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Kielb PJ, Teutloff C, Bittl R, Gray HB, Winkler JR. Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site? J Phys Chem B 2022; 126:7943-7949. [PMID: 36191240 PMCID: PMC10231039 DOI: 10.1021/acs.jpcb.2c04835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.
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Affiliation(s)
- Patrycja J. Kielb
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | | | - Robert Bittl
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
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2
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Novoa-Aponte L, Argüello JM. Unique underlying principles shaping copper homeostasis networks. J Biol Inorg Chem 2022; 27:509-528. [PMID: 35802193 PMCID: PMC9470648 DOI: 10.1007/s00775-022-01947-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 12/27/2022]
Abstract
Abstract Copper is essential in cells as a cofactor for key redox enzymes. Bacteria have acquired molecular components that sense, uptake, distribute, and expel copper ensuring that cuproenzymes are metallated and steady-state metal levels are maintained. Toward preventing deleterious reactions, proteins bind copper ions with high affinities and transfer the metal via ligand exchange, warranting that copper ions are always complexed. Consequently, the directional copper distribution within cell compartments and across cell membranes requires specific dynamic interactions and metal exchange between cognate holo-apo protein partners. These metal exchange reactions are determined by thermodynamic and kinetics parameters and influenced by mass action. Then, copper distribution can be conceptualized as a molecular system of singular interacting elements that maintain a physiological copper homeostasis. This review focuses on the impact of copper high-affinity binding and exchange reactions on the homeostatic mechanisms, the conceptual models to describe the cell as a homeostatic system, the various molecule functions that contribute to copper homeostasis, and the alternative system architectures responsible for copper homeostasis in model bacteria. Graphical Abstract ![]()
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Affiliation(s)
- Lorena Novoa-Aponte
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.,Genetics and Metabolism Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St, Worcester, MA, 01605, USA.
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3
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Structural Properties, Genomic Distribution of Laccases from Streptomyces and Their Potential Applications. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Lima NSM, Gomes-Pepe ES, Campanharo JC, de Macedo Lemos EG. Broad thermal spectrum metagenomic laccase with action for dye decolorization and fentin hydroxide treatment. AMB Express 2022; 12:38. [PMID: 35322306 PMCID: PMC8943092 DOI: 10.1186/s13568-022-01375-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/13/2022] [Indexed: 11/10/2022] Open
Abstract
Laccases are multicopper oxidases that act on various phenolic and non-phenolic compounds, enabling numerous applications including xenobiotic bioremediation, biofuel production, drug development, and cosmetic production, and they can be used as additives in the textile and food industries. This wide range of uses makes these enzymes extremely attractive for novel biotechnology applications. Here, we undertook the kinetic characterization of LacMeta, a predicted as homotrimeric (~ 107,93 kDa) small laccase, and demonstrated that this enzyme performs best at an acidic pH (pH 3–5) towards ABTS as substrate and has a broad thermal spectrum (10–60 °C), which can promote high plastic action potential through dynamic environmental temperature fluctuations. This enzyme showed following kinetic parameters: kcat = 6.377 s−1 ± 0.303, Km = 4.219 mM, and Vmax = 24.43 µM/min (against ABTS as substrate). LacMeta almost completely degraded malachite green (50 mg/mL) in only 2 h. Moreover, the enzyme was able to degrade seven dyes from four distinct classes and it respectively achieved 85% and 83% decolorization of methylene blue and trypan blue with ABTS as the mediator. In addition, LacMeta showed potential for the degradation of two thirds of an agricultural fungicide: fentin hydroxide, thus demonstrating its biotechnological aptitude for bioremediation. The results of this study suggest that LacMeta has potential in textile wastewater treatment and that it could help in the bioremediation of other human/environmental toxins such as pesticides and antibiotic compounds belonging to the same chemical classes as the degraded dyes. LacMeta is a new two-domain laccase with activity over a wide temperature range LacMeta maintained 50% activity after 5 months of storage at 4 °C. Laccase was able to degrade in 2 h the Malachite Green dye, and had the potential to degrade fentin hydroxide
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Athanasakoglou A, Fenner K. Toward Characterizing the Genetic Basis of Trace Organic Contaminant Biotransformation in Activated Sludge: The Role of Multicopper Oxidases as a Case Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:313-324. [PMID: 34932304 DOI: 10.1021/acs.est.1c05803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Activated sludge treatment leverages the ability of microbes to uptake and (co)-metabolize chemicals and has shown promise in eliminating trace organic contaminants (TrOCs) during wastewater treatment. However, targeted interventions to optimize the process are limited as the fundamental drivers of the observed reactions remain elusive. In this work, we present a comprehensive workflow for the identification and characterization of key enzymes involved in TrOCs biotransformation pathways in complex microbial communities. To demonstrate the applicability of the workflow, we investigated the role of the enzymatic group of multicopper oxidases (MCOs) as one putatively relevant driver of TrOCs biotransformation. To this end, we analyzed activated sludge metatranscriptomic data and selected, synthesized, and heterologously expressed three phylogenetically distinct MCO-encoding genes expressed in communities with different TrOCs oxidation potentials. Following the purification of the encoded enzymes, we screened their activities against different substrates. We saw that MCOs exhibit significant activities against selected TrOCs in the presence of the mediator compound 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulfonic acid and, in some cases, also in the presence of the wastewater contaminant 4'-hydroxy-benzotriazole. In the first case, we identified oxidation products previously reported from activated sludge communities and concluded that in the presence of appropriate mediators, bacterial MCOs could contribute to the biological removal of TrOCs. Similar investigations of other key enzyme systems may significantly advance our understanding of TrOCs biodegradation and assist the rational design of biology-based water treatment strategies in the future.
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Affiliation(s)
- Anastasia Athanasakoglou
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Kathrin Fenner
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland
- Department of Chemistry, University of Zürich, 8057 Zürich, Switzerland
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6
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Li B, Lu S. The Importance of Amine-degrading Enzymes on the Biogenic Amine Degradation in Fermented Foods: A review. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Gräff M, Buchholz PCF, Le Roes‐Hill M, Pleiss J. Multicopper oxidases: modular structure, sequence space, and evolutionary relationships. Proteins 2020; 88:1329-1339. [DOI: 10.1002/prot.25952] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/22/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Maike Gräff
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart Stuttgart Germany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart Stuttgart Germany
| | - Marilize Le Roes‐Hill
- Applied Microbial and Health Biotechnology Institute, Cape Peninsula University of Technology Bellville South Africa
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart Stuttgart Germany
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Wang L, Lim CK, Klotz MG. High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution. Microorganisms 2020; 8:E693. [PMID: 32397339 PMCID: PMC7285500 DOI: 10.3390/microorganisms8050693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/04/2020] [Indexed: 12/31/2022] Open
Abstract
The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world's oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C-107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.
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Affiliation(s)
- Lin Wang
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Chee Kent Lim
- Department of Biological Sciences, University of North Carolina, 9201 University City Boulevard, Charlotte, NC 28223, USA; (L.W.); (C.K.L.)
| | - Martin G. Klotz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, 2710 Crimson Way, Richland, WA 99354, USA
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Arregui L, Ayala M, Gómez-Gil X, Gutiérrez-Soto G, Hernández-Luna CE, Herrera de los Santos M, Levin L, Rojo-Domínguez A, Romero-Martínez D, Saparrat MCN, Trujillo-Roldán MA, Valdez-Cruz NA. Laccases: structure, function, and potential application in water bioremediation. Microb Cell Fact 2019; 18:200. [PMID: 31727078 PMCID: PMC6854816 DOI: 10.1186/s12934-019-1248-0] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/31/2019] [Indexed: 11/11/2022] Open
Abstract
The global rise in urbanization and industrial activity has led to the production and incorporation of foreign contaminant molecules into ecosystems, distorting them and impacting human and animal health. Physical, chemical, and biological strategies have been adopted to eliminate these contaminants from water bodies under anthropogenic stress. Biotechnological processes involving microorganisms and enzymes have been used for this purpose; specifically, laccases, which are broad spectrum biocatalysts, have been used to degrade several compounds, such as those that can be found in the effluents from industries and hospitals. Laccases have shown high potential in the biotransformation of diverse pollutants using crude enzyme extracts or free enzymes. However, their application in bioremediation and water treatment at a large scale is limited by the complex composition and high salt concentration and pH values of contaminated media that affect protein stability, recovery and recycling. These issues are also associated with operational problems and the necessity of large-scale production of laccase. Hence, more knowledge on the molecular characteristics of water bodies is required to identify and develop new laccases that can be used under complex conditions and to develop novel strategies and processes to achieve their efficient application in treating contaminated water. Recently, stability, efficiency, separation and reuse issues have been overcome by the immobilization of enzymes and development of novel biocatalytic materials. This review provides recent information on laccases from different sources, their structures and biochemical properties, mechanisms of action, and application in the bioremediation and biotransformation of contaminant molecules in water. Moreover, we discuss a series of improvements that have been attempted for better organic solvent tolerance, thermo-tolerance, and operational stability of laccases, as per process requirements.
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Affiliation(s)
- Leticia Arregui
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, C.P. 05348 Mexico City, Mexico
| | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Chamilpa, 62210 Cuernavaca, Morelos Mexico
| | - Ximena Gómez-Gil
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Guadalupe Gutiérrez-Soto
- Facultad de Agronomía, Universidad Autónoma de Nuevo León, Francisco Villa, 66059 Colonia Ex hacienda El Canadá, General Escobedo, Nuevo León Mexico
| | - Carlos Eduardo Hernández-Luna
- Laboratorio de Enzimología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, Pedro de Alba y Manuel L. Barragán, Cd. Universitaria, 66451 San Nicolás de los Garza, Nuevo León Mexico
| | - Mayra Herrera de los Santos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Laura Levin
- Laboratorio de Micología Experimental, DBBE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, INMIBO-CONICET, Ciudad Universitaria, Pabellón 2, Piso 4, C1428BGA Ciudad Autónoma de Buenos Aires, Argentina
| | - Arturo Rojo-Domínguez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, C.P. 05348 Mexico City, Mexico
| | - Daniel Romero-Martínez
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Mario C. N. Saparrat
- Instituto de Fisiología Vegetal (INFIVE), Universidad Nacional de La Plata (UNLP)-CCT-La Plata-Consejo Nacional de Investigaciones Científicas y técnicas (CONICET), Diag. 113 y 61, 327CC, 1900, La Plata, Argentina
- Instituto de Botánica Spegazzini, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, 53 # 477, 1900, La Plata, Argentina
| | - Mauricio A. Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
| | - Norma A. Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, AP. 70228, Mexico City, CP. 04510 Mexico
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10
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Dandare SU, Young JM, Kelleher BP, Allen CCR. The distribution of novel bacterial laccases in alpine paleosols is directly related to soil stratigraphy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:19-27. [PMID: 30927724 DOI: 10.1016/j.scitotenv.2019.03.250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 03/12/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
Bacterial laccases are now known to be abundant in soil and to function outside of the cell facilitating the bacterial degradation of lignin. In this study we wanted to test the hypotheses that: i) Such enzymes can be identified readily in stratified paleosols using metagenomics approaches, ii) The distribution of these genes as potential 'public good' proteins in soil is a function of the soil environment, iii) Such laccase genes can be readily retrieved and expressed in E. coli cloning systems to demonstrate that de novo assembly processes can be used to obtain similar metagenome-derived enzyme activities. To test these hypotheses, in silico gene-targeted assembly was employed to identify genes encoding novel type B two-domain bacterial laccases from alpine soil metagenomes sequenced on an Illumina MiSeq sequencer. The genes obtained from different strata were heterologously cloned, expressed and the gene products were shown to be active against two classical laccase substrates. The use of a metagenome-driven pipeline to obtain such active biocatalysts has demonstrated the potential for gene mining to be applied systematically for the discovery of such enzymes. These data ultimately further demonstrate the application of soil pedology methods to environmental enzyme discovery. As an interdisciplinary effort, we can now establish that paleosols can serve as a useful source of novel biocatalytic enzymes for various applications. We also, for the first time, link soil stratigraphy to enzyme profiling for widespread functional gene activity in paleosols.
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Affiliation(s)
| | | | | | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, UK; Institute for Global Food Security, Queen's University Belfast, UK.
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11
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Herrera-Zúñiga LD, Millán-Pacheco C, Viniegra-González G, Villegas E, Arregui L, Rojo-Domínguez A. Molecular dynamics on laccase from Trametes versicolor to examine thermal stability induced by salt bridges. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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12
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Wherland S, Pecht I. Radiation chemists look at damage in redox proteins induced by X-rays. Proteins 2018; 86:817-826. [DOI: 10.1002/prot.25521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Scot Wherland
- Department of Chemistry; Washington State University; Pullman Washington
| | - Israel Pecht
- Department of Immunology; The Weizmann Institute of Science; Rehovot 76100 Israel
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Hu J, Lu K, Dong S, Huang Q, Mao L. Inactivation of Laccase by the Attack of As (III) Reaction in Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:2945-2952. [PMID: 29405708 DOI: 10.1021/acs.est.7b05650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Laccase is a multicopper oxidase containing four coppers as reaction sites, including one type 1, one type 2, and two type 3. We here provide the first experimental data showing that As (III) can be effectively removed from water and transformed to As (V) through reactions mediated by laccase with the presence of oxygen. To this end, the As (III) removal, As (V) yields, total protein, active laccase, and copper concentrations in the aqueous phase were determined, respectively. Additionally, electron paramagnetic resonance spectra and UV-vis spectra were applied to probe possible structural changes of the laccase during the reaction. The data offer the first evidence that laccase can be inactivated by As (III) attack thus leading to the release of type 2 copper. The released copper has no reactivity with the As (III). These findings provide new ideas into a significant pathway likely to master the environmental transformation of arsenite, and advance the understanding of laccase inactivation mechanisms, thus providing a foundation for optimization of enzyme-based processes and potential development for removal and remediation of arsenite contamination in the environment.
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Affiliation(s)
- Jinyuan Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing 210093 , P. R. China
| | - Kun Lu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing 210093 , P. R. China
| | - Shipeng Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing 210093 , P. R. China
| | - Qingguo Huang
- College of Agricultural and Environmental Sciences, Department of Crop and Soil Sciences , University of Georgia , Griffin , Georgia 30223 , United States
| | - Liang Mao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing 210093 , P. R. China
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Heterocycle Thiazole Compounds Exhibit Antifungal Activity through Increase in the Production of Reactive Oxygen Species in the Cryptococcus neoformans-Cryptococcus gattii Species Complex. Antimicrob Agents Chemother 2017; 61:AAC.02700-16. [PMID: 28533240 DOI: 10.1128/aac.02700-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/08/2017] [Indexed: 01/09/2023] Open
Abstract
Human cryptococcosis can occur as a primary or opportunistic infection and develops as an acute, subacute, or chronic systemic infection involving different organs of the host. Given the limited therapeutic options and the occasional resistance to fluconazole, there is a need to develop novel drugs for the treatment of cryptococcosis. In this report, we describe promising thiazole compounds 1, 2, 3, and 4 and explore their possible modes of action against Cryptococcus To this end, we show evidence of interference in the Cryptococcus antioxidant system. The tested compounds exhibited MICs ranging from 0.25 to 2 μg/ml against Cryptococcus neoformans strains H99 and KN99α. Interestingly, the knockout strains for Cu oxidase and sarcosine oxidase were resistant to thiazoles. MIC values of thiazole compounds 1, 2, and 4 against these mutants were higher than for the parental strain. After the treatment of C. neoformans ATCC 24067 (or C. deneoformans) and C. gattii strain L27/01 (or C. deuterogattii) with thiazoles, we verified an increase in intracellular reactive oxygen species (ROS). Also, we verified the synergistic interactions among thiazoles and menadione, which generates superoxides, with fractional inhibitory concentrations (FICs) equal to 0.1874, 0.3024, 0.25, and 0.25 for the thiazole compounds 1, 2, 3, and 4, respectively. In addition, thiazoles exhibited antagonistic interactions with parasulphonatephenyl porphyrinato ferrate III (FeTPPS). Thus, in this work, we showed that the action of these thiazoles is related to an interference with the antioxidant system. These findings suggest that oxidative stress may be primarily related to the accumulation of superoxide radicals.
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The first acidobacterial laccase-like multicopper oxidase revealed by metagenomics shows high salt and thermo-tolerance. Appl Microbiol Biotechnol 2017; 101:6261-6276. [DOI: 10.1007/s00253-017-8345-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 01/10/2023]
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16
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Batth R, Singh K, Kumari S, Mustafiz A. Transcript Profiling Reveals the Presence of Abiotic Stress and Developmental Stage Specific Ascorbate Oxidase Genes in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:198. [PMID: 28261251 PMCID: PMC5314155 DOI: 10.3389/fpls.2017.00198] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/02/2017] [Indexed: 05/03/2023]
Abstract
Abiotic stress and climate change is the major concern for plant growth and crop yield. Abiotic stresses lead to enhanced accumulation of reactive oxygen species (ROS) consequently resulting in cellular damage and major losses in crop yield. One of the major scavengers of ROS is ascorbate (AA) which acts as first line of defense against external oxidants. An enzyme named ascorbate oxidase (AAO) is known to oxidize AA and deleteriously affect the plant system in response to stress. Genome-wide analysis of AAO gene family has led to the identification of five, three, seven, four, and six AAO genes in Oryza sativa, Arabidopsis, Glycine max, Zea mays, and Sorghum bicolor genomes, respectively. Expression profiling of these genes was carried out in response to various abiotic stresses and during various stages of vegetative and reproductive development using publicly available microarray database. Expression analysis in Oryza sativa revealed tissue specific expression of AAO genes wherein few members were exclusively expressed in either root or shoot. These genes were found to be regulated by both developmental cues as well as diverse stress conditions. The qRT-PCR analysis in response to salinity and drought stress in rice shoots revealed OsAAO2 to be the most stress responsive gene. On the other hand, OsAAO3 and OsAAO4 genes showed enhanced expression in roots under salinity/drought stresses. This study provides lead about important stress responsive AAO genes in various crop plants, which could be used to engineer climate resilient crop plants.
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Affiliation(s)
- Rituraj Batth
- Faculty of Life Sciences and Biotechnology, Plant Molecular Biology Laboratory, South Asian UniversityNew Delhi, India
| | - Kapil Singh
- Faculty of Life Sciences and Biotechnology, Plant Molecular Biology Laboratory, South Asian UniversityNew Delhi, India
| | - Sumita Kumari
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and TechnologyJammu, India
- *Correspondence: Ananda Mustafiz, Sumita Kumari,
| | - Ananda Mustafiz
- Faculty of Life Sciences and Biotechnology, Plant Molecular Biology Laboratory, South Asian UniversityNew Delhi, India
- *Correspondence: Ananda Mustafiz, Sumita Kumari,
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17
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Abstract
Prior to 1950, the consensus was that biological transformations occurred in two-electron steps, thereby avoiding the generation of free radicals. Dramatic advances in spectroscopy, biochemistry, and molecular biology have led to the realization that protein-based radicals participate in a vast array of vital biological mechanisms. Redox processes involving high-potential intermediates formed in reactions with O2 are particularly susceptible to radical formation. Clusters of tyrosine (Tyr) and tryptophan (Trp) residues have been found in many O2-reactive enzymes, raising the possibility that they play an antioxidant protective role. In blue copper proteins with plastocyanin-like domains, Tyr/Trp clusters are uncommon in the low-potential single-domain electron-transfer proteins and in the two-domain copper nitrite reductases. The two-domain muticopper oxidases, however, exhibit clusters of Tyr and Trp residues near the trinuclear copper active site where O2 is reduced. These clusters may play a protective role to ensure that reactive oxygen species are not liberated during O2 reduction.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
| | - Jay R Winkler
- Beckman Institute, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA 91125, USA
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18
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Wherland S, Miyazaki K, Pecht I. Intramolecular Electron Transfer in the Bacterial Two-Domain Multicopper Oxidase mgLAC. Biochemistry 2016; 55:2960-6. [PMID: 27126506 DOI: 10.1021/acs.biochem.6b00158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The kinetics of the intramolecular electron transfer process in mgLAC, a bacterial two-domain multicopper oxidase (MCO), were investigated by pulse radiolysis. The reaction is initiated by CO2(-) radicals produced in anaerobic, aqueous solutions of the enzyme by microsecond pulses of radiation. A sequence of pulses of CO2(-) radicals enables examination of the reductive half-cycle of the MCO catalysis. This is done by titrations of the Type 1 (T1) Cu(II) site and monitoring of the time course and amplitude of its reoxidation by internal electron transfer (ET) to the Type 3 site. Comparison of the internal ET kinetics observed for mgLAC with those of other MCOs studied by pulse radiolysis shows that they exhibit distinct reactivities. One main cause for the different reactivities is the broad range of T1 copper redox potentials, from the moderate potential of bacterial enzymes to the high potential of fungal laccases, and this possibly also reflects evolutionary quaternary structural adaptation of the MCO family to the wide range of reducing substrates that they oxidize while maintaining efficient reduction of the common substrate, molecular oxygen.
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Affiliation(s)
- Scot Wherland
- Department of Chemistry, Washington State University , Pullman, Washington 99164-4630, United States
| | - Kentaro Miyazaki
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology , Tsukuba Central 6, 10101 Higashi, Tsukuba, Ibaraki 205-8566, Japan
| | - Israel Pecht
- Department of Immunology, Weizmann Institute of Science , Rehovot 76100, Israel
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19
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Si W, Wu Z, Wang L, Yang M, Zhao X. Enzymological Characterization of Atm, the First Laccase from Agrobacterium sp. S5-1, with the Ability to Enhance In Vitro digestibility of Maize Straw. PLoS One 2015; 10:e0128204. [PMID: 26010258 PMCID: PMC4444218 DOI: 10.1371/journal.pone.0128204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/24/2015] [Indexed: 11/19/2022] Open
Abstract
Laccase is an enzyme that catalyzes oxidation of phenolic compounds, diamines and aromatic amines. In this study, a novel laccase-like gene (atm) in a ligninolyitic isolate Agrobacterium sp. S5-1 from soil humus was identified and heterologously expressed in Escherichia coli. Atm exhibited its maximal activity at pH 4.5 and at 50°C. This enzyme was tolerant to high temperature, a broad range of pH, heavy metal ions (Co3+, Mn2+, Cu2+ and Ni2+, 20 mM) and all tested organic solvents. Furthermore, Atm significantly (p<0.05) increased dry matter digestibility of maize straw from 23.44% to 27.96% and from 29.53% to 37.10% after 8 or 24 h of digestion and improved acid detergent fiber digestibility from 5.81% to 10.33% and from 12.80% to 19.07% after 8 or 24 h of digestion, respectively. The combination of Atm and fibrolytic enzymes significantly (p<0.05) enhanced neutral detergent fiber digestibility from 19.02% to 24.55% after 24 h of digestion respectively. Results showed treatment with Atm effectively improved in vitro digestibility of maize straw, thus suggesting that Atm has an application potential for bioconversion of lignin rich agricultural byproducts into animal feed and cellulosic ethanol.
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Affiliation(s)
- Wei Si
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - ZhaoWei Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - LiangLiang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
| | - MingMing Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
- * E-mail: (MY); (XZ)
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, People’s Republic of China
- Department of Animal Science, McGill University, Quebec, Canada
- * E-mail: (MY); (XZ)
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20
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Komori H, Higuchi Y. Structure and molecular evolution of multicopper blue proteins. Biomol Concepts 2015; 1:31-40. [PMID: 25961983 DOI: 10.1515/bmc.2010.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The multicopper blue protein family, which contains cupredoxin-like domains as a structural unit, is one of the most diverse groups of proteins. This protein family is divided into two functionally different types of enzymes: multicopper oxidase and nitrite reductase. Multicopper oxidase catalyzes the oxidation of the substrate and then reduces dioxygen. The structures of many multicopper oxidases are already known, and until recently they were classified into two main groups: the three- and six-domain types. Both function as monomers and have three spectroscopically different copper sites: Types I (blue), II, and III (tri-nuclear). Nitrite reductase is a closely related protein that contains Types I and II (mono-nuclear) coppers but reduces nitrite instead of dioxygen. Nitrite reductase, which consists of two domains, forms a homotrimer. Multicopper oxidase and nitrite reductase share similar structural architectures and also contain Type I copper. Therefore, it is proposed that they have a common ancestor protein. Recently, some two-domain type multicopper oxidases have been found and their crystal structures have been determined. They have a trimeric quaternary structure and contain an active site at the molecular interface such as nitrite reductase. These results support previous hypotheses and provide an insight into the molecular evolution of multicopper blue proteins.
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21
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Trubitsina LI, Tishchenko SV, Gabdulkhakov AG, Lisov AV, Zakharova MV, Leontievsky AA. Structural and functional characterization of two-domain laccase from Streptomyces viridochromogenes. Biochimie 2015; 112:151-9. [PMID: 25778839 DOI: 10.1016/j.biochi.2015.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/05/2015] [Indexed: 11/30/2022]
Abstract
Laccase (EC 1.10.3.2) is one of the most common copper-containing oxidases found in many organisms and catalyses oxidation of primarily phenolic compounds by oxygen. A recently found bacterial laccase whose molecule is formed by two domains - the so called two-domain laccase (2DLac) or small laccase - has unusual resistance to inhibitors and an alkaline optimum of activity. The causes of these properties, as well as the biological function of two-domain laccases, are poorly understood. We performed an enzymatic and structural characterization of 2DLac from Streptomyces viridochromogenes (SvSL). It was cloned and overproduced in Escherichia coli. Phenolic compounds were oxidized in the presence of the enzyme under alkaline but not acidic conditions. Conversely, nonphenolic compounds were oxidized at acidic but not alkaline pH. SvSL catalysed oxidation of nonphenolic compounds more efficiently than that of phenols. Moreover, this two-domain laccase displayed a cytochrome c oxidase activity and exhibited no ferroxidase activity. The enzyme was resistant to specific inhibitors of copper-containing oxidases, such as NaN3 and NaF. We succeeded in generating X-ray quality crystals and solved their structure to a resolution of 2.4 Å. SvSL is a homotrimer in its native state. Comparison of its structure with that of a three-domain laccase revealed differences in the second coordination sphere of the T2/T3 centre and solvent channels. The role of these differences in the resistance of the enzyme to inhibitors and the activity at alkaline pH is under discussion.
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Affiliation(s)
- L I Trubitsina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia; Pushchino State Institute of Life Sciences, Pushchino, Russia
| | - S V Tishchenko
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A G Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - A V Lisov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia.
| | - M V Zakharova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia
| | - A A Leontievsky
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences (IBPM RAS), Pushchino, Russia; Pushchino State Institute of Life Sciences, Pushchino, Russia
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22
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Hakulinen N, Rouvinen J. Three-dimensional structures of laccases. Cell Mol Life Sci 2015; 72:857-68. [PMID: 25586561 PMCID: PMC11113281 DOI: 10.1007/s00018-014-1827-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Abstract
Laccases are phenol oxidases that belong to the family of multi-copper oxidases and the superfamily of cupredoxins. A number of potential industrial applications for laccases have led to intensive structure-function studies and an increased amount of crystal structures has been solved. The objective of this review is to summarize and analyze available crystal structures of laccases. The experimental crystallographic data are now easily available from the websites and electron density maps can be used for the interpretation of the structural models. The crystal structures can give valuable insights into the functional mechanisms and may serve as the basis for the development of laccases for industrial applications.
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Affiliation(s)
- N Hakulinen
- Department of Chemistry, University of Eastern Finland, Joensuu Campus, PO Box 111, 80101, Joensuu, Finland,
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23
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Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Čapek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Front Microbiol 2014; 5:541. [PMID: 25360132 PMCID: PMC4199454 DOI: 10.3389/fmicb.2014.00541] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/29/2014] [Indexed: 01/04/2023] Open
Abstract
Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.
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Affiliation(s)
- Antje Gittel
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Department of Bioscience, Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Iva Kohoutová
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Jörg Schnecker
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Birgit Wild
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Petr Čapek
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Vigdis L. Torsvik
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Tim Urich
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
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24
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Moshkov KA, Zaitsev VN, Grishina TV, Stefanov VE. Multinuclear blue copper-proteins: the evolutionary design. J EVOL BIOCHEM PHYS+ 2014. [DOI: 10.1134/s0022093014030016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Diversity of two-domain laccase-like multicopper oxidase genes in Streptomyces spp.: identification of genes potentially involved in extracellular activities and lignocellulose degradation during composting of agricultural waste. Appl Environ Microbiol 2014; 80:3305-14. [PMID: 24657870 DOI: 10.1128/aem.00223-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Traditional three-domain fungal and bacterial laccases have been extensively studied for their significance in various biotechnological applications. Growing molecular evidence points to a wide occurrence of more recently recognized two-domain laccase-like multicopper oxidase (LMCO) genes in Streptomyces spp. However, the current knowledge about their ecological role and distribution in natural or artificial ecosystems is insufficient. The aim of this study was to investigate the diversity and composition of Streptomyces two-domain LMCO genes in agricultural waste composting, which will contribute to the understanding of the ecological function of Streptomyces two-domain LMCOs with potential extracellular activity and ligninolytic capacity. A new specific PCR primer pair was designed to target the two conserved copper binding regions of Streptomyces two-domain LMCO genes. The obtained sequences mainly clustered with Streptomyces coelicolor, Streptomyces violaceusniger, and Streptomyces griseus. Gene libraries retrieved from six composting samples revealed high diversity and a rapid succession of Streptomyces two-domain LMCO genes during composting. The obtained sequence types cluster in 8 distinct clades, most of which are homologous with Streptomyces two-domain LMCO genes, but the sequences of clades III and VIII do not match with any reference sequence of known streptomycetes. Both lignocellulose degradation rates and phenol oxidase activity at pH 8.0 in the composting process were found to be positively associated with the abundance of Streptomyces two-domain LMCO genes. These observations provide important clues that Streptomyces two-domain LMCOs are potentially involved in bacterial extracellular phenol oxidase activities and lignocellulose breakdown during agricultural waste composting.
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26
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Gunne M, Höppner A, Hagedoorn PL, Urlacher VB. Structural and redox properties of the small laccase Ssl1 fromStreptomyces sviceus. FEBS J 2014; 281:4307-18. [DOI: 10.1111/febs.12755] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Matthias Gunne
- Institute of Biochemistry; Heinrich-Heine-Universität Düsseldorf; Germany
| | - Astrid Höppner
- Crystal Farm and X-Ray Facility; Heinrich-Heine-Universität Düsseldorf; Germany
| | | | - Vlada B. Urlacher
- Institute of Biochemistry; Heinrich-Heine-Universität Düsseldorf; Germany
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27
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Argüello JM, Raimunda D, Padilla-Benavides T. Mechanisms of copper homeostasis in bacteria. Front Cell Infect Microbiol 2013; 3:73. [PMID: 24205499 PMCID: PMC3817396 DOI: 10.3389/fcimb.2013.00073] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 10/17/2013] [Indexed: 01/27/2023] Open
Abstract
Copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. However, free copper is a potential hazard because of its high chemical reactivity. Consequently, organisms exert a tight control on Cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. Recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a highly regulated system of transcriptional regulators, soluble chaperones, membrane transporters, and target cuproproteins distributed in the various bacterial compartments. As a result, new questions have emerged regarding the diversity and apparent redundancies of these components, their irregular presence in different organisms, functional interactions, and resulting system architectures.
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Affiliation(s)
- José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute Worcester, MA, USA
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28
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Multi-copper oxidases and human iron metabolism. Nutrients 2013; 5:2289-313. [PMID: 23807651 PMCID: PMC3738974 DOI: 10.3390/nu5072289] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/29/2013] [Accepted: 06/06/2013] [Indexed: 01/13/2023] Open
Abstract
Multi-copper oxidases (MCOs) are a small group of enzymes that oxidize their substrate with the concomitant reduction of dioxygen to two water molecules. Generally, multi-copper oxidases are promiscuous with regards to their reducing substrates and are capable of performing various functions in different species. To date, three multi-copper oxidases have been detected in humans—ceruloplasmin, hephaestin and zyklopen. Each of these enzymes has a high specificity towards iron with the resulting ferroxidase activity being associated with ferroportin, the only known iron exporter protein in humans. Ferroportin exports iron as Fe2+, but transferrin, the major iron transporter protein of blood, can bind only Fe3+ effectively. Iron oxidation in enterocytes is mediated mainly by hephaestin thus allowing dietary iron to enter the bloodstream. Zyklopen is involved in iron efflux from placental trophoblasts during iron transfer from mother to fetus. Release of iron from the liver relies on ferroportin and the ferroxidase activity of ceruloplasmin which is found in blood in a soluble form. Ceruloplasmin, hephaestin and zyklopen show distinctive expression patterns and have unique mechanisms for regulating their expression. These features of human multi-copper ferroxidases can serve as a basis for the precise control of iron efflux in different tissues. In this manuscript, we review the biochemical and biological properties of the three human MCOs and discuss their potential roles in human iron homeostasis.
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29
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Laccase versus laccase-like multi-copper oxidase: a comparative study of similar enzymes with diverse substrate spectra. PLoS One 2013; 8:e65633. [PMID: 23755261 PMCID: PMC3670849 DOI: 10.1371/journal.pone.0065633] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/26/2013] [Indexed: 11/19/2022] Open
Abstract
Laccases (EC 1.10.3.2) are multi-copper oxidases that catalyse the one-electron oxidation of a broad range of compounds including substituted phenols, arylamines and aromatic thiols to the corresponding radicals. Owing to their broad substrate range, copper-containing laccases are versatile biocatalysts, capable of oxidizing numerous natural and non-natural industry-relevant compounds, with water as the sole by-product. In the present study, 10 of the 11 multi-copper oxidases, hitherto considered to be laccases, from fungi, plant and bacterial origin were compared. A substrate screen of 91 natural and non-natural compounds was recorded and revealed a fairly broad but distinctive substrate spectrum amongst the enzymes. Even though the enzymes share conserved active site residues we found that the substrate ranges of the individual enzymes varied considerably. The EC classification is based on the type of chemical reaction performed and the actual name of the enzyme often refers to the physiological substrate. However, for the enzymes studied in this work such classification is not feasible, even more so as their prime substrates or natural functions are mainly unknown. The classification of multi-copper oxidases assigned as laccases remains a challenge. For the sake of simplicity we propose to introduce the term "laccase-like multi-copper oxidase" (LMCO) in addition to the term laccase that we use exclusively for the enzyme originally identified from the sap of the lacquer tree Rhus vernicifera.
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30
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Abstract
Multicopper blue proteins, composed of several repetitive copper-binding domains similar to one-domain cupredoxin-like proteins, were found in almost all organisms. They are classified into the three different groups, based on their two-, three- or six-domain organization. We found orthologs of chordate six-domain copper-binding proteins in animals, plants, bacteria and archea. The phylogenetic analysis of 183 multicopper blue proteins and their copper-binding sites comparison make us think that all the modern six-domain blue proteins have originated from the common ancestral six-domain protein in the process of gene duplication and copper-binding sites loss as a result of amino acid substitutions.
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31
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Characterization of a laccase-like multicopper oxidase from newly isolated Streptomyces sp. C1 in agricultural waste compost and enzymatic decolorization of azo dyes. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. PLoS One 2011; 6:e25724. [PMID: 22022440 PMCID: PMC3192119 DOI: 10.1371/journal.pone.0025724] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/09/2011] [Indexed: 11/19/2022] Open
Abstract
Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.
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33
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Farver O, Wherland S, Koroleva O, Loginov DS, Pecht I. Intramolecular electron transfer in laccases. FEBS J 2011; 278:3463-71. [PMID: 21790996 DOI: 10.1111/j.1742-4658.2011.08268.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Rate constants and activation parameters have been determined for the internal electron transfer from type 1 (T1) to type 3 (T3) copper ions in laccase from both the fungus Trametes hirsuta and the lacquer tree Rhus vernicifera, using the pulse radiolysis method. The rate constant at 298 K and the enthalpy and entropy of activation were 25 ± 1 s(-1), 39.7 ± 5.0 kJ·mol(-1) and -87 ± 9 J·mol(-1) ·K(-1) for the fungal enzyme and 1.1 ± 0.1 s(-1), 9.8 ± 0.2 kJ·mol(-1) and -211 ± 3 J·mol(-1) ·K(-1) for the tree enzyme. The initial reduction of the T1 site by pulse radiolytically produced radicals was direct in the case of T. hirsuta laccase, but occured indirectly via a disulfide radical in R. vernicifera. The equilibrium constant that characterizes the electron transfer from T1 to T3 copper ions was 0.4 for T. hirsuta laccase and 1.5 for R. vernicifera laccase, leading to full reduction of the T1 site occurring at 2.9 ± 0.2 electron equivalents for T. hirsuta and 4 electron equivalents for R. vernicifera laccase. These results were compared with each other and with those for the same process in other multicopper oxidases, ascorbate oxidase and Streptomyces coelicolor laccase, using available structural information and electron transfer theory.
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Affiliation(s)
- Ole Farver
- Institute of Analytical Chemistry, University of Copenhagen, Copenhagen, Denmark.
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34
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Abstract
Blue copper oxidase (BCO) is a multicopper oxidase (MCO) found in Nitrosomonas europaea as well as in other ammonia-oxidizing organisms. In this chapter, we detail methods used to detect, isolate, and characterize BCO from N. europaea. A method for identifying and classifying MCOs commonly found in nitrifiers based on primary sequence is also described.
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35
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Kosman DJ. Multicopper oxidases: a workshop on copper coordination chemistry, electron transfer, and metallophysiology. J Biol Inorg Chem 2009; 15:15-28. [PMID: 19816718 DOI: 10.1007/s00775-009-0590-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/15/2009] [Indexed: 01/01/2023]
Abstract
Multicopper oxidases (MCOs) are unique among copper proteins in that they contain at least one each of the three types of biologic copper sites, type 1, type 2, and the binuclear type 3. MCOs are descended from the family of small blue copper proteins (cupredoxins) that likely arose as a complement to the heme-iron-based cytochromes involved in electron transport; this event corresponded to the aerobiosis of the biosphere that resulted in the conversion of Fe(II) to Fe(III) as the predominant redox state of this essential metal and the solubilization of copper from Cu(2)S to Cu(H(2)O)( n ) (2+). MCOs are encoded in genomes in all three kingdoms and play essential roles in the physiology of essentially all aerobes. With four redox-active copper centers, MCOs share with terminal copper-heme oxidases the ability to catalyze the four-electron reduction of O(2) to two molecules of water. The electron transfers associated with this reaction are both outer and inner sphere in nature and their mechanisms have been fairly well established. A subset of MCO proteins exhibit specificity for Fe(2+), Cu(+), and/or Mn(2+) as reducing substrates and have been designated as metallooxidases. These enzymes, in particular the ferroxidases found in all fungi and metazoans, play critical roles in the metal metabolism of the expressing organism.
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Affiliation(s)
- Daniel J Kosman
- Department of Biochemistry, The University at Buffalo, NY 14214, USA.
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Sharma KK, Kuhad RC. An evidence of laccases in archaea. Indian J Microbiol 2009; 49:142-50. [PMID: 23100763 PMCID: PMC3450137 DOI: 10.1007/s12088-009-0039-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022] Open
Abstract
Laccases (benzenediol:oxygen oxidoreductase, EC 1.10.3.2) are a diverse group of multicopper oxidases that catalyze the oxidation of a variety of aromatic compounds. Here we present evidence for distribution of laccases among archaea and their probable functions. Putative laccase genes have been found in different archaeal groups that might have branched off early during evolution, e.g. Haloarcula marismortui ATCC 43049, Natronomonas pharaonis DSM2160, Pyrobaculum aerophilum IM2, Candidatus Nitrosopumilus maritimus SCM1, Halorubrum lacusprofundi ATCC 49239. Most of the archaeal multicopper oxidases reported here are of Type 1 and Type 2 whereas type 3 copper-binding domain could be found in Pyrobaculum aerophilum IM2 and Halorubrum lacusprofundi ATCC49239. An analysis of the genome sequence database revealed the presence of novel types of two-domain laccases in archaea. ed using this method. CyMVin the positive samples of Phalaenopsis sp. and Arachnis sp. was confirmed by DNA sequencing and cp gene homeology blast. The results showed that CyMV extracted from the leaves of orchid in Hangzhou, Zhejiang Province, China, could be derived from Kunming city (KM), Yunnan Province, China. This method characterized by high sensitivity, specificity, and precision is suitable for early diagnosis and quantitative detection of CyMV.
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Affiliation(s)
- Krishna Kant Sharma
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021 India
| | - Ramesh Chander Kuhad
- Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021 India
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Lawton TJ, Sayavedra-Soto LA, Arp DJ, Rosenzweig AC. Crystal structure of a two-domain multicopper oxidase: implications for the evolution of multicopper blue proteins. J Biol Chem 2009; 284:10174-80. [PMID: 19224923 PMCID: PMC2665071 DOI: 10.1074/jbc.m900179200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 02/06/2009] [Indexed: 11/06/2022] Open
Abstract
The two-domain multicopper oxidases are proposed to be key intermediates in the evolution of three-domain multicopper oxidases. A number of two-domain multicopper oxidases have been identified from genome sequences and are classified as type A, type B, or type C on the basis of the predicted location of the type 1 copper center. The crystal structure of blue copper oxidase, a type C two-domain multicopper oxidase from Nitrosomonas europaea, has been determined to 1.9 A resolution. Blue copper oxidase is a trimer, of which each subunit comprises two cupredoxin domains. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The coordination geometry at the trinuclear copper site is consistent with reduction of the copper ions. Although the overall architecture of blue copper oxidase is similar to nitrite reductases, detailed structural alignments show that the fold and domain orientation more closely resemble the three-domain multicopper oxidases. These observations have important implications for the evolution of nitrite reductases and multicopper oxidases.
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Affiliation(s)
- Thomas J Lawton
- Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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Komori H, Miyazaki K, Higuchi Y. X-ray structure of a two-domain type laccase: A missing link in the evolution of multi-copper proteins. FEBS Lett 2009; 583:1189-95. [DOI: 10.1016/j.febslet.2009.03.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 03/02/2009] [Accepted: 03/04/2009] [Indexed: 11/28/2022]
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Terzulli AJ, Kosman DJ. The Fox1 ferroxidase of Chlamydomonas reinhardtii: a new multicopper oxidase structural paradigm. J Biol Inorg Chem 2008; 14:315-25. [PMID: 19023602 DOI: 10.1007/s00775-008-0450-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 11/06/2008] [Indexed: 12/19/2022]
Abstract
Multicopper oxidases (MCO) contain at least four copper atoms arrayed in three distinct ligand fields supported by two canonical structural features: (1) multiples of the cupredoxin fold and (2) four unique sequence elements that include the ten histidine and one cysteine ligands to the four copper atoms. Ferroxidases are a subfamily of MCO proteins that contain residues supporting a specific reactivity towards ferrous iron; these MCOs play a vital role in iron metabolism in bacteria, algae, fungi, and mammals. In contrast to the fungal ferroxidases, e.g., Fet3p from Saccharomyces cerevisiae, the mammalian ceruloplasmin (Cp) is twice as large (six vs. three cupredoxin domains) and contains three type 1, or "blue," copper sites. Chlamydomonas reinhardtii expresses a putative ferroxidase, Fox1, which has sequence similarity to human Cp (hCp). Eschewing the standard sequence-based modeling paradigm, we have constructed a function-based model of the Fox1 protein which replicates hCp's six copper-site ligand arrays with an overall root mean square deviation of 1.4 A. Analysis of this model has led also to assignment of motifs in Fox1 that are unique to ferroxidases, the strongest evidence to date that the well-characterized fungal high-affinity iron uptake system is essential to iron homeostasis in green algae. The model of Fox1 also establishes a subfamily of MCO proteins with a noncanonical copper-ligand organization. These diverse structures suggest alternative mechanisms for intramolecular electron transfer and require a new trajectory for the evolution of the MCO superfamily.
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Affiliation(s)
- Alaina J Terzulli
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14214, USA
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Jones CM, Stres B, Rosenquist M, Hallin S. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol Biol Evol 2008; 25:1955-66. [PMID: 18614527 DOI: 10.1093/molbev/msn146] [Citation(s) in RCA: 263] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Denitrification is a facultative respiratory pathway in which nitrite (NO2(-)), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N(2)), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene.
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Affiliation(s)
- Christopher M Jones
- Department of Microbiology, Swedish Agricultural University, Uppsala, Sweden.
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Zhukhlistova NE, Zhukova YN, Lyashenko AV, Zaĭtsev VN, Mikhaĭlov AM. Three-dimensional organization of three-domain copper oxidases: A review. CRYSTALLOGR REP+ 2008. [DOI: 10.1134/s1063774508010124] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, Zhai M, Lapidus A, Copeland A, Kim E, Land M, Mavromatis K, Pitluck S, Richardson PM, Detter C, Brettin T, Saunders E, Lai B, Ravel B, Kemner KM, Wolf YI, Sorokin A, Gerasimova AV, Gelfand MS, Fredrickson JK, Koonin EV, Daly MJ. Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS One 2007; 2:e955. [PMID: 17895995 PMCID: PMC1978522 DOI: 10.1371/journal.pone.0000955] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 09/04/2007] [Indexed: 11/19/2022] Open
Abstract
Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (KM); (MD)
| | - Marina V. Omelchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elena K. Gaidamakova
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Vera Y. Matrosova
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Alexander Vasilenko
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Min Zhai
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
| | - Alla Lapidus
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alex Copeland
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edwin Kim
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Miriam Land
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Konstantinos Mavromatis
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Samuel Pitluck
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Paul M. Richardson
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Chris Detter
- US Department of Energy, Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Thomas Brettin
- US Department of Energy, Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Elizabeth Saunders
- US Department of Energy, Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Barry Lai
- Environmental Research Division and Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Bruce Ravel
- Environmental Research Division and Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Kenneth M. Kemner
- Environmental Research Division and Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander Sorokin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anna V. Gerasimova
- Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Mikhail S. Gelfand
- Institute for Information Transmission Problems of RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - James K. Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael J. Daly
- Department of Pathology, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (KM); (MD)
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Ellis MJ, Grossmann JG, Eady RR, Hasnain SS. Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases. J Biol Inorg Chem 2007; 12:1119-27. [PMID: 17712582 DOI: 10.1007/s00775-007-0282-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/19/2007] [Indexed: 10/22/2022]
Abstract
Recently, the structure of a Cu-containing nitrite reductase (NiR) from Hyphomicrobium denitrificans (HdNiR) has been reported, establishing the existence of a new family of Cu-NiR where an additional type 1 Cu (T1Cu) containing cupredoxin domain is located at the N-terminus (Nojiri et al. in Proc. Natl. Acad. Sci. USA 104:4315-4320, 2007). HdNiR retains the well-characterised coupled T1Cu-type 2 Cu (T2Cu) core, where the T2Cu catalytic site is also built utilising ligands from neighbouring monomers. We have undertaken a genome analysis and found the wide occurrence of these NiRs, with members clustering in two groups, one showing an amino acid sequence similarity of around 80% with HdNiR, and a second group, including the NiR from the extremophile Acidothermus cellulolyticus, clustering around 50% similarity to HdNiR. This is reminiscent of the difference observed between the blue (Alcaligenes xylosoxidans) and green (Achromobacter cycloclastes and Alcaligenes faecalis) NiRs which have been extensively studied and may indicate that these also form two distinct subclasses of the new family. Genome analysis also showed the presence of Cu-NiRs with a C-terminal extension of 160-190 residues containing a class I cytochrome c domain with a characteristic beta-sheet extension. Currently no structural information exists for any member of this family. Genome analysis suggests the widespread occurrence of these novel NiRs with representatives in the alpha, beta and gamma subclasses of the Proteobacteria and in two species of the fungus Aspergillus. We selected the enzyme from Ralstonia pickettii for comparative modelling and produced a plausible structure highlighting an electron transfer mode in which the cytochrome c haem at the C-terminus can come within 16-A reach of the T1Cu centre of the T1Cu-T2Cu core.
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Affiliation(s)
- Mark J Ellis
- Molecular Biophysics Group, Science and Technology Facilities Council, Daresbury Laboratory, Warrington, Cheshire, UK
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Klotz MG, Arp DJ, Chain PSG, El-Sheikh AF, Hauser LJ, Hommes NG, Larimer FW, Malfatti SA, Norton JM, Poret-Peterson AT, Vergez LM, Ward BB. Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Appl Environ Microbiol 2006; 72:6299-315. [PMID: 16957257 PMCID: PMC1563620 DOI: 10.1128/aem.00463-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H(+)-dependent F(0)F(1) type, one Na(+)-dependent V type).
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Affiliation(s)
- Martin G Klotz
- Department of Biology, University of Louisville, 139 Life Science Building, Louisville, KY 40292, USA.
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Battaini G, Granata A, Monzani E, Gullotti M, Casella L. Biomimetic Oxidations by Dinuclear and Trinuclear Copper Complexes. ADVANCES IN INORGANIC CHEMISTRY 2006. [DOI: 10.1016/s0898-8838(05)58005-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Wang HX, Ng TB. Purification of a laccase from fruiting bodies of the mushroom Pleurotus eryngii. Appl Microbiol Biotechnol 2005; 69:521-5. [PMID: 16075291 DOI: 10.1007/s00253-005-0086-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 06/30/2005] [Accepted: 07/03/2005] [Indexed: 11/30/2022]
Abstract
A purification scheme involving ion exchange chromatography on diethylaminoethyl (DEAE) cellulose, carboxymethyl (CM) cellulose, and Q-Sepharose, followed by fast protein liquid chromatography-gel filtration on Superdex 75, was utilized to isolate a laccase from the fruiting bodies of the mushroom Pleurotus eryngii. The laccase was adsorbed on DEAE-cellulose and Q-Sepharose and unadsorbed on CM-cellulose. The molecular mass of the laccase in sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 34 kDa. The laccase activity was maximal at 70 degrees C and remained high at 80 degrees C. High activity of the laccase was maintained at ph 3 to 5. The activity underwent an abrupt decline at pH 6 and 7 and was indiscernible at ph 8 and 9. The laccase exhibited an inhibitory activity toward HIV-1 reverse transcriptase with an IC50 of 2.2 microM. Its N-terminal sequence was dissimilar to those of laccase isoenzymes previously isolated from cultured mycelia of the same species.
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Affiliation(s)
- H X Wang
- State Key Laboratory for Agrobiotechnology and Department of Microbiology, China Agricultural University, 100094, Beijing, China
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