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Verma D, Kaushal N, Balhara R, Singh K. Genome-wide analysis of Catalase gene family reveal insights into abiotic stress response mechanism in Brassica juncea and B. rapa. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111620. [PMID: 36738937 DOI: 10.1016/j.plantsci.2023.111620] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Environmental stresses affect the yield and productivity of Brassica crops. Catalases are important antioxidant enzymes involved in reducing excess hydrogen peroxide produced by environmental stresses. In the present study, nine and seven CAT family members in two oilseed Brassica species (B. juncea and B. rapa) were identified with complete characterization based on gene and protein structure. Phylogenetic classification categorized CAT proteins into three classes and differentiated the monocot and dicot-specific CAT proteins. Further, the gene and protein characterizations revealed a high degree of conservation across the CAT family members. Differences were observed in the CAT-HEME binding affinity in CAT1, CAT2, and CAT3 isozymes, which could suggest their differential enzyme activities in different conditions. Furthermore, protein-protein interaction with other antioxidant proteins suggested their coordinated role in ROS scavenging mechanisms. Notably, the differential gene expression of BjuCATs and BraCATs and CAT enzyme activities suggested their crucial roles in major abiotic stresses faced by Brassica species. Promoter analysis in BjuCATs and BraCATs suggested the presence of abiotic-stress responsive cis-regulatory elements. Gene regulatory network analysis suggested miRNA and TF mediated stress response in BjuCATs and BraCATs. CAT family screening and characterization in Brassica sp. has established a basic ground for further functional validation in abiotic and heavy-metal stresses which can help in developing stress tolerant crops.
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Affiliation(s)
- Deepika Verma
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Nishant Kaushal
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Rinku Balhara
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India
| | - Kashmir Singh
- Department of Biotechnology, BMS Block I, Panjab University, Sector 25, Chandigarh 160014, India.
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2
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Hansberg W. Monofunctional Heme-Catalases. Antioxidants (Basel) 2022; 11:2173. [PMID: 36358546 PMCID: PMC9687031 DOI: 10.3390/antiox11112173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 09/17/2023] Open
Abstract
The review focuses on four issues that are critical for the understanding of monofunctional catalases. How hydrogen peroxide (H2O2) reaches the active site and outcompetes water molecules to be able to function at a very high rate is one of the issues examined. Part of the answer is a gate valve system that is instrumental to drive out solvent molecules from the final section of the main channel. A second issue relates to how the enzyme deals with an unproductive reactive compound I (Cpd I) intermediate. Peroxidatic two and one electron donors and the transfer of electrons to the active site from NADPH and other compounds are reviewed. The new ascribed catalase reactions are revised, indicating possible measurement pitfalls. A third issue concerns the heme b to heme d oxidation, why this reaction occurs only in some large-size subunit catalases (LSCs), and the possible role of singlet oxygen in this and other modifications. The formation of a covalent bond between the proximal tyrosine with the vicinal residue is analyzed. The last issue refers to the origin and function of the additional C-terminal domain (TD) of LSCs. The TD has a molecular chaperone activity that is traced to a gene fusion between a Hsp31-type chaperone and a small-size subunit catalase (SSC).
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Affiliation(s)
- Wilhelm Hansberg
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico
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Goc G, Balci S, Yorke BA, Pearson AR, Yuzugullu Karakus Y. Probing the role of Val228 on the catalytic activity of Scytalidium catalase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140662. [PMID: 33887466 DOI: 10.1016/j.bbapap.2021.140662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/17/2022]
Abstract
Scytalidium catalase is a homotetramer including heme d in each subunit. Its primary function is the dismutation of H2O2 to water and oxygen, but it is also able to oxidase various small organic compounds including catechol and phenol. The crystal structure of Scytalidium catalase reveals the presence of three linked channels providing access to the exterior like other catalases reported so far. The function of these channels has been extensively studied, revealing the possible routes for substrate flow and product release. In this report, we have focussed on the semi-conserved residue Val228, located near to the vinyl groups of the heme at the opening of the lateral channel. Its replacement with Ala, Ser, Gly, Cys, Phe and Ile were tested. We observed a significant decrease in catalytic efficiency in all mutants with the exception of a remarkable increase in oxidase activity when Val228 was mutated to either Ala, Gly or Ser. The reduced catalytic efficiencies are characterized in terms of the restriction of hydrogen peroxide as electron acceptor in the active centre resulting from the opening of lateral channel inlet by introducing the smaller side chain residues. On the other hand, the increased oxidase activity is explained by allowing the suitable electron donor to approach more closely to the heme. The crystal structures of V228C and V228I were determined at 1.41 and 1.47 Å resolution, respectively. The lateral channels of the V228C and V228I presented a broadly identical chain of arranged waters to that observed for wild-type enzyme.
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Affiliation(s)
- Gunce Goc
- Department of Biology, Kocaeli University, Umuttepe, Kocaeli 41380, Turkey
| | - Sinem Balci
- Department of Biology, Kocaeli University, Umuttepe, Kocaeli 41380, Turkey
| | - Briony A Yorke
- School of Chemistry and Bioscience, Faculty of Life Sciences, University of Bradford, Bradford West Yorkshire BD7 1DP, UK
| | - Arwen R Pearson
- The Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, 22761, Germany
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Hanaoka Y, Kimoto H, Yoshimume K, Hara I, Matsuyama H, Yumoto I. Relationship Between Main Channel Structure of Catalases and the Evolutionary Direction in Cold-Adapted Hydrogen Peroxide-Tolerant Exiguobacteium and Psychrobacter. Indian J Microbiol 2020; 60:353-362. [PMID: 32647394 DOI: 10.1007/s12088-020-00878-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Catalase has crucial role in adaptive response to H2O2. Main channel structure responsible for substrate selectivity was estimated to understand the relationship between the evolutionary direction of catalases from Exiguobacterium oxidotolerans and Psychrobacter piscatorii which survive in cold and high concentration of hydrogen peroxide, and their catalytic property. E. oxidotolerans catalase (EKTA) exhibited a higher ratio of compound I formation rate using peracetic acid (a substrate lager than H2O2)/catalase activity using H2O2 as the substrate than P. piscatori catalase (PKTA). It was considered that the ratio was attributed to the size of the amino acid residues locating at the bottle neck structure in the main channel. The differences in the ratio of the compound I formation rate with peracetic acid to catalase activity with H2O2 between the deeper branches in the phylogenetic tree in both EKTA and PKTA were large. This indicates that catalases from the hydrogen peroxide-tolerant bacteria have evolved in different directions, exhibiting effective catalytic activity and allowing broader substrates size or H2O2-specific substrate acceptability in EKTA and PKTA, respectively. It is considered that the main channel structure reflected the difference in the evolutionary direction of clade 1 and clade 3 catalases.
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Affiliation(s)
- Yoshiko Hanaoka
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
| | - Hideyuki Kimoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan.,School of Biological Science and Engineering, Tokai University, Sapporo, Japan
| | | | | | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Sapporo, Japan
| | - Isao Yumoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
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Chen L, Wu R, Feng J, Feng T, Wang C, Hu J, Zhan N, Li Y, Ma X, Ren B, Zhang J, Song CP, Li J, Zhou JM, Zuo J. Transnitrosylation Mediated by the Non-canonical Catalase ROG1 Regulates Nitric Oxide Signaling in Plants. Dev Cell 2020; 53:444-457.e5. [PMID: 32330424 DOI: 10.1016/j.devcel.2020.03.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 01/21/2020] [Accepted: 03/25/2020] [Indexed: 01/26/2023]
Abstract
The redox-based protein S-nitrosylation is a conserved mechanism modulating nitric oxide (NO) signaling and has been considered mainly as a non-enzymatic reaction. S-nitrosylation is regulated by the intracellular NO level that is tightly controlled by S-nitrosoglutathione reductase (GSNOR). However, the molecular mechanisms regulating S-nitrosylation selectivity remain elusive. Here, we characterize an Arabidopsis "repressor of" gsnor1 (rog1) mutation that specifically suppresses the gsnor1 mutant phenotype. ROG1, identical to the non-canonical catalase, CAT3, is a transnitrosylase that specifically modifies GSNOR1 at Cys-10. The transnitrosylase activity of ROG1 is regulated by a unique and highly conserved Cys-343 residue. A ROG1C343T mutant displays increased catalase but decreased transnitrosylase activities. Consistent with these results, the rog1 mutation compromises responses to NO under both normal and stress conditions. We propose that ROG1 functions as a transnitrosylase to regulate the NO-based redox signaling in plants.
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Affiliation(s)
- Lichao Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Feng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianpeng Feng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiliang Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ni Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Yansha Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Ren
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Collaborative Innovation Center of Crop Stress Biology, Henan University, Kaifeng 475001, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Biotic Interactions, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China.
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6
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Simin khataee, Dehghan G, Rashtbari S, Yekta R, Sheibani N. Synergistic inhibition of catalase activity by food colorants sunset yellow and curcumin: An experimental and MLSD simulation approach. Chem Biol Interact 2019; 311:108746. [DOI: 10.1016/j.cbi.2019.108746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/06/2019] [Accepted: 07/10/2019] [Indexed: 11/26/2022]
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7
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da Costa WLO, Araújo CLDA, Dias LM, Pereira LCDS, Alves JTC, Araújo FA, Folador EL, Henriques I, Silva A, Folador ARC. Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance. PLoS One 2018; 13:e0198965. [PMID: 29940001 PMCID: PMC6016940 DOI: 10.1371/journal.pone.0198965] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023] Open
Abstract
Exiguobacterium antarcticum strain B7 is a psychrophilic Gram-positive bacterium that possesses enzymes that can be used for several biotechnological applications. However, many proteins from its genome are considered hypothetical proteins (HPs). These functionally unknown proteins may indicate important functions regarding the biological role of this bacterium, and the use of bioinformatics tools can assist in the biological understanding of this organism through functional annotation analysis. Thus, our study aimed to assign functions to proteins previously described as HPs, present in the genome of E. antarcticum B7. We used an extensive in silico workflow combining several bioinformatics tools for function annotation, sub-cellular localization and physicochemical characterization, three-dimensional structure determination, and protein-protein interactions. This genome contains 2772 genes, of which 765 CDS were annotated as HPs. The amino acid sequences of all HPs were submitted to our workflow and we successfully attributed function to 132 HPs. We identified 11 proteins that play important roles in the mechanisms of adaptation to adverse environments, such as flagellar biosynthesis, biofilm formation, carotenoids biosynthesis, and others. In addition, three predicted HPs are possibly related to arsenic tolerance. Through an in vitro assay, we verified that E. antarcticum B7 can grow at high concentrations of this metal. The approach used was important to precisely assign function to proteins from diverse classes and to infer relationships with proteins with functions already described in the literature. This approach aims to produce a better understanding of the mechanism by which this bacterium adapts to extreme environments and to the finding of targets with biotechnological interest.
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Affiliation(s)
- Wana Lailan Oliveira da Costa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Carlos Leonardo de Aragão Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Larissa Maranhão Dias
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Lino César de Sousa Pereira
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Jorianne Thyeska Castro Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Fabrício Almeida Araújo
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraiba, João Pessoa, Paraíba, Brazil
| | - Isabel Henriques
- Biology Department & CESAM, University of Aveiro, Aveiro, Portugal
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil
- * E-mail: ,
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8
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Sepasi Tehrani H, Moosavi-Movahedi AA. Catalase and its mysteries. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018. [PMID: 29530789 DOI: 10.1016/j.pbiomolbio.2018.03.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Catalase is one of the firsts in every realm of biological sciences. At the same time it also has a number of unusual features. It has one of the highest turnover numbers of all enzymes. It is essential for neutralizing the noxious hydrogen peroxide both in the nature and the various industries such as dairy, textile and pharmaceutics. It also has the merit of being one of the first protein crystals to be isolated. Ironically its three-dimensional structure was discerned some forty years later. However through the times this senile enzyme has continued to intrigue the scientists by surprising facts and phenomena, such as peculiar interweaving of subunits and remarkable thermal stability. It is also known for suicide inactivation by its own substrate. Catalase is known to be implicated in various medical scenarios and its levels have served as a marker in that capacity. It has even been incorporated into several pharmaceuticals. This review strives to clarify these perspectives. It also draws attention to the biophysical contributions offered by thermodynamics and kinetics in these discoveries. The ultimate aim of this review, however, is to state that the venerable catalase will continue to bewilder us with its mysteries well into the twenty-first century.
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Affiliation(s)
- Hessam Sepasi Tehrani
- Department of Biology, Islamic Azad University, Science and Research Branch, Tehran, Iran.
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9
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Castro-Severyn J, Remonsellez F, Valenzuela SL, Salinas C, Fortt J, Aguilar P, Pardo-Esté C, Dorador C, Quatrini R, Molina F, Aguayo D, Castro-Nallar E, Saavedra CP. Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance. Front Microbiol 2017; 8:456. [PMID: 28377753 PMCID: PMC5360010 DOI: 10.3389/fmicb.2017.00456] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/06/2017] [Indexed: 11/13/2022] Open
Abstract
The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean lakes. Several heavy metals are found in the Atacama Desert, and microorganisms growing in this environment show varying levels of resistance/tolerance to copper, tellurium, and arsenic, among others. Herein, we report the genome sequence and comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Further, expression of the ars operon and acr3 was strongly induced in response to both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance in Exiguobacterium sp. SH31.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres BelloSantiago, Chile; Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés BelloSantiago, Chile
| | - Francisco Remonsellez
- Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte Antofagasta, Chile
| | - Sandro L Valenzuela
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello Santiago, Chile
| | - Cesar Salinas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Jonathan Fortt
- Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte Antofagasta, Chile
| | - Pablo Aguilar
- Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del NorteAntofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centre for Biotechnology and BioengineeringAntofagasta, Chile
| | - Raquel Quatrini
- Laboratorio de Ecofisiología Microbiana, Fundación Ciencia and Vida Santiago, Chile
| | | | - Daniel Aguayo
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés BelloSantiago, Chile; Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de ValparaísoValparaíso, Chile
| | - Eduardo Castro-Nallar
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bello Santiago, Chile
| | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello Santiago, Chile
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Studies to reveal the nature of interactions between catalase and curcumin using computational methods and optical techniques. Int J Biol Macromol 2016; 95:550-556. [PMID: 27865955 DOI: 10.1016/j.ijbiomac.2016.11.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 11/20/2022]
Abstract
Curcumin is an important antioxidant compound, and is widely reported as an effective component for reducing complications of many diseases. However, the detailed mechanisms of its activity remain poorly understood. We found that curcumin can significantly increase catalase activity of BLC (bovine liver catalase). The mechanism of curcumin action was investigated using a computational method. We suggested that curcumin may activate BLC by modifying the bottleneck of its narrow channel. The molecular dynamic simulation data showed that placing curcumin on the structure of enzyme can increase the size of the bottleneck in the narrow channel of BLC, and readily allow the access of substrate to the active site. Because of the increase of the distance between amino acids of the bottleneck in the presence of curcumin, the entrance space of substrate increased from 250Å3 to 440Å3. In addition, the increase in emission of intrinsic fluorescence of BLC in presence of curcumin demonstrated changes in tertiary structure of catalase, and possibility of less quenching. We also used circular dichroism (CD) spectropolarimetry to determine how curcumin may alter the enzyme secondary structure. Catalase spectra in the presence of various concentrations of curcumin showed an increase in the amount of α-helix content.
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Hospital A, Goñi JR, Orozco M, Gelpí JL. Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem 2015; 8:37-47. [PMID: 26604800 PMCID: PMC4655909 DOI: 10.2147/aabc.s70333] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
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Affiliation(s)
- Adam Hospital
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain
| | - Josep Ramon Goñi
- Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain ; Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Josep L Gelpí
- Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
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12
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Dong C, Zheng X, Diao Y, Wang Y, Zhou M, Hu Z. Molecular Cloning and Expression Analysis of a Catalase Gene (NnCAT) from Nelumbo nucifera. Appl Biochem Biotechnol 2015; 177:1216-28. [PMID: 26299377 DOI: 10.1007/s12010-015-1808-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/12/2015] [Indexed: 11/26/2022]
Abstract
Rapid amplification cDNA end (RACE) assay was established to achieve the complete cDNA sequence of a catalase gene (NnCAT) from Nelumbo nucifera. The obtained full-length cDNA was 1666 bp in size and contained a 1476-bp open reading frame. The 3D structural model of NnCAT was constructed by homology modeling. The putative NnCAT possessed all the main characteristic amino acid residues and motifs of catalase (CAT) protein family, and the phylogenetic analysis revealed that NnCAT grouped together with high plants. Moreover, recombinant NnCAT showed the CAT activity (758 U/mg) at room temperature, holding high activity during temperature range of 20-50 °C, then the optimal pH of recombinant protein was assessed from pH 4 to pH 11. Additionally, real-time PCR assay demonstrated that NnCAT mRNA was expressed in various tissues of N. nucifera, with the highest expression in young leaf and lowest level in the root, and mRNA level of NnCAT was significantly augmented in response to short-time mechanical wounding. Different expression pattern of NnCAT gene suggested that NnCAT probably played a defensive role in the initial stages of oxidative stress, regulating the level of reactive oxygen species (ROS) by extracellular stimuli such as short-time mechanical wounding.
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Affiliation(s)
- Chen Dong
- College of Biological Engineering, Henan University of Technology, Zhengzhou, Henan, 450051, China
| | - Xingfei Zheng
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Ying Diao
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Youwei Wang
- Lotus Center, Wuhan University, Wuhan, 430072, China
| | - Mingquan Zhou
- Lotus Center, Wuhan University, Wuhan, 430072, China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, 430072, China.
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13
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Abstract
The catalase enzyme decomposes the toxic concentrations of hydrogen peroxide into oxygen and water. Hydrogen peroxide is a highly reactive small molecule and its excessive concentration may cause significant damages to proteins, deoxyribonucleic acid, ribonucleic acid and lipids. Acatalasemia refers to inherited deficiency of the catalase enzyme. In this review the authors discuss the possible role of the human catalase enzyme, the metabolism of hydrogen peroxide, and the phenomenon of hydrogen peroxide paradox. In addition, they review data obtained from Hungarian acatalasemic patients indicating an increased frequency of type 2 diabetes mellitus, especially in female patients, and an early onset of type 2 diabetes in these patients. There are 10 catalase gene variants which appear to be responsible for decreased blood catalase activity in acatalasemic patients with type 2 diabetes. It is assumed that low levels of blood catalase may cause an increased concentration of hydrogen peroxide which may contribute to the pathogenesis of type 2 diabetes mellitus.
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Affiliation(s)
- László Góth
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Laboratóriumi és Képalkotó Diagnosztikai Tanszék Debrecen
| | - Teréz Nagy
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Laboratóriumi és Képalkotó Diagnosztikai Tanszék Debrecen
| | - Miklós Káplár
- Debreceni Egyetem, Klinikai Központ Belgyógyászati Intézet, Anyagcsere Betegségek Tanszék Debrecen
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14
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Purification, cloning, expression, and biochemical characterization of a monofunctional catalase, KatP, from Pigmentiphaga sp. DL-8. Protein Expr Purif 2015; 108:54-61. [PMID: 25665507 DOI: 10.1016/j.pep.2015.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 11/20/2022]
Abstract
Catalases are essential components of the cellular equipment used to cope with oxidative stress. The monofunctional catalase KatP was purified from Pigmentiphaga sp. using ammonium sulfate precipitation (ASP), diethylaminoethyl ion exchange chromatography (IEC), and hydrophobic interaction chromatography (HIC). The purified catalase formed polymer with an estimated monomer molecular mass of 54kDa, which were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymogram analysis. KatP exhibited a specific catalytic activity of 73,000U/mg, which was higher than that of catalase-1 of Comamonas terrigena N3H (55,900U/mg). Seven short tryptic fragments of this catalase were obtained by electrospray ionization quadrupole time-of-flight mass spectrometry (ESI-Q-TOF MS/MS), and the gene, katP, was cloned by PCR amplification and overexpressed in Escherichia coli BL21 (DE3). Based on the complete amino acid sequence, KatP was identified as a clade 3 monofunctional catalase. The specific activities of recombinant KatP for hydrogen peroxide (690,000U/mg) increased 9-fold over that of the parent strain. The Km and Vmax of recombinant KatP were 9.48mM and 81.2mol/minmg, respectively. The optimal pH and temperature for KatP were 7.0 and 37°C, respectively, and the enzyme displayed abroad pH-stable range of 4.0-11.0. The enzyme was inhibited by Zn(2+), Cu(2+), Cr(2+), and Mn(2+), whereas Fe(3+) and Mg(2+) stimulated KatP enzymatic activity. Interestingly, the catalase activity of recombinant KatP displayed high stability under different temperature and pH conditions, suggesting that KatP is a potential candidate for the production of catalase.
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15
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Manipulation of culture conditions for extensive extracellular catalase production by Exiguobacterium oxidotolerans T-2-2T. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0943-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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16
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Borges PT, Frazão C, Miranda CS, Carrondo MA, Romão CV. Structure of the monofunctional heme catalase DR1998 from Deinococcus radiodurans. FEBS J 2014; 281:4138-50. [PMID: 24975828 DOI: 10.1111/febs.12895] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/12/2014] [Accepted: 06/24/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Deinococcus radiodurans is an aerobic organism with the ability to survive under conditions of high radiation doses or desiccation. As part of its protection system against oxidative stress, this bacterium encodes three monofunctional catalases. The DR1998 catalase belongs to clade 1, and is present at high levels under normal growth conditions. The crystals of DR1998 diffracted very weakly, and the merged diffraction data showed an R sym of 0.308. Its crystal structure was determined and refined to 2.6 Å. The four molecules present in the asymmetric unit form, by crystallographic symmetry, two homotetramers with 222 point-group symmetry. The overall structure of DR1998 is similar to that of other monofunctional catalases, showing higher structural homology with the catalase structures of clade 1. Each monomer shows the typical catalase fold, and contains one heme b in the active site. The heme is coordinated by the proximal ligand Tyr369, and on the heme distal side the essential His81 and Asn159 are hydrogen-bonded to a water molecule. A 25-Å-long channel is the main channel connecting the active site to the external surface. This channel starts with a hydrophobic region from the catalytic heme site, which is followed by a hydrophilic region that begins on Asp139 and expands up to the protein surface. Apart from this channel, an alternative channel, also near the heme active site, is presented and discussed. DATABASE Coordinates and structure factors have been deposited in the Protein Data Bank in Europe under accession code 4CAB.
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Affiliation(s)
- Patrícia T Borges
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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17
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Borges PT, Miranda CS, Santos SP, Carita JN, Frazão C, Romão CV. Purification, crystallization and phase determination of the DR1998 haem b catalase from Deinococcus radiodurans. Acta Crystallogr F Struct Biol Commun 2014; 70:659-62. [PMID: 24817732 PMCID: PMC4014341 DOI: 10.1107/s2053230x1400764x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/04/2014] [Indexed: 11/10/2022] Open
Abstract
The protective mechanisms of Deinococcus radiodurans against primary reactive oxygen species involve nonenzymatic scavengers and a powerful enzymatic antioxidant system including catalases, peroxidases and superoxide dismutases that prevents oxidative damage. Catalase is an enzyme that is responsible for the conversion of H2O2 to O2 and H2O, protecting the organism from the oxidative effect of H2O2. This study reports the purification and crystallization of the DR1998 catalase from D. radiodurans. The crystals diffracted to 2.6 Å resolution and belonged to space group C2221, with unit-cell parameters a = 97.33, b = 311.88, c = 145.63 Å, suggesting that they contain four molecules per asymmetric unit. The initial phases were determined by molecular replacement and the obtained solution shows the typical catalase quaternary structure. A preliminary model of the protein structure has been built and refinement is currently in progress.
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Affiliation(s)
- Patrícia T. Borges
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Cecília S. Miranda
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Sandra P. Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - João N. Carita
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
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18
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Nonaka K, Yoon KS, Ogo S. Biochemical characterization of psychrophilic Mn-superoxide dismutase from newly isolated Exiguobacterium sp. OS-77. Extremophiles 2014; 18:363-73. [PMID: 24414928 DOI: 10.1007/s00792-013-0621-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/29/2013] [Indexed: 02/01/2023]
Abstract
Many types of superoxide dismutases have been purified and characterized from various bacteria, however, a psychrophilic Mn-superoxide dismutase (MnSOD) has not yet been reported. Here, we describe the purification and the biochemical characterization of the psychrophilic MnSOD from Exiguobacterium sp. strain OS-77 (EgMnSOD). According to 16S rRNA sequence analysis, a newly isolated bacterium strain OS-77 belongs to the genus Exiguobacterium. The optimum growth temperature of the strain OS-77 is 20 °C. The EgMnSOD is a homodimer of 23.5 kDa polypeptides determined by SDS-PAGE and gel filtration analysis. UV-Vis spectrum and ICP-MS analysis clearly indicated that the homogeneously purified enzyme contains only a Mn ion as a metal cofactor. The optimal reaction pH and temperature of the enzyme were pH 9.0 and 5 °C, respectively. Notably, the purified EgMnSOD was thermostable up to 45 °C and retained 50% activity after 21.2 min at 60 °C. The differential scanning calorimetry also indicated that the EgMnSOD is thermostable, exhibiting two protein denaturation peaks at 65 and 84 °C. The statistical analysis of amino acid sequence and composition of the EgMnSOD suggests that the enzyme retains psychrophilic characteristics.
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Affiliation(s)
- Kyoshiro Nonaka
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
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19
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Growth-dependent catalase localization in Exiguobacterium oxidotolerans T-2-2T reflected by catalase activity of cells. PLoS One 2013; 8:e76862. [PMID: 24204687 PMCID: PMC3800074 DOI: 10.1371/journal.pone.0076862] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/28/2013] [Indexed: 12/19/2022] Open
Abstract
A psychrotolerant and H2O2-resistant bacterium, Exiguobacterium oxidotolerans T-2-2T, exhibits extraordinary H2O2 resistance and produces catalase not only intracellularly but also extracellularly. The intracellular and extracellular catalases exhibited the same enzymatic characteristics, that is, they exhibited the temperature-dependent activity characteristic of a cold-adapted enzyme, their heat stabilities were similar to those of mesophilic enzymes and very high catalytic intensity. In addition, catalase gene analysis indicated that the bacterium possessed the sole clade 1 catalase gene corresponding to intracellular catalase. Hence, intracellular catalase is secreted into the extracellular space. In addition to intracellular and extracellular catalases, the inner circumference of the cells showed the localization of catalase in the mid-stationary growth phase, which was observed by immunoelectron microscopy using an antibody against the intracellular catalase of the strain. The cells demonstrated higher catalase activity in the mid-stationary growth phase than in the exponential growth phase. The catalase localized in the inner circumference can be dissociated by treatment with Tween 60. Thus, the localized catalase is not tightly bound to the inner circumference of the cells and may play a role in the oxidative defense of the cells under low metabolic state.
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20
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In silico 3D structure prediction and hydrogen peroxide binding study of wheat catalase. Interdiscip Sci 2013; 5:77-83. [PMID: 23605643 DOI: 10.1007/s12539-013-0154-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 11/27/2012] [Accepted: 12/04/2012] [Indexed: 10/26/2022]
Abstract
Catalase (CAT) is one of the most active enzyme catalysts found in plants, animals and in all aerobic microorganisms. The major function of the enzyme is to decompose H2O2, produced by cellular metabolic activities under normal and stressful conditions to water and oxygen. The present study involves 3D structure modeling of wheat catalase from Triticum aestivum by MODELLER9v7 and its binding study with H2O2. The Evaluation of the model was based on Discrete Optimized Protein Energy Score (DOPE). The structure was also validated using PROCHECK comprising of 95.0% amino acid residues in favored regions of Ramachandran plot, Verify3D and ProsA which confirm that the model is reliable. The 3D model of the molecule was found to consist of ten strands and seventeen helices having a common fold characterised by β-pleated sheet flanked either side by helices. The docking study with H2O2 indicates that Gln352 and Arg353 are two important determinant residues in binding H2O2 as these residues have strong hydrogen bonding contacts with the substrate. These hydrogen-bonding interactions play a significant role in the stability of the complex.
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21
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Yuzugullu Y, Trinh CH, Smith MA, Pearson AR, Phillips SEV, Sutay Kocabas D, Bakir U, Ogel ZB, McPherson MJ. Structure, recombinant expression and mutagenesis studies of the catalase with oxidase activity fromScytalidium thermophilum. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:398-408. [DOI: 10.1107/s0907444912049001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/29/2012] [Indexed: 11/10/2022]
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22
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Hospital A, Gelpi JL. High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Hansberg W, Salas-Lizana R, Domínguez L. Fungal catalases: Function, phylogenetic origin and structure. Arch Biochem Biophys 2012; 525:170-80. [DOI: 10.1016/j.abb.2012.05.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/16/2022]
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24
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Homology modeling and phylogenetic relationships of catalases of an opportunistic pathogen Rhizopus oryzae. Life Sci 2012; 91:115-26. [DOI: 10.1016/j.lfs.2012.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/24/2012] [Accepted: 06/15/2012] [Indexed: 11/19/2022]
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25
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Korth HG, Meier AC, Auferkamp O, Sicking W, de Groot H, Sustmann R, Kirsch M. Ascorbic acid reduction of compound I of mammalian catalases proceeds via specific binding to the NADPH binding pocket. Biochemistry 2012; 51:4693-703. [PMID: 22616883 DOI: 10.1021/bi2017602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mammalian (Clade 3) catalases utilize NADPH as a protective cofactor to prevent one-electron reduction of the central reactive intermediate Compound I (Cpd I) to the catalytically inactive Compound II (Cpd II) species by re-reduction of Cpd I to the enzyme's resting state (ferricatalase). It has long been known that ascorbate/ascorbic acid is capable of reducing Cpd I of NADPH-binding catalases to Cpd II, but the mode of this one-electron reduction had hitherto not been explored. We here demonstrate that ascorbate-mediated reduction of Cpd I, generated by addition of peroxoacetic acid to NADPH-free bovine liver catalase (BLC), requires specific binding of the ascorbate anion to the NADPH binding pocket. Ascorbate-mediated Cpd II formation was found to be suppressed by added NADPH in a concentration-dependent manner, for the achievement of complete suppression at a stoichiometric 1:1 NADPH:heme concentration ratio. Cpd I → Cpd II reduction by ascorbate was similarly inhibited by addition of NADH, NADP(+), thio-NADP(+), or NAD(+), though with 0.5-, 0.1-, 0.1-, and 0.01-fold reduced efficiencies, respectively, in agreement with the relative binding affinities of these dinucleotides. Unexpected was the observation that although Cpd II formation is not observed in the presence of NADP(+), the decay of Cpd I is slightly accelerated by ascorbate rather than retarded, leading to direct regeneration of ferricatalase. The experimental findings are supported by molecular mechanics docking computations, which show a similar binding of NADPH, NADP(+), and NADH, but not NAD(+), as found in the X-ray structure of NADPH-loaded human erythrocyte catalase. The computations suggest that two ascorbate molecules may occupy the empty NADPH pocket, preferably binding to the adenine binding site. The biological relevance of these findings is discussed.
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Affiliation(s)
- Hans-Gert Korth
- Institut für Organische Chemie, Universität Duisburg-Essen, Essen, Germany.
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26
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Characterization of catalase from psychrotolerant Psychrobacter piscatorii T-3 exhibiting high catalase activity. Int J Mol Sci 2012; 13:1733-1746. [PMID: 22408420 PMCID: PMC3291989 DOI: 10.3390/ijms13021733] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 01/16/2012] [Accepted: 01/30/2012] [Indexed: 12/30/2022] Open
Abstract
A psychrotolerant bacterium, strain T-3 (identified as Psychrobacter piscatorii), that exhibited an extraordinarily high catalase activity was isolated from the drain pool of a plant that uses H2O2 as a bleaching agent. Its cell extract exhibited a catalase activity (19,700 U·mg protein−1) that was higher than that of Micrococcus luteus used for industrial catalase production. Catalase was approximately 10% of the total proteins in the cell extract of the strain. The catalase (PktA) was purified homogeneously by only two purification steps, anion exchange and hydrophobic chromatographies. The purified catalase exhibited higher catalytic efficiency and higher sensitivity of activity at high temperatures than M. luteus catalase. The deduced amino acid sequence showed the highest homology with catalase of Psycrobacter cryohalolentis, a psychrotolelant bacterium obtained from Siberian permafrost. These findings suggest that the characteristics of the PktA molecule reflected the taxonomic relationship of the isolate as well as the environmental conditions (low temperatures and high concentrations of H2O2) under which the bacterium survives. Strain T-3 efficiently produces a catalase (PktA) at a higher rate than Exiguobacterium oxidotolerans, which produces a very strong activity of catalase (EktA) at a moderate rate, in order to adapt to high concentration of H2O2.
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27
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Thirty years of heme catalases structural biology. Arch Biochem Biophys 2011; 525:102-10. [PMID: 22209752 DOI: 10.1016/j.abb.2011.12.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/23/2022]
Abstract
About thirty years ago the crystal structures of the heme catalases from Penicillium vitale (PVC) and, a few months later, from bovine liver (BLC) were published. Both enzymes were compact tetrameric molecules with subunits that, despite their size differences and the large phylogenetic separation between the two organisms, presented a striking structural similarity for about 460 residues. The high conservation, confirmed in all the subsequent structures determined, suggested a strong pressure to preserve a functional catalase fold, which is almost exclusively found in these mono-functional heme catalases. However, even in the absence of the catalase fold an efficient catalase activity is also found in the heme containing catalase-peroxidase proteins. The structure of these broad substrate range enzymes, reported for the first time less than ten years ago from the halophilic archaebacterium Haloarcula marismortui (HmCPx) and from the bacterium Burkholderia pseudomallei (BpKatG), showed a heme pocket closely related to that of plant peroxidases, though with a number of unique modifications that enable the catalase reaction. Despite the wealth of structural information already available, for both monofunctional catalases and catalase-peroxidases, a number of unanswered major questions require continuing structural research with truly innovative approaches.
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28
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Enzymatic characterization of Catalase from Bacillus anthracis and prediction of critical residues using information theoretic measure of Relative Entropy. Biochem Biophys Res Commun 2011; 411:88-95. [DOI: 10.1016/j.bbrc.2011.06.099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 06/13/2011] [Indexed: 01/28/2023]
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29
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Lautier T, Ezanno P, Baffert C, Fourmond V, Cournac L, Fontecilla-Camps JC, Soucaille P, Bertrand P, Meynial-Salles I, Léger C. The quest for a functional substrate access tunnel in FeFe hydrogenase. Faraday Discuss 2011; 148:385-407; discussion 421-41. [DOI: 10.1039/c004099c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Kim S, Park J, Cho J. Layer-by-layer assembled multilayers using catalase-encapsulated gold nanoparticles. NANOTECHNOLOGY 2010; 21:375702. [PMID: 20724775 DOI: 10.1088/0957-4484/21/37/375702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We introduce a novel and versatile approach for the preparation of multilayers, based on catalase-encapsulated gold nanoparticles (CAT-Au(NP)), allowing electrostatic charge reversal and structural transformation through pH adjustment. CAT-Au(NP), which are synthesized directly from CAT stabilizer, can be electrostatically assembled with anionic and cationic PEs as a result of the charge reversal of the catalase stabilizers through pH control. In particular, at pH 5.2, near the pI of catalase, dispersed CAT-Au(NP) are structurally transformed into colloidal or network CAT-Au(NP) nanocomposites. Furthermore, we demonstrate that the layer-by-layer assembled multilayers composed of PEs and CAT-Au(NP) induce an effective electron transfer between CAT and the electrode as well as a high loading of CAT and Au(NP), and resultantly exhibit a highly catalytic activity toward H(2)O(2).
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Affiliation(s)
- Sungwoo Kim
- School of Advanced Materials Engineering, Kookmin University, Seoul, Korea
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31
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Anand P, Kwak Y, Simha R, Donaldson RP. Hydrogen peroxide induced oxidation of peroxisomal malate synthase and catalase. Arch Biochem Biophys 2009; 491:25-31. [PMID: 19800310 DOI: 10.1016/j.abb.2009.09.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 09/25/2009] [Accepted: 09/26/2009] [Indexed: 01/11/2023]
Abstract
Peroxisomes contain oxidases that produce H(2)O(2), which can result in protein oxidation. To test the vulnerability of peroxisomal proteins to oxidation in vivo the organelles were isolated from castor bean endosperm incubated with H(2)O(2). When peroxisomes were exposed to H(2)O(2)in vivo, the peroxisomal proteins exhibited an increase in carbonylation as detected in avidin blots of biotin hydrazide derivatized samples. Biotin-tagged peptides from trypsin digests of the proteins were analyzed by mass spectroscopy and compared to the masses of peptides from the same protein that had not been biotin-tagged and from proteins not exposed to excess H(2)O(2). H(2)O(2) exposure was found to increase the activity of catalase (CAT), and to increase the number of oxidized peptides found in CAT and malate synthase (MS). CAT had 10 peptides that were affected by in vivo exposure to H(2)O(2) and MS had 8. These sites of oxidation have definable locations within the proteins' structures.
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Affiliation(s)
- Pria Anand
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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32
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The Exiguobacterium genus: biodiversity and biogeography. Extremophiles 2009; 13:541-55. [DOI: 10.1007/s00792-009-0243-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2008] [Accepted: 03/30/2009] [Indexed: 10/20/2022]
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33
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Takahashi A, Kurahashi T, Fujii H. Effect of Imidazole and Phenolate Axial Ligands on the Electronic Structure and Reactivity of Oxoiron(IV) Porphyrin π-Cation Radical Complexes: Drastic Increase in Oxo-Transfer and Hydrogen Abstraction Reactivities. Inorg Chem 2009; 48:2614-25. [DOI: 10.1021/ic802123m] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Akihiro Takahashi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8787, Japan
| | - Takuya Kurahashi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8787, Japan
| | - Hiroshi Fujii
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, and Department of Functional Molecular Science, The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8787, Japan
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LaButti JN, Gates KS. Biologically relevant chemical properties of peroxymonophosphate (=O3POOH). Bioorg Med Chem Lett 2008; 19:218-21. [PMID: 19022671 DOI: 10.1016/j.bmcl.2008.10.133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 10/22/2008] [Accepted: 10/27/2008] [Indexed: 11/26/2022]
Abstract
It has been suggested that peroxymonophosphate could serve as an endogenous hydrogen peroxide-derived regulator of cellular protein tyrosine phosphatase activity under physiological or pathophysiological conditions. To facilitate further consideration of the potential role of peroxymonophosphate in biological systems we present studies related to the preparation, characterization, stability, and fluorometric detection of this agent.
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Affiliation(s)
- Jason N LaButti
- Departments of Chemistry and Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, MO 65211, USA
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Abstract
Excessive hydrogen peroxide is harmful for almost all cell components, so its rapid and efficient removal is of essential importance for aerobically living organisms. Conversely, hydrogen peroxide acts as a second messenger in signal-transduction pathways. H(2)O(2) is degraded by peroxidases and catalases, the latter being able both to reduce H(2)O(2) to water and to oxidize it to molecular oxygen. Nature has evolved three protein families that are able to catalyze this dismutation at reasonable rates. Two of the protein families are heme enzymes: typical catalases and catalase-peroxidases. Typical catalases comprise the most abundant group found in Eubacteria, Archaeabacteria, Protista, Fungi, Plantae, and Animalia, whereas catalase-peroxidases are not found in plants and animals and exhibit both catalatic and peroxidatic activities. The third group is a minor bacterial protein family with a dimanganese active site called manganese catalases. Although catalyzing the same reaction (2 H(2)O(2)--> 2 H(2)O+ O(2)), the three groups differ significantly in their overall and active-site architecture and the mechanism of reaction. Here, we present an overview of the distribution, phylogeny, structure, and function of these enzymes. Additionally, we report about their physiologic role, response to oxidative stress, and about diseases related to catalase deficiency in humans.
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Affiliation(s)
- Marcel Zamocky
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Applied Life Sciences, Vienna, Austria.
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Sicking W, Korth HG, de Groot H, Sustmann R. On the functional role of a water molecule in clade 3 catalases: a proposal for the mechanism by which NADPH prevents the formation of compound II. J Am Chem Soc 2008; 130:7345-56. [PMID: 18479132 DOI: 10.1021/ja077787e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
X-ray structures of the 13 different monofunctional heme catalases published to date were scrutinized in order to gain insight in the mechanism by which NADPH in Clade 3 catalases may protect the reactive ferryloxo intermediate Compound I (Cpd I; por (*+)Fe (IV)O) against deactivation to the catalytically inactive intermediate Compound II (Cpd II; porFe (IV)O). Striking similarities in the molecular network of the protein subunits encompassing the heme center and the surface-bound NADPH were found for all of the Clade 3 catalases. Unique features in this region are the presence of a water molecule (W1) adjacent to the 4-vinyl group of heme and a serine residue or a second water molecule hydrogen-bonded to both W1 and the carbonyl group of a threonine-proline linkage, with the proline in van der Waals contact with the dihydronicotinamide group of NADPH. A mechanism is proposed in which a hydroxyl anion released from W1 undergoes reversible nucleophilic addition to the terminal carbon of the 4-vinyl group of Cpd I, thereby producing a neutral porphyrin pi-radical ferryloxo (HO-por (*)Fe (IV)O) species of reduced reactivity. This structure is suggested to be the elusive Cpd II' intermediate proposed in previous studies. An accompanying proton-shifting process along the hydrogen-bonded network is believed to facilitate the NADPH-mediated reduction of Cpd I to ferricatalase and to serve as a funnel for electron transfer from NADPH to the heme center to restore the catalase Fe (III) resting state. The proposed reaction paths were fully supported as chemically reasonable and energetically feasible by means of density functional theory calculations at the (U)B3LYP/6-31G* level. A particularly attractive feature of the present mechanism is that the previously discussed formation of protein-derived radicals is avoided.
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Affiliation(s)
- Willi Sicking
- Institut für Organische Chemie, Universität Duisburg-Essen, 45117 Essen, Germany
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Takebe F, Hara I, Matsuyama H, Yumoto I. Effects of H2O2 under Low- and High-Aeration-Level Conditions on Growth and Catalase Activity in Exiguobacterium oxidotolerans T-2-2T. J Biosci Bioeng 2007; 104:464-9. [DOI: 10.1263/jbb.104.464] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 09/07/2007] [Indexed: 11/17/2022]
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Yoshimoto M, Sakamoto H, Yoshimoto N, Kuboi R, Nakao K. Stabilization of quaternary structure and activity of bovine liver catalase through encapsulation in liposomes. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.07.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Purification of beef heart cytochrome C by chromatography on an amberlite XE-64, polyacrylamide Bio-Gel P-60 and Bio-Gel P-300 “tandem” column. J Chromatogr A 1969. [DOI: 10.1016/0021-9673(64)80127-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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MORRISON M, HOLLOCHER T, STOTZ E. An evaluation of cytochrome c preparations in oxidation and phosphorylation. Arch Biochem Biophys 1961; 92:338-42. [PMID: 13772883 DOI: 10.1016/0003-9861(61)90358-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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MORRISON M, HOLLOCHER T, MURRAY R, MARINETTI G, STOTZ E. The isolation of cytochrome c by salt extraction. BIOCHIMICA ET BIOPHYSICA ACTA 1960; 41:334-7. [PMID: 14424376 DOI: 10.1016/0006-3002(60)90017-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
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