1
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Dort EN, Hamelin RC. Heterogeneity in establishment of polyethylene glycol-mediated plasmid transformations for five forest pathogenic Phytophthora species. PLoS One 2024; 19:e0306158. [PMID: 39255283 PMCID: PMC11386421 DOI: 10.1371/journal.pone.0306158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/26/2024] [Indexed: 09/12/2024] Open
Abstract
Plasmid-mediated DNA transformation is a foundational molecular technique and the basis for most CRISPR-Cas9 gene editing systems. While plasmid transformations are well established for many agricultural Phytophthora pathogens, development of this technique in forest Phytophthoras is lacking. Given our long-term research objective to develop CRISPR-Cas9 gene editing in a forest pathogenic Phytophthora species, we sought to establish the functionality of polyethylene glycol (PEG)-mediated plasmid transformation in five species: P. cactorum, P. cinnamomi, P. cryptogea, P. ramorum, and P. syringae. We used the agricultural pathogen P. sojae, a species for which PEG-mediated transformations are well-established, as a transformation control. Using a protocol previously optimized for P. sojae, we tested transformations in the five forest Phytophthoras with three different plasmids: two developed for CRISPR-Cas9 gene editing and one developed for fluorescent protein tagging. Out of the five species tested, successful transformation, as indicated by stable growth of transformants on a high concentration of antibiotic selective growth medium and diagnostic PCR, was achieved only with P. cactorum and P. ramorum. However, while transformations in P. cactorum were consistent and stable, transformations in P. ramorum were highly variable and yielded transformants with very weak mycelial growth and abnormal morphology. Our results indicate that P. cactorum is the best candidate to move forward with CRISPR-Cas9 protocol development and provide insight for future optimization of plasmid transformations in forest Phytophthoras.
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Affiliation(s)
- Erika N Dort
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard C Hamelin
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec City, Québec, Canada
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2
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Xing W, Li D, Wang W, Liu JJG, Chen C. Conformational dynamics of CasX (Cas12e) in mediating DNA cleavage revealed by single-molecule FRET. Nucleic Acids Res 2024; 52:9014-9027. [PMID: 38994558 PMCID: PMC11347132 DOI: 10.1093/nar/gkae604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
CasX (also known as Cas12e), a Class 2 CRISPR-Cas system, shows promise in genome editing due to its smaller size compared to the widely used Cas9 and Cas12a. Although the structures of CasX-sgRNA-DNA ternary complexes have been resolved and uncover a distinctive NTSB domain, the dynamic behaviors of CasX are not well characterized. In this study, we employed single-molecule and biochemical assays to investigate the conformational dynamics of two CasX homologs, DpbCasX and PlmCasX, from DNA binding to target cleavage and fragment release. Our results indicate that CasX cleaves the non-target strand and the target strand sequentially with relative irreversible dynamics. The two CasX homologs exhibited different cleavage patterns and specificities. The dynamic characterization of CasX also reveals a PAM-proximal seed region, providing guidance for CasX-based effector design. Further studies elucidate the mechanistic basis for why modification of sgRNA and the NTSB domain can affect its activity. Interestingly, CasX has less effective target search efficiency than Cas9 and Cas12a, potentially accounting for its lower genome editing efficiency. This observation opens a new avenue for future protein engineering.
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Affiliation(s)
- Wenjing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Danyuan Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenjuan Wang
- Technology Center for Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jun-Jie Gogo Liu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chunlai Chen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
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3
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Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA. CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606079. [PMID: 39131396 PMCID: PMC11312533 DOI: 10.1101/2024.07.31.606079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a-RNA-DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA engineering begins with local helix distortion by transient CRISPR-Cas protein binding.
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Affiliation(s)
- Katarzyna M. Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Joshua C. Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
| | - Owen T. Tuck
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley; Berkeley, CA, USA
| | - Honglue Shi
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
| | - Jennifer A. Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
- Innovative Genomics Institute; University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley; Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley; Berkeley CA, USA
- Gladstone-UCSF Institute of Genomic Immunology; San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory; Berkeley, CA, USA
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4
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Son JB, Kim S, Yang S, Ahn Y, Lee NK. Analysis of Fluorescent Proteins for Observing Single Gene Locus in a Live and Fixed Escherichia coli Cell. J Phys Chem B 2024; 128:6730-6741. [PMID: 38968413 PMCID: PMC11264270 DOI: 10.1021/acs.jpcb.4c01816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
Fluorescent proteins (FPs) are essential tools for advanced microscopy techniques such as super-resolution imaging, single-particle tracking, and quantitative single-molecule counting. Various FPs fused to DNA-binding proteins have been used to observe the subcellular location and movement of specific gene loci in living and fixed bacterial cells. However, quantitative assessments of the properties of FPs for gene locus measurements are still lacking. Here, we assessed various FPs to observe specific gene loci in live and fixed Escherichia coli cells using a fluorescent repressor-operator binding system (FROS), tet operator-Tet repressor proteins (TetR). Tsr-fused FPs were used to assess the intensity and photostability of various FPs (five red FPs: mCherry2, FusionRed, mRFP, mCrimson3, and dKatushka; and seven yellow FPs: SYFP2, Venus, mCitrine, YPet, mClover3, mTopaz, and EYFP) at the single-molecule level in living cells. These FPs were then used for gene locus measurements using FROS. Our results indicate that TetR-mCrimson3 (red) and TetR-EYFP (yellow) had better properties for visualizing gene loci than the other TetR-FPs. Furthermore, fixation procedures affected the clustering of diffusing TetR-FPs and altered the locations of the TetR-FP foci. Fixation with formaldehyde consistently disrupted proper DNA locus observations using TetR-FPs. Notably, the foci measured using TetR-mCrimson3 remained close to their original positions in live cells after glyoxal fixation. This in vivo study provides a cell-imaging guide for the use of FPs for gene-locus observation in E. coli and a scheme for evaluating the use of FPs for other cell-imaging purposes.
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Affiliation(s)
| | | | | | - Youmin Ahn
- Department of Chemistry, Seoul
National University, 08826 Seoul, South
Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul
National University, 08826 Seoul, South
Korea
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5
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [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] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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6
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Oberhofer G, Johnson ML, Ivy T, Antoshechkin I, Hay BA. Cleave and Rescue gamete killers create conditions for gene drive in plants. NATURE PLANTS 2024; 10:936-953. [PMID: 38886522 DOI: 10.1038/s41477-024-01701-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/16/2024] [Indexed: 06/20/2024]
Abstract
Gene drive elements promote the spread of linked traits and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Here we demonstrate the essential features of the ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61. Resistant alleles, which can slow or prevent drive, were not observed. Modelling shows plant ClvRs are robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications are discussed.
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Affiliation(s)
- Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michelle L Johnson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tobin Ivy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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7
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Yang C, Zhou Z, Sun X, Ju H, Yue X, Rao S, Xue C. PAMless SpRY exhibits a preference for the seed region for efficient targeting. Cell Rep 2024; 43:114225. [PMID: 38733582 DOI: 10.1016/j.celrep.2024.114225] [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: 12/18/2023] [Revised: 04/01/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Protospacer-adjacent motif (PAM) recognition licenses Cas nucleases for genome engineering applications, thereby restricting gene targeting to PAM-containing regions. Protein engineering has led to PAM-relaxed SpCas9 variants like SpG and SpRY. Given the evolved role of PAMs in facilitating target-searching kinetics, it remains unclear how these variants quickly locate their targets. We show that SpG and SpRY exhibit a preference for the seed region. To compensate for the relaxed PAM recognition, SpRY has evolved a sequence preference for the seed region through interactions with A61R and A1322R. Furthermore, SpCas9 exhibits a significant decrease in target search kinetics on high-PAM-density DNA, slowing down up to three orders of magnitude compared to low-PAM-density DNA, suggesting the necessity for sequence recognition even in PAM-relaxed variants. This underscores the importance of considering Cas9 target-searching kinetics in SpCas9 PAMless engineering, providing valuable insights for further PAMless Cas9 protein engineering efforts.
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Affiliation(s)
- Chen Yang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Xuanlong Sun
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Haiyan Ju
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinmin Yue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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8
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Olivi L, Bagchus C, Pool V, Bekkering E, Speckner K, Offerhaus H, Wu W, Depken M, Martens KA, Staals RJ, Hohlbein J. Live-cell imaging reveals the trade-off between target search flexibility and efficiency for Cas9 and Cas12a. Nucleic Acids Res 2024; 52:5241-5256. [PMID: 38647045 PMCID: PMC11109954 DOI: 10.1093/nar/gkae283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
CRISPR-Cas systems have widely been adopted as genome editing tools, with two frequently employed Cas nucleases being SpyCas9 and LbCas12a. Although both nucleases use RNA guides to find and cleave target DNA sites, the two enzymes differ in terms of protospacer-adjacent motif (PAM) requirements, guide architecture and cleavage mechanism. In the last years, rational engineering led to the creation of PAM-relaxed variants SpRYCas9 and impLbCas12a to broaden the targetable DNA space. By employing their catalytically inactive variants (dCas9/dCas12a), we quantified how the protein-specific characteristics impact the target search process. To allow quantification, we fused these nucleases to the photoactivatable fluorescent protein PAmCherry2.1 and performed single-particle tracking in cells of Escherichia coli. From our tracking analysis, we derived kinetic parameters for each nuclease with a non-targeting RNA guide, strongly suggesting that interrogation of DNA by LbdCas12a variants proceeds faster than that of SpydCas9. In the presence of a targeting RNA guide, both simulations and imaging of cells confirmed that LbdCas12a variants are faster and more efficient in finding a specific target site. Our work demonstrates the trade-off of relaxing PAM requirements in SpydCas9 and LbdCas12a using a powerful framework, which can be applied to other nucleases to quantify their DNA target search.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Cleo Bagchus
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Victor Pool
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ezra Bekkering
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Konstantin Speckner
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hidde Offerhaus
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Wen Y Wu
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Koen J A Martens
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | - Raymond H J Staals
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
- Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, The Netherlands
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9
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Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, Johnston B, Zhang Z, Potter J, Pineda L, Pflueger J, Swain T, Pflueger C, Lloyd JPB, Secco D, Small I, Kidd BN, Lister R. CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol 2024:10.1038/s41587-024-02236-w. [PMID: 38769424 DOI: 10.1038/s41587-024-02236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
The construction of synthetic gene circuits in plants has been limited by a lack of orthogonal and modular parts. Here, we implement a CRISPR (clustered regularly interspaced short palindromic repeats) interference (CRISPRi)-based reversible gene circuit platform in plants. We create a toolkit of engineered repressible promoters of different strengths and construct NOT and NOR gates in Arabidopsis thaliana protoplasts. We determine the optimal processing system to express single guide RNAs from RNA Pol II promoters to introduce NOR gate programmability for interfacing with host regulatory sequences. The performance of a NOR gate in stably transformed Arabidopsis plants demonstrates the system's programmability and reversibility in a complex multicellular organism. Furthermore, cross-species activity of CRISPRi-based logic gates is shown in Physcomitrium patens, Triticum aestivum and Brassica napus protoplasts. Layering multiple NOR gates together creates OR, NIMPLY and AND logic functions, highlighting the modularity of our system. Our CRISPRi circuits are orthogonal, compact, reversible, programmable and modular and provide a platform for sophisticated spatiotemporal control of gene expression in plants.
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Affiliation(s)
- Muhammad Adil Khan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Gabrielle Herring
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jia Yuan Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marina Oliva
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Elliott Fourie
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Benjamin Johnston
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhining Zhang
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jarred Potter
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Pineda
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Tessa Swain
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - David Secco
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Brendan N Kidd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland, Australia.
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Australian Research Council Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
- Harry Perkins Institute of Medical Research, The University of Western Australia, Perth, Western Australia, Australia.
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10
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Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun 2024; 15:3663. [PMID: 38688943 PMCID: PMC11061278 DOI: 10.1038/s41467-024-47830-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
CRISPR-Cas9 is a powerful tool for genome editing, but the strict requirement for an NGG protospacer-adjacent motif (PAM) sequence immediately next to the DNA target limits the number of editable genes. Recently developed Cas9 variants have been engineered with relaxed PAM requirements, including SpG-Cas9 (SpG) and the nearly PAM-less SpRY-Cas9 (SpRY). However, the molecular mechanisms of how SpRY recognizes all potential PAM sequences remains unclear. Here, we combine structural and biochemical approaches to determine how SpRY interrogates DNA and recognizes target sites. Divergent PAM sequences can be accommodated through conformational flexibility within the PAM-interacting region, which facilitates tight binding to off-target DNA sequences. Nuclease activation occurs ~1000-fold slower than for Streptococcus pyogenes Cas9, enabling us to directly visualize multiple on-pathway intermediate states. Experiments with SpG position it as an intermediate enzyme between Cas9 and SpRY. Our findings shed light on the molecular mechanisms of PAMless genome editing.
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Affiliation(s)
- Grace N Hibshman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| | - Matthew M Hooper
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Hongshan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kenneth A Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
- Interdisciplinary Life Sciences Graduate Programs, Austin, TX, 78712, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA.
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11
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Oberhofer G, Johnson ML, Ivy T, Antoshechkin I, Hay BA. Cleave and Rescue gamete killers create conditions for gene drive in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.13.562303. [PMID: 37873352 PMCID: PMC10592828 DOI: 10.1101/2023.10.13.562303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gene drive elements promote the spread of linked traits, even when their presence confers a fitness cost to carriers, and can be used to change the composition or fate of wild populations. Cleave and Rescue (ClvR) drive elements sit at a fixed chromosomal position and include a DNA sequence-modifying enzyme such as Cas9/gRNAs (the Cleaver/Toxin) that disrupts endogenous versions of an essential gene, and a recoded version of the essential gene resistant to cleavage (the Rescue/Antidote). ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. We demonstrate the essential features of ClvR gene drive in the plant Arabidopsis thaliana through killing of gametes that fail to inherit a ClvR that targets the essential gene YKT61, whose expression is required in male and female gametes for their survival. Resistant (uncleavable but functional) alleles, which can slow or prevent drive, were not observed. Modeling shows plant ClvRs are likely to be robust to certain failure modes and can be used to rapidly drive population modification or suppression. Possible applications in plant breeding, weed control, and conservation are discussed.
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Affiliation(s)
- Georg Oberhofer
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Michelle L. Johnson
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Tobin Ivy
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Igor Antoshechkin
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
| | - Bruce A. Hay
- California Institute of Technology. Division of Biology and Biological Engineering. 1200 East California Boulevard, MC156-29, Pasadena, CA 91125
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12
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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13
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Nam KM, Gunawardena J. The linear framework II: using graph theory to analyse the transient regime of Markov processes. Front Cell Dev Biol 2023; 11:1233808. [PMID: 38020901 PMCID: PMC10656611 DOI: 10.3389/fcell.2023.1233808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
The linear framework uses finite, directed graphs with labelled edges to model biomolecular systems. Graph vertices represent chemical species or molecular states, edges represent reactions or transitions and edge labels represent rates that also describe how the system is interacting with its environment. The present paper is a sequel to a recent review of the framework that focussed on how graph-theoretic methods give insight into steady states as rational algebraic functions of the edge labels. Here, we focus on the transient regime for systems that correspond to continuous-time Markov processes. In this case, the graph specifies the infinitesimal generator of the process. We show how the moments of the first-passage time distribution, and related quantities, such as splitting probabilities and conditional first-passage times, can also be expressed as rational algebraic functions of the labels. This capability is timely, as new experimental methods are finally giving access to the transient dynamic regime and revealing the computations and information processing that occur before a steady state is reached. We illustrate the concepts, methods and formulas through examples and show how the results may be used to illuminate previous findings in the literature.
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Affiliation(s)
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
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14
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Santos-Moreno J, Tasiudi E, Kusumawardhani H, Stelling J, Schaerli Y. Robustness and innovation in synthetic genotype networks. Nat Commun 2023; 14:2454. [PMID: 37117168 PMCID: PMC10147661 DOI: 10.1038/s41467-023-38033-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Genotype networks are sets of genotypes connected by small mutational changes that share the same phenotype. They facilitate evolutionary innovation by enabling the exploration of different neighborhoods in genotype space. Genotype networks, first suggested by theoretical models, have been empirically confirmed for proteins and RNAs. Comparative studies also support their existence for gene regulatory networks (GRNs), but direct experimental evidence is lacking. Here, we report the construction of three interconnected genotype networks of synthetic GRNs producing three distinct phenotypes in Escherichia coli. Our synthetic GRNs contain three nodes regulating each other by CRISPR interference and governing the expression of fluorescent reporters. The genotype networks, composed of over twenty different synthetic GRNs, provide robustness in face of mutations while enabling transitions to innovative phenotypes. Through realistic mathematical modeling, we quantify robustness and evolvability for the complete genotype-phenotype map and link these features mechanistically to GRN motifs. Our work thereby exemplifies how GRN evolution along genotype networks might be driving evolutionary innovation.
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Affiliation(s)
- Javier Santos-Moreno
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
- Department of Medicine and Life Sciences, Pompeu Fabra University, 00803, Barcelona, Spain
| | - Eve Tasiudi
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Hadiastri Kusumawardhani
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
| | - Joerg Stelling
- Department of Biosystems Science and Engineering, ETH Zurich and SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Yolanda Schaerli
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.
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15
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Arbel-Goren R, McKeithen-Mead SA, Voglmaier D, Afremov I, Teza G, Grossman A, Stavans J. Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer. Nucleic Acids Res 2023; 51:3116-3129. [PMID: 36762480 PMCID: PMC10123120 DOI: 10.1093/nar/gkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Dominik Voglmaier
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idana Afremov
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alan D Grossman
- Department of Biology Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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16
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Spasskaya DS, Davletshin AI, Bachurin SS, Tutyaeva VV, Garbuz DG, Karpov DS. Improving the on-target activity of high-fidelity Cas9 editors by combining rational design and random mutagenesis. Appl Microbiol Biotechnol 2023; 107:2385-2401. [PMID: 36917274 DOI: 10.1007/s00253-023-12469-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Genomic and post-genomic editors based on CRISPR/Cas systems are widely used in basic research and applied sciences, including human gene therapy. Most genome editing tools are based on the CRISPR/Cas9 type IIA system from Streptococcus pyogenes. Unfortunately, a number of drawbacks have hindered its application in therapeutic approaches, the most serious of which is the relatively high level of off-targets. To overcome this obstacle, various high-fidelity Cas9 variants have been created. However, they show reduced on-target activity compared to wild-type Cas9 possibly due to increased sensitivity to eukaryotic chromatin. Here, we combined a rational approach with random mutagenesis to create a set of new Cas9 variants showing high specificity and increased activity in Saccharomyces cerevisiae yeast. Moreover, a novel mutation in the PAM (protospacer adjacent motif)-interacting Cas9 domain was found, which increases the on-target activity of high-fidelity Cas9 variants while retaining their high specificity. The obtained data suggest that this mutation acts by weakening the eukaryotic chromatin barrier for Cas9 and rearranging the RuvC active center. Improved Cas9 variants should further advance genome and post-genome editing technologies. KEY POINTS: • D147Y and P411T mutations increase the activity of high-fidelity Cas9 variants. • The new L1206P mutation further increases the activity of high-fidelity Cas9 variants. • The L1206P mutation weakens the chromatin barrier for Cas9 editors.
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Affiliation(s)
- Daria S Spasskaya
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, 119991, Russia
| | - Artem I Davletshin
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, 119991, Russia
| | - Stanislav S Bachurin
- FSBEI HE Rostov State Medical University Ministry of Health, Nakhichevanskiy Lane 29, Rostov-On-Don, 344022, Russia
| | - Vera V Tutyaeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, 119991, Russia
| | - David G Garbuz
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, 119991, Russia
| | - Dmitry S Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, 119991, Russia.
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17
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Montagud-Martínez R, Márquez-Costa R, Rodrigo G. Programmable regulation of translation by harnessing the CRISPR-Cas13 system. Chem Commun (Camb) 2023; 59:2616-2619. [PMID: 36757178 DOI: 10.1039/d3cc00058c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ability to control protein expression at both the transcriptional and post-transcriptional levels is instrumental for the cell to integrate multiple molecular signals and then reach high operational sophistication. Although challenging, fully artificial regulations at different levels are required for boosting systems and synthetic biology. Here, we report the development of a novel framework to regulate translation by repurposing the CRISPR-Cas13 immune system, which uses an RNA-guided ribonuclease. By exploiting a cell-free expression system for prototyping gene regulatory structures, our results demonstrate that CRISPR-dCas13a ribonucleoproteins (d means catalytically dead) can be programmed to repress or activate translation initiation. The performance assessment of the engineered systems also revealed guide RNA design principles. Moreover, we show that the system can work in vivo. This development complements the ability to regulate transcription with other CRISPR-Cas systems and offers potential applications.
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Affiliation(s)
- Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Rosa Márquez-Costa
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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18
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Simmel FC. Nucleic acid strand displacement - from DNA nanotechnology to translational regulation. RNA Biol 2023; 20:154-163. [PMID: 37095744 PMCID: PMC10132225 DOI: 10.1080/15476286.2023.2204565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Nucleic acid strand displacement reactions involve the competition of two or more DNA or RNA strands of similar sequence for binding to a complementary strand, and facilitate the isothermal replacement of an incumbent strand by an invader. The process can be biased by augmenting the duplex comprising the incumbent with a single-stranded extension, which can act as a toehold for a complementary invader. The toehold gives the invader a thermodynamic advantage over the incumbent, and can be programmed as a unique label to activate a specific strand displacement process. Toehold-mediated strand displacement processes have been extensively utilized for the operation of DNA-based molecular machines and devices as well as for the design of DNA-based chemical reaction networks. More recently, principles developed initially in the context of DNA nanotechnology have been applied for the de novo design of gene regulatory switches that can operate inside living cells. The article specifically focuses on the design of RNA-based translational regulators termed toehold switches. Toehold switches utilize toehold-mediated strand invasion to either activate or repress translation of an mRNA in response to the binding of a trigger RNA molecule. The basic operation principles of toehold switches will be discussed as well as their applications in sensing and biocomputing. Finally, strategies for their optimization will be described as well as challenges for their operation in vivo.
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Affiliation(s)
- Friedrich C Simmel
- TU Munich, School of Natural Sciences, Department of Bioscience, Garching, Germany
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19
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Kiattisewee C, Karanjia AV, Legut M, Daniloski Z, Koplik SE, Nelson J, Kleinstiver BP, Sanjana NE, Carothers JM, Zalatan JG. Expanding the Scope of Bacterial CRISPR Activation with PAM-Flexible dCas9 Variants. ACS Synth Biol 2022; 11:4103-4112. [PMID: 36378874 PMCID: PMC10516241 DOI: 10.1021/acssynbio.2c00405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
CRISPR-Cas transcriptional tools have been widely applied for programmable regulation of complex biological networks. In comparison to eukaryotic systems, bacterial CRISPR activation (CRISPRa) has stringent target site requirements for effective gene activation. While genes may not always have an NGG protospacer adjacent motif (PAM) at the appropriate position, PAM-flexible dCas9 variants can expand the range of targetable sites. Here we systematically evaluate a panel of PAM-flexible dCas9 variants for their ability to activate bacterial genes. We observe that dxCas9-NG provides a high dynamic range of gene activation for sites with NGN PAMs while dSpRY permits modest activity across almost any PAM. Similar trends were observed for heterologous and endogenous promoters. For all variants tested, improved PAM-flexibility comes with the trade-off that CRISPRi-mediated gene repression becomes less effective. Weaker CRISPR interference (CRISPRi) gene repression can be partially rescued by expressing multiple sgRNAs to target many sites in the gene of interest. Our work provides a framework to choose the most effective dCas9 variant for a given set of gene targets, which will further expand the utility of CRISPRa/i gene regulation in bacterial systems.
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Affiliation(s)
- Cholpisit Kiattisewee
- Molecular Engineering & Sciences Institute and Center
for Synthetic Biology, University of Washington, Seattle, WA 98195, United
States
| | - Ava V. Karanjia
- Molecular Engineering & Sciences Institute and Center
for Synthetic Biology, University of Washington, Seattle, WA 98195, United
States
- Department of Chemical Engineering, University of
Washington, Seattle, WA 98195, United States
| | - Mateusz Legut
- New York Genome Center, New York, NY 10013, United
States
- Department of Biology, New York University, New York, NY
10013, United States
| | - Zharko Daniloski
- New York Genome Center, New York, NY 10013, United
States
- Department of Biology, New York University, New York, NY
10013, United States
| | - Samantha E. Koplik
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, United States
| | - Joely Nelson
- Molecular Engineering & Sciences Institute and Center
for Synthetic Biology, University of Washington, Seattle, WA 98195, United
States
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General
Hospital, Boston, MA 02114, United States
- Department of Pathology, Massachusetts General Hospital,
Boston, MA 02114, United States
- Department of Pathology, Harvard Medical School, Boston,
MA 02115, United States
| | - Neville E. Sanjana
- New York Genome Center, New York, NY 10013, United
States
- Department of Biology, New York University, New York, NY
10013, United States
| | - James M. Carothers
- Molecular Engineering & Sciences Institute and Center
for Synthetic Biology, University of Washington, Seattle, WA 98195, United
States
- Department of Chemical Engineering, University of
Washington, Seattle, WA 98195, United States
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, United States
| | - Jesse G. Zalatan
- Molecular Engineering & Sciences Institute and Center
for Synthetic Biology, University of Washington, Seattle, WA 98195, United
States
- Department of Chemical Engineering, University of
Washington, Seattle, WA 98195, United States
- Department of Chemistry, University of Washington,
Seattle, WA 98195, United States
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20
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Shaytan AK, Novikov RV, Vinnikov RS, Gribkova AK, Glukhov GS. From DNA-protein interactions to the genetic circuit design using CRISPR-dCas systems. Front Mol Biosci 2022; 9:1070526. [PMID: 36589238 PMCID: PMC9795063 DOI: 10.3389/fmolb.2022.1070526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023] Open
Abstract
In the last decade, the CRISPR-Cas technology has gained widespread popularity in different fields from genome editing and detecting specific DNA/RNA sequences to gene expression control. At the heart of this technology is the ability of CRISPR-Cas complexes to be programmed for targeting particular DNA loci, even when using catalytically inactive dCas-proteins. The repertoire of naturally derived and engineered dCas-proteins including fusion proteins presents a promising toolbox that can be used to construct functional synthetic genetic circuits. Rational genetic circuit design, apart from having practical relevance, is an important step towards a deeper quantitative understanding of the basic principles governing gene expression regulation and functioning of living organisms. In this minireview, we provide a succinct overview of the application of CRISPR-dCas-based systems in the emerging field of synthetic genetic circuit design. We discuss the diversity of dCas-based tools, their properties, and their application in different types of genetic circuits and outline challenges and further research directions in the field.
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Affiliation(s)
- A. K. Shaytan
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Computer Science, HSE University, Moscow, Russia,*Correspondence: A. K. Shaytan,
| | - R. V. Novikov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - R. S. Vinnikov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - A. K. Gribkova
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - G. S. Glukhov
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia,Faculty of Biology, MSU-BIT Shenzhen University, Shenzhen, China
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21
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Bravo JP, Hibshman GN, Taylor DW. Constructing next-generation CRISPR-Cas tools from structural blueprints. Curr Opin Biotechnol 2022; 78:102839. [PMID: 36371895 DOI: 10.1016/j.copbio.2022.102839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/18/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats - CRISPR-associated protein (CRISPR-Cas) systems are a critical component of the bacterial adaptive immune response. Since the discovery that they can be reengineered as programmable RNA-guided nucleases, there has been significant interest in using these systems to perform diverse and precise genetic manipulations. Here, we outline recent advances in the mechanistic understanding of CRISPR-Cas9, how these findings have been leveraged in the rational redesign of Cas9 variants with altered activities, and how these novel tools can be exploited for biotechnology and therapeutics. We also discuss the potential of the ubiquitous, yet often-overlooked, multisubunit CRISPR effector complexes for large-scale genomic deletions. Furthermore, we highlight how future structural studies will bolster these technologies.
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Affiliation(s)
- Jack Pk Bravo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
| | - Grace N Hibshman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA
| | - David W Taylor
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA; Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA
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22
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The Spatial Organization of Bacterial Transcriptional Regulatory Networks. Microorganisms 2022; 10:microorganisms10122366. [PMID: 36557619 PMCID: PMC9787925 DOI: 10.3390/microorganisms10122366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The transcriptional regulatory network (TRN) is the central pivot of a prokaryotic organism to receive, process and respond to internal and external environmental information. However, little is known about its spatial organization so far. In recent years, chromatin interaction data of bacteria such as Escherichia coli and Bacillus subtilis have been published, making it possible to study the spatial organization of bacterial transcriptional regulatory networks. By combining TRNs and chromatin interaction data of E. coli and B. subtilis, we explored the spatial organization characteristics of bacterial TRNs in many aspects such as regulation directions (positive and negative), central nodes (hubs, bottlenecks), hierarchical levels (top, middle, bottom) and network motifs (feed-forward loops and single input modules) of the TRNs and found that the bacterial TRNs have a variety of stable spatial organization features under different physiological conditions that may be closely related with biological functions. Our findings provided new insights into the connection between transcriptional regulation and the spatial organization of chromosome in bacteria and might serve as a factual foundation for trying spatial-distance-based gene circuit design in synthetic biology.
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23
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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/17/2022] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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24
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Specht DA, Cortes LB, Lambert G. Overcoming Leak Sensitivity in CRISPRi Circuits Using Antisense RNA Sequestration and Regulatory Feedback. ACS Synth Biol 2022; 11:2927-2937. [PMID: 36017994 PMCID: PMC9486968 DOI: 10.1021/acssynbio.2c00155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Indexed: 01/24/2023]
Abstract
The controlled binding of the catalytically dead CRISPR nuclease (dCas) to DNA can be used to create complex, programmable transcriptional genetic circuits, a fundamental goal of synthetic biology. This approach, called CRISPR interference (CRISPRi), is advantageous over existing methods because the programmable nature of CRISPR proteins in principle enables the simultaneous regulation of many different targets without crosstalk. However, the performance of dCas-based genetic circuits is limited by both the sensitivity to leaky repression within CRISPRi logic gates and retroactive effects due to a shared pool of dCas proteins. By utilizing antisense RNAs (asRNAs) to sequester gRNA transcripts as well as CRISPRi feedback to self-regulate asRNA production, we demonstrate a mechanism that suppresses unwanted repression by CRISPRi and improves logical gene circuit function in Escherichia coli. This improvement is particularly pronounced during stationary expression when CRISPRi circuits do not achieve the expected regulatory dynamics. Furthermore, the use of dual CRISPRi/asRNA inverters restores the logical performance of layered circuits such as a double inverter. By studying circuit induction at the single-cell level in microfluidic channels, we provide insight into the dynamics of antisense sequestration of gRNA and regulatory feedback on dCas-based repression and derepression. These results demonstrate how CRISPRi inverters can be improved for use in more complex genetic circuitry without sacrificing the programmability and orthogonality of dCas proteins.
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Affiliation(s)
- David A. Specht
- Applied Physics, Cornell University, Ithaca, New York 14853, United States
| | - Louis B. Cortes
- Applied Physics, Cornell University, Ithaca, New York 14853, United States
| | - Guillaume Lambert
- Applied Physics, Cornell University, Ithaca, New York 14853, United States
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25
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Dersch S, Rotter DA, Graumann PL. Heterogeneity of Subcellular Diffusion in Bacteria Based on Spatial Segregation of Ribosomes and Nucleoids. Microb Physiol 2022; 32:177-186. [PMID: 36070705 PMCID: PMC9827431 DOI: 10.1159/000526846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/18/2022] [Indexed: 01/12/2023]
Abstract
It has long become clear that in spite of generally lacking internal membrane systems, bacteria contain well-structured subcellular structures of usually filamentous proteins, and a preferred 3D arrangement of their chromosome(s). Some of these systems are set up by so-called cytoskeletal elements, or by polar landmark proteins, but the mechanism of specific localization is still unclear in most cases. Intriguingly, apart from such spatially organizing systems, the bacterial cytoplasm has unusual properties in terms of the diffusion of molecules, which varies between different sites within the cell. In many bacteria, chromosomes are compacted into centrally located nucleoids, being orderly folded as opposed to consisting of random coils of DNA. In these bacteria, there is a separation of transcription and translation, such that transcription by RNA polymerase occurs on the nucleoids, and translation takes place mostly at the cell poles and directly underneath the cell membrane, because 70S ribosomes accumulate at sites surrounding the nucleoids. Interestingly, accumulation of ribosomes appears to slow down diffusion of enzymes, noticeable for larger enzyme complexes, while nucleoids provide areas of confined motion for DNA-binding proteins, yet acceleration zones for non-DNA-binding proteins. Crowded regions at the cell poles set up zones of higher concentration of the translation machinery, shortening diffusion distances for rate-limiting translation factor/ribosome interactions, and of metabolic enzymes, possibly speeding up pathways containing low concentrations of metabolites. Thus, heterogeneous diffusion adds another layer of subcellular organization on top of cytoskeletal elements.
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26
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Wang T, Wang Y, Chen P, Yin BC, Ye BC. An Ultrasensitive, One-Pot RNA Detection Method Based on Rationally Engineered Cas9 Nickase-Assisted Isothermal Amplification Reaction. Anal Chem 2022; 94:12461-12471. [DOI: 10.1021/acs.analchem.2c02617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ting Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yan Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Pinru Chen
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
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27
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Mehra D, Adhikari S, Banerjee C, Puchner EM. Characterizing locus specific chromatin structure and dynamics with correlative conventional and super-resolution imaging in living cells. Nucleic Acids Res 2022; 50:e78. [PMID: 35524554 PMCID: PMC9303368 DOI: 10.1093/nar/gkac314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/08/2022] [Accepted: 05/02/2022] [Indexed: 11/23/2022] Open
Abstract
The dynamic rearrangement of chromatin is critical for gene regulation, but mapping both the spatial organization of chromatin and its dynamics remains a challenge. Many structural conformations are too small to be resolved via conventional fluorescence microscopy and the long acquisition time of super-resolution photoactivated localization microscopy (PALM) precludes the structural characterization of chromatin below the optical diffraction limit in living cells due to chromatin motion. Here we develop a correlative conventional fluorescence and PALM imaging approach to quantitatively map time-averaged chromatin structure and dynamics below the optical diffraction limit in living cells. By assigning localizations to a locus as it moves, we reliably discriminate between bound and unbound dCas9 molecules, whose mobilities overlap. Our approach accounts for changes in DNA mobility and relates local chromatin motion to larger scale domain movement. In our experimental system, we show that compacted telomeres move faster and have a higher density of bound dCas9 molecules, but the relative motion of those molecules is more restricted than in less compacted telomeres. Correlative conventional and PALM imaging therefore improves the ability to analyze the mobility and time-averaged nanoscopic structural features of locus specific chromatin with single molecule sensitivity and yields unprecedented insights across length and time scales.
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Affiliation(s)
- Dushyant Mehra
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester MN, USA
| | - Santosh Adhikari
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
| | - Chiranjib Banerjee
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
| | - Elias M Puchner
- School of Physics and Astronomy, University of Minnesota, Minneapolis MN, USA
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28
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da Costa LC, Bomfim LM, Dittz UVT, Velozo CDA, da Cunha RD, Tanuri A. Repression of HIV-1 reactivation mediated by CRISPR/dCas9-KRAB in lymphoid and myeloid cell models. Retrovirology 2022; 19:12. [PMID: 35733180 PMCID: PMC9215058 DOI: 10.1186/s12977-022-00600-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background Despite antiretroviral treatment efficacy, it does not lead to the complete eradication of HIV infection. Consequently, reactivation of the virus from latently infected cell reservoirs is a major challenge toward cure efforts. Two strategies targeting viral latency are currently under investigation: the “shock and kill” and the “block and lock.” The “Block and Lock” methodology aims to control HIV-1 latency reactivation, promoting a functional cure. We utilized the CRISPR/dCas9-KRAB platform, which was initially developed to suppress cellular genes transcription, to block drug-induced HIV-1 reactivation in latently infected T cells and myeloid cells. Results We identified a set of five sgRNAs targeting the HIV-1 proviral genome (LTR1-LTR5), having the lowest nominated off-target activity, and transduced them into the latently infected lymphoid (J-Lat 10.6) and myeloid (U1) cell lines. One of the sgRNAs (LTR5), which binds specifically in the HIV-1 LTR NFκB binding site, was able to promote robust repression of HIV-1 reactivation in latently infected T cells stimulated with Phorbol 12-Myristate 13-Acetate (PMA) and Ingenol B (IngB), both potent protein kinase C (PKC) stimulators. Reactivation with HDAC inhibitors, such as SAHA and Panobinostat, showed the same strong inhibition of reactivation. Additionally, we observed a hundred times reduction of HIV-1 RNA expression levels in the latently infected myeloid cell line, U1 induced with IngB. Conclusion Taken together, our results show that the KRAB fused CRISPR/dCas9 system can robustly prevent the HIV-1 latency reactivation process, mediated by PMA or IngB and SAHA or Panobinostat, both in myeloid and lymphoid HIV-1 latently infected cells. In addition, we demonstrated that KRAB repressor protein is crucial to reactivation resistance phenotype, and we have identified some useful hotspots sequences in HIV-1 LTR for the design sgRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-022-00600-9.
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Affiliation(s)
- Lendel Correia da Costa
- Departamento de Genética, Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av Carlos Chagas Filho 373, CCS, Bloco A, Sala 121, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Larissa Maciel Bomfim
- Departamento de Genética, Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av Carlos Chagas Filho 373, CCS, Bloco A, Sala 121, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Uilla Victoria Torres Dittz
- Departamento de Genética, Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av Carlos Chagas Filho 373, CCS, Bloco A, Sala 121, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Camila de Almeida Velozo
- Departamento de Genética, Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av Carlos Chagas Filho 373, CCS, Bloco A, Sala 121, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodrigo Delvecchio da Cunha
- Departamento de Genética, Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av Carlos Chagas Filho 373, CCS, Bloco A, Sala 121, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av Carlos Chagas Filho 373, CCS, Bloco A, Sala 121, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil.
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29
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Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
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Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
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30
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Govindarajan S, Borges A, Karambelkar S, Bondy-Denomy J. Distinct Subcellular Localization of a Type I CRISPR Complex and the Cas3 Nuclease in Bacteria. J Bacteriol 2022; 204:e0010522. [PMID: 35389256 PMCID: PMC9112876 DOI: 10.1128/jb.00105-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 12/30/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems are prokaryotic adaptive immune systems that have been well characterized biochemically, but in vivo spatiotemporal regulation and cell biology remain largely unaddressed. Here, we used fluorescent fusion proteins introduced at the chromosomal CRISPR-Cas locus to study the localization of the type I-F CRISPR-Cas system in Pseudomonas aeruginosa. When lacking a target in the cell, the Cascade complex is broadly nucleoid bound, while Cas3 is diffuse in the cytoplasm. When targeted to an integrated prophage, however, the CRISPR RNA (crRNA)-guided type I-F Cascade complex and a majority of Cas3 molecules in the cell are recruited to a single focus. Nucleoid association of the Csy proteins that form the Cascade complex is crRNA dependent and specifically inhibited by the expression of anti-CRISPR AcrIF2, which blocks protospacer adjacent motif (PAM) binding. The Cas9 nuclease is also nucleoid localized, only when single guide RNA (sgRNA) bound, which is abolished by the PAM-binding inhibitor AcrIIA4. Our findings reveal PAM-dependent nucleoid surveillance and spatiotemporal regulation in type I CRISPR-Cas that separates the nuclease-helicase Cas3 from the crRNA-guided surveillance complex. IMPORTANCE CRISPR-Cas systems, the prokaryotic adaptive immune systems, are largely understood using structural biology, biochemistry, and genetics. How CRISPR-Cas effectors are organized within cells is currently not well understood. By investigating the cell biology of the type I-F CRISPR-Cas system, we show that the surveillance complex, which "patrols" the cell to find targets, is largely nucleoid bound, while Cas3 nuclease is cytoplasmic. Nucleoid localization is also conserved for class 2 CRISPR-Cas single protein effector Cas9. Our observation of differential localization of the surveillance complex and Cas3 reveals a new layer of posttranslational spatiotemporal regulation to prevent autoimmunity.
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Affiliation(s)
- Sutharsan Govindarajan
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adair Borges
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Shweta Karambelkar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA
- Innovative Genomics Institute, Berkeley, California, USA
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31
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Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA. CRISPR-Cas9 bends and twists DNA to read its sequence. Nat Struct Mol Biol 2022; 29:395-402. [PMID: 35422516 PMCID: PMC9189902 DOI: 10.1038/s41594-022-00756-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 12/28/2022]
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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32
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Wu T, Cao Y, Liu Q, Wu X, Shang Y, Piao J, Li Y, Dong Y, Liu D, Wang H, Liu J, Ding B. Genetically Encoded Double-Stranded DNA-Based Nanostructure Folded by a Covalently Bivalent CRISPR/dCas System. J Am Chem Soc 2022; 144:6575-6582. [PMID: 35357193 DOI: 10.1021/jacs.2c01760] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA nanotechnology has been widely employed in the construction of various functional nanostructures. However, most DNA nanostructures rely on hybridization between multiple single-stranded DNAs. Herein, we report a general strategy for the construction of a double-stranded DNA-ribonucleoprotein (RNP) hybrid nanostructure by folding double-stranded DNA with a covalently bivalent clustered regularly interspaced short palindromic repeats (CRISPR)/nuclease-dead CRISPR-associated protein (dCas) system. In our design, dCas9 and dCas12a can be efficiently fused together through a flexible and stimuli-responsive peptide linker. After activation by guide RNAs, the covalently bivalent dCas9-12a RNPs (staples) can precisely recognize their target sequences in the double-stranded DNA scaffold and pull them together to construct a series of double-stranded DNA-RNP hybrid nanostructures. The genetically encoded hybrid nanostructure can protect genetic information in the folded state, similar to the natural DNA-protein hybrids present in chromosomes, and elicit efficient stimuli-responsive gene transcription in the unfolded form. This rationally developed double-stranded DNA folding and unfolding strategy presents a new avenue for the development of DNA nanotechnology.
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Affiliation(s)
- Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yuanwei Cao
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiafang Piao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Haoyi Wang
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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33
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dCas9-based gene editing for cleavage-free genomic knock-in of long sequences. Nat Cell Biol 2022; 24:268-278. [PMID: 35145221 PMCID: PMC8843813 DOI: 10.1038/s41556-021-00836-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 12/21/2021] [Indexed: 12/14/2022]
Abstract
Gene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering. Wang, Qu et al. developed a genome-editing system, utilizing catalytically inactive Cas9 fused to microbial single-strand annealing proteins, for kilobase-scale insertion in human cells without introducing DNA nicks or breaks.
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34
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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35
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Reint G, Li Z, Labun K, Keskitalo S, Soppa I, Mamia K, Tolo E, Szymanska M, Meza-Zepeda LA, Lorenz S, Cieslar-Pobuda A, Hu X, Bordin DL, Staerk J, Valen E, Schmierer B, Varjosalo M, Taipale J, Haapaniemi E. Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLife 2021; 10:75415. [PMID: 34898428 PMCID: PMC8747517 DOI: 10.7554/elife.75415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein-Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.
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Affiliation(s)
- Ganna Reint
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Zhuokun Li
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Kornel Labun
- Department of Informatics, Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Salla Keskitalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Inkeri Soppa
- Centre for Molecular Medicine, University of Oslo, Oslo, Finland
| | - Katariina Mamia
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eero Tolo
- Faculty of Social Sciences, University of Helsinki, Oslo, Finland
| | | | - Leonardo A Meza-Zepeda
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Xian Hu
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Diana L Bordin
- Department of Clinical Molecular Biology, Akershus University Hospital, Oslo, Norway
| | - Judith Staerk
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
| | - Eivind Valen
- Center for Biotechnology, University of Bergen, Bergen, Norway
| | - Bernhard Schmierer
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markku Varjosalo
- Centre for Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emma Haapaniemi
- Centre for Molecular Medicine, University of Oslo, Oslo, Norway
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36
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Aldag P, Welzel F, Jakob L, Schmidbauer A, Rutkauskas M, Fettes F, Grohmann D, Seidel R. Probing the stability of the SpCas9-DNA complex after cleavage. Nucleic Acids Res 2021; 49:12411-12421. [PMID: 34792162 PMCID: PMC8643700 DOI: 10.1093/nar/gkab1072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 and its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding stability of different Streptococcus pyogenes Cas9 variants after cleavage by challenging them with supercoiling. We find that different release mechanisms occur depending on which DNA strand is cleaved. After initial target strand cleavage, supercoils are only removed after the collapse of the R-loop. We identified several states with different stabilities of the R-loop. Most importantly, we find that the post-cleavage state of Cas9 exhibits a higher stability than the pre-cleavage state. After non-target strand cleavage, supercoils are immediately but slowly released by swiveling of the non-target strand around Cas9 bound to the target strand. Consequently, Cas9 and its non-target strand nicking mutant stay stably bound to the DNA for many hours even at elevated torsional stress.
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Affiliation(s)
- Pierre Aldag
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fabian Welzel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fergus Fettes
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
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37
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Zhang Q, Chen Z, Wang F, Zhang S, Chen H, Gu X, Wen F, Jin J, Zhang X, Huang X, Shen B, Sun B. Efficient DNA interrogation of SpCas9 governed by its electrostatic interaction with DNA beyond the PAM and protospacer. Nucleic Acids Res 2021; 49:12433-12444. [PMID: 34850124 PMCID: PMC8643646 DOI: 10.1093/nar/gkab1139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pyogenes Cas9 (SpCas9), a programmable RNA-guided DNA endonuclease, has been widely repurposed for biological and medical applications. Critical interactions between SpCas9 and DNA confer the high specificity of the enzyme in genome engineering. Here, we unveil that an essential SpCas9–DNA interaction located beyond the protospacer adjacent motif (PAM) is realized through electrostatic forces between four positively charged lysines among SpCas9 residues 1151–1156 and the negatively charged DNA backbone. Modulating this interaction by substituting lysines with amino acids that have distinct charges revealed a strong dependence of DNA target binding and cleavage activities of SpCas9 on the charge. Moreover, the SpCas9 mutants show markedly distinguishable DNA interaction sites beyond the PAM compared with wild-type SpCas9. Functionally, this interaction governs DNA sampling and participates in protospacer DNA unwinding during DNA interrogation. Overall, a mechanistic and functional understanding of this vital interaction explains how SpCas9 carries out efficient DNA interrogation.
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Affiliation(s)
- Qian Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziting Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fangzhu Wang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Siqi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyu Chen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Xueying Gu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Fengcai Wen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiachuan Jin
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Gene Editing Center, ShanghaiTech University, Shanghai 201210, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Gusu School, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Gene Editing Center, ShanghaiTech University, Shanghai 201210, China
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38
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Detection of pks Island mRNAs Using Toehold Sensors in Escherichia coli. Life (Basel) 2021; 11:life11111280. [PMID: 34833155 PMCID: PMC8625898 DOI: 10.3390/life11111280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/14/2022] Open
Abstract
Synthetic biologists have applied biomolecular engineering approaches toward the goal of novel biological devices and have shown progress in diverse areas of medicine and biotechnology. Especially promising is the application of synthetic biological devices towards a novel class of molecular diagnostics. As an example, a de-novo-designed riboregulator called toehold switch, with its programmability and compatibility with field-deployable devices showed promising in vitro applications for viral RNA detection such as Zika and Corona viruses. However, the in vivo application of high-performance RNA sensors remains challenging due to the secondary structure of long mRNA species. Here, we introduced ‘Helper RNAs’ that can enhance the functionality of toehold switch sensors by mitigating the effect of secondary structures around a target site. By employing the helper RNAs, previously reported mCherry mRNA sensor showed improved fold-changes in vivo. To further generalize the Helper RNA approaches, we employed automatic design pipeline for toehold sensors that target the essential genes within the pks island, an important target of biomedical research in connection with colorectal cancer. The toehold switch sensors showed fold-changes upon the expression of full-length mRNAs that apparently depended sensitively on the identity of the gene as well as the predicted local structure within the target region of the mRNA. Still, the helper RNAs could improve the performance of toehold switch sensors in many instances, with up to 10-fold improvement over no helper cases. These results suggest that the helper RNA approaches can further assist the design of functional RNA devices in vivo with the aid of the streamlined automatic design software developed here. Further, our solutions for screening and stabilizing single-stranded region of mRNA may find use in other in vivo mRNA-sensing applications such as cas13 crRNA design, transcriptome engineering, and trans-cleaving ribozymes.
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39
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Lu Q, Bhat D, Stepanenko D, Pigolotti S. Search and Localization Dynamics of the CRISPR-Cas9 System. PHYSICAL REVIEW LETTERS 2021; 127:208102. [PMID: 34860046 DOI: 10.1103/physrevlett.127.208102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The CRISPR-Cas9 system acts as the prokaryotic immune system and has important applications in gene editing. The protein Cas9 is one of its crucial components. The role of Cas9 is to search for specific target sequences on the DNA and cleave them. In this Letter, we introduce a model of facilitated diffusion for Cas9 and fit its parameters to single-molecule experiments. Our model confirms that Cas9 search for targets by sliding, but shows that its sliding length is rather short. We then investigate how Cas9 explores a long stretch of DNA containing randomly placed targets. We solve this problem by mapping it into the theory of Anderson localization in condensed matter physics. Our theoretical approach rationalizes experimental evidence on the distribution of Cas9 molecules along the DNA.
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Affiliation(s)
- Qiao Lu
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Deepak Bhat
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Darya Stepanenko
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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40
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Hirschenberger M, Stadler N, Fellermann M, Sparrer KMJ, Kirchhoff F, Barth H, Papatheodorou P. CRISPA: A Non-viral, Transient Cas9 Delivery System Based on Reengineered Anthrax Toxin. Front Pharmacol 2021; 12:770283. [PMID: 34733166 PMCID: PMC8558532 DOI: 10.3389/fphar.2021.770283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
Translating the CRISPR/Cas9 genome editing technology into clinics is still hampered by rather unspecific, unsafe and/or inconvenient approaches for the delivery of its main components - the Cas9 endonuclease and a guide RNA - into cells. Here, we describe the development of a novel transient and non-viral Cas9 delivery strategy based on the translocation machinery of the Bacillus anthracis anthrax toxin, PA (protective antigen). We show that Cas9 variants fused to the N-terminus of the lethal factor or to a hexahistidine tag are shuttled through channels formed by PA into the cytosol of human cells. As proof-of-principle, we applied our new approach, denoted as CRISPA, to knock out lipolysis-stimulated lipoprotein receptor (LSR) in the human colon cancer cell line HCT116 and green-fluorescent protein (GFP) in human embryonic kidney 293T cells stably expressing GFP. Notably, we confirmed that the transporter PA can be adapted to recognize specific host cell-surface receptor proteins and may be optimized for cell type-selective delivery of Cas9. Altogether, CRISPA provides a novel, transient and non-viral way to deliver Cas9 into specific cells. Thus, this system is an additional step towards safe translation of the CRISPR/Cas9 technology into clinics.
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Affiliation(s)
- Maximilian Hirschenberger
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany.,Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Nicole Stadler
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Maximilian Fellermann
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Holger Barth
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
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41
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Anderson DA, Voigt CA. Competitive dCas9 binding as a mechanism for transcriptional control. Mol Syst Biol 2021; 17:e10512. [PMID: 34747560 PMCID: PMC8574044 DOI: 10.15252/msb.202110512] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022] Open
Abstract
Catalytically dead Cas9 (dCas9) is a programmable transcription factor that can be targeted to promoters through the design of small guide RNAs (sgRNAs), where it can function as an activator or repressor. Natural promoters use overlapping binding sites as a mechanism for signal integration, where the binding of one can block, displace, or augment the activity of the other. Here, we implemented this strategy in Escherichia coli using pairs of sgRNAs designed to repress and then derepress transcription through competitive binding. When designed to target a promoter, this led to 27-fold repression and complete derepression. This system was also capable of ratiometric input comparison over two orders of magnitude. Additionally, we used this mechanism for promoter sequence-independent control by adopting it for elongation control, achieving 8-fold repression and 4-fold derepression. This work demonstrates a new genetic control mechanism that could be used to build analog circuit or implement cis-regulatory logic on CRISPRi-targeted native genes.
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Affiliation(s)
- Daniel A Anderson
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Christopher A Voigt
- Synthetic Biology CenterDepartment of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
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42
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Bergenholm D, Dabirian Y, Ferreira R, Siewers V, David F, Nielsen J. Rational gRNA design based on transcription factor binding data. Synth Biol (Oxf) 2021; 6:ysab014. [PMID: 34712839 PMCID: PMC8546606 DOI: 10.1093/synbio/ysab014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/21/2021] [Accepted: 06/08/2021] [Indexed: 11/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has become a standard tool in many genome engineering endeavors. The endonuclease-deficient version of Cas9 (dCas9) is also a powerful programmable tool for gene regulation. In this study, we made use of Saccharomyces cerevisiae transcription factor (TF) binding data to obtain a better understanding of the interplay between TF binding and binding of dCas9 fused to an activator domain, VPR. More specifically, we targeted dCas9–VPR toward binding sites of Gcr1–Gcr2 and Tye7 present in several promoters of genes encoding enzymes engaged in the central carbon metabolism. From our data, we observed an upregulation of gene expression when dCas9–VPR was targeted next to a TF binding motif, whereas a downregulation or no change was observed when dCas9 was bound on a TF motif. This suggests a steric competition between dCas9 and the specific TF. Integrating TF binding data, therefore, proved to be useful for designing guide RNAs for CRISPR interference or CRISPR activation applications.
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Affiliation(s)
- David Bergenholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yasaman Dabirian
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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43
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Yang M, Sun R, Deng P, Yang Y, Wang W, Liu JJG, Chen C. Nonspecific interactions between SpCas9 and dsDNA sites located downstream of the PAM mediate facilitated diffusion to accelerate target search. Chem Sci 2021; 12:12776-12784. [PMID: 34703564 PMCID: PMC8494019 DOI: 10.1039/d1sc02633j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/19/2021] [Indexed: 12/27/2022] Open
Abstract
RNA-guided Streptococcus pyogenes Cas9 (SpCas9) is a sequence-specific DNA endonuclease that works as one of the most powerful genetic editing tools. However, how Cas9 locates its target among huge amounts of dsDNAs remains elusive. Here, combining biochemical and single-molecule fluorescence assays, we revealed that Cas9 uses both three-dimensional and one-dimensional diffusion to find its target with high efficiency. We further observed surprising apparent asymmetric target search regions flanking PAM sites on dsDNA under physiological salt conditions, which accelerates the target search efficiency of Cas9 by ∼10-fold. Illustrated by a cryo-EM structure of the Cas9/sgRNA/dsDNA dimer, non-specific interactions between DNA ∼8 bp downstream of the PAM site and lysines within residues 1151–1156 of Cas9, especially lys1153, are the key elements to mediate the one-dimensional diffusion of Cas9 and cause asymmetric target search regions flanking the PAM. Disrupting these non-specific interactions, such as mutating these lysines to alanines, diminishes the contribution of one-dimensional diffusion and reduces the target search rate by several times. In addition, low ionic concentrations or mutations on PAM recognition residues that modulate interactions between Cas9 and dsDNA alter apparent asymmetric target search behaviors. Together, our results reveal a unique searching mechanism of Cas9 under physiological salt conditions, and provide important guidance for both in vitro and in vivo applications of Cas9. Nonspecific interactions between DNA ∼8 bp downstream of the PAM and lysines within residues 1151–1156 of Cas9 mediate one-dimensional diffusion and cause asymmetric target search regions flanking the PAM.![]()
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Affiliation(s)
- Mengyi Yang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University Beijing China .,Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institutue, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health Beijing 100045 China
| | - Ruirui Sun
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University Beijing China
| | - Pujuan Deng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University Beijing China
| | - Yuzhuo Yang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University Beijing China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University Beijing China
| | - Jun-Jie Gogo Liu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University Beijing China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University Beijing China
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44
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Zentout S, Smith R, Jacquier M, Huet S. New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells. Front Cell Dev Biol 2021; 9:730998. [PMID: 34589495 PMCID: PMC8473836 DOI: 10.3389/fcell.2021.730998] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
DNA repair requires a coordinated effort from an array of factors that play different roles in the DNA damage response from recognizing and signaling the presence of a break, creating a repair competent environment, and physically repairing the lesion. Due to the rapid nature of many of these events, live-cell microscopy has become an invaluable method to study this process. In this review we outline commonly used tools to induce DNA damage under the microscope and discuss spatio-temporal analysis tools that can bring added information regarding protein dynamics at sites of damage. In particular, we show how to go beyond the classical analysis of protein recruitment curves to be able to assess the dynamic association of the repair factors with the DNA lesions as well as the target-search strategies used to efficiently find these lesions. Finally, we discuss how the use of mathematical models, combined with experimental evidence, can be used to better interpret the complex dynamics of repair proteins at DNA lesions.
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Affiliation(s)
- Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Marine Jacquier
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, Rennes, France
- Institut Universitaire de France, Paris, France
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45
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Wiktor J, Gynnå AH, Leroy P, Larsson J, Coceano G, Testa I, Elf J. RecA finds homologous DNA by reduced dimensionality search. Nature 2021; 597:426-429. [PMID: 34471288 PMCID: PMC8443446 DOI: 10.1038/s41586-021-03877-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/04/2021] [Indexed: 11/21/2022]
Abstract
Homologous recombination is essential for the accurate repair of double-stranded DNA breaks (DSBs)1. Initially, the RecBCD complex2 resects the ends of the DSB into 3' single-stranded DNA on which a RecA filament assembles3. Next, the filament locates the homologous repair template on the sister chromosome4. Here we directly visualize the repair of DSBs in single cells, using high-throughput microfluidics and fluorescence microscopy. We find that, in Escherichia coli, repair of DSBs between segregated sister loci is completed in 15 ± 5 min (mean ± s.d.) with minimal fitness loss. We further show that the search takes less than 9 ± 3 min (mean ± s.d) and is mediated by a thin, highly dynamic RecA filament that stretches throughout the cell. We propose that the architecture of the RecA filament effectively reduces search dimensionality. This model predicts a search time that is consistent with our measurement and is corroborated by the observation that the search time does not depend on the length of the cell or the amount of DNA. Given the abundance of RecA homologues5, we believe this model to be widely conserved across living organisms.
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Affiliation(s)
- Jakub Wiktor
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arvid H Gynnå
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Prune Leroy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jimmy Larsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Giovanna Coceano
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ilaria Testa
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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46
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Ciurkot K, Gorochowski TE, Roubos JA, Verwaal R. Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a. Nucleic Acids Res 2021; 49:7775-7790. [PMID: 34197613 PMCID: PMC8287914 DOI: 10.1093/nar/gkab529] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/27/2022] Open
Abstract
CRISPR Cas12a is an RNA-programmable endonuclease particularly suitable for gene regulation. This is due to its preference for T-rich PAMs that allows it to more easily target AT-rich promoter sequences, and built-in RNase activity which can process a single CRISPR RNA array encoding multiple spacers into individual guide RNAs (gRNAs), thereby simplifying multiplexed gene regulation. Here, we develop a flexible dCas12a-based CRISPRi system for Saccharomyces cerevisiae and systematically evaluate its design features. This includes the role of the NLS position, use of repression domains, and the position of the gRNA target. Our optimal system is comprised of dCas12a E925A with a single C-terminal NLS and a Mxi1 or a MIG1 repression domain, which enables up to 97% downregulation of a reporter gene. We also extend this system to allow for inducible regulation via an RNAP II-controlled promoter, demonstrate position-dependent effects in crRNA arrays, and use multiplexed regulation to stringently control a heterologous β-carotene pathway. Together these findings offer valuable insights into the design constraints of dCas12a-based CRISPRi and enable new avenues for flexible and efficient gene regulation in S. cerevisiae.
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Affiliation(s)
- Klaudia Ciurkot
- DSM Biotechnology Center, Delft 2613 AX, The Netherlands.,Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK
| | | | - René Verwaal
- DSM Biotechnology Center, Delft 2613 AX, The Netherlands
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47
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Banerjee T, Takahashi H, Subekti DRG, Kamagata K. Engineering of the genome editing protein Cas9 to slide along DNA. Sci Rep 2021; 11:14165. [PMID: 34239016 PMCID: PMC8266852 DOI: 10.1038/s41598-021-93685-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022] Open
Abstract
The genome editing protein Cas9 faces engineering challenges in improving off-target DNA cleavage and low editing efficiency. In this study, we aimed to engineer Cas9 to be able to slide along DNA, which might facilitate genome editing and reduce off-target cleavage. We used two approaches to achieve this: reducing the sliding friction along DNA by removing the interactions of Cas9 residues with DNA and facilitating sliding by introducing the sliding-promoting tail of Nhp6A. Seven engineered mutants of Cas9 were prepared, and their performance was tested using single-molecule fluorescence microscopy. Comparison of the mutations enabled the identification of key residues of Cas9 to enhance the sliding along DNA in the presence and absence of single guide RNA (sgRNA). The attachment of the tail to Cas9 mutants enhanced sliding along DNA, particularly in the presence of sgRNA. Together, using the proposed approaches, the sliding ability of Cas9 was improved up to eightfold in the presence of sgRNA. A sliding model of Cas9 and its engineering action are discussed herein.
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Affiliation(s)
- Trishit Banerjee
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Hiroto Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Dwiky Rendra Graha Subekti
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.
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Khakimzhan A, Garenne D, Tickman B, Fontana J, Carothers J, Noireaux V. Complex dependence of CRISPR-Cas9 binding strength on guide RNA spacer lengths. Phys Biol 2021; 18:056003. [PMID: 34102625 DOI: 10.1088/1478-3975/ac091e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022]
Abstract
It is established that for CRISPR-Cas9 applications guide RNAs with 17-20 bp long spacer sequences are optimal for accurate target binding and cleavage. In this work we perform cell-free CRISPRa (CRISPR activation) and CRISPRi (CRISPR inhibition) experiments to demonstrate the existence of a complex dependence of CRISPR-Cas9 binding as a function of the spacer length and complementarity. Our results show that significantly truncated or mismatched spacer sequences can form stronger guide-target bonds than the conventional 17-20 bp long spacers. To explain this phenomenon, we take into consideration previous structural and single-molecule CRISPR-Cas9 experiments and develop a novel thermodynamic model of CRISPR-Cas9 target recognition.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States of America
| | - David Garenne
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States of America
| | - Benjamin Tickman
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States of America
| | - Jason Fontana
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States of America
| | - James Carothers
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, United States of America
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, United States of America
- Center for Synthetic Biology, University of Washington, Seattle, WA, 98195, United States of America
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street SE, Minneapolis, MN 55455, United States of America
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Wu X, Zhu J, Tao P, Rao VB. Bacteriophage T4 Escapes CRISPR Attack by Minihomology Recombination and Repair. mBio 2021; 12:e0136121. [PMID: 34154416 PMCID: PMC8262927 DOI: 10.1128/mbio.01361-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 01/05/2023] Open
Abstract
Bacteria and bacteriophages (phages) have evolved potent defense and counterdefense mechanisms that allowed their survival and greatest abundance on Earth. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) is a bacterial defense system that inactivates the invading phage genome by introducing double-strand breaks at targeted sequences. While the mechanisms of CRISPR defense have been extensively investigated, the counterdefense mechanisms employed by phages are poorly understood. Here, we report a novel counterdefense mechanism by which phage T4 restores the genomes broken by CRISPR cleavages. Catalyzed by the phage-encoded recombinase UvsX, this mechanism pairs very short stretches of sequence identity (minihomology sites), as few as 3 or 4 nucleotides in the flanking regions of the cleaved site, allowing replication, repair, and stitching of genomic fragments. Consequently, a series of deletions are created at the targeted site, making the progeny genomes completely resistant to CRISPR attack. Our results demonstrate that this is a general mechanism operating against both type II (Cas9) and type V (Cas12a) CRISPR-Cas systems. These studies uncovered a new type of counterdefense mechanism evolved by T4 phage where subtle functional tuning of preexisting DNA metabolism leads to profound impact on phage survival. IMPORTANCE Bacteriophages (phages) are viruses that infect bacteria and use them as replication factories to assemble progeny phages. Bacteria have evolved powerful defense mechanisms to destroy the invading phages by severing their genomes soon after entry into cells. We discovered a counterdefense mechanism evolved by phage T4 to stitch back the broken genomes and restore viral infection. In this process, a small amount of genetic material is deleted or another mutation is introduced, making the phage resistant to future bacterial attack. The mutant virus might also gain survival advantages against other restriction conditions or DNA damaging events. Thus, bacterial attack not only triggers counterdefenses but also provides opportunities to generate more fit phages. Such defense and counterdefense mechanisms over the millennia led to the extraordinary diversity and the greatest abundance of bacteriophages on Earth. Understanding these mechanisms will open new avenues for engineering recombinant phages for biomedical applications.
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Affiliation(s)
- Xiaorong Wu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Jingen Zhu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Pan Tao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
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Corbella M, Liao Q, Moreira C, Parracino A, Kasson PM, Kamerlin SCL. The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition. J Phys Chem B 2021; 125:6791-6806. [PMID: 34137249 PMCID: PMC8279559 DOI: 10.1021/acs.jpcb.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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DNA-binding proteins
play an important role in gene regulation
and cellular function. The transcription factors MarA and Rob are
two homologous members of the AraC/XylS family that regulate multidrug
resistance. They share a common DNA-binding domain, and Rob possesses
an additional C-terminal domain that permits binding of low-molecular
weight effectors. Both proteins possess two helix-turn-helix (HTH)
motifs capable of binding DNA; however, while MarA interacts with
its promoter through both HTH-motifs, prior studies indicate that
Rob binding to DNA via a single HTH-motif is sufficient for tight
binding. In the present work, we perform microsecond time scale all-atom
simulations of the binding of both transcription factors to different
DNA sequences to understand the determinants of DNA recognition and
binding. Our simulations characterize sequence-dependent changes in
dynamical behavior upon DNA binding, showcasing the role of Arg40
of the N-terminal HTH-motif in allowing for specific tight binding.
Finally, our simulations demonstrate that an acidic C-terminal loop
of Rob can control the DNA binding mode, facilitating interconversion
between the distinct DNA binding modes observed in MarA and Rob. In
doing so, we provide detailed molecular insight into DNA binding and
recognition by these proteins, which in turn is an important step
toward the efficient design of antivirulence agents that target these
proteins.
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Affiliation(s)
- Marina Corbella
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Cátia Moreira
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Antonietta Parracino
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-65124, Sweden.,Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, United States
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