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Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Thornton BW, Xu B, Trinidad MI, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. bioRxiv 2023:2023.12.14.571777. [PMID: 38168238 PMCID: PMC10760125 DOI: 10.1101/2023.12.14.571777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Thermostable CRISPR-Cas9 enzymes could improve genome editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold higher genome editing levels. Cryo-EM structures of the wildtype and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome editing activity.
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2
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Stahl EC, Sabo JK, Kang MH, Allen R, Applegate E, Kim SE, Kwon Y, Seth A, Lemus N, Salinas-Rios V, Soczek KM, Trinidad M, Vo LT, Jeans C, Wozniak A, Morris T, Kimberlin A, Foti T, Savage DF, Doudna JA. Genome editing in the mouse brain with minimally immunogenic Cas9 RNPs. Mol Ther 2023; 31:2422-2438. [PMID: 37403358 PMCID: PMC10422012 DOI: 10.1016/j.ymthe.2023.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023] Open
Abstract
Transient delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) into the central nervous system (CNS) for therapeutic genome editing could avoid limitations of viral vector-based delivery including cargo capacity, immunogenicity, and cost. Here, we tested the ability of cell-penetrant Cas9 RNPs to edit the mouse striatum when introduced using a convection-enhanced delivery system. These transient Cas9 RNPs showed comparable editing of neurons and reduced adaptive immune responses relative to one formulation of Cas9 delivered using AAV serotype 9. The production of ultra-low endotoxin Cas9 protein manufactured at scale further improved innate immunity. We conclude that injection-based delivery of minimally immunogenic CRISPR genome editing RNPs into the CNS provides a valuable alternative to virus-mediated genome editing.
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Affiliation(s)
- Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer K Sabo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Min Hyung Kang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Allen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth Applegate
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shin Eui Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yoonjin Kwon
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anmol Seth
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Lemus
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Viviana Salinas-Rios
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Linda T Vo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chris Jeans
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | | | | | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Gladstone Institutes, University of California, Berkeley, San Francisco, CA 94114, USA.
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3
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Wang JY, Tuck OT, Skopintsev P, Soczek KM, Li G, Al-Shayeb B, Zhou J, Doudna JA. Genome expansion by a CRISPR trimmer-integrase. Nature 2023:10.1038/s41586-023-06178-2. [PMID: 37316664 DOI: 10.1038/s41586-023-06178-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
CRISPR-Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity1. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1-Cas2 integrase is necessary but not sufficient2-5. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation6,7, but many CRISPR-Cas systems lack Cas48. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1-Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited9,10 exonucleases for faithful acquisition of new CRISPR immune sequences.
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Affiliation(s)
- Joy Y Wang
- Department of Chemistry, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Owen T Tuck
- Department of Chemistry, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Gary Li
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Julia Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
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4
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Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell 2022; 185:4574-4586.e16. [PMID: 36423580 DOI: 10.1016/j.cell.2022.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/10/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells.
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Affiliation(s)
- Basem Al-Shayeb
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Elizabeth C Stahl
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Zheng Li
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Evan Groover
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Dylan Smock
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Patrick Pausch
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Carolyn J Huang
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, CA, USA; Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA; University of Melbourne, Melbourne, Australia.
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, CA, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Gladstone Institutes, University of California, San Francisco, CA, USA.
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5
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Suwala A, Barger C, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF. EPCO-08. CONSERVED FEATURES OF TERT PROMOTER DUPLICATIONS REVEAL AN ACTIVATION MECHANISM THAT MIMICS HOTSPOT MUTATIONS IN CANCER. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Mutations in the TERT promoter are the single most common non-coding mutation in cancer and represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, G228A and G250A, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants in the TERT promoter are unknown. We identified duplications of wildtype sequence within the core promoter region of TERT in 7 different cancer types that have strikingly similar features including size, insertion position, and inclusion of one of the native ETS motifs. Each duplication activates the TERT promoter to a similar level as G228A and G250A and is critically dependent on the insertion site. The GABP tetramer binds to the TERT duplicated promoter sequence by virtue of the native ETS motif and its duplicated version with precise spacing, and it is necessary for the transcriptional activation by all duplications tested. Spatiotemporal analysis in a multifocal glioblastoma shows the duplication is clonal and its activation of TERT is readily detectable at the single cell level and in bulk tumor tissue. We conclude that recurrent TERT promoter duplications of the native ETS sequence are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.
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Affiliation(s)
| | | | | | | | | | | | | | - Susan M Chang
- University of California, San Francisco , San Francisco, CA , USA
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6
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Zukin SA, Marunde MR, Popova IK, Soczek KM, Nogales E, Patel AB. Structure and flexibility of the yeast NuA4 histone acetyltransferase complex. eLife 2022; 11:e81400. [PMID: 36263929 PMCID: PMC9643008 DOI: 10.7554/elife.81400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.
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Affiliation(s)
- Stefan A Zukin
- College of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Irina K Popova
- EpiCypher, Inc, Research Triangle ParkDurhamUnited States
| | - Katarzyna M Soczek
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Avinash B Patel
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
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7
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Barger CJ, Suwala AK, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF. Conserved features of TERT promoter duplications reveal an activation mechanism that mimics hotspot mutations in cancer. Nat Commun 2022; 13:5430. [PMID: 36114166 PMCID: PMC9481613 DOI: 10.1038/s41467-022-33099-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/01/2022] [Indexed: 12/13/2022] Open
Abstract
Mutations in the TERT promoter represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants is unknown. In seven cancer types, we identify duplications of wildtype sequence within the core promoter region of TERT that have strikingly similar features including an ETS motif, the duplication length and insertion site. The duplications recruit a GABP tetramer by virtue of the native ETS motif and its precisely spaced duplicated counterpart, activate the promoter and are clonal in a TERT expressing multifocal glioblastoma. We conclude that recurrent TERT promoter duplications are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.
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Affiliation(s)
- Carter J Barger
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Albert S Wang
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Min Y Kim
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - David A Solomon
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
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8
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Abstract
In bacterial defense and genome editing applications, the CRISPR-associated protein Cas9 searches millions of DNA base pairs to locate a 20-nucleotide, guide RNA-complementary target sequence that abuts a protospacer-adjacent motif (PAM). Target capture requires Cas9 to unwind DNA at candidate sequences using an unknown ATP-independent mechanism. Here we show that Cas9 sharply bends and undertwists DNA on PAM binding, thereby flipping DNA nucleotides out of the duplex and toward the guide RNA for sequence interrogation. Cryogenic-electron microscopy (cryo-EM) structures of Cas9-RNA-DNA complexes trapped at different states of the interrogation pathway, together with solution conformational probing, reveal that global protein rearrangement accompanies formation of an unstacked DNA hinge. Bend-induced base flipping explains how Cas9 'reads' snippets of DNA to locate target sites within a vast excess of nontarget DNA, a process crucial to both bacterial antiviral immunity and genome editing. This mechanism establishes a physical solution to the problem of complementarity-guided DNA search and shows how interrogation speed and local DNA geometry may influence genome editing efficiency.
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Affiliation(s)
- Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, CA, USA.
- Gladstone Institutes, University of California, San Francisco, CA, USA.
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
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9
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Syed AM, Taha TY, Tabata T, Chen IP, Ciling A, Khalid MM, Sreekumar B, Chen PY, Hayashi JM, Soczek KM, Ott M, Doudna JA. Rapid assessment of SARS-CoV-2-evolved variants using virus-like particles. Science 2021; 374:1626-1632. [PMID: 34735219 PMCID: PMC9005165 DOI: 10.1126/science.abl6184] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/29/2021] [Indexed: 01/16/2023]
Abstract
Efforts to determine why new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants demonstrate improved fitness have been limited to analyzing mutations in the spike (S) protein with the use of S-pseudotyped particles. In this study, we show that SARS-CoV-2 virus-like particles (SC2-VLPs) can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and at multiple steps in the viral life cycle. In SC2-VLPs, four nucleocapsid (N) mutations found universally in more-transmissible variants independently increased messenger RNA delivery and expression ~10-fold, and in a reverse genetics model, the serine-202→arginine (S202R) and arginine-203→methionine (R203M) mutations each produced >50 times as much virus. SC2-VLPs provide a platform for rapid testing of viral variants outside of a biosafety level 3 setting and demonstrate N mutations and particle assembly to be mechanisms that could explain the increased spread of variants, including B.1.617.2 (Delta, which contains the R203M mutation).
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Affiliation(s)
- Abdullah M. Syed
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Taha Y. Taha
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Takako Tabata
- Gladstone Institute of Virology, San Francisco, CA, USA
| | - Irene P. Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Alison Ciling
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Mir M. Khalid
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Pei-Yi Chen
- Gladstone Institute of Virology, San Francisco, CA, USA
| | | | - Katarzyna M. Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Melanie Ott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, CA, USA
| | - Jennifer A. Doudna
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
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Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA. DNA interference states of the hypercompact CRISPR-CasΦ effector. Nat Struct Mol Biol 2021; 28:652-661. [PMID: 34381246 PMCID: PMC8496406 DOI: 10.1038/s41594-021-00632-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-CasΦ, a small RNA-guided enzyme found uniquely in bacteriophages, achieves programmable DNA cutting as well as genome editing. To investigate how the hypercompact enzyme recognizes and cleaves double-stranded DNA, we determined cryo-EM structures of CasΦ (Cas12j) in pre- and post-DNA-binding states. The structures reveal a streamlined protein architecture that tightly encircles the CRISPR RNA and DNA target to capture, unwind and cleave DNA. Comparison of the pre- and post-DNA-binding states reveals how the protein rearranges for DNA cleavage upon target recognition. On the basis of these structures, we created and tested mutant forms of CasΦ that cut DNA up to 20-fold faster relative to wild type, showing how this system may be naturally attenuated to improve the fidelity of DNA interference. The structural and mechanistic insights into how CasΦ binds and cleaves DNA should allow for protein engineering for both in vitro diagnostics and genome editing.
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Affiliation(s)
- Patrick Pausch
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- VU LSC-EMBL Partnership for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Katarzyna M Soczek
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Dominik A Herbst
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Connor A Tsuchida
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, Baltimore, MD, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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Soczek KM, Grant T, Rosenthal PB, Mondragón A. CryoEM structures of open dimers of gyrase A in complex with DNA illuminate mechanism of strand passage. eLife 2018; 7:41215. [PMID: 30457554 PMCID: PMC6286129 DOI: 10.7554/elife.41215] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.
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Affiliation(s)
- Katarzyna M Soczek
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Tim Grant
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom
| | - Peter B Rosenthal
- Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom.,Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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Gunn KH, Soczek KM, Marko JF, Mondragon A. Studies of DNA Gyrase at the Single Molecule Level. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Gunn KH, Soczek KM, Critchelow CJ, Marko JF, Mondragon A. Studies of DNA Gyrase at the Single Molecule Level. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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