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Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024; 300:107295. [PMID: 38641067 PMCID: PMC11127173 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA-cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
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Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma, USA.
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2
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Deng X, Yuan J, Chen L, Chen H, Wei C, Nielsen PH, Wuertz S, Qiu G. CRISPR-Cas phage defense systems and prophages in Candidatus Accumulibacter. WATER RESEARCH 2023; 235:119906. [PMID: 37004306 DOI: 10.1016/j.watres.2023.119906] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR) from wastewater. Although bacteriophages have been shown to represent fatal threats to Ca. Accumulibacter organisms and thus interfere with the stability of the EBPR process, little is known about the ability of different Ca. Accumulibacter strains to resist phage infections. We conducted a systematic analysis of the occurrence and characteristics of clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR-Cas) systems and prophages in Ca. Accumulibacter lineage members (43 in total, including 10 newly recovered genomes). Results indicate that 28 Ca. Accumulibacter genomes encode CRISPR-Cas systems. They were likely acquired via horizontal gene transfer, conveying a distinct adaptivity to phage predation to different Ca. Accumulibacter members. Major differences in the number of spacers show the unique phage resistance of these members. A comparison of the spacers in closely related Ca. Accumulibacter members from distinct geographical locations indicates that habitat isolation may have resulted in the acquisition of resistance to different phages by different Ca. Accumulibacter. Long-term operation of three laboratory-scale EBPR bioreactors revealed high relative abundances of Ca. Accumulibacter with CRISPSR-Cas systems. Their specific resistance to phages in these reactors was indicated by spacer analysis. Metatranscriptomic analyses showed the activation of the CRISPR-Cas system under both anaerobic and aerobic conditions. Additionally, 133 prophage regions were identified in 43 Ca. Accumulibacter genomes. Twenty-seven of them (in 19 genomes) were potentially active. Major differences in the occurrence of CRISPR-Cas systems and prophages in Ca. Accumulibacter will lead to distinct responses to phage predation. This study represents the first systematic analysis of CRISPR-Cas systems and prophages in the Ca. Accumulibacter lineage, providing new perspectives on the potential impacts of phages on Ca. Accumulibacter and EBPR systems.
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Affiliation(s)
- Xuhan Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jing Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Hang Chen
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
| | - Per H Nielsen
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Centre for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg DK-9220, Denmark
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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3
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Shangguan Q, Graham S, Sundaramoorthy R, White M. Structure and mechanism of the type I-G CRISPR effector. Nucleic Acids Res 2022; 50:11214-11228. [PMID: 36305833 PMCID: PMC9638904 DOI: 10.1093/nar/gkac925] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 08/15/2023] Open
Abstract
Type I CRISPR systems are the most common CRISPR type found in bacteria. They use a multisubunit effector, guided by crRNA, to detect and bind dsDNA targets, forming an R-loop and recruiting the Cas3 enzyme to facilitate target DNA destruction, thus providing immunity against mobile genetic elements. Subtypes have been classified into families A-G, with type I-G being the least well understood. Here, we report the composition, structure and function of the type I-G Cascade CRISPR effector from Thioalkalivibrio sulfidiphilus, revealing key new molecular details. The unique Csb2 subunit processes pre-crRNA, remaining bound to the 3' end of the mature crRNA, and seven Cas7 subunits form the backbone of the effector. Cas3 associates stably with the effector complex via the Cas8g subunit and is important for target DNA recognition. Structural analysis by cryo-Electron Microscopy reveals a strikingly curved backbone conformation with Cas8g spanning the belly of the structure. These biochemical and structural insights shed new light on the diversity of type I systems and open the way to applications in genome engineering.
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Affiliation(s)
- Qilin Shangguan
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | | | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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4
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Hu C, Ni D, Nam KH, Majumdar S, McLean J, Stahlberg H, Terns MP, Ke A. Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Mol Cell 2022; 82:2754-2768.e5. [PMID: 35835111 PMCID: PMC9357151 DOI: 10.1016/j.molcel.2022.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/08/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022]
Abstract
Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degradation. Contrary to this model, here, we show that type I-A Cascade and Cas3 function as an integral effector complex. We provide four cryoelectron microscopy (cryo-EM) snapshots of the Pyrococcus furiosus (Pfu) type I-A effector complex in different stages of DNA recognition and degradation. The HD nuclease of Cas3 is autoinhibited inside the effector complex. It is only allosterically activated upon full R-loop formation, when the entire targeted region has been validated by the RNA guide. The mechanistic insights inspired us to convert Pfu Cascade-Cas3 into a high-sensitivity, low-background, and temperature-activated nucleic acid detection tool. Moreover, Pfu CRISPR-Cas3 shows robust bi-directional deletion-editing activity in human cells, which could find usage in allele-specific inactivation of disease-causing mutations.
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Affiliation(s)
- Chunyi Hu
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Institute of Physics, Faculty of Basic Sciences, Swiss Federal Institute of Technology (EPFL), Cubotron, Route de la Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Biology, Faculty of Biology and Medicine, University of Lausanne (UNIL), 1011 Lausanne, Switzerland
| | - Ki Hyun Nam
- Department of Life Science, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Sonali Majumdar
- Department of Biochemistry and Molecular Biology, Department of Genetics, and Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Justin McLean
- Department of Biochemistry and Molecular Biology, Department of Genetics, and Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, Faculty of Basic Sciences, Swiss Federal Institute of Technology (EPFL), Cubotron, Route de la Sorge, 1015 Lausanne, Switzerland; Department of Fundamental Biology, Faculty of Biology and Medicine, University of Lausanne (UNIL), 1011 Lausanne, Switzerland
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, Department of Genetics, and Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
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5
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Dynamic modulation of enzyme activity by synthetic CRISPR–Cas6 endonucleases. Nat Chem Biol 2022; 18:492-500. [DOI: 10.1038/s41589-022-01005-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/25/2022] [Indexed: 11/08/2022]
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6
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Hussain MS, Kumar M. Assembly of Cas7 subunits of Leptospira on the mature crRNA of CRISPR-Cas I-B is modulated by divalent ions. Gene X 2022; 818:146244. [PMID: 35074418 DOI: 10.1016/j.gene.2022.146244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/02/2023] Open
Abstract
The spirochete Leptospira interrogans serovar Copenhageni harbors the genetic elements of the CRISPR-Cas type I-B system in its genome. CRISPR-Cas is a CRISPR RNA (crRNA) mediated adaptive immune system in most prokaryotes against mobile genetic elements (MGEs). To eliminate the intruding MGEs, CRISPR-Cas type I systems utilize a Cascade (CRISPR-associated complex for antiviral defense) complex composed of Cas5, Cas6, Cas7, and Cas8 bound with a crRNA. The Cas7 is essentially known to constitute the major component of the Cascade complex. The present study reports the biochemical characterization of the Cas7 (LinCas7) from the CRISPR-Cas type I-B system of L. interrogans serovar Copenhageni. The pure recombinant LinCas7 (rLinCas7) exists as a monomer in the solution by size exclusion chromatography. The rLinCas7 demonstrates an endoDNase activity dependent upon divalent Mg2+ ions, monovalent ions, pH, temperature, and substrate size. Analysis of ribonucleoprotein composite (rLinCas7-crRNA) by electron microscopy and native-PAGE demonstrated that rLinCas7 could oligomerize on the mature CRISPR RNA (crRNA) framework in the presence of Mg2+ ions. The ribonucleoprotein composite attains a helical shape similar to the backbone of the Cascade complex. However, in the absence of Mg2+ ions, rLinCas7 acts as an RNase. The fluorescence spectroscopy disclosed a weak interaction (Kd = 26.81 mM) between rLinCas7 and Mg2+ ions, leading to an overall conformational change in rLinCas7 that modulates the rLinCas7's activity on DNA and RNA substrates. The nuclease activity of LinCas7 characterized in this study aids to the functional divergences among proteins of the Cas7 family from different CRISPR-Cas systems in various organisms.
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Affiliation(s)
- Md Saddam Hussain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 7810 39, Assam, India.
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Zink IA, Wimmer E, Schleper C. Heavily Armed Ancestors: CRISPR Immunity and Applications in Archaea with a Comparative Analysis of CRISPR Types in Sulfolobales. Biomolecules 2020; 10:E1523. [PMID: 33172134 PMCID: PMC7694759 DOI: 10.3390/biom10111523] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Prokaryotes are constantly coping with attacks by viruses in their natural environments and therefore have evolved an impressive array of defense systems. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system found in the majority of archaea and about half of bacteria which stores pieces of infecting viral DNA as spacers in genomic CRISPR arrays to reuse them for specific virus destruction upon a second wave of infection. In detail, small CRISPR RNAs (crRNAs) are transcribed from CRISPR arrays and incorporated into type-specific CRISPR effector complexes which further degrade foreign nucleic acids complementary to the crRNA. This review gives an overview of CRISPR immunity to newcomers in the field and an update on CRISPR literature in archaea by comparing the functional mechanisms and abundances of the diverse CRISPR types. A bigger fraction is dedicated to the versatile and prevalent CRISPR type III systems, as tremendous progress has been made recently using archaeal models in discerning the controlled molecular mechanisms of their unique tripartite mode of action including RNA interference, DNA interference and the unique cyclic-oligoadenylate signaling that induces promiscuous RNA shredding by CARF-domain ribonucleases. The second half of the review spotlights CRISPR in archaea outlining seminal in vivo and in vitro studies in model organisms of the euryarchaeal and crenarchaeal phyla, including the application of CRISPR-Cas for genome editing and gene silencing. In the last section, a special focus is laid on members of the crenarchaeal hyperthermophilic order Sulfolobales by presenting a thorough comparative analysis about the distribution and abundance of CRISPR-Cas systems, including arrays and spacers as well as CRISPR-accessory proteins in all 53 genomes available to date. Interestingly, we find that CRISPR type III and the DNA-degrading CRISPR type I complexes co-exist in more than two thirds of these genomes. Furthermore, we identified ring nuclease candidates in all but two genomes and found that they generally co-exist with the above-mentioned CARF domain ribonucleases Csx1/Csm6. These observations, together with published literature allowed us to draft a working model of how CRISPR-Cas systems and accessory proteins cross talk to establish native CRISPR anti-virus immunity in a Sulfolobales cell.
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8
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CRISPR-Cas adaptive immune systems in Sulfolobales: genetic studies and molecular mechanisms. SCIENCE CHINA-LIFE SCIENCES 2020; 64:678-696. [DOI: 10.1007/s11427-020-1745-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2020] [Indexed: 12/26/2022]
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9
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Nimkar S, Anand B. Cas3/I-C mediated target DNA recognition and cleavage during CRISPR interference are independent of the composition and architecture of Cascade surveillance complex. Nucleic Acids Res 2020; 48:2486-2501. [PMID: 31980818 PMCID: PMC7049708 DOI: 10.1093/nar/gkz1218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/17/2019] [Accepted: 01/22/2020] [Indexed: 12/26/2022] Open
Abstract
In type I CRISPR-Cas system, Cas3—a nuclease cum helicase—in cooperation with Cascade surveillance complex cleaves the target DNA. Unlike the Cascade/I-E, which is composed of five subunits, the Cascade/I-C is made of only three subunits lacking the CRISPR RNA processing enzyme Cas6, whose role is assumed by Cas5. How these differences in the composition and organization of Cascade subunits in type I-C influence the Cas3/I-C binding and its target cleavage mechanism is poorly understood. Here, we show that Cas3/I-C is intrinsically a single-strand specific promiscuous nuclease. Apart from the helicase domain, a constellation of highly conserved residues—which are unique to type I-C—located in the uncharacterized C-terminal domain appears to influence the nuclease activity. Recruited by Cascade/I-C, the HD nuclease of Cas3/I-C nicks the single-stranded region of the non-target strand and positions the helicase motor. Powered by ATP, the helicase motor reels in the target DNA, until it encounters the roadblock en route, which stimulates the HD nuclease. Remarkably, we show that Cas3/I-C supplants Cas3/I-E for CRISPR interference in type I-E in vivo, suggesting that the target cleavage mechanism is evolutionarily conserved between type I-C and type I-E despite the architectural difference exhibited by Cascade/I-C and Cascade/I-E.
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Affiliation(s)
- Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - B Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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Wittig S, Songailiene I, Schmidt C. Formation and Stoichiometry of CRISPR-Cascade Complexes with Varying Spacer Lengths Revealed by Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:538-546. [PMID: 32008319 DOI: 10.1021/jasms.9b00011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The adaptive immune system of bacteria and archaea against viral DNA is based on clustered, regularly interspaced, short palindromic repeats (CRISPRs) which are encoded in the host genome and translated into CRISPR RNAs (crRNAs) containing single spacer sequences complementary to foreign DNA. crRNAs assemble with CRISPR-associated (Cas) proteins forming surveillance complexes that base-pair with viral DNA and mediate its degradation. As specificity of degradation is provided by the crRNA spacer sequence, genetic engineering of the CRISPR system has emerged as a popular molecular tool, for instance, in gene silencing and programmed DNA degradation. Elongating or shortening the crRNA spacer sequence are therefore promising ventures to modify specificity toward the target DNA. However, even though the stoichiometry of wild-type complexes is well established, it is unknown how variations in crRNA spacer length affect their stoichiometry. The CRISPR-associated antiviral defense surveillance complexes of Streptococcus thermophilus (StCascade complexes) contain crRNA and five protein subunits. Using native mass spectrometry, we studied the formation and stoichiometry of StCascade complexes assembled on a set of crRNAs with different spacer lengths. We assigned all relevant complexes and gained insights into the stoichiometry of the complexes as well as their preferred assembly. We found that stable complexes, which incorporate or lose a (Cas7)2(Cse2)1-module, assemble on crRNA varied in length by 12-nucleotide units, while varying crRNA length in six-nucleotide units results in heterogeneous mixtures of complexes. Combining our results from the various variants, we generated an assembly pathway revealing general features of I-E type Cascade complex formation.
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Affiliation(s)
- Sabine Wittig
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
| | - Inga Songailiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, 7 Saulėtekio Avenue, 10257 Vilnius, Lithuania
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120 Halle, Germany
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Behler J, Hess WR. Approaches to study CRISPR RNA biogenesis and the key players involved. Methods 2020; 172:12-26. [PMID: 31325492 DOI: 10.1016/j.ymeth.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 07/15/2019] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins provide an inheritable and adaptive immune system against phages and foreign genetic elements in many bacteria and archaea. The three stages of CRISPR-Cas immunity comprise adaptation, CRISPR RNA (crRNA) biogenesis and interference. The maturation of the pre-crRNA into mature crRNAs, short guide RNAs that target invading nucleic acids, is crucial for the functionality of CRISPR-Cas defense systems. Mature crRNAs assemble with Cas proteins into the ribonucleoprotein (RNP) effector complex and guide the Cas nucleases to the cognate foreign DNA or RNA target. Experimental approaches to characterize these crRNAs, the specific steps toward their maturation and the involved factors, include RNA-seq analyses, enzyme assays, methods such as cryo-electron microscopy, the crystallization of proteins, or UV-induced protein-RNA crosslinking coupled to mass spectrometry analysis. Complex and multiple interactions exist between CRISPR-cas-encoded specific riboendonucleases such as Cas6, Cas5d and Csf5, endonucleases with dual functions in maturation and interference such as the enzymes of the Cas12 and Cas13 families, and nucleases belonging to the cell's degradosome such as RNase E, PNPase and RNase J, both in the maturation as well as in interference. The results of these studies have yielded a picture of unprecedented diversity of sequences, enzymes and biochemical mechanisms.
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Affiliation(s)
- Juliane Behler
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
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12
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Abstract
Liposomes are one of the most widely investigated carriers for CRISPR/Cas9 delivery. The surface properties of liposomal carriers, including the surface charge, PEGylation, and ligand modification can significantly affect the gene silencing efficiency. Three barriers of systemic CRISPR/Cas9 delivery (long blood circulation, efficient tumor penetration, and efficient cellular uptake/endosomal escape) are analyzed on liposomal carriers with different surface charges, PEGylations, and ligand modifications. Cationic formulations dominate CRISPR/Cas9 delivery and neutral formulations also have good performance while anionic formulations are generally not proper for CRISPR/Cas9 delivery. The PEG dilemma (prolonged blood circulation vs. reduced cellular uptake/endosomal escape) and the side effect of repeated PEGylated formulation (accelerated blood clearance) were discussed. Effects of ligand modification on cationic and neutral formulations were analyzed. Finally, we summarized the achievements in liposomal CRISPR/Cas9 delivery, outlined existing problems, and provided some future perspectives. Liposomes are one of the most widely investigated carriers for CRISPR/Cas9 delivery. The surface properties of liposomal carriers, including the surface charge, PEGylation, and ligand modification can significantly affect the gene silencing efficiency. Three barriers of systemic siRNA delivery (long blood circulation, efficient tumor penetration, and efficient cellular uptake/endosomal escape) are analyzed on liposomal carriers with different surface charges, PEGylations, and ligand modifications. Cationic formulations dominate CRISPR/Cas9 delivery and neutral formulations also have good performance while anionic formulations are generally not proper for CRISPR/Cas9 delivery. The PEG dilemma (prolonged blood circulation vs. reduced cellular uptake/endosomal escape) and the side effect of repeated PEGylated formulation (accelerated blood clearance) were discussed. Effects of ligand modification on cationic and neutral formulations were analyzed. Finally, we summarized the achievements in liposomal CRISPR/Cas9 delivery, outlined existing problems, and provided some future perspectives.
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13
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Özcan A, Pausch P, Linden A, Wulf A, Schühle K, Heider J, Urlaub H, Heimerl T, Bange G, Randau L. Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum. Nat Microbiol 2019; 4:89-96. [PMID: 30397343 DOI: 10.1038/s41564-018-0274-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/24/2018] [Indexed: 12/24/2022]
Abstract
Type IV CRISPR-Cas modules belong to class 1 prokaryotic adaptive immune systems, which are defined by the presence of multisubunit effector complexes. They usually lack the known Cas proteins involved in adaptation and target cleavage, and their function has not been experimentally addressed. To investigate RNA and protein components of this CRISPR-Cas type, we located a complete type IV cas gene locus and an adjacent CRISPR array on a megaplasmid of Aromatoleum aromaticum EbN1, which contains an additional type I-C system on its chromosome. RNA sequencing analyses verified CRISPR RNA (crRNA) production and maturation for both systems. Type IV crRNAs were shown to harbour unusually short 7 nucleotide 5'-repeat tags and stable 3' hairpin structures. A unique Cas6 variant (Csf5) was identified that generates crRNAs that are specifically incorporated into type IV CRISPR-ribonucleoprotein (crRNP) complexes. Structures of RNA-bound Csf5 were obtained. Recombinant production and purification of the type IV Cas proteins, together with electron microscopy, revealed that Csf2 acts as a helical backbone for type IV crRNPs that include Csf5, Csf3 and a large subunit (Csf1). Mass spectrometry analyses identified protein-protein and protein-RNA contact sites. These results highlight evolutionary connections between type IV and type I CRISPR-Cas systems and demonstrate that type IV CRISPR-Cas systems employ crRNA-guided effector complexes.
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Affiliation(s)
- Ahsen Özcan
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany
- Faculty of Chemistry, Philipps-University-Marburg, Marburg, Germany
| | - Andreas Linden
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karola Schühle
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Johann Heider
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Henning Urlaub
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany
- Faculty of Chemistry, Philipps-University-Marburg, Marburg, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- LOEWE Center for Synthetic Microbiology (Synmikro), Philipps University Marburg, Marburg, Germany.
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14
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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15
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Majumdar S, Terns MP. CRISPR RNA-guided DNA cleavage by reconstituted Type I-A immune effector complexes. Extremophiles 2018; 23:19-33. [PMID: 30284045 DOI: 10.1007/s00792-018-1057-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022]
Abstract
Diverse CRISPR-Cas immune systems protect archaea and bacteria from viruses and other mobile genetic elements. All CRISPR-Cas systems ultimately function by sequence-specific destruction of invading complementary nucleic acids. However, each CRISPR system uses compositionally distinct crRNP [CRISPR (cr) RNA/Cas protein] immune effector complexes to recognize and destroy invasive nucleic acids by unique molecular mechanisms. Previously, we found that Type I-A (Csa) effector crRNPs from Pyrococcus furiosus function in vivo to eliminate invader DNA. Here, we reconstituted functional Type I-A effector crRNPs in vitro with recombinant Csa proteins and synthetic crRNA and characterized properties of crRNP assembly, target DNA recognition and cleavage. Six proteins (Csa 4-1, Cas3″, Cas3', Cas5a, Csa2, Csa5) are essential for selective target DNA binding and cleavage. Native gel shift analysis and UV-induced RNA-protein crosslinking demonstrate that Cas5a and Csa2 directly interact with crRNA 5' tag and guide sequences, respectively. Mutational analysis revealed that Cas3″ is the effector nuclease of the complex. Together, our results indicate that DNA cleavage by Type I-A crRNPs requires crRNA-guided and protospacer adjacent motif-dependent target DNA binding to unwind double-stranded DNA and expose single strands for progressive ATP-dependent 3'-5' cleavage catalyzed by integral Cas3' helicase and Cas3″ nuclease crRNP components.
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Affiliation(s)
- Sonali Majumdar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA. .,Department of Genetics, University of Georgia, Athens, GA, 30602, USA. .,Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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16
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Drabavicius G, Sinkunas T, Silanskas A, Gasiunas G, Venclovas Č, Siksnys V. DnaQ exonuclease-like domain of Cas2 promotes spacer integration in a type I-E CRISPR-Cas system. EMBO Rep 2018; 19:e45543. [PMID: 29891635 PMCID: PMC6030702 DOI: 10.15252/embr.201745543] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas systems constitute an adaptive immune system that provides acquired resistance against phages and plasmids in prokaryotes. Upon invasion of foreign nucleic acids, some cells integrate short fragments of foreign DNA as spacers into the CRISPR locus to memorize the invaders and acquire resistance in the subsequent round of infection. This immunization step called adaptation is the least understood part of the CRISPR-Cas immunity. We have focused here on the adaptation stage of Streptococcus thermophilus DGCC7710 type I-E CRISPR4-Cas (St4) system. Cas1 and Cas2 proteins conserved in nearly all CRISPR-Cas systems are required for spacer acquisition. The St4 CRISPR-Cas system is unique because the Cas2 protein is fused to an additional DnaQ exonuclease domain. Here, we demonstrate that St4 Cas1 and Cas2-DnaQ form a multimeric complex, which is capable of integrating DNA duplexes with 3'-overhangs (protospacers) in vitro We further show that the DnaQ domain of Cas2 functions as a 3'-5'-exonuclease that processes 3'-overhangs of the protospacer to promote integration.
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Affiliation(s)
| | - Tomas Sinkunas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
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17
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Maier LK, Stachler AE, Brendel J, Stoll B, Fischer S, Haas KA, Schwarz TS, Alkhnbashi OS, Sharma K, Urlaub H, Backofen R, Gophna U, Marchfelder A. The nuts and bolts of the Haloferax CRISPR-Cas system I-B. RNA Biol 2018; 16:469-480. [PMID: 29649958 PMCID: PMC6546412 DOI: 10.1080/15476286.2018.1460994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Invading genetic elements pose a constant threat to prokaryotic survival, requiring an effective defence. Eleven years ago, the arsenal of known defence mechanisms was expanded by the discovery of the CRISPR-Cas system. Although CRISPR-Cas is present in the majority of archaea, research often focuses on bacterial models. Here, we provide a perspective based on insights gained studying CRISPR-Cas system I-B of the archaeon Haloferax volcanii. The system relies on more than 50 different crRNAs, whose stability and maintenance critically depend on the proteins Cas5 and Cas7, which bind the crRNA and form the Cascade complex. The interference machinery requires a seed sequence and can interact with multiple PAM sequences. H. volcanii stands out as the first example of an organism that can tolerate autoimmunity via the CRISPR-Cas system while maintaining a constitutively active system. In addition, the H. volcanii system was successfully developed into a tool for gene regulation.
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Affiliation(s)
| | | | | | | | | | - Karina A Haas
- a Biology II, Ulm University , Ulm , Germany.,b Microbiology and Biotechnology, Ulm University , Ulm , Germany
| | | | - Omer S Alkhnbashi
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany
| | - Kundan Sharma
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,f Ludwig Institute for Cancer Research, University of Oxford , Oxford , United Kingdom
| | - Henning Urlaub
- e Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, Göttingen , Germany.,g Institute for Clinical Chemistry, University Medical Center Göttingen , Robert Koch Straße 10, Göttingen , Germany
| | - Rolf Backofen
- c Freiburg Bioinformatics Group, Department of Computer Science , University of Freiburg , Georges-Köhler-Allee 106, Freiburg , Germany.,d Centre for Biological Signalling Studies (BIOSS), Cluster of Excellence, University of Freiburg , Germany
| | - Uri Gophna
- h School of Molecular Cell Biology & Biotechnology, George S. Wise, Faculty of Life Sciences, Tel Aviv University , Tel Aviv , Israel
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18
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Hille F, Richter H, Wong SP, Bratovič M, Ressel S, Charpentier E. The Biology of CRISPR-Cas: Backward and Forward. Cell 2018. [DOI: 10.1016/j.cell.2017.11.032] [Citation(s) in RCA: 333] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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He F, Vestergaard G, Peng W, She Q, Peng X. CRISPR-Cas type I-A Cascade complex couples viral infection surveillance to host transcriptional regulation in the dependence of Csa3b. Nucleic Acids Res 2017; 45:1902-1913. [PMID: 27980065 PMCID: PMC5389559 DOI: 10.1093/nar/gkw1265] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/07/2016] [Indexed: 12/25/2022] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats and the associated genes) constitute adaptive immune systems in bacteria and archaea and they provide sequence specific immunity against foreign nucleic acids. CRISPR-Cas systems are activated by viral infection. However, little is known about how CRISPR-Cas systems are activated in response to viral infection or how their expression is controlled in the absence of viral infection. Here, we demonstrate that both the transcriptional regulator Csa3b, and the type I-A interference complex Cascade, are required to transcriptionally repress the interference gene cassette in the archaeon Sulfolobus. Csa3b binds to two palindromic repeat sites in the promoter region of the cassette and facilitates binding of the Cascade to the promoter region. Upon viral infection, loading of Cascade complexes onto crRNA-matching protospacers leads to relief of the transcriptional repression. Our data demonstrate a mechanism coupling CRISPR-Cas surveillance of protospacers to transcriptional regulation of the interference gene cassette thereby allowing a fast response to viral infection.
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Affiliation(s)
- Fei He
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
| | - Gisle Vestergaard
- Helmholtz Zentrum München, Research Unit Environmental Genomics, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany
| | - Wenfang Peng
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
| | - Qunxin She
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
| | - Xu Peng
- Archaea Centre, Department of Biology, Copenhagen University, DK2200 Copenhagen N, Denmark
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20
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Abstract
Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.
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Affiliation(s)
- Marcus Thomas
- Computational Biology Department, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States of America. Joint Carnegie Mellon University/University of Pittsburgh Ph.D. Program in Computational Biology, 4400 Fifth Avenue, Pittsburgh, PA 15213, United States of America
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21
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Functional constraints on adaptive evolution of protein ubiquitination sites. Sci Rep 2017; 7:39949. [PMID: 28054638 PMCID: PMC5215434 DOI: 10.1038/srep39949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 11/23/2016] [Indexed: 12/29/2022] Open
Abstract
It is still unclear whether there exist functional constraints on the evolution of protein ubiquitination sites, because most previous studies regarded all protein ubiquitination sites as a whole or only focused on limited structural properties. We tried to clarify the relation between functional constraints and ubiquitination sites evolution. We investigated the evolutionary conservation of human ubiquitination sites in a broad evolutionary scale from G. gorilla to S. pombe, and we found that in organisms originated after the divergence of vertebrate, ubiquitination sites are more conserved than their flanking regions, while the opposite tendency is observed before this divergence time. By grouping the ubiquitination proteins into different functional categories, we confirm that many functional constraints like certain molecular functions, protein tissue expression specificity and protein connectivity in protein-protein interaction network enhance the evolutionary conservation of ubiquitination sites. Furthermore, by analyzing the gains of ubiquitination sites at different divergence time and their functional characters, we validate that the emergences of ubiquitination sites at different evolutionary time were also affected by the uncovered functional constraints. The above results suggest that functional constraints on the adaptive evolution of ubiquitination sites increase the opportunity for ubiquitination to synthetically regulate various cellular and developmental processes during evolution.
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22
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Tripp V, Martin R, Orell A, Alkhnbashi OS, Backofen R, Randau L. Plasticity of archaeal C/D box sRNA biogenesis. Mol Microbiol 2016; 103:151-164. [PMID: 27743417 DOI: 10.1111/mmi.13549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 01/11/2023]
Abstract
Archaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2'-O-methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes. We found that the majority of these genes do not possess independent promoters but are rather located at positions that allow for co-transcription with neighboring genes and their start or stop codons were frequently incorporated into the conserved boxC and D motifs. The biogenesis of plasmid-encoded C/D box sRNA variants was analyzed in vivo in Sulfolobus acidocaldarius. It was found that C/D box sRNA maturation occurs independent of their genetic context and relies solely on the presence of intact RNA kink-turn structures. The observed plasticity of C/D box sRNA biogenesis is suggested to enable their accelerated evolution and, consequently, allow for adjustments of the RNA modification landscape.
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Affiliation(s)
- Vanessa Tripp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
| | - Roman Martin
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany
| | - Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.,BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, University of Freiburg, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
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23
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Type III CRISPR-Cas Immunity: Major Differences Brushed Aside. Trends Microbiol 2016; 25:49-61. [PMID: 27773522 DOI: 10.1016/j.tim.2016.09.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 09/21/2016] [Accepted: 09/27/2016] [Indexed: 12/26/2022]
Abstract
For a long time the mechanism of immunity provided by the Type III CRISPR-Cas systems appeared to be inconsistent: the Type III-A Csm complex of Staphylococcus epidermidis was first reported to target DNA while Type III-B Cmr complexes were shown to target RNA. This long-standing conundrum has now been resolved by finding that the Type III CRISPR-Cas systems are both RNases and target RNA-activated DNA nucleases. The immunity is achieved by coupling binding and cleavage of RNA transcripts to the degradation of invading DNA. The base-pairing potential between the target RNA and the CRISPR RNA (crRNA) 5'-handle seems to play an important role in discriminating self and non-self nucleic acids; however, the detailed mechanism remains to be uncovered.
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24
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Mousaei M, Deng L, She Q, Garrett RA. Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type I-A CRISPR-Cas interference in Sulfolobus. RNA Biol 2016; 13:1166-1173. [PMID: 27618562 DOI: 10.1080/15476286.2016.1229735] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The stringency of crRNA-protospacer DNA base pair matching required for effective CRISPR-Cas interference is relatively low in crenarchaeal Sulfolobus species in contrast to that required in some bacteria. To understand its biological significance we studied crRNA-protospacer interactions in Sulfolobus islandicus REY15A which carries multiple, and functionally diverse, interference complexes. A range of mismatches were introduced into a vector-borne protospacer that was identical to spacer 1 of CRISPR locus 2, with a cognate CCN PAM sequence. Two important crRNA annealing regions were identified on the 39 bp protospacer, a strong primary site centered on nucleotides 3 - 7 and a weaker secondary site at nucleotides 21 - 25. Multiple mismatches introduced into remaining protospacer regions did not seriously impair interference. Extending the study to different protospacers demonstrated that the efficacy of the secondary site was greatest for protospacers with higher G+C contents. In addition, the interference effects were assigned specifically to the type I-A dsDNA-targeting module by repeating the experiments with mutated protospacer constructs that were transformed into an S. islandicus mutant lacking type III-Bα and III-Bβ interference gene cassettes, which showed similar interference levels to those of the wild-type strain. Parallels are drawn to the involvement of 2 annealing sites for microRNAs on some eukaryal mRNAs which provide enhanced binding capacity and specificity. A biological rationale for the relatively low crRNA-protospacer base pairing stringency among the Sulfolobales is considered.
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Affiliation(s)
- Marzieh Mousaei
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
| | - Ling Deng
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
| | - Qunxin She
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
| | - Roger A Garrett
- a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark
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25
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Reimann V, Alkhnbashi OS, Saunders SJ, Scholz I, Hein S, Backofen R, Hess WR. Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs. Nucleic Acids Res 2016; 45:915-925. [PMID: 27599840 PMCID: PMC5741207 DOI: 10.1093/nar/gkw786] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 11/14/2022] Open
Abstract
A hallmark of defense mechanisms based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated sequences (Cas) are the crRNAs that guide these complexes in the destruction of invading DNA or RNA. Three separate CRISPR-Cas systems exist in the cyanobacterium Synechocystis sp. PCC 6803. Based on genetic and transcriptomic evidence, two associated endoribonucleases, Cas6-1 and Cas6-2a, were postulated to be involved in crRNA maturation from CRISPR1 or CRISPR2, respectively. Here, we report a promiscuity of both enzymes to process in vitro not only their cognate transcripts, but also the respective non-cognate precursors, whereas they are specific in vivo. Moreover, while most of the repeats serving as substrates were cleaved in vitro, some were not. RNA structure predictions suggested that the context sequence surrounding a repeat can interfere with its stable folding. Indeed, structure accuracy calculations of the hairpin motifs within the repeat sequences explained the majority of analyzed cleavage reactions, making this a good measure for predicting successful cleavage events. We conclude that the cleavage of CRISPR1 and CRISPR2 repeat instances requires a stable formation of the characteristic hairpin motif, which is similar between the two types of repeats. The influence of surrounding sequences might partially explain variations in crRNA abundances and should be considered when designing artificial CRISPR arrays.
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Affiliation(s)
- Viktoria Reimann
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Sita J Saunders
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Ingeborg Scholz
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Stephanie Hein
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany .,Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany .,Centre for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, D-79104 Freiburg, Germany
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26
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Target DNA recognition and cleavage by a reconstituted Type I-G CRISPR-Cas immune effector complex. Extremophiles 2016; 21:95-107. [PMID: 27582008 DOI: 10.1007/s00792-016-0871-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/16/2016] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas immune systems defend prokaryotes against viruses and plasmids. CRISPR RNAs (crRNAs) associate with various CRISPR-associated (Cas) protein modules to form structurally and functionally diverse (Type I-VI) crRNP immune effector complexes. Previously, we identified three, co-existing effector complexes in Pyrococcus furiosus -Type I-A (Csa), Type I-G (Cst), and Type III-B (Cmr)-and demonstrated that each complex functions in vivo to eliminate invader DNA. Here, we reconstitute functional Cst crRNP complexes in vitro from recombinant Cas proteins and synthetic crRNAs and investigate mechanisms of crRNP assembly and invader DNA recognition and destruction. All four known Cst-affiliated Cas proteins (Cas5t, Cst1, Cst2, and Cas3) are required for activity, but each subunit plays a distinct role. Cas5t and Cst2 comprise a minimal set of proteins that selectively interact with crRNA. Further addition of Cst1, enables the four subunit crRNP (Cas5t, Cst1, Cst2, crRNA) to specifically bind complementary, double-stranded DNA targets and to recruit the Cas3 effector nuclease, which catalyzes cleavages at specific sites within the displaced, non-target DNA strand. Our results indicate that Type I-G crRNPs selectively bind target DNA in a crRNA and, protospacer adjacent motif dependent manner to recruit a dedicated Cas3 nuclease for invader DNA destruction.
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27
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Wright AV, Nuñez JK, Doudna JA. Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering. Cell 2016; 164:29-44. [PMID: 26771484 DOI: 10.1016/j.cell.2015.12.035] [Citation(s) in RCA: 684] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Indexed: 12/26/2022]
Abstract
Bacteria and archaea possess a range of defense mechanisms to combat plasmids and viral infections. Unique among these are the CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems, which provide adaptive immunity against foreign nucleic acids. CRISPR systems function by acquiring genetic records of invaders to facilitate robust interference upon reinfection. In this Review, we discuss recent advances in understanding the diverse mechanisms by which Cas proteins respond to foreign nucleic acids and how these systems have been harnessed for precision genome manipulation in a wide array of organisms.
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Affiliation(s)
- Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James K Nuñez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute HHMI, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, CA 94720, USA.
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28
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Gleditzsch D, Müller-Esparza H, Pausch P, Sharma K, Dwarakanath S, Urlaub H, Bange G, Randau L. Modulating the Cascade architecture of a minimal Type I-F CRISPR-Cas system. Nucleic Acids Res 2016; 44:5872-82. [PMID: 27216815 PMCID: PMC4937334 DOI: 10.1093/nar/gkw469] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/13/2016] [Indexed: 12/26/2022] Open
Abstract
Shewanella putrefaciens CN-32 contains a single Type I-Fv CRISPR-Cas system which confers adaptive immunity against bacteriophage infection. Three Cas proteins (Cas6f, Cas7fv, Cas5fv) and mature CRISPR RNAs were shown to be required for the assembly of an interference complex termed Cascade. The Cas protein-CRISPR RNA interaction sites within this complex were identified via mass spectrometry. Additional Cas proteins, commonly described as large and small subunits, that are present in all other investigated Cascade structures, were not detected. We introduced this minimal Type I system in Escherichia coli and show that it provides heterologous protection against lambda phage. The absence of a large subunit suggests that the length of the crRNA might not be fixed and recombinant Cascade complexes with drastically shortened and elongated crRNAs were engineered. Size-exclusion chromatography and small-angle X-ray scattering analyses revealed that the number of Cas7fv backbone subunits is adjusted in these shortened and extended Cascade variants. Larger Cascade complexes can still confer immunity against lambda phage infection in E. coli. Minimized Type I CRISPR-Cas systems expand our understanding of the evolution of Cascade assembly and diversity. Their adjustable crRNA length opens the possibility for customizing target DNA specificity.
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Affiliation(s)
- Daniel Gleditzsch
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Hanna Müller-Esparza
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Patrick Pausch
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Kundan Sharma
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany
| | - Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Henning Urlaub
- Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Centre, D-37075 Göttingen, Germany Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany Department of Chemistry, Philipps University Marburg, D-35043 Marburg, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany LOEWE Center for Synthetic Microbiology, Philipps University Marburg, D-35043 Marburg, Germany
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Elmore JR, Sheppard NF, Ramia N, Deighan T, Li H, Terns RM, Terns MP. Bipartite recognition of target RNAs activates DNA cleavage by the Type III-B CRISPR-Cas system. Genes Dev 2016; 30:447-59. [PMID: 26848045 PMCID: PMC4762429 DOI: 10.1101/gad.272153.115] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/03/2015] [Indexed: 12/18/2022]
Abstract
Here, Elmore et al. investigate how the Type III-B Cmr complex, which cleaves invader RNAs recognized by the CRISPR RNA (crRNA), functions. The findings demonstrate that the Cmr complex is a novel DNA nuclease activated by invader RNAs containing a crRNA target sequence and a protospacer-adjacent motif (rPAM). CRISPR–Cas systems eliminate nucleic acid invaders in bacteria and archaea. The effector complex of the Type III-B Cmr system cleaves invader RNAs recognized by the CRISPR RNA (crRNA ) of the complex. Here we show that invader RNAs also activate the Cmr complex to cleave DNA. As has been observed for other Type III systems, Cmr eliminates plasmid invaders in Pyrococcus furiosus by a mechanism that depends on transcription of the crRNA target sequence within the plasmid. Notably, we found that the target RNA per se induces DNA cleavage by the Cmr complex in vitro. DNA cleavage activity does not depend on cleavage of the target RNA but notably does require the presence of a short sequence adjacent to the target sequence within the activating target RNA (rPAM [RNA protospacer-adjacent motif]). The activated complex does not require a target sequence (or a PAM) in the DNA substrate. Plasmid elimination by the P. furiosus Cmr system also does not require the Csx1 (CRISPR-associated Rossman fold [CARF] superfamily) protein. Plasmid silencing depends on the HD nuclease and Palm domains of the Cmr2 (Cas10 superfamily) protein. The results establish the Cmr complex as a novel DNA nuclease activated by invader RNAs containing a crRNA target sequence and a rPAM.
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Affiliation(s)
- Joshua R Elmore
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Nolan F Sheppard
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Nancy Ramia
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32313, USA
| | - Trace Deighan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32313, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA; Department of Genetics, Florida State University, Tallahassee, Florida 32313, USA; Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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Elmore J, Deighan T, Westpheling J, Terns RM, Terns MP. DNA targeting by the type I-G and type I-A CRISPR-Cas systems of Pyrococcus furiosus. Nucleic Acids Res 2015; 43:10353-63. [PMID: 26519471 PMCID: PMC4666368 DOI: 10.1093/nar/gkv1140] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/16/2015] [Indexed: 12/26/2022] Open
Abstract
CRISPR–Cas systems silence plasmids and viruses in prokaryotes. CRISPR–Cas effector complexes contain CRISPR RNAs (crRNAs) that include sequences captured from invaders and direct CRISPR-associated (Cas) proteins to destroy corresponding invader nucleic acids. Pyrococcus furiosus (Pfu) harbors three CRISPR–Cas immune systems: a Cst (Type I-G) system with an associated Cmr (Type III-B) module at one locus, and a partial Csa (Type I-A) module (lacking known invader sequence acquisition and crRNA processing genes) at another locus. The Pfu Cmr complex cleaves complementary target RNAs, and Csa systems have been shown to target DNA, while the mechanism by which Cst complexes silence invaders is unknown. In this study, we investigated the function of the Cst as well as Csa system in Pfu strains harboring a single CRISPR–Cas system. Plasmid transformation assays revealed that the Cst and Csa systems both function by DNA silencing and utilize similar flanking sequence information (PAMs) to identify invader DNA. Silencing by each system specifically requires its associated Cas3 nuclease. crRNAs from the 7 shared CRISPR loci in Pfu are processed for use by all 3 effector complexes, and Northern analysis revealed that individual effector complexes dictate the profile of mature crRNA species that is generated.
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Affiliation(s)
- Joshua Elmore
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Trace Deighan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Jan Westpheling
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA Department of Genetics, University of Georgia, Athens, GA 30602, USA Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Dwarakanath S, Brenzinger S, Gleditzsch D, Plagens A, Klingl A, Thormann K, Randau L. Interference activity of a minimal Type I CRISPR-Cas system from Shewanella putrefaciens. Nucleic Acids Res 2015; 43:8913-23. [PMID: 26350210 PMCID: PMC4605320 DOI: 10.1093/nar/gkv882] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/26/2022] Open
Abstract
Type I CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR-associated) systems exist in bacterial and archaeal organisms and provide immunity against foreign DNA. The Cas protein content of the DNA interference complexes (termed Cascade) varies between different CRISPR-Cas subtypes. A minimal variant of the Type I-F system was identified in proteobacterial species including Shewanella putrefaciens CN-32. This variant lacks a large subunit (Csy1), Csy2 and Csy3 and contains two unclassified cas genes. The genome of S. putrefaciens CN-32 contains only five Cas proteins (Cas1, Cas3, Cas6f, Cas1821 and Cas1822) and a single CRISPR array with 81 spacers. RNA-Seq analyses revealed the transcription of this array and the maturation of crRNAs (CRISPR RNAs). Interference assays based on plasmid conjugation demonstrated that this CRISPR-Cas system is active in vivo and that activity is dependent on the recognition of the dinucleotide GG PAM (Protospacer Adjacent Motif) sequence and crRNA abundance. The deletion of cas1821 and cas1822 reduced the cellular crRNA pool. Recombinant Cas1821 was shown to form helical filaments bound to RNA molecules, which suggests its role as the Cascade backbone protein. A Cascade complex was isolated which contained multiple Cas1821 copies, Cas1822, Cas6f and mature crRNAs.
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Affiliation(s)
- Srivatsa Dwarakanath
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - Susanne Brenzinger
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Hessen D-35392, Germany
| | - Daniel Gleditzsch
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - André Plagens
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I, Biocentre LMU Munich, Großhaderner Str. 2-4, Planegg-Martinsried D-82152, Germany
| | - Kai Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-University Giessen, Giessen, Hessen D-35392, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Hessen D-35043, Germany LOEWE Center for Synthetic Microbiology (Synmikro), Marburg, Hessen D-35043, Germany
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33
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Dennis PP, Tripp V, Lui L, Lowe T, Randau L. C/D box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules. BMC Genomics 2015; 16:632. [PMID: 26296872 PMCID: PMC4644070 DOI: 10.1186/s12864-015-1839-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/13/2015] [Indexed: 11/26/2022] Open
Abstract
Background In archaea and eukaryotes, ribonucleoprotein complexes containing small C/D box s(no)RNAs use base pair complementarity to target specific sites within ribosomal RNA for 2'-O-ribose methylation. These modifications aid in the folding and stabilization of nascent rRNA molecules and their assembly into ribosomal particles. The genomes of hyperthermophilic archaea encode large numbers of C/D box sRNA genes, suggesting an increased necessity for rRNA stabilization at extreme growth temperatures. Results We have identified the complete sets of C/D box sRNAs from seven archaea using RNA-Seq methodology. In total, 489 C/D box sRNAs were identified, each containing two guide regions. A combination of computational and manual analyses predicts 719 guide interactions with 16S and 23S rRNA molecules. This first pan-archaeal description of guide sequences identifies (i) modified rRNA nucleotides that are frequently conserved between species and (ii) regions within rRNA that are hotspots for 2'-O-methylation. Gene duplication, rearrangement, mutational drift and convergent evolution of sRNA genes and guide sequences were observed. In addition, several C/D box sRNAs were identified that use their two guides to target locations distant in the rRNA sequence but close in the secondary and tertiary structure. We propose that they act as RNA chaperones and facilitate complex folding events between distant sequences. Conclusions This pan-archaeal analysis of C/D box sRNA guide regions identified conserved patterns of rRNA 2'-O-methylation in archaea. The interaction between the sRNP complexes and the nascent rRNA facilitates proper folding and the methyl modifications stabilize higher order rRNA structure within the assembled ribosome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1839-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick P Dennis
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany. .,Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Dr, Ashburn, VA, 20147, USA.
| | - Vanessa Tripp
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany.
| | - Lauren Lui
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Todd Lowe
- Department of Biomolecular Engineering, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Lennart Randau
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043, Marburg, Germany.
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Abstract
SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.
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Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RHJ, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods 2015; 89:138-48. [PMID: 26071038 DOI: 10.1016/j.ymeth.2015.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/19/2015] [Accepted: 06/04/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleoprotein (RNP) complexes play important roles in the cell by mediating basic cellular processes, including gene expression and its regulation. Understanding the molecular details of these processes requires the identification and characterization of protein-RNA interactions. Over the years various approaches have been used to investigate these interactions, including computational analyses to look for RNA binding domains, gel-shift mobility assays on recombinant and mutant proteins as well as co-crystallization and NMR studies for structure elucidation. Here we report a more specialized and direct approach using UV-induced cross-linking coupled with mass spectrometry. This approach permits the identification of cross-linked peptides and RNA moieties and can also pin-point exact RNA contact sites within the protein. The power of this method is illustrated by the application to different single- and multi-subunit RNP complexes belonging to the prokaryotic adaptive immune system, CRISPR-Cas (CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated). In particular, we identified the RNA-binding sites within three Cas7 protein homologs and mapped the cross-linking results to reveal structurally conserved Cas7 - RNA binding interfaces. These results demonstrate the strong potential of UV-induced cross-linking coupled with mass spectrometry analysis to identify RNA interaction sites on the RNA binding proteins.
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Affiliation(s)
- Kundan Sharma
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ajla Hrle
- Structural Cell Biology Department, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Katharina Kramer
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Timo Sachsenberg
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Elena Conti
- Structural Cell Biology Department, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
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Majumdar S, Zhao P, Pfister NT, Compton M, Olson S, Glover CVC, Wells L, Graveley BR, Terns RM, Terns MP. Three CRISPR-Cas immune effector complexes coexist in Pyrococcus furiosus. RNA (NEW YORK, N.Y.) 2015; 21:1147-58. [PMID: 25904135 PMCID: PMC4436667 DOI: 10.1261/rna.049130.114] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
CRISPR-Cas immune systems function to defend prokaryotes against potentially harmful mobile genetic elements including viruses and plasmids. The multiple CRISPR-Cas systems (Types I, II, and III) each target destruction of foreign nucleic acids via structurally and functionally diverse effector complexes (crRNPs). CRISPR-Cas effector complexes are comprised of CRISPR RNAs (crRNAs) that contain sequences homologous to the invading nucleic acids and Cas proteins specific to each immune system type. We have previously characterized a crRNP in Pyrococcus furiosus (Pfu) that contains Cmr (Type III-B) Cas proteins associated with one of two size classes of crRNAs and cleaves complementary target RNAs. Here, we have isolated and characterized two additional native Pfu crRNPs containing either Csa (Type I-A) or Cst (Type I-G) Cas proteins and distinct profiles of associated crRNAs. For each complex, the Cas proteins were identified by mass spectrometry and immunoblotting and the crRNAs by RNA sequencing and Northern blot analysis. The crRNAs associated with both the Csa and Cst complexes originate from all seven Pfu CRISPR loci and contain identical 5' ends (8-nt repeat-derived 5' tag sequences) but heterogeneous 3' ends (containing variable amounts of downstream repeat sequences). These crRNA forms are distinct from Cmr-associated crRNAs, indicating different 3' end processing pathways following primary cleavage of common pre-crRNAs. Like other previously characterized Type I CRISPR-Cas effector complexes, we predict that the newly identified Pfu Csa and Cst crRNPs each function to target invading DNA, adding an additional layer of protection beyond that afforded by the previously characterized RNA targeting Cmr complex.
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Affiliation(s)
- Sonali Majumdar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Neil T Pfister
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Mark Compton
- Department of Poultry Science, University of Georgia, Athens, Georgia 30602, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Claiborne V C Glover
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030-6403, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA Department of Genetics, University of Georgia, Athens, Georgia 30602, USA Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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Lum AG, Ly M, Santiago-Rodriguez TM, Naidu M, Boehm TK, Pride DT. Global transcription of CRISPR loci in the human oral cavity. BMC Genomics 2015; 16:401. [PMID: 25994215 PMCID: PMC4438527 DOI: 10.1186/s12864-015-1615-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 05/05/2015] [Indexed: 12/26/2022] Open
Abstract
Background Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment. Results We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage. Conclusions These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1615-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew G Lum
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Tasha M Santiago-Rodriguez
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Mayuri Naidu
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
| | - Tobias K Boehm
- College of Dental Medicine, Western University of Health Sciences, 309 E Second Street, Pomona, CA, 91766, USA.
| | - David T Pride
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. .,Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA.
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Charpentier E, Richter H, van der Oost J, White MF. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. FEMS Microbiol Rev 2015; 39:428-41. [PMID: 25994611 PMCID: PMC5965381 DOI: 10.1093/femsre/fuv023] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2015] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key elements in the interference step of the immune pathway. A CRISPR array composed of a series of repeats interspaced by spacer sequences acquired from invading mobile genomes is transcribed as a precursor crRNA (pre-crRNA) molecule. This pre-crRNA undergoes one or two maturation steps to generate the mature crRNAs that guide CRISPR-associated (Cas) protein(s) to cognate invading genomes for their destruction. Different types of CRISPR-Cas systems have evolved distinct crRNA biogenesis pathways that implicate highly sophisticated processing mechanisms. In Types I and III CRISPR-Cas systems, a specific endoribonuclease of the Cas6 family, either standalone or in a complex with other Cas proteins, cleaves the pre-crRNA within the repeat regions. In Type II systems, the trans-acting small RNA (tracrRNA) base pairs with each repeat of the pre-crRNA to form a dual-RNA that is cleaved by the housekeeping RNase III in the presence of the protein Cas9. In this review, we present a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the three CRISPR-Cas types. This review presents a detailed comparative analysis of pre-crRNA recognition and cleavage mechanisms involved in the biogenesis of guide crRNAs in the different bacterial and archaeal CRISPR-Cas immune systems.
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Affiliation(s)
- Emmanuelle Charpentier
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Hannover Medical School, Hannover 30625, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, the Netherlands
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
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Abstract
CRISPR (clustered regularly interspaced short palindromic repeat) systems provide bacteria and archaea with adaptive immunity to repel invasive genetic elements. Type I systems use 'cascade' [CRISPR-associated (Cas) complex for antiviral defence] ribonucleoprotein complexes to target invader DNA, by base pairing CRISPR RNA (crRNA) to protospacers. Cascade identifies PAMs (protospacer adjacent motifs) on invader DNA, triggering R-loop formation and subsequent DNA degradation by Cas3. Cas8 is a candidate PAM recognition factor in some cascades. We analysed Cas8 homologues from type IB CRISPR systems in archaea Haloferax volcanii (Hvo) and Methanothermobacter thermautotrophicus (Mth). Cas8 was essential for CRISPR interference in Hvo and purified Mth Cas8 protein responded to PAM sequence when binding to nucleic acids. Cas8 interacted physically with Cas5-Cas7-crRNA complex, stimulating binding to PAM containing substrates. Mutation of conserved Cas8 amino acid residues abolished interference in vivo and altered catalytic activity of Cas8 protein in vitro. This is experimental evidence that Cas8 is important for targeting Cascade to invader DNA.
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40
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Plagens A, Richter H, Charpentier E, Randau L. DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes. FEMS Microbiol Rev 2015; 39:442-63. [PMID: 25934119 PMCID: PMC5965380 DOI: 10.1093/femsre/fuv019] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2015] [Indexed: 12/26/2022] Open
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) adaptive immune systems use small guide RNAs, the CRISPR RNAs (crRNAs), to mark foreign genetic material, e.g. viral nucleic acids, for degradation. Archaea and bacteria encode a large variety of Cas proteins that bind crRNA molecules and build active ribonucleoprotein surveillance complexes. The evolution of CRISPR-Cas systems has resulted in a diversification of cas genes and a classification of the systems into three types and additional subtypes characterized by distinct surveillance and interfering complexes. Recent crystallographic and biochemical advances have revealed detailed insights into the assembly and DNA/RNA targeting mechanisms of the various complexes. Here, we review our knowledge on the molecular mechanism involved in the DNA and RNA interference stages of type I (Cascade: CRISPR-associated complex for antiviral defense), type II (Cas9) and type III (Csm, Cmr) CRISPR-Cas systems. We further highlight recently reported structural and mechanistic themes shared among these systems. This review details and compares the assembly and the DNA/RNA targeting mechanisms of the various surveillance complexes of prokaryotic CRISPR-Cas immune systems.
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Affiliation(s)
- André Plagens
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
| | - Hagen Richter
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany
| | - Emmanuelle Charpentier
- Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Hannover Medical School, Hannover 30625, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany
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41
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Rath D, Amlinger L, Rath A, Lundgren M. The CRISPR-Cas immune system: biology, mechanisms and applications. Biochimie 2015; 117:119-28. [PMID: 25868999 DOI: 10.1016/j.biochi.2015.03.025] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/31/2015] [Indexed: 12/26/2022]
Abstract
Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune system in prokaryotes, a type of system previously thought to be present only in vertebrates. The system, called CRISPR-Cas, provide sequence-specific adaptive immunity and fundamentally affect our understanding of virus-host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize and clear infections. There has been rapid advancement in our understanding of this immune system and its applications, but there are many aspects that await elucidation making the field an exciting area of research. This review provides an overview of the field and highlights unresolved issues.
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Affiliation(s)
- Devashish Rath
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Lina Amlinger
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Archana Rath
- Department of Biotechnology, University of Mumbai, Mumbai 400098, India
| | - Magnus Lundgren
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden.
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42
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Abstract
Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA-guided processes near the upper temperature limit of life. Archaea utilize the base-pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, trans-splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described.
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MESH Headings
- Archaea/genetics
- Base Sequence
- Evolution, Molecular
- Gene Expression Regulation, Archaeal
- Genome, Archaeal/genetics
- Hot Temperature
- Models, Genetic
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
- Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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43
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Garrett RA, Shah SA, Erdmann S, Liu G, Mousaei M, León-Sobrino C, Peng W, Gudbergsdottir S, Deng L, Vestergaard G, Peng X, She Q. CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity. Life (Basel) 2015; 5:783-817. [PMID: 25764276 PMCID: PMC4390879 DOI: 10.3390/life5010783] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/24/2015] [Accepted: 02/27/2015] [Indexed: 12/26/2022] Open
Abstract
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.
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Affiliation(s)
- Roger A Garrett
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Shiraz A Shah
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Susanne Erdmann
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052 Sydney NSW, Australia.
| | - Guannan Liu
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Marzieh Mousaei
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Carlos León-Sobrino
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Wenfang Peng
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Soley Gudbergsdottir
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Ling Deng
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Gisle Vestergaard
- Helmholtz Zentrum München, Research Unit Environmental Genomics, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Germany.
| | - Xu Peng
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
| | - Qunxin She
- Archaea Centre, Department of Biology, Copenhagen University, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
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44
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Beloglazova N, Kuznedelov K, Flick R, Datsenko KA, Brown G, Popovic A, Lemak S, Semenova E, Severinov K, Yakunin AF. CRISPR RNA binding and DNA target recognition by purified Cascade complexes from Escherichia coli. Nucleic Acids Res 2015; 43:530-43. [PMID: 25488810 PMCID: PMC4288178 DOI: 10.1093/nar/gku1285] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/22/2014] [Accepted: 11/24/2014] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of five different Cas proteins and a 61-nt-long guide RNA (crRNA). crRNAs contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). The spacer part of crRNA directs Cascade to DNA targets. Here, we show that the E. coli Cascade can be expressed and purified from cells lacking crRNAs and loaded in vitro with synthetic crRNAs, which direct it to targets complementary to crRNA spacer. The deletion of even one nucleotide from the crRNA 5' handle disrupted its binding to Cascade and target DNA recognition. In contrast, crRNA variants with just a single nucleotide downstream of the spacer part bound Cascade and the resulting ribonucleotide complex containing a 41-nt-long crRNA specifically recognized DNA targets. Thus, the E. coli Cascade-crRNA system exhibits significant flexibility suggesting that this complex can be engineered for applications in genome editing and opening the way for incorporation of site-specific labels in crRNA.
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Affiliation(s)
- Natalia Beloglazova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Konstantin Kuznedelov
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kirill A Datsenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Sofia Lemak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
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45
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Hochstrasser ML, Doudna JA. Cutting it close: CRISPR-associated endoribonuclease structure and function. Trends Biochem Sci 2014; 40:58-66. [PMID: 25468820 DOI: 10.1016/j.tibs.2014.10.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 12/26/2022]
Abstract
Many bacteria and archaea possess an adaptive immune system consisting of repetitive genetic elements known as clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Similar to RNAi pathways in eukaryotes, CRISPR-Cas systems require small RNAs for sequence-specific detection and degradation of complementary nucleic acids. Cas5 and Cas6 enzymes have evolved to specifically recognize and process CRISPR-derived transcripts into functional small RNAs used as guides by interference complexes. Our detailed understanding of these proteins has led to the development of several useful Cas6-based biotechnological methods. Here, we review the structures, functions, mechanisms, and applications of the enzymes responsible for CRISPR RNA (crRNA) processing, highlighting a fascinating family of endonucleases with exquisite RNA recognition and cleavage activities.
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Affiliation(s)
- Megan L Hochstrasser
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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46
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Luo ML, Mullis AS, Leenay RT, Beisel CL. Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. Nucleic Acids Res 2014. [PMID: 25326321 DOI: 10.1093/nar/gku971.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing and transcriptional regulation. Because these RNA-directed immune systems are found in most prokaryotes, an opportunity exists to harness the endogenous systems as convenient tools in these organisms. Here, we report that the Type I-E CRISPR-Cas system in Escherichia coli can be co-opted for programmable transcriptional repression. We found that deletion of the signature cas3 gene converted this immune system into a programmable gene regulator capable of reversible gene silencing of heterologous and endogenous genes. Targeting promoter regions yielded the strongest repression, whereas targeting coding regions showed consistent strand bias. Furthermore, multi-targeting CRISPR arrays could generate complex phenotypes. This strategy offers a simple approach to convert many endogenous Type I systems into transcriptional regulators, thereby expanding the available toolkit for CRISPR-mediated genetic control while creating new opportunities for genome-wide screens and pathway engineering.
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Affiliation(s)
- Michelle L Luo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Adam S Mullis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Ryan T Leenay
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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47
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Luo ML, Mullis AS, Leenay RT, Beisel CL. Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression. Nucleic Acids Res 2014; 43:674-81. [PMID: 25326321 PMCID: PMC4288209 DOI: 10.1093/nar/gku971] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems have shown tremendous promise as heterologous tools for genome editing and transcriptional regulation. Because these RNA-directed immune systems are found in most prokaryotes, an opportunity exists to harness the endogenous systems as convenient tools in these organisms. Here, we report that the Type I-E CRISPR-Cas system in Escherichia coli can be co-opted for programmable transcriptional repression. We found that deletion of the signature cas3 gene converted this immune system into a programmable gene regulator capable of reversible gene silencing of heterologous and endogenous genes. Targeting promoter regions yielded the strongest repression, whereas targeting coding regions showed consistent strand bias. Furthermore, multi-targeting CRISPR arrays could generate complex phenotypes. This strategy offers a simple approach to convert many endogenous Type I systems into transcriptional regulators, thereby expanding the available toolkit for CRISPR-mediated genetic control while creating new opportunities for genome-wide screens and pathway engineering.
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Affiliation(s)
- Michelle L Luo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Adam S Mullis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Ryan T Leenay
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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48
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Daume M, Plagens A, Randau L. DNA binding properties of the small cascade subunit Csa5. PLoS One 2014; 9:e105716. [PMID: 25148031 PMCID: PMC4141822 DOI: 10.1371/journal.pone.0105716] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/26/2014] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems provide immunity against viral attacks in archaeal and bacterial cells. Type I systems employ a Cas protein complex termed Cascade, which utilizes small CRISPR RNAs to detect and degrade the exogenic DNA. A small sequence motif, the PAM, marks the foreign substrates. Previously, a recombinant type I-A Cascade complex from the archaeon Thermoproteus tenax was shown to target and degrade DNA in vitro, dependent on a native PAM sequence. Here, we present the biochemical analysis of the small subunit, Csa5, of this Cascade complex. T. tenax Csa5 preferentially bound ssDNA and mutants that showed decreased ssDNA-binding and reduced Cascade-mediated DNA cleavage were identified. Csa5 oligomerization prevented DNA binding. Specific recognition of the PAM sequence was not observed. Phylogenetic analyses identified Csa5 as a universal member of type I-A systems and revealed three distinct groups. A potential role of Csa5 in R-loop stabilization is discussed.
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Affiliation(s)
- Michael Daume
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - André Plagens
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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49
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van der Oost J, Westra ER, Jackson RN, Wiedenheft B. Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol 2014; 12:479-92. [PMID: 24909109 PMCID: PMC4225775 DOI: 10.1038/nrmicro3279] [Citation(s) in RCA: 501] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments of foreign DNA into CRISPR loci, and following transcription and processing of these loci, the CRISPR RNAs (crRNAs) guide the Cas proteins to complementary invading nucleic acid, which results in target interference. In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR-Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.
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Affiliation(s)
- John van der Oost
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Edze R Westra
- 1] Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands. [2] Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Ryan N Jackson
- Department of Microbiology and Immunology, Montana State University, PO Box 173520, Bozeman, Montana 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, PO Box 173520, Bozeman, Montana 59717, USA
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50
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Sokolowski RD, Graham S, White MF. Cas6 specificity and CRISPR RNA loading in a complex CRISPR-Cas system. Nucleic Acids Res 2014; 42:6532-41. [PMID: 24753403 PMCID: PMC4041471 DOI: 10.1093/nar/gku308] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is an adaptive prokaryotic immune system, providing protection against viruses and other mobile genetic elements. In type I and type III CRISPR-Cas systems, CRISPR RNA (crRNA) is generated by cleavage of a primary transcript by the Cas6 endonuclease and loaded into multisubunit surveillance/effector complexes, allowing homology-directed detection and cleavage of invading elements. Highly studied CRISPR-Cas systems such as those in Escherichia coli and Pseudomonas aeruginosa have a single Cas6 enzyme that is an integral subunit of the surveillance complex. By contrast, Sulfolobus solfataricus has a complex CRISPR-Cas system with three types of surveillance complexes (Cascade/type I-A, CSM/type III-A and CMR/type III-B), five Cas6 paralogues and two different CRISPR-repeat families (AB and CD). Here, we investigate the kinetic properties of two different Cas6 paralogues from S. solfataricus. The Cas6-1 subtype is specific for CD-family CRISPR repeats, generating crRNA by multiple turnover catalysis whilst Cas6-3 has a broader specificity and also processes a non-coding RNA with a CRISPR repeat-related sequence. Deep sequencing of crRNA in surveillance complexes reveals a biased distribution of spacers derived from AB and CD loci, suggesting functional coupling between Cas6 paralogues and their downstream effector complexes.
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Affiliation(s)
- Richard D Sokolowski
- 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
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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