1
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Binder SC, Schneberger N, Schmitz M, Engeser M, Geyer M, Rouillon C, Hagelueken G. The SAVED domain of the type III CRISPR protease CalpL is a ring nuclease. Nucleic Acids Res 2024:gkae676. [PMID: 39166476 DOI: 10.1093/nar/gkae676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/18/2024] [Accepted: 07/27/2024] [Indexed: 08/23/2024] Open
Abstract
Prokaryotic CRISPR-Cas immune systems detect and cleave foreign nucleic acids. In type III CRISPR-Cas systems, the Cas10 subunit of the activated recognition complex synthesizes cyclic oligoadenylates (cOAs), second messengers that activate downstream ancillary effector proteins. Once the viral attack has been weathered, elimination of extant cOA is essential to limit the antiviral response and to allow cellular recovery. Various families of ring nucleases have been identified, specializing in the degradation of cOAs either as standalone enzymes or as domains of effector proteins. Here we describe the ring nuclease activity inherent in the SAVED domain of the cA4-activated CRISPR Lon protease CalpL. We characterize the kinetics of cA4 cleavage and identify key catalytic residues. We demonstrate that cA4-induced oligomerization of CalpL is essential not only for activation of the protease, but is also required for nuclease activity. Further, the nuclease activity of CalpL poses a limitation to the protease reaction, indicating a mechanism for regulation of the CalpL/T/S signaling cascade. This work is the first demonstration of a catalytic SAVED domain and gives new insights into the dynamics of transcriptional adaption in CRISPR defense systems.
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Affiliation(s)
- Sophie C Binder
- Institute of Structural Biology, Venusberg-Campus 1, University of Bonn, Bonn, Germany
| | - Niels Schneberger
- Institute of Structural Biology, Venusberg-Campus 1, University of Bonn, Bonn, Germany
| | - Maximilian Schmitz
- Institute of Structural Biology, Venusberg-Campus 1, University of Bonn, Bonn, Germany
| | - Marianne Engeser
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, Venusberg-Campus 1, University of Bonn, Bonn, Germany
| | - Christophe Rouillon
- Institut Pasteur, Université Paris Cité, Synthetic Biology, 75015 Paris, France
| | - Gregor Hagelueken
- Institute of Structural Biology, Venusberg-Campus 1, University of Bonn, Bonn, Germany
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2
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Zhang D, Du L, Gao H, Yuan C, Lin Z. Structural insight into the Csx1-Crn2 fusion self-limiting ribonuclease of type III CRISPR system. Nucleic Acids Res 2024; 52:8419-8430. [PMID: 38967023 PMCID: PMC11317161 DOI: 10.1093/nar/gkae569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
In the type III CRISPR system, cyclic oligoadenylate (cOA) molecules act as second messengers, activating various promiscuous ancillary nucleases that indiscriminately degrade host and viral DNA/RNA. Conversely, ring nucleases, by specifically cleaving cOA molecules, function as off-switches to protect host cells from dormancy or death, and allow viruses to counteract immune responses. The fusion protein Csx1-Crn2, combining host ribonuclease with viral ring nuclease, represents a unique self-limiting ribonuclease family. Here, we describe the structures of Csx1-Crn2 from the organism of Marinitoga sp., in both its full-length and truncated forms, as well as in complex with cA4. We show that Csx1-Crn2 operates as a homo-tetramer, a configuration crucial for preserving the structural integrity of the HEPN domain and ensuring effective ssRNA cleavage. The binding of cA4 to the CARF domain triggers significant conformational changes across the CARF, HTH, and into the HEPN domains, leading the two R-X4-6-H motifs to form a composite catalytic site. Intriguingly, an acetate ion was found to bind at this composite site by mimicking the scissile phosphate. Further molecular docking analysis reveals that the HEPN domain can accommodate a single ssRNA molecule involving both R-X4-6-H motifs, underscoring the importance of HEPN domain dimerization for its activation.
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Affiliation(s)
- Danping Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Liyang Du
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Haishan Gao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
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3
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Roberts A, Spang D, Sanozky-Dawes R, Nethery MA, Barrangou R. Characterization of Ligilactobacillus salivarius CRISPR-Cas systems. mSphere 2024; 9:e0017124. [PMID: 38990000 PMCID: PMC11288051 DOI: 10.1128/msphere.00171-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024] Open
Abstract
Ligilactobacillus is a diverse genus among lactobacilli with phenotypes that reflect adaptation to various hosts. CRISPR-Cas systems are highly prevalent within lactobacilli, and Ligilactobacillus salivarius, the most abundant species of Ligilactobacillus, possesses both DNA- and RNA-targeting CRISPR-Cas systems. In this study, we explore the presence and functional properties of I-B, I-C, I-E, II-A, and III-A CRISPR-Cas systems in over 500 Ligilactobacillus genomes, emphasizing systems found in L. salivarius. We examined the I-E, II-A, and III-A CRISPR-Cas systems of two L. salivarius strains and observed occurrences of split cas genes and differences in CRISPR RNA maturation in native hosts. This prompted testing of the single Cas9 and multiprotein Cascade and Csm CRISPR-Cas effector complexes in a cell-free context to demonstrate the functionality of these systems. We also predicted self-targeting spacers within L. salivarius CRISPR-Cas systems and found that nearly a third of L. salivarius genomes possess unique self-targeting spacers that generally target elements other than prophages. With these two L. salivarius strains, we performed prophage induction coupled with RNA sequencing and discovered that the prophages residing within these strains are inducible and likely active elements, despite targeting by CRISPR-Cas systems. These findings deepen our comprehension of CRISPR-Cas systems in L. salivarius, further elucidating their relationship with associated prophages and providing a functional basis for the repurposing of these Cas effectors for bacterial manipulation. IMPORTANCE Ligilactobacillus salivarius is a diverse bacterial species widely used in the food and dietary supplement industries. In this study, we investigate the occurrence and diversity of their adaptive immune systems, CRISPR-Cas, in over 500 genomes. We establish their function and provide insights into their role in the interplay between the bacterial host and the predatory phages that infect them. Such findings expand our knowledge about these important CRISPR-Cas immune systems widespread across the bacterial tree of life and also provide a technical basis for the repurposing of these molecular machines for the development of molecular biology tools and the manipulation and engineering of bacteria and other life forms.
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Affiliation(s)
- Avery Roberts
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Daniel Spang
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Rosemary Sanozky-Dawes
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | | | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
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4
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Goswami HN, Ahmadizadeh F, Wang B, Addo-Yobo D, Zhao Y, Whittington AC, He H, Terns MP, Li H. Molecular basis for cA6 synthesis by a type III-A CRISPR-Cas enzyme and its conversion to cA4 production. Nucleic Acids Res 2024:gkae603. [PMID: 38989619 DOI: 10.1093/nar/gkae603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024] Open
Abstract
The type III-A (Csm) CRISPR-Cas systems are multi-subunit and multipronged prokaryotic enzymes in guarding the hosts against viral invaders. Beyond cleaving activator RNA transcripts, Csm confers two additional activities: shredding single-stranded DNA and synthesizing cyclic oligoadenylates (cOAs) by the Cas10 subunit. Known Cas10 enzymes exhibit a fascinating diversity in cOA production. Three major forms-cA3, cA4 and cA6have been identified, each with the potential to trigger unique downstream effects. Whereas the mechanism for cOA-dependent activation is well characterized, the molecular basis for synthesizing different cOA isoforms remains unclear. Here, we present structural characterization of a cA6-producing Csm complex during its activation by an activator RNA. Analysis of the captured intermediates of cA6 synthesis suggests a 3'-to-5' nucleotidyl transferring process. Three primary adenine binding sites can be identified along the chain elongation path, including a unique tyrosine-threonine dyad found only in the cA6-producing Cas10. Consistently, disrupting the tyrosine-threonine dyad specifically impaired cA6 production while promoting cA4 production. These findings suggest that Cas10 utilizes a unique enzymatic mechanism for forming the phosphodiester bond and has evolved distinct strategies to regulate the cOA chain length.
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Affiliation(s)
- Hemant N Goswami
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Fozieh Ahmadizadeh
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Bing Wang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Doreen Addo-Yobo
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - A Carl Whittington
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Michael P Terns
- Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Hong Li
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
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5
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Hoikkala V, Graham S, White MF. Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families. Nucleic Acids Res 2024; 52:7129-7141. [PMID: 38808661 PMCID: PMC11229360 DOI: 10.1093/nar/gkae462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
Recognition of RNA from invading mobile genetic elements (MGE) prompts type III CRISPR systems to activate an HD nuclease domain and/or a nucleotide cyclase domain in the Cas10 subunit, eliciting an immune response. The cyclase domain can generate a range of nucleotide second messengers, which in turn activate a diverse family of ancillary effector proteins. These provide immunity by non-specific degradation of host and MGE nucleic acids or proteins, perturbation of membrane potentials, transcriptional responses, or the arrest of translation. The wide range of nucleotide activators and downstream effectors generates a complex picture that is gradually being resolved. Here, we carry out a global bioinformatic analysis of type III CRISPR loci in prokaryotic genomes, defining the relationships of Cas10 proteins and their ancillary effectors. Our study reveals that cyclic tetra-adenylate is by far the most common signalling molecule used and that many loci have multiple effectors. These typically share the same activator and may work synergistically to combat MGE. We propose four new candidate effector protein families and confirm experimentally that the Csm6-2 protein, a highly diverged, fused Csm6 effector, is a ribonuclease activated by cyclic hexa-adenylate.
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Affiliation(s)
- Ville Hoikkala
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
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6
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Fuentenebro Navas D, Steens JA, de Lannoy C, Noordijk B, Pfeffer M, de Ridder D, H.J. Staals R, Schmid S. Nanopores Reveal the Stoichiometry of Single Oligoadenylates Produced by Type III CRISPR-Cas. ACS NANO 2024; 18:16505-16515. [PMID: 38875527 PMCID: PMC11223493 DOI: 10.1021/acsnano.3c11769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Cyclic oligoadenylates (cOAs) are small second messenger molecules produced by the type III CRISPR-Cas system as part of the prokaryotic immune response. The role of cOAs is to allosterically activate downstream effector proteins that induce dormancy or cell death, and thus abort viral spread through the population. Interestingly, different type III systems have been reported to utilize different cOA stoichiometries (with 3 to 6 adenylate monophosphates). However, so far, their characterization has only been possible in bulk and with sophisticated equipment, while a portable assay with single-molecule resolution has been lacking. Here, we demonstrate the label-free detection of single cOA molecules using a simple protein nanopore assay. It sensitively identifies the stoichiometry of individual cOA molecules and their mixtures from synthetic and enzymatic origin. To achieve this, we trained a convolutional neural network (CNN) and validated it with a series of experiments on mono- and polydisperse cOA samples. Ultimately, we determined the stoichiometric composition of cOAs produced enzymatically by the CRISPR type III-A and III-B variants of Thermus thermophilus and confirmed the results by liquid chromatography-mass spectroscopy (LC-MS). Interestingly, both variants produce cOAs of nearly identical composition (within experimental uncertainties), and we discuss the biological implications of this finding. The presented nanopore-CNN workflow with single cOA resolution can be adapted to many other signaling molecules (including eukaryotic ones), and it may be integrated into portable handheld devices with potential point-of-care applications.
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Affiliation(s)
- David Fuentenebro Navas
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
| | - Jurre A. Steens
- Laboratory
of Microbiology, Wageningen University and
Research, Stippeneng
4, 6708WE Wageningen, The Netherlands
| | - Carlos de Lannoy
- Bioinformatics
Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department
of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Ben Noordijk
- Bioinformatics
Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Michael Pfeffer
- Department
of Chemistry, University of Basel, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Dick de Ridder
- Bioinformatics
Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Raymond H.J. Staals
- Laboratory
of Microbiology, Wageningen University and
Research, Stippeneng
4, 6708WE Wageningen, The Netherlands
| | - Sonja Schmid
- Laboratory
of Biophysics, Wageningen University and
Research, Stippeneng 4, 6708WE Wageningen, The Netherlands
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7
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Chi H, White MF. RNA processing by the CRISPR-associated NYN ribonuclease. Biochem J 2024; 481:793-804. [PMID: 38785320 PMCID: PMC11346440 DOI: 10.1042/bcj20240151] [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: 04/06/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 05/25/2024]
Abstract
CRISPR-Cas systems confer adaptive immunity in prokaryotes, facilitating the recognition and destruction of invasive nucleic acids. Type III CRISPR systems comprise large, multisubunit ribonucleoprotein complexes with a catalytic Cas10 subunit. When activated by the detection of foreign RNA, Cas10 generates nucleotide signalling molecules that elicit an immune response by activating ancillary effector proteins. Among these systems, the Bacteroides fragilis type III CRISPR system was recently shown to produce a novel signal molecule, SAM-AMP, by conjugating ATP and SAM. SAM-AMP regulates a membrane effector of the CorA family to provide immunity. Here, we focus on NYN, a ribonuclease encoded within this system, probing its potential involvement in crRNA maturation. Structural modelling and in vitro ribonuclease assays reveal that NYN displays robust sequence-nonspecific, Mn2+-dependent ssRNA-cleavage activity. Our findings suggest a role for NYN in trimming crRNA intermediates into mature crRNAs, which is necessary for type III CRISPR antiviral defence. This study sheds light on the functional relevance of CRISPR-associated NYN proteins and highlights the complexity of CRISPR-mediated defence strategies in bacteria.
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Affiliation(s)
- Haotian Chi
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, U.K
| | - Malcolm F. White
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, U.K
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8
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Agapov A, Panteleev V, Kropocheva E, Kanevskaya A, Esyunina D, Kulbachinskiy A. Prokaryotic Argonaute nuclease cooperates with co-encoded RNase to acquire guide RNAs and target invader DNA. Nucleic Acids Res 2024; 52:5895-5911. [PMID: 38716875 PMCID: PMC11162769 DOI: 10.1093/nar/gkae345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 06/11/2024] Open
Abstract
Argonautes are an evolutionary conserved family of programmable nucleases that identify target nucleic acids using small guide oligonucleotides. In contrast to eukaryotic Argonautes (eAgos) that act on RNA, most studied prokaryotic Argonautes (pAgos) recognize DNA targets. Similarly to eAgos, pAgos can protect prokaryotic cells from invaders, but the biogenesis of guide oligonucleotides that confer them specificity to their targets remains poorly understood. Here, we have identified a new group of RNA-guided pAgo nucleases and demonstrated that a representative pAgo from this group, AmAgo from the mesophilic bacterium Alteromonas macleodii, binds guide RNAs of varying lengths for specific DNA targeting. Unlike most pAgos and eAgos, AmAgo is strictly specific to hydroxylated RNA guides containing a 5'-adenosine. AmAgo and related pAgos are co-encoded with a conserved RNA endonuclease from the HEPN superfamily (Ago-associated protein, Agap-HEPN). In vitro, Agap cleaves RNA between guanine and adenine nucleotides producing hydroxylated 5'-A guide oligonucleotides bound by AmAgo. In vivo, Agap cooperates with AmAgo in acquiring guide RNAs and counteracting bacteriophage infection. The AmAgo-Agap pair represents the first example of a pAgo system that autonomously produces RNA guides for DNA targeting and antiviral defense, which holds promise for programmable DNA targeting in biotechnology.
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Affiliation(s)
- Aleksei Agapov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Vladimir Panteleev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | | | - Anna Kanevskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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9
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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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10
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Irmisch P, Mogila I, Samatanga B, Tamulaitis G, Seidel R. Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex. Nucleic Acids Res 2024; 52:3896-3910. [PMID: 38340341 DOI: 10.1093/nar/gkae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The type III CRISPR-Cas effector complex Csm functions as a molecular Swiss army knife that provides multilevel defense against foreign nucleic acids. The coordinated action of three catalytic activities of the Csm complex enables simultaneous degradation of the invader's RNA transcripts, destruction of the template DNA and synthesis of signaling molecules (cyclic oligoadenylates cAn) that activate auxiliary proteins to reinforce CRISPR-Cas defense. Here, we employed single-molecule techniques to connect the kinetics of RNA binding, dissociation, and DNA hydrolysis by the Csm complex from Streptococcus thermophilus. Although single-stranded RNA is cleaved rapidly (within seconds), dual-color FCS experiments and single-molecule TIRF microscopy revealed that Csm remains bound to terminal RNA cleavage products with a half-life of over 1 hour while releasing the internal RNA fragments quickly. Using a continuous fluorescent DNA degradation assay, we observed that RNA-regulated single-stranded DNase activity decreases on a similar timescale. These findings suggest that after fast target RNA cleavage the terminal RNA cleavage products stay bound within the Csm complex, keeping the Cas10 subunit activated for DNA destruction. Additionally, we demonstrate that during Cas10 activation, the complex remains capable of RNA turnover, i.e. of ongoing degradation of target RNA.
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Affiliation(s)
- Patrick Irmisch
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Irmantas Mogila
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Brighton Samatanga
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
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11
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Grüschow S, McQuarrie S, Ackermann K, McMahon S, Bode B, Gloster T, White M. CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23. Nucleic Acids Res 2024; 52:2761-2775. [PMID: 38471818 PMCID: PMC11014256 DOI: 10.1093/nar/gkae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae. Csx23 provides immunity against plasmids and phage when expressed in Escherichia coli along with its cognate type III CRISPR system. The Csx23 protein localises in the membrane using an N-terminal transmembrane α-helical domain and has a cytoplasmic C-terminal domain that binds cyclic tetra-adenylate (cA4), activating its defence function. Structural studies reveal a tetrameric structure with a novel fold that binds cA4 specifically. Using pulse EPR, we demonstrate that cA4 binding to the cytoplasmic domain of Csx23 results in a major perturbation of the transmembrane domain, consistent with the opening of a pore and/or disruption of membrane integrity. This work reveals a new class of cyclic nucleotide binding protein and provides key mechanistic detail on a membrane-associated CRISPR effector.
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Affiliation(s)
- Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Stephen McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife, KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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12
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Jungfer K, Sigg A, Jinek M. Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2. Nucleic Acids Res 2024; 52:462-473. [PMID: 38033326 PMCID: PMC10783487 DOI: 10.1093/nar/gkad1102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/26/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
Type III CRISPR-Cas systems provide adaptive immunity against foreign mobile genetic elements through RNA-guided interference. Sequence-specific recognition of RNA targets by the type III effector complex triggers the generation of cyclic oligoadenylate (cOA) second messengers that activate ancillary effector proteins, thus reinforcing the host immune response. The ancillary nuclease Can2 is activated by cyclic tetra-AMP (cA4); however, the mechanisms underlying cA4-mediated activation and substrate selectivity remain elusive. Here we report crystal structures of Thermoanaerobacter brockii Can2 (TbrCan2) in substrate- and product-bound complexes. We show that TbrCan2 is a single strand-selective DNase and RNase that binds substrates via a conserved SxTTS active site motif, and reveal molecular interactions underpinning its sequence preference for CA dinucleotides. Furthermore, we identify a molecular interaction relay linking the cA4 binding site and the nuclease catalytic site to enable divalent metal cation coordination and catalytic activation. These findings provide key insights into the molecular mechanisms of Can2 nucleases in type III CRISPR-Cas immunity and may guide their technological development for nucleic acid detection applications.
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Affiliation(s)
- Kenny Jungfer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Annina Sigg
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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13
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Stella G, Marraffini L. Type III CRISPR-Cas: beyond the Cas10 effector complex. Trends Biochem Sci 2024; 49:28-37. [PMID: 37949766 PMCID: PMC10844953 DOI: 10.1016/j.tibs.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/12/2023]
Abstract
Type III CRISPR-Cas loci encode some of the most abundant, yet complex, immune systems of prokaryotes. They are composed of a Cas10 complex that uses an RNA guide to recognize transcripts from bacteriophage and plasmid invaders. Target recognition triggers three activities within this complex: ssDNA degradation, synthesis of cyclic oligoadenylates (cOA) that act as second messengers to activate CARF-domain effectors, and cleavage of target RNA. This review covers recent research in type III CRISPR-Cas systems that looked beyond the activity of the canonical Cas10 complexes towards: (i) ancillary nucleases and understanding how they provide defense by sensing cOA molecules; (ii) ring nucleases and their role in regulating cOA production; and (iii) CRISPR-associated proteases, including the function of the Craspase complex in a transcriptional response to phage infection.
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Affiliation(s)
- Gianna Stella
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Luciano Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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14
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Du L, Zhu Q, Lin Z. Molecular mechanism of allosteric activation of the CRISPR ribonuclease Csm6 by cyclic tetra-adenylate. EMBO J 2024; 43:304-315. [PMID: 38177499 PMCID: PMC10897365 DOI: 10.1038/s44318-023-00017-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
Type III CRISPR systems are innate immune systems found in bacteria and archaea, which produce cyclic oligoadenylate (cOA) second messengers in response to viral infections. In these systems, Csm6 proteins serve as ancillary nucleases that degrade single-stranded RNA (ssRNA) upon activation by cOA. In addition, Csm6 proteins also possess cOA-degrading activity as an intrinsic off-switch to avoid degradation of host RNA and DNA that would eventually lead to cell dormancy or cell death. Here, we present the crystal structures of Thermus thermophilus (Tt) Csm6 alone, and in complex with cyclic tetra-adenylate (cA4) in both pre- and post-cleavage states. These structures establish the molecular basis of the long-range allosteric activation of TtCsm6 ribonuclease by cA4. cA4 binding induces significant conformational changes, including closure of the CARF domain, dimerization of the HTH domain, and reorganization of the R-X4-6-H motif within the HEPN domain. The cleavage of cA4 by the CARF domain restores each domain to a conformation similar to its apo state. Furthermore, we have identified hyperactive TtCsm6 variants that exhibit sustained cA4-activated RNase activity, showing great promise for their applications in genome editing and diagnostics.
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Affiliation(s)
- Liyang Du
- College of Chemistry, Fuzhou University, 350108, Fuzhou, China
| | - Qinwei Zhu
- College of Chemistry, Fuzhou University, 350108, Fuzhou, China
| | - Zhonghui Lin
- College of Chemistry, Fuzhou University, 350108, Fuzhou, China.
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15
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Mogila I, Tamulaitiene G, Keda K, Timinskas A, Ruksenaite A, Sasnauskas G, Venclovas Č, Siksnys V, Tamulaitis G. Ribosomal stalk-captured CARF-RelE ribonuclease inhibits translation following CRISPR signaling. Science 2023; 382:1036-1041. [PMID: 38033086 DOI: 10.1126/science.adj2107] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023]
Abstract
Prokaryotic type III CRISPR-Cas antiviral systems employ cyclic oligoadenylate (cAn) signaling to activate a diverse range of auxiliary proteins that reinforce the CRISPR-Cas defense. Here we characterize a class of cAn-dependent effector proteins named CRISPR-Cas-associated messenger RNA (mRNA) interferase 1 (Cami1) consisting of a CRISPR-associated Rossmann fold sensor domain fused to winged helix-turn-helix and a RelE-family mRNA interferase domain. Upon activation by cyclic tetra-adenylate (cA4), Cami1 cleaves mRNA exposed at the ribosomal A-site thereby depleting mRNA and leading to cell growth arrest. The structures of apo-Cami1 and the ribosome-bound Cami1-cA4 complex delineate the conformational changes that lead to Cami1 activation and the mechanism of Cami1 binding to a bacterial ribosome, revealing unexpected parallels with eukaryotic ribosome-inactivating proteins.
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Affiliation(s)
- Irmantas Mogila
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Konstanty Keda
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Audrone Ruksenaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania
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16
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McQuarrie S, Athukoralage JS, McMahon SA, Graham S, Ackermann K, Bode BE, White MF, Gloster TM. Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open. Nucleic Acids Res 2023; 51:10590-10605. [PMID: 37747760 DOI: 10.1093/nar/gkad739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
Type III CRISPR systems synthesize cyclic oligoadenylate (cOA) second messengers as part of a multi-faceted immune response against invading mobile genetic elements (MGEs). cOA activates non-specific CRISPR ancillary defence nucleases to create a hostile environment for MGE replication. Csm6 ribonucleases bind cOA using a CARF (CRISPR-associated Rossmann Fold) domain, resulting in activation of a fused HEPN (Higher Eukaryotes and Prokaryotes Nucleotide binding) ribonuclease domain. Csm6 enzymes are widely used in a new generation of diagnostic assays for the detection of specific nucleic acid species. However, the activation mechanism is not fully understood. Here we characterised the cyclic hexa-adenylate (cA6) activated Csm6' ribonuclease from the industrially important bacterium Streptococcus thermophilus. Crystal structures of Csm6' in the inactive and cA6 bound active states illuminate the conformational changes which trigger mRNA destruction. Upon binding of cA6, there is a close to 60° rotation between the CARF and HEPN domains, which causes the 'jaws' of the HEPN domain to open and reposition active site residues. Key to this transition is the 6H domain, a right-handed solenoid domain connecting the CARF and HEPN domains, which transmits the conformational changes for activation.
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Affiliation(s)
- Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Januka S Athukoralage
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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17
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McBride TM, Cameron SC, Fineran PC, Fagerlund RD. The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochem J 2023; 480:471-488. [PMID: 37052300 DOI: 10.1042/bcj20220073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 04/14/2023]
Abstract
Prokaryotes have adaptive defence mechanisms that protect them from mobile genetic elements and viral infection. One defence mechanism is called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins). There are six different types of CRISPR-Cas systems and multiple subtypes that vary in composition and mode of action. Type I and III CRISPR-Cas systems utilise multi-protein complexes, which differ in structure, nucleic acid binding and cleaving preference. The type I-D system is a chimera of type I and III systems. Recently, there has been a burst of research on the type I-D CRISPR-Cas system. Here, we review the mechanism, evolution and biotechnological applications of the type I-D CRISPR-Cas system.
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Affiliation(s)
- Tess M McBride
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Shaharn C Cameron
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, 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
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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18
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Du L, Zhang D, Luo Z, Lin Z. Molecular basis of stepwise cyclic tetra-adenylate cleavage by the type III CRISPR ring nuclease Crn1/Sso2081. Nucleic Acids Res 2023; 51:2485-2495. [PMID: 36807980 PMCID: PMC10018336 DOI: 10.1093/nar/gkad101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/22/2023] Open
Abstract
The cyclic oligoadenylates (cOAs) act as second messengers of the type III CRISPR immunity system through activating the auxiliary nucleases for indiscriminate RNA degradation. The cOA-degrading nucleases (ring nucleases) provide an 'off-switch' regulation of the signaling, thereby preventing cell dormancy or cell death. Here, we describe the crystal structures of the founding member of CRISPR-associated ring nuclease 1 (Crn1) Sso2081 from Saccharolobus solfataricus, alone, bound to phosphate ions or cA4 in both pre-cleavage and cleavage intermediate states. These structures together with biochemical characterizations establish the molecular basis of cA4 recognition and catalysis by Sso2081. The conformational changes in the C-terminal helical insert upon the binding of phosphate ions or cA4 reveal a gate-locking mechanism for ligand binding. The critical residues and motifs identified in this study provide a new insight to distinguish between cOA-degrading and -nondegrading CARF domain-containing proteins.
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Affiliation(s)
- Liyang Du
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Danping Zhang
- College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhipu Luo
- Correspondence may also be addressed to Zhipu Luo.
| | - Zhonghui Lin
- To whom correspondence should be addressed. Tel: +86 0591 22867273;
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19
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Abstract
CRISPR-Cas is a widespread adaptive immune system in bacteria and archaea that protects against viral infection by targeting specific invading nucleic acid sequences. Whereas some CRISPR-Cas systems sense and cleave viral DNA, type III and type VI CRISPR-Cas systems sense RNA that results from viral transcription and perhaps invasion by RNA viruses. The sequence-specific detection of viral RNA evokes a cell-wide response that typically involves global damage to halt the infection. How can one make sense of an immune strategy that encompasses broad, collateral effects rather than specific, targeted destruction? In this Review, we summarize the current understanding of RNA-targeting CRISPR-Cas systems. We detail the composition and properties of type III and type VI systems, outline the cellular defence processes that are instigated upon viral RNA sensing and describe the biological rationale behind the broad RNA-activated immune responses as an effective strategy to combat viral infection.
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20
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Patel DJ, Yu Y, Jia N. Bacterial origins of cyclic nucleotide-activated antiviral immune signaling. Mol Cell 2022; 82:4591-4610. [PMID: 36460008 PMCID: PMC9772257 DOI: 10.1016/j.molcel.2022.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Second-messenger-mediated signaling by cyclic oligonucleotides (cOs) composed of distinct base, ring size, and 3'-5'/2'-5' linkage combinations constitutes the initial trigger resulting in activation of signaling pathways that have an impact on immune-mediated antiviral defense against invading viruses and phages. Bacteria and archaea have evolved CRISPR, CBASS, Pycsar, and Thoeris surveillance complexes that involve cO-mediated activation of effectors resulting in antiviral defense through either targeted nuclease activity, effector oligomerization-mediated depletion of essential cellular metabolites or disruption of host cell membrane functions. Notably, antiviral defense capitalizes on an abortive infection mechanism, whereby infected cells die prior to completion of the phage replication cycle. In turn, phages have evolved small proteins that target and degrade/sequester cOs, thereby suppressing host immunity. This review presents a structure-based mechanistic perspective of recent advances in the field of cO-mediated antiviral defense, in particular highlighting the ancient evolutionary adaptation by metazoans of bacterial cell-autonomous innate immune mechanisms.
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Affiliation(s)
- Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
| | - You Yu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Ning Jia
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
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21
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Nemudraia A, Nemudryi A, Buyukyoruk M, Scherffius AM, Zahl T, Wiegand T, Pandey S, Nichols JE, Hall LN, McVey A, Lee HH, Wilkinson RA, Snyder LR, Jones JD, Koutmou KS, Santiago-Frangos A, Wiedenheft B. Sequence-specific capture and concentration of viral RNA by type III CRISPR system enhances diagnostic. Nat Commun 2022; 13:7762. [PMID: 36522348 PMCID: PMC9751510 DOI: 10.1038/s41467-022-35445-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Type-III CRISPR-Cas systems have recently been adopted for sequence-specific detection of SARS-CoV-2. Here, we repurpose the type III-A CRISPR complex from Thermus thermophilus (TtCsm) for programmable capture and concentration of specific RNAs from complex mixtures. The target bound TtCsm complex generates two cyclic oligoadenylates (i.e., cA3 and cA4) that allosterically activate ancillary nucleases. We show that both Can1 and Can2 nucleases cleave single-stranded RNA, single-stranded DNA, and double-stranded DNA in the presence of cA4. We integrate the Can2 nuclease with type III-A RNA capture and concentration for direct detection of SARS-CoV-2 RNA in nasopharyngeal swabs with 15 fM sensitivity. Collectively, this work demonstrates how type-III CRISPR-based RNA capture and concentration simultaneously increases sensitivity, limits time to result, lowers cost of the assay, eliminates solvents used for RNA extraction, and reduces sample handling.
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Affiliation(s)
- Anna Nemudraia
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Artem Nemudryi
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Murat Buyukyoruk
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Andrew M. Scherffius
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Trevor Zahl
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Tanner Wiegand
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Shishir Pandey
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Joseph E. Nichols
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Laina N. Hall
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Aidan McVey
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Helen H. Lee
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Royce A. Wilkinson
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Laura R. Snyder
- grid.214458.e0000000086837370Department of Chemistry, University of Michigan, Ann Arbor, MI 48105 USA
| | - Joshua D. Jones
- grid.214458.e0000000086837370Department of Chemistry, University of Michigan, Ann Arbor, MI 48105 USA
| | - Kristin S. Koutmou
- grid.214458.e0000000086837370Department of Chemistry, University of Michigan, Ann Arbor, MI 48105 USA
| | - Andrew Santiago-Frangos
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
| | - Blake Wiedenheft
- grid.41891.350000 0001 2156 6108Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717 USA
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22
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Ding J, Schuergers N, Baehre H, Wilde A. Enzymatic properties of CARF-domain proteins in Synechocystis sp. PCC 6803. Front Microbiol 2022; 13:1046388. [DOI: 10.3389/fmicb.2022.1046388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) systems provide immunity against invading genetic elements such as bacteriophages and plasmids. In type III CRISPR systems, the recognition of target RNA leads to the synthesis of cyclic oligoadenylate (cOA) second messengers that activate ancillary effector proteins via their CRISPR-associated Rossmann fold (CARF) domains. Commonly, these are ribonucleases (RNases) that unspecifically degrade both invader and host RNA. To mitigate adverse effects on cell growth, ring nucleases can degrade extant cOAs to switch off ancillary nucleases. Here we show that the model organism Synechocystis sp. PCC 6803 harbors functional CARF-domain effector and ring nuclease proteins. We purified and characterized the two ancillary CARF-domain proteins from the III-D type CRISPR system of this cyanobacterium. The Csx1 homolog, SyCsx1, is a cyclic tetraadenylate(cA4)-dependent RNase with a strict specificity for cytosine nucleotides. The second CARF-domain protein with similarity to Csm6 effectors, SyCsm6, did not show RNase activity in vitro but was able to break down cOAs and attenuate SyCsx1 RNase activity. Our data suggest that the CRISPR systems in Synechocystis confer a multilayered cA4-mediated defense mechanism.
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23
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Steens JA, Salazar CRP, Staals RH. The diverse arsenal of type III CRISPR-Cas-associated CARF and SAVED effectors. Biochem Soc Trans 2022; 50:1353-1364. [PMID: 36282000 PMCID: PMC9704534 DOI: 10.1042/bst20220289] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 09/14/2023]
Abstract
Type III CRISPR-Cas systems make use of a multi-subunit effector complex to target foreign (m)RNA transcripts complementary to the guide/CRISPR RNA (crRNA). Base-pairing of the target RNA with specialized regions in the crRNA not only triggers target RNA cleavage, but also activates the characteristic Cas10 subunit and sets in motion a variety of catalytic activities that starts with the production of cyclic oligoadenylate (cOA) second messenger molecules. These messenger molecules can activate an extensive arsenal of ancillary effector proteins carrying the appropriate sensory domain. Notably, the CARF and SAVED effector proteins have been responsible for renewed interest in type III CRISPR-Cas due to the extraordinary diversity of defenses against invading genetic elements. Whereas only a handful of CARF and SAVED proteins have been studied so far, many of them seem to provoke abortive infection, aimed to kill the host and provide population-wide immunity. A defining feature of these effector proteins is the variety of in silico-predicted catalytic domains they are fused to. In this mini-review, we discuss all currently characterized type III-associated CARF and SAVED effector proteins, highlight a few examples of predicted CARF and SAVED proteins with interesting predicted catalytic activities, and speculate how they could contribute to type III immunity.
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Affiliation(s)
- Jurre A. Steens
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Raymond H.J. Staals
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
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24
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Abstract
Advances in our understanding of prokaryotic antiphage defense mechanisms in the past few years have revealed a multitude of new cyclic nucleotide signaling molecules that play a crucial role in switching infected cells into an antiviral state. Defense pathways including type III CRISPR (clustered regularly interspaced palindromic repeats), CBASS (cyclic nucleotide-based antiphage signaling system), PYCSAR (pyrimidine cyclase system for antiphage resistance), and Thoeris all use cyclic nucleotides as second messengers to activate a diverse range of effector proteins. These effectors typically degrade or disrupt key cellular components such as nucleic acids, membranes, or metabolites, slowing down viral replication kinetics at great cost to the infected cell. Mechanisms to manipulate the levels of cyclic nucleotides are employed by cells to regulate defense pathways and by viruses to subvert them. Here we review the discovery and mechanism of the key pathways, signaling molecules and effectors, parallels and differences between the systems, open questions, and prospects for future research in this area.
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Affiliation(s)
- Januka S Athukoralage
- Department of Microbiology and Immunology, University of California, San Francisco, California, USA
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews, United Kingdom;
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25
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Zhang Y, Lin J, Tian X, Wang Y, Zhao R, Wu C, Wang X, Zhao P, Bi X, Yu Z, Han W, Peng N, Liang YX, She Q. Inactivation of Target RNA Cleavage of a III-B CRISPR-Cas System Induces Robust Autoimmunity in Saccharolobus islandicus. Int J Mol Sci 2022; 23:ijms23158515. [PMID: 35955649 PMCID: PMC9368842 DOI: 10.3390/ijms23158515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 12/04/2022] Open
Abstract
Type III CRISPR-Cas systems show the target (tg)RNA-activated indiscriminate DNA cleavage and synthesis of oligoadenylates (cOA) and a secondary signal that activates downstream nuclease effectors to exert indiscriminate RNA/DNA cleavage, and both activities are regulated in a spatiotemporal fashion. In III-B Cmr systems, cognate tgRNAs activate the two Cmr2-based activities, which are then inactivated via tgRNA cleavage by Cmr4, but how Cmr4 nuclease regulates the Cmr immunization remains to be experimentally characterized. Here, we conducted mutagenesis of Cmr4 conserved amino acids in Saccharolobus islandicus, and this revealed that Cmr4α RNase-dead (dCmr4α) mutation yields cell dormancy/death. We also found that plasmid-borne expression of dCmr4α in the wild-type strain strongly reduced plasmid transformation efficiency, and deletion of CRISPR arrays in the host genome reversed the dCmr4α inhibition. Expression of dCmr4α also strongly inhibited plasmid transformation with Cmr2αHD and Cmr2αPalm mutants, but the inhibition was diminished in Cmr2αHD,Palm. Since dCmr4α-containing effectors lack spatiotemporal regulation, this allows an everlasting interaction between crRNA and cellular RNAs to occur. As a result, some cellular RNAs, which are not effective in mediating immunity due to the presence of spatiotemporal regulation, trigger autoimmunity of the Cmr-α system in the S. islandicus cells expressing dCmr4α. Together, these results pinpoint the crucial importance of tgRNA cleavage in autoimmunity avoidance and in the regulation of immunization of type III systems.
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Affiliation(s)
- Yan Zhang
- Henan Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang 453007, China;
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark;
| | - Xuhui Tian
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Yuan Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Chenwei Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (C.W.); (X.W.); (P.Z.); (X.B.); (Z.Y.)
| | - Xiaoning Wang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (C.W.); (X.W.); (P.Z.); (X.B.); (Z.Y.)
| | - Pengpeng Zhao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (C.W.); (X.W.); (P.Z.); (X.B.); (Z.Y.)
| | - Xiaonan Bi
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (C.W.); (X.W.); (P.Z.); (X.B.); (Z.Y.)
| | - Zhenxiao Yu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (C.W.); (X.W.); (P.Z.); (X.B.); (Z.Y.)
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Yun Xiang Liang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
| | - Qunxin She
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.T.); (Y.W.); (R.Z.); (W.H.); (N.P.); (Y.X.L.)
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark;
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (C.W.); (X.W.); (P.Z.); (X.B.); (Z.Y.)
- Correspondence:
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26
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Nemudraia A, Nemudryi A, Buyukyoruk M, Scherffius AM, Zahl T, Wiegand T, Pandey S, Nichols JE, Hall L, McVey A, Lee HH, Wilkinson RA, Snyder LR, Jones JD, Koutmou KS, Santiago-Frangos A, Wiedenheft B. Sequence-specific capture and concentration of viral RNA by type III CRISPR system enhances diagnostic. RESEARCH SQUARE 2022:rs.3.rs-1466718. [PMID: 35475170 PMCID: PMC9040678 DOI: 10.21203/rs.3.rs-1466718/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Type-III CRISPR-Cas systems have recently been adopted for sequence-specific detection of SARS-CoV-2. Here, we make two major advances that simultaneously limit sample handling and significantly enhance the sensitivity of SARS-CoV-2 RNA detection directly from patient samples. First, we repurpose the type III-A CRISPR complex from Thermus thermophilus (TtCsm) for programmable capture and concentration of specific RNAs from complex mixtures. The target bound TtCsm complex primarily generates two cyclic oligoadenylates (i.e., cA3 and cA4) that allosterically activate ancillary nucleases. To improve sensitivity of the diagnostic, we identify and test several ancillary nucleases (i.e., Can1, Can2, and NucC). We show that Can1 and Can2 are activated by both cA3 and cA4, and that different activators trigger changes in the substrate specificity of these nucleases. Finally, we integrate the type III-A CRISPR RNA-guided capture technique with the Can2 nuclease for 90 fM (5x104 copies/ul) detection of SARS-CoV-2 RNA directly from nasopharyngeal swab samples.
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Affiliation(s)
- Anna Nemudraia
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA,These authors contributed equally
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA,These authors contributed equally
| | - Murat Buyukyoruk
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA,These authors contributed equally
| | - Andrew M. Scherffius
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA,These authors contributed equally
| | - Trevor Zahl
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Shishir Pandey
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Joseph E. Nichols
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Laina Hall
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Aidan McVey
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Helen H Lee
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Royce A. Wilkinson
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Laura R. Snyder
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48105, USA
| | - Joshua D. Jones
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48105, USA
| | - Kristin S. Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48105, USA
| | - Andrew Santiago-Frangos
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA,Correspondence: and
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA,Lead contact,Correspondence: and
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27
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Sohail M, Xie S, Zhang X, Li B. Methodologies in visualizing the activation of CRISPR/Cas: The last mile in developing CRISPR-Based diagnostics and biosensing – A review. Anal Chim Acta 2022; 1205:339541. [DOI: 10.1016/j.aca.2022.339541] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
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28
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. Nat Chem Biol 2021; 17:982-988. [PMID: 34354262 PMCID: PMC10184463 DOI: 10.1038/s41589-021-00842-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided RNA recognition that triggers cleavage and release of a fluorescent reporter molecule, but long reaction times hamper their detection sensitivity and speed. Here, we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 molecules per µl of RNA in 20 min. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA extracted from respiratory swab samples with quantitative reverse transcriptase PCR (qRT-PCR)-derived cycle threshold (Ct) values up to 33, using a compact detector. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables sensitive, direct RNA detection in a format that is amenable to point-of-care infection diagnosis as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria, Australia
| | - Dylan C J Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Emeric J Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Brittney W Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Stephanie I Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - G Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shineui Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- UC Berkeley, UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Berkeley Stem Cell Center, University of California, Berkeley, Berkeley, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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29
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Jia N, Patel DJ. Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins. Nat Rev Mol Cell Biol 2021; 22:563-579. [PMID: 34089013 DOI: 10.1038/s41580-021-00371-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
CRISPR loci and Cas proteins provide adaptive immunity in prokaryotes against invading bacteriophages and plasmids. In response, bacteriophages have evolved a broad spectrum of anti-CRISPR proteins (anti-CRISPRs) to counteract and overcome this immunity pathway. Numerous anti-CRISPRs have been identified to date, which suppress single-subunit Cas effectors (in CRISPR class 2, type II, V and VI systems) and multisubunit Cascade effectors (in CRISPR class 1, type I and III systems). Crystallography and cryo-electron microscopy structural studies of anti-CRISPRs bound to effector complexes, complemented by functional experiments in vitro and in vivo, have identified four major CRISPR-Cas suppression mechanisms: inhibition of CRISPR-Cas complex assembly, blocking of target binding, prevention of target cleavage, and degradation of cyclic oligonucleotide signalling molecules. In this Review, we discuss novel mechanistic insights into anti-CRISPR function that have emerged from X-ray crystallography and cryo-electron microscopy studies, and how these structures in combination with function studies provide valuable tools for the ever-growing CRISPR-Cas biotechnology toolbox, to be used for precise and robust genome editing and other applications.
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Affiliation(s)
- Ning Jia
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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30
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Athukoralage JS, White MF. Cyclic oligoadenylate signalling and regulation by ring nucleases during type III CRISPR defence. RNA (NEW YORK, N.Y.) 2021; 27:rna.078739.121. [PMID: 33986148 PMCID: PMC8284326 DOI: 10.1261/rna.078739.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/08/2021] [Indexed: 06/12/2023]
Abstract
In prokaryotes, CRISPR-Cas immune systems recognise and cleave foreign nucleic acids to defend against Mobile Genetic Elements (MGEs). Type III CRISPR-Cas complexes also synthesise cyclic oligoadenylate (cOA) second messengers, which activate CRISPR ancillary proteins involved in antiviral defence. In particular, cOA-stimulated nucleases degrade RNA and DNA non-specifically, which slows MGE replication but also impedes cell growth, necessitating mechanisms to eliminate cOA in order to mitigate collateral damage. Extant cOA is degraded by a new class of enzyme termed a 'ring nuclease', which cleaves cOA specifically and switches off CRISPR ancillary enzymes. Several ring nuclease families have been characterised to date, including a family used by MGEs to circumvent CRISPR immunity, and encompass diverse protein folds and distinct cOA cleavage mechanisms. In this review we outline cOA signalling, discuss how different ring nucleases regulate the cOA signalling pathway, and reflect on parallels between cyclic nucleotide-based immune systems to reveal new areas for exploration.
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31
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Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim SE, Dugan EJ, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Accelerated RNA detection using tandem CRISPR nucleases. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.19.21253328. [PMID: 33791736 PMCID: PMC8010768 DOI: 10.1101/2021.03.19.21253328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.
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Affiliation(s)
- Tina Y. Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J. Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, VIC 3800, Australia
| | - Dylan C. J. Smock
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - John J. Desmarais
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Shrutee Jakhanwal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Shreeya Agrawal
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Neil A. Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R. Harris
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Emeric J. Charles
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brittney W. Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Parinaz Fozouni
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey Shu
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie I. Stephens
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chunyu Zhao
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Shin E. Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Katherine S. Pollard
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | | | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley-UC San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Liana F. Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Patrick D. Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
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32
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Huang F, Zhu B. The Cyclic Oligoadenylate Signaling Pathway of Type III CRISPR-Cas Systems. Front Microbiol 2021; 11:602789. [PMID: 33552016 PMCID: PMC7854544 DOI: 10.3389/fmicb.2020.602789] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/11/2020] [Indexed: 12/24/2022] Open
Abstract
Type III CRISPR-Cas systems, which are widespread in both bacteria and archaea, provide immunity against DNA viruses and plasmids in a transcription-dependent manner. Since an unprecedented cyclic oligoadenylate (cOA) signaling pathway was discovered in type III systems in 2017, the cOA signaling has been extensively studied in recent 3 years, which has expanded our understanding of type III systems immune defense and also its counteraction by viruses. In this review, we summarized recent advances in cOA synthesis, cOA-activated effector protein, cOA signaling-mediated immunoprotection, and cOA signaling inhibition, and highlighted the crosstalk between cOA signaling and other cyclic oligonucleotide-mediated immunity discovered very recently.
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Affiliation(s)
- Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology and Shenzhen College, Huazhong University of Science and Technology, Wuhan, China
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Mckay A, Burgio G. Harnessing CRISPR-Cas system diversity for gene editing technologies. J Biomed Res 2021; 35:91-106. [PMID: 33797415 PMCID: PMC8038530 DOI: 10.7555/jbr.35.20200184] [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] [Indexed: 12/05/2022] Open
Abstract
The discovery and utilization of RNA-guided surveillance complexes, such as CRISPR-Cas9, for sequence-specific DNA or RNA cleavage, has revolutionised the process of gene modification or knockdown. To optimise the use of this technology, an exploratory race has ensued to discover or develop new RNA-guided endonucleases with the most flexible sequence targeting requirements, coupled with high cleavage efficacy and specificity. Here we review the constraints of existing gene editing and assess the merits of exploiting the diversity of CRISPR-Cas effectors as a methodology for surmounting these limitations.
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Affiliation(s)
- Alexander Mckay
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
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