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Liang C, Yang Y, Ning P, Chang C, Cao W. Structural and functional coupling in cross-linking uracil-DNA glycosylase UDGX. Biosci Rep 2024; 44:BSR20231551. [PMID: 38059429 PMCID: PMC10776899 DOI: 10.1042/bsr20231551] [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: 09/11/2023] [Revised: 11/14/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023] Open
Abstract
Enzymes in uracil-DNA glycosylase (UDG) superfamily are involved in removal of deaminated nucleobases such as uracil, methylcytosine derivatives such as formylcytosine and carboxylcytosine, and other base damage in DNA repair. UDGX is the latest addition of a new class to the UDG superfamily with a sporadic distribution in bacteria. UDGX type enzymes have a distinct biochemical property of cross-linking itself to the resulting AP site after uracil removal. Built on previous biochemical and structural analyses, this work comprehensively investigated the kinetic and enzymatic properties of Mycobacterium smegmatis UDGX. Kinetics and mutational analyses, coupled with structural information, defined the roles of E52, D56, D59, F65 of motif 1, H178 of motif 2 and N91, K94, R107 and H109 of motif 3 play in uracil excision and cross-linking. More importantly, a series of quantitative analyses underscored the structural coupling through inter-motif and intra-motif interactions and subsequent functional coupling of the uracil excision and cross-linking reactions. A catalytic model is proposed, which underlies this catalytic feature unique to UDGX type enzymes. This study offers new insight on the catalytic mechanism of UDGX and provides a unique example of enzyme evolution.
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Affiliation(s)
- Chuan Liang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Ye Yang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Ping Ning
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Chenyan Chang
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
| | - Weiguo Cao
- Department of Genetics and Biochemistry, Clemson University, Room 049 Life Sciences Facility, 190 Collings Street, Clemson, SC 29634, U.S.A
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2
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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [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] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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3
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Computational design of a thermolabile uracil-DNA glycosylase of Escherichia coli. Biophys J 2022; 121:1276-1288. [PMID: 35183522 PMCID: PMC9034189 DOI: 10.1016/j.bpj.2022.02.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Abstract
Polymerase chain reaction (PCR) is a powerful tool to diagnose infectious diseases. Uracil DNA glycosylase (UDG) is broadly used to remove carryover contamination in PCR. However, UDG can contribute to false negative results when not inactivated completely, leading to DNA degradation during the amplification step. In this study, we designed novel thermolabile UDG derivatives by supercomputing molecular dynamic simulations and residual network analysis. Based on enzyme activity analysis, thermolability, thermal stability, and biochemical experiments of Escherichia coli-derived UDG and 22 derivatives, we uncovered that the UDG D43A mutant eliminated the false negative problem, demonstrated high efficiency, and offered great benefit for use in PCR diagnosis. We further obtained structural and thermodynamic insights into the role of the D43A mutation, including perturbed protein structure near D43; weakened pairwise interactions of D43 with K42, N46, and R80; and decreased melting temperature and native fraction of the UDG D43A mutant compared with wild-type UDG.
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4
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Coppola D, Lauritano C, Palma Esposito F, Riccio G, Rizzo C, de Pascale D. Fish Waste: From Problem to Valuable Resource. Mar Drugs 2021; 19:116. [PMID: 33669858 PMCID: PMC7923225 DOI: 10.3390/md19020116] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
Following the growth of the global population and the subsequent rapid increase in urbanization and industrialization, the fisheries and aquaculture production has seen a massive increase driven mainly by the development of fishing technologies. Accordingly, a remarkable increase in the amount of fish waste has been produced around the world; it has been estimated that about two-thirds of the total amount of fish is discarded as waste, creating huge economic and environmental concerns. For this reason, the disposal and recycling of these wastes has become a key issue to be resolved. With the growing attention of the circular economy, the exploitation of underused or discarded marine material can represent a sustainable strategy for the realization of a circular bioeconomy, with the production of materials with high added value. In this study, we underline the enormous role that fish waste can have in the socio-economic sector. This review presents the different compounds with high commercial value obtained by fish byproducts, including collagen, enzymes, and bioactive peptides, and lists their possible applications in different fields.
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Affiliation(s)
- Daniela Coppola
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (D.C.); (C.L.); (F.P.E.); (G.R.); (C.R.)
| | - Chiara Lauritano
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (D.C.); (C.L.); (F.P.E.); (G.R.); (C.R.)
| | - Fortunato Palma Esposito
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (D.C.); (C.L.); (F.P.E.); (G.R.); (C.R.)
| | - Gennaro Riccio
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (D.C.); (C.L.); (F.P.E.); (G.R.); (C.R.)
| | - Carmen Rizzo
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (D.C.); (C.L.); (F.P.E.); (G.R.); (C.R.)
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (D.C.); (C.L.); (F.P.E.); (G.R.); (C.R.)
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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5
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Wollenberg Valero KC, Pathak R, Prajapati I, Bankston S, Thompson A, Usher J, Isokpehi RD. A candidate multimodal functional genetic network for thermal adaptation. PeerJ 2014; 2:e578. [PMID: 25289178 PMCID: PMC4183952 DOI: 10.7717/peerj.578] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/24/2014] [Indexed: 01/20/2023] Open
Abstract
Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken. We first established a framework of candidate functions for such markers, and then compiled the literature on genes known to adapt to the thermal environment in different lineages of vertebrates. We then identified them in the genomes of human, chicken, and the lizard Anolis carolinensis, and established a functional genetic interaction network in the chicken. Surprisingly, markers initially identified from diverse lineages of vertebrates such as human and fish were all in close functional relationship with each other and more associated than expected by chance. This indicates that the general genetic functional network for thermoregulation and/or thermal adaptation to the environment might be regulated via similar evolutionarily conserved pathways in different vertebrate lineages. We were able to identify seven functions that were statistically overrepresented in this network, corresponding to four of our originally predicted functions plus three unpredicted functions. We describe this network as multimodal: central regulator genes with the function of relaying thermal signal (1), affect genes with different cellular functions, namely (2) lipoprotein metabolism, (3) membrane channels, (4) stress response, (5) response to oxidative stress, (6) muscle contraction and relaxation, and (7) vasodilation, vasoconstriction and regulation of blood pressure. This network constitutes a novel resource for the study of thermal adaptation in the closely related nonavian reptiles and other vertebrate ectotherms.
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Affiliation(s)
| | - Rachana Pathak
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Indira Prajapati
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Shannon Bankston
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Aprylle Thompson
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Jaytriece Usher
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
| | - Raphael D Isokpehi
- College of Science, Engineering and Mathematics, Bethune-Cookman University , Daytona Beach, FL , USA
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6
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Assefa NG, Niiranen L, Johnson KA, Leiros HKS, Smalås AO, Willassen NP, Moe E. Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2093-100. [PMID: 25084329 PMCID: PMC4118823 DOI: 10.1107/s1399004714011699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/20/2014] [Indexed: 12/01/2022]
Abstract
Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme-substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG-Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG-Ugi complex with previously determined structures of UNG-Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (Kb) which is one order of magnitude larger than that for hUNG-Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein-Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.
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Affiliation(s)
- Netsanet Gizaw Assefa
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Laila Niiranen
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland
| | - Kenneth A. Johnson
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | - Arne Oskar Smalås
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Nils Peder Willassen
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Elin Moe
- Department of Chemistry/Norstruct, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Instituto de Tecnologia Quimica e Biologica (ITQB), Universidade Nova de Lisboa, Avenida da Republica (EAN), 2780-157 Oeiras, Portugal
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7
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Olsen RL, Toppe J, Karunasagar I. Challenges and realistic opportunities in the use of by-products from processing of fish and shellfish. Trends Food Sci Technol 2014. [DOI: 10.1016/j.tifs.2014.01.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Hsieh K, Mage PL, Csordas AT, Eisenstein M, Soh HT. Simultaneous elimination of carryover contamination and detection of DNA with uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification (UDG-LAMP). Chem Commun (Camb) 2014; 50:3747-9. [PMID: 24577617 DOI: 10.1039/c4cc00540f] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a one-pot, closed-vessel enzymatic assay that eliminates carryover contamination while preserving robust DNA amplification in loop-mediated isothermal amplification (LAMP), providing reliable and rapid detection of target DNA in contaminated samples.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA.
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9
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Sartmatova D, Nash T, Schormann N, Nuth M, Ricciardi R, Banerjee S, Chattopadhyay D. Crystallization and preliminary X-ray diffraction analysis of three recombinant mutants of Vaccinia virus uracil DNA glycosylase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:295-301. [PMID: 23519808 PMCID: PMC3606578 DOI: 10.1107/s1744309113002716] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/27/2013] [Indexed: 11/10/2022]
Abstract
Amino-acid residues located at a highly flexible area in the uracil DNA glycosylase of Vaccinia virus were mutated. In the crystal structure of wild-type D4 these residues lie at the dimer interface. Specifically, three mutants were generated: (i) residue Arg167 was replaced with an alanine (R167AD4), (ii) residues Glu171, Ser172 and Pro173 were substituted with three glycine residues (3GD4) and (iii) residues Glu171 and Ser172 were deleted (Δ171-172D4). Mutant proteins were expressed, purified and crystallized in order to investigate the effects of these mutations on the structure of the protein.
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Affiliation(s)
- Darika Sartmatova
- Science and Technology Honors Program, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Taishayla Nash
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Norbert Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Manunya Nuth
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert Ricciardi
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Surajit Banerjee
- North-Eastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, IL 60439, USA
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10
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Assefa NG, Niiranen L, Willassen NP, Smalås A, Moe E. Thermal unfolding studies of cold adapted uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). A comparative study with human UNG. Comp Biochem Physiol B Biochem Mol Biol 2012; 161:60-8. [DOI: 10.1016/j.cbpb.2011.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 09/12/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
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11
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Mereghetti P, Riccardi L, Brandsdal BO, Fantucci P, De Gioia L, Papaleo E. Near native-state conformational landscape of psychrophilic and mesophilic enzymes: probing the folding funnel model. J Phys Chem B 2010; 114:7609-19. [PMID: 20518574 DOI: 10.1021/jp911523h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, increased interest has been directed to the study of enzyme adaptation to low temperatures. In particular, a peculiar folding funnel model was proposed for the free energy landscape of a psychrophilic alpha-amylase and other cold-adapted enzymes. In the present contribution, the comparison between the near native-state dynamics and conformational landscape in the essential subspace of different cold-adapted enzymes with their mesophilic counterparts, as obtained by more than 0.1 micros molecular dynamics simulations at different temperatures, allows the folding funnel model to be probed. Common characteristics were highlighted in the near native-state dynamics of psychrophilic enzymes belonging to different enzymatic families when compared to the mesophilic counterparts. According to the model, a cold-adapted enzyme in its native-state consists of a large population of conformations which can easily interconvert and result in high structural flexibility.
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Affiliation(s)
- Paolo Mereghetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, 2, 20126 Milan, Italy
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12
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Raeder ILU, Moe E, Willassen NP, Smalås AO, Leiros I. Structure of uracil-DNA N-glycosylase (UNG) from Vibrio cholerae: mapping temperature adaptation through structural and mutational analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:130-6. [PMID: 20124707 PMCID: PMC2815677 DOI: 10.1107/s1744309109052063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/03/2009] [Indexed: 11/10/2022]
Abstract
The crystal structure of Vibrio cholerae uracil-DNA N-glycosylase (vcUNG) has been determined to 1.5 A resolution. Based on this structure, a homology model of Aliivibrio salmonicida uracil-DNA N-glycosylase (asUNG) was built. A previous study demonstrated that asUNG possesses typical cold-adapted features compared with vcUNG, such as a higher catalytic efficiency owing to increased substrate affinity. Specific amino-acid substitutions in asUNG were suggested to be responsible for the increased substrate affinity and the elevated catalytic efficiency by increasing the positive surface charge in the DNA-binding region. The temperature adaptation of these enzymes has been investigated using structural and mutational analyses, in which mutations of vcUNG demonstrated an increased substrate affinity that more resembled that of asUNG. Visualization of surface potentials revealed a more positive potential for asUNG compared with vcUNG; a modelled double mutant of vcUNG had a potential around the substrate-binding region that was more like that of asUNG, thus rationalizing the results obtained from the kinetic studies.
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Affiliation(s)
- Inger Lin Uttakleiv Raeder
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Elin Moe
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Nils Peder Willassen
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
- Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
| | - Arne O. Smalås
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
| | - Ingar Leiros
- Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
- The Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
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13
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Kim GA, Sun Y, Song JG, Bae H, Kim JH, Kwon ST. Properties of cold-active uracil-DNA glycosylase from Photobacterium aplysiae GMD509, and its PCR application for carryover contamination control. Enzyme Microb Technol 2009. [DOI: 10.1016/j.enzmictec.2008.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Characterization of cold-active uracil-DNA glycosylase from Bacillus sp. HJ171 and its use for contamination control in PCR. Appl Microbiol Biotechnol 2008; 80:785-94. [PMID: 18626641 DOI: 10.1007/s00253-008-1585-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 06/16/2008] [Accepted: 06/17/2008] [Indexed: 10/21/2022]
Abstract
In this study, the gene encoding Bacillus sp. HJ171 uracil-DNA glycosylase (Bsp HJ171 UDG) was cloned and sequenced. The Bsp HJ171 UDG gene consists of a 738-bp DNA sequence, which encodes for a protein that is 245-amino-acid residues in length. The deduced amino acid sequence of the Bsp HJ171 UDG had a high sequence similarity with other bacterial UDGs. The molecular mass of the protein derived from this amino acid sequence was 27.218 kDa. The Bsp HJ171 UDG gene was expressed under the control of a T7lac promoter in the pTYB1 plasmid in Escherichia coli BL21 (DE3). The expressed enzyme was purified in one step using the Intein Mediated Purification with an Affinity Chitin-binding Tag purification system. The optimal temperature range, pH, NaCl concentration, and KCl concentration of the purified enzyme was 20-25 degrees C, 8.0, 25 and 25 mM, respectively. The half-life of the enzyme at 40 degrees C and 50 degrees C were approximately 131 and 45 s, respectively. These heat-labile characteristics enabled Bsp HJ171 UDG to control carry-over contamination in the polymerase chain reaction product (PCR) without losing the PCR product.
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15
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Ræder ILU, Leiros I, Willassen NP, Smalås AO, Moe E. Uracil-DNA N-glycosylase (UNG) from the marine, psychrophilic bacterium Vibrio salmonicida shows cold adapted features. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Tvete T, Haugan K. Purification and characterization of a 630 kDa bacterial killing metalloprotease (KilC) isolated from plaice Pleuronectes platessa (L.), epidermal mucus. JOURNAL OF FISH DISEASES 2008; 31:343-352. [PMID: 18355181 DOI: 10.1111/j.1365-2761.2008.00906.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Antibacterial chemicals in the mucus of fish such as lysozyme, lectins, peptides and proteases provide an efficient first line of defence against pathogens. This study shows that there are at least three antibacterial proteins in plaice skin mucus in addition to lysozyme. One of these proteins is responsible for approximately 74% of the antibacterial activity and is a 630 kDa protease complex designated KilC (bacterial killing metalloprotease C). Purified KilC kills the bacteria Staphylococcus aureus, Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa efficiently. The protease activity of KilC is dependent upon the divalent cation Mg(2+) and shows pH dual optima of 5.0 and 8.0. The enzyme has a temperature optimum of 25 degrees C and is made up of at least five different sized peptides. Studies with protease inhibitors show that the catalytic site of KilC may be cysteine- or serine protease-like. KilC may kill bacterial cells by acting directly upon the bacteria or by producing low molecular weight bioactive compounds such as peptides.
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Affiliation(s)
- T Tvete
- Nord-Trondelag University College, Faculty of Education, Engineering and Nursing, Rostad, Levanger, Norway
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17
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Olufsen M, Papaleo E, Smalås AO, Brandsdal BO. Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase. Proteins 2007; 71:1219-30. [DOI: 10.1002/prot.21815] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Olufsen M, Brandsdal BO, Smalås AO. Comparative unfolding studies of psychrophilic and mesophilic uracil DNA glycosylase: MD simulations show reduced thermal stability of the cold-adapted enzyme. J Mol Graph Model 2007; 26:124-34. [PMID: 17134924 DOI: 10.1016/j.jmgm.2006.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 10/17/2006] [Accepted: 10/18/2006] [Indexed: 11/22/2022]
Abstract
Uracil DNA glycosylase (UDG) is a DNA repair enzyme involved in the base excision repair (BER) pathway, removing misincorporated uracil from the DNA strand. The native and mutant forms of Atlantic cod and human UDG have previously been characterized in terms of kinetic and thermodynamic properties as well as the determination of several crystal structures. This data shows that the cold-adapted enzyme is more catalytically efficient but at the same time less resistant to heat compared to its warm-active counterpart. In this study, the structure-function relationship is further explored by means of comparative molecular dynamics (MD) simulations at three different temperatures (375, 400 and 425K) to gain a deeper insight into the structural features responsible for the reduced thermostability of the cold-active enzyme. The simulations show that there are distinct structural differences in the unfolding pathway between the two homologues, particularly evident in the N- and C-terminals. Distortion of the mesophilic enzyme is initiated simultaneously in the N- and C-terminal, while the C-terminal part plays a key role for the stability of the psychrophilic enzyme. The simulations also show that at certain temperatures the cold-adapted enzyme unfolds faster than the warm-active homologues in accordance with the lower thermal stability found experimentally.
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Affiliation(s)
- Magne Olufsen
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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Moe E, Leiros I, Smalås AO, McSweeney S. The Crystal Structure of Mismatch-specific Uracil-DNA Glycosylase (MUG) from Deinococcus radiodurans Reveals a Novel Catalytic Residue and Broad Substrate Specificity. J Biol Chem 2006; 281:569-77. [PMID: 16223719 DOI: 10.1074/jbc.m508032200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deinococcus radiodurans is extremely resistant to the effects of ionizing radiation. The source of the radiation resistance is not known, but an expansion of specific protein families related to stress response and damage control has been observed. DNA repair enzymes are among the expanded protein families in D. radiodurans, and genes encoding five different uracil-DNA glycosylases are identified in the genome. Here we report the three-dimensional structure of the mismatch-specific uracil-DNA glycosylase (MUG) from D. radiodurans (drMUG) to a resolution of 1.75 angstroms. Structural analyses suggest that drMUG possesses a novel catalytic residue, Asp-93. Activity measurements show that drMUG has a modified and broadened substrate specificity compared with Escherichia coli MUG. The importance of Asp-93 for activity was confirmed by structural analysis and abolished activity for the mutant drMUGD93A. Two other microorganisms, Bradyrhizobium japonicum and Rhodopseudomonas palustris, possess genes that encode MUGs with the highest sequence identity to drMUG among all of the bacterial MUGs examined. A phylogenetic analysis indicates that these three MUGs form a new MUG/thymidine-DNA glycosylase subfamily, here called the MUG2 family. We suggest that the novel catalytic residue (Asp-93) has evolved to provide drMUG with broad substrate specificity to increase the DNA repair repertoire of D. radiodurans.
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Affiliation(s)
- Elin Moe
- Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
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20
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Olufsen M, Smalås AO, Moe E, Brandsdal BO. Increased Flexibility as a Strategy for Cold Adaptation. J Biol Chem 2005; 280:18042-8. [PMID: 15749696 DOI: 10.1074/jbc.m500948200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Uracil DNA glycosylase (UDG) is a DNA repair enzyme in the base excision repair pathway and removes uracil from the DNA strand. Atlantic cod UDG (cUDG), which is a cold-adapted enzyme, has been found to be up to 10 times more catalytically active in the temperature range 15-37 degrees C as compared with the warm-active human counterpart. The increased catalytic activity of cold-adapted enzymes as compared with their mesophilic homologues are partly believed to be caused by an increase in the structural flexibility. However, no direct experimental evidence supports the proposal of increased flexibility of cold-adapted enzymes. We have used molecular dynamics simulations to gain insight into the structural flexibility of UDG. The results from these simulations show that an important loop involved in DNA recognition (the Leu(272) loop) is the most flexible part of the cUDG structure and that the human counterpart has much lower flexibility in the Leu(272) loop. The flexibility in this loop correlates well with the experimental k(cat)/K(m) values. Thus, the data presented here add strong support to the idea that flexibility plays a central role in adaptation to cold environments.
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Affiliation(s)
- Magne Olufsen
- Norwegian Structural Biology Centre, University of Tromsø, N-9037 Tromsø, Norway
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Moe E, Leiros I, Riise EK, Olufsen M, Lanes O, Smalås A, Willassen NP. Optimisation of the surface electrostatics as a strategy for cold adaptation of uracil-DNA N-glycosylase (UNG) from Atlantic cod (Gadus morhua). J Mol Biol 2004; 343:1221-30. [PMID: 15491608 DOI: 10.1016/j.jmb.2004.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Revised: 09/01/2004] [Accepted: 09/03/2004] [Indexed: 11/29/2022]
Abstract
Cold-adapted enzymes are characterised by an increased catalytic efficiency and reduced temperature stability compared to their mesophilic counterparts. Lately, it has been suggested that an optimisation of the electrostatic surface potential is a strategy for cold adaptation for some enzymes. A visualisation of the electrostatic surface potential of cold-adapted uracil-DNA N-glycosylase (cUNG) from Atlantic cod indicates a more positively charged surface near the active site compared to human UNG (hUNG). In order to investigate the importance of the altered surface potential for the cold-adapted features of cod UNG, six mutants have been characterised and compared to cUNG and hUNG. The cUNG quadruple mutant (V171E, K185V, H250Q and H275Y) and four corresponding single mutants all comprise substitutions of residues present in the human enzyme. A human UNG mutant, E171V, comprises the equivalent residue found in cod UNG. In addition, crystal structures of the single mutants V171E and E171V have been determined. Results from the study show that a more negative electrostatic surface potential reduces the activity and increases the stability of cod UNG, and suggest an optimisation of the surface potential as a strategy for cold-adaptation of this enzyme. Val171 in cod UNG is especially important in this respect.
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Affiliation(s)
- Elin Moe
- Department of Molecular Biotechnology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, N-9037 Tromsø, Norway
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Cavicchioli R, Siddiqui KS, Andrews D, Sowers KR. Low-temperature extremophiles and their applications. Curr Opin Biotechnol 2002; 13:253-61. [PMID: 12180102 DOI: 10.1016/s0958-1669(02)00317-8] [Citation(s) in RCA: 289] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Psychrophilic (cold-adapted) organisms and their products have potential applications in a broad range of industrial, agricultural and medical processes. In order for growth to occur in low-temperature environments, all cellular components must adapt to the cold. This fact, in combination with the diversity of Archaea, Bacteria and Eucarya isolated from cold environments, highlights the breadth and type of biological products and processes that might be exploited for biotechnology. Relative to this undisputed potential, psychrophiles and their products are under-utilised in biotechnology; however, recent advances, particularly with cold-active enzymes, herald rapid growth for this burgeoning field.
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Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, UNSW 2052, Australia.
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