1
|
Zhang X, Blumenthal RM, Cheng X. Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins. Curr Opin Struct Biol 2024; 87:102836. [PMID: 38754172 DOI: 10.1016/j.sbi.2024.102836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
C2H2 zinc-finger (ZF) proteins form the largest family of DNA-binding transcription factors coded by mammalian genomes. In a typical DNA-binding ZF module, there are twelve residues (numbered from -1 to -12) between the last zinc-coordinating cysteine and the first zinc-coordinating histidine. The established C2H2-ZF "recognition code" suggests that residues at positions -1, -4, and -7 recognize the 5', central, and 3' bases of a DNA base-pair triplet, respectively. Structural studies have highlighted that additional residues at positions -5 and -8 also play roles in specific DNA recognition. The presence of bulky and either charged or polar residues at these five positions determines specificity for given DNA bases: guanine is recognized by arginine, lysine, or histidine; adenine by asparagine or glutamine; thymine or 5-methylcytosine by glutamate; and unmodified cytosine by aspartate. This review discusses recent structural characterizations of C2H2-ZFs that add to our understanding of the principles underlying the C2H2-ZF recognition code.
Collapse
Affiliation(s)
- Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
2
|
Foster MP, Benedek MJ, Billings TD, Montgomery JS. Dynamics in Cre-loxP site-specific recombination. Curr Opin Struct Biol 2024; 88:102878. [PMID: 39029281 DOI: 10.1016/j.sbi.2024.102878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/21/2024]
Abstract
Cre recombinase is a phage-derived enzyme that has found utility for precise manipulation of DNA sequences. Cre recognizes and recombines pairs of loxP sequences characterized by an inverted repeat and asymmetric spacer. Cre cleaves and religates its DNA targets such that error-prone repair pathways are not required to generate intact DNA products. Major obstacles to broader applications are lack of knowledge of how Cre recognizes its targets, and how its activity is controlled. The picture emerging from high resolution methods is that the dynamic properties of both the enzyme and its DNA target are important determinants of its activity in both sequence recognition and DNA cleavage. Improved understanding of the role of dynamics in the key steps along the pathway of Cre-loxP recombination should significantly advance our ability to both redirect Cre to new sequences and to control its DNA cleavage activity in the test tube and in cells.
Collapse
Affiliation(s)
- Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
| | - Matthew J Benedek
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tyler D Billings
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
3
|
Bisht D, Salave S, Desai N, Gogoi P, Rana D, Biswal P, Sarma G, Benival D, Kommineni N, Desai D. Genome editing and its role in vaccine, diagnosis, and therapeutic advancement. Int J Biol Macromol 2024; 269:131802. [PMID: 38670178 DOI: 10.1016/j.ijbiomac.2024.131802] [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: 11/05/2023] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
Genome editing involves precise modification of specific nucleotides in the genome using nucleases like CRISPR/Cas, ZFN, or TALEN, leading to increased efficiency of homologous recombination (HR) for gene editing, and it can result in gene disruption events via non-homologous end joining (NHEJ) or homology-driven repair (HDR). Genome editing, particularly CRISPR-Cas9, revolutionizes vaccine development by enabling precise modifications of pathogen genomes, leading to enhanced vaccine efficacy and safety. It allows for tailored antigen optimization, improved vector design, and deeper insights into host genes' impact on vaccine responses, ultimately enhancing vaccine development and manufacturing processes. This review highlights different types of genome editing methods, their associated risks, approaches to overcome the shortcomings, and the diverse roles of genome editing.
Collapse
Affiliation(s)
- Deepanker Bisht
- ICAR- Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India
| | - Purnima Gogoi
- School of Medicine and Public Health, University of Wisconsin and Madison, Madison, WI 53726, USA
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Prachurya Biswal
- College of Veterinary and Animal Sciences, Bihar Animal Sciences University, Kishanganj 855115, Bihar, India
| | - Gautami Sarma
- College of Veterinary & Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, U.S. Nagar, Uttarakhand, India
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India.
| | | | - Dhruv Desai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
4
|
Li X, Chen Z, Ye W, Yu J, Zhang X, Li Y, Niu Y, Ran S, Wang S, Luo Z, Zhao J, Hao Y, Zong J, Xia C, Xia J, Wu J. High-throughput CRISPR technology: a novel horizon for solid organ transplantation. Front Immunol 2024; 14:1295523. [PMID: 38239344 PMCID: PMC10794540 DOI: 10.3389/fimmu.2023.1295523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.
Collapse
Affiliation(s)
- Xiaohan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weicong Ye
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhang Yu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Niu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuan Ran
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Song Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilong Luo
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiulu Zhao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanglin Hao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjie Zong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengkun Xia
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Jie Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| |
Collapse
|
5
|
Sherkatghanad Z, Abdar M, Charlier J, Makarenkov V. Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review. Brief Bioinform 2023; 24:7130974. [PMID: 37080758 DOI: 10.1093/bib/bbad131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9) is a popular and effective two-component technology used for targeted genetic manipulation. It is currently the most versatile and accurate method of gene and genome editing, which benefits from a large variety of practical applications. For example, in biomedicine, it has been used in research related to cancer, virus infections, pathogen detection, and genetic diseases. Current CRISPR/Cas9 research is based on data-driven models for on- and off-target prediction as a cleavage may occur at non-target sequence locations. Nowadays, conventional machine learning and deep learning methods are applied on a regular basis to accurately predict on-target knockout efficacy and off-target profile of given single-guide RNAs (sgRNAs). In this paper, we present an overview and a comparative analysis of traditional machine learning and deep learning models used in CRISPR/Cas9. We highlight the key research challenges and directions associated with target activity prediction. We discuss recent advances in the sgRNA-DNA sequence encoding used in state-of-the-art on- and off-target prediction models. Furthermore, we present the most popular deep learning neural network architectures used in CRISPR/Cas9 prediction models. Finally, we summarize the existing challenges and discuss possible future investigations in the field of on- and off-target prediction. Our paper provides valuable support for academic and industrial researchers interested in the application of machine learning methods in the field of CRISPR/Cas9 genome editing.
Collapse
Affiliation(s)
- Zeinab Sherkatghanad
- Departement d'Informatique, Universite du Quebec a Montreal, H2X 3Y7, Montreal, QC, Canada
| | - Moloud Abdar
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, 3216, Geelong, VIC, Australia
| | - Jeremy Charlier
- Departement d'Informatique, Universite du Quebec a Montreal, H2X 3Y7, Montreal, QC, Canada
| | - Vladimir Makarenkov
- Departement d'Informatique, Universite du Quebec a Montreal, H2X 3Y7, Montreal, QC, Canada
| |
Collapse
|
6
|
Sufyan M, Daraz U, Hyder S, Zulfiqar U, Iqbal R, Eldin SM, Rafiq F, Mahmood N, Shahzad K, Uzair M, Fiaz S, Ali I. An overview of genome engineering in plants, including its scope, technologies, progress and grand challenges. Funct Integr Genomics 2023; 23:119. [PMID: 37022538 DOI: 10.1007/s10142-023-01036-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
Genome editing is a useful, adaptable, and favored technique for both functional genomics and crop enhancement. Over the years, rapidly evolving genome editing technologies, including clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas), transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs), have shown broad application prospects in gene function research and improvement of critical agronomic traits in many crops. These technologies have also opened up opportunities for plant breeding. These techniques provide excellent chances for the quick modification of crops and the advancement of plant science in the future. The current review describes various genome editing techniques and how they function, particularly CRISPR/Cas9 systems, which can contribute significantly to the most accurate characterization of genomic rearrangement and plant gene functions as well as the enhancement of critical traits in field crops. To accelerate the use of gene-editing technologies for crop enhancement, the speed editing strategy of gene-family members was designed. As it permits genome editing in numerous biological systems, the CRISPR technology provides a valuable edge in this regard that particularly captures the attention of scientists.
Collapse
Affiliation(s)
- Muhammad Sufyan
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Umar Daraz
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Sajjad Hyder
- Department of Botant, Government College Women University, Sialkot, Pakistan
| | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Rashid Iqbal
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Sayed M Eldin
- Center of Research, Faculty of Engineering, Future University in Egypt, New Cairo, 11835, Egypt
| | - Farzana Rafiq
- School of Environmental Sciences and Engineering, NCEPU, Beijing, China
| | - Naveed Mahmood
- College of Biological Sciences, China Agricultural University, Beijing, 100083, China
| | - Khurram Shahzad
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Park Road, Islamabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan
| | - Iftikhar Ali
- Center for Plant Sciences and Biodiversity, University of Swat, Charbagh, 19120, Pakistan.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| |
Collapse
|
7
|
Luo S, Xiong D, Zhao X, Duan L. An Attempt of Seeking Favorable Binding Free Energy Prediction Schemes Considering the Entropic Effect on Fis-DNA Binding. J Phys Chem B 2023; 127:1312-1324. [PMID: 36735878 DOI: 10.1021/acs.jpcb.2c07811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein-DNA binding mechanisms in a complex manner are essential for understanding many biological processes. Over the past decades, numerous experiments and calculations have analyzed the specificity of protein-DNA binding. However, the accuracy of binding free energy prediction for multi-base DNA systems still needs to be improved. Fis is a DNA-binding protein that regulates various transcription and recombination reactions. In the present work, we tested several methods of predict binding free energy based on this system to find a favorable prediction scheme and explore the binding mechanism of Fis protein and DNA. Two solvent models (explicit and implicit solvent models) were chosen for the dynamics process, and the predicted binding free energy was more accurate under the explicit solvent model. When different Poisson-Boltzmann/Generalized Born (PB/GB) models were tested for DNA force fields (BSC1 and OL15), it was found that the binding free energy predicted by the selected OL15 force field performed better and the correlation between predicted and experimental values was improved with the increasing interior dielectric constant (Dk). Finally, using Dk = 8, the GBOBC1 model combined with interaction entropy (IE), which was calculated for entropic contribution (GBOBC1_IE_8), was screened out for the binding free energy prediction and analysis of the Fis-DNA system, and the validity of the method was further verified by testing the Cren7-DNA system. By performing conformational analysis of the minor groove, it was found that mutation of the DNA central sequence A/T to C/G and deletion of the guanine 2-amino group would change the minor groove width and thus affect the formation of the major groove, altering the interaction and atomic contact between the protein and the major groove, thus changing the binding affinity of Fis and DNA. Hopefully, the series of tests in this work can shed some light on the related studies of protein and DNA systems.
Collapse
Affiliation(s)
- Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| | - Danyang Xiong
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan, Shandong250014, China
| |
Collapse
|
8
|
Talluri S. Engineering and Design of Programmable Genome Editors. J Phys Chem B 2022; 126:5140-5150. [PMID: 35819243 DOI: 10.1021/acs.jpcb.2c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Programmable genome editors are enzymes that can be targeted to a specific location in the genome for making site-specific alterations or deletions. The engineering, design, and development of sequence-specific editors has resulted in a dramatic increase in the precision of editing for nucleotide sequences. These editors can target specific locations in a genome, in vivo. The genome editors are being deployed for the development of genetically modified organisms for agriculture and industry, and for gene therapy of inherited human genetic disorders, cancer, and immunotherapy. Experimental and computational studies of structure, binding, activity, dynamics, and folding, reviewed here, have provided valuable insights that have the potential for increasing the functional efficiency of these gene/genome editors. Biochemical and biophysical studies of the specificities of natural and engineered genome editors reveal that increased binding affinity can be detrimental because of the increase of off-target effects and that the engineering and design of genome editors with higher specificity may require modulation and control of the conformational dynamics.
Collapse
Affiliation(s)
- Sekhar Talluri
- Department of Biotechnology, GITAM, Visakhapatnam, India 530045
| |
Collapse
|
9
|
Chaturvedi S, Pablo M, Wolf M, Rosas-Rivera D, Calia G, Kumar AJ, Vardi N, Du K, Glazier J, Ke R, Chan MF, Perelson AS, Weinberger LS. Disrupting autorepression circuitry generates "open-loop lethality" to yield escape-resistant antiviral agents. Cell 2022; 185:2086-2102.e22. [PMID: 35561685 PMCID: PMC9097017 DOI: 10.1016/j.cell.2022.04.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 12/27/2022]
Abstract
Across biological scales, gene-regulatory networks employ autorepression (negative feedback) to maintain homeostasis and minimize failure from aberrant expression. Here, we present a proof of concept that disrupting transcriptional negative feedback dysregulates viral gene expression to therapeutically inhibit replication and confers a high evolutionary barrier to resistance. We find that nucleic-acid decoys mimicking cis-regulatory sites act as "feedback disruptors," break homeostasis, and increase viral transcription factors to cytotoxic levels (termed "open-loop lethality"). Feedback disruptors against herpesviruses reduced viral replication >2-logs without activating innate immunity, showed sub-nM IC50, synergized with standard-of-care antivirals, and inhibited virus replication in mice. In contrast to approved antivirals where resistance rapidly emerged, no feedback-disruptor escape mutants evolved in long-term cultures. For SARS-CoV-2, disruption of a putative feedback circuit also generated open-loop lethality, reducing viral titers by >1-log. These results demonstrate that generating open-loop lethality, via negative-feedback disruption, may yield a class of antimicrobials with a high genetic barrier to resistance.
Collapse
Affiliation(s)
- Sonali Chaturvedi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA.
| | - Michael Pablo
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marie Wolf
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Daniel Rosas-Rivera
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Giuliana Calia
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Arjun J Kumar
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Noam Vardi
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelvin Du
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joshua Glazier
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ruian Ke
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Matilda F Chan
- Francis I. Proctor Foundation, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Leor S Weinberger
- Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
10
|
Pant P, Pathak A, Jayaram B. Bicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations. J Biomol Struct Dyn 2022; 41:4040-4047. [PMID: 35403569 DOI: 10.1080/07391102.2022.2061594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA-protein interactions occur at all levels of DNA expression and replication and are crucial determinants for the survival of a cell. Several modified nucleotides have been utilized to manipulate these interactions and have implications in drug discovery. In the present article, we evaluated the binding of bicyclo-nucleotides (generated by forming a methylene bridge between C1' and C5' in sugar, leading to a bicyclo system with C2' axis of symmetry at the nucleotide level) to proteins. We utilized four ssDNA-protein complexes with experimentally known binding free energies and investigated the binding of modified nucleotides to proteins via all-atom explicit solvent molecular dynamics (MD) simulations (200 ns), and compared the binding with control ssDNA-protein systems. The modified ssDNA displayed enhanced binding to proteins as compared to the control ssDNA, as seen by means of MD simulations followed by MM-PBSA calculations. Further, the Delphi-based electrostatic estimation revealed that the high binding of modified ssDNA to protein might be related to the enhanced electrostatic complementarity displayed by the modified ssDNA molecules in all the four systems considered for the study. The improved binding achieved with modified nucleotides can be utilized to design and develop anticancer/antisense molecules capable of targeting proteins or ssRNAs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Pradeep Pant
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, India
| | - Amita Pathak
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, India
| | - B Jayaram
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India.,Supercomputing Facility for Bioinformatics & Computational Biology, Hauz Khas, New Delhi, India.,Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| |
Collapse
|
11
|
Peterson CW, Venkataraman R, Reddy SS, Pande D, Enstrom MR, Radtke S, Humbert O, Kiem HP. Intracellular RNase activity dampens zinc finger nuclease-mediated gene editing in hematopoietic stem and progenitor cells. Mol Ther Methods Clin Dev 2022; 24:30-39. [PMID: 34977270 PMCID: PMC8671732 DOI: 10.1016/j.omtm.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022]
Abstract
Over the past decade, numerous gene-editing platforms which alter host DNA in a highly specific and targeted fashion have been described. Two notable examples are zinc finger nucleases (ZFNs), the first gene-editing platform to be tested in clinical trials, and more recently, CRISPR/Cas9. Although CRISPR/Cas9 approaches have become arguably the most popular platform in the field, the therapeutic advantages and disadvantages of each strategy are only beginning to emerge. We have established a nonhuman primate (NHP) model that serves as a strong predictor of successful gene therapy and gene-editing approaches in humans; our recent work shows that ZFN-edited hematopoietic stem and progenitor cells (HSPCs) engraft at lower levels than CRISPR/Cas9-edited cells. Here, we investigate the mechanisms underlying this difference. We show that optimized culture conditions, including defined serum-free media, augment engraftment of gene-edited NHP HSPCs in a mouse xenograft model. Furthermore, we identify intracellular RNases as major barriers for mRNA-encoded nucleases relative to preformed enzymatically active CRISPR/Cas9 ribonucleoprotein (RNP) complexes. We conclude that CRISPR/Cas9 RNP gene editing is more stable and efficient than ZFN mRNA-based delivery and identify co-delivered RNase inhibitors as a strategy to enhance the expression of gene-editing proteins from mRNA intermediates.
Collapse
Affiliation(s)
- Christopher W. Peterson
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rasika Venkataraman
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Sowmya S. Reddy
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Dnyanada Pande
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Mark R. Enstrom
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Stefan Radtke
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Olivier Humbert
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
12
|
Nawimanage R, Yuan Z, Casares M, Joshi R, Lohman JR, Gimble FS. Structure-function studies of two yeast homing endonucleases that evolved to cleave identical targets with dissimilar rates and specificities. J Mol Biol 2022; 434:167550. [DOI: 10.1016/j.jmb.2022.167550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
|
13
|
Wang P, Fang X, Du R, Wang J, Liu M, Xu P, Li S, Zhang K, Ye S, You Q, Yang Y, Wang C. Principles of Amino Acid and Nucleotide Revealed by Binding Affinities between Homogeneous Oligopeptides and Single-stranded DNA Molecule s. Chembiochem 2022; 23:e202200048. [PMID: 35191574 DOI: 10.1002/cbic.202200048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Indexed: 11/11/2022]
Abstract
We have determined the binding strengths between nucleotides of adenine, thymine, guanine and cytosine in homogeneous single stranded DNAs and homo-octapeptides consisting of 20 common amino acids. We use a bead-based fluorescence assay for these measurements in which octapeptides are immobilized on the bead surface and ssDNAs are in solutions. The results provide a molecular basis for analyzing selectivity, specificity and polymorphisms of amino-acid-nucleotide interactions. Comparative analyses of the distribution of the binding energies reveal unique binding strengths patterns assignable to each pair of DNA nucleotide and amino acid originating from the chemical structures. Pronounced favorable (such as Arg-G , etc.) and unfavorable (such as Ile-T , etc.) binding interactions can be identified in selected groups of amino acid and nucleotide pairs that could provide basis to elucidate energetics of amino-acid-nucleotide interactions. Such interaction selectivity, specificity and polymorphism manifest the contributions from DNA backbone, DNA bases, as well as main chain and side chain of the amino acids.
Collapse
Affiliation(s)
- Pengyu Wang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Xiaocui Fang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Rong Du
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Jiali Wang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Mingpeng Liu
- Tsinghua University, Department of Chemistry, CHINA
| | - Peng Xu
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Shiqi Li
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Kaiyue Zhang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Siyuan Ye
- Tsinghua University, Department of Chemistry, CHINA
| | - Qing You
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Yanlian Yang
- NCNST: National Center for Nanoscience and Technology, Key Laboratory for Biological Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences), and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, CHINA
| | - Chen Wang
- National Center for NanoScience and Technology, China(NCNST), Beijing, CHINA
| |
Collapse
|
14
|
Stachowski K, Norris A, Potter D, Wysocki V, Foster M. Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM. Nucleic Acids Res 2022; 50:1753-1769. [PMID: 35104890 PMCID: PMC8860596 DOI: 10.1093/nar/gkac032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022] Open
Abstract
Cre recombinase selectively recognizes DNA and prevents non-specific DNA cleavage through an orchestrated series of assembly intermediates. Cre recombines two loxP DNA sequences featuring a pair of palindromic recombinase binding elements and an asymmetric spacer region, by assembly of a tetrameric synaptic complex, cleavage of an opposing pair of strands, and formation of a Holliday junction intermediate. We used Cre and loxP variants to isolate the monomeric Cre-loxP (54 kDa), dimeric Cre2-loxP (110 kDa), and tetrameric Cre4-loxP2 assembly intermediates, and determined their structures using cryo-EM to resolutions of 3.9, 4.5 and 3.2 Å, respectively. Progressive and asymmetric bending of the spacer region along the assembly pathway enables formation of increasingly intimate interfaces between Cre protomers and illuminates the structural bases of biased loxP strand cleavage order and half-the-sites activity. Application of 3D variability analysis to the tetramer data reveals constrained conformational sampling along the pathway between protomer activation and Holliday junction isomerization. These findings underscore the importance of protein and DNA flexibility in Cre-mediated site selection, controlled activation of alternating protomers, the basis for biased strand cleavage order, and recombination efficiency. Such considerations may advance development of site-specific recombinases for use in gene editing applications.
Collapse
Affiliation(s)
- Kye Stachowski
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew S Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Devante Potter
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
15
|
Roueinfar M, Templeton HN, Sheng JA, Hong KL. An Update of Nucleic Acids Aptamers Theranostic Integration with CRISPR/Cas Technology. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031114. [PMID: 35164379 PMCID: PMC8839139 DOI: 10.3390/molecules27031114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system is best known for its role in genomic editing. It has also demonstrated great potential in nucleic acid biosensing. However, the specificity limitation in CRISPR/Cas has created a hurdle for its advancement. More recently, nucleic acid aptamers known for their high affinity and specificity properties for their targets have been integrated into CRISPR/Cas systems. This review article gives a brief overview of the aptamer and CRISPR/Cas technology and provides an updated summary and discussion on how the two distinctive nucleic acid technologies are being integrated into modern diagnostic and therapeutic applications
Collapse
Affiliation(s)
- Mina Roueinfar
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
| | - Hayley N. Templeton
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Julietta A. Sheng
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (M.R.); (H.N.T.); (J.A.S.)
| | - Ka Lok Hong
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, 84 W. South Street, Wilkes-Barre, PA 18766, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, Notre Dame of Maryland University, 4701 North Charles Street, Baltimore, MD 21210, USA
- Correspondence: ; Tel.: +1-410-532-5044
| |
Collapse
|
16
|
Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C. Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182. ACS OMEGA 2022; 7:129-139. [PMID: 35036684 PMCID: PMC8756438 DOI: 10.1021/acsomega.1c04148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Zta, the Epstein-Barr virus bZIP transcription factor (TF), binds both unmethylated and methylated double-stranded DNA (dsDNA) in a sequence-specific manner. We studied the contribution of a conserved asparagine (N182) to sequence-specific dsDNA binding to four types of dsDNA: (i) dsDNA with cytosine in both strands ((DNA(C|C)), (ii, iii) dsDNA with 5-methylcytosine (5mC, M) or 5-hydroxymethylcytosine (5hmC, H) in one strand and cytosine in the second strand ((DNA(5mC|C) and DNA(5hmC|C)), and (iv) dsDNA with methylated cytosine in both strands in all CG dinucleotides ((DNA(5mCG)). We replaced asparagine with five similarly sized amino acids (glutamine (Q), serine (S), threonine (T), isoleucine (I), or valine (V)) and used protein binding microarrays to evaluate sequence-specific dsDNA binding. Zta preferentially binds the pseudo-palindrome TRE (AP1) motif (T-4G-3A-2G/C 0T2C3A4 ). Zta (N182Q) changes binding to A3 in only one half-site. Zta(N182S) changes binding to G3 in one or both halves of the motif. Zta(N182S) and Zta(N182Q) have 34- and 17-fold weaker median dsDNA binding, respectively. Zta(N182V) and Zta(N182I) have increased binding to dsDNA(5mC|C). Molecular dynamics simulations rationalize some of these results, identifying hydrogen bonds between glutamine and A3 , but do not reveal why serine preferentially binds G3 , suggesting that entropic interactions may mediate this new binding specificity.
Collapse
Affiliation(s)
- Sreejana Ray
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Desiree Tillo
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
- Cancer
Genetics Branch, National Cancer Institute,
National Institutes of Health, Building 37, Bethesda, Maryland 20892, United States
| | - Nima Assad
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Aniekanabasi Ufot
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Aleksey Porollo
- Center
for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, United States
- Department
of Pediatrics, University of Cincinnati
College of Medicine, Cincinnati, Ohio 45267, United States
| | - Stewart R. Durell
- Laboratory
of Cell Biology, National Cancer Institute,
National Institutes of Health, Building 37, Bethesda, Maryland 20892, United States
| | - Charles Vinson
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| |
Collapse
|
17
|
Selvaraj D, Dawar R, Sivakumar PK, Devi A. Clustered regularly interspaced short palindromic repeats, a glimpse - impacts in molecular biology, trends and highlights. Horm Mol Biol Clin Investig 2021; 43:105-112. [PMID: 34881529 DOI: 10.1515/hmbci-2021-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 11/10/2021] [Indexed: 11/15/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a novel molecular tool. In recent days, it has been highlighted a lot, as the Nobel prize was awarded for this sector in 2020, and also for its recent use in Covid-19 related diagnostics. Otherwise, it is an eminent gene-editing technique applied in diverse medical zones of therapeutics in genetic diseases, hematological diseases, infectious diseases, etc., research related to molecular biology, cancer, hereditary diseases, immune and inflammatory diseases, etc., diagnostics related to infectious diseases like viral hemorrhagic fevers, Covid-19, etc. In this review, its discovery, working mechanisms, challenges while handling the technique, recent advancements, applications, alternatives have been discussed. It is a cheaper, faster technique revolutionizing the medicinal field right now. However, their off-target effects and difficulties in delivery into the desired cells make CRISPR, not easily utilizable. We conclude that further robust research in this field may promise many interesting, useful results.
Collapse
Affiliation(s)
- Dhivya Selvaraj
- Department of Biochemistry, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India.,Department of Biochemistry, SGT University, Gurgaon, India
| | - Rajni Dawar
- Department of Biochemistry, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | | | - Anita Devi
- Department of Biochemistry, Dr Rajendra Prasad Government Medical College, Tanda, Kangra, India
| |
Collapse
|
18
|
Hassan MM, Zhang Y, Yuan G, De K, Chen JG, Muchero W, Tuskan GA, Qi Y, Yang X. Construct design for CRISPR/Cas-based genome editing in plants. TRENDS IN PLANT SCIENCE 2021; 26:1133-1152. [PMID: 34340931 DOI: 10.1016/j.tplants.2021.06.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 05/06/2023]
Abstract
CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.
Collapse
Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| |
Collapse
|
19
|
Irving M, Lanitis E, Migliorini D, Ivics Z, Guedan S. Choosing the Right Tool for Genetic Engineering: Clinical Lessons from Chimeric Antigen Receptor-T Cells. Hum Gene Ther 2021; 32:1044-1058. [PMID: 34662233 PMCID: PMC8697565 DOI: 10.1089/hum.2021.173] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
T cell modification with genes that encode chimeric antigen receptors (CAR-T cells) has shown tremendous promise for the treatment of B cell malignancies. The successful translation of CAR-T cell therapy to other tumor types, including solid tumors, is the next big challenge. As the field advances from second- to next-generation CAR-T cells comprising multiple genetic modifications, more sophisticated methods and tools to engineer T cells are being developed. Viral vectors, especially γ-retroviruses and lentiviruses, are traditionally used for CAR-T cell engineering due to their high transduction efficiency. However, limited genetic cargo, high costs of production under good manufacturing practice (GMP) conditions, and the high regulatory demands are obstacles for widespread clinical translation. To overcome these limitations, different nonviral approaches are being explored at a preclinical or clinical level, including transposon/transposase systems and mRNA electroporation and nonintegrating DNA nanovectors. Genome editing tools that allow efficient knockout of particular genes and/or site-directed integration of the CAR and/or other transgenes into the genome are also being evaluated for CAR-T cell engineering. In this review, we discuss the development of viral and nonviral vectors used to generate CAR-T cells, focusing on their advantages and limitations. We also discuss the lessons learned from clinical trials using the different genetic engineering tools, with special focus on safety and efficacy.
Collapse
Affiliation(s)
- Melita Irving
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Evripidis Lanitis
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Denis Migliorini
- Department of Oncology, Geneva University Hospitals, Geneva, Switzerland.,Center for Translational Research in Onco-Hematology, University of Geneva, Geneva, Switzerland.,Swiss Cancer Center Léman, Geneva and Lausanne, Switzerland
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Sonia Guedan
- Department of Hematology and Oncology, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| |
Collapse
|
20
|
Nakamura K, Nakao T, Mori T, Ohno S, Fujita Y, Masaoka K, Sakabayashi K, Mori K, Tobimatsu T, Sera T. Necessity of Flanking Repeats R1' and R8' of Human Pumilio1 Protein for RNA Binding. Biochemistry 2021; 60:3007-3015. [PMID: 34541851 DOI: 10.1021/acs.biochem.1c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human Pumilio (hPUM) is a structurally well-analyzed RNA-binding protein that has been used recently for artificial RNA binding. Structural analysis revealed that amino acids at positions 12, 13, and 16 in the repeats from R1 to R8 each contact one specific RNA base in the eight-nucleotide RNA target. The functions of the N- and C-terminal flanking repeats R1' and R8', however, remain unclear. Here, we report how the repeats contribute to overall RNA binding. We first prepared three mutants in which R1' and/or R8' were deleted and then analyzed RNA binding using gel shift assays. The assays showed that all deletion mutants bound to their target less than the original hPUM, but that R1' contributed more than R8', unlike Drosophila PUM. We next investigated which amino acid residues of R1' or R8' were responsible for RNA binding. With detailed analysis of the protein tertiary structure, we found a hydrophobic core in each of the repeats. We therefore mutated all hydrophobic amino residues in each core to alanine. The gel shift assays with the resulting mutants revealed that both hydrophobic cores contributed to the RNA binding: especially the hydrophobic core of R1' had a significant influence. In the present study, we demonstrated that the flanking R1' and R8' repeats are indispensable for RNA binding of hPUM and suggest that hydrophobic R1'-R1 interactions may stabilize the whole hPUM structure.
Collapse
Affiliation(s)
- Kento Nakamura
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Taishu Nakao
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Tomoaki Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Serika Ohno
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Fujita
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Keisuke Masaoka
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuki Sakabayashi
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Koichi Mori
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takamasa Tobimatsu
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Takashi Sera
- Department of Applied Chemistry and Biotechnology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| |
Collapse
|
21
|
Čermák T. Sequence modification on demand: search and replace tools for precise gene editing in plants. Transgenic Res 2021; 30:353-379. [PMID: 34086167 DOI: 10.1007/s11248-021-00253-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Until recently, our ability to generate allelic diversity in plants was limited to introduction of variants from domesticated and wild species by breeding via uncontrolled recombination or the use of chemical and physical mutagens-processes that are lengthy and costly or lack specificity, respectively. Gene editing provides a faster and more precise way to create new variation, although its application in plants has been dominated by the creation of short insertion and deletion mutations leading to loss of gene function, mostly due to the dependence of editing outcomes on DNA repair pathway choices intrinsic to higher eukaryotes. Other types of edits such as point mutations and precise and pre-designed targeted sequence insertions have rarely been implemented, despite providing means to modulate the expression of target genes or to engineer the function and stability of their protein products. Several advancements have been developed in recent years to facilitate custom editing by regulation of repair pathway choices or by taking advantage of alternative types of DNA repair. We have seen the advent of novel gene editing tools that are independent of DNA double-strand break repair, and methods completely independent of host DNA repair processes are being increasingly explored. With the aim to provide a comprehensive review of the state-of-the-art methodology for allele replacement in plants, I discuss the adoption of these improvements for plant genome engineering.
Collapse
|
22
|
Elias A, Kassis H, Elkader SA, Gritsenko N, Nahmad A, Shir H, Younis L, Shannan A, Aihara H, Prag G, Yagil E, Kolot M. HK022 bacteriophage Integrase mediated RMCE as a potential tool for human gene therapy. Nucleic Acids Res 2020; 48:12804-12816. [PMID: 33270859 PMCID: PMC7736782 DOI: 10.1093/nar/gkaa1140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/31/2020] [Accepted: 11/08/2020] [Indexed: 12/25/2022] Open
Abstract
HK022 coliphage site-specific recombinase Integrase (Int) can catalyze integrative site-specific recombination and recombinase-mediated cassette exchange (RMCE) reactions in mammalian cell cultures. Owing to the promiscuity of the 7 bp overlap sequence in its att sites, active ‘attB’ sites flanking human deleterious mutations were previously identified that may serve as substrates for RMCE reactions for future potential gene therapy. However, the wild type Int proved inefficient in catalyzing such RMCE reactions. To address this low efficiency, variants of Int were constructed and examined by integrative site-specific recombination and RMCE assays in human cells using native ‘attB’ sites. As a proof of concept, various Int derivatives have demonstrated successful RMCE reactions using a pair of native ‘attB’ sites that were inserted as a substrate into the human genome. Moreover, successful RMCE reactions were demonstrated in native locations of the human CTNS and DMD genes whose mutations are responsible for Cystinosis and Duchene Muscular Dystrophy diseases, respectively. This work provides a steppingstone for potential downstream therapeutic applications.
Collapse
Affiliation(s)
- Amer Elias
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Hala Kassis
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Suha Abd Elkader
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Natasha Gritsenko
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Alessio Nahmad
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Hodaya Shir
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Liana Younis
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Atheer Shannan
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota TwinCities, Minneapolis, MN, 55455, USA
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Ezra Yagil
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| | - Mikhail Kolot
- Department of Biochemistry and Molecular Biology, School of Neurobiology, Biochemistry &Biophysics, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
23
|
Antón Z, Mullally G, Ford HC, van der Kamp MW, Szczelkun MD, Lane JD. Mitochondrial import, health and mtDNA copy number variability seen when using type II and type V CRISPR effectors. J Cell Sci 2020; 133:jcs.248468. [PMID: 32843580 DOI: 10.1242/jcs.248468] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Current methodologies for targeting the mitochondrial genome for research and/or therapy development in mitochondrial diseases are restricted by practical limitations and technical inflexibility. A molecular toolbox for CRISPR-mediated mitochondrial genome editing is desirable, as this could enable targeting of mtDNA haplotypes using the precision and tuneability of CRISPR enzymes. Such 'MitoCRISPR' systems described to date lack reproducibility and independent corroboration. We have explored the requirements for MitoCRISPR in human cells by CRISPR nuclease engineering, including the use of alternative mitochondrial protein targeting sequences and smaller paralogues, and the application of guide (g)RNA modifications for mitochondrial import. We demonstrate varied mitochondrial targeting efficiencies and effects on mitochondrial dynamics/function of different CRISPR nucleases, with Lachnospiraceae bacterium ND2006 (Lb) Cas12a being better targeted and tolerated than Cas9 variants. We also provide evidence of Cas9 gRNA association with mitochondria in HeLa cells and isolated yeast mitochondria, even in the absence of a targeting RNA aptamer. Our data link mitochondrial-targeted LbCas12a/crRNA with increased mtDNA copy number dependent upon DNA binding and cleavage activity. We discuss reproducibility issues and the future steps necessary for MitoCRISPR.
Collapse
Affiliation(s)
- Zuriñe Antón
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Grace Mullally
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Holly C Ford
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Marc W van der Kamp
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.,Centre for Computational Chemistry, School of Chemistry, Faculty of Science, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK .,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Jon D Lane
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK .,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| |
Collapse
|
24
|
Reddy P, Vilella F, Izpisua Belmonte JC, Simón C. Use of Customizable Nucleases for Gene Editing and Other Novel Applications. Genes (Basel) 2020; 11:E976. [PMID: 32842577 PMCID: PMC7565838 DOI: 10.3390/genes11090976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/13/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022] Open
Abstract
The development of novel genome editing tools has unlocked new opportunities that were not previously possible in basic and biomedical research. During the last two decades, several new genome editing methods have been developed that can be customized to modify specific regions of the genome. However, in the past couple of years, many newer and more exciting genome editing techniques have been developed that are more efficient, precise, and easier to use. These genome editing tools have helped to improve our understanding of genetic disorders by modeling them in cells and animal models, in addition to correcting the disease-causing mutations. Among the genome editing tools, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has proven to be the most popular one due to its versatility and has been successfully used in a wide variety of laboratory animal models and plants. In this review, we summarize the customizable nucleases currently used for genome editing and their uses beyond the modification of genome. We also discuss the potential future applications of gene editing tools for both basic research and clinical purposes.
Collapse
Affiliation(s)
- Pradeep Reddy
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA;
| | - Felipe Vilella
- Igenomix Foundation, Instituto de Investigación Sanitaria Hospital Clínico (INCLIVA), 46010 Valencia, Spain; (F.V.); (C.S.)
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA 02215, USA
| | | | - Carlos Simón
- Igenomix Foundation, Instituto de Investigación Sanitaria Hospital Clínico (INCLIVA), 46010 Valencia, Spain; (F.V.); (C.S.)
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA 02215, USA
- Department of Pediatrics, Obstetrics and Gynecology, School of Medicine, University of Valencia, 46010 Valencia, Spain
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
25
|
Lambert AR, Hallinan JP, Werther R, Glöw D, Stoddard BL. Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition. Structure 2020; 28:760-775.e8. [PMID: 32359399 PMCID: PMC7347439 DOI: 10.1016/j.str.2020.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/17/2020] [Accepted: 04/11/2020] [Indexed: 01/07/2023]
Abstract
The redesign of a macromolecular binding interface and corresponding alteration of recognition specificity is a challenging endeavor that remains recalcitrant to computational approaches. This is particularly true for the redesign of DNA binding specificity, which is highly dependent upon bending, hydrogen bonds, electrostatic contacts, and the presence of solvent and counterions throughout the molecular interface. Thus, redesign of protein-DNA binding specificity generally requires iterative rounds of amino acid randomization coupled to selections. Here, we describe the importance of scaffold thermostability for protein engineering, coupled with a strategy that exploits the protein's specificity profile, to redesign the specificity of a pair of meganucleases toward three separate genomic targets. We determine and describe a series of changes in protein sequence, stability, structure, and activity that accumulate during the engineering process, culminating in fully retargeted endonucleases.
Collapse
Affiliation(s)
- Abigail R. Lambert
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle WA 98109 USA
| | - Jazmine P. Hallinan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle WA 98109 USA
| | - Rachel Werther
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle WA 98109 USA
| | - Dawid Glöw
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle WA 98109 USA,Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle WA 98109 USA,Corresponding Author and Lead Contact:
| |
Collapse
|
26
|
Chen J, Qi Y, Duan Y, Duan M, Yang M. C1188D mutation abolishes specific recognition between MLL1-CXXC domain and CpG site by inducing conformational switch of flexible N-terminal. Proteins 2020; 88:1401-1412. [PMID: 32519403 DOI: 10.1002/prot.25960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/22/2020] [Accepted: 06/06/2020] [Indexed: 01/19/2023]
Abstract
Mixed lineage leukemia protein (MLL1 protein) recognizes the CpG site via its CXXC domain and is frequently associated with leukemia. The specific recognition is abolished by C1188D mutation, which also prevents MLL-related leukemia. In this paper, multiple molecular dynamic (MD) simulations were performed to investigate the mechanism of recognition and influences of C1188D mutation. Started from fully dissociated DNA and MLL1-CXXC domain, remarkably, the center of mass (COM) of MLL1-CXXC domain quickly concentrates on the vicinity of the CpG site in all 53 short MD simulations. Extended simulations of the wild type showed that the native complex formed in 500 ns among 4 of 53 simulations. In contrast, the C1188D mutant COM distributed broadly around the DNA and the native complex was not observed in any of the extended simulations. Simulations on the apo MLL1-CXXC domain further suggest that the wild type protein remained predominantly in an open form that closely resembles its structure in the native complex whereas C1188D mutant formed predominantly compact structures in which the N- terminal bends to D1188. This conformational switch hinders the formation of encounter complex, thus abolishes the recognition. Our study also provides clues to the study mechanism of recognition, by the CXXC domain from proteins like DNA methyltransferase and ten-eleven translocation enzymes.
Collapse
Affiliation(s)
- Jiawen Chen
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonances in Wuhan, State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Yanping Qi
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonances in Wuhan, State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China.,College of Physical Science and Technology, Central China Normal University, Wuhan, China
| | - Yong Duan
- Department of Biomedical Engineering and UC Davis Genome Center, University of California at Davis, Davis, California, USA
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonances in Wuhan, State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonances in Wuhan, State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China.,Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
27
|
Naeem M, Majeed S, Hoque MZ, Ahmad I. Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing. Cells 2020; 9:E1608. [PMID: 32630835 PMCID: PMC7407193 DOI: 10.3390/cells9071608] [Citation(s) in RCA: 205] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/24/2022] Open
Abstract
Gene editing that makes target gene modification in the genome by deletion or addition has revolutionized the era of biomedicine. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 emerged as a substantial tool due to its simplicity in use, less cost and extraordinary efficiency than the conventional gene-editing tools, including zinc finger nucleases (ZFNs) and Transcription activator-like effector nucleases (TALENs). However, potential off-target activities are crucial shortcomings in the CRISPR system. Numerous types of approaches have been developed to reduce off-target effects. Here, we review several latest approaches to reduce the off-target effects, including biased or unbiased off-target detection, cytosine or adenine base editors, prime editing, dCas9, Cas9 paired nickase, ribonucleoprotein (RNP) delivery and truncated gRNAs. This review article provides extensive information to cautiously interpret off-target effects to assist the basic and clinical applications in biomedicine.
Collapse
Affiliation(s)
- Muhammad Naeem
- Department of Life Sciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; (M.N.); (M.Z.H.)
| | - Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA;
| | - Mubasher Zahir Hoque
- Department of Life Sciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; (M.N.); (M.Z.H.)
| | - Irshad Ahmad
- Department of Life Sciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; (M.N.); (M.Z.H.)
| |
Collapse
|
28
|
Lanigan TM, Kopera HC, Saunders TL. Principles of Genetic Engineering. Genes (Basel) 2020; 11:E291. [PMID: 32164255 PMCID: PMC7140808 DOI: 10.3390/genes11030291] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic engineering is the use of molecular biology technology to modify DNA sequence(s) in genomes, using a variety of approaches. For example, homologous recombination can be used to target specific sequences in mouse embryonic stem (ES) cell genomes or other cultured cells, but it is cumbersome, poorly efficient, and relies on drug positive/negative selection in cell culture for success. Other routinely applied methods include random integration of DNA after direct transfection (microinjection), transposon-mediated DNA insertion, or DNA insertion mediated by viral vectors for the production of transgenic mice and rats. Random integration of DNA occurs more frequently than homologous recombination, but has numerous drawbacks, despite its efficiency. The most elegant and effective method is technology based on guided endonucleases, because these can target specific DNA sequences. Since the advent of clustered regularly interspaced short palindromic repeats or CRISPR/Cas9 technology, endonuclease-mediated gene targeting has become the most widely applied method to engineer genomes, supplanting the use of zinc finger nucleases, transcription activator-like effector nucleases, and meganucleases. Future improvements in CRISPR/Cas9 gene editing may be achieved by increasing the efficiency of homology-directed repair. Here, we describe principles of genetic engineering and detail: (1) how common elements of current technologies include the need for a chromosome break to occur, (2) the use of specific and sensitive genotyping assays to detect altered genomes, and (3) delivery modalities that impact characterization of gene modifications. In summary, while some principles of genetic engineering remain steadfast, others change as technologies are ever-evolving and continue to revolutionize research in many fields.
Collapse
Affiliation(s)
- Thomas M. Lanigan
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C. Kopera
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Biomedical Research Core Facilities, Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
29
|
Lansing F, Paszkowski-Rogacz M, Schmitt LT, Schneider PM, Rojo Romanos T, Sonntag J, Buchholz F. A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus. Nucleic Acids Res 2020; 48:472-485. [PMID: 31745551 PMCID: PMC7107906 DOI: 10.1093/nar/gkz1078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
Site-specific recombinases (SSRs) such as the Cre/loxP system are useful genome engineering tools that can be repurposed by altering their DNA-binding specificity. However, SSRs that delete a natural sequence from the human genome have not been reported thus far. Here, we describe the generation of an SSR system that precisely excises a 1.4 kb fragment from the human genome. Through a streamlined process of substrate-linked directed evolution we generated two separate recombinases that, when expressed together, act as a heterodimer to delete a human genomic sequence from chromosome 7. Our data indicates that designer-recombinases can be generated in a manageable timeframe for precision genome editing. A large-scale bioinformatics analysis suggests that around 13% of all human protein-coding genes could be targetable by dual designer-recombinase induced genomic deletion (dDRiGD). We propose that heterospecific designer-recombinases, which work independently of the host DNA repair machinery, represent an efficient and safe alternative to nuclease-based genome editing technologies.
Collapse
Affiliation(s)
- Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Paul Martin Schneider
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Teresa Rojo Romanos
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Jan Sonntag
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| |
Collapse
|
30
|
Laforet M, McMurrough TA, Vu M, Brown CM, Zhang K, Junop MS, Gloor GB, Edgell DR. Modifying a covarying protein-DNA interaction changes substrate preference of a site-specific endonuclease. Nucleic Acids Res 2019; 47:10830-10841. [PMID: 31602462 PMCID: PMC6847045 DOI: 10.1093/nar/gkz866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/17/2019] [Accepted: 10/09/2019] [Indexed: 12/23/2022] Open
Abstract
Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not all redesigns successfully reprogram specificity. To gain a global overview of residues that influence meganuclease specificity, we used information theory to identify protein-DNA covariation. Directed evolution experiments of one predicted pair, 227/+3, revealed variants with surprising shifts in I-OnuI substrate preference at the central 4 bases where cleavage occurs. Structural studies showed significant remodeling distant from the covarying position, including restructuring of an inter-hairpin loop, DNA distortions near the scissile phosphates, and new base-specific contacts. Our findings are consistent with a model whereby the functional impacts of covariation can be indirectly propagated to neighboring residues outside of direct contact range, allowing meganucleases to adapt to target site variation and indirectly expand the sequence space accessible for cleavage. We suggest that some engineered meganucleases may have unexpected cleavage profiles that were not rationally incorporated during the design process.
Collapse
Affiliation(s)
- Marc Laforet
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Thomas A McMurrough
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Michael Vu
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Christopher M Brown
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Kun Zhang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Murray S Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| |
Collapse
|
31
|
McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR. Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases. Nucleic Acids Res 2019; 46:11990-12007. [PMID: 30357419 PMCID: PMC6294521 DOI: 10.1093/nar/gky976] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/05/2018] [Indexed: 12/30/2022] Open
Abstract
LAGLIDADG homing endonucleases (meganucleases) are site-specific mobile endonucleases that can be adapted for genome-editing applications. However, one problem when reprogramming meganucleases on non-native substrates is indirect readout of DNA shape and flexibility at the central 4 bases where cleavage occurs. To understand how the meganuclease active site regulates DNA cleavage, we used functional selections and deep sequencing to profile the fitness landscape of 1600 I-LtrI and I-OnuI active site variants individually challenged with 67 substrates with central 4 base substitutions. The wild-type active site was not optimal for cleavage on many substrates, including the native I-LtrI and I-OnuI targets. Novel combinations of active site residues not observed in known meganucleases supported activity on substrates poorly cleaved by the wild-type enzymes. Strikingly, combinations of E or D substitutions in the two metal-binding residues greatly influenced cleavage activity, and E184D variants had a broadened cleavage profile. Analyses of I-LtrI E184D and the wild-type proteins co-crystallized with the non-cognate AACC central 4 sequence revealed structural differences that correlated with kinetic constants for cleavage of individual DNA strands. Optimizing meganuclease active sites to enhance cleavage of non-native central 4 target sites is a straightforward addition to engineering workflows that will expand genome-editing applications.
Collapse
Affiliation(s)
- Thomas A McMurrough
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Christopher M Brown
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Kun Zhang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Georg Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
| | - Murray S Junop
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - Gregory B Gloor
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1
| |
Collapse
|
32
|
Bessen JL, Afeyan LK, Dančík V, Koblan LW, Thompson DB, Leichner C, Clemons PA, Liu DR. High-resolution specificity profiling and off-target prediction for site-specific DNA recombinases. Nat Commun 2019; 10:1937. [PMID: 31028261 PMCID: PMC6486577 DOI: 10.1038/s41467-019-09987-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/05/2019] [Indexed: 12/26/2022] Open
Abstract
The development of site-specific recombinases (SSRs) as genome editing agents is limited by the difficulty of altering their native DNA specificities. Here we describe Rec-seq, a method for revealing the DNA specificity determinants and potential off-target substrates of SSRs in a comprehensive and unbiased manner. We applied Rec-seq to characterize the DNA specificity determinants of several natural and evolved SSRs including Cre, evolved variants of Cre, and other SSR family members. Rec-seq profiling of these enzymes and mutants thereof revealed previously uncharacterized SSR interactions, including specificity determinants not evident from SSR:DNA structures. Finally, we used Rec-seq specificity profiles to predict off-target substrates of Tre and Brec1 recombinases, including endogenous human genomic sequences, and confirmed their ability to recombine these off-target sequences in human cells. These findings establish Rec-seq as a high-resolution method for rapidly characterizing the DNA specificity of recombinases with single-nucleotide resolution, and for informing their further development. The development of site-specific recombinases as genome editing tools is limited by the difficulty of altering their DNA sequence specificity. Here the authors present Rec-seq, a method for identifying specificity determinants and off-target substrates of recombinases in an unbiased manner.
Collapse
Affiliation(s)
- Jeffrey L Bessen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Lena K Afeyan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Vlado Dančík
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - David B Thompson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | | | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
33
|
Abstract
Inherited retinal degeneration (IRD), a group of rare retinal diseases that primarily lead to the progressive loss of retinal photoreceptor cells, can be inherited in all modes of inheritance: autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), and mitochondrial. Based on the pattern of inheritance of the dystrophy, retinal gene therapy has 2 main strategies. AR, XL, and AD IRDs with haploinsufficiency can be treated by inserting a functional copy of the gene using either viral or nonviral vectors (gene augmentation). Different types of viral vectors and nonviral vectors are used to transfer plasmid DNA both in vitro and in vivo. AD IRDs with gain-of-function mutations or dominant-negative mutations can be treated by disrupting the mutant allele with (and occasionally without) gene augmentation. This review article aims to provide an overview of ocular gene therapy for treating IRDs using gene augmentation with viral or nonviral vectors or gene disruption through different gene-editing tools, especially with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system.
Collapse
Affiliation(s)
- Amirmohsen Arbabi
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Amelia Liu
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Hossein Ameri
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, California
| |
Collapse
|
34
|
Li H, Sharp R, Rutherford K, Gupta K, Van Duyne GD. Serine Integrase attP Binding and Specificity. J Mol Biol 2018; 430:4401-4418. [PMID: 30227134 DOI: 10.1016/j.jmb.2018.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 01/31/2023]
Abstract
Serine integrases catalyze the site-specific insertion of viral DNA into a host's genome. The minimal requirements and irreversible nature of this integration reaction have led to the use of serine integrases in applications ranging from bacterial memory storage devices to gene therapy. Our understanding of how the integrase proteins recognize the viral (attP) and host (attB) attachment sites is limited, with structural data available for only a Listeria integrase C-terminal domain (CTD) bound to an attP half-site. Here we report quantitative binding and saturation mutagenesis analyses for the Listeria innocua prophage attP site and a new 2.8-Å crystal structure of the CTD•attP half site. We find that Int binds with high affinity to attP (6.9 nM), but the Int CTD binds to attP half-sites with only 7- to 10-fold lower affinity, supporting the idea that free energy is expended to open an Int dimer for attP binding. Despite the 50-bp Int-attP interaction surface, only 20 residues are sensitive to mutagenesis, and of these, only 6 require a specific residue for efficient Int binding and integration activity. One of the integrase DNA-binding domains, the recombinase domain, appears to be primarily non-specific. Several substitutions result in an improved attP site, indicating that higher-efficiency attachment sites can be obtained through site engineering. These findings advance our understanding of serine integrase function and provide important data for efforts towards engineering this family of enzymes for a variety of biotechnology applications.
Collapse
Affiliation(s)
- Huiguang Li
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert Sharp
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karen Rutherford
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kushol Gupta
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|