1
|
Oliveira-Junior SD, Silva GL, Pessoa VA, Vasconcelos AS, Silva DF, Soares LBN, Chevreuil LR, Santos ES, Sales-Campos C. Adding-value to Ganoderma lingzhi by producing enzymes and antioxidant compounds under submerged fermentation using different culture media. BRAZ J BIOL 2024; 84:e283882. [PMID: 39383366 DOI: 10.1590/1519-6984.283882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/20/2024] [Indexed: 10/11/2024] Open
Abstract
Ganoderma lingzhi is widely reported for its medicinal properties, presenting several bioactive substances with potential pharmaceutical and industrial application. This study aimed to evaluate the production of mycelial biomass, extracellular enzymes and antioxidant compounds by G. lingzhi under submerged fermentation. G. lingzhi was cultured in Polysaccharide (POL) and Melin-Norkrans (MNM) media for 7 days. The cellulases, xylanases, pectinases, laccases, and proteases activities were quantified in the culture broth, while the antioxidant potential was evaluated for the mycelial biomass. G. lingzhi showed higher biomass production in MNM. However, it exhibited similar microstructural characteristics in both culture media. In the POL there was greater activity of CMCase (0.229 U/mL), xylanase (0.780 U/mL), pectinase (0.447 U/mL) and proteases (16.13 U/mL). FPase did not differ (0.01 U/mL), and laccase was detected only in MNM (0.122 U/mL). The biomass water extract from MNM showed high levels of phenolic compounds (951.97 mg AGE/100 g). DPPH• inhibition (90.55%) and reducing power (0.456) were higher in MNM medium, while ABTS•+ inhibition (99.95%) and chelating ability (54.86%) were higher in POL. Thus, the MNM medium was more favorable to the production of mycelial biomass and phenolic compounds, while the POL medium favored the synthesis and excretion of hydrolytic enzymes.
Collapse
Affiliation(s)
- S D Oliveira-Junior
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
| | - G L Silva
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
- Universidade Federal do Amazonas - UFAM, Programa de Pós-Graduação em Biotecnologia - PPGBIOTEC, Manaus, AM, Brasil
| | - V A Pessoa
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
- Universidade Federal do Amazonas - UFAM, Programa de Pós-Graduação em Biotecnologia - PPGBIOTEC, Manaus, AM, Brasil
| | - A S Vasconcelos
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
- Universidade Federal do Amazonas - UFAM, Programa de Pós-Graduação em Biotecnologia - PPGBIOTEC, Manaus, AM, Brasil
- Universidade do Estado do Amazonas - UEA, Centro Multiusuário para Análise de Fenômenos Biomédicos - CMABio, Manaus, AM, Brasil
| | - D F Silva
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
- Universidade do Estado do Amazonas - UEA, Programa de Pós-Graduação em Biodiversidade e Biotecnologia da rede BIONORTE - PPGBIONORTE, Manaus, AM, Brasil
| | - L B N Soares
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
- Universidade do Estado do Amazonas - UEA, Programa de Pós-Graduação em Biodiversidade e Biotecnologia da rede BIONORTE - PPGBIONORTE, Manaus, AM, Brasil
| | - L R Chevreuil
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
| | - E S Santos
- Universidade Federal do Rio Grande do Norte - UFRN, Laboratório de Engenharia Bioquímica - LEB, Departamento de Engenharia Química - DEQ, Natal, RN, Brasil
| | - C Sales-Campos
- Instituto Nacional de Pesquisas da Amazônia - INPA, Laboratório de Cultivo de Fungos Comestíveis - LCFC, Manaus, AM, Brasil
- Universidade Federal do Amazonas - UFAM, Programa de Pós-Graduação em Biotecnologia - PPGBIOTEC, Manaus, AM, Brasil
- Universidade do Estado do Amazonas - UEA, Programa de Pós-Graduação em Biodiversidade e Biotecnologia da rede BIONORTE - PPGBIONORTE, Manaus, AM, Brasil
| |
Collapse
|
2
|
Ban H, Liu Q, Xiu L, Cai D, Liu J. Effect of Solid-State Fermentation of Hericium erinaceus on the Structure and Physicochemical Properties of Soluble Dietary Fiber from Corn Husk. Foods 2024; 13:2895. [PMID: 39335822 PMCID: PMC11431227 DOI: 10.3390/foods13182895] [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: 08/26/2024] [Revised: 09/03/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
Corn husk, a by-product of corn starch production and processing, contains high-quality dietary fiber (DF). Our study compares and analyzes the impact of Hericium erinaceus solid-state fermentation (SSF) on the structure and physicochemical characteristics of soluble dietary fiber (SDF) of corn husks. The study also investigates the kinetics of SSF of H. erinaceus in this process. The scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) results revealed significant structural changes in corn husk SDF before and after fermentation, with a significant elevation in the functional group numbers. The data indicate that the fermented corn husk SDF's water-holding, swelling, and oil-holding capacities increased to 1.57, 1.95, and 1.80 times those of the pre-fermentation SDF, respectively. Additionally, the results suggest that changes in extracellular enzyme activity and nutrient composition during SSF of H. erinaceus are closely associated with the mycelium growth stage, with a mutual promotion or inhibition relationship between the two. Our study offers a foundation for corn husk SDF fermentation and is relevant to the bioconversion of maize processing by-products.
Collapse
Affiliation(s)
- He Ban
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (H.B.); (Q.L.); (L.X.); (J.L.)
- National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, China
| | - Qiannan Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (H.B.); (Q.L.); (L.X.); (J.L.)
- National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, China
| | - Lin Xiu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (H.B.); (Q.L.); (L.X.); (J.L.)
- National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, China
| | - Dan Cai
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (H.B.); (Q.L.); (L.X.); (J.L.)
- National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, China
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (H.B.); (Q.L.); (L.X.); (J.L.)
- National Engineering Research Center for Wheat and Corn Deep Processing, Changchun 130118, China
| |
Collapse
|
3
|
Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
Collapse
Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| |
Collapse
|
4
|
Shamshitov A, Kadžienė G, Supronienė S. The Role of Soil Microbial Consortia in Sustainable Cereal Crop Residue Management. PLANTS (BASEL, SWITZERLAND) 2024; 13:766. [PMID: 38592825 PMCID: PMC10974107 DOI: 10.3390/plants13060766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
The global escalation in cereal production, essential to meet growing population demands, simultaneously augments the generation of cereal crop residues, estimated annually at approximately 3107 × 106 Mg/year. Among different crop residue management approaches, returning them to the soil can be essential for various ecological benefits, including nutrient recycling and soil carbon sequestration. However, the recalcitrant characteristics of cereal crop residues pose significant challenges in their management, particularly in the decomposition rate. Therefore, in this review, we aim to summarize the influence of different agricultural practices on enhancing soil microbial decomposer communities, thereby effectively managing cereal crop residues. Moreover, this manuscript provides indirect estimates of cereal crop residue production in Northern Europe and Lithuania, and highlights the diverse roles of lignocellulolytic microorganisms in the decomposition process, with a particular focus on enzymatic activities. This review bridges the knowledge gap and indicates future research directions concerning the influence of agricultural practices on cereal crop residue-associated microbial consortia.
Collapse
Affiliation(s)
- Arman Shamshitov
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
| | - Gražina Kadžienė
- Department of Soil and Crop Management, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania
| | - Skaidrė Supronienė
- Laboratory of Microbiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Instituto al. 1, Akademija, LT-58344 Kedainiai, Lithuania;
| |
Collapse
|
5
|
Serbent MP, Magario I, Saux C. Immobilizing white-rot fungi laccase: Toward bio-derived supports as a circular economy approach in organochlorine removal. Biotechnol Bioeng 2024; 121:434-455. [PMID: 37990982 DOI: 10.1002/bit.28591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/23/2023] [Accepted: 10/28/2023] [Indexed: 11/23/2023]
Abstract
Despite their high persistence in the environment, organochlorines (OC) are widely used in the pharmaceutical industry, in plastics, and in the manufacture of pesticides, among other applications. These compounds and the byproducts of their decomposition deserve attention and efficient proposals for their treatment. Among sustainable alternatives, the use of ligninolytic enzymes (LEs) from fungi stands out, as these molecules can catalyze the transformation of a wide range of pollutants. Among LEs, laccases (Lac) are known for their efficiency as biocatalysts in the conversion of organic pollutants. Their application in biotechnological processes is possible, but the enzymes are often unstable and difficult to recover after use, driving up costs. Immobilization of enzymes on a matrix (support or solid carrier) allows recovery and stabilization of this catalytic capacity. Agricultural residual biomass is a passive environmental asset. Although underestimated and still treated as an undesirable component, residual biomass can be used as a low-cost adsorbent and as a support for the immobilization of enzymes. In this review, the adsorption capacity and immobilization of fungal Lac on supports made from residual biomass, including compounds such as biochar, for the removal of OC compounds are analyzed and compared with the use of synthetic supports. A qualitative and quantitative comparison of the reported results was made. In this context, the use of peanut shells is highlighted in view of the increasing peanut production worldwide. The linkage of methods with circular economy approaches that can be applied in practice is discussed.
Collapse
Affiliation(s)
- Maria Pilar Serbent
- Centro de Investigación y Tecnología Química (CITeQ), Facultad Regional Córdoba, Universidad Tecnológica Nacional (CONICET), Córdoba, Argentina
- Programa de Pós-Graduação em Ciências Ambientais (PPGCAMB), Universidade do Estado de Santa Catarina, Lages, Santa Catarina, Brasil
| | - Ivana Magario
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos y Química Aplicada (IPQA), Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba (CONICET), Córdoba, Argentina
| | - Clara Saux
- Centro de Investigación y Tecnología Química (CITeQ), Facultad Regional Córdoba, Universidad Tecnológica Nacional (CONICET), Córdoba, Argentina
| |
Collapse
|
6
|
Yu H, Jiang N, Yan M, Cheng X, Zhang L, Zhai D, Liu J, Zhang M, Song C, Yu H, Li Q. Comparative analysis of proteomes and transcriptomes revealed the molecular mechanism of development and nutrition of Pleurotus giganteus at different fruiting body development stages. Front Nutr 2023; 10:1197983. [PMID: 37545588 PMCID: PMC10402744 DOI: 10.3389/fnut.2023.1197983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
Pleurotus giganteus is a commercially cultivated high-temperature mushroom. Investigating the molecular mechanism of fruiting body development will help us to better understand the regulation of substrates and energy in this process. However, little information has been reported on the development and nutrients of the P. giganteus fruiting body. In the present study, P. giganteus is cultivated in a climate chamber, and comparative transcriptome, proteome, and nutritional analysis of P. giganteus fruiting bodies were performed. Our results revealed that Cytochrome P450 monooxygenases and hydrophobin proteins play important roles during the differentiation in the elongation stage. Later, carbon metabolism dominate the fruiting body metabolism and genes related to the carbohydrate metabolic process, glycolytic process, and gluconeogenesis were up-regulated in the mature fruiting bodies. The up-regulation of carbohydrate substrates utilization CAZymes genes and inconsistent protein expression in pileus indicated a reverse transportation of mRNA from the fruiting body to vegetative mycelia. In addition, protein concentration in the pileus is higher than that in the stem, while the stem is the major nitrogen metabolic and amino acid synthetic location. The integrated transcriptomic, proteomic, and nutritional analysis indicated a two-way transportation of substrates and mRNAs in P. giganteus. Stem synthesizes amino acids and transported them to pileus with reducing sugars, while pileus induces the expression of substrate degradation mRNA according to the needs of growth and development and transports them in the other direction.
Collapse
Affiliation(s)
- Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ning Jiang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Miaomiao Yan
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuan Cheng
- Agricultural Specialty Industry Development Center, Qujiang, Zhejiang, China
| | - Lujun Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dandan Zhai
- Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China
| | - Jianyu Liu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunyan Song
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hao Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiaozhen Li
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
7
|
Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
Collapse
Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| |
Collapse
|
8
|
Singh G, Kumar S, Afreen S, Bhalla A, Khurana J, Chandel S, Aggarwal A, Arya SK. Laccase mediated delignification of wasted and non-food agricultural biomass: Recent developments and challenges. Int J Biol Macromol 2023; 235:123840. [PMID: 36849073 DOI: 10.1016/j.ijbiomac.2023.123840] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
Utilization of microbial laccases is considered as the cleaner and target specific biocatalytic mechanism for the recovery of cellulose and hemicelluloses from nonfood and wasted agricultural, lignocellulosic biomass (LCB). The extent of lignin removal by laccase depends on the biochemical composition of biomass and the redox potential (E0) of the biocatalyst. Intensive research efforts are going on all over the world for the recognition of appropriate and easily available agricultural lignocellulosic feedstocks to exploit maximally for the production of value-added bioproducts and biofuels. In such circumstances, laccase can play a major role as a leading biocatalyst and potent substitute for chemical based deconstruction of the lignocellulosic materials. The limited commercialization of laccase at an industrial scale has been feasible due to its full working efficiency mostly expressed in the presence of cost intensive redox mediators only. Although, recently there are some reports that came on the mediator free biocatalysis of enzyme but still not considerably explored and neither understood in depth. The present review will address the various research gaps and shortcomings that acted as the big hurdles before the complete exploitation of laccases at an industrial scale. Further, this article also reveals insights on different microbial laccases and their diverse functional environmental conditions that affect the deconstruction process of LCB.
Collapse
Affiliation(s)
- Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Shiv Kumar
- Department of Microbiology, Guru Gobind Singh Medical College and Hospital, Baba Farid University of Health Sciences, Faridkot 151203, Punjab, India
| | - Sumbul Afreen
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India
| | - Aditya Bhalla
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Jyoti Khurana
- Biotechnology Department, Arka Jain University, Jamshedpur, Jharkhand, India
| | - Sanjeev Chandel
- GHG College of Pharmacy, Raikot Road, Ludhiana, -141109, India
| | | | | |
Collapse
|
9
|
Yu J, Sun M, Wang X, Qi D, Han C. Poly-pathways metabolomics for high-yielding cordycepin of Cordyceps militaris. Biomed Chromatogr 2023; 37:e5551. [PMID: 36408993 DOI: 10.1002/bmc.5551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/02/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
Cordycepin is an important quality control marker in Cordyceps militaris. This study aimed to explain the metabolic mechanisms for high-yielding cordycepin of C. militaris. In this study, high-yielding strains of cordycepin were obtained by ultraviolet mutagenesis, and the polysaccharide and protein contents were also changed. In high-yielding strains, the protein content significantly increased, whereas the polysaccharide content decreased. Simultaneously, metabolic differences for high- and low-yielding cordycepin strains were detected by metabolomics. Metabolomics results showed that the relative content of most metabolites decreased in high-yielding cordycepin strains. Various metabolic pathways have been altered in high-yielding cordycepin strains, such as the citric acid cycle, purine metabolism, and pyrimidine metabolism, leading to an increase in cordycepin content. In addition, changes in metabolic poly-pathways related to polysaccharide and protein synthesis, such as galactose metabolism and amino acid metabolism, promoted an increase in cordycepin content. This study analyzes the high yield of cordycepin in C. militaris at the metabolic level and provides a theoretical basis for further increasing cordycepin content.
Collapse
Affiliation(s)
- Jinyan Yu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Min Sun
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaoyu Wang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Dongmei Qi
- Experimental center, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chunchao Han
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| |
Collapse
|
10
|
Wang L, Ding X, Huang Q, Hu B, Liang L, Wang Q. Gllac7 Is Induced by Agricultural and Forestry Residues and Exhibits Allelic Expression Bias in Ganoderma lucidum. Front Microbiol 2022; 13:890686. [PMID: 35847055 PMCID: PMC9279560 DOI: 10.3389/fmicb.2022.890686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Ganoderma lucidum has a wide carbon spectrum, while the expression profile of key genes relevant to carbon metabolism on different carbon sources has been seldom studied. Here, the transcriptomes of G. lucidum mycelia cultured on each of 19 carbon sources were conducted. In comparison with glucose, 16 to 1,006 genes were upregulated and 7 to 1,865 genes were downregulated. Significant gene expression dynamics and induced activity were observed in laccase genes when using agricultural and forestry residues (AFRs) as solo carbon sources. Furthermore, study of laccase gene family in two haploids of G. lucidum GL0102 was conducted. Totally, 15 and 16 laccase genes were identified in GL0102_53 and GL0102_8, respectively, among which 15 pairs were allelic genes. Gene structures were conserved between allelic laccase genes, while sequence variations (most were SNPs) existed. Nine laccase genes rarely expressed on all the tested carbon sources, while the other seven genes showed high expression level on AFRs, especially Gllac2 and Gllac7, which showed 5- to 1,149-fold and 4- to 94-fold upregulation in mycelia cultured for 5 days, respectively. The expression of H53lac7 was consistently higher than that of H8lac7_1 on all the carbon sources except XM, exhibiting a case of allelic expression bias. A total of 47 SNPs and 3 insertions/deletions were observed between promoters of H53lac7 and H8lac7_1, which lead to differences in predicted binding sites of zinc fingers. These results provide scientific data for understanding the gene expression profile and regulatory role on different carbon sources and may support further functional research of laccase.
Collapse
Affiliation(s)
- Lining Wang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qinghua Huang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Biao Hu
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Lei Liang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingfu Wang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| |
Collapse
|
11
|
Abstract
Plant-derived biomass is the most abundant biogenic carbon source on Earth. Despite this, only a small clade of organisms known as white-rot fungi (WRF) can efficiently break down both the polysaccharide and lignin components of plant cell walls. This unique ability imparts a key role for WRF in global carbon cycling and highlights their potential utilization in diverse biotechnological applications. To date, research on WRF has primarily focused on their extracellular ‘digestive enzymes’ whereas knowledge of their intracellular metabolism remains underexplored. Systems biology is a powerful approach to elucidate biological processes in numerous organisms, including WRF. Thus, here we review systems biology methods applied to WRF to date, highlight observations related to their intracellular metabolism, and conduct comparative extracellular proteomic analyses to establish further correlations between WRF species, enzymes, and cultivation conditions. Lastly, we discuss biotechnological opportunities of WRF as well as challenges and future research directions.
Collapse
|
12
|
Rigobello A, Ayres P. Compressive behaviour of anisotropic mycelium-based composites. Sci Rep 2022; 12:6846. [PMID: 35477970 PMCID: PMC9046257 DOI: 10.1038/s41598-022-10930-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Mycelium based composites (MBC) exhibit many properties that make them promising alternatives for less sustainable materials. However, there is no unified approach to their testing. We hypothesise that the two-phase particulate composite model and use of ASTM D1037 could provide a basis for systematisation. An experimental series of MBC were produced using four substrate particle sizes and subjected to compression testing. We report on their effect over Young’s modulus and ultimate strength. We extend the study by investigating three anisotropic substrate designs through orientated fibre placement as a strategy for modifying compressive behaviour. We find that the two-phase particulate model is appropriate for describing the mechanical behaviour of MBC and that mechanical behaviour can be modified through anisotropic designs using orientated fibres. We also confirm that fibre orientation and particle size are significant parameters in determining ultimate strength.
Collapse
Affiliation(s)
- Adrien Rigobello
- Centre for IT and Architecture, Royal Danish Academy, 1435, Copenhagen, Denmark.
| | - Phil Ayres
- Centre for IT and Architecture, Royal Danish Academy, 1435, Copenhagen, Denmark
| |
Collapse
|
13
|
Cai M, Tan Z, Wu X, Liang X, Liu Y, Xie Y, Li X, Xiao C, Gao X, Chen S, Hu H, Wu Q. Comparative transcriptome analysis of genes and metabolic pathways involved in sporulation in Ganoderma lingzhi. G3 (BETHESDA, MD.) 2022; 12:jkab448. [PMID: 35079793 PMCID: PMC8895980 DOI: 10.1093/g3journal/jkab448] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/14/2021] [Indexed: 11/21/2022]
Abstract
Over the past decades, Ganoderma lingzhi spores have received considerable attention as a great potential pharmaceutical resource. However, the genetic regulation of sporulation is not well understood. In this study, a comparative transcriptome analysis of the low-sporing HZ203 and high-sporing YW-1 was performed to characterize the mechanism underlying sporulation. A total of 917 differentially expressed genes were identified in HZ203 and 1,450 differentially expressed genes in YW-1. Differentially expressed genes involved in sporulation were identified, which included HOP1, Mek1, MSH4, MSH5, and Spo5 in meiosis. Positive regulatory pathways of sporulation were proposed as 2 transcriptional factors had high connectivity with MSH4 and Spo5. Furthermore, we found that the pathways associated with energy production were enriched in the high-sporing genotype, such as the glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism. Finally, we performed a weighted gene coexpression network analysis and found that the hub genes of the module which exhibit strong positive relationship with the high-sporing phase purportedly participate in signal transduction, carbohydrate transport and metabolism. The dissection of differentially expressed genes during sporulation extends our knowledge about the genetic and molecular networks mediating spore morphogenesis and sheds light on the importance of energy source during sporulation.
Collapse
Affiliation(s)
- Manjun Cai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Zengdong Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoxian Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiaowei Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Yuanchao Liu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Yuewei Edible Fungi Technology Co. Ltd., Guangzhou 510663, China
| | - Yizhen Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
- Guangdong Yuewei Edible Fungi Technology Co. Ltd., Guangzhou 510663, China
| | - Xiangmin Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Chun Xiao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Xiong Gao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Shaodan Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Huiping Hu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| |
Collapse
|
14
|
Chan YS, Chong KP. Bioactive Compounds of Ganoderma boninense Inhibited Methicillin-Resistant Staphylococcus aureus Growth by Affecting Their Cell Membrane Permeability and Integrity. Molecules 2022; 27:838. [PMID: 35164103 PMCID: PMC8840476 DOI: 10.3390/molecules27030838] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 12/31/2022] Open
Abstract
Some species of Ganoderma, such as G. lucidum, are well-known as traditional Chinese medicine (TCM), and their pharmacological value was scientifically proven in modern days. However, G. boninense is recognized as an oil palm pathogen, and its biological activity is scarcely reported. Hence, this study aimed to investigate the antibacterial properties of G. boninense fruiting bodies, which formed by condensed mycelial, produced numerous and complex profiles of natural compounds. Extract was cleaned up with normal-phase SPE and its metabolites were analyzed using liquid chromatography-mass spectrometry (LCMS). From the disc diffusion and broth microdilution assays, strong susceptibility was observed in methicillin-resistant Staphylococcus aureus (MRSA) in elute fraction with zone inhibition of 41.08 ± 0.04 mm and MIC value of 0.078 mg mL-1. A total of 23 peaks were detected using MS, which were putatively identified based on their mass-to-charge ratio (m/z), and eight compounds, which include aristolochic acid, aminoimidazole ribotide, lysine sulfonamide 11v, carbocyclic puromycin, fenbendazole, acetylcaranine, tigecycline, and tamoxifen, were reported in earlier literature for their antimicrobial activity. Morphological observation via scanning electron microscope (SEM), cell membrane permeability, and integrity assessment suggest G. boninense extract induces irreversible damage to the cell membrane of MRSA, thus causing cellular lysis and death.
Collapse
Affiliation(s)
| | - Khim-Phin Chong
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| |
Collapse
|
15
|
Guo H, He T, Lee DJ. Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review. BIORESOURCE TECHNOLOGY 2022; 344:126263. [PMID: 34728359 DOI: 10.1016/j.biortech.2021.126263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.
Collapse
Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China; College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Tongyuan He
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong.
| |
Collapse
|
16
|
Wan JN, Li Y, Guo T, Ji GY, Luo SZ, Ji KP, Cao Y, Tan Q, Bao DP, Yang RH. Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development. Front Microbiol 2021; 12:732458. [PMID: 34659161 PMCID: PMC8511702 DOI: 10.3389/fmicb.2021.732458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023] Open
Abstract
Phlebopus portentosus (Berk. and Broome) Boedijin, a widely consumed mushroom in China and Thailand, is the first species in the order Boletaceae to have been industrially cultivated on a large scale. However, to date, the lignocellulose degradation system and molecular basis of fruiting body development in P. portentosus have remained cryptic. In the present study, genome and transcriptome sequencing of P. portentosus was performed during the mycelium (S), primordium (P), and fruiting body (F) stages. A genome of 32.74 Mb with a 48.92% GC content across 62 scaffolds was obtained. A total of 9,464 putative genes were predicted from the genome, of which the number of genes related to plant cell wall-degrading enzymes was much lower than that of some saprophytic mushrooms with specific ectomycorrhizal niches. Principal component analysis of RNA-Seq data revealed that the gene expression profiles at all three stages were different. The low expression of plant cell wall-degrading genes also confirmed the limited ability to degrade lignocellulose. The expression profiles also revealed that some conserved and specific pathways were enriched in the different developmental stages of P. portentosus. Starch and sucrose metabolic pathways were enriched in the mycelium stage, while DNA replication, the proteasome and MAPK signaling pathways may be associated with maturation. These results provide a new perspective for understanding the key pathways and hub genes involved in P. portentosus development.
Collapse
Affiliation(s)
- Jia-Ning Wan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ting Guo
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guang-Yan Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Shun-Zhen Luo
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Kai-Ping Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Yang Cao
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Qi Tan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Rui-Heng Yang
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| |
Collapse
|
17
|
Integrative Analysis of Selected Metabolites and the Fungal Transcriptome during the Developmental Cycle of Ganoderma lucidum Strain G0119 Correlates Lignocellulose Degradation with Carbohydrate and Triterpenoid Metabolism. Appl Environ Microbiol 2021; 87:e0053321. [PMID: 33893114 DOI: 10.1128/aem.00533-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To systemically understand the biosynthetic pathways of bioactive substances, including triterpenoids and polysaccharides, in Ganoderma lucidum, the correlation between substrate degradation and carbohydrate and triterpenoid metabolism during growth was analyzed by combining changes in metabolite content and changes in related enzyme expression in G. lucidum over 5 growth phases. Changes in low-polarity triterpenoid content were correlated with changes in glucose and mannitol contents in fruiting bodies. Additionally, changes in medium-polarity triterpenoid content were correlated with changes in the lignocellulose content of the substrate and with the glucose, trehalose, and mannitol contents of fruiting bodies. Weighted gene coexpression network analysis (WGCNA) indicated that changes in trehalose and polyol contents were related to carbohydrate catabolism and polysaccharide synthesis. Changes in triterpenoid content were related to expression of the carbohydrate catabolic enzymes laccase, cellulase, hemicellulase, and polysaccharide synthase and to the expression of several cytochrome P450 monooxygenases (CYPs). It was concluded that the products of cellulose and hemicellulose degradation participate in polyol, trehalose, and polysaccharide synthesis during initial fruiting body formation. These carbohydrates accumulate in the early phase of fruiting body formation and are utilized when the fruiting bodies mature and a large number of spores are ejected. An increase in carbohydrate metabolism provides additional precursors for the synthesis of triterpenoids. IMPORTANCE Most studies of G. lucidum have focused on its medicinal function and on the mechanism of its activity, whereas the physiological metabolism and synthesis of bioactive substances during the growth of this species have been less studied. Therefore, theoretical guidance for cultivation methods to increase the production of bioactive compounds remains lacking. This study integrated changes in the lignocellulose, carbohydrate, and triterpenoid contents of G. lucidum with enzyme expression from transcriptomics data using WGCNA. The findings helped us better understand the connections between substrate utilization and the synthesis of polysaccharides and triterpenoids during the cultivation cycle of G. lucidum. The results of WGCNA suggest that the synthesis of triterpenoids can be enhanced not only through regulating the expression of enzymes in the triterpenoid pathway, but also through regulating carbohydrate metabolism and substrate degradation. This study provides a potential approach and identifies enzymes that can be targeted to regulate lignocellulose degradation and accelerate the accumulation of bioactive substances by regulating substrate degradation in G. lucidum.
Collapse
|
18
|
Evaluation of Basidiomycetes Wild Strains Grown in Agro-Industrial Residues for Their Anti-Tyrosinase and Antioxidant Potential and for the Production of Biocatalysts. FERMENTATION 2021. [DOI: 10.3390/fermentation7010019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
White-rot basidiomycetes are the only microorganisms with the ability to produce both hydrolytic (cellulases and hemicellulases) and oxidative (ligninolytic) enzymes for degrading cellulose/hemicellulose and lignin. In addition, they produce biologically active natural products with important application in cosmetic formulations, either as pure compounds or as standardized extracts. In the present work, three wild strains of Basidiomycetes fungi (Pleurotus citrinopileatus, Abortiporus biennis and Ganoderma resinaceum) from Greek habitats were grown in agro-industrial residues (oil mill wastewater, and corn cob) and evaluated for their anti-tyrosinase and antioxidant activity and for the production of biotechnologically relevant enzymes. P. citrinopileatus showed the most interesting tyrosinase inhibitory activity, while A. biennis showed the highest DPPH(2,2-diphenyl-1-picryl-hydrazyl) scavenging potential. Corn cobs were the most appropriate carbon source for maximizing the inhibitory effect of fungal biomasses on both activities, while the use of oil mill wastewater selectively increased the anti-tyrosinase potential of P. citrinopileatus culture filtrate. All strains were found to be preferential lignin degraders, similarly to most white-rot fungi. Bioinformatic analyses were performed on the proteome of the strains P. citrinopileatus and A. biennis, focusing on CAZymes with biotechnological relevance, and the results were compared with the enzyme activities of culture supernatants. Overall, all three strains showed strong production of oxidative enzymes for biomass conversion applications.
Collapse
|
19
|
Wang S, Han J, Xia J, Hu Y, Shi L, Ren A, Zhu J, Zhao M. Overexpression of nicotinamide mononucleotide adenylyltransferase (nmnat) increases the growth rate, Ca 2+ concentration and cellulase production in Ganoderma lucidum. Appl Microbiol Biotechnol 2020; 104:7079-7091. [PMID: 32632475 DOI: 10.1007/s00253-020-10763-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022]
Abstract
Identifying new and economical means to utilize diverse lignocellulosic biomass is an urgent task. Ganoderma lucidum is a well-known edible and medicinal basidiomycete with an excellent ability to degrade a wide range of cellulosic biomass, and its nutrient use efficiency is closely related to the activity of extracellular cellulase. Intracellular nicotinamide adenine dinucleotide (NAD+) biosynthesis is controlled in response to nutritional status, and NAD+ is an essential metabolite involved in diverse cellular processes. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a common enzyme in three NAD+ synthesis pathways. In this study, a homologous gene of nmnat was cloned from G. lucidum and two G. lucidum overexpression strains, OE::nmnat4 and OE::nmnat19, were constructed using an Agrobacterium tumefaciens-mediated transformation method. The G. lucidum nmnat overexpression strains showed obviously increased colony growth on different carbon sources, and intracellular Ca2+ concentrations in the G. lucidum OE::nmnat4 and OE::nmnat19 strains were increased by 2.04- and 2.30-fold, respectively, compared with those in the wild-type (WT) strains. In the G. lucidum OE::nmnat4 and OE::nmnat19 strains, endo-β-glucanase (CMCase) activity increased by approximately 2.8- and 3-fold, while β-glucosidase (pNPGase) activity increased by approximately 1.9- and 2.1-fold, respectively, compared with the activity in the WT strains. Furthermore, overexpression of NAD+ synthesis pathways was found to elicit cellulase production by increasing the intracellular Ca2+ concentration. In summary, this study is the first to demonstrate that increased intracellular NAD+ contents through overexpression of the nmnat gene of NAD+ synthesis pathways may increase cellulase production by increasing intracellular Ca2+ concentrations in G. lucidum. KEY POINTS: • The concentration of NAD+influences cellulase production in G. lucidum. • The concentration of NAD+influences the intracellular Ca2+concentration in G. lucidum. • The concentration of NAD+influences cellulase production by eliciting a change in intracellular Ca2+in G. lucidum.
Collapse
Affiliation(s)
- Shengli Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jing Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jiale Xia
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Yanru Hu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Ang Ren
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China.
| |
Collapse
|
20
|
Ramzi AB, Che Me ML, Ruslan US, Baharum SN, Nor Muhammad NA. Insight into plant cell wall degradation and pathogenesis of Ganoderma boninense via comparative genome analysis. PeerJ 2019; 7:e8065. [PMID: 31879570 PMCID: PMC6927665 DOI: 10.7717/peerj.8065] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 10/20/2019] [Indexed: 12/20/2022] Open
Abstract
Background G. boninense is a hemibiotrophic fungus that infects oil palms (Elaeis guineensis Jacq.) causing basal stem rot (BSR) disease and consequent massive economic losses to the oil palm industry. The pathogenicity of this white-rot fungus has been associated with cell wall degrading enzymes (CWDEs) released during saprophytic and necrotrophic stage of infection of the oil palm host. However, there is a lack of information available on the essentiality of CWDEs in wood-decaying process and pathogenesis of this oil palm pathogen especially at molecular and genome levels. Methods In this study, comparative genome analysis was carried out using the G. boninense NJ3 genome to identify and characterize carbohydrate-active enzyme (CAZymes) including CWDE in the fungal genome. Augustus pipeline was employed for gene identification in G. boninense NJ3 and the produced protein sequences were analyzed via dbCAN pipeline and PhiBase 4.5 database annotation for CAZymes and plant-host interaction (PHI) gene analysis, respectively. Comparison of CAZymes from G. boninense NJ3 was made against G. lucidum, a well-studied model Ganoderma sp. and five selected pathogenic fungi for CAZymes characterization. Functional annotation of PHI genes was carried out using Web Gene Ontology Annotation Plot (WEGO) and was used for selecting candidate PHI genes related to cell wall degradation of G. boninense NJ3. Results G. boninense was enriched with CAZymes and CWDEs in a similar fashion to G. lucidum that corroborate with the lignocellulolytic abilities of both closely-related fungal strains. The role of polysaccharide and cell wall degrading enzymes in the hemibiotrophic mode of infection of G. boninense was investigated by analyzing the fungal CAZymes with necrotrophic Armillaria solidipes, A. mellea, biotrophic Ustilago maydis, Melampsora larici-populina and hemibiotrophic Moniliophthora perniciosa. Profiles of the selected pathogenic fungi demonstrated that necrotizing pathogens including G. boninense NJ3 exhibited an extensive set of CAZymes as compared to the more CAZymes-limited biotrophic pathogens. Following PHI analysis, several candidate genes including polygalacturonase, endo β-1,3-xylanase, β-glucanase and laccase were identified as potential CWDEs that contribute to the plant host interaction and pathogenesis. Discussion This study employed bioinformatics tools for providing a greater understanding of the biological mechanisms underlying the production of CAZymes in G. boninense NJ3. Identification and profiling of the fungal polysaccharide- and lignocellulosic-degrading enzymes would further facilitate in elucidating the infection mechanisms through the production of CWDEs by G. boninense. Identification of CAZymes and CWDE-related PHI genes in G. boninense would serve as the basis for functional studies of genes associated with the fungal virulence and pathogenicity using systems biology and genetic engineering approaches.
Collapse
Affiliation(s)
- Ahmad Bazli Ramzi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Muhammad Lutfi Che Me
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Ummul Syafiqah Ruslan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | | | | |
Collapse
|
21
|
Jasińska A, Soboń A, Góralczyk-Bińkowska A, Długoński J. Analysis of decolorization potential of Myrothecium roridum in the light of its secretome and toxicological studies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:26313-26323. [PMID: 31286376 PMCID: PMC6717178 DOI: 10.1007/s11356-019-05324-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
To identify the enzymes potentially useful for the decolorization of azo dyes, the secretome of the ascomycetous fungus Myrothecium roridum IM6482 was studied by using a bottom-up proteomic approach. Among the identified proteins, the most promising for dye removal was laccase, which decolorized respectively, 66, 91, 79, and 80% of Acid Blue 113 (AB 113), Acid Red 27 (AR 27), Direct Blue 14 (DB 14), and Acid Orange 7 (AO 7). The degradation of dyes was enhanced at the wide range of pH from 4 to 8. The addition of redox mediators allowed eliminating AB 113 in concentrations up to 400 mg/L and decolorization of the simulated textile effluent. Microbial toxicity and phytotoxicity tests indicated that dyes are converted into low-toxicity metabolites. This is the first insight into the M. roridum secretome, its identification and its application for removal of select azo dyes. Obtained results extended knowledge concerning biodegradative potential of ascomycetous, ligninolytic fungi and will contribute to the improvement of dye removal by fungi.
Collapse
Affiliation(s)
- Anna Jasińska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland.
| | - Adrian Soboń
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| | - Aleksandra Góralczyk-Bińkowska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| | - Jerzy Długoński
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237, Lodz, Poland
| |
Collapse
|
22
|
Champreda V, Mhuantong W, Lekakarn H, Bunterngsook B, Kanokratana P, Zhao XQ, Zhang F, Inoue H, Fujii T, Eurwilaichitr L. Designing cellulolytic enzyme systems for biorefinery: From nature to application. J Biosci Bioeng 2019; 128:637-654. [PMID: 31204199 DOI: 10.1016/j.jbiosc.2019.05.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/06/2019] [Accepted: 05/11/2019] [Indexed: 12/14/2022]
Abstract
Cellulolytic enzymes play a key role on conversion of lignocellulosic plant biomass to biofuels and biochemicals in sugar platform biorefineries. In this review, we survey composite carbohydrate-active enzymes (CAZymes) among groups of cellulolytic fungi and bacteria that exist under aerobic and anaerobic conditions. Recent advances in designing effective cellulase mixtures are described, starting from the most complex microbial consortium-based enzyme preparations, to single-origin enzymes derived from intensively studied cellulase producers such as Trichoderma reesei, Talaromyces cellulolyticus, and Penicellium funiculosum, and the simplest minimal enzyme systems comprising selected sets of mono-component enzymes tailor-made for specific lignocellulosic substrates. We provide a comprehensive update on studies in developing high-performance cellulases for biorefineries.
Collapse
Affiliation(s)
- Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand.
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Hataikarn Lekakarn
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Benjarat Bunterngsook
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Inoue
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Tatsuya Fujii
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Hiroshima 739-0046, Japan
| | - Lily Eurwilaichitr
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| |
Collapse
|