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Zhang LB, Yang WWJ, Qiu TT. Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation. BMC Genomics 2023; 24:504. [PMID: 37649000 PMCID: PMC10466755 DOI: 10.1186/s12864-023-09606-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Laccases are green biocatalysts with wide industrial applications. The study of efficient and specific laccase producers remains a priority. Cerrena species have been shown to be promising basidiomycete candidates for laccase production. Although two sets of Cerrena genome data have been publicly published, no comprehensive bioinformatics study of laccase gene family in C. unicolor has been reported, particularly concerning the analysis of their three-dimensional (3D) structures and molecular docking to substrates, like ABTS and aflatoxin B1 (AFB1). RESULTS In this study, we conducted a comprehensive genome-wide analysis of laccase gene family in C. unicolor 87613. We identified eighteen laccase genes (CuLacs) and classified them into three clades using phylogenetic analysis. We characterized these laccases, including their location in contig 5,6,9,12,15,19,26,27, gene structures of different exon-intron arrangements, molecular weight ranging from 47.89 to 141.41 kDa, acidic pI value, 5-15 conserved protein motifs, signaling peptide of extracellular secretion (harbored by 13 CuLacs) and others. In addition, the analysis of cis-acting element in laccase promoters indicated that the transcription response of CuLac gene family was regulatable and complex under different environmental cues. Furthermore, analysis of transcription pattern revealed that CuLac8, 12 and CuLac2, 13 were the predominant laccases in response to copper ions or oxidative stress, respectively. Finally, we focused on the 3D structure analysis of CuLac proteins. Seven laccases with extra transmembrane domains or special sequences were particularly interesting. Predicted structures of each CuLac protein with or without these extra sequences showed altered interacting amino acid residues and binding sites, leading to varied affinities to both ABTS and AFB1. As far as we know, it is the first time to discuss the influence of the extra sequence on laccase's affinity to substrates. CONCLUSIONS Our findings provide robust genetic data for a better understanding of the laccase gene family in C. unicolor 87613, and create a foundation for the molecular redesign of CuLac proteins to enhance their industrial applications.
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Affiliation(s)
- Long-Bin Zhang
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China.
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China.
| | - Wu-Wei-Jie Yang
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
| | - Ting-Ting Qiu
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350116, Fujian, China
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Viel T, Manfra L, Zupo V, Libralato G, Cocca M, Costantini M. Biodegradation of Plastics Induced by Marine Organisms: Future Perspectives for Bioremediation Approaches. Polymers (Basel) 2023; 15:2673. [PMID: 37376319 DOI: 10.3390/polym15122673] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Plastic pollution is a distinctive element of the globalized world. In fact, since the 1970s the expansion and use of plastics, particularly in the consumer and commercial sectors, has given this material a permanent place in our lives. The increasing use of plastic products and the wrong management of end-of-life plastic products have contributed to increasing environmental pollution, with negative impacts on our ecosystems and the ecological functions of natural habitats. Nowadays, plastic pollution is pervasive in all environmental compartments. As aquatic environments are the dumping points for poorly managed plastics, biofouling and biodegradation have been proposed as promising approaches for plastic bioremediation. Known for the high stability of plastics in the marine environment, this represents a very important issue to preserve marine biodiversity. In this review, we have summarized the main cases reported in the literature on the degradation of plastics by bacteria, fungi, and microalgae and the degradation mechanisms involved, to highlight the potential of bioremediation approaches to reduce macro and microplastic pollution.
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Affiliation(s)
- Thomas Viel
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- Institute for Polymers, Composites and Biomaterials, National Research Council of Italy, Via Campi Flegri, 34, 80078 Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Napoli, Italy
| | - Loredana Manfra
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- Institute for Environmental Protection and Research (ISPRA), Via Vitaliano Brancati 48, 00144 Rome, Italy
| | - Valerio Zupo
- Stazione Zoologica, Ecosustainable Biotechnology Department, Ischia Marine Centre, Via Buonocore 42, 80077 Ischia, Italy
| | - Giovanni Libralato
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Napoli, Italy
| | - Mariacristina Cocca
- Institute for Polymers, Composites and Biomaterials, National Research Council of Italy, Via Campi Flegri, 34, 80078 Pozzuoli, Italy
| | - Maria Costantini
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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Current and emerging tools of computational biology to improve the detoxification of mycotoxins. Appl Environ Microbiol 2021; 88:e0210221. [PMID: 34878810 DOI: 10.1128/aem.02102-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Biological organisms carry a rich potential for removing toxins from our environment, but identifying suitable candidates and improving them remain challenging. We explore the use of computational tools to discover strains and enzymes that detoxify harmful compounds. In particular, we will focus on mycotoxins-fungi-produced toxins that contaminate food and feed-and biological enzymes that are capable of rendering them less harmful. We discuss the use of established and novel computational tools to complement existing empirical data in three directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and improving the performance of detoxifying enzymes. We hope to create a synergistic conversation between researchers in computational biology and those in the bioremediation field. We showcase open bioremediation questions where computational researchers can contribute and highlight relevant existing and emerging computational tools that could benefit bioremediation researchers.
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de Jesus Fontes B, Kleingesinds EK, Giovanella P, Junior AP, Sette LD. Laccases produced by Peniophora from marine and terrestrial origin: A comparative study. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Purification and Characterization of Two Novel Laccases from Peniophora lycii. J Fungi (Basel) 2020; 6:jof6040340. [PMID: 33291231 PMCID: PMC7762197 DOI: 10.3390/jof6040340] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 01/09/2023] Open
Abstract
Although, currently, more than 100 laccases have been purified from basidiomycete fungi, the majority of these laccases were obtained from fungi of the Polyporales order, and only scarce data are available about the laccases from other fungi. In this article, laccase production by the white-rot basidiomycete fungus Peniophora lycii, belonging to the Russulales order, was investigated. It was shown that, under copper induction, this fungus secreted three different laccase isozymes. Two laccase isozymes—Lac5 and LacA—were purified and their corresponding nucleotide sequences were determined. Both purified laccases were relatively thermostable with periods of half-life at 70 °C of 10 and 8 min for Lac5 and LacA, respectively. The laccases demonstrated the highest activity toward ABTS (97 U·mg−1 for Lac5 and 121 U·mg−1 for LacA at pH 4.5); Lac5 demonstrated the lowest activity toward 2,6-DMP (2.5 U·mg−1 at pH 4.5), while LacA demonstrated this towards gallic acid (1.4 U·mg−1 at pH 4.5). Both Lac5 and LacA were able to efficiently decolorize such dyes as RBBR and Bromcresol Green. Additionally, phylogenetic relationships among laccases of Peniophora spp. were reconstructed, and groups of orthologous genes were determined. Based on these groups, all currently available data about laccases of Peniophora spp. were systematized.
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Novel redox-active enzymes for ligninolytic applications revealed from multiomics analyses of Peniophora sp. CBMAI 1063, a laccase hyper-producer strain. Sci Rep 2019; 9:17564. [PMID: 31772294 PMCID: PMC6879535 DOI: 10.1038/s41598-019-53608-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/04/2019] [Indexed: 11/08/2022] Open
Abstract
The repertoire of redox-active enzymes produced by the marine fungus Peniophora sp. CBMAI 1063, a laccase hyper-producer strain, was characterized by omics analyses. The genome revealed 309 Carbohydrate-Active Enzymes (CAZymes) genes, including 48 predicted genes related to the modification and degradation of lignin, whith 303 being transcribed under cultivation in optimized saline conditions for laccase production. The secretome confirmed that the fungus can produce a versatile ligninolytic enzyme cocktail. It secretes 56 CAZymes, including 11 oxidative enzymes classified as members of auxiliary activity families (AAs), comprising two laccases, Pnh_Lac1 and Pnh_Lac2, the first is the major secretory protein of the fungi. The Pnh_Lac1-mediator system was able to promote the depolymerization of lignin fragments and polymeric lignin removal from pretreated sugarcane bagasse, confirming viability of this fungus enzymatic system for lignocellulose-based bioproducts applications.
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Morlighem JÉRL, Radis-Baptista G. The Place for Enzymes and Biologically Active Peptides from Marine Organisms for Application in Industrial and Pharmaceutical Biotechnology. Curr Protein Pept Sci 2019; 20:334-355. [PMID: 30255754 DOI: 10.2174/1389203719666180926121722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/10/2018] [Accepted: 09/15/2018] [Indexed: 01/07/2023]
Abstract
Since the beginning of written history, diverse texts have reported the use of enzymatic preparations in food processing and have described the medicinal properties of crude and fractionated venoms to treat various diseases and injuries. With the biochemical characterization of enzymes from distinct sources and bioactive polypeptides from animal venoms, the last sixty years have testified the advent of industrial enzymology and protein therapeutics, which are currently applicable in a wide variety of industrial processes, household products, and pharmaceuticals. Bioprospecting of novel biocatalysts and bioactive peptides is propelled by their unsurpassed properties that are applicable for current and future green industrial processes, biotechnology, and biomedicine. The demand for both novel enzymes with desired characteristics and novel peptides that lead to drug development, has experienced a steady increase in response to the expanding global market for industrial enzymes and peptidebased drugs. Moreover, although largely unexplored, oceans and marine realms, with their unique ecosystems inhabited by a large variety of species, including a considerable number of venomous animals, are recognized as untapped reservoirs of molecules and macromolecules (enzymes and bioactive venom-derived peptides) that can potentially be converted into highly valuable biopharmaceutical products. In this review, we have focused on enzymes and animal venom (poly)peptides that are presently in biotechnological use, and considering the state of prospection of marine resources, on the discovery of useful industrial biocatalysts and drug leads with novel structures exhibiting selectivity and improved performance.
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Affiliation(s)
- Jean-Étienne R L Morlighem
- Institute for Marine Sciences, Federal University of Ceara, Av da Abolicao 3207. Fortaleza/CE. 60165081, Brazil
| | - Gandhi Radis-Baptista
- Institute for Marine Sciences, Federal University of Ceara, Av da Abolicao 3207. Fortaleza/CE. 60165081, Brazil
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Vasconcelos MRS, Vieira GAL, Otero IVR, Bonugli-Santos RC, Rodrigues MVN, Rehder VLG, Ferro M, Boaventura S, Bacci M, Sette LD. Pyrene degradation by marine-derived ascomycete: process optimization, toxicity, and metabolic analyses. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:12412-12424. [PMID: 30847811 DOI: 10.1007/s11356-019-04518-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Marine-derived fungi are relevant genetic resources for bioremediation of saline environments/processes. Among the five fungi recovered from marine sponges able to degrade pyrene (Py) and benzo[a]pyrene (BaP), Tolypocladium sp. strain CBMAI 1346 and Xylaria sp. CBMAI 1464 presented the best removal rates of Py and BaP, respectively. Since the decrease in BaP was related to mycelial adsorption, a combined strategy was applied for the investigation of Py degradation by the fungus Tolypocladium sp. CBMAI 1346. The selected fungus was able to degrade about 95% of Py after 7 days of incubation (optimized conditions), generating metabolites different from the ones found before optimization. Metabolites and transcriptomic data revealed that the degradation occurred mainly by the cytochrome P450 pathway. Putative monooxygenases and dioxygenases found in the transcriptome may play an important role. After 21 days of degradation, no toxicity was found in the optimized culture conditions. The findings from the present study highlight the potential of marine-derived fungi to degrade environmental pollutants and convey innovative information related to the metabolism of pyrene.
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Affiliation(s)
- Maria R S Vasconcelos
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - Gabriela A L Vieira
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 24A, 1515 - Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Igor V R Otero
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 24A, 1515 - Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Rafaella C Bonugli-Santos
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Paulínia, SP, Brazil
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration (UNILA), Paraná, PR, Brazil
| | - Marili V N Rodrigues
- Divisão de Química Orgânica e Farmacêutica, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - Vera L G Rehder
- Divisão de Química Orgânica e Farmacêutica, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - Milene Ferro
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Sinésio Boaventura
- Divisão de Química Orgânica e Farmacêutica, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - Maurício Bacci
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 24A, 1515 - Bela Vista, Rio Claro, SP, 13506-900, Brazil
- Centro de Estudos de Insetos Sociais, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Lara D Sette
- Divisão de Recursos Microbianos, Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, Paulínia, SP, Brazil.
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), 24A, 1515 - Bela Vista, Rio Claro, SP, 13506-900, Brazil.
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Balabanova L, Slepchenko L, Son O, Tekutyeva L. Biotechnology Potential of Marine Fungi Degrading Plant and Algae Polymeric Substrates. Front Microbiol 2018; 9:1527. [PMID: 30050513 PMCID: PMC6052901 DOI: 10.3389/fmicb.2018.01527] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the metabolic capacity to degrade environment organic matter, much of which is the plant and algae material enriched with the cell wall carbohydrates and polyphenol complexes that frequently can be assimilated by only marine fungi. As the most renewable energy feedstock on the Earth, the plant or algae polymeric substrates induce an expression of microbial extracellular enzymes that catalyze their cleaving up to the component sugars. However, the question of what the marine fungi contributes to the plant and algae material biotransformation processes has yet to be highlighted sufficiently. In this review, we summarized the potential of marine fungi alternatively to terrestrial fungi to produce the biotechnologically valuable extracellular enzymes in response to the plant and macroalgae polymeric substrates as sources of carbon for their bioconversion used for industries and bioremediation.
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Affiliation(s)
- Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Lubov Slepchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Oksana Son
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Liudmila Tekutyeva
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
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