DNA. These results explain the interplay between Csa3a functions in activating CRISPR adaptation and DNA repair systems, and expands our understanding of the lost link between CRISPR self-immunity and genome stability.
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Affiliation(s)
- Zhenzhen Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Mengmeng Sun
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jilin Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Tao Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qing Ye
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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24
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Kumar P, Malik YS, Ganesh B, Rahangdale S, Saurabh S, Natesan S, Srivastava A, Sharun K, Yatoo MI, Tiwari R, Singh RK, Dhama K. CRISPR-Cas System: An Approach With Potentials for COVID-19 Diagnosis and Therapeutics. Front Cell Infect Microbiol 2020; 10:576875. [PMID: 33251158 PMCID: PMC7673385 DOI: 10.3389/fcimb.2020.576875] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
COVID-19, the human coronavirus disease caused by SARS-CoV-2, was reported for the first time in Wuhan, China in late 2019. COVID-19 has no preventive vaccine or proven standard pharmacological treatment, and consequently, the outbreak swiftly became a pandemic affecting more than 215 countries around the world. For the diagnosis of COVID-19, the only reliable diagnostics is a qPCR assay. Among other diagnostic tools, the CRISPR-Cas system is being investigated for rapid and specific diagnosis of COVID-19. The CRISPR-Cas-based methods diagnose the SARS-CoV-2 infections within an hour. Apart from its diagnostic ability, CRISPR-Cas system is also being assessed for antiviral therapy development; however, till date, no CRISPR-based therapy has been approved for human use. The Prophylactic Antiviral CRISPR in huMAN cells (PAC-MAN), which is Cas 13 based strategy, has been developed against coronavirus. Although this strategy has the potential to be developed as a therapeutic modality, it may face significant challenges for approval in human clinical trials. This review is focused on describing potential use and challenges of CRISPR-Cas based approaches for the development of rapid and accurate diagnostic technique and/or a possible therapeutic alternative for combating COVID-19. The assessment of potential risks associated with use of CRISPR will be important for future clinical advancements.
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Affiliation(s)
- Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, India
| | - Balasubramanian Ganesh
- Laboratory Division, Indian Council of Medical Research—National Institute of Epidemiology, Ministry of Health & Family Welfare, Chennai, India
| | - Somnath Rahangdale
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, India
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Sharad Saurabh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Mohd. Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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25
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Xu Z, Li Y, Li M, Xiang H, Yan A. Harnessing the type I CRISPR-Cas systems for genome editing in prokaryotes. Environ Microbiol 2020; 23:542-558. [PMID: 32510745 DOI: 10.1111/1462-2920.15116] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/26/2022]
Abstract
Genetic analysis is crucial to the understanding, exploitation, and control of microorganisms. The advent of CRISPR-Cas-based genome-editing techniques, particularly those mediated by the single-effector (Cas9 and Cas12a) class 2 CRISPR-Cas systems, has revolutionized the genetics in model eukaryotic organisms. However, their applications in prokaryotes are rather limited, largely owing to the exceptional diversity of DNA homeostasis in microorganisms and severe cytotoxicity of overexpressing these nuclease proteins in certain genotypes. Remarkably, CRISPR-Cas systems belonging to different classes and types are continuously identified in prokaryotic genomes and serve as a deep reservoir for expansion of the CRISPR-based genetic toolkits. ~90% of the CRISPR-Cas systems identified so far belong to the class 1 system which hinges on multi-protein effector complexes for DNA interference. Harnessing these widespread native CRISPR-Cas systems for 'built-in' genome editing represents an emerging and powerful genetic tool in prokaryotes, especially in the genetically recalcitrant non-model species and strains. In this progress review, we introduce the general workflow of this emerging editing platform and summarize its establishment in a growing number of prokaryotes by harnessing the most widespread, diverse type I CRISPR-Cas systems present in their genomes. We also discuss the various factors affecting the success and efficiency of this editing platform and the corresponding solutions.
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Affiliation(s)
- Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yanran Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 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
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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26
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Wiegand T, Karambelkar S, Bondy-Denomy J, Wiedenheft B. Structures and Strategies of Anti-CRISPR-Mediated Immune Suppression. Annu Rev Microbiol 2020; 74:21-37. [PMID: 32503371 DOI: 10.1146/annurev-micro-020518-120107] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
More than 50 protein families have been identified that inhibit CRISPR (clustered regularly interspaced short palindromic repeats)-Cas-mediated adaptive immune systems. Here, we analyze the available anti-CRISPR (Acr) structures and describe common themes and unique mechanisms of stoichiometric and enzymatic suppressors of CRISPR-Cas. Stoichiometric inhibitors often function as molecular decoys of protein-binding partners or nucleic acid targets, while enzymatic suppressors covalently modify Cas ribonucleoprotein complexes or degrade immune signaling molecules. We review mechanistic insights that have been revealed by structures of Acrs, discuss some of the trade-offs associated with each of these strategies, and highlight how Acrs are regulated and deployed in the race to overcome adaptive immunity.
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Affiliation(s)
- Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
| | - Shweta Karambelkar
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, California 94143, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA;
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27
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Francisella novicida CRISPR-Cas Systems Can Functionally Complement Each Other in DNA Defense while Providing Target Flexibility. J Bacteriol 2020; 202:JB.00670-19. [PMID: 32284320 DOI: 10.1128/jb.00670-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/11/2020] [Indexed: 01/03/2023] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immune systems that facilitate protection of bacteria and archaea against infection by external mobile genetic elements. The model pathogen Francisella novicida encodes a CRISPR-Cas12a (FnoCas12a) system and a CRISPR-Cas9 (FnoCas9) system, the latter of which has an additional and noncanonical function in bacterial virulence. Here, we investigated and compared the functional roles of the FnoCas12a and FnoCas9 systems in transformation inhibition and bacterial virulence. Unlike FnoCas9, FnoCas12a was not required for F. novicida virulence. However, both systems were highly effective at plasmid restriction and acted independently of each other. We further identified a critical protospacer-adjacent motif (PAM) necessary for transformation inhibition by FnoCas12a, demonstrating a greater flexibility for target identification by FnoCas12a than previously appreciated and a specificity that is distinct from that of FnoCas9. The effectors of the two systems exhibited different patterns of expression at the mRNA level, suggesting that they may confer distinct benefits to the bacterium in diverse environments. These data suggest that due to the differences between the two CRISPR-Cas systems, together they may provide F. novicida with a more comprehensive defense against foreign nucleic acids. Finally, we demonstrated that the FnoCas12a and FnoCas9 machineries could be simultaneously engineered to restrict the same nonnative target, thereby expanding the toolset for prokaryotic genome manipulation.IMPORTANCE CRISPR-Cas9 and CRISPR-Cas12a systems have been widely commandeered for genome engineering. However, they originate in prokaryotes, where they function as adaptive immune systems. The details of this activity and relationship between these systems within native host organisms have been minimally explored. The human pathogen Francisella novicida contains both of these systems, with the Cas9 system also exhibiting a second activity, modulating virulence through transcriptional regulation. We compared and contrasted the ability of these two systems to control virulence and restrict DNA within their native host bacterium, highlighting differences and similarities in these two functions. Collectively, our results indicate that these two distinct and reprogrammable endogenous systems provide F. novicida with a more comprehensive defense against mobile genetic elements.
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Kumar P, Malik YS, Ganesh B, Rahangdale S, Saurabh S, Natesan S, Srivastava A, Sharun K, Yatoo MI, Tiwari R, Singh RK, Dhama K. CRISPR-Cas System: An Approach With Potentials for COVID-19 Diagnosis and Therapeutics. Front Cell Infect Microbiol 2020. [PMID: 33251158 DOI: 10.3389/fcimb] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
COVID-19, the human coronavirus disease caused by SARS-CoV-2, was reported for the first time in Wuhan, China in late 2019. COVID-19 has no preventive vaccine or proven standard pharmacological treatment, and consequently, the outbreak swiftly became a pandemic affecting more than 215 countries around the world. For the diagnosis of COVID-19, the only reliable diagnostics is a qPCR assay. Among other diagnostic tools, the CRISPR-Cas system is being investigated for rapid and specific diagnosis of COVID-19. The CRISPR-Cas-based methods diagnose the SARS-CoV-2 infections within an hour. Apart from its diagnostic ability, CRISPR-Cas system is also being assessed for antiviral therapy development; however, till date, no CRISPR-based therapy has been approved for human use. The Prophylactic Antiviral CRISPR in huMAN cells (PAC-MAN), which is Cas 13 based strategy, has been developed against coronavirus. Although this strategy has the potential to be developed as a therapeutic modality, it may face significant challenges for approval in human clinical trials. This review is focused on describing potential use and challenges of CRISPR-Cas based approaches for the development of rapid and accurate diagnostic technique and/or a possible therapeutic alternative for combating COVID-19. The assessment of potential risks associated with use of CRISPR will be important for future clinical advancements.
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Affiliation(s)
- Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, India
| | - Balasubramanian Ganesh
- Laboratory Division, Indian Council of Medical Research-National Institute of Epidemiology, Ministry of Health & Family Welfare, Chennai, India
| | - Somnath Rahangdale
- Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, India
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Sharad Saurabh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University, Noida, India
| | - Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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29
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Environmentally applied nucleic acids and proteins for purposes of engineering changes to genes and other genetic material. BIOSAFETY AND HEALTH 2019. [DOI: 10.1016/j.bsheal.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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30
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Gu DH, Ha SC, Kim JS. A CRISPR RNA Is Closely Related With the Size of the Cascade Nucleoprotein Complex. Front Microbiol 2019; 10:2458. [PMID: 31736904 PMCID: PMC6828817 DOI: 10.3389/fmicb.2019.02458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/14/2019] [Indexed: 12/26/2022] Open
Abstract
The currently known prokaryotic adaptive immune system against mobile genetic elements is based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated (Cas) proteins and the transcribed short CRISPR RNA (crRNA) molecule form a heterologous ribonucleoprotein complex that neutralizes invading foreign nucleic acids, wherein the crRNA molecule base-pairs with the exogenous genetic elements. In the ribonucleoprotein complexes of the type I CRISPR system, a helical backbone of six identical subunits is commonly found. However, it is not clear how this ribonucleoprotein complex is assembled and what is the determinant factor for its size. We elucidated the crystal structure of the Csy3 subunit of the type I-F ribonucleoprotein complex from Zymomonas mobilis (ZmCsy3), in which seven ZmCsy3 protomers in the asymmetric unit form a molecular helix that is part of a filamentous structure in the entire crystal system. This ZmCsy3 helical structure is remarkably similar to the crRNA-bound hexameric Csy3 backbone from Pseudomonas aeruginosa, with conserved interactions between neighboring subunits. The monomeric ZmCsy3 in solution is transformed into different oligomeric states depending on the added crRNAs. These results suggest that a crRNA and Csy3 subunit play a determinant role in the stepwise formation of the functional Cascade ribonucleoprotein complex and the recruitment of other subunits, and crRNA functions as a molecular ruler for determining the size of the Cascade silencing complex.
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Affiliation(s)
- Do-Heon Gu
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory, Pohang, South Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
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31
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Zhang L, Sun R, Yang M, Peng S, Cheng Y, Chen C. Conformational Dynamics and Cleavage Sites of Cas12a Are Modulated by Complementarity between crRNA and DNA. iScience 2019; 19:492-503. [PMID: 31437752 PMCID: PMC6710298 DOI: 10.1016/j.isci.2019.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/15/2019] [Accepted: 08/02/2019] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease, which displays great potentials and several advantages over the well-known Cas9 in genome editing and engineering. Here, we established a quantitative kinetic scheme to describe the conformational dynamics of Cas12a/crRNA/dsDNA ternary complexes. The highly dynamic nature of Cas12a complexes, including their reversible formation, disassembly, and transition between different conformational states, is likely to be one of the key aspects contributing to their high specificity. The non-target strand is cleaved when its cleavage sites are released from DNA duplex after DNase activation of Cas12a. Cleaved non-target strand stabilizes target strand pre-cleavage states to permit subsequent cleavage and to ensure two DNA strands cleaved in a well-defined order. The extent of complementarity between crRNA and DNA modulates the relative stabilities of target strand pre-cleavage states targeting different cleavage sites. Our discoveries provide insights to fully elucidate the working mechanisms of Cas12a and to optimize it for genome engineering. Dynamic processes of Cas12a contribute to its high specificity Cleavage sites of non-target strand are released from duplex after DNase activation Cleaved non-target strand stabilizes target strand pre-cleavage states Multiple target strand pre-cleavage states target different cleavage sites
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Affiliation(s)
- Lujia Zhang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Ruirui Sun
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Mengyi Yang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Sijia Peng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yongxin Cheng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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32
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Han W, Stella S, Zhang Y, Guo T, Sulek K, Peng-Lundgren L, Montoya G, She Q. A Type III-B Cmr effector complex catalyzes the synthesis of cyclic oligoadenylate second messengers by cooperative substrate binding. Nucleic Acids Res 2019; 46:10319-10330. [PMID: 30239876 PMCID: PMC6212834 DOI: 10.1093/nar/gky844] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022] Open
Abstract
Recently, Type III-A CRISPR-Cas systems were found to catalyze the synthesis of cyclic oligoadenylates (cOAs), a second messenger that specifically activates Csm6, a Cas accessory RNase and confers antiviral defense in bacteria. To test if III-B CRISPR-Cas systems could mediate a similar CRISPR signaling pathway, the Sulfolobus islandicus Cmr-α ribonucleoprotein complex (Cmr-α-RNP) was purified from the native host and tested for cOA synthesis. We found that the system showed a robust production of cyclic tetra-adenylate (c-A4), and that c-A4 functions as a second messenger to activate the III-B-associated RNase Csx1 by binding to its CRISPR-associated Rossmann Fold domain. Investigation of the kinetics of cOA synthesis revealed that Cmr-α-RNP displayed positively cooperative binding to the adenosine triphosphate (ATP) substrate. Furthermore, mutagenesis of conserved domains in Cmr2α confirmed that, while Palm 2 hosts the active site of cOA synthesis, Palm 1 domain serves as the primary site in the enzyme-substrate interaction. Together, our data suggest that the two Palm domains cooperatively interact with ATP molecules to achieve a robust cOA synthesis by the III-B CRISPR-Cas system.
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Affiliation(s)
- Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N DK-2200, Denmark
| | - Stefano Stella
- Structural Molecular Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Yan Zhang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tong Guo
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N DK-2200, Denmark
| | - Karolina Sulek
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Li Peng-Lundgren
- Protein Production and Characterization Platform, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen 2200, Denmark
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N DK-2200, Denmark
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33
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Ka D, Jang DM, Han BW, Bae E. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Nucleic Acids Res 2019; 46:9805-9815. [PMID: 30102386 PMCID: PMC6182153 DOI: 10.1093/nar/gky702] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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Reversible Gene Expression Control in Yersinia pestis by Using an Optimized CRISPR Interference System. Appl Environ Microbiol 2019; 85:AEM.00097-19. [PMID: 30979834 DOI: 10.1128/aem.00097-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/02/2019] [Indexed: 12/26/2022] Open
Abstract
Many genes in the bacterial pathogen Yersinia pestis, the causative agent of three plague pandemics, remain uncharacterized, greatly hampering the development of measures for plague prevention and control. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been shown to be an effective tool for gene knockdown in model bacteria. In this system, a catalytically dead Cas9 (dCas9) and a small guide RNA (sgRNA) form a complex, binding to the specific DNA target through base pairing, thereby impeding RNA polymerase binding and causing target gene repression. Here, we introduce an optimized CRISPRi system using Streptococcus pyogenes Cas9-derived dCas9 for gene knockdown in Y. pestis Multiple genes harbored on either the chromosome or plasmids of Y. pestis were efficiently knocked down (up to 380-fold) in a strictly anhydrotetracycline-inducible manner using this CRISPRi approach. Knockdown of hmsH (responsible for biofilm formation) or cspB (encoding a cold shock protein) resulted in greatly decreased biofilm formation or impaired cold tolerance in in vitro phenotypic assays. Furthermore, silencing of the virulence-associated genes yscB or ail using this CRISPRi system resulted in attenuation of virulence in HeLa cells and mice similar to that previously reported for yscB and ail null mutants. Taken together, our results confirm that this optimized CRISPRi system can reversibly and efficiently repress the expression of target genes in Y. pestis, providing an alternative to conventional gene knockdown techniques, as well as a strategy for high-throughput phenotypic screening of Y. pestis genes with unknown functions.IMPORTANCE Yersinia pestis is a lethal pathogen responsible for millions of human deaths in history. It has also attracted much attention for potential uses as a bioweapon or bioterrorism agent, against which new vaccines are desperately needed. However, many Y. pestis genes remain uncharacterized, greatly hampering the development of measures for plague prevention and control. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been successfully used in a variety of bacteria in functional genomic studies, but no such genetic tool has been reported in Y. pestis Here, we systematically optimized the CRISPRi approach for use in Y. pestis, which ultimately repressed target gene expression with high efficiency in a reversible manner. Knockdown of functional genes using this method produced phenotypes that were readily detected by in vitro assays, cell infection assays, and mouse infection experiments. This is a report of a CRISPRi approach in Y. pestis and highlights the potential use of this approach in high-throughput functional genomics studies of this pathogen.
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35
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36
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Hameed A, Shan-E-Ali Zaidi S, Sattar MN, Iqbal Z, Tahir MN. CRISPR technology to combat plant RNA viruses: A theoretical model for Potato virus Y (PVY) resistance. Microb Pathog 2019; 133:103551. [PMID: 31125685 DOI: 10.1016/j.micpath.2019.103551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/17/2019] [Indexed: 12/26/2022]
Abstract
RNA viruses are the most diverse phytopathogens which cause severe epidemics in important agricultural crops and threaten the global food security. Being obligatory intracellular pathogens, these viruses have developed fine-tuned evading mechanisms and are non-responsive to most of the prophylactic treatments. Additionally, their sprint ability to overcome host defense demands a broad-spectrum and durable mechanism of resistance. In context of CRISPR-Cas discoveries, some variants of Cas effectors have been characterized as programmable RNA-guided RNases in the microbial genomes and could be reprogramed in mammalian and plant cells with guided RNase activity. Recently, the RNA variants of CRISPR-Cas systems have been successfully employed in plants to engineer resistance against RNA viruses. Some variants of CRISPR-Cas9 have been tamed either for directly targeting plant RNA viruses' genome or through targeting the host genes/factors assisting in viral proliferation. The new frontiers in CRISPR-Cas discoveries, and more importantly shifting towards RNA targeting will pyramid the opportunities in plant virus research. The current review highlights the probable implications of CRISPR-Cas system to confer the pathogen-derived or host-mediated resistance against phytopathogenic RNA viruses. Furthermore, a multiplexed CRISPR-Cas13a methodology is proposed here to combat Potato virus Y (PVY); a globally diverse phytopathogen infecting multiple crops.
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Affiliation(s)
- Amir Hameed
- Akhuwat Faisalabad Institute of Research Science and Technology, Faisalabad, Pakistan; Department of Bioinformatics & Biotechnology, Government College University, Allama Iqbal Road, Faisalabad, Pakistan.
| | | | - Muhammad Naeem Sattar
- Department of Biotechnology, College of Agriculture and Food Science, King Faisal University, Box 400, Al-Ahsa, 3192, Saudi Arabia
| | - Zafar Iqbal
- Department of Plant Pathology, University of Florida, Gainesville, 32611, FL, USA
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Pan S, Li Q, Deng L, Jiang S, Jin X, Peng N, Liang Y, She Q, Li Y. A seed motif for target RNA capture enables efficient immune defence by a type III-B CRISPR-Cas system. RNA Biol 2019; 16:1166-1178. [PMID: 31096876 DOI: 10.1080/15476286.2019.1618693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide an adaptive defence against foreign nucleic acids guided by small RNAs (crRNAs) in archaea and bacteria. The Type III CRISPR systems are reported to carry RNase, RNA-activated DNase and cyclic oligoadenylate (cOA) synthetase activity, and are significantly different from other CRISPR systems. However, detailed features of target recognition, which are essential for enhancing target specificity remain unknown in Type III CRISPR systems. Here, we show that the Type III-B Cmr-α system in S. islandicus generates two constant lengths of crRNA independent of the length of the spacer. Either mutation at the 3'-end of crRNA or target truncation greatly influences the target capture and cleavage by the Cmr-α effector complex. Furthermore, we found that cleavage at the tag-proximal site on the target RNA by the Cmr-α RNP complex is delayed relative to the other sites, which probably provides Cas10 more time to function as a guard against invaders. Using a mutagenesis assay in vivo, we discovered that a seed motif located at the tag-distal region of the crRNA is required by Cmr1α for target RNA capture by the Cmr-α system thereby enhancing target specificity and efficiency. These findings further refine the model for immune defence of Type III-B CRISPR-Cas system, commencing on capture, cleavage and regulation.
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Affiliation(s)
- Saifu Pan
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Qi Li
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Ling Deng
- b Archaea Centre, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Suping Jiang
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Xuexia Jin
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Nan Peng
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Yunxiang Liang
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
| | - Qunxin She
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China.,b Archaea Centre, Department of Biology, University of Copenhagen , Copenhagen , Denmark
| | - Yingjun Li
- a State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University , Wuhan , China
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38
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Koonin EV, Makarova KS. Origins and evolution of CRISPR-Cas systems. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180087. [PMID: 30905284 PMCID: PMC6452270 DOI: 10.1098/rstb.2018.0087] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2018] [Indexed: 12/11/2022] Open
Abstract
CRISPR-Cas, the bacterial and archaeal adaptive immunity systems, encompass a complex machinery that integrates fragments of foreign nucleic acids, mostly from mobile genetic elements (MGE), into CRISPR arrays embedded in microbial genomes. Transcripts of the inserted segments (spacers) are employed by CRISPR-Cas systems as guide (g)RNAs for recognition and inactivation of the cognate targets. The CRISPR-Cas systems consist of distinct adaptation and effector modules whose evolutionary trajectories appear to be at least partially independent. Comparative genome analysis reveals the origin of the adaptation module from casposons, a distinct type of transposons, which employ a homologue of Cas1 protein, the integrase responsible for the spacer incorporation into CRISPR arrays, as the transposase. The origin of the effector module(s) is far less clear. The CRISPR-Cas systems are partitioned into two classes, class 1 with multisubunit effectors, and class 2 in which the effector consists of a single, large protein. The class 2 effectors originate from nucleases encoded by different MGE, whereas the origin of the class 1 effector complexes remains murky. However, the recent discovery of a signalling pathway built into the type III systems of class 1 might offer a clue, suggesting that type III effector modules could have evolved from a signal transduction system involved in stress-induced programmed cell death. The subsequent evolution of the class 1 effector complexes through serial gene duplication and displacement, primarily of genes for proteins containing RNA recognition motif domains, can be hypothetically reconstructed. In addition to the multiple contributions of MGE to the evolution of CRISPR-Cas, the reverse flow of information is notable, namely, recruitment of minimalist variants of CRISPR-Cas systems by MGE for functions that remain to be elucidated. Here, we attempt a synthesis of the diverse threads that shed light on CRISPR-Cas origins and evolution. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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39
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Faure G, Shmakov SA, Makarova KS, Wolf YI, Crawley AB, Barrangou R, Koonin EV. Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems. RNA Biol 2019; 16:435-448. [PMID: 30103650 PMCID: PMC6546382 DOI: 10.1080/15476286.2018.1493331] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/12/2018] [Indexed: 11/01/2022] Open
Abstract
Trans-activating CRISPR (tracr) RNA is a distinct RNA species that interacts with the CRISPR (cr) RNA to form the dual guide (g) RNA in type II and subtype V-B CRISPR-Cas systems. The tracrRNA-crRNA interaction is essential for pre-crRNA processing as well as target recognition and cleavage. The tracrRNA consists of an antirepeat, which forms an imperfect hybrid with the repeat in the crRNA, and a distal region containing a Rho-independent terminator. Exhaustive comparative analysis of the sequences and predicted structures of the Class 2 CRISPR guide RNAs shows that all these guide RNAs share distinct structural features, in particular, the nexus stem-loop that separates the repeat-antirepeat hybrid from the distal portion of the tracrRNA and the conserved GU pair at that end of the hybrid. These structural constraints might ensure full exposure of the spacer for target recognition. Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection. An evolutionary scenario is proposed whereby tracrRNAs evolved on multiple occasions, via rearrangement of a CRISPR array to form the antirepeat in different locations with respect to the array. A functional tracrRNA would form if, in the new location, the antirepeat is flanked by sequences that meet the minimal requirements for a promoter and a Rho-independent terminator. Alternatively, or additionally, the antirepeat sequence could be occasionally 'reset' by recombination with a repeat, restoring the functionality of tracrRNAs that drift beyond the required minimal hybrid stability.
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Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sergey A. Shmakov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Alexandra B. Crawley
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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40
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Hadidi A. Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics. Viruses 2019; 11:E120. [PMID: 30699972 PMCID: PMC6409718 DOI: 10.3390/v11020120] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022] Open
Abstract
Viroid discovery as well as the economic significance of viroids and biological properties are presented. Next-generation sequencing (NGS) technologies combined with informatics have been applied to viroid research and diagnostics for almost a decade. NGS provides highly efficient, rapid, low-cost high-throughput sequencing of viroid genomes and of the 21⁻24 nt vd-sRNAs generated by the RNA silencing defense of the host. NGS has been utilized in various viroid studies which are presented. The discovery during the last few years that prokaryotes have heritable adaptive immunity mediated through clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated Cas proteins, have led to transformative advances in molecular biology, notably genome engineering and most recently molecular diagnostics. The potential application of the CRISPR-Cas13a system for engineering viroid interference in plants is suggested by targeting specific motifs of three economically important viroids. The CRISPR-Cas13 system has been utilized recently for the accurate detection of human RNA viruses by visual read out in 90 min or less and by paper-based assay. Multitarget RNA tests by this technology have a good potential for application as a rapid and accurate diagnostic assay for known viroids. The CRISPR/Cas system will work only for known viroids in contrast to NGS, but it should be much faster.
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Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA.
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41
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Watters KE, Fellmann C, Bai HB, Ren SM, Doudna JA. Systematic discovery of natural CRISPR-Cas12a inhibitors. Science 2018; 362:236-239. [PMID: 30190307 DOI: 10.1126/science.aau5138] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/23/2018] [Indexed: 12/18/2022]
Abstract
Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility for synthetic genome engineering, agricultural genomics, and biomedical applications. Although bacteria harboring CRISPR-Cas9 or CRISPR-Cas3 adaptive immune systems sometimes acquire mobile genetic elements encoding anti-CRISPR proteins that inhibit Cas9, Cas3, or the DNA-binding Cascade complex, no such inhibitors have been found for CRISPR-Cas12a. Here we use a comprehensive bioinformatic and experimental screening approach to identify three different inhibitors that block or diminish CRISPR-Cas12a-mediated genome editing in human cells. We also find a widespread connection between CRISPR self-targeting and inhibitor prevalence in prokaryotic genomes, suggesting a straightforward path to the discovery of many more anti-CRISPRs from the microbial world.
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Affiliation(s)
- Kyle E Watters
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | - Hua B Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shawn M Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Li Ka Shing Biomedical and Health Sciences Center, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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42
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Faure G, Makarova KS, Koonin EV. CRISPR-Cas: Complex Functional Networks and Multiple Roles beyond Adaptive Immunity. J Mol Biol 2018; 431:3-20. [PMID: 30193985 DOI: 10.1016/j.jmb.2018.08.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/26/2023]
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system that functions by incorporating fragments of foreign DNA into CRISPR arrays. The arrays containing spacers derived from foreign DNA are transcribed, and the transcripts are processed to generate spacer-containing mature CRISPR-RNAs that are employed as guides to specifically recognize and cleave the DNA or RNA of the cognate parasitic genetic elements. The CRISPR-Cas systems show remarkable complexity and diversity of molecular organization and appear to be involved in various cellular functions that are distinct from, even if connected to, adaptive immunity. In this review, we discuss some of such functional links of CRISPR-Cas systems including their effect on horizontal gene transfer that can be either inhibitory or stimulatory, connections between CRISPR-Cas and DNA repair systems as well as programmed cell death and signal transduction mechanisms, and potential role of CRISPR-Cas in transposon integration and plasmid maintenance. The interplay between the primary function of CRISPR-Cas as an adaptive immunity mechanism and these other roles defines the richness of the biological effects of these systems and affects their spread among bacteria and archaea.
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Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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43
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Jeon Y, Choi YH, Jang Y, Yu J, Goo J, Lee G, Jeong YK, Lee SH, Kim IS, Kim JS, Jeong C, Lee S, Bae S. Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Nat Commun 2018; 9:2777. [PMID: 30018371 PMCID: PMC6050341 DOI: 10.1038/s41467-018-05245-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/20/2018] [Indexed: 12/24/2022] Open
Abstract
Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.
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Affiliation(s)
- Yongmoon Jeon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - You Hee Choi
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Yunsu Jang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jiyoung Goo
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - Gyejun Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - You Kyeong Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Seung Hwan Lee
- Center for Genome Engineering, Institute for Basic Science, Seoul, 08826, South Korea
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, 28116, South Korea
| | - In-San Kim
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, 08826, South Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Cherlhyun Jeong
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea.
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea.
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea.
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44
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Wei W, Zhang S, Fleming J, Chen Y, Li Z, Fan S, Liu Y, Wang W, Wang T, Liu Y, Ren B, Wang M, Jiao J, Chen Y, Zhou Y, Zhou Y, Gu S, Zhang X, Wan L, Chen T, Zhou L, Chen Y, Zhang XE, Li C, Zhang H, Bi L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features. FASEB J 2018; 33:1496-1509. [PMID: 29979631 DOI: 10.1096/fj.201800557rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are prokaryotic adaptive immune systems against invading nucleic acids. CRISPR locus variability has been exploited in evolutionary and epidemiological studies of Mycobacterium tuberculosis, the causative agent of tuberculosis, for over 20 yr, yet the biological function of this type III-A system is largely unexplored. Here, using cell biology and biochemical, mutagenic, and RNA-seq approaches, we show it is active in invader defense and has features atypical of type III-A systems: mature CRISPR RNA (crRNA) in its crRNA-CRISPR/Cas protein complex are of uniform length (∼71 nt) and appear not to be subject to 3'-end processing after Cas6 cleavage of repeat RNA 8 nt from its 3' end. crRNAs generated resemble mature crRNA in type I systems, having both 5' (8 nt) and 3' (28 nt) repeat tags. Cas6 cleavage of repeat RNA is ion dependent, and accurate cleavage depends on the presence of a 3' hairpin in the repeat RNA and the sequence of its stem base nucleotides. This study unveils further diversity among CRISPR/Cas systems and provides insight into the crRNA recognition mechanism in M. tuberculosis, providing a foundation for investigating the potential of a type III-A-based genome editing system.-Wei, W., Zhang, S., Fleming, J., Chen, Y., Li, Z., Fan, S., Liu, Y., Wang, W., Wang, T., Liu, Y., Ren, B., Wang, M., Jiao, J., Chen, Y., Zhou, Y., Zhou, Y., Gu, S., Zhang, X., Wan, L., Chen, T., Zhou, L., Chen, Y., Zhang, X.-E., Li, C., Zhang, H., Bi, L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features.
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Affiliation(s)
- Wenjing Wei
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Ying Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shanghua Fan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yi Liu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Wei Wang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Baiguang Ren
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ming Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianjian Jiao
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Yafeng Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Shoujin Gu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Xiaoli Zhang
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Li Wan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tao Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Yong Chen
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Xian-En Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Chuanyou Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lijun Bi
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China.,Guangdong Province Key Laboratory of Tuberculosis Systems Biology and Translational Medicine, Foshan, China
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45
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Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis. Proc Natl Acad Sci U S A 2018; 115:E5307-E5316. [PMID: 29784811 DOI: 10.1073/pnas.1803440115] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity consist of direct repeat arrays separated by unique spacers and multiple CRISPR-associated (cas) genes encoding proteins that mediate all stages of the CRISPR response. In addition to the relatively small set of core cas genes that are typically present in all CRISPR-Cas systems of a given (sub)type and are essential for the defense function, numerous genes occur in CRISPR-cas loci only sporadically. Some of these have been shown to perform various ancillary roles in CRISPR response, but the functional relevance of most remains unknown. We developed a computational strategy for systematically detecting genes that are likely to be functionally linked to CRISPR-Cas. The approach is based on a "CRISPRicity" metric that measures the strength of CRISPR association for all protein-coding genes from sequenced bacterial and archaeal genomes. Uncharacterized genes with CRISPRicity values comparable to those of cas genes are considered candidate CRISPR-linked genes. We describe additional criteria to predict functionally relevance for genes in the candidate set and identify 79 genes as strong candidates for functional association with CRISPR-Cas systems. A substantial majority of these CRISPR-linked genes reside in type III CRISPR-cas loci, which implies exceptional functional versatility of type III systems. Numerous candidate CRISPR-linked genes encode integral membrane proteins suggestive of tight membrane association of CRISPR-Cas systems, whereas many others encode proteins implicated in various signal transduction pathways. These predictions provide ample material for improving annotation of CRISPR-cas loci and experimental characterization of previously unsuspected aspects of CRISPR-Cas system functionality.
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46
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He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X. Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 2018; 3:461-469. [PMID: 29507349 PMCID: PMC11249088 DOI: 10.1038/s41564-018-0120-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/30/2018] [Indexed: 11/09/2022]
Abstract
Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enzymatic function using anti-CRISPR proteins (Acrs). Acrs have been found in many bacteriophages but so far not in archaeal viruses, despite the near ubiquity of CRISPR-Cas systems in archaea. Here, we report the functional and structural characterization of two archaeal Acrs from the lytic rudiviruses, SIRV2 and SIRV3. We show that a 4 kb deletion in the SIRV2 genome dramatically reduces infectivity in Sulfolobus islandicus LAL14/1 that carries functional CRISPR-Cas subtypes I-A, I-D and III-B. Subsequent insertion of a single gene from SIRV3, gp02 (AcrID1), which is conserved in the deleted fragment, successfully restored infectivity. We demonstrate that AcrID1 protein inhibits the CRISPR-Cas subtype I-D system by interacting directly with Cas10d protein, which is required for the interference stage. Sequence and structural analysis of AcrID1 show that it belongs to a conserved family of compact, dimeric αβ-sandwich proteins characterized by extreme pH and temperature stability and a tendency to form protein fibres. We identify about 50 homologues of AcrID1 in four archaeal viral families demonstrating the broad distribution of this group of anti-CRISPR proteins.
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Affiliation(s)
- Fei He
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Lan B Van
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anders L Kjeldsen
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Dedola
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Ditlev E Brodersen
- Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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47
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Klompe SE, Sternberg SH. Harnessing "A Billion Years of Experimentation": The Ongoing Exploration and Exploitation of CRISPR-Cas Immune Systems. CRISPR J 2018; 1:141-158. [PMID: 31021200 PMCID: PMC6636882 DOI: 10.1089/crispr.2018.0012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The famed physicist-turned-biologist, Max Delbrück, once remarked that, for physicists, "the field of bacterial viruses is a fine playground for serious children who ask ambitious questions." Early discoveries in that playground helped establish molecular genetics, and half a century later, biologists delving into the same field have ushered in the era of precision genome engineering. The focus has of course shifted-from bacterial viruses and their mechanisms of infection to the bacterial hosts and their mechanisms of immunity-but it is the very same evolutionary arms race that continues to awe and inspire researchers worldwide. In this review, we explore the remarkable diversity of CRISPR-Cas adaptive immune systems, describe the molecular components that mediate nucleic acid targeting, and outline the use of these RNA-guided machines for biotechnology applications. CRISPR-Cas research has yielded far more than just Cas9-based genome-editing tools, and the wide-reaching, innovative impacts of this fascinating biological playground are sure to be felt for years to come.
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Affiliation(s)
- Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University , New York, New York
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48
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Zhang X, Liu X, Yang F, Chen L. Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation. Front Microbiol 2018; 9:577. [PMID: 29636744 PMCID: PMC5880901 DOI: 10.3389/fmicb.2018.00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
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Zhang J, Zong W, Hong W, Zhang ZT, Wang Y. Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production. Metab Eng 2018. [PMID: 29530750 DOI: 10.1016/j.ymben.2018.03.007] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although CRISPR-Cas9/Cpf1 have been employed as powerful genome engineering tools, heterologous CRISPR-Cas9/Cpf1 are often difficult to introduce into bacteria and archaea due to their severe toxicity. Since most prokaryotes harbor native CRISPR-Cas systems, genome engineering can be achieved by harnessing these endogenous immune systems. Here, we report the exploitation of Type I-B CRISPR-Cas of Clostridium tyrobutyricum for genome engineering. In silico CRISPR array analysis and plasmid interference assay revealed that TCA or TCG at the 5'-end of the protospacer was the functional protospacer adjacent motif (PAM) for CRISPR targeting. With a lactose inducible promoter for CRISPR array expression, we significantly decreased the toxicity of CRISPR-Cas and enhanced the transformation efficiency, and successfully deleted spo0A with an editing efficiency of 100%. We further evaluated effects of the spacer length on genome editing efficiency. Interestingly, spacers ≤ 20 nt led to unsuccessful transformation consistently, likely due to severe off-target effects; while a spacer of 30-38 nt is most appropriate to ensure successful transformation and high genome editing efficiency. Moreover, multiplex genome editing for the deletion of spo0A and pyrF was achieved in a single transformation, with an editing efficiency of up to 100%. Finally, with the integration of the alcohol dehydrogenase gene (adhE1 or adhE2) to replace cat1 (the key gene responsible for butyrate production and previously could not be deleted), two mutants were created for n-butanol production, with the butanol titer reached historically record high of 26.2 g/L in a batch fermentation. Altogether, our results demonstrated the easy programmability and high efficiency of endogenous CRISPR-Cas. The developed protocol herein has a broader applicability to other prokaryotes containing endogenous CRISPR-Cas systems. C. tyrobutyricum could be employed as an excellent platform to be engineered for biofuel and biochemical production using the CRISPR-Cas based genome engineering toolkit.
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Affiliation(s)
- Jie Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA
| | - Wenming Zong
- Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA; School of Engineering, Anhui Agricultural University, Hefei 230036, China
| | - Wei Hong
- Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA; Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University), Ministry of Education, Guiyang 550000, China
| | - Zhong-Tian Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL 36849, USA; Center for Bioenergy and Bioproducts, Auburn University, Auburn, AL 36849, USA.
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50
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Silas S, Jain N, Stadler M, Fu BXH, Sánchez-Amat A, Fire AZ, Arribere J. A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria. Bio Protoc 2018; 8:e2727. [PMID: 29600253 PMCID: PMC5870890 DOI: 10.21769/bioprotoc.2727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 11/02/2022] Open
Abstract
Next generation high-throughput sequencing has enabled sensitive and unambiguous analysis of RNA populations in cells. Here, we describe a method for isolation and strand-specific sequencing of small RNA pools from bacteria that can be multiplexed to accommodate multiple biological samples in a single experiment. Small RNAs are isolated by polyacrylamide gel electrophoresis and treated with T4 polynucleotide kinase. This allows for 3' adapter ligation to CRISPR RNAs, which don't have pre-existing 3'-OH ends. Pre-adenylated adapters are then ligated using T4 RNA ligase 1 in the absence of ATP and with a high concentration of polyethylene glycol (PEG). The 3' capture step enables precise determination of the 3' ends of diverse RNA molecules. Additionally, a random hexamer in the ligated adapter helps control for potential downstream amplification bias. Following reverse-transcription, the cDNA product is circularized and libraries are prepared by PCR. We show that the amplified library need not be visible by gel electrophoresis for efficient sequencing of the desired product. Using this method, we routinely prepare RNA sequencing libraries from minute amounts of purified small RNA. This protocol is tailored to assay for CRISPR RNA biogenesis in bacteria through sequencing of mature CRISPR RNAs, but can be used to sequence diverse classes of small RNAs. We also provide a fully worked example of our data processing pipeline, with instructions for running the provided scripts.
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Affiliation(s)
- Sukrit Silas
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Nimit Jain
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael Stadler
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Becky Xu Hua Fu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Andrew Z. Fire
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joshua Arribere
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of MCD Biology, University of California, Santa Cruz, CA, USA
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