1
|
Hoikkala V, Graham S, White MF. Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families. Nucleic Acids Res 2024:gkae462. [PMID: 38808661 DOI: 10.1093/nar/gkae462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [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.
Collapse
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
| |
Collapse
|
2
|
Rechkoblit O, Sciaky D, Kreitler DF, Buku A, Kottur J, Aggarwal AK. Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides. Nat Struct Mol Biol 2024; 31:767-776. [PMID: 38321146 DOI: 10.1038/s41594-024-01220-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024]
Abstract
The bacterial cyclic oligonucleotide-based antiphage signaling system (CBASS) is similar to the cGAS-STING system in humans, containing an enzyme that synthesizes a cyclic nucleotide on viral infection and an effector that senses the second messenger for the antiviral response. Cap5, containing a SAVED domain coupled to an HNH DNA endonuclease domain, is the most abundant CBASS effector, yet the mechanism by which it becomes activated for cell killing remains unknown. We present here high-resolution structures of full-length Cap5 from Pseudomonas syringae (Ps) with second messengers. The key to PsCap5 activation is a dimer-to-tetramer transition, whereby the binding of second messenger to dimer triggers an open-to-closed transformation of the SAVED domains, furnishing a surface for assembly of the tetramer. This movement propagates to the HNH domains, juxtaposing and converting two HNH domains into states for DNA destruction. These results show how Cap5 effects bacterial cell suicide and we provide proof-in-principle data that the CBASS can be extrinsically activated to limit bacterial infections.
Collapse
Affiliation(s)
- Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Daniela Sciaky
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dale F Kreitler
- Center for BioMolecular Structure NSLS‑II, Brookhaven National Laboratory, Upton, NY, USA
| | - Angeliki Buku
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Antiviral Research, Institute of Advanced Virology, Thiruvananthapuram, India
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
3
|
Prostova M, Kanevskaya A, Panteleev V, Lisitskaya L, Perfilova Tugaeva KV, Sluchanko NN, Esyunina D, Kulbachinskiy A. DNA-targeting short Argonautes complex with effector proteins for collateral nuclease activity and bacterial population immunity. Nat Microbiol 2024; 9:1368-1381. [PMID: 38622379 DOI: 10.1038/s41564-024-01654-5] [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: 11/25/2023] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
Two prokaryotic defence systems, prokaryotic Argonautes (pAgos) and CRISPR-Cas, detect and cleave invader nucleic acids using complementary guides and the nuclease activities of pAgo or Cas proteins. However, not all pAgos are active nucleases. A large clade of short pAgos bind nucleic acid guides but lack nuclease activity, suggesting a different mechanism of action. Here we investigate short pAgos associated with a putative effector nuclease, NbaAgo from Novosphingopyxis baekryungensis and CmeAgo from Cupriavidus metallidurans. We show that these pAgos form a heterodimeric complex with co-encoded effector nucleases (short prokaryotic Argonaute, DNase and RNase associated (SPARDA)). RNA-guided target DNA recognition unleashes the nuclease activity of SPARDA leading to indiscriminate collateral cleavage of DNA and RNA. Activation of SPARDA by plasmids or phages results in degradation of cellular DNA and cell death or dormancy, conferring target-specific population protection and expanding the range of known prokaryotic immune systems.
Collapse
Affiliation(s)
- Maria Prostova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Anna Kanevskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
| | | | - Lidia Lisitskaya
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kristina V Perfilova Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Li X, Han J, Yang J, Zhang H. The structural biology of type III CRISPR-Cas systems. J Struct Biol 2024; 216:108070. [PMID: 38395113 DOI: 10.1016/j.jsb.2024.108070] [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: 10/27/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
CRISPR-Cas system is an RNA-guided adaptive immune system widespread in bacteria and archaea. Among them, type III CRISPR-Cas systems are the most ancient throughout the CRISPR-Cas family, proving anti-phage defense through a crRNA-guided RNA targeting manner and possessing multiple enzymatic activities. Type III CRISPR-Cas systems comprise four typical members (type III-A to III-D) and two atypical members (type III-E and type III-F), providing immune defense through distinct mechanisms. Here, we delve into structural studies conducted on three well-characterized members: the type III-A, III-B, and III-E systems, provide an overview of the structural insights into the crRNA-guided target RNA cleavage, self/non-self discrimination, and the target RNA-dependent regulation of enzymatic subunits in the effector complex.
Collapse
Affiliation(s)
- Xuzichao Li
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jie Han
- Department of Anatomy and Histology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jie Yang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Heng Zhang
- State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.
| |
Collapse
|
8
|
Aviram N, Shilton AK, Lyn NG, Reis BS, Brivanlou A, Marraffini LA. The Cas10 nuclease activity relieves host dormancy to facilitate spacer acquisition and retention during type III-A CRISPR immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579731. [PMID: 38405743 PMCID: PMC10888962 DOI: 10.1101/2024.02.11.579731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A hallmark of CRISPR immunity is the acquisition of short viral DNA sequences, known as spacers, that are transcribed into guide RNAs to recognize complementary sequences. The staphylococcal type III-A CRISPR-Cas system uses guide RNAs to locate viral transcripts and start a response that displays two mechanisms of immunity. When immunity is triggered by an early-expressed phage RNA, degradation of viral ssDNA can cure the host from infection. In contrast, when the RNA guide targets a late-expressed transcript, defense requires the activity of Csm6, a non-specific RNase. Here we show that Csm6 triggers a growth arrest of the host that provides immunity at the population level which hinders viral propagation to allow the replication of non-infected cells. We demonstrate that this mechanism leads to defense against not only the target phage but also other viruses present in the population that fail to replicate in the arrested cells. On the other hand, dormancy limits the acquisition and retention of spacers that trigger it. We found that the ssDNase activity of type III-A systems is required for the re-growth of a subset of the arrested cells, presumably through the degradation of the phage DNA, ending target transcription and inactivating the immune response. Altogether, our work reveals a built-in mechanism within type III-A CRISPR-Cas systems that allows the exit from dormancy needed for the subsistence of spacers that provide broad-spectrum immunity.
Collapse
Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amanda K Shilton
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Nia G Lyn
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Amir Brivanlou
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. Mol Microbiol 2024; 121:152-166. [PMID: 38104967 PMCID: PMC10842292 DOI: 10.1111/mmi.15206] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
Small proteins (<50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance, are poorly understood. Here, we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene neighborhoods support that MntS evolved from the signal peptide of an ancestral SitA protein, acquiring a life of its own with a distinct function in Mn homeostasis.
Collapse
Affiliation(s)
- Zachary Wright
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Mackenzie Seymour
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Kalista Paszczak
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Taylor Truttmann
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Katherine Senn
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Samuel Stilp
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Nickolas Jansen
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Magdalyn Gosz
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Lindsay Goeden
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lauren S. Waters
- Department of Chemistry, 800 Algoma Blvd, University of Wisconsin, Oshkosh, WI 54901, USA
| |
Collapse
|
13
|
Baca CF, Yu Y, Rostøl JT, Majumder P, Patel DJ, Marraffini LA. The CRISPR effector Cam1 mediates membrane depolarization for phage defence. Nature 2024; 625:797-804. [PMID: 38200316 PMCID: PMC10808066 DOI: 10.1038/s41586-023-06902-y] [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: 09/14/2022] [Accepted: 11/27/2023] [Indexed: 01/12/2024]
Abstract
Prokaryotic type III CRISPR-Cas systems provide immunity against viruses and plasmids using CRISPR-associated Rossman fold (CARF) protein effectors1-5. Recognition of transcripts of these invaders with sequences that are complementary to CRISPR RNA guides leads to the production of cyclic oligoadenylate second messengers, which bind CARF domains and trigger the activity of an effector domain6,7. Whereas most effectors degrade host and invader nucleic acids, some are predicted to contain transmembrane helices without an enzymatic function. Whether and how these CARF-transmembrane helix fusion proteins facilitate the type III CRISPR-Cas immune response remains unknown. Here we investigate the role of cyclic oligoadenylate-activated membrane protein 1 (Cam1) during type III CRISPR immunity. Structural and biochemical analyses reveal that the CARF domains of a Cam1 dimer bind cyclic tetra-adenylate second messengers. In vivo, Cam1 localizes to the membrane, is predicted to form a tetrameric transmembrane pore, and provides defence against viral infection through the induction of membrane depolarization and growth arrest. These results reveal that CRISPR immunity does not always operate through the degradation of nucleic acids, but is instead mediated via a wider range of cellular responses.
Collapse
Affiliation(s)
- Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - You Yu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Puja Majumder
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
14
|
Altae-Tran H, Kannan S, Suberski AJ, Mears KS, Demircioglu FE, Moeller L, Kocalar S, Oshiro R, Makarova KS, Macrae RK, Koonin EV, Zhang F. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. Science 2023; 382:eadi1910. [PMID: 37995242 PMCID: PMC10910872 DOI: 10.1126/science.adi1910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/28/2023] [Indexed: 11/25/2023]
Abstract
Microbial systems underpin many biotechnologies, including CRISPR, but the exponential growth of sequence databases makes it difficult to find previously unidentified systems. In this work, we develop the fast locality-sensitive hashing-based clustering (FLSHclust) algorithm, which performs deep clustering on massive datasets in linearithmic time. We incorporated FLSHclust into a CRISPR discovery pipeline and identified 188 previously unreported CRISPR-linked gene modules, revealing many additional biochemical functions coupled to adaptive immunity. We experimentally characterized three HNH nuclease-containing CRISPR systems, including the first type IV system with a specified interference mechanism, and engineered them for genome editing. We also identified and characterized a candidate type VII system, which we show acts on RNA. This work opens new avenues for harnessing CRISPR and for the broader exploration of the vast functional diversity of microbial proteins.
Collapse
Affiliation(s)
- Han Altae-Tran
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Soumya Kannan
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Anthony J. Suberski
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Kepler S. Mears
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - F. Esra Demircioglu
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Lukas Moeller
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Selin Kocalar
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Rachel Oshiro
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD 20894, USA
| | - Rhiannon K. Macrae
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD 20894, USA
| | - Feng Zhang
- Howard Hughes Medical Institute; Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT; Cambridge, MA 02139, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| |
Collapse
|
15
|
Xie W, Lama L, Yang X, Kuryavyi V, Bhattacharya S, Nudelman I, Yang G, Ouerfelli O, Glickman JF, Jones RA, Tuschl T, Patel DJ. Arabinose- and xylose-modified analogs of 2',3'-cGAMP act as STING agonists. Cell Chem Biol 2023; 30:1366-1376.e7. [PMID: 37536341 PMCID: PMC10808274 DOI: 10.1016/j.chembiol.2023.07.002] [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: 11/10/2021] [Revised: 04/19/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023]
Abstract
Stimulator of interferon genes (STING) agonists are promising candidates for vaccine adjuvants and antitumor immune stimulants. The most potent natural agonist of STING, 2',3'-cyclic GMP-AMP (2',3'-cGAMP), is subject to nuclease-mediated inherent metabolic instability, thereby placing limits on its clinical efficacy. Here, we report on a new class of chemically synthesized sugar-modified analogs of 2',3'-cGAMP containing arabinose and xylose sugar derivatives that bind mouse and human STING alleles with high affinity. The co-crystal structures demonstrate that such analogs act as 2',3'-cGAMP mimetics that induce the "closed" conformation of human STING. These analogs show significant resistance to hydrolysis mediated by ENPP1 and increased stability in human serum, while retaining similar potency as 2',3'-cGAMP at inducing IFN-β secretion from human THP1 cells. The arabinose- and xylose-modified 2',3'-cGAMP analogs open a new strategy for overcoming the inherent nuclease-mediated vulnerability of natural ribose cyclic nucleotides, with the additional benefit of high translational potential as cancer therapeutics and vaccine adjuvants.
Collapse
Affiliation(s)
- Wei Xie
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lodoe Lama
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Vitaly Kuryavyi
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | | | - Ilona Nudelman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Guangli Yang
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - J Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Roger A Jones
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
16
|
Lin J, Alfastsen L, Bhoobalan-Chitty Y, Peng X. Molecular basis for inhibition of type III-B CRISPR-Cas by an archaeal viral anti-CRISPR protein. Cell Host Microbe 2023; 31:1837-1849.e5. [PMID: 37909049 DOI: 10.1016/j.chom.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 11/02/2023]
Abstract
Despite a wide presence of type III clustered regularly interspaced short palindromic repeats, CRISPR-associated (CRISPR-Cas) in archaea and bacteria, very few anti-CRISPR (Acr) proteins inhibiting type III immunity have been identified, and even less is known about their inhibition mechanism. Here, we present the discovery of a type III CRISPR-Cas inhibitor, AcrIIIB2, encoded by Sulfolobus virus S. islandicus rod-shaped virus 3 (SIRV3). AcrIIIB2 inhibits type III-B CRISPR-Cas immune response to protospacers encoded in middle/late-expressed viral genes. Investigation of the interactions between S. islandicus type III-B CRISPR-Cas Cmr-α-related proteins and AcrIIIB2 reveals that the Acr does not bind to Csx1 but rather interacts with the Cmr-α effector complex. Furthermore, in vitro assays demonstrate that AcrIIIB2 can block the dissociation of cleaved target RNA from the Cmr-α complex, thereby inhibiting the Cmr-α turnover, thus preventing host cellular dormancy and further viral genome degradation by the type III-B CRISPR-Cas immunity.
Collapse
Affiliation(s)
- Jinzhong Lin
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Lauge Alfastsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | | | - Xu Peng
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark.
| |
Collapse
|
17
|
Song X, Lei S, Liu S, Liu Y, Fu P, Zeng Z, Yang K, Chen Y, Li M, She Q, Han W. Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection. Nat Commun 2023; 14:6970. [PMID: 37914725 PMCID: PMC10620215 DOI: 10.1038/s41467-023-42793-3] [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: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.
Collapse
Affiliation(s)
- Xinmi Song
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sheng Lei
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shunhang Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yanqiu Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pan Fu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, 266237, Jimo, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Attrill EL, Łapińska U, Westra ER, Harding SV, Pagliara S. Slow growing bacteria survive bacteriophage in isolation. ISME COMMUNICATIONS 2023; 3:95. [PMID: 37684358 PMCID: PMC10491631 DOI: 10.1038/s43705-023-00299-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023]
Abstract
The interactions between bacteria and bacteriophage have important roles in the global ecosystem; in turn changes in environmental parameters affect the interactions between bacteria and phage. However, there is a lack of knowledge on whether clonal bacterial populations harbour different phenotypes that respond to phage in distinct ways and whether the abundance of such phenotypes within bacterial populations is affected by variations in environmental parameters. Here we study the impact of variations in nutrient availability, bacterial growth rate and phage abundance on the interactions between the phage T4 and individual Escherichia coli cells confined in spatial refuges. Surprisingly, we found that fast growing bacteria survive together with all of their clonal kin cells, whereas slow growing bacteria survive in isolation. We also discovered that the number of bacteria that survive in isolation decreases at increasing phage doses possibly due to lysis inhibition in the presence of secondary adsorptions. We further show that these changes in the phenotypic composition of the E. coli population have important consequences on the bacterial and phage population dynamics and should therefore be considered when investigating bacteria-phage interactions in ecological, health or food production settings in structured environments.
Collapse
Affiliation(s)
- Erin L Attrill
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK
| | - Edze R Westra
- Environment and Sustainability Institute and Biosciences, University of Exeter, Penryn, UK
| | - Sarah V Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, UK.
| |
Collapse
|
20
|
Wright Z, Seymour M, Paszczak K, Truttmann T, Senn K, Stilp S, Jansen N, Gosz M, Goeden L, Anantharaman V, Aravind L, Waters LS. The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543501. [PMID: 37398132 PMCID: PMC10312517 DOI: 10.1101/2023.06.02.543501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Small proteins (< 50 amino acids) are emerging as ubiquitous and important regulators in organisms ranging from bacteria to humans, where they commonly bind to and regulate larger proteins during stress responses. However, fundamental aspects of small proteins, such as their molecular mechanism of action, downregulation after they are no longer needed, and their evolutionary provenance are poorly understood. Here we show that the MntS small protein involved in manganese (Mn) homeostasis binds and inhibits the MntP Mn transporter. Mn is crucial for bacterial survival in stressful environments, but is toxic in excess. Thus, Mn transport is tightly controlled at multiple levels to maintain optimal Mn levels. The small protein MntS adds a new level of regulation for Mn transporters, beyond the known transcriptional and post-transcriptional control. We also found that MntS binds to itself in the presence of Mn, providing a possible mechanism of downregulating MntS activity to terminate its inhibition of MntP Mn export. MntS is homologous to the signal peptide of SitA, the periplasmic metal-binding subunit of a Mn importer. Remarkably, the homologous signal peptide regions can substitute for MntS, demonstrating a functional relationship between MntS and these signal peptides. Conserved gene-neighborhoods support that MntS evolved from an ancestral SitA, acquiring a life of its own with a distinct function in Mn homeostasis. Significance This study demonstrates that the MntS small protein binds and inhibits the MntP Mn exporter, adding another layer to the complex regulation of Mn homeostasis. MntS also interacts with itself in cells with Mn, which could prevent it from regulating MntP. We propose that MntS and other small proteins might sense environmental signals and shut off their own regulation via binding to ligands (e.g., metals) or other proteins. We also provide evidence that MntS evolved from the signal peptide region of the Mn importer, SitA. Homologous SitA signal peptides can recapitulate MntS activities, showing that they have a second function beyond protein secretion. Overall, we establish that small proteins can emerge and develop novel functionalities from gene remnants.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Chen Y, Zeng Z, She Q, Han W. The abortive infection functions of CRISPR-Cas and Argonaute. Trends Microbiol 2023; 31:405-418. [PMID: 36463018 DOI: 10.1016/j.tim.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
CRISPR-Cas and prokaryotic Argonaute (pAgo) are nucleic acid (NA)-guided defense systems that protect prokaryotes against the invasion of mobile genetic elements. Previous studies established that they are directed by NA fragments (guides) to recognize invading complementary NA (targets), and that they cleave the targets to silence the invaders. Nevertheless, growing evidence indicates that many CRISPR-Cas and pAgo systems exploit the abortive infection (Abi) strategy to confer immunity. The CRISPR-Cas and pAgo Abi systems typically sense invaders using the NA recognition ability and activate various toxic effectors to kill the infected cells to prevent the invaders from spreading. This review summarizes the diverse mechanisms of these CRISPR-Cas and pAgo systems, and highlights their critical roles in the arms race between microbes and invaders.
Collapse
Affiliation(s)
- Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Jimo, 266237, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China.
| |
Collapse
|
23
|
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.
Collapse
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;
| |
Collapse
|
24
|
Cannone G, Kompaniiets D, Graham S, White MF, Spagnolo L. Structure of the Saccharolobus solfataricus type III-D CRISPR effector. Curr Res Struct Biol 2023; 5:100098. [PMID: 36843655 PMCID: PMC9945777 DOI: 10.1016/j.crstbi.2023.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
CRISPR-Cas is a prokaryotic adaptive immune system, classified into six different types, each characterised by a signature protein. Type III systems, classified based on the presence of a Cas10 subunit, are rather diverse multi-subunit assemblies with a range of enzymatic activities and downstream ancillary effectors. The broad array of current biotechnological CRISPR applications is mainly based on proteins classified as Type II, however recent developments established the feasibility and efficacy of multi-protein Type III CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes. The crenarchaeon Saccharolobus solfataricus has two type III system subtypes (III-B and III-D). Here, we report the cryo-EM structure of the Csm Type III-D complex from S. solfataricus (SsoCsm), which uses CRISPR RNA to bind target RNA molecules, activating the Cas10 subunit for antiviral defence. The structure reveals the complex organisation, subunit/subunit connectivity and protein/guide RNA interactions of the SsoCsm complex, one of the largest CRISPR effectors known.
Collapse
Affiliation(s)
- Giuseppe Cannone
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom
| | - Dmytro Kompaniiets
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Malcolm F. White
- School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Laura Spagnolo
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
25
|
Yu Z, Xu J, She Q. Harnessing the LdCsm RNA Detection Platform for Efficient microRNA Detection. Int J Mol Sci 2023; 24:ijms24032857. [PMID: 36769177 PMCID: PMC9918065 DOI: 10.3390/ijms24032857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
In cancer diagnosis, diverse microRNAs (miRNAs) are used as biomarkers for carcinogenesis of distinctive human cancers. Thus, the detection of these miRNAs and their quantification are very important in prevention of cancer diseases in human beings. However, efficient RNA detection often requires RT-PCR, which is very complex for miRNAs. Recently, the development of CRISPR-based nucleic acid detection tools has brought new promises to efficient miRNA detection. Three CRISPR systems can be explored for miRNA detection, including type III, V, and VI, among which type III (CRISPR-Cas10) systems have a unique property as they recognize RNA directly and cleave DNA collaterally. In particular, a unique type III-A Csm system encoded by Lactobacillus delbrueckii subsp. bulgaricus (LdCsm) exhibits robust target RNA-activated DNase activity, which makes it a promising candidate for developing efficient miRNA diagnostic tools. Herein, LdCsm was tested for RNA detection using fluorescence-quenched DNA reporters. We found that the system is capable of specific detection of miR-155, a microRNA implicated in the carcinogenesis of human breast cancer. The RNA detection system was then improved by various approaches including assay conditions and modification of the 5'-repeat tag of LdCsm crRNAs. Due to its robustness, the resulting LdCsm detection platform has the potential to be further developed as a better point-of-care miRNA diagnostics relative to other CRISPR-based RNA detection tools.
Collapse
Affiliation(s)
| | | | - Qunxin She
- Correspondence: ; Tel.: +86-532-58631522
| |
Collapse
|
26
|
Rouillon C, Schneberger N, Chi H, Blumenstock K, Da Vela S, Ackermann K, Moecking J, Peter MF, Boenigk W, Seifert R, Bode BE, Schmid-Burgk JL, Svergun D, Geyer M, White MF, Hagelueken G. Antiviral signalling by a cyclic nucleotide activated CRISPR protease. Nature 2023; 614:168-174. [PMID: 36423657 DOI: 10.1038/s41586-022-05571-7] [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: 12/06/2021] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
CRISPR defence systems such as the well-known DNA-targeting Cas9 and the RNA-targeting type III systems are widespread in prokaryotes1,2. The latter orchestrates a complex antiviral response that is initiated through the synthesis of cyclic oligoadenylates after recognition of foreign RNA3-5. Among the large set of proteins that are linked to type III systems and predicted to bind cyclic oligoadenylates6,7, a CRISPR-associated Lon protease (CalpL) stood out to us. CalpL contains a sensor domain of the SAVED family7 fused to a Lon protease effector domain. However, the mode of action of this effector is unknown. Here we report the structure and function of CalpL and show that this soluble protein forms a stable tripartite complex with two other proteins, CalpT and CalpS, that are encoded on the same operon. After activation by cyclic tetra-adenylate (cA4), CalpL oligomerizes and specifically cleaves the MazF homologue CalpT, which releases the extracytoplasmic function σ factor CalpS from the complex. Our data provide a direct connection between CRISPR-based detection of foreign nucleic acids and transcriptional regulation. Furthermore, the presence of a SAVED domain that binds cyclic tetra-adenylate in a CRISPR effector reveals a link to the cyclic-oligonucleotide-based antiphage signalling system.
Collapse
Affiliation(s)
- Christophe Rouillon
- Institute of Structural Biology, University of Bonn, Bonn, Germany.
- Max Planck Institute for Neurobiology of Behavior-caesar, Bonn, Germany.
| | | | - Haotian Chi
- School of Biology, University of St Andrews, St Andrews, UK
| | - Katja Blumenstock
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory (EMBL), Hamburg Site, Hamburg, Germany
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, UK
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Martin F Peter
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Wolfgang Boenigk
- Max Planck Institute for Neurobiology of Behavior-caesar, Bonn, Germany
| | - Reinhard Seifert
- Max Planck Institute for Neurobiology of Behavior-caesar, Bonn, Germany
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, UK
| | - Jonathan L Schmid-Burgk
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Site, Hamburg, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | | | | |
Collapse
|
27
|
Ecology and evolution of phages encoding anti-CRISPR proteins. J Mol Biol 2023; 435:167974. [PMID: 36690071 DOI: 10.1016/j.jmb.2023.167974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
CRISPR-Cas are prokaryotic defence systems that provide protection against invasion by mobile genetic elements (MGE), including bacteriophages. MGE can overcome CRISPR-Cas defences by encoding anti-CRISPR (Acr) proteins. These proteins are produced in the early stages of the infection and inhibit the CRISPR-Cas machinery to allow phage replication. While research on Acr has mainly focused on their discovery, structure and mode of action, and their applications in biotechnology, the impact of Acr on the ecology of MGE as well as on the coevolution with their bacterial hosts only begins to be unravelled. In this review, we summarise our current understanding on the distribution of anti-CRISPR genes in MGE, the ecology of phages encoding Acr, and their coevolution with bacterial defence mechanisms. We highlight the need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in MGE-host interactions.
Collapse
|
28
|
Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA. Nature 2023; 613:588-594. [PMID: 36599979 PMCID: PMC9811890 DOI: 10.1038/s41586-022-05559-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/11/2022] [Indexed: 01/05/2023]
Abstract
Bacterial abortive-infection systems limit the spread of foreign invaders by shutting down or killing infected cells before the invaders can replicate1,2. Several RNA-targeting CRISPR-Cas systems (that is, types III and VI) cause abortive-infection phenotypes by activating indiscriminate nucleases3-5. However, a CRISPR-mediated abortive mechanism that leverages indiscriminate DNase activity of an RNA-guided single-effector nuclease has yet to be observed. Here we report that RNA targeting by the type V single-effector nuclease Cas12a2 drives abortive infection through non-specific cleavage of double-stranded DNA (dsDNA). After recognizing an RNA target with an activating protospacer-flanking sequence, Cas12a2 efficiently degrades single-stranded RNA (ssRNA), single-stranded DNA (ssDNA) and dsDNA. Within cells, the activation of Cas12a2 induces an SOS DNA-damage response and impairs growth, preventing the dissemination of the invader. Finally, we harnessed the collateral activity of Cas12a2 for direct RNA detection, demonstrating that Cas12a2 can be repurposed as an RNA-guided RNA-targeting tool. These findings expand the known defensive abilities of CRISPR-Cas systems and create additional opportunities for CRISPR technologies.
Collapse
|
29
|
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.
Collapse
|
30
|
RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2. Nature 2023; 613:582-587. [PMID: 36599980 PMCID: PMC9849127 DOI: 10.1038/s41586-022-05560-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2023]
Abstract
Cas12a2 is a CRISPR-associated nuclease that performs RNA-guided, sequence-nonspecific degradation of single-stranded RNA, single-stranded DNA and double-stranded DNA following recognition of a complementary RNA target, culminating in abortive infection1. Here we report structures of Cas12a2 in binary, ternary and quaternary complexes to reveal a complete activation pathway. Our structures reveal that Cas12a2 is autoinhibited until binding a cognate RNA target, which exposes the RuvC active site within a large, positively charged cleft. Double-stranded DNA substrates are captured through duplex distortion and local melting, stabilized by pairs of 'aromatic clamp' residues that are crucial for double-stranded DNA degradation and in vivo immune system function. Our work provides a structural basis for this mechanism of abortive infection to achieve population-level immunity, which can be leveraged to create rational mutants that degrade a spectrum of collateral substrates.
Collapse
|
31
|
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [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.
Collapse
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
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
|
34
|
Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Mol Cell 2022; 82:4471-4486.e9. [PMID: 36395770 DOI: 10.1016/j.molcel.2022.10.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/13/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
Abstract
Bacteria have diverse defenses against phages. In response, jumbo phages evade multiple DNA-targeting defenses by protecting their DNA inside a nucleus-like structure. We previously demonstrated that RNA-targeting type III CRISPR-Cas systems provide jumbo phage immunity by recognizing viral mRNA exported from the nucleus for translation. Here, we demonstrate that recognition of phage mRNA by the type III system activates a cyclic triadenylate-dependent accessory nuclease, NucC. Although unable to access phage DNA in the nucleus, NucC degrades the bacterial chromosome, triggers cell death, and disrupts phage replication and maturation. Hence, type-III-mediated jumbo phage immunity occurs via abortive infection, with suppression of the viral epidemic protecting the population. We further show that type III systems targeting jumbo phages have diverse accessory nucleases, including RNases that provide immunity. Our study demonstrates how type III CRISPR-Cas systems overcome the inaccessibility of jumbo phage DNA to provide robust immunity.
Collapse
|
35
|
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: 10] [Impact Index Per Article: 5.0] [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.
Collapse
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
| |
Collapse
|
36
|
Molina R, Garcia-Martin R, López-Méndez B, Jensen ALG, Ciges-Tomas JR, Marchena-Hurtado J, Stella S, Montoya G. Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases. Nucleic Acids Res 2022; 50:11199-11213. [PMID: 36271789 PMCID: PMC9638899 DOI: 10.1093/nar/gkac923] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
Standalone ring nucleases are CRISPR ancillary proteins, which downregulate the immune response of Type III CRISPR-Cas systems by cleaving cyclic oligoadenylates (cA) second messengers. Two genes with this function have been found within the Sulfolobus islandicus (Sis) genome. They code for a long polypeptide composed by a CARF domain fused to an HTH domain and a short polypeptide constituted by a CARF domain with a 40 residue C-terminal insertion. Here, we determine the structure of the apo and substrate bound states of the Sis0455 enzyme, revealing an insertion at the C-terminal region of the CARF domain, which plays a key role closing the catalytic site upon substrate binding. Our analysis reveals the key residues of Sis0455 during cleavage and the coupling of the active site closing with their positioning to proceed with cA4 phosphodiester hydrolysis. A time course comparison of cA4 cleavage between the short, Sis0455, and long ring nucleases, Sis0811, shows the slower cleavage kinetics of the former, suggesting that the combination of these two types of enzymes with the same function in a genome could be an evolutionary strategy to regulate the levels of the second messenger in different infection scenarios.
Collapse
Affiliation(s)
- Rafael Molina
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark
| | - Ricardo Garcia-Martin
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark
| | - Blanca López-Méndez
- The Novo Nordisk Foundation Center for Protein Research, Protein Structure & Function Programme, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anne Louise Grøn Jensen
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark
| | - J Rafael Ciges-Tomas
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark
| | - Javier Marchena-Hurtado
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark
| | - Stefano Stella
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, 2200 Copenhagen, Denmark.,The Novo Nordisk Foundation Center for Protein Research, Protein Structure & Function Programme, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| |
Collapse
|
37
|
Cellier MFM. Nramp: Deprive and conquer? Front Cell Dev Biol 2022; 10:988866. [PMID: 36313567 PMCID: PMC9606685 DOI: 10.3389/fcell.2022.988866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.
Collapse
|
38
|
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.
Collapse
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;
| |
Collapse
|
39
|
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.
Collapse
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:
| |
Collapse
|
40
|
Marino ND, Pinilla-Redondo R, Bondy-Denomy J. CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity. Nucleic Acids Res 2022; 50:6414-6422. [PMID: 35670674 PMCID: PMC9226536 DOI: 10.1093/nar/gkac462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/12/2022] [Accepted: 05/23/2022] [Indexed: 12/17/2022] Open
Abstract
CRISPR-Cas12a (Cpf1) is a bacterial RNA-guided nuclease that cuts double-stranded DNA (dsDNA) at sites specified by a CRISPR RNA (crRNA) guide. Additional activities have been ascribed to this enzyme in vitro: site-specific (cis) single-stranded DNA (ssDNA) cleavage and indiscriminate (trans) degradation of ssDNA, RNA, and dsDNA after activation by a complementary target. The ability of Cas12a to cleave nucleic acids indiscriminately has been harnessed for many applications, including diagnostics, but it remains unknown if it contributes to bacterial immunity. Here, we provide evidence that cleavage of ssDNA in cis or in trans by Cas12a is insufficient to impact immunity. Using LbCas12a expressed in either Pseudomonas aeruginosa or Escherichia coli, we observed that cleavage of dsDNA targets did not elicit cell death or dormancy, suggesting insignificant levels of collateral damage against host RNA or DNA. Canonical immunity against invasive dsDNA also had no impact on the replicative fitness of co-infecting dsDNA phage, ssDNA phage or plasmid in trans. Lastly, crRNAs complementary to invasive ssDNA did not provide protection, suggesting that ssDNA cleavage does not occur in vivo or is insignificant. Overall, these results suggest that CRISPR-Cas12a immunity predominantly occurs via canonical targeting of dsDNA, and that the other activities do not significantly impact infection outcomes.
Collapse
Affiliation(s)
- Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Innovative Genomics Institute, Berkeley, CA 94720, USA
| |
Collapse
|
41
|
Smith EM, Ferrell S, Tokars VL, Mondragón A. Structures of an active type III-A CRISPR effector complex. Structure 2022; 30:1109-1128.e6. [PMID: 35714601 PMCID: PMC9357104 DOI: 10.1016/j.str.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) provide many prokaryotes with an adaptive immune system against invading genetic material. Type III CRISPR systems are unique in that they can degrade both RNA and DNA. In response to invading nucleic acids, they produce cyclic oligoadenylates that act as secondary messengers, activating cellular nucleases that aid in the immune response. Here, we present seven single-particle cryo-EM structures of the type III-A Staphylococcus epidermidis CRISPR effector complex. The structures reveal the intact S. epidermidis effector complex in an apo, ATP-bound, cognate target RNA-bound, and non-cognate target RNA-bound states and illustrate how the effector complex binds and presents crRNA. The complexes bound to target RNA capture the type III-A effector complex in a post-RNA cleavage state. The ATP-bound structures give details about how ATP binds to Cas10 to facilitate cyclic oligoadenylate production.
Collapse
Affiliation(s)
- Eric M Smith
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sé Ferrell
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Valerie L Tokars
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA. Nat Microbiol 2022; 7:530-541. [PMID: 35314780 PMCID: PMC7612570 DOI: 10.1038/s41564-022-01074-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/01/2022] [Indexed: 11/08/2022]
Abstract
CRISPR-Cas systems store fragments of foreign DNA called spacers as immunological recordings used to combat future infections. Of the many spacers stored in a CRISPR array, the newest spacers are known to be prioritized for immune defense. However, the underlying mechanism remains unclear. Here we show that the leader region upstream of CRISPR arrays in CRISPR-Cas9 systems enhances CRISPR RNA (crRNA) processing from the newest spacer, prioritizing defense against the matching invader. Using the CRISPR-Cas9 system from Streptococcus pyogenes as a model, we found that the transcribed leader interacts with the conserved repeats bordering the newest spacer. The resulting interaction promotes tracrRNA hybridization with the second repeat, accelerating crRNA processing. Accordingly, disrupting this structure reduces the abundance of the associated crRNA and immune defense against targeted plasmids and bacteriophages. Beyond the S. pyogenes system, bioinformatics analyses revealed that leader-repeat structures appear across CRISPR-Cas9 systems. CRISPR-Cas systems thus possess an RNA-based mechanism to prioritize defense against the most recently encountered invaders.
Collapse
|
44
|
Duncan-Lowey B, Kranzusch PJ. CBASS phage defense and evolution of antiviral nucleotide signaling. Curr Opin Immunol 2022; 74:156-163. [PMID: 35123147 DOI: 10.1016/j.coi.2022.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/16/2022]
Abstract
Cyclic oligonucleotide-based antiphage signaling system (CBASS) immunity is a widespread form of antiphage defense in bacteria and archaea. Each CBASS operon encodes a cGAS/DncV-like Nucleotidyltransferase (CD-NTase) enzyme that synthesizes a nucleotide second messenger in response to viral infection. An associated Cap effector protein then binds the nucleotide signal and executes cell death to destroy the host cell and block phage propagation. Here we build upon recent advances to establish rules controlling each step of CBASS activation and antiphage defense. Comparative analysis of CBASS, CRISPR, Pycsar, and cGAS-STING immunity provides insight into the evolution of phage defense and animal innate immunity and highlights new questions emerging in the role of nucleotide second messenger signaling in host-virus interactions.
Collapse
Affiliation(s)
- Brianna Duncan-Lowey
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA.
| |
Collapse
|
45
|
Das A, Goswami HN, Whyms CT, Sridhara S, Li H. Structural Principles of CRISPR-Cas Enzymes Used in Nucleic Acid Detection. J Struct Biol 2022; 214:107838. [PMID: 35123001 PMCID: PMC8924977 DOI: 10.1016/j.jsb.2022.107838] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-based technology has revolutionized the field of biomedicine with broad applications in genome editing, therapeutics and diagnostics. While a majority of applications involve the RNA-guided site-specific DNA or RNA cleavage by CRISPR enzymes, recent successes in nucleic acid detection rely on their collateral and non-specific cleavage activated by viral DNA or RNA. Ranging in enzyme composition, the mechanism for distinguishing self- from foreign-nucleic acids, the usage of second messengers, and enzymology, the CRISPR enzymes provide a diverse set of diagnosis tools in further innovations. Structural biology plays an important role in elucidating the mechanisms of these CRISPR enzymes. Here we summarize and compare structures of three types of CRISPR enzymes used in nucleic acid detection captured in their respective functional forms and illustrate the current understanding of their activation mechanism.
Collapse
Affiliation(s)
- Anuska Das
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Hemant N Goswami
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Charlisa T Whyms
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Sagar Sridhara
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, 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.
| |
Collapse
|
46
|
Xia P, Dutta A, Gupta K, Batish M, Parashar V. Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems. J Biol Chem 2022; 298:101591. [PMID: 35038453 PMCID: PMC8844856 DOI: 10.1016/j.jbc.2022.101591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/28/2023] Open
Abstract
RNA interference by type III CRISPR systems results in the synthesis of cyclic oligoadenylate (cOA) second messengers, which are known to bind and regulate various CARF domain-containing nuclease receptors. The CARF domain-containing Csa3 family of transcriptional factors associated with the DNA-targeting type I CRISPR systems regulate expression of various CRISPR and DNA repair genes in many prokaryotes. In this study, we extend the known receptor repertoire of cOA messengers to include transcriptional factors by demonstrating specific binding of cyclic tetra-adenylate (cA4) to Saccharolobus solfataricus Csa3 (Csa3Sso). Our 2.0-Å resolution X-ray crystal structure of cA4-bound full-length Csa3Sso reveals the binding of its CARF domain to an elongated conformation of cA4. Using cA4 binding affinity analyses of Csa3Sso mutants targeting the observed Csa3Sso•cA4 structural interface, we identified a Csa3-specific cA4 binding motif distinct from a more widely conserved cOA-binding CARF motif. Using a rational surface engineering approach, we increased the cA4 binding affinity of Csa3Sso up to ∼145-fold over the wildtype, which has potential applications for future second messenger-driven CRISPR gene expression and editing systems. Our in-solution Csa3Sso structural analysis identified cA4-induced allosteric and asymmetric conformational rearrangement of its C-terminal winged helix-turn-helix effector domains, which could potentially be incompatible to DNA binding. However, specific in vitro binding of the purified Csa3Sso to its putative promoter (PCas4a) was found to be cA4 independent, suggesting a complex mode of Csa3Sso regulation. Overall, our results support cA4-and Csa3-mediated cross talk between type III and type I CRISPR systems.
Collapse
Affiliation(s)
- Pengjun Xia
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Anirudha Dutta
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Kushol Gupta
- The Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Vijay Parashar
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA; Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA.
| |
Collapse
|
47
|
Aviram N, Thornal AN, Zeevi D, Marraffini LA. Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system. Nucleic Acids Res 2022; 50:1661-1672. [PMID: 35048966 PMCID: PMC8860600 DOI: 10.1093/nar/gkab1299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called ‘spacers’, into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.
Collapse
Affiliation(s)
- Naama Aviram
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Ashley N Thornal
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - David Zeevi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Luciano A Marraffini
- Laboratory of Bacteriology, the Rockefeller University, 1230 York Ave, New York, NY 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| |
Collapse
|
48
|
Alternative functions of CRISPR-Cas systems in the evolutionary arms race. Nat Rev Microbiol 2022; 20:351-364. [PMID: 34992260 DOI: 10.1038/s41579-021-00663-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
CRISPR-Cas systems of bacteria and archaea comprise chromosomal loci with typical repetitive clusters and associated genes encoding a range of Cas proteins. Adaptation of CRISPR arrays occurs when virus-derived and plasmid-derived sequences are integrated as new CRISPR spacers. Cas proteins use CRISPR-derived RNA guides to specifically recognize and cleave nucleic acids of invading mobile genetic elements. Apart from this role as an adaptive immune system, some CRISPR-associated nucleases are hijacked by mobile genetic elements: viruses use them to attack their prokaryotic hosts, and transposons have adopted CRISPR systems for guided transposition. In addition, some CRISPR-Cas systems control the expression of genes involved in bacterial physiology and virulence. Moreover, pathogenic bacteria may use their Cas nuclease activity indirectly to evade the human immune system or directly to invade the nucleus and damage the chromosomal DNA of infected human cells. Thus, the evolutionary arms race has led to the expansion of exciting variations in CRISPR mechanisms and functionalities. In this Review, we explore the latest insights into the diverse functions of CRISPR-Cas systems beyond adaptive immunity and discuss the implications for the development of CRISPR-based applications.
Collapse
|
49
|
Abstract
The principal biological function of bacterial and archaeal CRISPR systems is RNA-guided adaptive immunity against viruses and other mobile genetic elements (MGEs). These systems show remarkable evolutionary plasticity and functional versatility at multiple levels, including both the defense mechanisms that lead to direct, specific elimination of the target DNA or RNA and those that cause programmed cell death (PCD) or induction of dormancy. This flexibility is also evident in the recruitment of CRISPR systems for nondefense functions. Defective CRISPR systems or individual CRISPR components have been recruited by transposons for RNA-guided transposition, by plasmids for interplasmid competition, and by viruses for antidefense and interviral conflicts. Additionally, multiple highly derived CRISPR variants of yet unknown functions have been discovered. A major route of innovation in CRISPR evolution is the repurposing of diverged repeat variants encoded outside CRISPR arrays for various structural and regulatory functions. The evolutionary plasticity and functional versatility of CRISPR systems are striking manifestations of the ubiquitous interplay between defense and “normal” cellular functions. The CRISPR systems show remarkable functional versatility beyond their principal function as an adaptive immune mechanism. This Essay discusses how derived CRISPR systems have been recruited by transposons on multiple occasions and mediate RNA-guided transposition; derived CRISPR RNAs are frequently recruited for regulatory functions.
Collapse
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
50
|
Cao Y, Yang R, Wang W, Jiang S, Yang C, Liu N, Dai H, Lee I, Meng X, Yuan Z. Probing the Formation, Structure and Free Energy Relationships of M Protein Dimers of SARS-CoV-2. Comput Struct Biotechnol J 2022; 20:573-582. [PMID: 35047128 PMCID: PMC8756865 DOI: 10.1016/j.csbj.2022.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The M protein of the novel coronavirus 2019 (SARS-CoV-2) is the major structural component of the viral envelope and is also the minimum requirement for virus particle budding. M proteins generally exist as dimers. In virus assembly, they are the main driving force for envelope formation through lateral interactions and interactions with other viral structural proteins that play a central role. We built 100 candidate models and finally analyzed the six most convincing structural features of the SARS-CoV-2 M protein dimer based on long-timescale molecular dynamics (MD) simulations, multiple free energy analyses (potential mean force (PMF) and molecular mechanics Poisson-Boltzmann surface area (MMPBSA)) and principal component analysis (PCA) to obtain the most reasonable structure. The dimer stability was found to depend on the Leu-Ile zipper motif and aromatic amino acids in the transmembrane domain (TMD). Furthermore, the C-terminal domain (CTD) effects were relatively small. These results highlight a model in which there is sufficient binding affinity between the TMDs of M proteins to form dimers through the residues at the interface of the three transmembrane helices (TMHs). This study aims to help find more effective inhibitors of SARS-CoV-2 M dimers and to develop vaccines based on structural information.
Collapse
Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
- National Supercomputer Center in Tianjin, 300457 PR China
| | - Rui Yang
- Department of Infection and Immunity, Tianjin Union Medical Center, Nankai University Affiliated Hospital. 300031, PR China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Shengpeng Jiang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Chengwen Yang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Ningbo Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
| | - Hongji Dai
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
- College of Physics, Nankai University, Tianjin 300071, PR China
| | - Imshik Lee
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, PR China
| | - Xiangfei Meng
- National Supercomputer Center in Tianjin, 300457 PR China
- Corresponding authors.
| | - Zhiyong Yuan
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060 PR China
- Corresponding authors.
| |
Collapse
|