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Karpenko MN, Muruzheva ZM, Ilyechova EY, Babich PS, Puchkova LV. Abnormalities in Copper Status Associated with an Elevated Risk of Parkinson's Phenotype Development. Antioxidants (Basel) 2023; 12:1654. [PMID: 37759957 PMCID: PMC10525645 DOI: 10.3390/antiox12091654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
In the last 15 years, among the many reasons given for the development of idiopathic forms of Parkinson's disease (PD), copper imbalance has been identified as a factor, and PD is often referred to as a copper-mediated disorder. More than 640 papers have been devoted to the relationship between PD and copper status in the blood, which include the following markers: total copper concentration, enzymatic ceruloplasmin (Cp) concentration, Cp protein level, and non-ceruloplasmin copper level. Most studies measure only one of these markers. Therefore, the existence of a correlation between copper status and the development of PD is still debated. Based on data from the published literature, meta-analysis, and our own research, it is clear that there is a connection between the development of PD symptoms and the number of copper atoms, which are weakly associated with the ceruloplasmin molecule. In this work, the link between the risk of developing PD and various inborn errors related to copper metabolism, leading to decreased levels of oxidase ceruloplasmin in the circulation and cerebrospinal fluid, is discussed.
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Affiliation(s)
- Marina N. Karpenko
- I.P. Pavlov Department of Physiology, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia; (M.N.K.); (Z.M.M.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;
| | - Zamira M. Muruzheva
- I.P. Pavlov Department of Physiology, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia; (M.N.K.); (Z.M.M.)
- State Budgetary Institution of Health Care “Leningrad Regional Clinical Hospital”, 194291 St. Petersburg, Russia
| | - Ekaterina Yu. Ilyechova
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;
- Research Center of Advanced Functional Materials and Laser Communication Systems, ADTS Institute, ITMO University, 197101 St. Petersburg, Russia
- Department of Molecular Genetics, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Polina S. Babich
- Department of Zoology and Genetics, Faculty of Biology, Herzen State Pedagogical University of Russia, 191186 St. Petersburg, Russia;
| | - Ludmila V. Puchkova
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;
- Research Center of Advanced Functional Materials and Laser Communication Systems, ADTS Institute, ITMO University, 197101 St. Petersburg, Russia
- Department of Molecular Genetics, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia
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Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins. J Mol Evol 2022; 90:418-428. [PMID: 36181519 DOI: 10.1007/s00239-022-10071-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 08/26/2022] [Indexed: 10/06/2022]
Abstract
Vertebrate blood coagulation is controlled by a cascade containing more than 20 proteins. The cascade proteins are found in the blood in their zymogen forms and when the cascade is triggered by tissue damage, zymogens are activated and in turn activate their downstream proteins by serine protease activity. In this study, we examined proteomes of 21 chordates, of which 18 are vertebrates, to reveal the modular evolution of the blood coagulation cascade. Additionally, two Arthropoda species were used to compare domain arrangements of the proteins belonging to the hemolymph clotting and the blood coagulation cascades. Within the vertebrate coagulation protein set, almost half of the studied proteins are shared with jawless vertebrates. Domain similarity analyses revealed that there are multiple possible evolutionary trajectories for each coagulation protein. During the evolution of higher vertebrate clades, gene and genome duplications led to the formation of other coagulation cascade proteins.
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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: 166] [Impact Index Per Article: 33.2] [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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Puchkova LV, Broggini M, Polishchuk EV, Ilyechova EY, Polishchuk RS. Silver Ions as a Tool for Understanding Different Aspects of Copper Metabolism. Nutrients 2019; 11:E1364. [PMID: 31213024 PMCID: PMC6627586 DOI: 10.3390/nu11061364] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/12/2019] [Indexed: 12/11/2022] Open
Abstract
In humans, copper is an important micronutrient because it is a cofactor of ubiquitous and brain-specific cuproenzymes, as well as a secondary messenger. Failure of the mechanisms supporting copper balance leads to the development of neurodegenerative, oncological, and other severe disorders, whose treatment requires a detailed understanding of copper metabolism. In the body, bioavailable copper exists in two stable oxidation states, Cu(I) and Cu(II), both of which are highly toxic. The toxicity of copper ions is usually overcome by coordinating them with a wide range of ligands. These include the active cuproenzyme centers, copper-binding protein motifs to ensure the safe delivery of copper to its physiological location, and participants in the Cu(I) ↔ Cu(II) redox cycle, in which cellular copper is stored. The use of modern experimental approaches has allowed the overall picture of copper turnover in the cells and the organism to be clarified. However, many aspects of this process remain poorly understood. Some of them can be found out using abiogenic silver ions (Ag(I)), which are isoelectronic to Cu(I). This review covers the physicochemical principles of the ability of Ag(I) to substitute for copper ions in transport proteins and cuproenzyme active sites, the effectiveness of using Ag(I) to study copper routes in the cells and the body, and the limitations associated with Ag(I) remaining stable in only one oxidation state. The use of Ag(I) to restrict copper transport to tumors and the consequences of large-scale use of silver nanoparticles for human health are also discussed.
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Affiliation(s)
- Ludmila V Puchkova
- Laboratory of Trace elements metabolism, ITMO University, Kronverksky av., 49, St.-Petersburg 197101, Russia.
- Department of Molecular Genetics, Research Institute of Experimental Medicine, Acad. Pavlov str., 12, St.-Petersburg 197376, Russia.
- Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, Politekhnicheskaya str., 29, St.-Petersburg 195251, Russia.
| | - Massimo Broggini
- Laboratory of Trace elements metabolism, ITMO University, Kronverksky av., 49, St.-Petersburg 197101, Russia.
- Laboratory of molecular pharmacology, Istituto di Ricerche Farmacologiche "Mario Negri" IRCCS, Via La Masa, 19, Milan 20156, Italy.
| | - Elena V Polishchuk
- Laboratory of Trace elements metabolism, ITMO University, Kronverksky av., 49, St.-Petersburg 197101, Russia.
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, Pozzuoli (NA) 80078, Italy.
| | - Ekaterina Y Ilyechova
- Laboratory of Trace elements metabolism, ITMO University, Kronverksky av., 49, St.-Petersburg 197101, Russia.
| | - Roman S Polishchuk
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, Pozzuoli (NA) 80078, Italy.
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Das S, Sahoo PK. Ceruloplasmin, a moonlighting protein in fish. FISH & SHELLFISH IMMUNOLOGY 2018; 82:460-468. [PMID: 30144565 DOI: 10.1016/j.fsi.2018.08.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/15/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
Ceruloplasmin is an ancient multicopper oxidase evolved to insure a safe handling of oxygen in some metabolic pathways of vertebrates. The current knowledge of its structure provides a glimpse of its plasticity, revealing a multitude of binding sites that point to an elaborate mechanism of multifunctional activity. Ceruloplasmin is highly conserved throughout the vertebrate evolution. Cupredoxin, a multi-cupper blue protein is believed to be the evolutionary precursor of ceruloplasmin with three trinuclear and three mononuclear copper binding sites. There are 20 copper-binding residues in ceruloplasmin gene out of which 16 residues are conserved in fish. This ceruloplasmin gene is being characterized in zebrafish (Danio rerio), rohu (Labeo rohita), Indian medaka (Oryzias melastigama), catfish (Ictalurus punctatus), icefish (Chionodraco rastrospinosus), goldfish (Carassius auratus) and yellow perch (Perca flaviscens). The complete coding sequence of fish ceruloplasmin gene is around 3.2 kb which codes for 1000 to 1100 amino acid residues. The size of ceruloplasmin gene sequence in fish ranges around 13 kb containing 20 exons and 19 introns. Liver is the major site of synthesis in fish. Increased expression of this gene during bacterial infection in channel catfish and rohu suggested its potential involvement in bacterial disease response in fish. It has been found to serve as an indirect marker for selection against Aeromonas hydrophila resistance in rohu carp. Ceruloplasmin expression is also evident during parasitic infection in few fish species. The role of this gene is well studied during inflammatory response to hormonal, drug and heavy metal mediated toxicity in fish. Overall, ceruloplasmin represents an example of a 'moonlighting' protein that overcomes the one gene-one structure-one function concept to follow the changes of the organism in its physiological and pathological conditions.
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Affiliation(s)
- Sweta Das
- Peninsular and Marine Fish Genetic Resources Centre, ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Kochi 682 018, India
| | - Pramoda Kumar Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar 751 002, India.
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6
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Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx. Nat Commun 2017; 8:746. [PMID: 28963463 PMCID: PMC5622069 DOI: 10.1038/s41467-017-00896-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 08/02/2017] [Indexed: 12/28/2022] Open
Abstract
Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase in Bacillus sp. PL-12, Mnx, is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins, MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant to crystallization, so its structure is unknown. Here, we show that native mass spectrometry defines the subunit topology and copper binding of Mnx, while high-resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for understanding Mn biomineralization by such unexplored enzymes. Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products
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Orlov IA, Sankova TP, Babich PS, Sosnin IM, Ilyechova EY, Kirilenko DA, Brunkov PN, Ataev GL, Romanov AE, Puchkova LV. New silver nanoparticles induce apoptosis-like process in E. coli and interfere with mammalian copper metabolism. Int J Nanomedicine 2016; 11:6561-6574. [PMID: 28008247 PMCID: PMC5170787 DOI: 10.2147/ijn.s117745] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Silver nanoparticles (SNPs) are new functional materials that are widely used in biomedical and industrial technologies. Two main features that make SNPs valuable are their strong antibacterial effects and low toxicity to eukaryotes. In this study, SNPs were synthesized using a modified method of reducing the metal ions to their atomic state followed by crystallization. SNPs were characterized by UV/vis spectroscopy, X-ray diffractometry, atomic force microscopy, and transmission electron microscopy (TEM). The SNPs were spherically shaped with an average linear dimension of 20 nm. In aqueous solution, the SNPs were beige-yellow in color, and they formed a black color in bacteria-rich growth media. The toxicity and bioavailability of the SNPs were tested using Escherichia coli cells and C57Bl/6 mice. Although the SNPs displayed bactericidal activity, an E. coli cell strain transformed with an expression plasmid carrying a human CTR1 ectodomain with three motives that bind Cu(II), Cu(I), and Ag(I) demonstrated increased resistance to treatment with SNPs. TEM showed that the SNPs were absorbed by the E. coli cell, and flow cytometry showed that the SNPs induced apoptosis-like death. In mice treated with SNPs (daily intraperitoneal injection of 10 μg SNPs/g body weight over 4 days), the ceruloplasmin (Cp) oxidase activity in the blood serum decreased. However, level of Cp gene expression, the relative contents of the Cp protein in the Golgi complex and in the serum did not change. Treatment with SNPs did not influence the activity of superoxide dismutase 1 in the liver and had no apparent toxic effects in mice. These findings expand the scope of application for the use of new SNPs. The data are discussed in a paradigm, in which the effects of SNPs are caused by the interference of silver ions with copper metabolism.
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Affiliation(s)
- Iurii A Orlov
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Department of Biophysics, Peter the Great St Petersburg Polytechnic University
| | - Tatiana P Sankova
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Department of Biophysics, Peter the Great St Petersburg Polytechnic University
| | - Polina S Babich
- Department of Zoology, Herzen State Pedagogical University of Russia, St Petersburg
| | - Ilya M Sosnin
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Nanocatalysts and Functional Materials Laboratory, Togliatti State University, Togliatti
| | - Ekaterina Yu Ilyechova
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Department of Molecular Genetics, Research Institute of Experimental Medicine
| | - Demid A Kirilenko
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Ioffe Institute, St Petersburg, Russia
| | - Pavel N Brunkov
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Ioffe Institute, St Petersburg, Russia
| | - Gennadii L Ataev
- Department of Zoology, Herzen State Pedagogical University of Russia, St Petersburg
| | - Alexey E Romanov
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Nanocatalysts and Functional Materials Laboratory, Togliatti State University, Togliatti; Ioffe Institute, St Petersburg, Russia
| | - Ludmila V Puchkova
- International Research and Education Center "Functional materials and devices of optoelectronics and microelectronics", ITMO University; Department of Biophysics, Peter the Great St Petersburg Polytechnic University; Department of Molecular Genetics, Research Institute of Experimental Medicine
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Takeuchi T, Yamada L, Shinzato C, Sawada H, Satoh N. Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics. PLoS One 2016; 11:e0156424. [PMID: 27253604 PMCID: PMC4890752 DOI: 10.1371/journal.pone.0156424] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/14/2016] [Indexed: 11/19/2022] Open
Abstract
Despite the importance of stony corals in many research fields related to global issues, such as marine ecology, climate change, paleoclimatogy, and metazoan evolution, very little is known about the evolutionary origin of coral skeleton formation. In order to investigate the evolution of coral biomineralization, we have identified skeletal organic matrix proteins (SOMPs) in the skeletal proteome of the scleractinian coral, Acropora digitifera, for which large genomic and transcriptomic datasets are available. Scrupulous gene annotation was conducted based on comparisons of functional domain structures among metazoans. We found that SOMPs include not only coral-specific proteins, but also protein families that are widely conserved among cnidarians and other metazoans. We also identified several conserved transmembrane proteins in the skeletal proteome. Gene expression analysis revealed that expression of these conserved genes continues throughout development. Therefore, these genes are involved not only skeleton formation, but also in basic cellular functions, such as cell-cell interaction and signaling. On the other hand, genes encoding coral-specific proteins, including extracellular matrix domain-containing proteins, galaxins, and acidic proteins, were prominently expressed in post-settlement stages, indicating their role in skeleton formation. Taken together, the process of coral skeleton formation is hypothesized as: 1) formation of initial extracellular matrix between epithelial cells and substrate, employing pre-existing transmembrane proteins; 2) additional extracellular matrix formation using novel proteins that have emerged by domain shuffling and rapid molecular evolution and; 3) calcification controlled by coral-specific SOMPs.
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Affiliation(s)
- Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
- * E-mail:
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517–0004, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517–0004, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904–0495, Japan
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Tian JH, Pourcher AM, Bouchez T, Gelhaye E, Peu P. Occurrence of lignin degradation genotypes and phenotypes among prokaryotes. Appl Microbiol Biotechnol 2014; 98:9527-44. [PMID: 25343973 DOI: 10.1007/s00253-014-6142-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/24/2022]
Abstract
A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNA sequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.
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Affiliation(s)
- Jiang-Hao Tian
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, 35044, Rennes, France
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