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Waheed A, Chen Y, Rizwan HM, Adnan M, Ma X, Liu G. Genomic characterization and expression profiling of the lytic polysaccharide monooxygenases AA9 family in thermophilic fungi Thermothelomyces fergusii in response to carbon source media. Int J Biol Macromol 2024; 265:130740. [PMID: 38462117 DOI: 10.1016/j.ijbiomac.2024.130740] [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: 12/04/2023] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Enhancing enzyme activity and stability in biomass degradation can improve substrate saccharification and, increases biorefinery efficiency. For the first time, we identified 20 lytic polysaccharide monooxygenases (LPMOs) AA9 genes in the genome of Thermothelomyces fergusii. Our results showed that TfAA9 was categorized into LPMOs1, LPMOs2, and LPMOs3 subgroups based on protein diversity. Protein- 3D structure analysis showed strong interactions between Myceliophthora thermophila AA9 proteins and 17 TfAA9 proteins. Gene ontology analysis indicated a high enrichment of cellulase activity in TfAA9 genes. KEGG pathways analysis revealed the role of TfAA9 proteins in the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose. Numerous TfAA9s gene transcripts were up-regulated on avicel, cellobiose, and glucose, with a higher proportion on avicel. Protein concentration, endoglucanase, and cellulase activity were also boosted on avicel. However, limited fungal biomass was observed on avicel, despite the abundance of AA9 LPMOs in the T. fergusii genome. These findings expand our understanding of fungal AA9 genes and their role in lignocellulolytic degradation. The disparity between biomass and enzymatic activity suggests screening TfAA9 genes for highly active enzymes and redundant genes via heterologous expression. In short, functional characterization of these genes could contribute to improving the saccharification process of industrial raw materials.
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Affiliation(s)
- Abdul Waheed
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Yi Chen
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hafiz Muhammad Rizwan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen 518060, China; Shenzhen Key Laboratory of Food Nutrition and Health, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Muhammad Adnan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xuekun Ma
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Gang Liu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
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Ferrario E, Kallio JP, Strømland Ø, Ziegler M. Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase. Biochemistry 2023; 62:3293-3302. [PMID: 37934975 PMCID: PMC10666276 DOI: 10.1021/acs.biochem.3c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential molecule in all kingdoms of life, mediating energy metabolism and cellular signaling. Recently, a new class of highly active fungal surface NADases was discovered. The enzyme from the opportunistic human pathogen Aspergillus fumigatus was thoroughly characterized. It harbors a catalytic domain that resembles that of the tuberculosis necrotizing toxin from Mycobacterium tuberculosis, which efficiently cleaves NAD+ to nicotinamide and ADP-ribose, thereby depleting the dinucleotide pool. Of note, the A. fumigatus NADase has an additional Ca2+-binding motif at the C-terminus of the protein. Despite the presence of NADases in several fungal divisions, the Ca2+-binding motif is uniquely found in the Eurotiales order, which contains species that have immense health and economic impacts on humans. To identify the potential roles of the metal ion-binding site in catalysis or protein stability, we generated and characterized A. fumigatus NADase variants lacking the ability to bind calcium. X-ray crystallographic analyses revealed that the mutation causes a drastic and dynamic structural rearrangement of the homodimer, resulting in decreased thermal stability. Even though the calcium-binding site is at a long distance from the catalytic center, the structural reorganization upon the loss of calcium binding allosterically alters the active site, thereby negatively affecting NAD-glycohydrolase activity. Together, these findings reveal that this unique calcium-binding site affects the protein fold, stabilizing the dimeric structure, but also mediates long-range effects resulting in an increased catalytic rate.
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Affiliation(s)
- Eugenio Ferrario
- Department
of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Juha P. Kallio
- Department
of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Øyvind Strømland
- Department
of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
| | - Mathias Ziegler
- Department
of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen 5009, Norway
- Leibniz
Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbargstraße 11A, Jena 07745, Germany
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Dadwal A, Singh V, Sharma S, Sahoo AK, Satyanarayana T. Structural and thermostability insights into cellobiohydrolase of a thermophilic mould Myceliophthora thermophila: in-silico studies. J Biomol Struct Dyn 2023; 41:8373-8382. [PMID: 36238990 DOI: 10.1080/07391102.2022.2133012] [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: 08/08/2022] [Accepted: 10/02/2022] [Indexed: 10/17/2022]
Abstract
Cellobiohydrolase (CBH) is one of the cellulases with a wide range of industrial applications; it plays a pivotal role in cellulose hydrolysis and thus in biofuel production. The structural and thermostability analysis of a CBHII of the thermophilic mold Myceliophthora thermophila (MtCel6A) had been carried out using various in-silico approaches. The validation of 3 D model by the Ramachandran plot indicated 88.5% amino acid residues in the favoured regions. Docking analysis suggested MtCel6A to display a high affinity towards cellotetraose as compared to other substrates. The enzyme exhibited a high tolerance to the end product, cellobiose. The thermostability evaluation by molecular dynamic simulations and principal component analysis confirmed its tolerance to elevated temperatures. The identified thermolabile regions could be targeted for site-directed mutagenesis in order to ameliorate thermostability further. Our experimental data published earlier confirmed the present findings of in-silico studies. The structural and functional characteristics of MtCel6A highlighted its critical features that make it a useful biocatalyst in several industrial processes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Department of Applied Sciences and Humanities (Faculty of Technology), University of Delhi, Delhi, India
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Department of Applied Sciences and Humanities (Faculty of Technology), University of Delhi, Delhi, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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Correa CZ, de Tavares Machado Bolonhesi IB, Lopes DD, Prates KVMC, Panagio LA, Ratuchne A, Damianovic MHRZ. Removal of organic matter and nitrogen from dairy effluents in a structured bed reactor operated with intermittent aeration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:91060-91073. [PMID: 37464210 DOI: 10.1007/s11356-023-28581-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 06/29/2023] [Indexed: 07/20/2023]
Abstract
The objective of this research was to evaluate the performance of a structured bed reactor (SBRIA), carried out with intermittent aeration (IA), in the removal of organic matter and nitrogen from dairy effluent, when run with different organic loading rates (OLR). The SBRIA was operated for 227 days, with 2:1 AI cycles (2 h with aeration on and 1 h off) and Hydraulic Retention Time (HRT) of 16 h. Three phases, with different OLR, were evaluated: phases A (1000 gCOD m-3 day-1 - 63 days), B (1400 gCOD m-3 day-1 - 94 days), and C (1800 gCOD m-3 day-1 - 70 days). The percentage of COD, NH4+-N removal, and nitrogen removal, respectively, were above 85 ± 7%, 73 ± 27%, and 83 ± 5, in all phases. There was no accumulation of the oxidized forms of nitrogen in the reactor. The kinetic test, performed to evaluate the nitrification and denitrification in the system, indicated that even in dissolved oxygen concentrations of 4.5 mg L-1, it was possible to obtain the denitrification process in the system. The results demonstrate that the reactor under study has positive characteristics to be used as an alternative for removing the removal of organic material and nitrogen in the biological treatment of dairy effluents.
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Affiliation(s)
- Camila Zoe Correa
- Department of Civil Construction, State University of Londrina, Rodovia Celso Garcia Cid, Km 380, Campus Universitario, CEP, Londrina, Parana, 86057-970, Brazil.
| | | | - Deize Dias Lopes
- Department of Civil Construction, State University of Londrina, Rodovia Celso Garcia Cid, Km 380, Campus Universitario, CEP, Londrina, Parana, 86057-970, Brazil
| | - Kátia Valéria Marques Cardoso Prates
- Department of Environmental Engineering, Federal Technological University of Paraná, Av. Dos Pioneiros 3131, Londrina, Parana, CEP 86036-370, Brazil
| | - Luciano Aparecido Panagio
- Department of Microbiology, State University of Londrina, Rodovia Celso Garcia Cid, Km 380, Campus Universitario, Londrina, Parana, CEP 86057-970, Brazil
| | - Aline Ratuchne
- Department of Microbiology, State University of Londrina, Rodovia Celso Garcia Cid, Km 380, Campus Universitario, Londrina, Parana, CEP 86057-970, Brazil
| | - Márcia Helena Rissato Zamariolli Damianovic
- Laboratory of Biological Processes, São Carlos School of Engineering, University of São Paulo (USP), 1100, João Dagnone Ave., Santa Angelina, Sao Carlos, São Paulo, 13563-120, Brazil
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Liu X, Zhou W, Wang X, Wu H, Dong W. Microbial gradual shifts during the process of species replacement in Taihang Mountain. Front Microbiol 2023; 14:1158731. [PMID: 37089536 PMCID: PMC10113637 DOI: 10.3389/fmicb.2023.1158731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
IntroductionUnderstanding microbial gradual shifts along species replacement can help elucidate the mechanisms driving secondary succession, and predict microbial responses to changing environments. However, how climate-induced species replacement alters microbial processes, and whether microbial shifts follow predictable assembly trajectories remain unclear.MethodsUsing space-for-time substitution approach, we studied shifts in bacterial and fungal communities in the succession from Leptodermis oblonga to Vitex negundo var. heterophylla shrubland in Taihang Mountain.Results and DiscussionSpecies replacement, induced by climate related environmental change, significantly increased the above-ground biomass of shrublands, and TP and TK contents in topsoil. The succession from L. oblonga to V. negundo var. heterophylla communities resulted in the gradually replacement of cold-tolerant microbes with warm-affinity ones, and alterations of microbial communities involved in soil biogeochemical processes. Soil and plant variables, such as above-ground biomass, soil pH, total phosphorus, and total potassium, well explained the variations in microbial communities, indicating that the coordinated changes in plant communities and soil properties during secondary succession caused accompanied shifts in microbial diversity and composition.
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Affiliation(s)
- Xiuping Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wangming Zhou
- School of Life Sciences, Anqing Normal University, Anqing, China
| | - Xinzhen Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Hongliang Wu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- *Correspondence: Wenxu Dong,
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Xiong J, Su Y, He X, Han L, Huang G. Effects of functional membrane coverings on carbon and nitrogen evolution during aerobic composting: Insight into the succession of bacterial and fungal communities. BIORESOURCE TECHNOLOGY 2023; 369:128463. [PMID: 36503091 DOI: 10.1016/j.biortech.2022.128463] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Carbon and nitrogen evolution and bacteria and fungi succession in two functional membrane-covered aerobic composting (FMCAC) systems and a conventional aerobic composting system were investigated. The micro-positive pressure in each FMCAC system altered the composting microenvironment, significantly increased the oxygen uptake rates of microbes (p < 0.05), and increased the abundance of cellulose- and hemicellulose-degrading microorganisms. Bacteria and fungi together influenced the conversion between carbon and nitrogen forms. FMCAC made the systems less anaerobic and decreased CH4 production and emissions by 22.16 %-23.37 % and N2O production and emissions by 41.34 %-45.37 % but increased organic matter degradation and NH3 production and emissions by 16.91 %-90.13 %. FMCAC decreased carbon losses, nitrogen losses, and the global warming potential by 7.97 %-11.24 %, 15.43 %-34.00 %, and 39.45 %-42.16 %, respectively. The functional membrane properties (pore size distribution and air permeability) affected fermentation process and gaseous emissions. A comprehensive assessment indicated that FMCAC has excellent prospects for application.
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Affiliation(s)
- Jinpeng Xiong
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Ya Su
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Xueqin He
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Lujia Han
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Guangqun Huang
- Engineering Laboratory for AgroBiomass Recycling & Valorizing, College of Engineering, China Agricultural University, Beijing 100083, China.
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7
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Steindorff AS, Seong K, Carver A, Calhoun S, Fischer MS, Stillman K, Liu H, Drula E, Henrissat B, Simpson HJ, Schilling JS, Lipzen A, He G, Yan M, Andreopoulos B, Pangilinan J, LaButti K, Ng V, Traxler M, Bruns TD, Grigoriev IV. Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development. THE NEW PHYTOLOGIST 2022; 236:1154-1167. [PMID: 35898177 DOI: 10.1111/nph.18407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire-responsive fungal colonizers of post-fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora. A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions - growing on charcoal, and during sexual development - identified modules of genes that are co-expressed in the charcoal and light-induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum.
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Affiliation(s)
- Andrei S Steindorff
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kyungyong Seong
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Akiko Carver
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sara Calhoun
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Monika S Fischer
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Kyra Stillman
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Haowen Liu
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy, 13288 Aix Marseille Université, Marseille, France
- INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, 13009, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Hunter J Simpson
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN, 55108, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Anna Lipzen
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Guifen He
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mi Yan
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bill Andreopoulos
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Matthew Traxler
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Thomas D Bruns
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Plant and Microbial Biology Department, University of California Berkeley, Berkeley, CA, 94720, USA
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Viegas MF, Neves RPP, Ramos MJ, Fernandes PA. QM/MM Study of the Reaction Mechanism of Thermophilic Glucuronoyl Esterase for Biomass Treatment. Chemphyschem 2022; 23:e202200269. [PMID: 35925549 DOI: 10.1002/cphc.202200269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/23/2022] [Indexed: 11/06/2022]
Abstract
Hydrolysis of lignocellulosic biomass, composed of a lignin-carbohydrate-complex (LCC) matrix, is critical for producing bioethanol from glucose. However, current methods for LCC processing require costly and polluting processes. The fungal Thermothelomyces thermophila glucuronoyl esterase (TtGE) is a promising thermophilic enzyme that hydrolyses LCC ester bonds. This study describes the TtGE catalytic mechanism using QM/MM methods. Two nearly-degenerate rate-determining transition states were found, with barriers of 16 and 17 kcal ⋅ mol-1 , both with a zwitterionic nature that results from a proton interplay from His346 to either the Ser213-hydroxyl or the lignin leaving group and the rehybridisation of the ester moiety of the substrate to an alkoxide. An oxyanion hole, characteristic of esterases, was provided by the conserved Arg214 through its backbone and sidechain. Our work further suggests that a mutation of Glu267 to a non-negative residue will decrease the energetic barrier in ca. -5 kcal ⋅ mol-1 , improving the catalytic rate of TtGE.
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Affiliation(s)
- Matilde F Viegas
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Rui P P Neves
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro A Fernandes
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
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Bazzicalupo AL, Erlandson S, Branine M, Ratz M, Ruffing L, Nguyen NH, Branco S. Fungal Community Shift Along Steep Environmental Gradients from Geothermal Soils in Yellowstone National Park. MICROBIAL ECOLOGY 2022; 84:33-43. [PMID: 34468785 DOI: 10.1007/s00248-021-01848-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Geothermal soils offer unique insight into the way extreme environmental factors shape communities of organisms. However, little is known about the fungi growing in these environments and in particular how localized steep abiotic gradients affect fungal diversity. We used metabarcoding to characterize soil fungi surrounding a hot spring-fed thermal creek with water up to 84 °C and pH 10 in Yellowstone National Park. We found a significant association between fungal communities and soil variable principal components, and we identify the key trends in co-varying soil variables that explain the variation in fungal community. Saprotrophic and ectomycorrhizal fungi community profiles followed, and were significantly associated with, different soil variable principal components, highlighting potential differences in the factors that structure these different fungal trophic guilds. In addition, in vitro growth experiments in four target fungal species revealed a wide range of tolerances to pH levels but not to heat. Overall, our results documenting turnover in fungal species within a few hundred meters suggest many co-varying environmental factors structure the diverse fungal communities found in the soils of Yellowstone National Park.
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Affiliation(s)
- Anna L Bazzicalupo
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada.
| | - Sonya Erlandson
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Margaret Branine
- Graduate Field of Microbiology, Cornell University, Ithaca, NY, USA
| | - Megan Ratz
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Lauren Ruffing
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Nhu H Nguyen
- Department of Tropical Plant and Soil Sciences, University of Hawaii At Manoa, Honolulu, HI, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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10
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Santander-Jimenez S, Vega-Rodriguez MA, Sousa L. Inter-Algorithm Multiobjective Cooperation for Phylogenetic Reconstruction on Amino Acid Data. IEEE TRANSACTIONS ON CYBERNETICS 2022; 52:3577-3591. [PMID: 32915754 DOI: 10.1109/tcyb.2020.2995464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inter-algorithm cooperative approaches are increasingly gaining interest as a way to boost the search capabilities of evolutionary algorithms (EAs). However, the growing complexity of real-world optimization problems demands new cooperative designs that implement performance-driven strategies to improve the solution quality. This article explores multiobjective cooperation to address an important problem in bioinformatics: the reconstruction of phylogenetic histories from amino acid data. The proposed method is built using representative algorithms from the three main multiobjective design trends: 1) nondominated sorting genetic algorithm II; 2) indicator-based evolutionary algorithm; and 3) multiobjective evolutionary algorithm based on decomposition. The cooperation is supervised by an Elite island component that, along with managing migrations, retrieves multitrend performance feedback from each approach to run additional instantiations of the most satisfying algorithm in each stage of the execution. Experimentation on five real-world problem instances shows the benefits of the proposal to handle complex optimization tasks, in comparison to stand-alone algorithms, standard island models, and other state-of-the-art methods.
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11
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Talhi I, Dehimat L, Jaouani A, Cherfia R, Berkani M, Almomani F, Vasseghian Y, Chaouche NK. Optimization of thermostable proteases production under agro-wastes solid-state fermentation by a new thermophilic Mycothermus thermophilus isolated from a hydrothermal spring Hammam Debagh, Algeria. CHEMOSPHERE 2022; 286:131479. [PMID: 34315081 DOI: 10.1016/j.chemosphere.2021.131479] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The present work investigates for the first time the presence and isolation of the thermophilic fungi from hydrothermal spring situated at the locality of Guelma, in the Northeast of Algeria. The production of the thermostable proteases and the optimization of culture conditions under agro-wastes solid-state fermentation to achieve optimal production capacity were explored. A statistical experimental approach consisting of two designs was used to determine the optimum culture conditions and to attain the greatest enzyme production. Besides, different agricultural wastes were initially evaluated as a substrate, whereby wheat bran was selected for enzyme production by the isolate under solid-state conditions. The isolate thermophilic fungi were identified as Mycothermus thermophilus by sequencing the ITS region of the rDNA (NCBI Accession No: MK770356.1). Among the various screened variables: the temperature, the inoculum size, and the moisture were proved to have the most significant effects on protease activity. Employing two-level fractional Plackett-Burman and a Box-Behnken designs statistical approach helped in identifying optimum values of screened factors and their interactions. The analysis showed up 6.17-fold improvement in the production of proteases (~1187.03 U/mL) was achieved under the optimal conditions of moisture content 47%, inoculum 5 × 105 spores/g, and temperature at 42 °C. These significant findings highlight the importance of the statistical design in isolation of Mycothermus thermophilus species from a specific location as well as identifying the optimal culture conditions for maximum yield.
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Affiliation(s)
- Imen Talhi
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri, Constantine 1, BP, 325 Route de Aïn El Bey, Constantine 25017, Algeria
| | - Laid Dehimat
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri, Constantine 1, BP, 325 Route de Aïn El Bey, Constantine 25017, Algeria
| | - Atef Jaouani
- Laboratoire de Microorganismes et Biomolécules Actives (LMBA) Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire 2092 El Manar, Tunisie
| | - Radia Cherfia
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri, Constantine 1, BP, 325 Route de Aïn El Bey, Constantine 25017, Algeria
| | - Mohammed Berkani
- Laboratoire Biotechnologies, Ecole Nationale Supérieure de Biotechnologie, Ville Universitaire Ali Mendjeli, BP E66, 25100 Constantine, Algeria.
| | - Fares Almomani
- Department of Chemical Engineering, College of Engineering, Qatar University, P. O. Box, Doha, 2713, Qatar.
| | - Yasser Vasseghian
- Department of Chemical Engineering, Quchan University of Technology, Quchan, Iran.
| | - Noreddine Kacem Chaouche
- Laboratoire de Mycologie, de Biotechnologie et de l'Activité Microbienne (LaMyBAM), Département de Biologie Appliquée, Université des Frères Mentouri, Constantine 1, BP, 325 Route de Aïn El Bey, Constantine 25017, Algeria
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12
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Dadwal A, Sharma S, Satyanarayana T. Recombinant cellobiohydrolase of Myceliophthora thermophila: characterization and applicability in cellulose saccharification. AMB Express 2021; 11:148. [PMID: 34735642 PMCID: PMC8568750 DOI: 10.1186/s13568-021-01311-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 12/31/2022] Open
Abstract
A codon optimized cellobiohydrolase (CBH) encoding synthetic gene of 1188 bp from a thermophilic mold Myceliophthora thermophila (MtCel6A) was cloned and heterologously expressed in Escherichia coli for the first time. In silico analysis suggested that MtCel6A is a GH6 CBH and belongs to CBHII family, which is structurally similar to Cel6A of Humicola insolens. The recombinant MtCel6A is expressed as active inclusion bodies, and the molecular mass of the purified enzyme is ~ 45 kDa. The rMtCel6A is active in a wide range of pH (4-12) and temperatures (40-100 °C) with optima at pH 10.0 and 60 °C. It exhibits T1/2 of 6.0 and 1.0 h at 60 and 90 °C, respectively. The rMtCel6A is an extremozyme with organic solvent, salt and alkali tolerance. The Km, Vmax, kcat and kcat/Km values of the enzyme are 3.2 mg mL-1, 222.2 μmol mg-1 min-1, 2492 s-1 and 778.7 s-1 mg-1 mL-1, respectively. The product analysis of rMtCel6A confirmed that it is an exoenzyme that acts from the non-reducing end of cellulose. The addition of rMtCel6A to the commercial cellulase mix (Cellic CTec2) led to 1.9-fold increase in saccharification of the pre-treated sugarcane bagasse. The rMtCel6A is a potential CBH that finds utility in industrial processes such as in bioethanol, paper pulp and textile industries.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences & Engineering, Netaji Subhas Institute of Technology (University of Delhi), Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India
| | - Shilpa Sharma
- Department of Biological Sciences & Engineering, Netaji Subhas Institute of Technology (University of Delhi), Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India
- Department of Biological Sciences & Engineering, Netaji Subhas University of Technology, Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences & Engineering, Netaji Subhas Institute of Technology (University of Delhi), Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India.
- Department of Biological Sciences & Engineering, Netaji Subhas University of Technology, Azad Hind Fauj Marg, Sector-3 Dwarka, New Delhi, 110078, India.
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13
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Antonelli MA, Gaglioti AL, Silva PRDA, Knob A. Thermophilic fungi in Araucaria Forest, Atlantic Forest Biome, Brazil. AN ACAD BRAS CIENC 2021; 93:e20210714. [PMID: 34706012 DOI: 10.1590/0001-3765202120210714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/31/2021] [Indexed: 11/21/2022] Open
Abstract
Thermophilic fungi constitute an ecologically well-defined group, commonly found in environments wherever decomposition of organic matter takes place, making them self-heating. The importance of thermophilic fungus in ecosystems contrasts with the incompleteness of our understanding of the group's biogeography patterns, phylogenies and coevolution relationships. Actually, the lack of data about thermophilic fungi from the Brazil is a limiting factor that also contributes for this scenario. In order to reduce this gap of knowledge, we aimed to characterize thermophilic filamentous fungi in Araucaria Forest, Atlantic Forest biome. Species identification was achieved by using internal transcribed spacers (ITS) as molecular ribosomal markers. In total, 240 heat-tolerant fungal strains were isolated and identified as Thermothielavioides terrestris, Thielavia sp., Thermoascus crustaceus, Aspergillus fumigatus, Rhizomucor miehei, Rhizomucor pusillus, and Rhizopus microsporus. All thermophilic strains exhibited optimal growth at 45 °C. T. crustaceus, T. miehei e R. pusillus were the dominant species, with the frequencies of occurrence of 35.00%, 28.33% and 23.33%, respectively. Our data reveals the apparent diversity of the Neotropical realm and may serve as reference to future studies that will try to elucidate important aspects of group.
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Affiliation(s)
- Marcio André Antonelli
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
| | - André Luiz Gaglioti
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
| | - Paulo Roberto DA Silva
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
| | - Adriana Knob
- Midwest State University State, Department of Biological Sciences, Alameda Élio Antonio Dalla Vecchia, 838, 85040-167 Guarapuava, PR, Brazil
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Ratuchne A, Knob A. A new and unusual β-glucosidase from Aspergillus fumigatus: Catalytic activity at high temperatures and glucose tolerance. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102064] [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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A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01710-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.
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Krska D, Mazurkewich S, Brown HA, Theibich Y, Poulsen JCN, Morris AL, Koropatkin NM, Lo Leggio L, Larsbrink J. Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii. Biochemistry 2021; 60:2206-2220. [PMID: 34180241 PMCID: PMC8280721 DOI: 10.1021/acs.biochem.1c00305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The hyperthermophilic bacterium Caldicellulosiruptor kristjansonii encodes an unusual enzyme, CkXyn10C-GE15A, which
incorporates two catalytic domains, a xylanase and a glucuronoyl esterase,
and five carbohydrate-binding modules (CBMs) from families 9 and 22.
The xylanase and glucuronoyl esterase catalytic domains were recently
biochemically characterized, as was the ability of the individual
CBMs to bind insoluble polysaccharides. Here, we further probed the
abilities of the different CBMs from CkXyn10C-GE15A
to bind to soluble poly- and oligosaccharides using affinity gel electrophoresis,
isothermal titration calorimetry, and differential scanning fluorimetry.
The results revealed additional binding properties of the proteins
compared to the former studies on insoluble polysaccharides. Collectively,
the results show that all five CBMs have their own distinct binding
preferences and appear to complement each other and the catalytic
domains in targeting complex cell wall polysaccharides. Additionally,
through renewed efforts, we have achieved partial structural characterization
of this complex multidomain protein. We have determined the structures
of the third CBM9 domain (CBM9.3) and the glucuronoyl esterase (GE15A)
by X-ray crystallography. CBM9.3 is the second CBM9 structure determined
to date and was shown to bind oligosaccharide ligands at the same
site but in a different binding mode compared to that of the previously
determined CBM9 structure from Thermotoga maritima. GE15A represents a unique intermediate between reported fungal
and bacterial glucuronoyl esterase structures as it lacks two inserted
loop regions typical of bacterial enzymes and a third loop has an
atypical structure. We also report small-angle X-ray scattering measurements
of the N-terminal CBM22.1–CBM22.2–Xyn10C construct,
indicating a compact arrangement at room temperature.
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Affiliation(s)
- Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Yusuf Theibich
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | | | - Adeline L Morris
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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17
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Gao J, Li Q, Li D. Novel Proteome and N-Glycoproteome of the Thermophilic Fungus Chaetomium thermophilum in Response to High Temperature. Front Microbiol 2021; 12:644984. [PMID: 34163440 PMCID: PMC8216556 DOI: 10.3389/fmicb.2021.644984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
Thermophilic fungi are eukaryotic species that grow at high temperatures, but little is known about the underlying basis of thermophily at cell and molecular levels. Here the proteome and N-glycoproteome of Chaetomium thermophilum at varying culture temperatures (30, 50, and 55°C) were studied using hydrophilic interaction liquid chromatography enrichment and high-resolution liquid chromatography–tandem mass spectroscopy analysis. With respect to the proteome, the numbers of differentially expressed proteins were 1,274, 1,374, and 1,063 in T50/T30, T55/T30, and T55/T50, respectively. The upregulated proteins were involved in biological processes, such as protein folding and carbohydrate metabolism. Most downregulated proteins were involved in molecular functions, including structural constituents of the ribosome and other protein complexes. For the N-glycoproteome, the numbers of differentially expressed N-glycoproteins were 160, 176, and 128 in T50/T30, T55/T30, and T55/T50, respectively. The differential glycoproteins were mainly involved in various types of N-glycan biosynthesis, mRNA surveillance pathway, and protein processing in the endoplasmic reticulum. These results indicated that an efficient protein homeostasis pathway plays an essential role in the thermophily of C. thermophilum, and N-glycosylation is involved by affecting related proteins. This is the novel study to reveal thermophilic fungi’s physiological response to high-temperature adaptation using omics analysis, facilitating the exploration of the thermophily mechanism of thermophilic fungi.
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Affiliation(s)
- Jinpeng Gao
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Qingchao Li
- Department of Mycology, Shandong Agricultural University, Taian, China
| | - Duochuan Li
- Department of Mycology, Shandong Agricultural University, Taian, China
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18
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Improved strategies to efficiently isolate thermophilic, thermotolerant, and heat-resistant fungi from compost and soil. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThermophilic, thermotolerant and heat-resistant fungi developed different physiological traits, enabling them to sustain or even flourish under elevated temperatures, which are life-hostile for most other eukaryotes. With the growing demand of heat-stable molecules in biotechnology and industry, the awareness of heat-adapted fungi as a promising source of respective enzymes and biomolecules is still increasing. The aim of this study was to test two different strategies for the efficient isolation and identification of distinctly heat-adapted fungi from easily accessible substrates and locations. Eight compost piles and ten soil sites were sampled in combination with different culture-dependent approaches to describe suitable strategies for the isolation and selection of thermophilous fungi. Additionally, an approach with a heat-shock treatment, but without elevated temperature incubation led to the isolation of heat-resistant mesophilic species. The cultures were identified based on morphology, DNA barcodes, and microsatellite fingerprinting. In total, 191 obtained isolates were assigned to 31 fungal species, from which half are truly thermophilic or thermotolerant, while the other half are heat-resistant fungi. A numerous amount of heat-adapted fungi was isolated from both compost and soil samples, indicating the suitability of the used approaches and that the richness and availability of those organisms in such environments are substantially high.
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19
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Diversity and composition of the North Sikkim hot spring mycobiome using a culture-independent method. Folia Microbiol (Praha) 2021; 66:457-468. [PMID: 33755859 DOI: 10.1007/s12223-021-00859-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
Fungi are considered to be the most resilient and economically important microbial community that can easily survive and optimally grow under a wide range of growth conditions. Thermophilic fungi from the geothermal sources have been less pondered upon and lie unexplored. Here, a microbiome approach was conducted to understand the concealed world of the environmental mycobiota from the two hot springs of North Sikkim district located in North-east India. The solfataric muds from the hot springs were analyzed. In both the samples, on the basis of genus level classification, genus Fusarium had the highest abundance followed by Colletotrichum, Pochonia, Pyricularia, Neurospora, etc. Analyzing the predicted genes, the functional proteins of New Yume Samdung mycobiome were found to be dominated by the genera Fusarium (22%), Trichoderma (12%), and Aspergillus (11%), whereas in the case of Old Yume Samdung, it was dominated by the genera Aspergillus (11%), Saccharomyces (6%), and Fusarium (5%). Interestingly, in the studied mycobiome, environmental yeasts were also detected. From the functional metagenomics, sulfate adenylatetransferase (SAT) proteins for sulfur assimilation were found in some of the fungal reads. Toxin protein reads such as AM-toxin biosynthesis proteins, AF-toxin biosynthesis proteins, Gliotoxin biosynthesis proteins, and aflatoxin biosynthesis proteins were detected in the mycobiomes.
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20
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Dadwal A, Singh V, Sharma S, Satyanarayana T. Structural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking. J Biomol Struct Dyn 2021; 40:5211-5228. [PMID: 33413029 DOI: 10.1080/07391102.2020.1869095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulases are the enzymes with diverse range of industrial applications. Cellulases degrade cellulose into monomeric glucose units by hydrolysing β-1,4-glycosidic bonds. There are three components of cellulases: a) endoglucanase, b) exoglucanase and c) β-glucosidase which act synergistically in cellulose bioconversion. The cellulases are the third largest industrial enzymes with a great potential in bioethanol production. In this investigation, a β-glucosidase of a thermophilic fungus Myceliophthora thermophila (MtBgl3c) was analysed for its structural characterization using in silico approaches. The protein structure of MtBgl3c is unknown, therefore an attempt has been made to model 3D structure using Modeller 9.23 software. The MtBgl3c protein model generated was validated from Verify 3D and ERRAT scores of 89.37% and 71.25%, respectively derived from SAVES. Using RAMPAGE the Ramachandran plot was generated, which predicted the accuracy of the 3D model with 91.5% amino acid residues in the favored region. The ion binding and N-glycosylation sites were also predicted. The generated model was docked with cellobiose to predict the most favorable binding sites of MtBgl3c. The key amino acid residues involved in cellobiose bonding are Val88, Asp106, Asp287, Tyr255, Arg170, Glu514. The catalytic conserved amino residues of MtBgl3c were identified. The dock score of cellobiose with MtBgl3c is much lower (-6.46 kcal/mol) than that of glucose (-5.61 kcal/mol), suggesting its high affinity for cellobiose. The docking data of MtBgl3c with glucose illustrate its tolerance to glucose. The present study provides insight into structural characteristics of the MtBgl3c which can be further validated by experimental data. Highlights3D structure of β-glucosidase (MtBgl3c) of Myceliophthora thermophila is being proposed based on computational analysesThe amino acid residues Asp106, Asp287, Tyr255, Arg170 and Glu514 have been identified to play catalytically important role in substrate bindingDocking and interaction of MtBgl3c with cellobiose and glucose has been confirmedDocking analysis of MtBgl3c with glucose suggested its glucose toleranceThe data would be useful in engineering enzymes for attaining higher catalytic efficiencyCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
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21
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Bioprospecting of Thermophilic Fungal Enzymes and Potential Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Muggia L, Ametrano CG, Sterflinger K, Tesei D. An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) 2020; 10:E356. [PMID: 33348904 PMCID: PMC7765829 DOI: 10.3390/life10120356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/26/2022] Open
Abstract
Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.
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Affiliation(s)
- Lucia Muggia
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Claudio G. Ametrano
- Grainger Bioinformatics Center, Department of Science and Education, The Field Museum, Chicago, IL 60605, USA;
| | - Katja Sterflinger
- Academy of Fine Arts Vienna, Institute of Natual Sciences and Technology in the Arts, 1090 Vienna, Austria;
| | - Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
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23
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Chovanová K, Böhmer M, Poljovka A, Budiš J, Harichová J, Szemeš T, Zámocký M. Parallel Molecular Evolution of Catalases and Superoxide Dismutases-Focus on Thermophilic Fungal Genomes. Antioxidants (Basel) 2020; 9:antiox9111047. [PMID: 33120873 PMCID: PMC7712995 DOI: 10.3390/antiox9111047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/17/2022] Open
Abstract
Catalases (CAT) and superoxide dismutases (SOD) represent two main groups of enzymatic antioxidants that are present in almost all aerobic organisms and even in certain anaerobes. They are closely interconnected in the catabolism of reactive oxygen species because one product of SOD reaction (hydrogen peroxide) is the main substrate of CAT reaction finally leading to harmless products (i.e., molecular oxygen and water). It is therefore interesting to compare the molecular evolution of corresponding gene families. We have used a phylogenomic approach to elucidate the evolutionary relationships among these two main enzymatic antioxidants with a focus on the genomes of thermophilic fungi. Distinct gene families coding for CuZnSODs, FeMnSODs, and heme catalases are very abundant in thermophilic Ascomycota. Here, the presented results demonstrate that whereas superoxide dismutase genes remained rather constant during long-term evolution, the total count of heme catalase genes was reduced in thermophilic fungi in comparison with their mesophilic counterparts. We demonstrate here, for the newly discovered ascomycetous genes coding for thermophilic superoxide dismutases and catalases (originating from our sequencing project), the expression patterns of corresponding mRNA transcripts and further analyze translated protein sequences. Our results provide important implications for the physiology of reactive oxygen species metabolism in eukaryotic cells at elevated temperatures.
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Affiliation(s)
- Katarína Chovanová
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
| | - Miroslav Böhmer
- Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkovičova 8, SK-84104 Bratislava, Slovakia; (M.B.); (J.B.); (T.S.)
| | - Andrej Poljovka
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
| | - Jaroslav Budiš
- Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkovičova 8, SK-84104 Bratislava, Slovakia; (M.B.); (J.B.); (T.S.)
| | - Jana Harichová
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
| | - Tomáš Szemeš
- Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkovičova 8, SK-84104 Bratislava, Slovakia; (M.B.); (J.B.); (T.S.)
| | - Marcel Zámocký
- Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; (K.C.); (A.P.); (J.H.)
- Department of Chemistry, Institute of Biochemistry, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- Correspondence:
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Huang WP, Du YJ, Yang Y, He JN, Lei Q, Yang XY, Zhang KQ, Niu XM. Two CRISPR/Cas9 Systems Developed in Thermomyces dupontii and Characterization of Key Gene Functions in Thermolide Biosynthesis and Fungal Adaptation. Appl Environ Microbiol 2020; 86:e01486-20. [PMID: 32769197 PMCID: PMC7531979 DOI: 10.1128/aem.01486-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/23/2020] [Indexed: 11/20/2022] Open
Abstract
Thermomyces dupontii, a widely distributed thermophilic fungus, is an ideal organism for investigating the mechanism of thermophilic fungal adaptation to diverse environments. However, genetic analysis of this fungus is hindered by a lack of available and efficient gene-manipulating tools. In this study, two different Cas9 proteins from mesophilic and thermophilic bacteria, with in vivo expression of a single guide RNA (sgRNA) under the control of tRNAGly, were successfully adapted for genome editing in T. dupontii We demonstrated the feasibility of applying these two gene editing systems to edit one or two genes in T. dupontii The mesophilic CRISPR/Cas9 system displayed higher editing efficiency (50 to 86%) than the thermophilic CRISPR/Cas9 system (40 to 67%). However, the thermophilic CRISPR/Cas9 system was much less time-consuming than the mesophilic CRISPR/Cas9 system. Combining the CRISPR/Cas9 systems with homologous recombination, a constitutive promoter was precisely knocked in to activate a silent polyketide synthase-nonribosomal peptide synthase (PKS-NRPS) biosynthetic gene, leading to the production of extra metabolites that did not exist in the parental strains. Metabolic analysis of the generated biosynthetic gene mutants suggested that a key biosynthetic pathway existed for the biosynthesis of thermolides in T. dupontii, with the last two steps being different from those in the heterologous host Aspergillus Further analysis suggested that these biosynthetic genes might be involved in fungal mycelial growth, conidiation, and spore germination, as well as in fungal adaptation to osmotic, oxidative, and cell wall-perturbing agents.IMPORTANCE Thermomyces represents a unique ecological taxon in fungi, but a lack of flexible genetic tools has greatly hampered the study of gene function in this taxon. The biosynthesis of potent nematicidal thermolides in T. dupontii remains largely unknown. In this study, mesophilic and thermophilic CRISPR/Cas9 gene editing systems were successfully established for both disrupting and activating genes in T. dupontii In this study, a usable thermophilic CRISPR/Cas9 gene editing system derived from bacteria was constructed in thermophilic fungi. Chemical analysis of the mutants generated by these two gene editing systems identified the key biosynthetic genes and pathway for the biosynthesis of nematocidal thermolides in T. dupontii Phenotype analysis and chemical stress experiments revealed potential roles of secondary metabolites or their biosynthetic genes in fungal development and adaption to chemical stress conditions. These two genomic editing systems will not only accelerate investigations into the biosynthetic mechanisms of unique natural products and functions of cryptic genes in T. dupontii but also offer an example for setting up CRISPR/Cas9 systems in other thermophilic fungi.
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Affiliation(s)
- Wei-Ping Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Yuan-Jiang Du
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Yun Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Jia-Ning He
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Qian Lei
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Xiao-Yu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
| | - Xue-Mei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, People's Republic of China
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25
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Sokolyanskaya LO, Ivanov MV, Ikkert OP, Kalinina AE, Evseev VA, Glukhova LB, Karnachuk OV. Copper Precipitation as Insoluble Oxalates by Thermotolerant Aspergillus spp. from Burning Wastes of Coal Mining. Microbiology (Reading) 2020. [DOI: 10.1134/s002626172004013x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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26
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Godon JJ, Galès A, Latrille E, Ouichanpagdee P, Seyer JP. An “overlooked” habitat for thermophilic bacteria: the phyllosphere. BIODISCOVERY 2020. [DOI: 10.3897/biodiscovery.23.e47033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Thermophilic microbes are present everywhere around us and their only known natural biotope is far away and most usually associated with geothermal energy. To answer this paradox, we explore the hypothesis that the phyllosphere (surface of leaves), due to its exposition to the sun, could well be a thermophilic habitat for microbes and thus a source of thermophilic microbes growing around 50°C – 60°C. To support this hypothesis, we reviewed the heat sources on earth and associated microbial habitats, as well as the difficult identification of thermophilic microbes. We further present an experiment to show the presence and activity of thermophilic bacteria in the phyllosphere. Leaves were collected from eleven tree species from five locations on three continents belonging to three different biomes. On fresh leaves, 16S rDNA sequencing reveals the presence of 0.2 to 7% of clearly identified thermophilic bacteria. Moreover, after incubation at 55°C under aerobic and anaerobic conditions, 16S rDNA sequencing reveals the presence of 4 to 99% of clearly identified thermophilic bacteria. The accumulation of observations provides coherence to our hypothesis and allows the emergence of a new vision of leaves as a thermophilic biotope. We then propose a life cycle of microbes belonging to the thermophilic biotope associated with leaf surfaces.
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Yang XY, Zhang JX, Ding QY, He ZC, Zhu CY, Zhang KQ, Niu XM. Metabolites from Two Dominant Thermophilic Fungal Species Thermomyces lanuginosus and Scytalidium thermophilum. Chem Biodivers 2020; 17:e2000137. [PMID: 32207881 DOI: 10.1002/cbdv.202000137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Thermomyces lanuginosus and Scytalidium thermophilum are among the most ubiquitous thermophilic fungi in compost and soil. Chemical study on these two prevalent strains collected from Yunnan led to isolation of 23 metabolites, including one new metabolite, therlanubutanolide, and 15 known compounds, isolated from the YGP culture broth of Thermomyces lanuginosus and 7 known compounds isolated from Scytalidium thermophilum, respectively. Therlanubutanolide shared the quite similar features of the same carbon skeleton and saturation as natural hexadecanoic acids. This was the first reported discovery of such a lactone as natural occurring metabolite. All the compounds were reported for the first time from thermophilic fungi. Among them, N-[(2S,3R,4E,8E)-1,3-dihydroxy-9-methyloctadeca-4,8-dien-2-yl]acetamide was for the first time reported to be a naturally occurring metabolite and its NMR data was first provided in this study. A type of PKS-derived metabolites, three 3,4-dihydronaphthalen-1(2H)-ones, which were widely found in plant pathogenic fungi as phytotoxins and reported to have antimicrobial activity, were obtained from both dominant thermophilic fungi. The frequent occurrence of such PKS phytotoxins in these two thermophilic fungi might suggest particular ecological interest.
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Affiliation(s)
- Xiao-Yu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
| | - Jun-Xian Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
| | - Qiu-Yan Ding
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
| | - Zi-Cong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
| | - Chun-Yan Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
| | - Xue-Mei Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, School of life Sciences, Yunnan University, Kunming, 650091, P. R. China
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28
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Zhu J, Ren Z, Huang B, Cao A, Wang Q, Yan D, Ouyang C, Wu J, Li Y. Effects of Fumigation with Allyl Isothiocyanate on Soil Microbial Diversity and Community Structure of Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1226-1236. [PMID: 31922739 DOI: 10.1021/acs.jafc.9b07292] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As a substitute for methyl bromide, effects of allyl isothiocyanate (AITC) on nontarget microorganisms in soil are poorly understood. This study measured the half-life of AITC in the soil as well as its effects on the soil substrate-induced respiration (SIR) and on communities of soil bacteria and fungi. The results showed that AITC had a short half-life and a short-term inhibition of SIR; high-throughput sequencing analysis showed that AITC had less effect on bacterial than fungal communities. Fumigation reduced the diversity of soil bacteria temporarily, but stimulated the diversity of soil fungi in the long-term and significantly changed the structure of the fungal community. Following AITC fumigation there were significant increases in the relative abundance of probiotics such as Sphingomonas, Streptomyces, Hypocreales, Acremonium, Aspergillus, and Pseudallescheria that help to control plant diseases. Our study provided useful information for assessing the ecological safety of AITC.
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Affiliation(s)
- Jiahong Zhu
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Zongjie Ren
- National Agricultural Technology Extension Service Center , Ministry of Agriculture and Rural Affairs , Beijing 100125 , China
| | - Bin Huang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Aocheng Cao
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Qiuxia Wang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Dongdong Yan
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Canbin Ouyang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Jiajia Wu
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Yuan Li
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
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29
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Molecular Approaches for Analyzing Environmental Chaetomium Diversity and Exploitation of Chaetomium thermophilum for Biochemical Analyses. Fungal Biol 2020. [DOI: 10.1007/978-3-030-31612-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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30
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Isolation and Molecular Characterization of Thermophilic Coprophilous Fungus Malbranchea cinnamomea GSMBKU from Goat Dung. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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31
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Discovery and Expression of Thermostable LPMOs from Thermophilic Fungi for Producing Efficient Lignocellulolytic Enzyme Cocktails. Appl Biochem Biotechnol 2019; 191:463-481. [DOI: 10.1007/s12010-019-03198-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/23/2019] [Indexed: 01/18/2023]
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32
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Ellingham O, David J, Culham A. Enhancing identification accuracy for powdery mildews using previously underexploited DNA loci. Mycologia 2019; 111:798-812. [DOI: 10.1080/00275514.2019.1643644] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Oliver Ellingham
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - John David
- Royal Horticultural Society Garden Wisley, Woking, Surrey, GU23 6QB, UK
| | - Alastair Culham
- School of Biological Sciences, University of Reading, Whiteknights, Reading, RG6 6AS, UK
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33
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Sandona K, Billingsley Tobias TL, Hutchinson MI, Natvig DO, Porras-Alfaro A. Diversity of thermophilic and thermotolerant fungi in corn grain. Mycologia 2019; 111:719-729. [PMID: 31348716 DOI: 10.1080/00275514.2019.1631137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Corn bins in the midwestern United States can reach temperatures up to 52 C. High temperatures combined with sufficient moisture and humidity in bins provide the perfect environment to promote the growth of thermophilic and thermotolerant fungi. In this article, we characterize for the first time thermophilic and thermotolerant fungi in corn grain bins using culture-based methods and pyrosequencing techniques. Corn samples were collected from local farms in western Illinois. Samples were plated and incubated at 50 C using a variety of approaches. Of several hundred kernels examined, more than 90% showed colonization. Species identified using culture methods included Thermomyces lanuginosus, Thermomyces dupontii, Aspergillus fumigatus, Thermoascus crustaceus, and Rhizomucor pusillus. Pyrosequencing was also performed directly on corn grain using fungal-specific primers to determine whether thermophilic fungi could be detected using this technique. Sequences were dominated by pathogenic fungi, and thermophiles were represented by less than 2% of the sequences despite being isolated from 90% of the grain samples using culturing techniques. The high abundance of previously undocumented viable fungi in corn could have negative implications for grain quality and pose a potential risk for workers and consumers of corn-derived products in the food industry. Members of the Sordariales were absent among thermophile isolates and were not represented in nuc rDNA internal transcribed spacer (ITS) sequences. This is in striking contrast with results obtained with other substrates such as litter, dung, and soils, where mesophilic and thermophilic members of the Sordariaceae and Chaetomiaceae are common. This absence appears to reflect an important difference between the ecology of Sordariales and other orders within the Ascomycota in terms of their ability to compete in microhabitats rich in sugars and living tissues.
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Affiliation(s)
- Katrina Sandona
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Terri L Billingsley Tobias
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Miriam I Hutchinson
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Donald O Natvig
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Andrea Porras-Alfaro
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455.,Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
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34
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Kavalecz N, Ág N, Karaffa L, Scazzocchio C, Flipphi M, Fekete E. A spliceosomal twin intron (stwintron) participates in both exon skipping and evolutionary exon loss. Sci Rep 2019; 9:9940. [PMID: 31289343 PMCID: PMC6616335 DOI: 10.1038/s41598-019-46435-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/28/2019] [Indexed: 01/06/2023] Open
Abstract
Spliceosomal twin introns (stwintrons) are introns where any of the three consensus sequences involved in splicing is interrupted by another intron (internal intron). In Aspergillus nidulans, a donor-disrupted stwintron (intron-1) is extant in the transcript encoding a reticulon-like protein. The orthologous transcript of Aspergillus niger can be alternatively spliced; the exon downstream the stwintron could be skipped by excising a sequence that comprises this stwintron, the neighbouring intron-2, and the exon bounded by these. This process involves the use of alternative 3' splice sites for the internal intron, the resulting alternative intervening sequence being a longer 3'-extended stwintron. In 29 species of Onygenales, a multi-step splicing process occurs in the orthologous transcript, in which a complex intervening sequence including the stwintron and neigbouring intron-2, generates by three splicing reactions a "second order intron" which must then be excised with a fourth splicing event. The gene model in two species can be envisaged as one canonical intron (intron-1) evolved from this complex intervening sequence of nested canonical introns found elsewhere in Onygenales. Postulated splicing intermediates were experimentally verified in one or more species. This work illustrates a role of stwintrons in both alternative splicing and the evolution of intron structure.
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Affiliation(s)
- Napsugár Kavalecz
- Department of Biochemical Engineering, University of Debrecen, Debrecen, 4032, Hungary
| | - Norbert Ág
- Department of Biochemical Engineering, University of Debrecen, Debrecen, 4032, Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, University of Debrecen, Debrecen, 4032, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College London, London, SW7 2AZ, UK.,Institut de Biologie Intégrative de la Cellule, Centre National de la Recherche Scientifique - Unité Mixte de Recherche 9198, Gif-sur-Yvette, 91405, France
| | - Michel Flipphi
- Department of Biochemical Engineering, University of Debrecen, Debrecen, 4032, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, University of Debrecen, Debrecen, 4032, Hungary.
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Santander-Jiménez S, Vega-Rodríguez MA, Sousa L. A multiobjective adaptive approach for the inference of evolutionary relationships in protein-based scenarios. Inf Sci (N Y) 2019. [DOI: 10.1016/j.ins.2019.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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36
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Surveying of acid-tolerant thermophilic lignocellulolytic fungi in Vietnam reveals surprisingly high genetic diversity. Sci Rep 2019; 9:3674. [PMID: 30842513 PMCID: PMC6403320 DOI: 10.1038/s41598-019-40213-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/23/2019] [Indexed: 12/28/2022] Open
Abstract
Thermophilic fungi can represent a rich source of industrially relevant enzymes. Here, 105 fungal strains capable of growing at 50 °C and pH 2.0 were isolated from compost and decaying plant matter. Maximum growth temperatures of the strains were in the range 50 °C to 60 °C. Sequencing of the internal transcribed spacer (ITS) regions indicated that 78 fungi belonged to 12 species of Ascomycota and 3 species of Zygomycota, while no fungus of Basidiomycota was detected. The remaining 27 strains could not be reliably assigned to any known species. Phylogenetically, they belonged to the genus Thielavia, but they represented 23 highly divergent genetic groups different from each other and from the closest known species by 12 to 152 nucleotides in the ITS region. Fungal secretomes of all 105 strains produced during growth on untreated rice straw were studied for lignocellulolytic activity at different pH and temperatures. The endoglucanase and xylanase activities differed substantially between the different species and strains, but in general, the enzymes produced by the novel Thielavia spp. strains exhibited both higher thermal stability and tolerance to acidic conditions. The study highlights the vast potential of an untapped diversity of thermophilic fungi in the tropics.
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Hüttner S, Granchi Z, Nguyen TT, van Pelt S, Larsbrink J, Thanh VN, Olsson L. Genome sequence of Rhizomucor pusillus FCH 5.7, a thermophilic zygomycete involved in plant biomass degradation harbouring putative GH9 endoglucanases. ACTA ACUST UNITED AC 2018; 20:e00279. [PMID: 30211016 PMCID: PMC6132078 DOI: 10.1016/j.btre.2018.e00279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 11/12/2022]
Abstract
R. pusillus encodes cellulose-, xylan- and chitin-degrading proteins. Two putative GH9 endoglucanases were identified. Enzyme system of R. pusillus is suited to consume easily accessible sugars. Endoglucanase and xylanase activity detected when the fungus was grown on wheat bran and xylan.
We report here the annotated draft genome sequence of the thermophilic zygomycete Rhizomucor pusillus strain FCH 5.7, isolated from compost soil in Vietnam. The genome assembly contains 25.59 Mb with an overall GC content of 44.95%, and comprises 10,898 protein coding genes. Genes encoding putative cellulose-, xylan- and chitin-degrading proteins were identified, including two putative endoglucanases (EC 3.2.1.4) from glycoside hydrolase family 9, which have so far been mostly assigned to bacteria and plants.
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Affiliation(s)
- Silvia Hüttner
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Thanh Thuy Nguyen
- Centre for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Ha Noi, Viet Nam
| | - Sake van Pelt
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | - Johan Larsbrink
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Vu Nguyen Thanh
- Centre for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Ha Noi, Viet Nam
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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Couger B, Weirick T, Damásio ARL, Segato F, Polizeli MDLTDM, de Almeida RSC, Goldman GH, Prade RA. The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatus. Front Microbiol 2018; 9:1827. [PMID: 30154766 PMCID: PMC6102483 DOI: 10.3389/fmicb.2018.01827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/23/2018] [Indexed: 11/16/2022] Open
Abstract
Biotechnologists are interested in thermo tolerant fungi to manufacture enzymes active and stable at high temperatures, because they provide improved catalytic efficiency, strengthen enzyme substrate interactions, accelerate substrate enzyme conversion rates, enhance mass transfer, lower substrate viscosity, lessen contamination risk and offer the potential for enzyme recycling. Members of the genus Aspergillus live a wide variety of lifestyles, some embrace GRAS status routinely employed in food processing while others such as Aspergillus fumigatus are human pathogens. A. fumigatus produces melanins, pyomelanin protects the fungus against reactive oxygen species and DHN melanin produced by the pksP gene cluster confers the gray-greenish color. pksP mutants are attenuated in virulence. Here we report on the genomic DNA sequence of a thermo tolerant albino Aspergillus isolated from rain forest composted floors. Unexpectedly, the nucleotide sequence was 95.7% identical to the reported by Aspergillus fumigatus Af293. Genome size and predicted gene models were also highly similar, however differences in DNA content and conservation were observed. The albino strain, classified as Aspergillus fumigatus var. niveus, had 160 gene models not present in A. fumigatus Af293 and A. fumigatus Af293 had 647 not found in the albino strain. Furthermore, the major pigment generating gene cluster pksP appeared to have undergone genomic rearrangements and a key tyrosinase present in many aspergilli was missing from the genome. Remarkably however, despite the lack of pigmentation A. fumigatus var. niveus killed neutropenic mice and survived macrophage engulfment at similar rates as A. fumigatus Af293.
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Affiliation(s)
- Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Tyler Weirick
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - André R. L. Damásio
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, São Paulo, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas São Paulo, Brazil
| | - Fernando Segato
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas São Paulo, Brazil
- Departamento de Biotecnologia da Escola de Engenharia de Lorena, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Gustavo H. Goldman
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas São Paulo, Brazil
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, São Paulo, Brazil
| | - Rolf A. Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Campinas São Paulo, Brazil
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40
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Kamlárová A, Chovanová K, Zámocký M. Peculiar genes for thermostable bifunctional catalase-peroxidases in Chaetomium thermophilum and their molecular evolution. Gene 2018; 666:83-91. [DOI: 10.1016/j.gene.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/26/2018] [Accepted: 05/02/2018] [Indexed: 11/25/2022]
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Abstract
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
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42
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Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors. Extremophiles 2018; 22:525-535. [DOI: 10.1007/s00792-018-1014-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/11/2018] [Indexed: 10/18/2022]
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43
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Liu Y, Freeman A, Déclais AC, Gartner A, Lilley DMJ. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes. Methods Enzymol 2018; 600:543-568. [PMID: 29458774 DOI: 10.1016/bs.mie.2017.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Four-way Holliday junctions in DNA are the central intermediates of genetic recombination and must be processed into regular duplex species. One mechanism for achieving this is called resolution, brought about by structure-selective nucleases. GEN1 is an important junction-resolving enzyme in eukaryotic cells, a member of the FEN1/EXO1 superfamily of nucleases. While human GEN1 is difficult to work with because of aggregation, orthologs from thermophilic fungi have been identified using bioinformatics and have proved to have excellent properties. Here, the expression and purification of this enzyme from Chaetomium thermophilum is described, together with the means of investigating its biochemical properties. The enzyme is quite similar to junction-resolving enzymes from lower organisms, binding to junctions in dimeric form, introducing symmetrical bilateral cleavages, the second of which is accelerated to promote productive resolution. Crystallization of C. thermophilum GEN1 is described, and the structure of a DNA-product complex. Juxtaposition of complexes in the crystal lattice suggests how the structure of a dimeric enzyme with an intact junction is organized.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Alasdair Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - Anton Gartner
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom.
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44
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Laluce C, Igbojionu LI, Dussán KJ. Fungal Enzymes Applied to Industrial Processes for Bioethanol Production. Fungal Biol 2018. [DOI: 10.1007/978-3-319-90379-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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45
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Hüttner S, Nguyen TT, Granchi Z, Chin-A-Woeng T, Ahrén D, Larsbrink J, Thanh VN, Olsson L. Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:265. [PMID: 29158777 PMCID: PMC5683368 DOI: 10.1186/s13068-017-0956-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/04/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The information obtained enables the investigation and discovery of genes encoding proteins involved in plant cell wall degradation, which are crucial for saccharification of lignocellulosic biomass in second-generation biorefinery applications. The thermophilic fungus Malbranchea cinnamomea is an efficient producer of many industrially relevant enzymes and a detailed analysis of its genomic content will considerably enhance our understanding of its lignocellulolytic system and promote the discovery of novel proteins. RESULTS The 25-million-base-pair genome of M. cinnamomea FCH 10.5 was sequenced with 225× coverage. A total of 9437 protein-coding genes were predicted and annotated, among which 301 carbohydrate-active enzyme (CAZyme) domains were found. The putative CAZymes of M. cinnamomea cover cellulases, hemicellulases, chitinases and pectinases, equipping the fungus with the ability to grow on a wide variety of biomass types. Upregulation of 438 and 150 genes during growth on wheat bran and xylan, respectively, in comparison to growth on glucose was revealed. Among the most highly upregulated CAZymes on xylan were glycoside hydrolase family GH10 and GH11 xylanases, as well as a putative glucuronoyl esterase and a putative lytic polysaccharide monooxygenase (LPMO). AA9-domain-containing proteins were also found to be upregulated on wheat bran, as well as a putative cutinase and a protein harbouring a CBM9 domain. Several genes encoding secreted proteins of unknown function were also more abundant on wheat bran and xylan than on glucose. CONCLUSIONS The comprehensive combined genome and transcriptome analysis of M. cinnamomea provides a detailed insight into its response to growth on different types of biomass. In addition, the study facilitates the further exploration and exploitation of the repertoire of industrially relevant lignocellulolytic enzymes of this fungus.
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Affiliation(s)
- Silvia Hüttner
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Thanh Thuy Nguyen
- Centre for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Ha Noi, Vietnam
| | - Zoraide Granchi
- GenomeScan B.V., Plesmanlaan 1/D, 2333 BZ Leiden, The Netherlands
| | | | - Dag Ahrén
- National Bioinformatics Infrastructure Sweden (NBIS), Institute of Biology, Lund University, 223 62 Lund, Sweden
| | - Johan Larsbrink
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Vu Nguyen Thanh
- Centre for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Ha Noi, Vietnam
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Wallenberg Wood Science Center, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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46
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Wilhelm RC, Cardenas E, Maas KR, Leung H, McNeil L, Berch S, Chapman W, Hope G, Kranabetter JM, Dubé S, Busse M, Fleming R, Hazlett P, Webster KL, Morris D, Scott DA, Mohn WW. Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities. THE ISME JOURNAL 2017; 11:2552-2568. [PMID: 28753210 PMCID: PMC5649165 DOI: 10.1038/ismej.2017.109] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/03/2017] [Accepted: 05/19/2017] [Indexed: 11/09/2022]
Abstract
The growing demand for renewable, carbon-neutral materials and energy is leading to intensified forest land-use. The long-term ecological challenges associated with maintaining soil fertility in managed forests are not yet known, in part due to the complexity of soil microbial communities and the heterogeneity of forest soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal soil populations in 11- to 17-year-old reforested coniferous plantations at 18 sites across North America. Analysis of highly replicated 16 S rRNA gene and ITS region pyrotag libraries and shotgun metagenomes demonstrated consistent changes in microbial communities in harvested plots that included the expansion of desiccation- and heat-tolerant organisms and decline in diversity of ectomycorrhizal fungi. However, the majority of taxa, including the most abundant and cosmopolitan groups, were unaffected by harvesting. Shifts in microbial populations that corresponded to increased temperature and soil dryness were moderated by OM retention, which also selected for sub-populations of fungal decomposers. Biogeographical differences in the distribution of taxa as well as local edaphic and environmental conditions produced substantial variation in the effects of harvesting. This extensive molecular-based investigation of forest soil advances our understanding of forest disturbance and lays the foundation for monitoring long-term impacts of timber harvesting.
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Affiliation(s)
- Roland C Wilhelm
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erick Cardenas
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kendra R Maas
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Leung
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Larisa McNeil
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shannon Berch
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, British Columbia, Canada
| | - William Chapman
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, British Columbia, Canada
| | - Graeme Hope
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, British Columbia, Canada
| | - J M Kranabetter
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, British Columbia, Canada
| | - Stephane Dubé
- College of New Caledonia, Prince George, British Columbia, Canada
| | | | - Robert Fleming
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Paul Hazlett
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Kara L Webster
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - David Morris
- Ontario Ministry of Natural Resources, Thunder Bay, Ontario, Canada
| | | | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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47
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Gu W, Lu Y, Tan Z, Xu P, Xie K, Li X, Sun L. Fungi diversity from different depths and times in chicken manure waste static aerobic composting. BIORESOURCE TECHNOLOGY 2017; 239:447-453. [PMID: 28538200 DOI: 10.1016/j.biortech.2017.04.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 06/07/2023]
Abstract
The Dirichlet multinomial mixtures mode was used to analyse illumina sequencing data to reveal both temporal and spatial variations of the fungi community present in the aerobic composting. Results showed that 670 operational taxonomic units (OTUs) were detected, and the dominant phylum was Ascomycota. There were four types of samples fungi communities during the composting process. Samples from the early composting stage were mainly grouped into type I and Saccharomycetales sp. was dominant. Fungi community in the medium composting stage were fallen into type II and III, Sordariales sp. and Acremonium alcalophilum, Saccharomycetales sp. and Scedosporium minutisporum were the dominant OTUs respectively. Samples from the late composting stage were mainly grouped into type IV and Scedosporium minutisporum was the dominant OTU; Scedosporium minutisporum was significantly affected by depth (P<0.05). Results indicate that time and depth both are factors that influence fungi distribution and variation in c waste during static aerobic composting.
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Affiliation(s)
- Wenjie Gu
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China; Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Yusheng Lu
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Zhiyuan Tan
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| | - Peizhi Xu
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Kaizhi Xie
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Xia Li
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Lili Sun
- Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture/Guangdong Key Laboratory of Nutrient Cycling and Farmland Conservation/Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
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48
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Genome Sequence of the Thermophilic Biomass-Degrading Fungus Malbranchea cinnamomea FCH 10.5. GENOME ANNOUNCEMENTS 2017; 5:5/33/e00779-17. [PMID: 28818895 PMCID: PMC5604768 DOI: 10.1128/genomea.00779-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the annotated draft genome sequence of the thermophilic biomass-degrading fungus Malbranchea cinnamomea strain FCH 10.5, isolated from compost at a waste treatment plant in Vietnam. The genome sequence contains 24.96 Mb with an overall GC content of 49.79% and comprises 9,437 protein-coding genes.
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49
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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50
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Natvig DO, Taylor JW, Tsang A, Hutchinson MI, Powell AJ. Mycothermus thermophilusgen. et comb. nov., a new home for the itinerant thermophileScytalidium thermophilum(Torula thermophila). Mycologia 2017; 107:319-27. [DOI: 10.3852/13-399] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Donald O. Natvig
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, H4B 1R6 Canada
| | | | - Amy J. Powell
- Sandia National Laboratories, Albuquerque, New Mexico 87123
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