Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3
Significance Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, whic...
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| Published in | Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 46; pp. 16359 - 16364 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
National Academy of Sciences
18.11.2014
National Acad Sciences |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0027-8424 1091-6490 1091-6490 |
| DOI | 10.1073/pnas.1410806111 |
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| Abstract | Significance Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, which can be transcribed and activated into short RNA molecules (crRNA) with sequences complementary to invader DNA or RNA. In some CRISPR-Cas systems, crRNA is assembled into a targeting complex called “Cascade” that seeks invader DNA to form an R-loop that triggers recruitment of a nuclease-helicase, Cas3, to destroy invader DNA. In this study, we show atomic resolution structures of a full-length Cas3, revealing how Cas3 coordinates binding, ATP-dependent translocation, and nuclease digestion of invader DNA.
Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum , with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3′ to 5′ nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3′ to 5′ translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. |
|---|---|
| AbstractList | Significance Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, which can be transcribed and activated into short RNA molecules (crRNA) with sequences complementary to invader DNA or RNA. In some CRISPR-Cas systems, crRNA is assembled into a targeting complex called “Cascade” that seeks invader DNA to form an R-loop that triggers recruitment of a nuclease-helicase, Cas3, to destroy invader DNA. In this study, we show atomic resolution structures of a full-length Cas3, revealing how Cas3 coordinates binding, ATP-dependent translocation, and nuclease digestion of invader DNA. Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum , with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3′ to 5′ nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3′ to 5′ translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. Significance Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, which can be transcribed and activated into short RNA molecules (crRNA) with sequences complementary to invader DNA or RNA. In some CRISPR-Cas systems, crRNA is assembled into a targeting complex called “Cascade” that seeks invader DNA to form an R-loop that triggers recruitment of a nuclease-helicase, Cas3, to destroy invader DNA. In this study, we show atomic resolution structures of a full-length Cas3, revealing how Cas3 coordinates binding, ATP-dependent translocation, and nuclease digestion of invader DNA. Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum , with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3′ to 5′ nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3′ to 5′ translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, which can be transcribed and activated into short RNA molecules (crRNA) with sequences complementary to invader DNA or RNA. In some CRISPR-Cas systems, crRNA is assembled into a targeting complex called “Cascade” that seeks invader DNA to form an R-loop that triggers recruitment of a nuclease-helicase, Cas3, to destroy invader DNA. In this study, we show atomic resolution structures of a full-length Cas3, revealing how Cas3 coordinates binding, ATP-dependent translocation, and nuclease digestion of invader DNA. Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum , with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3′ to 5′ nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3′ to 5′ translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems.Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a "Cascade" ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called "interference." After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3' to 5' nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3' to 5' translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats (CRISPRs)-Cas. CRISPR loci in a host genome are a repository of DNA fragments obtained from previous encounters with an invader, which can be transcribed and activated into short RNA molecules (crRNA) with sequences complementary to invader DNA or RNA. In some CRISPR-Cas systems, crRNA is assembled into a targeting complex called “Cascade” that seeks invader DNA to form an R-loop that triggers recruitment of a nuclease-helicase, Cas3, to destroy invader DNA. In this study, we show atomic resolution structures of a full-length Cas3, revealing how Cas3 coordinates binding, ATP-dependent translocation, and nuclease digestion of invader DNA. Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins. Type I CRISPR-Cas systems use a “Cascade” ribonucleoprotein complex to guide RNA specifically to complementary sequence in invader double-stranded DNA (dsDNA), a process called “interference.” After target recognition by Cascade, formation of an R-loop triggers recruitment of a Cas3 nuclease-helicase, completing the interference process by destroying the invader dsDNA. To elucidate the molecular mechanism of CRISPR interference, we analyzed crystal structures of Cas3 from the bacterium Thermobaculum terrenum, with and without a bound ATP analog. The structures reveal a histidine-aspartate (HD)-type nuclease domain fused to superfamily-2 (SF2) helicase domains and a distinct C-terminal domain. Binding of ATP analog at the interface of the SF2 helicase RecA-like domains rearranges a motif V with implications for the enzyme mechanism. The HD-nucleolytic site contains two metal ions that are positioned at the end of a proposed nucleic acid-binding tunnel running through the SF2 helicase structure. This structural alignment suggests a mechanism for 3′ to 5′ nucleolytic processing of the displaced strand of invader DNA that is coordinated with ATP-dependent 3′ to 5′ translocation of Cas3 along DNA. In agreement with biochemical studies, the presented Cas3 structures reveal important mechanistic details on the neutralization of genetic invaders by type I CRISPR-Cas systems. |
| Author | Shin, Minsang Jung, Che-Hun Sun, Jiali Gong, Bei Kim, Jeong-Sun Bolt, Edward L. van der Oost, John |
| Author_xml | – sequence: 1 givenname: Bei surname: Gong fullname: Gong, Bei – sequence: 2 givenname: Minsang surname: Shin fullname: Shin, Minsang – sequence: 3 givenname: Jiali surname: Sun fullname: Sun, Jiali – sequence: 4 givenname: Che-Hun surname: Jung fullname: Jung, Che-Hun – sequence: 5 givenname: Edward L. surname: Bolt fullname: Bolt, Edward L. – sequence: 6 givenname: John surname: van der Oost fullname: van der Oost, John – sequence: 7 givenname: Jeong-Sun surname: Kim fullname: Kim, Jeong-Sun |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25368186$$D View this record in MEDLINE/PubMed |
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| Keywords | CRISPR Cas3 Cas proteins bacterial immunity Cascade |
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| Notes | http://dx.doi.org/10.1073/pnas.1410806111 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-2 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 Author contributions: B.G., M.S., J.S., and J.-S.K. designed research; B.G., M.S., J.S., and J.-S.K. performed research; B.G., M.S., J.S., C.-H.J., E.L.B., J.v.d.O., and J.-S.K. analyzed data; and B.G., M.S., E.L.B., J.v.d.O., and J.-S.K. wrote the paper. 1B.G. and M.S. contributed equally to this work. Edited by Wei Yang, National Institutes of Health, Bethesda, MD, and approved September 26, 2014 (received for review June 10, 2014) |
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| Snippet | Significance Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic... Mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (CRISPRs) and... Bacteria can repel invader DNA and RNA molecules by using an adaptive immunity mechanism called clustered regularly interspaced short palindromic repeats... |
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| SubjectTerms | Active sites adaptive immunity Adenosine triphosphatase Adenosine triphosphatases Adenosine Triphosphate - metabolism Amino Acid Motifs Amino Acid Sequence antiviral defense ATP bacteria Bacteria - enzymology Bacteria - genetics Bacteria - immunology bacterial immune-system Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Binding sites Biochemistry Biological Sciences cascade Clustered Regularly Interspaced Short Palindromic Repeats - physiology complex CRISPR-Associated Proteins - chemistry CRISPR-Associated Proteins - genetics CRISPR-Associated Proteins - metabolism CRISPR-Cas Systems - physiology Crystal structure Crystallography, X-Ray Deoxyribonucleases - chemistry Deoxyribonucleases - genetics Deoxyribonucleases - metabolism Deoxyribonucleic acid DNA DNA - metabolism DNA fragmentation DNA Helicases - chemistry DNA Helicases - genetics DNA Helicases - metabolism DNA, Bacterial - metabolism DNA, Single-Stranded - metabolism escherichia-coli genome Host-Pathogen Interactions in-vitro reconstitution Interspersed Repetitive Sequences loci Magnesium - metabolism Manganese - metabolism Metal ions Models, Molecular Molecular Sequence Data Molecular structure Molecules Mutagenesis, Site-Directed Neutralization Nucleic acids Protein Binding Protein Conformation Protein Structure, Tertiary Proteins Recombinant Fusion Proteins - chemistry Recombinant Fusion Proteins - genetics Recombinant Fusion Proteins - metabolism RNA RNA, Bacterial - metabolism Sequence Alignment Sequence Homology, Amino Acid structural basis transcription (genetics) Translocation Tunnels |
| Title | Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3 |
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