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Clement PC, Sapam T, Nair DT. A conserved polar residue plays a critical role in mismatch detection in A-family DNA polymerases. Int J Biol Macromol 2024; 269:131965. [PMID: 38697428 DOI: 10.1016/j.ijbiomac.2024.131965] [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: 01/29/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
In A-family DNA polymerases (dPols), a functional 3'-5' exonuclease activity is known to proofread newly synthesized DNA. The identification of a mismatch in substrate DNA leads to transfer of the primer strand from the polymerase active site to the exonuclease active site. To shed more light regarding the mechanism responsible for the detection of mismatches, we have utilized DNA polymerase 1 from Aquifex pyrophilus (ApPol1). The enzyme synthesized DNA with high fidelity and exhibited maximal exonuclease activity with DNA substrates bearing mismatches at the -2 and - 3 positions. The crystal structure of apo-ApPol1 was utilized to generate a computational model of the functional ternary complex of this enzyme. The analysis of the model showed that N332 forms interactions with minor groove atoms of the base pairs at the -2 and - 3 positions. The majority of known A-family dPols show the presence of Asn at a position equivalent to N332. The N332L mutation led to a decrease in the exonuclease activity for representative purine-pyrimidine, and pyrimidine-pyrimidine mismatches at -2 and - 3 positions, respectively. Overall, our findings suggest that conserved polar residues located towards the minor groove may facilitate the detection of position-specific mismatches to enhance the fidelity of DNA synthesis.
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Affiliation(s)
- Patterson C Clement
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, Haryana (NCR Delhi), India
| | - Tuleshwori Sapam
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, Haryana (NCR Delhi), India
| | - Deepak T Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121 001, Haryana (NCR Delhi), India.
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2
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Botto MM, Borsellini A, Lamers MH. A four-point molecular handover during Okazaki maturation. Nat Struct Mol Biol 2023; 30:1505-1515. [PMID: 37620586 DOI: 10.1038/s41594-023-01071-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 07/17/2023] [Indexed: 08/26/2023]
Abstract
DNA replication introduces thousands of RNA primers into the lagging strand that need to be removed for replication to be completed. In Escherichia coli when the replicative DNA polymerase Pol IIIα terminates at a previously synthesized RNA primer, DNA Pol I takes over and continues DNA synthesis while displacing the downstream RNA primer. The displaced primer is subsequently excised by an endonuclease, followed by the sealing of the nick by a DNA ligase. Yet how the sequential actions of Pol IIIα, Pol I polymerase, Pol I endonuclease and DNA ligase are coordinated is poorly defined. Here we show that each enzymatic activity prepares the DNA substrate for the next activity, creating an efficient four-point molecular handover. The cryogenic-electron microscopy structure of Pol I bound to a DNA substrate with both an upstream and downstream primer reveals how it displaces the primer in a manner analogous to the monomeric helicases. Moreover, we find that in addition to its flap-directed nuclease activity, the endonuclease domain of Pol I also specifically cuts at the RNA-DNA junction, thus marking the end of the RNA primer and creating a 5' end that is a suitable substrate for the ligase activity of LigA once all RNA has been removed.
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Affiliation(s)
- Margherita M Botto
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
- Department of Molecular and Cellular Biology, Geneva University, Geneva, Switzerland
| | - Alessandro Borsellini
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands
- Department of Structural Biology, Human Technopole, Milan, Italy
| | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Leiden, the Netherlands.
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3
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Dupuy P, Ghosh S, Fay A, Adefisayo O, Gupta R, Shuman S, Glickman MS. Roles for mycobacterial DinB2 in frameshift and substitution mutagenesis. eLife 2023; 12:e83094. [PMID: 37141254 PMCID: PMC10159617 DOI: 10.7554/elife.83094] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/18/2023] [Indexed: 05/05/2023] Open
Abstract
Translesion synthesis by translesion polymerases is a conserved mechanism of DNA damage tolerance. In bacteria, DinB enzymes are the widely distributed promutagenic translesion polymerases. The role of DinBs in mycobacterial mutagenesis was unclear until recent studies revealed a role for mycobacterial DinB1 in substitution and frameshift mutagenesis, overlapping with that of translesion polymerase DnaE2. Mycobacterium smegmatis encodes two additional DinBs (DinB2 and DinB3) and Mycobacterium tuberculosis encodes DinB2, but the roles of these polymerases in mycobacterial damage tolerance and mutagenesis is unknown. The biochemical properties of DinB2, including facile utilization of ribonucleotides and 8-oxo-guanine, suggest that DinB2 could be a promutagenic polymerase. Here, we examine the effects of DinB2 and DinB3 overexpression in mycobacterial cells. We demonstrate that DinB2 can drive diverse substitution mutations conferring antibiotic resistance. DinB2 induces frameshift mutations in homopolymeric sequences, both in vitro and in vivo. DinB2 switches from less to more mutagenic in the presence of manganese in vitro. This study indicates that DinB2 may contribute to mycobacterial mutagenesis and antibiotic resistance acquisition in combination with DinB1 and DnaE2.
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Affiliation(s)
- Pierre Dupuy
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Shreya Ghosh
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Allison Fay
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Oyindamola Adefisayo
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
| | - Richa Gupta
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Stewart Shuman
- Molecular Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Michael S Glickman
- Immunology Program, Sloan Kettering InstituteNew YorkUnited States
- Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate SchoolNew YorkUnited States
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Hao J, Wang J, Dong Y, Yang J, Wang Z, Zhao X, Zeng T, Zhao X, Liang H, Li J. Homogeneous, Simple, and Direct Analysis of Exosomal PD-L1 via Aptamer-Bivalent-Cholesterol-Anchor Assembly of DNAzyme (ABCzyme) for Tumor Immunotherapy. Anal Chem 2023; 95:6854-6862. [PMID: 37027485 DOI: 10.1021/acs.analchem.2c05461] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Breakthroughs in immune checkpoint inhibitor (ICI) therapy have revolutionized clinical tumor therapy. Immunohistochemistry (IHC) analysis of PD-L1 in tumor tissue has been used to predict the response to tumor immunotherapy, but the results are not reproducible, and IHC is invasive and cannot be used to monitor the dynamic changes in PD-L1 expression during treatment. Monitoring the expression level of the PD-L1 protein on exosomes (exosomal PD-L1) is promising for both tumor diagnosis and tumor immunotherapy. Here, we established an aptamer-bivalent-cholesterol-anchor assembly of DNAzyme (ABCzyme) analytical strategy that can directly detect exosomal PD-L1 with a minimum lower limit of detection of 5.21 pg/mL. In this way, we found that the levels of exosomal PD-L1 are significantly elevated in the peripheral blood of patients with progressive disease. The precise analysis of exosomal PD-L1 by the proposed ABCzyme strategy provides a potentially convenient method for the dynamic monitoring of tumor progression in patients who receive immunotherapy and proves to be a potential and effective liquid biopsy method for tumor immunotherapy.
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Affiliation(s)
- Jie Hao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Junyi Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Yan Dong
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jingyao Yang
- The Department of Hyperbaric Oxygen, Xingcheng Special Service Sanatorium of Strategic Support Force, Liaoning 125105, China
| | - Zhe Wang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiaoxin Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Tian Zeng
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Xiang Zhao
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Houjie Liang
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
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Jomova K, Makova M, Alomar SY, Alwasel SH, Nepovimova E, Kuca K, Rhodes CJ, Valko M. Essential metals in health and disease. Chem Biol Interact 2022; 367:110173. [PMID: 36152810 DOI: 10.1016/j.cbi.2022.110173] [Citation(s) in RCA: 195] [Impact Index Per Article: 97.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 11/03/2022]
Abstract
In total, twenty elements appear to be essential for the correct functioning of the human body, half of which are metals and half are non-metals. Among those metals that are currently considered to be essential for normal biological functioning are four main group elements, sodium (Na), potassium (K), magnesium (Mg), and calcium (Ca), and six d-block transition metal elements, manganese (Mn), iron (Fe), cobalt (Co), copper (Cu), zinc (Zn) and molybdenum (Mo). Cells have developed various metallo-regulatory mechanisms for maintaining a necessary homeostasis of metal-ions for diverse cellular processes, most importantly in the central nervous system. Since redox active transition metals (for example Fe and Cu) may participate in electron transfer reactions, their homeostasis must be carefully controlled. The catalytic behaviour of redox metals which have escaped control, e.g. via the Fenton reaction, results in the formation of reactive hydroxyl radicals, which may cause damage to DNA, proteins and membranes. Transition metals are integral parts of the active centers of numerous enzymes (e.g. Cu,Zn-SOD, Mn-SOD, Catalase) which catalyze chemical reactions at physiologically compatible rates. Either a deficiency, or an excess of essential metals may result in various disease states arising in an organism. Some typical ailments that are characterized by a disturbed homeostasis of redox active metals include neurological disorders (Alzheimer's, Parkinson's and Huntington's disorders), mental health problems, cardiovascular diseases, cancer, and diabetes. To comprehend more deeply the mechanisms by which essential metals, acting either alone or in combination, and/or through their interaction with non-essential metals (e.g. chromium) function in biological systems will require the application of a broader, more interdisciplinary approach than has mainly been used so far. It is clear that a stronger cooperation between bioinorganic chemists and biophysicists - who have already achieved great success in understanding the structure and role of metalloenzymes in living systems - with biologists, will access new avenues of research in the systems biology of metal ions. With this in mind, the present paper reviews selected chemical and biological aspects of metal ions and their possible interactions in living systems under normal and pathological conditions.
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Affiliation(s)
- Klaudia Jomova
- Department of Chemistry, Faculty of Natural Sciences and Informatics, Constantine The Philosopher University in Nitra, 949 01, Nitra, Slovakia
| | - Marianna Makova
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, 812 37, Bratislava, Slovakia
| | - Suliman Y Alomar
- King Saud University, Zoology Department, College of Science, Riyadh, 11451, Saudi Arabia
| | - Saleh H Alwasel
- King Saud University, Zoology Department, College of Science, Riyadh, 11451, Saudi Arabia
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic; Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - Marian Valko
- Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, 812 37, Bratislava, Slovakia; King Saud University, Zoology Department, College of Science, Riyadh, 11451, Saudi Arabia.
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Feng S, Liang L, Shen C, Lin D, Li J, Lyu L, Liang W, Zhong LL, Cook GM, Doi Y, Chen C, Tian GB. A CRISPR-guided mutagenic DNA polymerase strategy for the detection of antibiotic-resistant mutations in M. tuberculosis. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:354-367. [PMID: 35950213 PMCID: PMC9358013 DOI: 10.1016/j.omtn.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
A sharp increase in multidrug-resistant tuberculosis (MDR-TB) threatens human health. Spontaneous mutation in essential gene confers an ability of Mycobacterium tuberculosis resistance to anti-TB drugs. However, conventional laboratory strategies for identification and prediction of the mutations in this slowly growing species remain challenging. Here, by combining XCas9 nickase and the error-prone DNA polymerase A from M. tuberculosis, we constructed a CRISPR-guided DNA polymerase system, CAMPER, for effective site-directed mutagenesis of drug-target genes in mycobacteria. CAMPER was able to generate mutagenesis of all nucleotides at user-defined loci, and its bidirectional mutagenesis at nick sites allowed editing windows with lengths up to 80 nucleotides. Mutagenesis of drug-targeted genes in Mycobacterium smegmatis and M. tuberculosis with this system significantly increased the fraction of the antibiotic-resistant bacterial population to a level approximately 60- to 120-fold higher than that in unedited cells. Moreover, this strategy could facilitate the discovery of the mutation conferring antibiotic resistance and enable a rapid verification of the growth phenotype-mutation genotype association. Our data demonstrate that CAMPER facilitates targeted mutagenesis of genomic loci and thus may be useful for broad functions such as resistance prediction and development of novel TB therapies.
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Czernecki D, Hu H, Romoli F, Delarue M. Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8. Nucleic Acids Res 2021; 49:11974-11985. [PMID: 34751404 PMCID: PMC8599892 DOI: 10.1093/nar/gkab955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 11/12/2022] Open
Abstract
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3′-5′ exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.
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Affiliation(s)
- Dariusz Czernecki
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France.,Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Haidai Hu
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Filippo Romoli
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
| | - Marc Delarue
- Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France
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Zhou X, Chen X, An Y, Lu H, Wang L, Xu H, Tian B, Zhao Y, Hua Y. Biochemical characterization of a unique DNA polymerase A from the extreme radioresistant organism Deinococcus radiodurans. Biochimie 2021; 185:22-32. [PMID: 33727139 DOI: 10.1016/j.biochi.2021.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/30/2021] [Accepted: 02/19/2021] [Indexed: 01/07/2023]
Abstract
Deinococcus radiodurans survives extraordinary doses of ionizing radiation and desiccation that cause numerous DNA strand breaks. D. radiodurans DNA polymerase A (DrPolA) is essential for reassembling the shattered genome, while its biochemical property has not been fully demonstrated. In this study, we systematically examined the enzymatic activities of DrPolA and characterized its unique features. DrPolA contains an N-terminal nuclease domain (DrPolA-NTD) and a C-terminal Klenow fragment (KlenDr). Compared with the Klenow fragment of E. coli Pol I, KlenDr shows higher fidelity despite the lacking of 3'-5' exonuclease proofreading activity and prefers double-strand DNA rather than Primer-Template substrates. Apart from the well-annotated 5'-3' exonuclease and flap endonuclease activities, DrPolA-NTD displays approximately 140-fold higher gap endonuclease activity than its homolog in E. coli and Human FEN1. Its 5'-3' exonuclease activity on ssDNA, gap endonuclease, and Holliday junction cleavage activities are greatly enhanced by Mn2+. The DrPolA-NTD deficient strain shows increased sensitivity to UV and gamma-ray radiation. Collectively, our results reveal distinct biochemical characteristics of DrPolA during DNA degradation and re-synthesis, which provide new insight into the outstanding DNA repair capacity of D. radiodurans.
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Affiliation(s)
- Xingru Zhou
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Xuanyi Chen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Ying An
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Huizhi Lu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Liangyan Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Hong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Bing Tian
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Ye Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Yuejin Hua
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China.
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