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Borsley S, Leigh DA, Roberts BMW. Molecular Ratchets and Kinetic Asymmetry: Giving Chemistry Direction. Angew Chem Int Ed Engl 2024; 63:e202400495. [PMID: 38568047 DOI: 10.1002/anie.202400495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Indexed: 05/03/2024]
Abstract
Over the last two decades ratchet mechanisms have transformed the understanding and design of stochastic molecular systems-biological, chemical and physical-in a move away from the mechanical macroscopic analogies that dominated thinking regarding molecular dynamics in the 1990s and early 2000s (e.g. pistons, springs, etc), to the more scale-relevant concepts that underpin out-of-equilibrium research in the molecular sciences today. Ratcheting has established molecular nanotechnology as a research frontier for energy transduction and metabolism, and has enabled the reverse engineering of biomolecular machinery, delivering insights into how molecules 'walk' and track-based synthesisers operate, how the acceleration of chemical reactions enables energy to be transduced by catalysts (both motor proteins and synthetic catalysts), and how dynamic systems can be driven away from equilibrium through catalysis. The recognition of molecular ratchet mechanisms in biology, and their invention in synthetic systems, is proving significant in areas as diverse as supramolecular chemistry, systems chemistry, dynamic covalent chemistry, DNA nanotechnology, polymer and materials science, molecular biology, heterogeneous catalysis, endergonic synthesis, the origin of life, and many other branches of chemical science. Put simply, ratchet mechanisms give chemistry direction. Kinetic asymmetry, the key feature of ratcheting, is the dynamic counterpart of structural asymmetry (i.e. chirality). Given the ubiquity of ratchet mechanisms in endergonic chemical processes in biology, and their significance for behaviour and function from systems to synthesis, it is surely just as fundamentally important. This Review charts the recognition, invention and development of molecular ratchets, focussing particularly on the role for which they were originally envisaged in chemistry, as design elements for molecular machinery. Different kinetically asymmetric systems are compared, and the consequences of their dynamic behaviour discussed. These archetypal examples demonstrate how chemical systems can be driven inexorably away from equilibrium, rather than relax towards it.
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Affiliation(s)
- Stefan Borsley
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
| | - David A Leigh
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
| | - Benjamin M W Roberts
- Department of Chemistry, The University of Manchester, Oxford Road, M13 9PL, Manchester, United Kingdom
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Zia S, Sumon MM, Ashik MA, Basar A, Lim S, Oh Y, Park Y, Rahman MM. Potential Inhibitors of Lumpy Skin Disease's Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches. Animals (Basel) 2024; 14:1283. [PMID: 38731287 PMCID: PMC11083254 DOI: 10.3390/ani14091283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024] Open
Abstract
Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle. This spreads through direct contact and insect vectors, significantly affecting global cattle farming. Despite the availability of vaccines, their efficacy is limited by poor prophylaxis and adverse effects. Our study aimed to identify the potential inhibitors targeting the LSDV-encoded DNA polymerase protein (gene LSDV039) for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as being potent binders among 380 phytocompounds, with respective affinities of -8.97 and -7.20 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.86 and -8.86 kcal/mol) among 718 FDA-approved antiviral drugs. Simulating the molecular dynamics of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF, but fluctuated in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. This study highlights the promising potential of using repurposed drugs and phytocompounds as potential LSD therapeutics. However, extensive validation through in vitro and in vivo testing and clinical trials is crucial for their practical application.
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Affiliation(s)
- Sabbir Zia
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Md-Mehedi Sumon
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Md-Ashiqur Ashik
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Abul Basar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
| | - Sangjin Lim
- College of Forest & Environmental Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Yeonsu Oh
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Yungchul Park
- College of Forest & Environmental Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea;
| | - Md-Mafizur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh; (S.Z.); (M.-M.S.); (M.-A.A.); (A.B.)
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Kuznetsova AA, Senchurova SI, Gavrilova AA, Tyugashev TE, Mikushina ES, Kuznetsov NA. Substrate Specificity Diversity of Human Terminal Deoxynucleotidyltransferase May Be a Naturally Programmed Feature Facilitating Its Biological Function. Int J Mol Sci 2024; 25:879. [PMID: 38255952 PMCID: PMC10815903 DOI: 10.3390/ijms25020879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Terminal 2'-deoxynucleotidyl transferase (TdT) is a unique enzyme capable of catalysing template-independent elongation of DNA 3' ends during V(D)J recombination. The mechanism controlling the enzyme's substrate specificity, which is necessary for its biological function, remains unknown. Accordingly, in this work, kinetic and mutational analyses of human TdT were performed and allowed to determine quantitative characteristics of individual stages of the enzyme-substrate interaction, which overall may ensure the enzyme's operation either in the distributive or processive mode of primer extension. It was found that conformational dynamics of TdT play an important role in the formation of the catalytic complex. Meanwhile, the nature of the nitrogenous base significantly affected both the dNTP-binding and catalytic-reaction efficiency. The results indicated that neutralisation of the charge and an increase in the internal volume of the active site caused a substantial increase in the activity of the enzyme and induced a transition to the processive mode in the presence of Mg2+ ions. Surrogate metal ions Co2+ or Mn2+ also may regulate the switching of the enzymatic process to the processive mode. Thus, the totality of individual factors affecting the activity of TdT ensures effective execution of its biological function.
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Affiliation(s)
- Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; (A.A.K.); (S.I.S.); (A.A.G.); (T.E.T.)
| | - Svetlana I. Senchurova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; (A.A.K.); (S.I.S.); (A.A.G.); (T.E.T.)
| | - Anastasia A. Gavrilova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; (A.A.K.); (S.I.S.); (A.A.G.); (T.E.T.)
| | - Timofey E. Tyugashev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; (A.A.K.); (S.I.S.); (A.A.G.); (T.E.T.)
| | - Elena S. Mikushina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; (A.A.K.); (S.I.S.); (A.A.G.); (T.E.T.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; (A.A.K.); (S.I.S.); (A.A.G.); (T.E.T.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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Wang W, Lin L, Zhang Q, Yang J, Kamili E, Chu J, Li X, Yang S, Xu Y. Heteroplasmy and Individual Mitogene Pools: Characteristics and Potential Roles in Ecological Studies. BIOLOGY 2023; 12:1452. [PMID: 37998051 PMCID: PMC10669347 DOI: 10.3390/biology12111452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
The mitochondrial genome (mitogenome or mtDNA), the extrachromosomal genome, is a multicopy circular DNA with high mutation rates due to replication and repair errors. A mitochondrion, cell, tissue, organ, or an individual body may hold multiple variants, both inherited and developed over a lifetime, which make up individual mitogene pools. This phenomenon is also called mtDNA heteroplasmy. MtDNA variants influence cellular and tissular functions and are consequently subjected to selection. Although it has long been recognized that only inheritable germline heteroplasmies have evolutionary significance, non-inheritable somatic heteroplasmies have been overlooked since they directly affect individual fitness and thus indirectly affect the fate of heritable germline variants. This review focuses on the characteristics, dynamics, and functions of mtDNA heteroplasmy and proposes the concept of individual mitogene pools to discuss individual genetic diversity from multiple angles. We provide a unique perspective on the relationship between individual genetic diversity and heritable genetic diversity and guide how the individual mitogene pool with novel genetic markers can be applied to ecological research.
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Affiliation(s)
| | | | | | | | | | | | | | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (W.W.); (L.L.); (Q.Z.); (J.Y.); (E.K.); (J.C.); (X.L.)
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (W.W.); (L.L.); (Q.Z.); (J.Y.); (E.K.); (J.C.); (X.L.)
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Qin T, Hu B, Zhao Q, Wang Y, Wang S, Luo D, Lyu J, Chen Y, Gan J, Huang Z. Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom. Int J Mol Sci 2023; 24:15758. [PMID: 37958741 PMCID: PMC10647396 DOI: 10.3390/ijms242115758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
DNA synthesis catalyzed by DNA polymerase is essential for all life forms, and phosphodiester bond formation with phosphorus center inversion is a key step in this process. Herein, by using a single-selenium-atom-modified dNTP probe, we report a novel strategy to visualize the reaction stereochemistry and catalysis. We capture the before- and after-reaction states and provide explicit evidence of the center inversion and in-line attacking SN2 mechanism of DNA polymerization, while solving the diastereomer absolute configurations. Further, our kinetic and thermodynamic studies demonstrate that in the presence of Mg2+ ions (or Mn2+), the binding affinity (Km) and reaction selectivity (kcat/Km) of dGTPαSe-Rp were 51.1-fold (or 19.5-fold) stronger and 21.8-fold (or 11.3-fold) higher than those of dGTPαSe-Sp, respectively, indicating that the diastereomeric Se-Sp atom was quite disruptive of the binding and catalysis. Our findings reveal that the third metal ion is much more critical than the other two metal ions in both substrate recognition and bond formation, providing insights into how to better design the polymerase inhibitors and discover the therapeutics.
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Affiliation(s)
- Tong Qin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Bei Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Qianwei Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Yali Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Yibin 644000, China;
| | - Shaoxin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Danyan Luo
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acid Institute, Chengdu 618000, China;
| | - Jiazhen Lyu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
| | - Yiqing Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China; (T.Q.); (B.H.); (Q.Z.); (S.W.); (J.L.)
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acid Institute, Chengdu 618000, China;
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 610000, China
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Kuznetsova AA, Kuznetsov NA. Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches. Bioengineering (Basel) 2023; 10:1150. [PMID: 37892880 PMCID: PMC10604792 DOI: 10.3390/bioengineering10101150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
DNA-dependent DNA polymerases have been intensively studied for more than 60 years and underlie numerous biotechnological and diagnostic applications. In vitro, DNA polymerases are used for DNA manipulations, including cloning, PCR, site-directed mutagenesis, sequencing, and others. Understanding the mechanisms of action of DNA polymerases is important for the creation of new enzymes possessing improved or modified properties. This review is focused on archaeal family B DNA polymerases. These enzymes have high fidelity and thermal stability and are finding many applications in molecular biological methods. Nevertheless, the search for and construction of new DNA polymerases with altered properties is constantly underway, including enzymes for synthetic biology. This brief review describes advances in the development of family B DNA polymerases for PCR, synthesis of xeno-nucleic acids, and reverse transcription.
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Affiliation(s)
- Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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Petronek MS, Allen BG. Maintenance of genome integrity by the late-acting cytoplasmic iron-sulfur assembly (CIA) complex. Front Genet 2023; 14:1152398. [PMID: 36968611 PMCID: PMC10031043 DOI: 10.3389/fgene.2023.1152398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.
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Characterization and genome analysis of Escherichia phage fBC-Eco01, isolated from wastewater in Tunisia. Arch Virol 2023; 168:44. [PMID: 36609878 PMCID: PMC9825357 DOI: 10.1007/s00705-022-05680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/01/2022] [Indexed: 01/09/2023]
Abstract
The rise of antibiotic resistance in bacterial strains has led to vigorous exploration for alternative treatments. To this end, phage therapy has been revisited, and it is gaining increasing attention, as it may represent an efficient alternative for treating multiresistant pathogenic bacteria. Phage therapy is considered safe, and phages do not infect eukaryotic cells. There have been many studies investigating phage-host bacteria interactions and the ability of phages to target specific hosts. Escherichia coli is the causative agent of a multitude of infections, ranging from urinary tract infections to sepsis, with growing antibiotic resistance. In this study, we characterized the Escherichia phage fBC-Eco01, which was isolated from a water sample collected at Oued, Tunis. Electron microscopy showed that fBC-Eco01 phage particles have siphovirus morphology, with an icosahedral head of 61 ± 3 nm in diameter and a non-contractile tail of 94 ± 2 nm in length and 12 ± 0.9 nm in width. The genome of fBC-Eco01 is a linear double-stranded DNA of 43.466 bp with a GC content of 50.4%. Comparison to databases allowed annotation of the functions to 39 of the 78 predicted gene products. A single-step growth curve revealed that fBC-Eco01 has a latent period of 30 minutes and a burst size of 175 plaque-forming units (PFU) per infected cell. Genomic analysis indicated that fBC-Eco01 is a member of the subfamily Guernseyvirinae. It is most closely related to a group of phages of the genus Kagunavirus that infect Enterobacter, Raoultella, and Escherichia strains.
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Tsai YC, Chen WY, Chiu CC. Molecular effects of site-specific phosphate-methylated primer on the structure and motions of Taq DNA polymerase. Comput Struct Biotechnol J 2023; 21:1820-1827. [PMID: 36923470 PMCID: PMC10009445 DOI: 10.1016/j.csbj.2023.02.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Conventional DNA primers for PCR often suffer from poor sensitivity in specific gene detection. Recently, oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. Yet, site-specific MPTE-modifications on DNA primers have been reported to affect PCR amplification efficiencies while the detailed mechanism remains elusive. Here, we utilized molecular dynamics (MD) simulation to examine the effects of site-specific MPTE-modified primers on the structure and motions of DNA/Taq polymerase complexes. All tested MPTE-DNA/Taq complexes exhibited RMSD values below 2 Å, indicating insignificant effects of all methylation sites on the complex stability. The energetic and hydrogen-bonding analyses suggest minor effects of methylation at t-3, t-4, t-6, and t-7 positions on the DNA-Taq interaction. Principal component analyses further reveal that only t-3, and t-7 methylations preserve the motions of the Taq thumb domain. The site-specific methylation affects the interaction between DNA and the surrounding protein residues, resulting in allosteric-like effects on the DNA/Taq complex. The MD data complement the best experimentally observed PCR efficacies for the t-3 and t-7 positions among all tested MPTE-primers. The unveiled molecular insights can benefit the design of novel PCR primers for improving genetic testing platforms.
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Affiliation(s)
- Yi-Chen Tsai
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Wen-Yih Chen
- Department of Chemical and Materials Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Chi-Cheng Chiu
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.,Hierarchical Green-Energy Materials (Hi-GEM) Research Center, National Cheng Kung University, Tainan 701, Taiwan
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Cohen-Paes A, de Alcântara AL, de Souza Menezes E, Moreira FC, Fernandes MR, Guerreiro JF, Ribeiro-Dos-Santos Â, Dos Santos SEB, dos Santos NPC. Characterization of DNA Polymerase Genes in Amazonian Amerindian Populations. Genes (Basel) 2022; 14:53. [PMID: 36672794 PMCID: PMC9859017 DOI: 10.3390/genes14010053] [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: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 12/28/2022] Open
Abstract
Due to their continuing geographic isolation, the Amerindian populations of the Brazilian Amazon present a different genetic profile when compared to other continental populations. Few studies have investigated genetic variants present in these populations, especially in the context of next-generation sequencing. Knowledge of the molecular profile of a population is one of the bases for inferences about human evolutionary history, in addition, it has the ability to assist in the validation of molecular biomarkers of susceptibility to complex and rare diseases, and in the improvement of specific precision medicine protocols applied to these populations and to populations with high Amerindian ancestry, such as Brazilians. DNA polymerases play essential roles in DNA replication, repair, recombination, or damage repair, and their influence on various clinical phenotypes has been demonstrated in the specialized literature. Thus, the aim of this study is to characterize the molecular profile of POLA1, POLE, POLG, POLQ, and REV3L genes in Amerindian populations from the Brazilian Amazon, comparing these findings with genomic data from five continental populations described in the gnomAD database, and with data from the Brazilian population described in ABraOM. We performed the whole exome sequencing (WES) of 63 Indigenous individuals. Our study described for the first time the allele frequency of 45 variants already described in the other continental populations, but never before described in the investigated Amerindian populations. Our results also describe eight unique variants of the investigated Amerindians populations, with predictions of moderate, modifier and high clinical impact. Our findings demonstrate the unique genetic profile of the Indigenous population of the Brazilian Amazon, reinforcing the need for further studies on these populations, and may contribute to the creation of public policies that optimize not only the quality of life of this population, but also of the Brazilian population.
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Affiliation(s)
- Amanda Cohen-Paes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
| | | | - Elisa de Souza Menezes
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
| | | | | | - João Farias Guerreiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Sidney Emanuel Batista Dos Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, PA, Brazil
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
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Zhou ZX, Kunkel TA. Extrinsic proofreading. DNA Repair (Amst) 2022; 117:103369. [PMID: 35850061 PMCID: PMC9561950 DOI: 10.1016/j.dnarep.2022.103369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/24/2022]
Abstract
The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes. Correct rather than incorrect dNTPs are almost always incorporated by the three major replicases, DNA polymerases α, δ and ε. When an incorrect base is occasionally inserted, the latter Pols δ and ε also have a 3 ´ to 5 ´ exonuclease activity that can remove the mismatch to allow correct DNA synthesis to proceed. Lastly, rare mismatches that escape proofreading activity and are present in newly replicated DNA can be removed by DNA mismatch repair. In this review, we consider evidence supporting the hypothesis that the second mechanism, proofreading, can operate in two different ways. Primer terminal mismatches made by either Pol δ or Pol ε can be 'intrinsically' proofread. This mechanism occurs by direct transfer of a misinserted base made at the polymerase active site to the exonuclease active site that is located a short distance away. Intrinsic proofreading allows mismatch excision without intervening enzyme dissociation. Alternatively, considerable evidence suggests that mismatches made by any of the three replicases can also be proofread by 'extrinsic' proofreading by Pol δ. Extrinsic proofreading occurs when a mismatch made by any of the three replicases is initially abandoned, thereby allowing the exonuclease active site of Pol δ to bind directly to and remove the mismatch before replication continues. Here we review the evidence that extrinsic proofreading significantly enhances the fidelity of nuclear DNA replication, and we then briefly consider the implications of this process for evolution and disease.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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13
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Adebayo IA, Habib MAH, Sarmiento ME, Acosta A, Yaacob NS, Ismail MN. Proteomic analysis of Malaysian Horseshoe crab (Tachypleus gigas) hemocytes gives insights into its innate immunity host defence system and other biological processes. PLoS One 2022; 17:e0272799. [PMID: 35947629 PMCID: PMC9365167 DOI: 10.1371/journal.pone.0272799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Horseshoe crabs are one of the most studied invertebrates due to their remarkable innate immunity mechanism and biological processes. In this work, the proteins of the lipopolysaccharides (LPS)-stimulated and non-stimulated hemocytes of Malaysian Tachypleus gigas were profiled using LC-MS/MS. A total of 154 proteins were identified in both types of samples. Additionally, seventy-seven proteins were commonly found in both conditions, while 52 and 25 proteins were uniquely found in the LPS-stimulated and non-stimulated hemocytes, respectively. ATP-dependent energy-generating proteins such as actins and BLTX actin-related proteins were detected in both stimulated and non-stimulated T. gigas hemocytes, but more of such proteins were found in the former type. Proteins such as tachylectin-2, coagulogen, c-reactive proteins, histones, hemocyanin, and DNA polymerase, which play key roles in the organism’s innate immunity, were differentially expressed in the hemocytes following LPS challenge. In conclusion, the proteins identified in the hemolymph of T. gigas are vital for the organism’s molecular functions, biological processes, and activation of innate immunity.
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Affiliation(s)
- Ismail Abiola Adebayo
- Faculty of Biomedical Sciences, Department of Microbiology and Immunology, Kampala International University, Ishaka, Bushenyi, Uganda
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Department of Clinical Biology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
| | - Maria E. Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kelantan, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
- * E-mail:
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14
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Dorawa S, Werbowy O, Plotka M, Kaczorowska AK, Makowska J, Kozlowski LP, Fridjonsson OH, Hreggvidsson GO, Aevarsson A, Kaczorowski T. Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity. Int J Mol Sci 2022; 23:ijms23147945. [PMID: 35887293 PMCID: PMC9324360 DOI: 10.3390/ijms23147945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
We present a structural and functional analysis of the DNA polymerase of thermophilic Thermus thermophilus MAT72 phage vB_Tt72. The enzyme shows low sequence identity (<30%) to the members of the type-A family of DNA polymerases, except for two yet uncharacterized DNA polymerases of T. thermophilus phages: φYS40 (91%) and φTMA (90%). The Tt72 polA gene does not complement the Escherichia colipolA− mutant in replicating polA-dependent plasmid replicons. It encodes a 703-aa protein with a predicted molecular weight of 80,490 and an isoelectric point of 5.49. The enzyme contains a nucleotidyltransferase domain and a 3′-5′ exonuclease domain that is engaged in proofreading. Recombinant enzyme with His-tag at the N-terminus was overproduced in E. coli, subsequently purified by immobilized metal affinity chromatography, and biochemically characterized. The enzyme exists in solution in monomeric form and shows optimum activity at pH 8.5, 25 mM KCl, and 0.5 mM Mg2+. Site-directed analysis proved that highly-conserved residues D15, E17, D78, D180, and D184 in 3′-5′ exonuclease and D384 and D615 in the nucleotidyltransferase domain are critical for the enzyme’s activity. Despite the source of origin, the Tt72 DNA polymerase has not proven to be highly thermoresistant, with a temperature optimum at 55 °C. Above 60 °C, the rapid loss of function follows with no activity > 75 °C. However, during heat treatment (10 min at 75 °C), trehalose, trimethylamine N-oxide, and betaine protected the enzyme against thermal inactivation. A midpoint of thermal denaturation at Tm = 74.6 °C (ΔHcal = 2.05 × 104 cal mol−1) and circular dichroism spectra > 60 °C indicate the enzyme’s moderate thermal stability.
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Affiliation(s)
- Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland;
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland;
| | - Lukasz P. Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | | | - Gudmundur O. Hreggvidsson
- Matis, 113 Reykjavik, Iceland; (O.H.F.); (G.O.H.); (A.A.)
- Department of Biology, School of Engineering and Natural Sciences, University of Iceland, 102 Reykjavik, Iceland
| | | | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland; (S.D.); (O.W.); (M.P.)
- Correspondence:
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15
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Structural and Molecular Kinetic Features of Activities of DNA Polymerases. Int J Mol Sci 2022; 23:ijms23126373. [PMID: 35742812 PMCID: PMC9224347 DOI: 10.3390/ijms23126373] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 02/01/2023] Open
Abstract
DNA polymerases catalyze DNA synthesis during the replication, repair, and recombination of DNA. Based on phylogenetic analysis and primary protein sequences, DNA polymerases have been categorized into seven families: A, B, C, D, X, Y, and RT. This review presents generalized data on the catalytic mechanism of action of DNA polymerases. The structural features of different DNA polymerase families are described in detail. The discussion highlights the kinetics and conformational dynamics of DNA polymerases from all known polymerase families during DNA synthesis.
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16
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Park J, Baruch-Torres N, Iwai S, Herrmann GK, Brieba LG, Yin YW. Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability. Front Mol Biosci 2022; 9:808036. [PMID: 35355510 PMCID: PMC8959595 DOI: 10.3389/fmolb.2022.808036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022] Open
Abstract
Human mitochondrial DNA contains more UV-induced lesions than the nuclear DNA due to lack of mechanism to remove bulky photoproducts. Human DNA polymerase gamma (Pol γ) is the sole DNA replicase in mitochondria, which contains a polymerase (pol) and an exonuclease (exo) active site. Previous studies showed that Pol γ only displays UV lesion bypassing when its exonuclease activity is obliterated. To investigate the reaction environment on Pol γ translesion activity, we tested Pol γ DNA activity in the presence of different metal ions. While Pol γ is unable to replicate through UV lesions on DNA templates in the presence of Mg2+, it exhibits robust translesion DNA synthesis (TLS) on cyclobutane pyrimidine dimer (CPD)-containing template when Mg2+ was mixed with or completely replaced by Mn2+. Under these conditions, the efficiency of Pol γ′s TLS opposite CPD is near to that on a non-damaged template and is 800-fold higher than that of exonuclease-deficient Pol γ. Interestingly, Pol γ exhibits higher exonuclease activity in the presence of Mn2+ than with Mg2+, suggesting Mn2+-stimulated Pol γ TLS is not via suppressing its exonuclease activity. We suggest that Mn2+ ion expands Pol γ′s pol active site relative to Mg2+ so that a UV lesion can be accommodated and blocks the communication between pol and exo active sites to execute translesion DNA synthesis.
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Affiliation(s)
- Joon Park
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Noe Baruch-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Japan
| | - Geoffrey K. Herrmann
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
- *Correspondence: Luis G. Brieba, ; Y. Whitney Yin,
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, United States
- *Correspondence: Luis G. Brieba, ; Y. Whitney Yin,
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17
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PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. Biomolecules 2022; 12:biom12020248. [PMID: 35204749 PMCID: PMC8961649 DOI: 10.3390/biom12020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with conventional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a DNA primase, elongating primers that PrimPol itself sythesizes, or as translesion synthesis (TLS) DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only acts as a DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer.
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18
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Morcinek-Orłowska J, Zdrojewska K, Węgrzyn A. Bacteriophage-Encoded DNA Polymerases-Beyond the Traditional View of Polymerase Activities. Int J Mol Sci 2022; 23:635. [PMID: 35054821 PMCID: PMC8775771 DOI: 10.3390/ijms23020635] [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: 11/30/2021] [Revised: 12/28/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
DNA polymerases are enzymes capable of synthesizing DNA. They are involved in replication of genomes of all cellular organisms as well as in processes of DNA repair and genetic recombination. However, DNA polymerases can also be encoded by viruses, including bacteriophages, and such enzymes are involved in viral DNA replication. DNA synthesizing enzymes are grouped in several families according to their structures and functions. Nevertheless, there are examples of bacteriophage-encoded DNA polymerases which are significantly different from other known enzymes capable of catalyzing synthesis of DNA. These differences are both structural and functional, indicating a huge biodiversity of bacteriophages and specific properties of their enzymes which had to evolve under certain conditions, selecting unusual properties of the enzymes which are nonetheless crucial for survival of these viruses, propagating as special kinds of obligatory parasites. In this review, we present a brief overview on DNA polymerases, and then we discuss unusual properties of different bacteriophage-encoded enzymes, such as those able to initiate DNA synthesis using the protein-priming mechanisms or even start this process without any primer, as well as able to incorporate untypical nucleotides. Apart from being extremely interesting examples of biochemical biodiversity, bacteriophage-encoded DNA polymerases can also be useful tools in genetic engineering and biotechnology.
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Affiliation(s)
- Joanna Morcinek-Orłowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Karolina Zdrojewska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.M.-O.); (K.Z.)
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdansk, Poland
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19
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Rosenstein AH, Walker VK. Fidelity of a Bacterial DNA Polymerase in Microgravity, a Model for Human Health in Space. Front Cell Dev Biol 2021; 9:702849. [PMID: 34912795 PMCID: PMC8666419 DOI: 10.3389/fcell.2021.702849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Long-term space missions will expose crew members, their cells as well as their microbiomes to prolonged periods of microgravity and ionizing radiation, environmental stressors for which almost no earth-based organisms have evolved to survive. Despite the importance of maintaining genomic integrity, the impact of these stresses on DNA polymerase-mediated replication and repair has not been fully explored. DNA polymerase fidelity and replication rates were assayed under conditions of microgravity generated by parabolic flight and compared to earth-like gravity. Upon commencement of a parabolic arc, primed synthetic single-stranded DNA was used as a template for one of two enzymes (Klenow fragment exonuclease+/-; with and without proofreading exonuclease activity, respectively) and were quenched immediately following the 20 s microgravitational period. DNA polymerase error rates were determined with an algorithm developed to identify experimental mutations. In microgravity Klenow exonuclease+ showed a median 1.1-fold per-base decrease in polymerization fidelity for base substitutions when compared to earth-like gravity (p = 0.02), but in the absence of proofreading activity, a 2.4-fold decrease was observed (p = 1.98 × 10-11). Similarly, 1.1-fold and 1.5-fold increases in deletion frequencies in the presence or absence of exonuclease activity (p = 1.51 × 10-7 and p = 8.74 × 10-13), respectively, were observed in microgravity compared to controls. The development of this flexible semi-autonomous payload system coupled with genetic and bioinformatic approaches serves as a proof-of-concept for future space health research.
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Affiliation(s)
- Aaron H Rosenstein
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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20
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Caracciolo D, Riillo C, Di Martino MT, Tagliaferri P, Tassone P. Alternative Non-Homologous End-Joining: Error-Prone DNA Repair as Cancer's Achilles' Heel. Cancers (Basel) 2021; 13:cancers13061392. [PMID: 33808562 PMCID: PMC8003480 DOI: 10.3390/cancers13061392] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Cancer onset and progression lead to a high rate of DNA damage, due to replicative and metabolic stress. To survive in this dangerous condition, cancer cells switch the DNA repair machinery from faithful systems to error-prone pathways, strongly increasing the mutational rate that, in turn, supports the disease progression and drug resistance. Although DNA repair de-regulation boosts genomic instability, it represents, at the same time, a critical cancer vulnerability that can be exploited for synthetic lethality-based therapeutic intervention. We here discuss the role of the error-prone DNA repair, named Alternative Non-Homologous End Joining (Alt-NHEJ), as inducer of genomic instability and as a potential therapeutic target. We portray different strategies to drug Alt-NHEJ and discuss future challenges for selecting patients who could benefit from Alt-NHEJ inhibition, with the aim of precision oncology. Abstract Error-prone DNA repair pathways promote genomic instability which leads to the onset of cancer hallmarks by progressive genetic aberrations in tumor cells. The molecular mechanisms which foster this process remain mostly undefined, and breakthrough advancements are eagerly awaited. In this context, the alternative non-homologous end joining (Alt-NHEJ) pathway is considered a leading actor. Indeed, there is experimental evidence that up-regulation of major Alt-NHEJ components, such as LIG3, PolQ, and PARP1, occurs in different tumors, where they are often associated with disease progression and drug resistance. Moreover, the Alt-NHEJ addiction of cancer cells provides a promising target to be exploited by synthetic lethality approaches for the use of DNA damage response (DDR) inhibitors and even as a sensitizer to checkpoint-inhibitors immunotherapy by increasing the mutational load. In this review, we discuss recent findings highlighting the role of Alt-NHEJ as a promoter of genomic instability and, therefore, as new cancer’s Achilles’ heel to be therapeutically exploited in precision oncology.
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21
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Selective Metal Ion Utilization Contributes to the Transformation of the Activity of Yeast Polymerase η from DNA Polymerization toward RNA Polymerization. Int J Mol Sci 2020; 21:ijms21218248. [PMID: 33158019 PMCID: PMC7672554 DOI: 10.3390/ijms21218248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/16/2022] Open
Abstract
Polymerase eta (Polη) is a translesion synthesis DNA polymerase directly linked to cancer development. It can bypass several DNA lesions thereby rescuing DNA damage-stalled replication complexes. We previously presented evidence implicating Saccharomyces cerevisiae Polη in transcription elongation, and identified its specific RNA extension and translesion RNA synthetic activities. However, RNA synthesis by Polη proved rather inefficient under conditions optimal for DNA synthesis. Searching for factors that could enhance its RNA synthetic activity, we have identified the divalent cation of manganese. Here, we show that manganese triggers drastic changes in the activity of Polη. Kinetics experiments indicate that manganese increases the efficiency of ribonucleoside incorporation into RNA by ~400–2000-fold opposite undamaged DNA, and ~3000 and ~6000-fold opposite TT dimer and 8oxoG, respectively. Importantly, preference for the correct base is maintained with manganese during RNA synthesis. In contrast, activity is strongly impaired, and base discrimination is almost lost during DNA synthesis by Polη with manganese. Moreover, Polη shows strong preference for manganese during RNA synthesis even at a 25-fold excess magnesium concentration. Based on this, we suggest that a new regulatory mechanism, selective metal cofactor utilization, modulates the specificity of Polη helping it to perform distinct activities needed for its separate functions during replication and transcription.
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22
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Li S, Shi B, Liu X, An HX. Acetylation and Deacetylation of DNA Repair Proteins in Cancers. Front Oncol 2020; 10:573502. [PMID: 33194676 PMCID: PMC7642810 DOI: 10.3389/fonc.2020.573502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Hundreds of DNA repair proteins coordinate together to remove the diverse damages for ensuring the genomic integrity and stability. The repair system is an extensive network mainly encompassing cell cycle arrest, chromatin remodeling, various repair pathways, and new DNA fragment synthesis. Acetylation on DNA repair proteins is a dynamic epigenetic modification orchestrated by lysine acetyltransferases (HATs) and lysine deacetylases (HDACs), which dramatically affects the protein functions through multiple mechanisms, such as regulation of DNA binding ability, protein activity, post-translational modification (PTM) crosstalk, and protein–protein interaction. Accumulating evidence has indicated that the aberrant acetylation of DNA repair proteins contributes to the dysfunction of DNA repair ability, the pathogenesis and progress of cancer, as well as the chemosensitivity of cancer cells. In the present scenario, targeting epigenetic therapy is being considered as a promising method at par with the conventional cancer therapeutic strategies. This present article provides an overview of the recent progress in the functions and mechanisms of acetylation on DNA repair proteins involved in five major repair pathways, which warrants the possibility of regulating acetylation on repair proteins as a therapeutic target in cancers.
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Affiliation(s)
- Shiqin Li
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Bingbing Shi
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Han-Xiang An
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
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23
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Understanding the Effect of Multiple Domain Deletion in DNA Polymerase I from Geobacillus Sp. Strain SK72. Catalysts 2020. [DOI: 10.3390/catal10080936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic polymerase activity with additional traits that used isothermal amplification. However, the 3′-5′ exonuclease domain that carries a proofreading activity was disabled. Yet, the structure remained attached to the 5′-3′ polymerization domain without affecting its ability. The purpose of this non-functional domain still remains scarce. It either gives negative effects or provides structural support to the DNA polymerase. Here, we compared the effect of deleting each domain against the polymerase activity. The recombinant wild type and its variants were successfully purified and characterized. Interestingly, SK72-Exo (a large fragment excluding the 5′-3′ exonuclease domain) exhibited better catalytic activity than the native SK72 (with all three domains) at similar optimum temperature and pH profile, and it showed longer stability at 70 °C. Meanwhile, SK72-Exo2 (polymerization domain without both the 5′-3′ and 3′-5′ exonuclease domain) displayed the lowest activity with an optimum at 40 °C and favored a more neutral environment. It was also the least stable among the variants, with almost no activity at 50 °C for the first 10 min. In conclusion, cutting both exonuclease domains in DNA polymerase I has a detrimental effect on the polymerization activity and structural stability.
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24
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Zhang L, Jiang D, Shi H, Wu M, Gan Q, Yang Z, Oger P. Characterization and application of a family B DNA polymerase from the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans. Int J Biol Macromol 2020; 156:217-224. [PMID: 32229210 DOI: 10.1016/j.ijbiomac.2020.03.204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/07/2020] [Accepted: 03/24/2020] [Indexed: 11/19/2022]
Abstract
Thermococcus gammatolerans is anaerobic euryarchaeon which grows optimally at 88 °C and its genome encodes a family B DNA polymerase (Tga PolB). Herein, we cloned the gene of Tga PolB, expressed and purified the gene product, and characterized the enzyme biochemically. The recombinant Tga PolB can efficiently synthesize DNA at high temperature, and retain 93% activity after heated at 95 °C for 1.0 h, suggesting that the enzyme is thermostable. Furthermore, the optimal pH for the enzyme activity was measured to be 7.0-9.0. Tga PolB activity is dependent on a divalent cation, among which magnesium ion is optimal. NaCl at low concentration stimulates the enzyme activity but at high concentration inhibits enzyme activity. Interestingly, Tga PolB is able to efficiently bypass uracil in DNA, which is distinct from other archaeal family B DNA pols. By contrast, Tga PolB is halted by an AP site in DNA, as observed in other archaeal family B DNA polymerases. Furthermore, Tga PolB extends the mismatched ends with reduced efficiencies. The enzyme possesses 3'-5' exonuclease activity and this activity is inhibited by dNTPs. The DNA binding assays showed that Tga PolB can efficiently bind to ssDNA and primed DNA, and have a marked preference for primed DNA. Last, Tga PolB can be used in routine PCR.
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Affiliation(s)
- Likui Zhang
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China; Guangling College, Yangzhou University, China.
| | - Donghao Jiang
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Haoqiang Shi
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Mai Wu
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Qi Gan
- Marine Science & Technology Institute, College of Environmental Science and Engineering, Yangzhou University, Jiangsu Province 225127, China
| | - Zhihui Yang
- College of Plant Protection, Agricultural University of Hebei, Baoding, City, Hebei Province 071001, China.
| | - Philippe Oger
- Univ Lyon, INSA de Lyon, CNRS UMR 5240, Villeurbanne, France.
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25
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Farag MR, Alagawany M, Bin-Jumah M, Othman SI, Khafaga AF, Shaheen HM, Samak D, Shehata AM, Allam AA, Abd El-Hack ME. The Toxicological Aspects of the Heat-Borne Toxicant 5-Hydroxymethylfurfural in Animals: A Review. Molecules 2020; 25:E1941. [PMID: 32331408 PMCID: PMC7221839 DOI: 10.3390/molecules25081941] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/17/2023] Open
Abstract
The incidence of adverse reactions in food is very low, however, some food products contain toxins formed naturally due to their handling, processing and storage conditions. 5-(Hydroxymethyl)-2-furfural (HMF) can be formed by hydrogenation of sugar substances in some of manufactured foodstuffs and honey under elevated temperatures and reduced pH conditions following Maillard reactions. In previous studies, it was found that HMF was responsible for harmful (mutagenic, genotoxic, cytotoxic and enzyme inhibitory) effects on human health. HMF occurs in a wide variety of food products like dried fruit, juice, caramel products, coffee, bakery, malt and vinegar. The formation of HMF is not only an indicator of food storage conditions and quality, but HMF could also be used as an indicator of the potential occurrence of contamination during heat-processing of some food products such as coffee, milk, honey and processed fruits. This review focuses on HMF formation and summarizes the adverse effects of HMF on human health.
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Affiliation(s)
- Mayada R. Farag
- Forensic Medicine and Toxicology Department, Veterinary Medicine Faculty, Zagazig University, Zagazig 44519, Egypt
| | - Mahmoud Alagawany
- Poultry Department, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt;
| | - May Bin-Jumah
- Biology Department, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia; (M.B.-J.); (S.I.O.)
| | - Sarah I. Othman
- Biology Department, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia; (M.B.-J.); (S.I.O.)
| | - Asmaa F. Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt;
| | - Hazem M. Shaheen
- Department of Pharmacology, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt;
| | - Dalia Samak
- Department of Veterinary Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt;
| | - Abdelrazeq M. Shehata
- Department of Animal Production, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt;
- Department of Dairy Science & Food Technology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ahmed A. Allam
- Department of Zoology, Faculty of Science, Beni-suef University, Beni-suef 65211, Egypt;
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26
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Acharya N, Khandagale P, Thakur S, Sahu JK, Utkalaja BG. Quaternary structural diversity in eukaryotic DNA polymerases: monomeric to multimeric form. Curr Genet 2020; 66:635-655. [PMID: 32236653 DOI: 10.1007/s00294-020-01071-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Sixteen eukaryotic DNA polymerases have been identified and studied so far. Based on the sequence similarity of the catalytic subunits of DNA polymerases, these have been classified into four A, B, X and Y families except PrimPol, which belongs to the AEP family. The quaternary structure of these polymerases also varies depending upon whether they are composed of one or more subunits. Therefore, in this review, we used a quaternary structure-based classification approach to group DNA polymerases as either monomeric or multimeric and highlighted functional significance of their accessory subunits. Additionally, we have briefly summarized various DNA polymerase discoveries from a historical perspective, emphasized unique catalytic mechanism of each DNA polymerase and highlighted recent advances in understanding their cellular functions.
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Affiliation(s)
- Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Shweta Thakur
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Jugal Kishor Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
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27
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Dong Y, Sun F, Ping Z, Ouyang Q, Qian L. DNA storage: research landscape and future prospects. Natl Sci Rev 2020; 7:1092-1107. [PMID: 34692128 PMCID: PMC8288837 DOI: 10.1093/nsr/nwaa007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/06/2020] [Accepted: 01/18/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
The global demand for data storage is currently outpacing the world's storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.
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Affiliation(s)
- Yiming Dong
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fajia Sun
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qi Ouyang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Long Qian
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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28
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Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci 2020; 77:35-59. [PMID: 31722068 PMCID: PMC7050493 DOI: 10.1007/s00018-019-03368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Max S Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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29
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Zhu J, Wang J, Cheng K, Chen H, An R, Zhang Y, Komiyama M, Liang X. Effective Characterization of DNA Ligation Kinetics by High-Resolution Melting Analysis. Chembiochem 2019; 21:785-788. [PMID: 31592561 DOI: 10.1002/cbic.201900489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/07/2019] [Indexed: 12/31/2022]
Abstract
High-resolution melting (HRM) analysis has been improved and applied for the first time to quantitative analysis of enzymatic reactions. By using the relative ratios of peak intensities of substrates and products, the quantitativity of conventional HRM analysis has been improved to allow detailed kinetic analysis. As an example, the ligation of sticky ends through the action of T4 DNA ligase has been kinetically analyzed, with comprehensive data on substrate specificity and other properties having been obtained. For the first time, the kinetic parameters (kobs and apparent Km ) of sticky-end ligation were obtained for both fully matched and mismatched sticky ends. The effect of ATP concentration on sticky-end ligation was also investigated. The improved HRM method should also be applicable to versatile DNA-transforming enzymes, because the only requirement is that the products have Tm values different enough from the substrates.
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Affiliation(s)
- Jianming Zhu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Jing Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,CAS Key laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, P. R. China
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30
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Combined immunodeficiency caused by a loss-of-function mutation in DNA polymerase delta 1. J Allergy Clin Immunol 2019; 145:391-401.e8. [PMID: 31629014 DOI: 10.1016/j.jaci.2019.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/11/2019] [Accepted: 10/04/2019] [Indexed: 01/29/2023]
Abstract
BACKGROUND Mutations affecting DNA polymerases have been implicated in genomic instability and cancer development, but the mechanisms by which they can affect the immune system remain largely unexplored. OBJECTIVE We sought to establish the role of DNA polymerase δ1 catalytic subunit (POLD1) as the cause of a primary immunodeficiency in an extended kindred. METHODS We performed whole-exome and targeted gene sequencing, lymphocyte characterization, molecular and functional analyses of the DNA polymerase δ (Polδ) complex, and T- and B-cell antigen receptor repertoire analysis. RESULTS We identified a missense mutation (c. 3178C>T; p.R1060C) in POLD1 in 3 related subjects who presented with recurrent, especially herpetic, infections and T-cell lymphopenia with impaired T-cell but not B-cell proliferation. The mutation destabilizes the Polδ complex, leading to ineffective recruitment of replication factor C to initiate DNA replication. Molecular dynamics simulation revealed that the R1060C mutation disrupts the intramolecular interaction between the POLD1 CysB motif and the catalytic domain and also between POLD1 and the Polδ subunit POLD2. The patients exhibited decreased numbers of naive CD4 and especially CD8 T cells in favor of effector memory subpopulations. This skewing was associated with oligoclonality and restricted T-cell receptor β-chain V-J pairing in CD8+ but not CD4+ T cells, suggesting that POLD1R1060C differentially affects peripheral CD8+ T-cell expansion and possibly thymic selection. CONCLUSION These results identify gene defects in POLD1 as a novel cause of T-cell immunodeficiency.
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31
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Abstract
Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.
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32
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Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters. FRONTIERS IN PLANT SCIENCE 2019; 10:1055. [PMID: 31543887 PMCID: PMC6728418 DOI: 10.3389/fpls.2019.01055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
Base excision repair (BER) is a critical genome defense pathway that deals with a broad range of non-voluminous DNA lesions induced by endogenous or exogenous genotoxic agents. BER is a complex process initiated by the excision of the damaged base, proceeds through a sequence of reactions that generate various DNA intermediates, and culminates with restoration of the original DNA structure. BER has been extensively studied in microbial and animal systems, but knowledge in plants has lagged behind until recently. Results obtained so far indicate that plants share many BER factors with other organisms, but also possess some unique features and combinations. Plant BER plays an important role in preserving genome integrity through removal of damaged bases. However, it performs additional important functions, such as the replacement of the naturally modified base 5-methylcytosine with cytosine in a plant-specific pathway for active DNA demethylation.
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Affiliation(s)
- Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Rafael R. Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
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33
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Lushnikov A, Hooy R, Sohn J, Krasnoslobodtsev A. Characterization of DNA bound cyclic GMP-AMP synthase using atomic force microscopy imaging. Methods Enzymol 2019; 625:157-166. [PMID: 31455525 DOI: 10.1016/bs.mie.2019.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The protocol described herein allows for acquiring topography images of DNA-protein complexes using Atomic Force Microscopy imaging. Since the very beginning of this method, AFM has been an indispensable tool for characterization of biomolecular complexes with exceptional capability of observing single complexes. This method can visualize structural characteristics of DNA-protein assemblies and evaluate differences between individual complexes. Although this protocol is generally applicable to a large number of various proteins complexed with DNA, we use cyclic G/AMP synthase (cGAS) enzyme as a case study for the protocol description.
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Affiliation(s)
- Alexander Lushnikov
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE, United States
| | - Richard Hooy
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD, United States
| | - Jungsan Sohn
- Department of Biophysics and Biophysical Chemistry, John Hopkins School of Medicine, Baltimore, MD, United States
| | - Alexey Krasnoslobodtsev
- Nanoimaging Core Facility at the University of Nebraska Medical Center, Omaha, NE, United States; Department of Physics, University of Nebraska Omaha, Omaha, NE, United States.
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34
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de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ. High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic Acids Res 2019; 46:e78. [PMID: 29718339 PMCID: PMC6061839 DOI: 10.1093/nar/gky296] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/12/2018] [Indexed: 02/06/2023] Open
Abstract
DNA polymerase fidelity is affected by both intrinsic properties and environmental conditions. Current strategies for measuring DNA polymerase error rate in vitro are constrained by low error subtype sensitivity, poor scalability, and lack of flexibility in types of sequence contexts that can be tested. We have developed the Magnification via Nucleotide Imbalance Fidelity (MagNIFi) assay, a scalable next-generation sequencing assay that uses a biased deoxynucleotide pool to quantitatively shift error rates into a range where errors are frequent and hence measurement is robust, while still allowing for accurate mapping to error rates under typical conditions. This assay is compatible with a wide range of fidelity-modulating conditions, and enables high-throughput analysis of sequence context effects on base substitution and single nucleotide deletion fidelity using a built-in template library. We validate this assay by comparing to previously established fidelity metrics, and use it to investigate neighboring sequence-mediated effects on fidelity for several DNA polymerases. Through these demonstrations, we establish the MagNIFi assay for robust, high-throughput analysis of DNA polymerase fidelity.
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Affiliation(s)
- Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
| | - Adam H Marblestone
- Biophysics Program, Harvard University, Boston, MA 02115, USA.,Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Bradley M Zamft
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Biophysics Program, Harvard University, Boston, MA 02115, USA.,Wyss Institute, Harvard University, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Konrad P Kording
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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35
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Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH. Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). Virology 2019; 529:29-42. [PMID: 30660046 PMCID: PMC6502252 DOI: 10.1016/j.virol.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
We developed a computational approach called Domain-architecture Aware Inference of Orthologs (DAIO) for the analysis of protein orthology by combining phylogenetic and protein domain-architecture information. Using DAIO, we performed a systematic study of the proteomes of all human Herpesviridae species to define Strict Ortholog Groups (SOGs). In addition to assessing the taxonomic distribution for each protein based on sequence similarity, we performed a protein domain-architecture analysis for every protein family and computationally inferred gene duplication events. While many herpesvirus proteins have evolved without any detectable gene duplications or domain rearrangements, numerous herpesvirus protein families do exhibit complex evolutionary histories. Some proteins acquired additional domains (e.g., DNA polymerase), whereas others show a combination of domain acquisition and gene duplication (e.g., betaherpesvirus US22 family), with possible functional implications. This novel classification system of SOGs for human Herpesviridae proteins is available through the Virus Pathogen Resource (ViPR, www.viprbrc.org).
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Affiliation(s)
| | - David M Knipe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip E Pellett
- Department of Biochemistry, Microbiology & Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego, CA 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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36
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Sassa A, Yasui M, Honma M. Current perspectives on mechanisms of ribonucleotide incorporation and processing in mammalian DNA. Genes Environ 2019; 41:3. [PMID: 30700998 PMCID: PMC6346524 DOI: 10.1186/s41021-019-0118-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/08/2019] [Indexed: 01/09/2023] Open
Abstract
Ribonucleotides, which are RNA precursors, are often incorporated into DNA during replication. Although embedded ribonucleotides in the genome are efficiently removed by canonical ribonucleotide excision repair (RER), inactivation of RER causes genomic ribonucleotide accumulation, leading to various abnormalities in cells. Mutation of genes encoding factors involved in RER is associated with the neuroinflammatory autoimmune disorder Aicardi–Goutières syndrome. Over the last decade, the biological impact of ribonucleotides in the genome has attracted much attention. In the present review, we particularly focus on recent studies that have elucidated possible mechanisms of ribonucleotide incorporation and repair and their significance in mammals.
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Affiliation(s)
- Akira Sassa
- 1Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522 Japan
| | - Manabu Yasui
- 2Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501 Japan
| | - Masamitsu Honma
- 2Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501 Japan
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37
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Zhang C, Wang B, Zhao X, Li X, Lou Z, Chen X, Zhang F. Iron deficiency accelerates intervertebral disc degeneration through affecting the stability of DNA polymerase epsilon complex. Am J Transl Res 2018; 10:3430-3442. [PMID: 30662597 PMCID: PMC6291718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/05/2018] [Indexed: 06/09/2023]
Abstract
Iron serves as an important cofactor of iron-containing proteins that play critical roles in the maintenance of DNA stability and cell cycle progression. The disturbed iron homeostasis results in the pathogenesis of many diseases such as cancer and anemia. In this study, we found a clear correlation between iron deficiency and intervertebral disc degeneration (IDD). Through microarray experiments, we found that a large number of genes were differentially expressed in tissues with different degrees of degeneration. Among them, an iron-containing gene, PolE, the catalytic subunit of DNA polymerase epsilon (Polε), and the other two Polε subunits, including PolE2 and PolE3, were markedly downregulated, while some proteins involved in apoptosis such as Caspase-3 and -8 were significantly upregulated. By supplementation with an iron chelator deferoxamine (DFO) or knocking down either iron divalentmetal transporter 1 (DMT1) or transferrin receptor 1 (TfR1) in the nucleus pulposus (NP) cells, we found that the protein levels of PolE complex members were dramatically reduced, whereas the intrinsic apoptotic pathway was activated. Interestingly, overexpression of PolE in NP cells knocked down with either DMT1 or TfR could not reverse the stability of PolE complex and apoptosis status. In summary, our study suggests that iron deficiency is an important factor in the aggravation of IDD. Proper iron supplementation may be an effective strategy to alleviate the symptoms of patients with IDD.
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Affiliation(s)
- Chunqiang Zhang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical UniversityKunming 650032, Yunnan, China
| | - Bing Wang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical UniversityKunming 650032, Yunnan, China
| | - Xueling Zhao
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical UniversityKunming 650032, Yunnan, China
| | - Xingguo Li
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical UniversityKunming 650032, Yunnan, China
| | - Zhenkai Lou
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical UniversityKunming 650032, Yunnan, China
| | - Xun Chen
- Department of Orthopedics, Hong-Hui Hospital, Xi’an Jiaotong UniversityXi’an 710054, Shaanxi, China
| | - Fan Zhang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical UniversityKunming 650032, Yunnan, China
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38
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Burioli EAV, Varello K, Lavazza A, Bozzetta E, Prearo M, Houssin M. A novel divergent group of Ostreid herpesvirus 1 μVar variants associated with a mortality event in Pacific oyster spat in Normandy (France) in 2016. JOURNAL OF FISH DISEASES 2018; 41:1759-1769. [PMID: 30151980 DOI: 10.1111/jfd.12883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/21/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
The acute course of disease in young oysters infected by OsHV-1 and the rapid tissue degradation often preclude histological examination of specimens collected during outbreaks in field. Herein, live spat originated from two geographical areas were sampled just at the onset of a mortality event that occurred in Normandy (France) in June 2016. The lesions, associated with high OsHV-1 DNA quantities, were characterized by severe and diffuse haemocytosis mainly involving blast-like cells, myocyte degeneration and large, irregularly shaped degenerate eosinophilic cells in the connective tissue. The herpesvirus was identified by negative staining TEM and real-time PCR. Sequencing of the C region and ORFs 42/43 confirmed that the variants met the definition of OsHV-1 μVar. We sequenced 30 other ORFs in twenty OsHV-1-positive individuals and compared them to the μVar specimens isolated between 2009 and 2011. The ORFs encoding putative membrane proteins showed the highest number of variations. Seven different genotypes were identified, confirming the presence of relevant genetic diversity. Phylogenetic analysis provided evidence for a well-separated μVar new group, with an evolutionary divergence estimated at 0.0013 from the other μVar variants. The geographical distribution of these newly described variants and their effective virulence should be investigated in future.
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Affiliation(s)
- Erika A V Burioli
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy
- LABÉO Frank Duncombe, Caen, France
| | - Katia Varello
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Elena Bozzetta
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy
| | - Marino Prearo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Torino, Italy
| | - Maryline Houssin
- LABÉO Frank Duncombe, Caen, France
- Université de Caen Normandie, UMR BOREA MNHN, UPMC, UCN, CNRS 7208, IRD 207, Caen, France
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39
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Cremen MCM, Leliaert F, Marcelino VR, Verbruggen H. Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta). Genome Biol Evol 2018; 10:1048-1061. [PMID: 29635329 PMCID: PMC5888179 DOI: 10.1093/gbe/evy063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.
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Affiliation(s)
| | - Frederik Leliaert
- Botanic Garden Meise, 1860 Meise, Belgium.,Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Vanessa R Marcelino
- School of BioSciences, University of Melbourne, Parkville, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, New South Wales, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Australia
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40
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Raper AT, Reed AJ, Suo Z. Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion. Chem Rev 2018; 118:6000-6025. [DOI: 10.1021/acs.chemrev.7b00685] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Austin T. Raper
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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41
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Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018; 46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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42
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Yang X, Wang B, Luan J, Xie Y, Liu S, Zhou X. Molecular variation of tomato yellow leaf curl virus in the insect vector Bemisia tabaci. Sci Rep 2017; 7:16427. [PMID: 29180745 PMCID: PMC5703973 DOI: 10.1038/s41598-017-16330-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/08/2017] [Indexed: 12/19/2022] Open
Abstract
Insect vectors play significant roles in geminivirus spread and evolution in nature. To date little is known about the population dynamics of begomoviruses in their insect vector Bemisia tabaci. In this study we analyzed the genetic variation of tomato yellow leaf curl virus (TYLCV) in its host plant, Solanum lycopersicum, in its transmission vector B. tabaci raised on TYLCV-infected S. lycopersicum plants, and in B. tabaci after being transferred from S. lycopersicum to Gossypium hirsutum. We found that the levels of variability of TYLCV remained stable in S. lycopersicum plants, but increased significantly in both invasive and indigenous species of B. tabaci. We also presented evidence that the elevated mutation frequencies in TYLCV populations from vector whiteflies were caused mainly by mutations that occurred at several distinct sites within the TYLCV genome. Simultaneous introduction of mutations in the hot spots did not affect the ability of TYLCV to be transmitted by B. tabaci, but reduced its pathogenicity in both S. lycopersicum and Nicotiana benthamiana. Our findings provide new information on population variability of TYLCV in its insect vector, extending the knowledge of the influence of insect vector on plant virus population dynamics.
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Affiliation(s)
- Xiuling Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Junbo Luan
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shusheng Liu
- Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Baruch-Torres N, Brieba LG. Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases. Nucleic Acids Res 2017; 45:10751-10763. [PMID: 28977655 PMCID: PMC5737093 DOI: 10.1093/nar/gkx744] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/14/2017] [Indexed: 02/01/2023] Open
Abstract
Genomes acquire lesions that can block the replication fork and some lesions must be bypassed to allow survival. The nuclear genome of flowering plants encodes two family-A DNA polymerases (DNAPs), the result of a duplication event, that are the sole DNAPs in plant organelles. These DNAPs, dubbed Plant Organellar Polymerases (POPs), resemble the Klenow fragment of bacterial DNAP I and are not related to metazoan and fungal mitochondrial DNAPs. Herein we report that replicative POPs from the plant model Arabidopsis thaliana (AtPolI) efficiently bypass one the most insidious DNA lesions, an apurinic/apyrimidinic (AP) site. AtPolIs accomplish lesion bypass with high catalytic efficiency during nucleotide insertion and extension. Lesion bypass depends on two unique polymerization domain insertions evolutionarily unrelated to the insertions responsible for lesion bypass by DNAP θ, an analogous lesion bypass polymerase. AtPolIs exhibit an insertion fidelity that ranks between the fidelity of replicative and lesion bypass DNAPs, moderate 3′-5′ exonuclease activity and strong strand-displacement. AtPolIs are the first known example of a family-A DNAP evolved to function in both DNA replication and lesion bypass. The lesion bypass capabilities of POPs may be required to prevent replication fork collapse in plant organelles.
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Affiliation(s)
- Noe Baruch-Torres
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821 Irapuato Guanajuato, México
| | - Luis G Brieba
- Langebio-Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera. Irapuato-León, 36821 Irapuato Guanajuato, México
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44
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Origins of mtDNA mutations in ageing. Essays Biochem 2017; 61:325-337. [PMID: 28698307 DOI: 10.1042/ebc20160090] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022]
Abstract
MtDNA mutations are one of the hallmarks of ageing and age-related diseases. It is well established that somatic point mutations accumulate in mtDNA of multiple organs and tissues with increasing age and heteroplasmy is universal in mammals. However, the origin of these mutations remains controversial. The long-lasting hypothesis stating that mtDNA mutations emanate from oxidative damage via a self-perpetuating mechanism has been extensively challenged in recent years. Contrary to this initial ascertainment, mtDNA appears to be well protected from action of reactive oxygen species (ROS) through robust protein coating and endomitochondrial microcompartmentalization. Extensive development of scrupulous high-throughput DNA sequencing methods suggests that an imperfect replication process, rather than oxidative lesions are the main sources of mtDNA point mutations, indicating that mtDNA polymerase γ (POLG) might be responsible for the majority of mtDNA mutagenic events. Here, we summarize the recent knowledge in prevention and defence of mtDNA oxidative lesions and discuss the plausible mechanisms of mtDNA point mutation generation and fixation.
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45
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DNA polymerases eta and kappa exchange with the polymerase delta holoenzyme to complete common fragile site synthesis. DNA Repair (Amst) 2017; 57:1-11. [PMID: 28605669 DOI: 10.1016/j.dnarep.2017.05.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/25/2017] [Accepted: 05/29/2017] [Indexed: 12/21/2022]
Abstract
Common fragile sites (CFSs) are inherently unstable genomic loci that are recurrently altered in human tumor cells. Despite their instability, CFS are ubiquitous throughout the human genome and associated with large tumor suppressor genes or oncogenes. CFSs are enriched with repetitive DNA sequences, one feature postulated to explain why these loci are inherently difficult to replicate, and sensitive to replication stress. We have shown that specialized DNA polymerases (Pols) η and κ replicate CFS-derived sequences more efficiently than the replicative Pol δ. However, we lacked an understanding of how these enzymes cooperate to ensure efficient CFS replication. Here, we designed a model of lagging strand replication with RFC loaded PCNA that allows for maximal activity of the four-subunit human Pol δ holoenzyme, Pol η, and Pol κ in polymerase mixing assays. We discovered that Pol η and κ are both able to exchange with Pol δ stalled at repetitive CFS sequences, enhancing Normalized Replication Efficiency. We used this model to test the impact of PCNA mono-ubiquitination on polymerase exchange, and found no change in polymerase cooperativity in CFS replication compared with unmodified PCNA. Finally, we modeled replication stress in vitro using aphidicolin and found that Pol δ holoenzyme synthesis was significantly inhibited in a dose-dependent manner, preventing any replication past the CFS. Importantly, Pol η and κ were still proficient in rescuing this stalled Pol δ synthesis, which may explain, in part, the CFS instability phenotype of aphidicolin-treated Pol η and Pol κ-deficient cells. In total, our data support a model wherein Pol δ stalling at CFSs allows for free exchange with a specialized polymerase that is not driven by PCNA.
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46
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Guo J, Zhang W, Coker AR, Wood SP, Cooper JB, Ahmad S, Ali S, Rashid N, Akhtar M. Structure of the family B DNA polymerase from the hyperthermophilic archaeon Pyrobaculum calidifontis. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:420-427. [PMID: 28471366 DOI: 10.1107/s2059798317004090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/13/2017] [Indexed: 11/10/2022]
Abstract
The family B DNA polymerase from Pyrobaculum calidifontis (Pc-polymerase) consists of 783 amino acids and is magnesium-ion dependent. It has an optimal pH of 8.5, an optimal temperature of 75°C and a half-life of 4.5 h at 95°C, giving it greater thermostability than the widely used Taq DNA polymerase. The enzyme is also capable of PCR-amplifying larger DNA fragments of up to 7.5 kb in length. It was shown to have functional, error-correcting 3'-5' exonuclease activity, as do the related high-fidelity DNA polymerases from Pyrococcus furiosus, Thermococcus kodakarensis KOD1 and Thermococcus gorgonarius, which have extensive commercial applications. Pc-polymerase has a quite low sequence identity of approximately 37% to these enzymes, which, in contrast, have very high sequence identity to each other, suggesting that the P. calidifontis enzyme is distinct. Here, the structure determination of Pc-polymerase is reported, which has been refined to an R factor of 24.47% and an Rfree of 28.81% at 2.80 Å resolution. The domains of the enzyme are arranged in a circular fashion to form a disc with a narrow central channel. One face of the disc has a number of connected crevices in it, which allow the protein to bind duplex and single-stranded DNA. The central channel is thought to allow incoming nucleoside triphosphates to access the active site. The enzyme has a number of unique structural features which distinguish it from other archaeal DNA polymerases and may account for its high processivity. A model of the complex with the primer-template duplex of DNA indicates that the largest conformational change that occurs upon DNA binding is the movement of the thumb domain, which rotates by 7.6° and moves by 10.0 Å. The surface potential of the enzyme is dominated by acidic groups in the central region of the molecule, where catalytic magnesium ions bind at the polymerase and exonuclease active sites. The outer regions are richer in basic amino acids that presumably interact with the sugar-phosphate backbone of DNA. The large number of salt bridges may contribute to the high thermal stability of this enzyme.
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Affiliation(s)
- Jingxu Guo
- Wolfson Institute for Biomedical Research, Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Wenling Zhang
- School of Pharmacy, UCL, 29-39 Brunswick Square, London WC1N 1AX, England
| | - Alun R Coker
- Wolfson Institute for Biomedical Research, Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Steve P Wood
- Wolfson Institute for Biomedical Research, Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Jonathan B Cooper
- Wolfson Institute for Biomedical Research, Division of Medicine, UCL, Gower Street, London WC1E 6BT, England
| | - Shazeel Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Syed Ali
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Muhummad Akhtar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
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Zarrouk K, Piret J, Boivin G. Herpesvirus DNA polymerases: Structures, functions and inhibitors. Virus Res 2017; 234:177-192. [PMID: 28153606 DOI: 10.1016/j.virusres.2017.01.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/10/2017] [Accepted: 01/22/2017] [Indexed: 11/25/2022]
Abstract
Human herpesviruses are large double-stranded DNA viruses belonging to the Herpesviridae family. These viruses have the ability to establish lifelong latency into the host and to periodically reactivate. Primary infections and reactivations of herpesviruses cause a large spectrum of diseases and may lead to severe complications in immunocompromised patients. The viral DNA polymerase is a key enzyme in the lytic phase of the infection by herpesviruses. This review focuses on the structures and functions of viral DNA polymerases of herpes simplex virus (HSV) and human cytomegalovirus (HCMV). DNA polymerases of HSV (UL30) and HCMV (UL54) belong to B family DNA polymerases with which they share seven regions of homology numbered I to VII as well as a δ-region C which is homologous to DNA polymerases δ. These DNA polymerases are multi-functional enzymes exhibiting polymerase, 3'-5' exonuclease proofreading and ribonuclease H activities. Furthermore, UL30 and UL54 DNA polymerases form a complex with UL42 and UL44 processivity factors, respectively. The mechanisms involved in their polymerisation activity have been elucidated based on structural analyses of the DNA polymerase of bacteriophage RB69 crystallized under different conformations, i.e. the enzyme alone or in complex with DNA and with both DNA and incoming nucleotide. All antiviral agents currently used for the prevention or treatment of HSV and HCMV infections target the viral DNA polymerases. However, long-term administration of these antivirals may lead to the emergence of drug-resistant isolates harboring mutations in genes encoding viral enzymes that phosphorylate drugs (i.e., nucleoside analogues) and/or DNA polymerases.
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Affiliation(s)
- Karima Zarrouk
- Research Center in Infectious Diseases, CHU de Québec and Laval University, Quebec City, Quebec, Canada
| | - Jocelyne Piret
- Research Center in Infectious Diseases, CHU de Québec and Laval University, Quebec City, Quebec, Canada
| | - Guy Boivin
- Research Center in Infectious Diseases, CHU de Québec and Laval University, Quebec City, Quebec, Canada.
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Krasich R, Copeland WC. DNA polymerases in the mitochondria: A critical review of the evidence. FRONT BIOSCI-LANDMRK 2017; 22:692-709. [PMID: 27814640 PMCID: PMC5485829 DOI: 10.2741/4510] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Since 1970, the DNA polymerase gamma (PolG) has been known to be the DNA polymerase responsible for replication and repair of mitochondrial DNA, and until recently it was generally accepted that this was the only polymerase present in mitochondria. However, recent data has challenged that opinion, as several polymerases are now proposed to have activity in mitochondria. To date, their exact role of these other DNA polymerases is unclear and the amount of evidence supporting their role in mitochondria varies greatly. Further complicating matters, no universally accepted standards have been set for definitive proof of the mitochondrial localization of a protein. To gain an appreciation of these newly proposed DNA polymerases in the mitochondria, we review the evidence and standards needed to establish the role of a polymerase in the mitochondria. Employing PolG as an example, we established a list of criteria necessary to verify the existence and function of new mitochondrial proteins. We then apply this criteria towards several other putative mitochondrial polymerases. While there is still a lot left to be done in this exciting new direction, it is clear that PolG is not acting alone in mitochondria, opening new doors for potential replication and repair mechanisms.
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Affiliation(s)
- Rachel Krasich
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Dr., Bldg. 101, Rm. E316, Research Triangle Park, NC 27709,
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Shawon J, Khan AM, Rahman A, Hoque MM, Khan MAK, Sarwar MG, Halim MA. Molecular Recognition of Azelaic Acid and Related Molecules with DNA Polymerase I Investigated by Molecular Modeling Calculations. Interdiscip Sci 2016; 10:525-537. [PMID: 27696206 DOI: 10.1007/s12539-016-0186-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/20/2016] [Accepted: 09/12/2016] [Indexed: 12/18/2022]
Abstract
Molecular recognition has central role on the development of rational drug design. Binding affinity and interactions are two key components which aid to understand the molecular recognition in drug-receptor complex and crucial for structure-based drug design in medicinal chemistry. Herein, we report the binding affinity and the nonbonding interactions of azelaic acid and related compounds with the receptor DNA polymerase I (2KFN). Quantum mechanical calculation was employed to optimize the modified drugs using B3LYP/6-31G(d,p) level of theory. Charge distribution, dipole moment and thermodynamic properties such as electronic energy, enthalpy and free energy of these optimized drugs are also explored to evaluate how modifications impact the drug properties. Molecular docking calculation was performed to evaluate the binding affinity and nonbonding interactions between designed molecules and the receptor protein. We notice that all modified drugs are thermodynamically more stable and some of them are more chemically reactive than the unmodified drug. Promise in enhancing hydrogen bonds is found in case of fluorine-directed modifications as well as in the addition of trifluoroacetyl group. Fluorine participates in forming fluorine bonds and also stimulates alkyl, pi-alkyl interactions in some drugs. Designed drugs revealed increased binding affinity toward 2KFN. A1, A2 and A3 showed binding affinities of -8.7, -8.6 and -7.9 kcal/mol, respectively against 2KFN compared to the binding affinity -6.7 kcal/mol of the parent drug. Significant interactions observed between the drugs and Thr358 and Asp355 residues of 2KFN. Moreover, designed drugs demonstrated improved pharmacokinetic properties. This study disclosed that 9-octadecenoic acid and drugs containing trifluoroacetyl and trifluoromethyl groups are the best 2KFN inhibitors. Overall, these results can be useful for the design of new potential candidates against DNA polymerase I.
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Affiliation(s)
- Jakaria Shawon
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Adhip Rahman
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh
| | - Mohammad Abdul Kader Khan
- Department of General Studies, Jubail University College, Jubail Industrial City, 31961, Saudi Arabia
| | - Mohammed G Sarwar
- Fakultät für Chemie und Biochemie, Organische Chemie I, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, BICCB, Green Research Centre, 38 Green Road West, Dhaka, 1205, Bangladesh.
- Institut Lumière Matière, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France.
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50
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Abellón-Ruiz J, Waldron KJ, Connolly BA. Archaeoglobus Fulgidus DNA Polymerase D: A Zinc-Binding Protein Inhibited by Hypoxanthine and Uracil. J Mol Biol 2016; 428:2805-13. [PMID: 27320386 PMCID: PMC4942837 DOI: 10.1016/j.jmb.2016.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/28/2016] [Accepted: 06/13/2016] [Indexed: 02/03/2023]
Abstract
Archaeal family-D DNA polymerases (Pol-D) comprise a small (DP1) proofreading subunit and a large (DP2) polymerase subunit. Pol-D is one of the least studied polymerase families, and this publication investigates the enzyme from Archaeoglobus fulgidus (Afu Pol-D). The C-terminal region of DP2 contains two conserved cysteine clusters, and their roles are investigated using site-directed mutagenesis. The cluster nearest the C terminus is essential for polymerase activity, and the cysteines are shown to serve as ligands for a single, critical Zn(2+) ion. The cysteines farthest from the C terminal were not required for activity, and a role for these amino acids has yet to be defined. Additionally, it is shown that Afu Pol-D activity is slowed by the template strand hypoxanthine, extending previous results that demonstrated inhibition by uracil. Hypoxanthine was a weaker inhibitor than uracil. Investigations with isolated DP2, which has a measurable polymerase activity, localised the deaminated base binding site to this subunit. Uracil and hypoxanthine slowed Afu Pol-D "in trans", that is, a copied DNA strand could be inhibited by a deaminated base in the alternate strand of a replication fork. The error rate of Afu Pol-D, measured in vitro, was 0.24×10(-5), typical for a polymerase that has been proposed to carry out genome replication in the Archaea. Deleting the 3'-5' proofreading exonuclease activity reduced fidelity twofold. The results presented in this publication considerably increase our knowledge of Pol-D.
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Affiliation(s)
- Javier Abellón-Ruiz
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Kevin J Waldron
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Bernard A Connolly
- Institute for Cell and Molecular Biology, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
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