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Rajtar NN, Kielsmeier-Cook JC, Held BW, Toapanta-Alban CE, Ordonez ME, Barnes CW, Blanchette RA. Diverse Xylaria in the Ecuadorian Amazon and their mode of wood degradation. BOTANICAL STUDIES 2023; 64:30. [PMID: 37878199 PMCID: PMC10600087 DOI: 10.1186/s40529-023-00403-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Xylaria is a diverse and ecologically important genus in the Ascomycota. This paper describes the xylariaceous fungi present in an Ecuadorian Amazon Rainforest and investigates the decay potential of selected Xylaria species. Fungi were collected at Yasuní National Park, Ecuador during two collection trips to a single hectare plot divided into a 10-m by 10-m grid, providing 121 collection points. All Xylaria fruiting bodies found within a 1.2-m radius of each grid point were collected. Dried fruiting bodies were used for culturing and the internal transcribed spacer region was sequenced to identify Xylaria samples to species level. Agar microcosms were used to assess the decay potential of three selected species, two unknown species referred to as Xylaria 1 and Xylaria 2 and Xylaria curta, on four different types of wood from trees growing in Ecuador including balsa (Ochroma pyramidale), melina (Gmelina arborea), saman (Samanea saman), and moral (Chlorophora tinctoria). ANOVA and post-hoc comparisons were used to test for differences in biomass lost between wood blocks inoculated with Xylaria and uninoculated control blocks. Scanning electron micrographs of transverse sections of each wood and assay fungus were used to assess the type of degradation present. RESULTS 210 Xylaria collections were sequenced, with 106 collections belonging to 60 taxa that were unknown species, all with less than 97% match to NCBI reference sequences. Xylaria with sequence matches of 97% or greater included X. aff. comosa (28 isolates), X. cuneata (9 isolates) X. curta and X. oligotoma (7 isolates), and X. apiculta (6 isolates)., All Xylaria species tested were able to cause type 1 or type 2 soft rot degradation in the four wood types and significant biomass loss was observed compared to the uninoculated controls. Balsa and melina woods had the greatest amount of biomass loss, with as much as 60% and 25% lost, respectively, compared to the controls. CONCLUSIONS Xylaria species were found in extraordinary abundance in the Ecuadorian rainforest studied. Our study demonstrated that the Xylaria species tested can cause a soft rot type of wood decay and with the significant amount of biomass loss that occurred within a short incubation time, it indicates these fungi likely play a significant role in nutrient cycling in the Amazonian rainforest.
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Affiliation(s)
- Nickolas N Rajtar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
| | | | - Benjamin W Held
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Maria E Ordonez
- QCAM Fungarium, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Department of Microbiology and Plant Pathology, University of California, Riverside, 92521, USA
| | - Charles W Barnes
- Forest Health Protection-Region 5, USDA Forest Service, San Bernardino, CA, 92408, USA
| | - Robert A Blanchette
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
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2
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Pan L, Zhang Y, Zhang F, Wang Z, Zheng J. α-L-rhamnosidase: production, properties, and applications. World J Microbiol Biotechnol 2023; 39:191. [PMID: 37160824 DOI: 10.1007/s11274-023-03638-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/30/2023] [Indexed: 05/11/2023]
Abstract
α-L-rhamnosidase [EC 3.2.1.40] belongs to glycoside hydrolase (GH) families (GH13, GH78, and GH106 families) in the carbohydrate-active enzymes (CAZy) database, which specifically hydrolyzes the non-reducing end of α-L-rhamnose. Αccording to the sites of catalytic hydrolysis, α-L-rhamnosidase can be divided into α-1, 2-rhamnosidase, α-1, 3-rhamnosidase, α-1, 4-rhamnosidase and α-1, 6-rhamnosidase. α-L-rhamnosidase is an important enzyme for various biotechnological applications, especially in food, beverage, and pharmaceutical industries. α-L-rhamnosidase has a wide range of sources and is commonly found in animals, plants, and microorganisms, and its microbial source includes a variety of bacteria, molds and yeasts (such as Lactobacillus sp., Aspergillus sp., Pichia angusta and Saccharomyces cerevisiae). In recent years, a series of advances have been achieved in various aspects of α-validates the above-described-rhamnosidase research. A number of α-L-rhamnosidases have been successfully recombinant expressed in prokaryotic systems as well as eukaryotic systems which involve Pichia pastoris, Saccharomyces cerevisiae and Aspergillus niger, and the catalytic properties of the recombinant enzymes have been improved by enzyme modification techniques. In this review, the sources and production methods, general and catalytic properties and biotechnological applications of α-L-rhamnosidase in different fields are summarized and discussed, concluding with the directions for further in-depth research on α-L-rhamnosidase.
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Affiliation(s)
- Lixia Pan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Yueting Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Fei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, People's Republic of China.
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Yu B, Luo S, Ding Y, Gong Z, Nie T. Insights into glycosidic bond specificity of an engineered selective α-L-rhamnosidase N12-Rha via activity assays and molecular modelling. AMB Express 2022; 12:143. [DOI: 10.1186/s13568-022-01489-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractαL-rhamnosidase (EC 3.2.1.40) has been widely used in food processing and pharmaceutical preparation. The recombinant α-L-rhamnosidase N12-Rha from Aspergillus niger JMU-TS528 had significantly higher catalytic activity on α-1,6 glycosidic bond than α-1,2 glycosidic bond, and had no activity on α-1,3 glycosidic bond. The activities of hydrolyzed hesperidin and naringin were 7240 U/mL and 945 U/mL, respectively, which are 10.63 times that of native α-L-rhamnosidase. The activity could maintain more than 80% at pH 3–6 and 40–60℃. Quantum chemistry calculations showed that charge difference of the C-O atoms of the α-1,2, α-1,3 and α-1,6 bonds indicated that α-1,6 bond is most easily broken and α-1,3 bond is the most stable. Molecular dynamics simulations revealed that the key residue Trp359 that may affect substrate specificity and the main catalytic sites of N12-Rha are located in the (α/α)6-barrel domain.
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Knauer JF, Liers C, Hahn S, Wuestenhagen DA, Zemella A, Kellner H, Haueis L, Hofrichter M, Kubick S. Cell-free production of the bifunctional glycoside hydrolase GH78 from Xylaria polymorpha. Enzyme Microb Technol 2022; 161:110110. [PMID: 35939898 DOI: 10.1016/j.enzmictec.2022.110110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/28/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022]
Abstract
The ability to catalyze diverse reactions with relevance for chemical and pharmaceutical research and industry has led to an increasing interest in fungal enzymes. There is still an enormous potential considering the sheer amount of new enzymes from the huge diversity of fungi. Most of these fungal enzymes have not been characterized yet due to the lack of high throughput synthesis and analysis methods. This bottleneck could be overcome by means of cell-free protein synthesis. In this study, cell-free protein synthesis based on eukaryotic cell lysates was utilized to produce a functional glycoside hydrolase (GH78) from the soft-rot fungus Xylaria polymorpha (Ascomycota). The enzyme was successfully synthesized under different reaction conditions. We characterized its enzymatic activities and immobilized the protein via FLAG-Tag interaction. Alteration of several conditions including reaction temperature, template design and lysate supplementation had an influence on the activity of cell-free synthesized GH78. Consequently this led to a production of purified GH78 with a specific activity of 15.4 U mg- 1. The results of this study may be foundational for future high throughput fungal enzyme screenings, including substrate spectra analysis and mutant screenings.
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Affiliation(s)
- Jan Felix Knauer
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Takustr. 6, 14195 Berlin, Germany
| | - Christiane Liers
- Technische Universität Dresden, Internationales Hochschulinstitut Zittau, Markt 23, 02763 Zittau
| | - Stephanie Hahn
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; Berliner Hochschule für Technik, Luxemburger Str. 10, 13353 Berlin, Germany
| | - Doreen A Wuestenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Harald Kellner
- Technische Universität Dresden, Internationales Hochschulinstitut Zittau, Markt 23, 02763 Zittau
| | - Lisa Haueis
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany
| | - Martin Hofrichter
- Technische Universität Dresden, Internationales Hochschulinstitut Zittau, Markt 23, 02763 Zittau
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476 Potsdam, Germany; Freie Universität Berlin, Institute of Chemistry and Biochemistry - Biochemistry, Takustr. 6, 14195 Berlin, Germany; Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes. Appl Microbiol Biotechnol 2022; 106:2993-3007. [PMID: 35435459 PMCID: PMC9064869 DOI: 10.1007/s00253-022-11923-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 01/13/2023]
Abstract
Abstract Fungal dye-decolorizing peroxidases (DyPs) have found applications in the treatment of dye-contaminated industrial wastes or to improve biomass digestibility. Their roles in fungal biology are uncertain, although it has been repeatedly suggested that they could participate in lignin degradation and/or modification. Using a comprehensive set of 162 fully sequenced fungal species, we defined seven distinct fungal DyP clades on basis of a sequence similarity network. Sequences from one of these clades clearly diverged from all others, having on average the lower isoelectric points and hydropathy indices, the highest number of N-glycosylation sites, and N-terminal sequence peptides for secretion. Putative proteins from this clade are absent from brown-rot and ectomycorrhizal species that have lost the capability of degrading lignin enzymatically. They are almost exclusively present in white-rot and other saprotrophic Basidiomycota that digest lignin enzymatically, thus lending support for a specific role of DyPs from this clade in biochemical lignin modification. Additional nearly full-length fungal DyP genes were isolated from the environment by sequence capture by hybridization; they all belonged to the clade of the presumably secreted DyPs and to another related clade. We suggest focusing our attention on the presumably intracellular DyPs from the other clades, which have not been characterized thus far and could represent enzyme proteins with novel catalytic properties. Key points • A fungal DyP phylogeny delineates seven main sequence clades. • Putative extracellular DyPs form a single clade of Basidiomycota sequences. • Extracellular DyPs are associated to white-rot fungi. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11923-0.
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Degradation activity of fungal communities on avocado peel (Persea americana Mill.) in a solid-state process: mycobiota successions and trophic guild shifts. Arch Microbiol 2021; 204:2. [PMID: 34870719 DOI: 10.1007/s00203-021-02600-3] [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: 07/15/2020] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 10/19/2022]
Abstract
To explore the capability of soil mycobiota to degrade avocado peel waste and identify relevant successions and trophic guild shifts, fungal communities from three environments with different land uses were evaluated in a solid-state process. Soil samples used as inoculum were collected from a pristine mature tropical forest, a traditionally managed Mayan land, and an intensively managed monospecific avocado plantation. Soil-substrate mixes were evaluated for 52 weeks to evaluate organic matter decay and the carbon-to-nitrogen ratio. Amplicon-based high-throughput sequencing from internally transcribed spacer (ITS) analysis revealed significant differences in fungal communities widely dominated by Fusarium sp. and Clonostachys sp.; however, less represented taxa showed relevant shifts concomitantly with organic matter content drops. Trophic guild assignment revealed different behaviors in fungal communities between treatments over the 52 weeks, suggesting distinct preconditioning of fungal communities in these environments. Overall, the results lead to the identification of promising degradation moments and inoculum sources for further consortia enrichment or bioprospecting efforts.
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Liers C, Ullrich R, Kellner H, Chi DH, Quynh DT, Luyen ND, Huong LM, Hofrichter M, Nghi DH. Bioconversion of Lignocellulosic Materials with the Contribution of a Multifunctional GH78 Glycoside Hydrolase from Xylaria polymorpha to Release Aromatic Fragments and Carbohydrates. J Microbiol Biotechnol 2021; 31:1438-1445. [PMID: 34409952 PMCID: PMC9705965 DOI: 10.4014/jmb.2106.06053] [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: 06/18/2021] [Revised: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
A bifunctional glycoside hydrolase GH78 from the ascomycete Xylaria polymorpha (XpoGH78) possesses catalytic versatility towards both glycosides and esters, which may be advantageous for the efficient degradation of the plant cell-wall complex that contains both diverse sugar residues and esterified structures. The contribution of XpoGH78 to the conversion of lignocellulosic materials without any chemical pretreatment to release the water-soluble aromatic fragments, carbohydrates, and methanol was studied. The disintegrating effect of enzymatic lignocellulose treatment can be significantly improved by using different kinds of hydrolases and phenoloxidases. The considerable changes in low (3 kDa), medium (30 kDa), and high (> 200 kDa) aromatic fragments were observed after the treatment with XpoGH78 alone or with this potent cocktail. Synergistic conversion of rape straw also resulted in a release of 17.3 mg of total carbohydrates (e.g., arabinose, galactose, glucose, mannose, xylose) per gram of substrate after incubating for 72 h. Moreover, the treatment of rape straw with XpoGH78 led to a marginal methanol release of approximately 17 μg/g and improved to 270 μg/g by cooperation with the above accessory enzymes. In the case of beech wood conversion, the combined catalysis by XpoGH78 and laccase caused an effect comparable with that of fungal strain X. polymorpha in woody cultures concerning the liberation of aromatic lignocellulose fragments.
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Affiliation(s)
- Christiane Liers
- International Graduate School of Zittau (IHI Zittau), Dresden University of Technology, D-03583 Zittau, Germany
| | - René Ullrich
- International Graduate School of Zittau (IHI Zittau), Dresden University of Technology, D-03583 Zittau, Germany
| | - Harald Kellner
- International Graduate School of Zittau (IHI Zittau), Dresden University of Technology, D-03583 Zittau, Germany
| | - Do Huu Chi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Dang Thu Quynh
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Nguyen Dinh Luyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Le Mai Huong
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Martin Hofrichter
- International Graduate School of Zittau (IHI Zittau), Dresden University of Technology, D-03583 Zittau, Germany
| | - Do Huu Nghi
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam,Corresponding author Phone: +84 (0)916670188 Fax: +84 (043) 7564 390 E-mail:
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Mushroom Nutrition as Preventative Healthcare in Sub-Saharan Africa. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11094221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The defining characteristics of the traditional Sub-Saharan Africa (SSA) cuisine have been the richness in indigenous foods and ingredients, herbs and spices, fermented foods and beverages, and healthy and whole ingredients used. It is crucial to safeguard the recognized benefits of mainstream traditional foods and ingredients, which gradually eroded in the last decades. Notwithstanding poverty, chronic hunger, malnutrition, and undernourishment in the region, traditional eating habits have been related to positive health outcomes and sustainability. The research prevailed dealing with food availability and access rather than the health, nutrition, and diet quality dimensions of food security based on what people consume per country and on the missing data related to nutrient composition of indigenous foods. As countries become more economically developed, they shift to “modern” occidental foods rich in saturated fats, salt, sugar, fizzy beverages, and sweeteners. As a result, there are increased incidences of previously unreported ailments due to an unbalanced diet. Protein-rich foods in dietary guidelines enhance only those of animal or plant sources, while rich protein sources such as mushrooms have been absent in these charts, even in developed countries. This article considers the valorization of traditional African foodstuffs and ingredients, enhancing the importance of establishing food-based dietary guidelines per country. The crux of this review highlights the potential of mushrooms, namely some underutilized in the SSA, which is the continent’s little exploited gold mine as one of the greatest untapped resources for feeding and providing income for Africa’s growing population, which could play a role in shielding Sub-Saharan Africans against the side effects of an unhealthy stylish diet.
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Bioactive Attributes of Xylaria Species from the Scrub Jungles of Southwest India. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wang Y, Huang Q, Liu C, Ding Y, Liu L, Tian Y, Wu X, Li H, Awasthi MK, Zhao Z. Mulching practices alter soil microbial functional diversity and benefit to soil quality in orchards on the Loess Plateau. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110985. [PMID: 32579532 DOI: 10.1016/j.jenvman.2020.110985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/26/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
To improve our understanding about the responses of microbial functional diversity to different mulching practices, this study used a metagenomic approach to reveal soil microbial functional specificity under four tillage regimes: conventional tillage (CT), organic mulch practices with ryegrass (Lolium perenne L.) intercropping cover (RE) and cornstalk mulch (CS), and inorganic mulching with black ground fabric (BF) in a 7-year field experiment in an apple orchard of the Loess Plateau in China. Enzyme activity and soil physicochemical properties were measured. A redundancy analysis showed that the RE and CS treatments had positive effects on soil nutrient and enzyme activity compared to that of the BF and CT treatments. The CS and RE treatments increased β-glucosidase, cellobiohydrolase, and β-xylosidase activities. In addition, the CS treatment significantly enhanced the β-N-acetylglucosaminidase and urease activities compared to that under CT treatment. However, the activity of these enzyme was reduced in the BF treatment compared with that of the CT treatment. The results also indicated that the enzymes activities were not completely consistent with the changing trends of the genes encoding these enzymes. In addition, the RE and CS treatments also increased the abundance of genes encoding carbohydrate enzymes. It is interesting that the RE and CS treatments had more pathway genes associated with the carbon cycle, nitrogen cycle, and amino acid metabolism compared with the BF treatment. Remarkably, RE and CS treatments effectively increased the abundance of carbon fixation gene cbbL compared to CT treatment. In summary, organic mulching practices increased the soil microbiological functional diversity related to the carbon and nitrogen cycle, while inorganic mulching practice reduced them. This study enhanced our understanding of how mulching practices may alter soil microbial functional diversity and benefit soil quality.
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Affiliation(s)
- Yuanji Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qianqian Huang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chen Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuanyuan Ding
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Liu
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuli Tian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoping Wu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Huike Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Zhengyang Zhao
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Gu X, Ding J, Liu W, Yang X, Yao L, Gao X, Zhang M, Yang S, Wen J. Comparative genomics and association analysis identifies virulence genes of Cercospora sojina in soybean. BMC Genomics 2020; 21:172. [PMID: 32075575 PMCID: PMC7032006 DOI: 10.1186/s12864-020-6581-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/13/2020] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Recently, a new strain of Cercospora sojina (Race15) has been identified, which has caused the breakdown of resistance in most soybean cultivars in China. Despite this serious yield reduction, little is known about why this strain is more virulent than others. Therefore, we sequenced the Race15 genome and compared it to the Race1 genome sequence, as its virulence is significantly lower. We then re-sequenced 30 isolates of C. sojina from different regions to identifying differential virulence genes using genome-wide association analysis (GWAS). RESULTS The 40.12-Mb Race15 genome encodes 12,607 predicated genes and contains large numbers of gene clusters that have annotations in 11 different common databases. Comparative genomics revealed that although these two genomes had a large number of homologous genes, their genome structures have evolved to introduce 245 specific genes. The most important 5 candidate virulence genes were located on Contig 3 and Contig 1 and were mainly related to the regulation of metabolic mechanisms and the biosynthesis of bioactive metabolites, thereby putatively affecting fungi self-toxicity and reducing host resistance. Our study provides insight into the genomic basis of C. sojina pathogenicity and its infection mechanism, enabling future studies of this disease. CONCLUSIONS Via GWAS, we identified five candidate genes using three different methods, and these candidate genes are speculated to be related to metabolic mechanisms and the biosynthesis of bioactive metabolites. Meanwhile, Race15 specific genes may be linked with high virulence. The genes highly prevalent in virulent isolates should also be proposed as candidates, even though they were not found in our SNP analysis. Future work should focus on using a larger sample size to confirm and refine candidate gene identifications and should study the functional roles of these candidates, in order to investigate their potential roles in C. sojina pathogenicity.
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Affiliation(s)
- Xin Gu
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xiaohe Yang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jingzhi Wen
- Department of Plant Protection, College of Agriculture, Northeast Agricultural University, Harbin, China.
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Extracellular Fungal Peroxidases and Laccases for Waste Treatment: Recent Improvement. RECENT ADVANCEMENT IN WHITE BIOTECHNOLOGY THROUGH FUNGI 2019. [DOI: 10.1007/978-3-030-25506-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Pachl P, Škerlová J, Šimčíková D, Kotik M, Křenková A, Mader P, Brynda J, Kapešová J, Křen V, Otwinowski Z, Řezáčová P. Crystal structure of native α-L-rhamnosidase from Aspergillus terreus. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1078-1084. [DOI: 10.1107/s2059798318013049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/10/2022]
Abstract
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.
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Reina R, García-Sánchez M, Liers C, García-Romera I, Aranda E. An Overview of Fungal Applications in the Valorization of Lignocellulosic Agricultural By-Products: The Case of Two-Phase Olive Mill Wastes. Fungal Biol 2018. [DOI: 10.1007/978-3-319-77386-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Chi DH, Giap VD, Anh LPH, Nghi DH. Feruloyl esterase from Alternaria tenuissima that hydrolyses lignocellulosic material to release hydroxycinnamic acids. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817060047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Beisl S, Friedl A, Miltner A. Lignin from Micro- to Nanosize: Applications. Int J Mol Sci 2017; 18:E2367. [PMID: 29117142 PMCID: PMC5713336 DOI: 10.3390/ijms18112367] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 01/08/2023] Open
Abstract
Micro- and nanosize lignin has recently gained interest due to improved properties compared to standard lignin available today. As the second most abundant biopolymer after cellulose, lignin is readily available but used for rather low-value applications. This review focuses on the application of micro- and nanostructured lignin in final products or processes that all show potential for high added value. The fields of application are ranging from improvement of mechanical properties of polymer nanocomposites, bactericidal and antioxidant properties and impregnations to hollow lignin drug carriers for hydrophobic and hydrophilic substances. Also, a carbonization of lignin nanostructures can lead to high-value applications such as use in supercapacitors for energy storage. The properties of the final product depend on the surface properties of the nanomaterial and, therefore, on factors like the lignin source, extraction method, and production/precipitation methods, as discussed in this review.
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Affiliation(s)
- Stefan Beisl
- Institute of Chemical, Environmental and Biological Engineering, TU Wien, 1060 Vienna, Austria.
| | - Anton Friedl
- Institute of Chemical, Environmental and Biological Engineering, TU Wien, 1060 Vienna, Austria.
| | - Angela Miltner
- Institute of Chemical, Environmental and Biological Engineering, TU Wien, 1060 Vienna, Austria.
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Draft Genome Sequence of the Wood-Degrading Ascomycete Kretzschmaria deusta DSM 104547. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01076-17. [PMID: 29074647 PMCID: PMC5658485 DOI: 10.1128/genomea.01076-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genome of Kretzschmaria (Ustulina) deusta, an ascomycetous fungus that colonizes and substantially degrades hardwood and can infest living broad-leaved trees. The genome was assembled into 858 contigs, with a total size of 46.5 Mb, and 11,074 protein-coding genes were predicted.
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Ishikawa M, Shiono Y, Koseki T. Biochemical characterization of Aspergillus oryzae recombinant α-l-rhamnosidase expressed in Pichia pastoris. J Biosci Bioeng 2017; 124:630-634. [PMID: 28800907 DOI: 10.1016/j.jbiosc.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 11/30/2022]
Abstract
An α-l-rhamnosidase-encoding gene from Aspergillus oryzae, which belongs to the glycoside hydrolase family 78, was cloned and expressed in Pichia pastoris. SDS-PAGE of the purified recombinant α-l-rhamnosidase protein revealed smeared bands with apparent molecular mass of 90-130 kDa. After N-deglycosylation, the recombinant enzyme showed a molecular mass of 70 kDa. The enzyme exhibited optimal activity at a pH of 5.0 and a temperature of 70 °C. Specific activity of the enzyme was higher toward hesperidin than toward naringin, which consist of α-1,6 and α-1,2 linkages, respectively. The activity was also higher toward hesperidin than toward rutin, which consist of 7-O- and 3-O-glycosyl linkages of flavonoids, respectively. Kinetic analysis of the enzyme showed that the Michaelis constant (Km) was lowest toward rutin, moderate toward naringin, and higher toward p-nitrophenyl-α-l-rhamnopyranoside and hesperidin. Its high catalytic efficiency (kcat/Km) toward rutin was results of its low Km value while its high catalytic efficiency toward hesperidin was results of a considerably high kcat value.
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Affiliation(s)
- Mai Ishikawa
- Department of Food and Applied Life Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka 997-8555, Japan
| | - Yoshihito Shiono
- Department of Food and Applied Life Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka 997-8555, Japan
| | - Takuya Koseki
- Department of Food and Applied Life Sciences, Faculty of Agriculture, Yamagata University, 1-23 Wakaba-machi, Tsuruoka 997-8555, Japan.
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Long L, Ding D, Han Z, Zhao H, Lin Q, Ding S. Thermotolerant hemicellulolytic and cellulolytic enzymes from Eupenicillium parvum 4-14 display high efficiency upon release of ferulic acid from wheat bran. J Appl Microbiol 2017; 121:422-34. [PMID: 27171788 DOI: 10.1111/jam.13177] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/13/2016] [Accepted: 05/05/2016] [Indexed: 11/28/2022]
Abstract
AIMS To characterize the hemicellulolytic and cellulolytic enzymes from novel fungi, and evaluate the potential of novel enzyme system in releasing ferulic acid (FA) from biomass resource. METHODS AND RESULTS A hemicellulolytic and cellulolytic enzyme-producing fungus 4-14 was isolated from soil by Congo red staining method, and identified as Eupenicillium parvum based on the morphologic and molecular phylogenetic analysis. The optimum temperature of fungal growth was 37°C. Hemicellulolytic and cellulolytic enzymes were produced by this fungus in solid-state fermentation (SSF), and their maximum activities were 554, 385, 218, 2·62 and 5·25 U g(-1) for CMCase, xylanase, β-glucosidase, FPase and FAE respectively. These enzymes displayed the best catalytic ability at low pH values (pH 4·5-5·0). The optimum temperatures were 70°C, 70°C, 75°C and 55°C for CMCase, β-glucosidase, xylanase and FAE respectively. CMCase, xylanase and FAE were stable at different pHs or high temperature (60°C). Enzymatic hydrolysis experiment indicated that the maximum (76·8 ± 4)% of total alkali-extractable FA was released from de-starched wheat bran by the fungal enzyme system. CONCLUSIONS High activities of thermotolerant CMCase, β-glucosidase, xylanase and FAE were produced by the newly isolated fungus E. parvum 4-14 in SSF. The fungal enzyme system displayed high efficiency at releasing FA from wheat bran. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides a new fungal strain for researches of novel hemicellulolytic and cellulolytic enzymes and will improve the bioconversion and utilization of agricultural by-products.
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Affiliation(s)
- L Long
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - D Ding
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Z Han
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - H Zhao
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Q Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing, China
| | - S Ding
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
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20
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Purahong W, Wubet T, Lentendu G, Schloter M, Pecyna MJ, Kapturska D, Hofrichter M, Krüger D, Buscot F. Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition. Mol Ecol 2016; 25:4059-74. [DOI: 10.1111/mec.13739] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 06/08/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023]
Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
| | - Tesfaye Wubet
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e D-04103 Leipzig Germany
| | - Guillaume Lentendu
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
| | - Michael Schloter
- Helmholtz Zentrum München; Research Unit for Environmental Genomics; Ingolstädter Landstr. 1 D-85758 Oberschleissheim Germany
| | - Marek J. Pecyna
- Technische Universität Dresden; International Institute (IHI) Zittau; Markt 23 D-02763 Zittau Germany
| | - Danuta Kapturska
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
- Technische Universität Dresden; International Institute (IHI) Zittau; Markt 23 D-02763 Zittau Germany
| | - Martin Hofrichter
- Technische Universität Dresden; International Institute (IHI) Zittau; Markt 23 D-02763 Zittau Germany
| | - Dirk Krüger
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
| | - François Buscot
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e D-04103 Leipzig Germany
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21
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Purahong W, Krüger D, Buscot F, Wubet T. Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2016.04.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Dilokpimol A, Mäkelä MR, Aguilar-Pontes MV, Benoit-Gelber I, Hildén KS, de Vries RP. Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:231. [PMID: 27795736 PMCID: PMC5084320 DOI: 10.1186/s13068-016-0651-6] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
Feruloyl esterases (FAEs) represent a diverse group of carboxyl esterases that specifically catalyze the hydrolysis of ester bonds between ferulic (hydroxycinnamic) acid and plant cell wall polysaccharides. Therefore, FAEs act as accessory enzymes to assist xylanolytic and pectinolytic enzymes in gaining access to their site of action during biomass conversion. Their ability to release ferulic acid and other hydroxycinnamic acids from plant biomass makes FAEs potential biocatalysts in a wide variety of applications such as in biofuel, food and feed, pulp and paper, cosmetics, and pharmaceutical industries. This review provides an updated overview of the knowledge on fungal FAEs, in particular describing their role in plant biomass degradation, diversity of their biochemical properties and substrate specificities, their regulation and conditions needed for their induction. Furthermore, the discovery of new FAEs using genome mining and phylogenetic analysis of current publicly accessible fungal genomes will also be presented. This has led to a new subfamily classification of fungal FAEs that takes into account both phylogeny and substrate specificity.
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Affiliation(s)
- Adiphol Dilokpimol
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Miia R. Mäkelä
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Isabelle Benoit-Gelber
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Kristiina S. Hildén
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Ronald P. de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
- Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
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Gopalan N, Rodríguez-Duran LV, Saucedo-Castaneda G, Nampoothiri KM. Review on technological and scientific aspects of feruloyl esterases: A versatile enzyme for biorefining of biomass. BIORESOURCE TECHNOLOGY 2015; 193:534-44. [PMID: 26159377 DOI: 10.1016/j.biortech.2015.06.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 05/11/2023]
Abstract
With increasing focus on sustainable energy, bio-refining from lignocellulosic biomass has become a thrust area of research. With most of the works being focused on biofuels, significant efforts are also being directed towards other value added products. Feruloyl esterases (EC. 3.1.1.73) can be used as a tool for bio-refining of lignocellulosic material for the recovery and purification of ferulic acid and related hydroxycinnamic acids ubiquitously found in the plant cell wall. More and more genes coding for feruloyl esterases have been mined out from various sources to allow efficient enzymatic release of ferulic acid and allied hydroxycinnamic acids (HCAs) from plant-based biomass. A sum up on enzymatic extraction of HCAs and its recovery from less explored agro residual by-products is still a missing link and this review brushes up the achieved landmarks so far in this direction and also covers a detailed patent search on this biomass refining enzyme.
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Affiliation(s)
- Nishant Gopalan
- Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, New Delhi, India
| | - L V Rodríguez-Duran
- Metropolitan Autonomous University Campus Iztapalapa, Biotechnology Department, Mexico City, Iztapalapa Z.C. 09340, Mexico
| | - G Saucedo-Castaneda
- Metropolitan Autonomous University Campus Iztapalapa, Biotechnology Department, Mexico City, Iztapalapa Z.C. 09340, Mexico
| | - K Madhavan Nampoothiri
- Biotechnology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, New Delhi, India.
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The ascomycete Xylaria polymorpha produces an acetyl esterase that solubilises beech wood material to release water-soluble lignin fragments. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0061-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. mBio 2014; 5:e01464-14. [PMID: 25028429 PMCID: PMC4161256 DOI: 10.1128/mbio.01464-14] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The emergence of distinct populations of Cryptococcus gattii in the temperate North American Pacific Northwest (PNW) was surprising, as this species was previously thought to be confined to tropical and semitropical regions. Beyond a new habitat niche, the dominant emergent population displayed increased virulence and caused primary pulmonary disease, as opposed to the predominantly neurologic disease seen previously elsewhere. Whole-genome sequencing was performed on 118 C. gattii isolates, including the PNW subtypes and the global diversity of molecular type VGII, to better ascertain the natural source and genomic adaptations leading to the emergence of infection in the PNW. Overall, the VGII population was highly diverse, demonstrating large numbers of mutational and recombinational events; however, the three dominant subtypes from the PNW were of low diversity and were completely clonal. Although strains of VGII were found on at least five continents, all genetic subpopulations were represented or were most closely related to strains from South America. The phylogenetic data are consistent with multiple dispersal events from South America to North America and elsewhere. Numerous gene content differences were identified between the emergent clones and other VGII lineages, including genes potentially related to habitat adaptation, virulence, and pathology. Evidence was also found for possible gene introgression from Cryptococcus neoformans var. grubii that is rarely seen in global C. gattii but that was present in all PNW populations. These findings provide greater understanding of C. gattii evolution in North America and support extensive evolution in, and dispersal from, South America. Cryptococcus gattii emerged in the temperate North American Pacific Northwest (PNW) in the late 1990s. Beyond a new environmental niche, these emergent populations displayed increased virulence and resulted in a different pattern of clinical disease. In particular, severe pulmonary infections predominated in contrast to presentation with neurologic disease as seen previously elsewhere. We employed population-level whole-genome sequencing and analysis to explore the genetic relationships and gene content of the PNW C. gattii populations. We provide evidence that the PNW strains originated from South America and identified numerous genes potentially related to habitat adaptation, virulence expression, and clinical presentation. Characterization of these genetic features may lead to improved diagnostics and therapies for such fungal infections. The data indicate that there were multiple recent introductions of C. gattii into the PNW. Public health vigilance is warranted for emergence in regions where C. gattii is not thought to be endemic.
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Fungal laccases and their applications in bioremediation. Enzyme Res 2014; 2014:163242. [PMID: 24959348 PMCID: PMC4052089 DOI: 10.1155/2014/163242] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/22/2014] [Indexed: 12/25/2022] Open
Abstract
Laccases are blue multicopper oxidases, which catalyze the monoelectronic oxidation of a broad spectrum of substrates, for example, ortho- and para-diphenols, polyphenols, aminophenols, and aromatic or aliphatic amines, coupled with a full, four-electron reduction of O2 to H2O. Hence, they are capable of degrading lignin and are present abundantly in many white-rot fungi. Laccases decolorize and detoxify the industrial effluents and help in wastewater treatment. They act on both phenolic and nonphenolic lignin-related compounds as well as highly recalcitrant environmental pollutants, and they can be effectively used in paper and pulp industries, textile industries, xenobiotic degradation, and bioremediation and act as biosensors. Recently, laccase has been applied to nanobiotechnology, which is an increasing research field, and catalyzes electron transfer reactions without additional cofactors. Several techniques have been developed for the immobilization of biomolecule such as micropatterning, self-assembled monolayer, and layer-by-layer techniques, which immobilize laccase and preserve their enzymatic activity. In this review, we describe the fungal source of laccases and their application in environment protection.
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Abstract
“Trees in miniemulsion” – the biopolymer lignin was used to generate biodegradable nanocontainers via an interfacial polyaddition reaction.
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Affiliation(s)
| | - Grit Baier
- Max-Planck-Institut für Polymerforschung
- 55128 Mainz, Germany
| | - Eckhard Thines
- IBWF e.V
- Institute of Biotechnology and Drug Research
- 67663 Kaiserslautern, Germany
- Institute of Biotechnology
- Johannes Gutenberg-University
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Arfi Y, Chevret D, Henrissat B, Berrin JG, Levasseur A, Record E. Characterization of salt-adapted secreted lignocellulolytic enzymes from the mangrove fungus Pestalotiopsis sp. Nat Commun 2013; 4:1810. [PMID: 23651998 DOI: 10.1038/ncomms2850] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 04/08/2013] [Indexed: 11/09/2022] Open
Abstract
Fungi are important for biomass degradation processes in mangrove forests. Given the presence of sea water in these ecosystems, mangrove fungi are adapted to high salinity. Here we isolate Pestalotiopsis sp. NCi6, a halotolerant and lignocellulolytic mangrove fungus of the order Xylariales. We study its lignocellulolytic enzymes and analyse the effects of salinity on its secretomes. De novo transcriptome sequencing and assembly indicate that this fungus possesses of over 400 putative lignocellulolytic enzymes, including a large fraction involved in lignin degradation. Proteomic analyses of the secretomes suggest that the presence of salt modifies lignocellulolytic enzyme composition, with an increase in the secretion of xylanases and cellulases and a decrease in the production of oxidases. As a result, cellulose and hemicellulose hydrolysis is enhanced but lignin breakdown is reduced. This study highlights the adaptation to salt of mangrove fungi and their potential for biotechnological applications.
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Affiliation(s)
- Yonathan Arfi
- INRA, UMR1163-Biotechnologie des Champignons Filamenteux, ESIL-Polytech, Aix-Marseille University, 13288 Marseille, France.
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