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Sloan DB, Broz AK, Kuster SA, Muthye V, Peñafiel-Ayala A, Marron JR, Lavrov DV, Brieba LG. Expansion of the MutS Gene Family in Plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603841. [PMID: 39071318 PMCID: PMC11275761 DOI: 10.1101/2024.07.17.603841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The MutS gene family is distributed across the tree of life and is involved in recombination, DNA repair, and protein translation. Multiple evolutionary processes have expanded the set of MutS genes in plants relative to other eukaryotes. Here, we investigate the origins and functions of these plant-specific genes. Land plants, green algae, red algae, and glaucophytes share cyanobacterial-like MutS1 and MutS2 genes that presumably were gained via plastid endosymbiotic gene transfer. MutS1 was subsequently lost in some taxa, including seed plants, whereas MutS2 was duplicated in Viridiplantae (i.e., land plants and green algae) with widespread retention of both resulting paralogs. Viridiplantae also have two anciently duplicated copies of the eukaryotic MSH6 gene (i.e., MSH6 and MSH7) and acquired MSH1 via horizontal gene transfer - potentially from a nucleocytovirus. Despite sharing the same name, "plant MSH1" is not directly related to the gene known as MSH1 in some fungi and animals, which may be an ancestral eukaryotic gene acquired via mitochondrial endosymbiosis and subsequently lost in most eukaryotic lineages. There has been substantial progress in understanding the functions of MSH1 and MSH6/MSH7 in plants, but the roles of the cyanobacterial-like MutS1 and MutS2 genes remain uncharacterized. Known functions of bacterial homologs and predicted protein structures, including fusions to diverse nuclease domains, provide hypotheses about potential molecular mechanisms. Because most plant-specific MutS proteins are targeted to the mitochondria and/or plastids, the expansion of this family appears to have played a large role in shaping plant organelle genetics.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Shady A Kuster
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Viraj Muthye
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Alejandro Peñafiel-Ayala
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
| | - Jennifer R Marron
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Luis G Brieba
- Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Gto, México
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2
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. Nucleic Acids Res 2024; 52:6347-6359. [PMID: 38661211 PMCID: PMC11194089 DOI: 10.1093/nar/gkae308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lia M Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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3
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He Y, Han Y, Ma Y, Liu S, Fan T, Liang Y, Tang X, Zheng X, Wu Y, Zhang T, Qi Y, Zhang Y. Expanding plant genome editing scope and profiles with CRISPR-FrCas9 systems targeting palindromic TA sites. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38713743 DOI: 10.1111/pbi.14363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 05/09/2024]
Abstract
CRISPR-Cas9 is widely used for genome editing, but its PAM sequence requirements limit its efficiency. In this study, we explore Faecalibaculum rodentium Cas9 (FrCas9) for plant genome editing, especially in rice. FrCas9 recognizes a concise 5'-NNTA-3' PAM, targeting more abundant palindromic TA sites in plant genomes than the 5'-NGG-3' PAM sites of the most popular SpCas9. FrCas9 shows cleavage activities at all tested 5'-NNTA-3' PAM sites with editing outcomes sharing the same characteristics of a typical CRISPR-Cas9 system. FrCas9 induces high-efficiency targeted mutagenesis in stable rice lines, readily generating biallelic mutants with expected phenotypes. We augment FrCas9's ability to generate larger deletions through fusion with the exonuclease, TREX2. TREX2-FrCas9 generates much larger deletions than FrCas9 without compromise in editing efficiency. We demonstrate TREX2-FrCas9 as an efficient tool for genetic knockout of a microRNA gene. Furthermore, FrCas9-derived cytosine base editors (CBEs) and adenine base editors (ABE) are developed to produce targeted C-to-T and A-to-G base edits in rice plants. Whole-genome sequencing-based off-target analysis suggests that FrCas9 is a highly specific nuclease. Expression of TREX2-FrCas9 in plants, however, causes detectable guide RNA-independent off-target mutations, mostly as single nucleotide variants (SNVs). Together, we have established an efficient CRISPR-FrCas9 system for targeted mutagenesis, large deletions, C-to-T base editing, and A-to-G base editing in plants. The simple palindromic TA motif in the PAM makes the CRISPR-FrCas9 system a promising tool for genome editing in plants with an expanded targeting scope.
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Affiliation(s)
- Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Yangshuo Han
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Yanqin Ma
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingting Fan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanling Liang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xu Tang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
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Ma Y, Wang J, He X, Liu Y, Zhen S, An L, Yang Q, Niu F, Wang H, An B, Tai X, Yan Z, Wu C, Yang X, Liu X. Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA. Nucleic Acids Res 2024; 52:1878-1895. [PMID: 38153123 PMCID: PMC10899777 DOI: 10.1093/nar/gkad1210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αβα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.
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Affiliation(s)
- Yinliang Ma
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Jiaxu Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- College of Life Sciences, State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453002 Henan, China
| | - Xingyi He
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Yuhang Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Shuo Zhen
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Lina An
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Qian Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Fumin Niu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Hong Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Boran An
- Affiliated Hospital of Hebei University, Hebei University, Baoding 071002 Hebei, China
| | - Xinyue Tai
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Zhenzhen Yan
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Chen Wu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Xiaoyun Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xiuhua Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
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5
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Manthei KA, Munson LM, Nandakumar J, Simmons LA. Structural and biochemical characterization of the mitomycin C repair exonuclease MrfB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580553. [PMID: 38405983 PMCID: PMC10889028 DOI: 10.1101/2024.02.15.580553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitomycin C (MMC) repair factor A (mrfA) and factor B (mrfB), encode a conserved helicase and exonuclease that repair DNA damage in the soil-dwelling bacterium Bacillus subtilis. Here we have focused on the characterization of MrfB, a DEDDh exonuclease in the DnaQ superfamily. We solved the structure of the exonuclease core of MrfB to a resolution of 2.1 Å, in what appears to be an inactive state. In this conformation, a predicted α-helix containing the catalytic DEDDh residue Asp172 adopts a random coil, which moves Asp172 away from the active site and results in the occupancy of only one of the two catalytic Mg2+ ions. We propose that MrfB resides in this inactive state until it interacts with DNA to become activated. By comparing our structure to an AlphaFold prediction as well as other DnaQ-family structures, we located residues hypothesized to be important for exonuclease function. Using exonuclease assays we show that MrfB is a Mg2+-dependent 3'-5' DNA exonuclease. We show that Leu113 aids in coordinating the 3' end of the DNA substrate, and that a basic loop is important for substrate binding. This work provides insight into the function of a recently discovered bacterial exonuclease important for the repair of MMC-induced DNA adducts.
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Affiliation(s)
- Kelly A. Manthei
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lia M. Munson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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6
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Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
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Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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7
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Wang Y, Feng YL, Liu Q, Xiao JJ, Liu SC, Huang ZC, Xie AY. TREX2 enables efficient genome disruption mediated by paired CRISPR-Cas9 nickases that generate 3'-overhanging ends. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102072. [PMID: 38028195 PMCID: PMC10661556 DOI: 10.1016/j.omtn.2023.102072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
Paired SpCas9 nickases (SpCas9n) are an effective strategy to reduce off-target effect in genome editing. However, this approach is not efficient with 3'-overhanging ends, limiting its applications. In order to expand the utility of paired SpCas9n in genome editing, we tested the effect of the TREX2 3'-5' exonuclease on repair of 3'-overhanging ends. We found ectopic overexpression of Trex2 stimulates the efficiency of paired SpCas9n in genome disruption with 3'-overhanging ends up to 400-fold with little stimulation of off-target editing. TREX2 overexpressed preferentially deletes entire 3' overhangs but has no significant effect on 5' overhangs. Trex2 overexpression also stimulates genome disruption by paired SpCas9n that potentially generate short 3'-overhanging ends at overlapping SpCas9n target sites, suggesting sequential nicking of overlapping target sites by SpCas9n. This approach is further simplified with improved efficiency and safety by fusion of TREX2 and particularly its DNA-binding-deficient mutant to SpCas9n. Junction analysis at overlapping targets revealed the different extent of end resection of 3' single-stranded DNA (ssDNA) by free TREX2 and TREX2 fused to SpCas9n. SpCas9n-TREX2 fusion is more convenient and safer than overexpression of free TREX2 to process 3'-overhanging ends for efficient genome disruption by paired SpCas9n, allowing practical use of this TREX2-based strategy in genome editing.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Hangzhou Qiantang Hospital, Hangzhou, Zhejiang 310018, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Yi-Li Feng
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Hangzhou Qiantang Hospital, Hangzhou, Zhejiang 310018, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Qian Liu
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Jing-Jing Xiao
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Si-Cheng Liu
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - Zhi-Cheng Huang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
| | - An-Yong Xie
- Key Laboratory of Laparoscopic Technology of Zhejiang Province, Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, P.R. China
- Hangzhou Qiantang Hospital, Hangzhou, Zhejiang 310018, P.R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, Hangzhou, Zhejiang 310029, P.R. China
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8
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Huang KW, Wu CY, Toh SI, Liu TC, Tu CI, Lin YH, Cheng AJ, Kao YT, Chu JW, Hsiao YY. Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids. Nucleic Acids Res 2023; 51:11927-11940. [PMID: 37870446 PMCID: PMC10681709 DOI: 10.1093/nar/gkad910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
In various autoimmune diseases, dysfunctional TREX1 (Three prime Repair Exonuclease 1) leads to accumulation of endogenous single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and DNA/RNA hybrids in the cytoplasm and triggers immune activation through the cGAS-STING pathway. Although inhibition of TREX1 could be a useful strategy for cancer immunotherapy, profiling cellular functions in terms of its potential substrates is a key step. Particularly important is the functionality of processing DNA/RNA hybrids and RNA substrates. The exonuclease activity measurements conducted here establish that TREX1 can digest both ssRNA and DNA/RNA hybrids but not dsRNA. The newly solved structures of TREX1-RNA product and TREX1-nucleotide complexes show that 2'-OH does not impose steric hindrance or specific interactions for the recognition of RNA. Through all-atom molecular dynamics simulations, we illustrate that the 2'-OH-mediated intra-chain hydrogen bonding in RNA would affect the binding with TREX1 and thereby reduce the exonuclease activity. This notion of higher conformational rigidity in RNA leading TREX1 to exhibit weaker catalytic cleavage is further validated by the binding affinity measurements with various synthetic DNA-RNA junctions. The results of this work thus provide new insights into the mechanism by which TREX1 processes RNA and DNA/RNA hybrids and contribute to the molecular-level understanding of the complex cellular functions of TREX1 as an exonuclease.
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Affiliation(s)
- Kuan-Wei Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chia-Yun Wu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tung-Chang Liu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chun-I Tu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yin-Hsin Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - An-Ju Cheng
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ya-Ting Kao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jhih-Wei Chu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yu-Yuan Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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9
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Mathavarajah S, Vergunst KL, Habib EB, Williams SK, He R, Maliougina M, Park M, Salsman J, Roy S, Braasch I, Roger A, Langelaan D, Dellaire G. PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates. Nucleic Acids Res 2023; 51:3185-3204. [PMID: 36912092 PMCID: PMC10123124 DOI: 10.1093/nar/gkad152] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
We have uncovered a role for the promyelocytic leukemia (PML) gene and novel PML-like DEDDh exonucleases in the maintenance of genome stability through the restriction of LINE-1 (L1) retrotransposition in jawed vertebrates. Although the mammalian PML protein forms nuclear bodies, we found that the spotted gar PML ortholog and related proteins in fish function as cytoplasmic DEDDh exonucleases. In contrast, PML proteins from amniote species localized both to the cytoplasm and formed nuclear bodies. We also identified the PML-like exon 9 (Plex9) genes in teleost fishes that encode exonucleases. Plex9 proteins resemble TREX1 but are unique from the TREX family and share homology to gar PML. We also characterized the molecular evolution of TREX1 and the first non-mammalian TREX1 homologs in axolotl. In an example of convergent evolution and akin to TREX1, gar PML and zebrafish Plex9 proteins suppressed L1 retrotransposition and could complement TREX1 knockout in mammalian cells. Following export to the cytoplasm, the human PML-I isoform also restricted L1 through its conserved C-terminus by enhancing ORF1p degradation through the ubiquitin-proteasome system. Thus, PML first emerged as a cytoplasmic suppressor of retroelements, and this function is retained in amniotes despite its new role in the assembly of nuclear bodies.
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Affiliation(s)
| | - Kathleen L Vergunst
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Elias B Habib
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Shelby K Williams
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Raymond He
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Maria Maliougina
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Mika Park
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Jayme Salsman
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Stéphane Roy
- Department of Stomatology, Faculty of Dentistry, Université de Montréal, Montréal, QB, Canada
| | - Ingo Braasch
- Michigan State University, Department of Integrative Biology and Ecology, Evolution, and Behavior Program, East Lansing, MI, USA
| | - Andrew J Roger
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - David N Langelaan
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
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10
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Yu CC, Raj N, Chu JW. Statistical Learning of Protein Elastic Network from Positional Covariance Matrix. Comput Struct Biotechnol J 2023; 21:2524-2535. [PMID: 37095762 PMCID: PMC10121796 DOI: 10.1016/j.csbj.2023.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Positional fluctuation and covariance during protein dynamics are key observables for understanding the molecular origin of biological functions. A frequently employed potential energy function for describing protein structural variation at the coarse-gained level is elastic network model (ENM). A long-standing issue in biomolecular simulation is thus the parametrization of ENM spring constants from the components of positional covariance matrix (PCM). Based on sensitivity analysis of PCM, the direct-coupling statistics of each spring, which is a specific combination of position fluctuation and covariance, is found to exhibit prominent signal of parameter dependence. This finding provides the basis for devising the objective function and the scheme of running through the effective one-dimensional optimization of every spring by self-consistent iteration. Formal derivation of the positional covariance statistical learning (PCSL) method also motivates the necessary data regularization for stable calculations. Robust convergence of PCSL is achieved in taking an all-atom molecular dynamics trajectory or an ensemble of homologous structures as input data. The PCSL framework can also be generalized with mixed objective functions to capture specific property such as the residue flexibility profile. Such physical chemistry-based statistical learning thus provides a useful platform for integrating the mechanical information encoded in various experimental or computational data.
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11
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Huang KW, Chen JW, Hua TY, Chu YY, Chiu TY, Liu JY, Tu CI, Hsu KC, Kao YT, Chu JW, Hsiao YY. Targeted Covalent Inhibitors Allosterically Deactivate the DEDDh Lassa Fever Virus NP Exonuclease from Alternative Distal Sites. JACS AU 2021; 1:2315-2327. [PMID: 34977900 PMCID: PMC8715546 DOI: 10.1021/jacsau.1c00420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Indexed: 06/14/2023]
Abstract
For using targeted covalent inhibitors (TCIs) as anticancer and antiviral drugs, we establish that the model compounds PCMPS (p-chloromercuriphenyl sulfate) and PCMB (p-chloromercuribenzoate) are inhibitors of the DEDDh family of exonucleases. The underlying mechanism is analyzed by X-ray crystallography, activity/nucleic acid-binding assays, and all-atom molecular dynamics (MD) simulations. The first TCI-complexed structures of a DEDDh enzyme, the Lassa fever virus NP exonuclease (NPexo), are resolved to elucidate that the Cys409 binding site is away from the active site and the RNA-binding lid. The NPexo C409A structures indicate Cys461 as the alternative distal site for obstructing the equally active mutant. All-atom MD simulations of the wild type and mutant NPexos in explicit solvent uncover an allosteric inhibition mechanism that the local perturbation induced by PCMPS sulfonate propagates to impact the RNA-binding lid conformation. Binding assay studies confirm that PCMPS does affect the RNA binding of NPexo. The predicted relative potency between PCMPS and PCMB is also in line with experiments. The structural data and inhibition mechanism established in this work provide an important molecular basis for the drug development of TCIs.
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Affiliation(s)
- Kuan-Wei Huang
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jing-Wen Chen
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Tzu-Yu Hua
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Yu-Yu Chu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Tsai-Yuan Chiu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jung-Yu Liu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chun-I Tu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Kai-Cheng Hsu
- Graduate
Institute of Cancer Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program
for Cancer Molecular Biology and Drug Discovery, College of Medical
Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D.
Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan
- Biomedical
Commercialization Center, Taipei Medical
University, Taipei 11031, Taiwan
| | - Ya-Ting Kao
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jhih-Wei Chu
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yu-Yuan Hsiao
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute
of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute
of Bioinformatics and Systems Biology, National
Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan
- Center
for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Drug
Development and Value Creation Research Center, Center for Cancer
Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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12
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Bruand M, Barras D, Mina M, Ghisoni E, Morotti M, Lanitis E, Fahr N, Desbuisson M, Grimm A, Zhang H, Chong C, Dagher J, Chee S, Tsianou T, Dorier J, Stevenson BJ, Iseli C, Ronet C, Bobisse S, Genolet R, Walton J, Bassani-Sternberg M, Kandalaft LE, Ren B, McNeish I, Swisher E, Harari A, Delorenzi M, Ciriello G, Irving M, Rusakiewicz S, Foukas PG, Martinon F, Dangaj Laniti D, Coukos G. Cell-autonomous inflammation of BRCA1-deficient ovarian cancers drives both tumor-intrinsic immunoreactivity and immune resistance via STING. Cell Rep 2021; 36:109412. [PMID: 34289354 PMCID: PMC8371260 DOI: 10.1016/j.celrep.2021.109412] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/18/2020] [Accepted: 06/25/2021] [Indexed: 12/23/2022] Open
Abstract
In this study, we investigate mechanisms leading to inflammation and immunoreactivity in ovarian tumors with homologous recombination deficiency (HRD). BRCA1 loss is found to lead to transcriptional reprogramming in tumor cells and cell-intrinsic inflammation involving type I interferon (IFN) and stimulator of IFN genes (STING). BRCA1-mutated (BRCA1mut) tumors are thus T cell inflamed at baseline. Genetic deletion or methylation of DNA-sensing/IFN genes or CCL5 chemokine is identified as a potential mechanism to attenuate T cell inflammation. Alternatively, in BRCA1mut cancers retaining inflammation, STING upregulates VEGF-A, mediating immune resistance and tumor progression. Tumor-intrinsic STING elimination reduces neoangiogenesis, increases CD8+ T cell infiltration, and reverts therapeutic resistance to dual immune checkpoint blockade (ICB). VEGF-A blockade phenocopies genetic STING loss and synergizes with ICB and/or poly(ADP-ribose) polymerase (PARP) inhibitors to control the outgrowth of Trp53-/-Brca1-/- but not Brca1+/+ ovarian tumors in vivo, offering rational combinatorial therapies for HRD cancers.
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Affiliation(s)
- Marine Bruand
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marco Mina
- Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Computational Biology, UNIL, Lausanne, Switzerland
| | - Eleonora Ghisoni
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Matteo Morotti
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Evripidis Lanitis
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Noémie Fahr
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Mathieu Desbuisson
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Alizée Grimm
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Hualing Zhang
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland; Department of Gynecology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chloe Chong
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Julien Dagher
- Institute of Pathology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Sora Chee
- Ludwig Institute for Cancer Research and University of California, La Jolla, CA, USA
| | - Theodora Tsianou
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Julien Dorier
- Swiss Institute of Bioinformatics, Lausanne, Switzerland; Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | | | | | - Catherine Ronet
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Josephine Walton
- Department of Surgery & Cancer, Ovarian Cancer Action Research Centre, Hammersmith Hospital, Imperial College London, London, UK
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Bing Ren
- Ludwig Institute for Cancer Research and University of California, La Jolla, CA, USA
| | - Iain McNeish
- Department of Surgery & Cancer, Ovarian Cancer Action Research Centre, Hammersmith Hospital, Imperial College London, London, UK
| | | | - Alexandre Harari
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Mauro Delorenzi
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Giovanni Ciriello
- Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Computational Biology, UNIL, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Periklis G Foukas
- 2nd Department of Pathology, Attikon Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.
| | - George Coukos
- Ludwig Institute for Cancer Research, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.
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13
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Dürr SL, Bohuszewicz O, Berta D, Suardiaz R, Jambrina PG, Peter C, Shao Y, Rosta E. The Role of Conserved Residues in the DEDDh Motif: the Proton-Transfer Mechanism of HIV-1 RNase H. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Simon L. Dürr
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Olga Bohuszewicz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | - Dénes Berta
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
| | - Reynier Suardiaz
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
| | | | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Edina Rosta
- Department of Chemistry, King’s College London, London SE1 1DB, U.K
- Department of Physics and Astronomy, University College London; London WC1E 6BT, U.K
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14
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Fusing T5 exonuclease with Cas9 and Cas12a increases the frequency and size of deletion at target sites. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1918-1927. [DOI: 10.1007/s11427-020-1671-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
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