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Jamontas R, Laurynėnas A, Povilaitytė D, Meškys R, Aučynaitė A. RudS: bacterial desulfidase responsible for tRNA 4-thiouridine de-modification. Nucleic Acids Res 2024:gkae716. [PMID: 39166491 DOI: 10.1093/nar/gkae716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
In this study, we present an extensive analysis of a widespread group of bacterial tRNA de-modifying enzymes, dubbed RudS, which consist of a TudS desulfidase fused to a Domain of Unknown Function 1722 (DUF1722). RudS enzymes exhibit specific de-modification activity towards the 4-thiouridine modification (s4U) in tRNA molecules, as indicated by our experimental findings. The heterologous overexpression of RudS genes in Escherichia coli significantly reduces the tRNA 4-thiouridine content and diminishes UVA-induced growth delay, indicating the enzyme's role in regulating photosensitive tRNA s4U modification. Through a combination of protein modeling, docking studies, and molecular dynamics simulations, we have identified amino acid residues involved in catalysis and tRNA binding. Experimental validation through targeted mutagenesis confirms the TudS domain as the catalytic core of RudS, with the DUF1722 domain facilitating tRNA binding in the anticodon region. Our results suggest that RudS tRNA modification eraser proteins may play a role in regulating tRNA during prokaryotic stress responses.
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Affiliation(s)
- Rapolas Jamontas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Audrius Laurynėnas
- Department of Bioanalysis, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Deimantė Povilaitytė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, 10257 Vilnius, Lithuania
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2
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Vosough P, Vafadar A, Naderi S, Alashti SK, Karimi S, Irajie C, Savardashtaki A, Taghizadeh S. Escherichia coli cytosine deaminase: Structural and biotechnological aspects. Biotechnol Appl Biochem 2024; 71:5-16. [PMID: 37743549 DOI: 10.1002/bab.2516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Suicide gene therapy involves introducing viral or bacterial genes into tumor cells, which enables the conversion of a nontoxic prodrug into a toxic-lethal drug. The application of the bacterial cytosine deaminase (bCD)/5-fluorocytosine (5-FC) approach has been beneficial and progressive within the current field of cancer therapy because of the enhanced bystander effect. The basis of this method is the preferential deamination of 5-FC to 5-fluorouracil by cancer cells expressing cytosine deaminase (CD), which strongly inhibits DNA synthesis and RNA function, effectively targeting tumor cells. However, the poor binding affinity of toward 5-FC compared to the natural substrate cytosine and/or inappropriate thermostability limits the clinical applications of this gene therapy approach. Nowadays, many genetic engineering studies have been carried out to solve and improve the activity of this enzyme. In the current review, we intend to discuss the biotechnological aspects of Escherichia coli CD, including its structure, functions, molecular cloning, and protein engineering. We will also explore its relevance in cancer clinical trials. By examining these aspects, we hope to provide a thorough understanding of E. coli CD and its potential applications in cancer therapy.
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Affiliation(s)
- Parisa Vosough
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Asma Vafadar
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Samaneh Naderi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shayan Khalili Alashti
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Karimi
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Taghizadeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Guo W, Li X, Fan J, Li H, Wen Y, Meng C, Chen H, Zhao Z, Zhang Y, Du Y, Wu B. Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy. iScience 2023; 26:107672. [PMID: 37680460 PMCID: PMC10481359 DOI: 10.1016/j.isci.2023.107672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023] Open
Abstract
Non-natural nucleobase isocytosine (IC) is the isomer of cytosine; its chemical derivate 5-fluoroisocytosine (5-FIC) together with the isocytosine-specific deaminase (ICD) VCZ was suggested to be potential practical enzyme/prodrug pair for cancer therapy through gene-directed enzyme-prodrug therapy (GDEPT) method. In this study, we have determined the crystal structures of apo-VCZ and its complex with 5-FU. We identified the critical residues for substrate binding and catalytic reaction. We also captured the substrate-induced conformational changes of VCZ, then proposed the conjectural reaction procedures of VCZ for converting the IC into the uracil. Moreover, we evaluated the therapeutic effect of wildtype or the mutated VCZ protein in the colorectal cancer cell lines. Our studies will shed light on optimizing the ICD/5-FIC pairs by modifying either the enzyme or the prodrug based on the structural observations, thereby improving the possibility of applying the ICD/5-FIC pair in clinical trials.
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Affiliation(s)
- Wenting Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xiaojia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jingyu Fan
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hongwei Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Cardiology, Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology and Guangzhou Key Laboratory of Molecular Mechanism and Translation in Major Cardiovascular Disease, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yan Wen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Chunyan Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Haitao Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhipeng Zhao
- Department of Basic Medical Sciences, Taizhou University, Taizhou, Zhejiang 318000, China
| | - Yuling Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Cardiology, Guangdong Province Key Laboratory of Arrhythmia and Electrophysiology and Guangzhou Key Laboratory of Molecular Mechanism and Translation in Major Cardiovascular Disease, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yushen Du
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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Zhou N, Wang J, Wang W, Wu X. Purification, characterization, and catalytic mechanism of N-Isopropylammelide isopropylaminohydrolase (AtzC) involved in the degradation of s-triazine herbicides. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115803. [PMID: 33158617 DOI: 10.1016/j.envpol.2020.115803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Deamination is ubiquitous in nature and has important biological significance. Leucobacter triazinivorans JW-1, recently isolated from sludge, can rapidly degrade s-triazine herbicides. The responsible enzymes, however, have not been purified and characterized. Herein, we purified an amidohydrolase, i.e., N-isopropylammelide isopropylaminohydrolase (AtzC) from JW-1 cells by ammonium sulfate precipitation and three chromatography steps. The purified AtzC catalyzed amidohydrolysis of N-isopropylammelide to cyanuric acid. The optimal catalytic conditions of the purified AtzC were 42 °C and pH 7.0, and the Km and Vmax of AtzC was 0.811 mM and 28.19 mmol/min·mg. AtzC could catalyze amidohydrolysis of an N-alkyl substituent from dihydroxy s-triazines to cyanuric acid. Molecular docking and structural alignments were used to infer AtzC catalytic mechanism. The structural architecture of AtzC resembled that of cytosine deaminase in class III amidohydrolase, with a single Zn2+ coordinated by His and Asp. Interestingly, the AtzC lacks an acidic residue putatively to activate water for hydrolysis as compared to the other amidohydrolases. His253 in AtzC probably functions as a single general acid-base catalyst. These findings further enhance our understanding how aminohydrolases catalyze the metabolism of s-triazine herbicides.
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Affiliation(s)
- Nan Zhou
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Jie Wang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Wenbo Wang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei, 230036, China.
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Shek R, Hilaire T, Sim J, French JB. Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. Biochemistry 2019; 58:3280-3292. [PMID: 31283204 DOI: 10.1021/acs.biochem.9b00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine deaminase is a metabolic enzyme, found in all forms of life, which catalyzes the conversion of guanine to xanthine. Despite the availability of several crystal structures, the molecular determinants of substrate orientation and mechanism remain to be elucidated for the amidohydrolase family of guanine deaminase enzymes. Here, we report the crystal structures of Escherichia coli and Saccharomyces cerevisiae guanine deaminase enzymes (EcGuaD and Gud1, respectively), both members of the amidohydrolase superfamily. EcGuaD and Gud1 retain the overall TIM barrel tertiary structure conserved among amidohydrolase enzymes. Both proteins also possess a single zinc cation with trigonal bipyrimidal coordination geometry within their active sites. We also determined a liganded structure of Gud1 bound to the product, xanthine. Analysis of this structure, along with kinetic data of native and site-directed mutants of EcGuaD, identifies several key residues that are responsible for substrate recognition and catalysis. In addition, after a small library of compounds had been screened, two guanine derivatives, 8-azaguanine and 1-methylguanine, were identified as EcGuaD substrates. Interestingly, both EcGuaD and Gud1 also exhibit secondary ammeline deaminase activity. Overall, this work details key structural features of substrate recognition and catalysis of the amidohydrolase family of guanine deaminase enzymes in support of our long-term goal to engineer these enzymes with altered activity and substrate specificity.
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Affiliation(s)
- Roger Shek
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Tylene Hilaire
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jasper Sim
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jarrod B French
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
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Aučynaitė A, Rutkienė R, Tauraitė D, Meškys R, Urbonavičius J. Discovery of Bacterial Deaminases That Convert 5-Fluoroisocytosine Into 5-Fluorouracil. Front Microbiol 2018; 9:2375. [PMID: 30349513 PMCID: PMC6186785 DOI: 10.3389/fmicb.2018.02375] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/18/2018] [Indexed: 11/29/2022] Open
Abstract
Cytosine is one of the four letters of a standard genetic code, found both in DNA and in RNA. This heterocyclic base can be converted into uracil upon the action of the well-known cytosine deaminase. Isocytosine (2-aminouracil) is an isomer of cytosine, yet the enzymes that could convert it into uracil were previously mainly overlooked. In order to search for the isocytosine deaminases we used a selection strategy that is based on uracil auxotrophy and the metagenomic libraries, which provide a random pool of genes from uncultivated soil bacteria. Several genes that encode isocytosine deaminases were found and two respective recombinant proteins were purified. It was established that both novel deaminases do not use cytosine as a substrate. Instead, these enzymes are able to convert not only isocytosine into uracil, but also 5-fluoroisocytosine into 5-fluorouracil. Our findings suggest that novel isocytosine deaminases have a potential to be efficiently used in targeted cancer therapy instead of the classical cytosine deaminases. Use of isocytosine instead of cytosine would produce fewer side effects since deaminases produced by the commensal E. coli gut flora are ten times less efficient in degrading isocytosine than cytosine. In addition, there are no known homologs of isocytosine deaminases in human cells that would induce the toxicity when 5-fluoroisocytosine would be used as a prodrug.
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Affiliation(s)
- Agota Aučynaitė
- Institute of Biochemistry, Department of Molecular Microbiology and Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rasa Rutkienė
- Institute of Biochemistry, Department of Molecular Microbiology and Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daiva Tauraitė
- Institute of Biochemistry, Department of Molecular Microbiology and Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Institute of Biochemistry, Department of Molecular Microbiology and Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jaunius Urbonavičius
- Institute of Biochemistry, Department of Molecular Microbiology and Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
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7
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Golime G, Bogonda G, Kim HY, Oh K. Biomimetic Oxidative Deamination Catalysis via ortho-Naphthoquinone-Catalyzed Aerobic Oxidation Strategy. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00992] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Gangadhararao Golime
- Center for Metareceptome Research, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro,
Dongjak, Seoul 06974, Republic of Korea
| | - Ganganna Bogonda
- Center for Metareceptome Research, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro,
Dongjak, Seoul 06974, Republic of Korea
| | - Hun Young Kim
- Center for Metareceptome Research, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro,
Dongjak, Seoul 06974, Republic of Korea
| | - Kyungsoo Oh
- Center for Metareceptome Research, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro,
Dongjak, Seoul 06974, Republic of Korea
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Gaded V, Anand R. Nucleobase deaminases: a potential enzyme system for new therapies. RSC Adv 2018; 8:23567-23577. [PMID: 35540270 PMCID: PMC9081823 DOI: 10.1039/c8ra04112a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 11/21/2022] Open
Abstract
This review presents an overview of the structure, function and mechanism of CDA deaminases and their potential as enzyme systems for development of new antimicrobial therapies.
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Affiliation(s)
- Vandana Gaded
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
| | - Ruchi Anand
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
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Gaded V, Anand R. Selective Deamination of Mutagens by a Mycobacterial Enzyme. J Am Chem Soc 2017; 139:10762-10768. [DOI: 10.1021/jacs.7b04967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Vandana Gaded
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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10
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Ferraboschi P, Ciceri S, Grisenti P. Synthesis of Antitumor Fluorinated Pyrimidine Nucleosides. ORG PREP PROCED INT 2017. [DOI: 10.1080/00304948.2017.1290994] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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11
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Wu GH, Shi XB, Lian YF, Xiang HB, Xiong J. Crystal structure of N, N-diethyl-5-bromo-3,4-dihydro-2,4-dioxopyrimidine-1(2 H)-carboxamide, C 9H 12BrN 3O 3. Z KRIST-NEW CRYST ST 2017. [DOI: 10.1515/ncrs-2016-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C9H12BrN3O3, monoclinic, P21/c, a = 12.0359(15) Å, b = 5.4815(6) Å, c = 20.1931(18) Å, β = 120.780(5)°, V = 1144.6(2) Å3, Z = 4, R
gt(F) = 0.0234, wR
ref(F
2) = 0.0984, T = 298(2) K.
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Affiliation(s)
- Guang-Hui Wu
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, People’s Republic of China
| | - Xian-Bo Shi
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, People’s Republic of China
| | - Yu-Feng Lian
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, People’s Republic of China
| | - Hua-Bin Xiang
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, People’s Republic of China
| | - Jing Xiong
- College of Chemistry and Materials Engineering, Wenzhou University, Wenzhou 325035, P. R. China
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