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Gourlie R, McDonald M, Hafez M, Ortega-Polo R, Low KE, Abbott DW, Strelkov SE, Daayf F, Aboukhaddour R. The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB. BMC Biol 2022; 20:239. [PMID: 36280878 PMCID: PMC9594970 DOI: 10.1186/s12915-022-01433-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements. RESULTS A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr's adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr's effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb 'Starship' transposon (dubbed 'Horizon') with a clearly defined target site and target site duplications. 'Horizon' was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative 'Starship' (dubbed 'Icarus') in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and 'Icarus' were both present in a different non-coding isolate. This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as 'one-compartment' based on calculated gene distances and evolutionary rates. CONCLUSIONS These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr.
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Affiliation(s)
- Ryan Gourlie
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Megan McDonald
- grid.6572.60000 0004 1936 7486School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, UK
| | - Mohamed Hafez
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Rodrigo Ortega-Polo
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Kristin E. Low
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - D. Wade Abbott
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
| | - Stephen E. Strelkov
- grid.17089.370000 0001 2190 316XFaculty of Agricultural, Life, and Environmental Sciences, University of Alberta, Edmonton, AB Canada
| | - Fouad Daayf
- grid.21613.370000 0004 1936 9609Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB Canada
| | - Reem Aboukhaddour
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, Lethbridge, AB Canada
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Identification of Gene Modules and Hub Genes Associated with Sporisorium scitamineum Infection Using Weighted Gene Co-Expression Network Analysis. J Fungi (Basel) 2022; 8:jof8080852. [PMID: 36012840 PMCID: PMC9409688 DOI: 10.3390/jof8080852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus responsible for sugarcane smut disease. To investigate the key genes involved in S. scitamineum infection, we conducted RNA sequencing of sugarcane sprouts inoculated with S. scitamineum teliospores. A weighted gene co-expression network analysis (WGCNA) showed that two co-expressed gene modules, MEdarkturquoise and MEpurple—containing 66 and 208 genes, respectively—were associated with S. scitamineum infection. The genes in these two modules were further studied using Gene Ontology (GO) enrichment analysis, pathogen-host interaction (PHI) database BLASTp, and small secreted cysteine-rich proteins (SCRPs) prediction. The top ten hub genes in each module were identified using the Cytohubba plugin. The GO enrichment analysis found that endoplasmic reticulum-related and catabolism-related genes were expressed during S. scitamineum infection. A total of 83 genes had homologs in the PHI database, 62 of which correlated with pathogen virulence. A total of 21 proteins had the characteristics of small secreted cysteine-rich proteins (SCRPs), a common source of fungal effectors. The top ten hub genes in each module were identified, and seven were annotated as Mig1-Mig1 protein, glycosyl hydrolase, beta-N-acetylglucosaminidase, secreted chorismate mutase, collagen, mRNA export factor, and pleckstrin homology domain protein, while the remaining three were unknown. Two SCRPs—SPSC_06609 and SPSC_04676—and three proteins—SPSC_01958, SPSC_02155, and SPSC_00940—identified in the PHI database were also among the top ten hub genes in the MEdarkturquoise and MEpurple modules, suggesting that they may play important roles in S. scitamineum infection. A S. scitamineum infection model was postulated based on current findings. These findings help to deepen the current understanding of early events in S. scitamineum infection.
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Screening of Cellulolytic Bacteria from Various Ecosystems and Their Cellulases Production under Multi-Stress Conditions. Catalysts 2022. [DOI: 10.3390/catal12070769] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cellulose represents the most abundant component of plant biomass on earth; it is degraded by cellulases, specific enzymes produced by microorganisms. However, cellulases of bacterial origin attract more interest due to their natural diversity and ability to inhabit a variety of niches, allowing the selection of cellulolytic strains resistant to environmental stresses. The screening of the cellulolytic activity of 398 bacteria isolated from various ecosystems in Algeria (cave, ruins, chott, thermal station, and rhizosphere of arid and semi-arid regions) was performed by the appearance of a hydrolysis zone on carboxymethylcellulose (CMC) medium. The cellulase activity on CMC (1%) broth allowed to select 26 strains among which 12 had the best activity (0.3 U/mL to 2.2 U/mL). Optimization of physicochemical parameters (salinity: 0–1 M NaCl; pH: 3, 4, 7, 9, and 11; temperature: 30, 45, and 50 °C; PEG8000: 0 and 30%) involved in growth and cellulose production showed that the majority of strains were mesophilic, neutrophilic, or alkali- tolerant and tolerant to 30% of PEG8000. The cellulase activity and stability under different stress allowed to retain five strains, which the most efficient. Based on the 16S-rRNA sequencing results, they belonged to the genus Bacillus. The physicochemical properties of cellulases (crude extract) showed a CMCase active over a wide range of pH (4 to 11), optimal at 50 °C and 60 °C. The inhibiting salinity effect on the activity was not detected and was negligible on the enzymatic stability. The residual CMCase activity remained between 40 and 70% in a temperature range between 40 and 70 °C, was stable over a wide range of saline concentrations (0–2000 mM), and was weakly affected at 30% of PEG8000. The crude enzyme extract was able to hydrolyze both soluble and insoluble cellulosic substrates. The evaluation of the hydrolysis capacity of lignocellulosic waste revealed the ability of tested strains to degrade wheat bran, barley bran, and corncob. In addition, the enzyme showed significant multi-stress resistance on solid and liquid media. By these characteristics, these cellulolytic bacteria could be attractive to be used in various industrial and biotechnology applications.
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Reppke MJ, Gerstner R, Windeisen-Holzhauser E, Richter K, Benz JP. Press water from the mechanical drying of Douglas-fir wood chips has multiple beneficial effects on lignocellulolytic fungi. Fungal Biol Biotechnol 2022; 9:10. [PMID: 35606847 PMCID: PMC9128199 DOI: 10.1186/s40694-022-00141-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/10/2022] [Indexed: 12/05/2022] Open
Abstract
Background The mechanical drying of wood chips is an innovative method that improves the heating value of sawmill by-products in an energy-efficient continuous process. The liquid that comes out of the wood chips as press water (PW), however, contains a variety of undissolved as well as dissolved organic substances. The disposal of the PW as wastewater would generate additional costs due to its high organic load, offsetting the benefits in energy costs associated with the enhanced heating value of the wood chips. Our research explored if the organic load in PW could be utilized as a substrate by cellulolytic filamentous fungi. Hence, using the industrially relevant Ascomycete Trichoderma reesei RUT-C30 as well as several Basidiomycete wood-rotting fungi, we examined the potential of press water obtained from Douglas-fir wood chips to be used in the growth and enzyme production media. Results The addition of PW supernatant to liquid cultures of T. reesei RUT-C30 resulted in a significant enhancement of the endoglucanase and endoxylanase activities with a substantially shortened lag-phase. A partial replacement of Ca2+, Mg2+, K+, as well as a complete replacement of Fe2+, Mn2+, Zn2+ by supplementing PW of the liquid media was achieved without negative effects on enzyme production. Concentrations of PW above 50% showed no adverse effects regarding the achievable endoglucanase activity but affected the endoxylanase activity to some extent. Exploring the enhancing potential of several individual PW components after chemical analysis revealed that the observed lag-phase reduction of T. reesei RUT-C30 was not caused by the dissolved sugars and ions, nor the wood particles in the PW sediment, suggesting that other, so far non-identified, compounds are responsible. However, also the growth rate of several basidiomycetes was significantly enhanced by the supplementation of raw PW to the agar medium. Moreover, their cultivation in liquid cultures reduced the turbidity of the PW substantially. Conclusions PW was identified as a suitable media supplement for lignocellulolytic fungi, including the cellulase and xylanase producer T. reesei RUT-C30 and several wood-degrading basidiomycetes. The possibility to replace several minerals, trace elements and an equal volume of fresh water in liquid media with PW and the ability of fungal mycelia to filter out the suspended solids is a promising way to combine biological wastewater treatment with value-adding biotechnological applications. Supplementary Information The online version contains supplementary material available at 10.1186/s40694-022-00141-y.
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Wang YH, Hou LL, Wu XQ, Zhu ML, Dai Y, Zhao YJ. Mycorrhiza helper bacterium Bacillus pumilus HR10 improves growth and nutritional status of Pinus thunbergii by promoting mycorrhizal proliferation. TREE PHYSIOLOGY 2022; 42:907-918. [PMID: 34730183 DOI: 10.1093/treephys/tpab139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Mycorrhizal helper bacteria (MHB) play an important role in mediating mycorrhizal symbiosis, which improves the growth and nutrient uptake of plants. This study examined the growth-promoting effects and mechanisms of pine growth after inoculation with the MHB Bacillus pumilus HR10 and/or Hymenochaete sp. Rl. The effect of B. pumilus HR10 on Hymenochaete sp. Rl growth, enzyme activity and gene expression related to mycorrhiza formation were determined. The growth, root activity, nitrogen, phosphorus, and potassium content and chlorophyll fluorescence activity of Pinus thunbergii and the mycorrhizal colonization intensity of Hymenochaete sp. Rl-inoculated pine seedlings after inoculation with B. pumilus HR10 were also evaluated. The results showed that B. pumilus HR10 promoted growth, regulated the expression of mycorrhizal-related genes and affected the β-1,3-glucanase activity of Hymenochaete sp. Rl. The mycorrhizal colonization intensity of pine seedlings co-inoculated with B. pumilus HR10 and Hymenochaete sp. Rl was 1.58-fold higher than seedlings inoculated with only Hymenochaete sp. Rl. Inoculation with B. pumilus HR10 and/or Hymenochaete sp. Rl increased lateral root number and root activity of pine seedlings and chlorophyll fluorescence activity of pine needles compared with the control. Bacillus pumilus HR10 facilitated nutrient uptake by enhancing the mycorrhizal proliferation of pine and induced greater photosynthesis and root activity of pine seedlings, which confirms its role as an outstanding plant-growth-promoting rhizobacterium. These findings improve our understanding of the mechanism of B. pumilus HR10 promotion of mycorrhizal symbiosis.
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Affiliation(s)
- Ya-Hui Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Liang-Liang Hou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Mei-Ling Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yun Dai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yin-Juan Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
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Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
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Lamit LJ, Romanowicz KJ, Potvin LR, Lennon JT, Tringe SG, Chimner RA, Kolka RK, Kane ES, Lilleskov EA. Peatland microbial community responses to plant functional group and drought are depth-dependent. Mol Ecol 2021; 30:5119-5136. [PMID: 34402116 DOI: 10.1111/mec.16125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022]
Abstract
Peatlands store one-third of Earth's soil carbon, the stability of which is uncertain due to climate change-driven shifts in hydrology and vegetation, and consequent impacts on microbial communities that mediate decomposition. Peatland carbon cycling varies over steep physicochemical gradients characterizing vertical peat profiles. However, it is unclear how drought-mediated changes in plant functional groups (PFGs) and water table (WT) levels affect microbial communities at different depths. We combined a multiyear mesocosm experiment with community sequencing across a 70-cm depth gradient, to test the hypotheses that vascular PFGs (Ericaceae vs. sedges) and WT (high vs. low) structure peatland microbial communities in depth-dependent ways. Several key results emerged. (i) Both fungal and prokaryote (bacteria and archaea) community structure shifted with WT and PFG manipulation, but fungi were much more sensitive to PFG whereas prokaryotes were much more sensitive to WT. (ii) PFG effects were largely driven by Ericaceae, although sedge effects were evident in specific cases (e.g., methanotrophs). (iii) Treatment effects varied with depth: the influence of PFG was strongest in shallow peat (0-10, 10-20 cm), whereas WT effects were strongest at the surface and middle depths (0-10, 30-40 cm), and all treatment effects waned in the deepest peat (60-70 cm). Our results underline the depth-dependent and taxon-specific ways that plant communities and hydrologic variability shape peatland microbial communities, pointing to the importance of understanding how these factors integrate across soil profiles when examining peatland responses to climate change.
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Affiliation(s)
- Louis J Lamit
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Karl J Romanowicz
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Lynette R Potvin
- USDA Forest Service Northern Research Station, Houghton, Michigan, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rodney A Chimner
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Randall K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, Minnesota, USA
| | - Evan S Kane
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA.,USDA Forest Service Northern Research Station, Houghton, Michigan, USA
| | - Erik A Lilleskov
- USDA Forest Service Northern Research Station, Houghton, Michigan, USA
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Quo vadis: signaling molecules and small secreted proteins from mycorrhizal fungi at the early stage of mycorrhiza formation. Symbiosis 2021. [DOI: 10.1007/s13199-021-00793-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Conlon BH, Gostinčar C, Fricke J, Kreuzenbeck NB, Daniel JM, Schlosser MS, Peereboom N, Aanen DK, de Beer ZW, Beemelmanns C, Gunde-Cimerman N, Poulsen M. Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis. iScience 2021; 24:102680. [PMID: 34189441 PMCID: PMC8220239 DOI: 10.1016/j.isci.2021.102680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/07/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
Insights into the genomic consequences of symbiosis for basidiomycete fungi associated with social insects remain sparse. Capitalizing on viability of spores from centuries-old herbarium specimens of free-living, facultative, and specialist termite-associated Podaxis fungi, we obtained genomes of 10 specimens, including two type species described by Linnaeus >240 years ago. We document that the transition to termite association was accompanied by significant reductions in genome size and gene content, accelerated evolution in protein-coding genes, and reduced functional capacities for oxidative stress responses and lignin degradation. Functional testing confirmed that termite specialists perform worse under oxidative stress, while all lineages retained some capacity to cleave lignin. Mitochondrial genomes of termite associates were significantly larger; possibly driven by smaller population sizes or reduced competition, supported by apparent loss of certain biosynthetic gene clusters. Our findings point to relaxed selection that mirrors genome traits observed among obligate endosymbiotic bacteria of many insects.
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Affiliation(s)
- Benjamin H. Conlon
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Janis Fricke
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Nina B. Kreuzenbeck
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Jan-Martin Daniel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Malte S.L. Schlosser
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Nils Peereboom
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Duur K. Aanen
- Department of Plant Sciences, Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Z. Wilhelm de Beer
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoll-Institute, Chemical Biology, 07745 Jena, Germany
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
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Lee DS, Lee YG, Cho EJ, Song Y, Bae HJ. Hydrolysis pattern analysis of xylem tissues of woody plants pretreated with hydrogen peroxide and acetic acid: rapid saccharification of softwood for economical bioconversion. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:37. [PMID: 33549141 PMCID: PMC7866737 DOI: 10.1186/s13068-021-01889-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/25/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Woody plants with high glucose content are alternative bioresources for the production of biofuels and biochemicals. Various pretreatment methods may be used to reduce the effects of retardation factors such as lignin interference and cellulose structural recalcitrance on the degradation of the lignocellulose material of woody plants. RESULTS A hydrogen peroxide-acetic acid (HPAC) pretreatment was used to reduce the lignin content of several types of woody plants, and the effect of the cellulose structural recalcitrance on the enzymatic hydrolysis was analyzed. The cellulose structural recalcitrance and the degradation patterns of the wood fibers in the xylem tissues of Quercus acutissima (hardwood) resulted in greater retardation in the enzymatic saccharification than those in the tracheids of Pinus densiflora (softwood). In addition to the HPAC pretreatment, the application of supplementary enzymes (7.5 FPU cellulase for 24 h) further increased the hydrolysis rate of P. densiflora from 61.42 to 91.94% whereas the same effect was not observed for Q. acutissima. It was also observed that endoxylanase synergism significantly affected the hydrolysis of P. densiflora. However, this synergistic effect was lower for other supplementary enzymes. The maximum concentration of the reducing sugars produced from 10% softwood was 89.17 g L-1 after 36 h of hydrolysis with 15 FPU cellulase and other supplementary enzymes. Approximately 80 mg mL-1 of reducing sugars was produced with the addition of 7.5 FPU cellulase and other supplementary enzymes after 36 h, achieving rapid saccharification. CONCLUSION HPAC pretreatment removed the interference of lignin, reduced structural recalcitrance of cellulose in the P. densiflora, and enabled rapid saccharification of the woody plants including a high concentration of insoluble substrates with only low amounts of cellulase. HPAC pretreatment may be a viable alternative for the cost-efficient production of biofuels or biochemicals from softwood plant tissues.
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Affiliation(s)
- Dae-Seok Lee
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Yoon-Gyo Lee
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Eun Jin Cho
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Younho Song
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Hyeun-Jong Bae
- Bio-Energy Research Center, Chonnam National University, Gwangju, 500-757, Republic of Korea.
- Department of Bioenergy Science and Technology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, Republic of Korea.
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Hess J, Skrede I, Chaib De Mares M, Hainaut M, Henrissat B, Pringle A. Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita. Mol Biol Evol 2018; 35:2786-2804. [PMID: 30239843 PMCID: PMC6231487 DOI: 10.1093/molbev/msy179] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.
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Affiliation(s)
- Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Maryam Chaib De Mares
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille University, Marseille, France
- INRA, USC1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin, Madison, Madison, WI
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Partial Purification and Characterization of Cellulolytic Enzymes Extracted from Trichoderma reesei Inoculated Digested Biogas Slurry. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.4.37] [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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Stappler E, Walton JD, Beier S, Schmoll M. Abundance of Secreted Proteins of Trichoderma reesei Is Regulated by Light of Different Intensities. Front Microbiol 2017; 8:2586. [PMID: 29375497 PMCID: PMC5770571 DOI: 10.3389/fmicb.2017.02586] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022] Open
Abstract
In Trichoderma reesei light is an important factor in the regulation of glycoside hydrolase gene expression. We therefore investigated the influence of different light intensities on cellulase activity and protein secretion. Differentially secreted proteins in light and darkness as identified by mass spectrometry included members of different glycoside hydrolase families, such as CBH1, Cel3A, Cel61B, XYN2, and XYN4. Several of the associated genes showed light-dependent regulation on the transcript level. Deletion of the photoreceptor genes blr1 and blr2 resulted in a diminished difference of protein abundance between light and darkness. The amount of secreted proteins including that of the major exo-acting beta-1,4-glucanases CBH1 and CBH2 was generally lower in light-grown cultures than in darkness. In contrast, cbh1 transcript levels increased with increasing light intensity from 700 to 2,000 lux but dopped at high light intensity (5,000 lux). In the photoreceptor mutants Δblr1 and Δblr2 cellulase activity in light was reduced compared to activity in darkness, showing a discrepancy between transcript levels and secreted cellulase activity. Furthermore, evaluation of different light sensitivities revealed an increased light tolerance with respect to cellulase expression of QM9414 compared to its parental strain QM6a. Investigation of one of the differentially expressed proteins between light and darkness, CLF1, revealed its function as a factor involved in regulation of secreted protease activity. T. reesei secretes a different set of proteins in light compared to darkness, this difference being mainly due to the function of the major known photoreceptors. Moreover, cellulase regulation is adjusted to light intensity and improved light tolerance was correlated with increased cellulase production. Our findings further support the hypothesis of a light intensity dependent post-transcriptional regulation of cellulase gene expression in T. reesei.
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Affiliation(s)
- Eva Stappler
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Jonathan D. Walton
- MSU-DOE Plant Research Laboratory, Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Sabrina Beier
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Monika Schmoll
- Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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Imran M, Hussain A, Anwar Z, Irshad M, Jabeen F. Beta-Glucosidase Production Optimization from Newly Isolated Aspergillus tubingensis IMMIS2 Using Taguchi Statistical Design. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY TRANSACTION A-SCIENCE 2017. [DOI: 10.1007/s40995-017-0462-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Schuelke TA, Wu G, Westbrook A, Woeste K, Plachetzki DC, Broders K, MacManes MD. Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia. Genome Biol Evol 2017; 9:3312-3327. [PMID: 29186370 PMCID: PMC5737690 DOI: 10.1093/gbe/evx242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2017] [Indexed: 12/29/2022] Open
Abstract
Geosmithia morbida is an emerging fungal pathogen which serves as a model for examining the evolutionary processes behind pathogenicity because it is one of two known pathogens within a genus of mostly saprophytic, beetle-associated, fungi. This pathogen causes thousand cankers disease in black walnut trees and is vectored into the host via the walnut twig beetle. Geosmithia morbida was first detected in western United States and currently threatens the timber industry concentrated in eastern United States. We sequenced the genomes of G. morbida in a previous study and two nonpathogenic Geosmithia species in this work and compared these species to other fungal pathogens and nonpathogens to identify genes under positive selection in G. morbida that may be associated with pathogenicity. Geosmithia morbida possesses one of the smallest genomes among the fungal species observed in this study, and one of the smallest fungal pathogen genomes to date. The enzymatic profile in this pathogen is very similar to its nonpathogenic relatives. Our findings indicate that genome reduction or retention of a smaller genome may be an important adaptative force during the evolution of a specialized lifestyle in fungal species that occupy a specificniche, such as beetle vectored tree pathogens. We also present potential genes under selection in G. morbida that could be important for adaptation to a pathogenic lifestyle.
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Affiliation(s)
- Taruna A Schuelke
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire
| | - Guangxi Wu
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
| | | | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University
| | - David C Plachetzki
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University
| | - Matthew D MacManes
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire
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Smith GR, Finlay RD, Stenlid J, Vasaitis R, Menkis A. Growing evidence for facultative biotrophy in saprotrophic fungi: data from microcosm tests with 201 species of wood-decay basidiomycetes. THE NEW PHYTOLOGIST 2017; 215:747-755. [PMID: 28382741 DOI: 10.1111/nph.14551] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Ectomycorrhizal (ECM) symbioses have evolved a minimum of 78 times independently from saprotrophic lineages, indicating the potential for functional overlap between ECM and saprotrophic fungi. ECM fungi have the capacity to decompose organic matter, and although there is increasing evidence that some saprotrophic fungi exhibit the capacity to enter into facultative biotrophic relationships with plant roots without causing disease symptoms, this subject is still not well studied. In order to determine the extent of biotrophic capacity in saprotrophic wood-decay fungi and which systems may be useful models, we investigated the colonization of conifer seedling roots in vitro using an array of 201 basidiomycete wood-decay fungi. Microtome sectioning, differential staining and fluorescence microscopy were used to visualize patterns of root colonization in microcosm systems containing Picea abies or Pinus sylvestris seedlings and each saprotrophic fungus. Thirty-four (16.9%) of the tested fungal species colonized the roots of at least one tree species. Two fungal species showed formation of a mantle and one showed Hartig net-like structures. These features suggest the possibility of an active functional symbiosis between fungus and plant. The data indicate that the capacity for facultative biotrophic relationships in free-living saprotrophic basidiomycetes may be greater than previously supposed.
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Affiliation(s)
- Gabriel R Smith
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
| | - Roger D Finlay
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala, SE-75007, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala, SE-75007, Sweden
| | - Rimvydas Vasaitis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala, SE-75007, Sweden
| | - Audrius Menkis
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, Uppsala, SE-75007, Sweden
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Persistence of ecto- and ectendomycorrhizal fungi associated with Pinus montezumae in experimental microcosms. Symbiosis 2017. [DOI: 10.1007/s13199-017-0496-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mayerhofer MS, Fraser E, Kernaghan G. Acid protease production in fungal root endophytes. Mycologia 2017; 107:1-11. [DOI: 10.3852/14-106] [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)
| | | | - Gavin Kernaghan
- Department of Biology, Mount Saint Vincent University, 166 Bedford Highway, Halifax, Nova Scotia, Canada, B3M 2J6
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Sillo F, Fangel JU, Henrissat B, Faccio A, Bonfante P, Martin F, Willats WGT, Balestrini R. Understanding plant cell-wall remodelling during the symbiotic interaction between Tuber melanosporum and Corylus avellana using a carbohydrate microarray. PLANTA 2016; 244:347-59. [PMID: 27072675 DOI: 10.1007/s00425-016-2507-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/24/2016] [Indexed: 05/09/2023]
Abstract
A combined approach, using a carbohydrate microarray as a support for genomic data, has revealed subtle plant cell-wall remodelling during Tuber melanosporum and Corylus avellana interaction. Cell walls are involved, to a great extent, in mediating plant-microbe interactions. An important feature of these interactions concerns changes in the cell-wall composition during interaction with other organisms. In ectomycorrhizae, plant and fungal cell walls come into direct contact, and represent the interface between the two partners. However, very little information is available on the re-arrangement that could occur within the plant and fungal cell walls during ectomycorrhizal symbiosis. Taking advantage of the Comprehensive Microarray Polymer Profiling (CoMPP) technology, the current study has had the aim of monitoring the changes that take place in the plant cell wall in Corylus avellana roots during colonization by the ascomycetous ectomycorrhizal fungus T. melanosporum. Additionally, genes encoding putative plant cell-wall degrading enzymes (PCWDEs) have been identified in the T. melanosporum genome, and RT-qPCRs have been performed to verify the expression of selected genes in fully developed C. avellana/T. melanosporum ectomycorrhizae. A localized degradation of pectin seems to occur during fungal colonization, in agreement with the growth of the ectomycorrhizal fungus through the middle lamella and with the fungal gene expression of genes acting on these polysaccharides.
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Affiliation(s)
- Fabiano Sillo
- Dipartimento di Scienze Della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, Grugliasco, 10095, Turin, Italy
| | - Jonatan U Fangel
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, Copenhagen, Denmark
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique, UMR 7257, 13288, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, 13288, Marseille, France
- INRA, USC 1408 AFMB, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Antonella Faccio
- Istituto per la Protezione Sostenibile delle Piante (IPSP) del CNR, Torino Unit, Viale Mattioli 25, 10125, Torino, Italy
| | - Paola Bonfante
- Dipartimento di Scienze Della Vita e Biologia dei Sistemi, Università di Torino, Torino, Italy
| | - Francis Martin
- Laboratoire d'excellence ARBRE, Institut National de la Recherche Agronomique (INRA), UMR 1136 Interactions Arbres/Microorganismes, INRA-Nancy, 54 280, Champenoux, France
| | - William G T Willats
- Section for Plant Glycobiology, Department of Plant and Environmental Sciences, Copenhagen University, Copenhagen, Denmark
| | - Raffaella Balestrini
- Istituto per la Protezione Sostenibile delle Piante (IPSP) del CNR, Torino Unit, Viale Mattioli 25, 10125, Torino, Italy.
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Stöckli M, Lin CW, Sieber R, Plaza DF, Ohm RA, Künzler M. Coprinopsis cinerea intracellular lactonases hydrolyze quorum sensing molecules of Gram-negative bacteria. Fungal Genet Biol 2016; 102:49-62. [PMID: 27475110 DOI: 10.1016/j.fgb.2016.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Biofilm formation on fungal hyphae and production of antifungal molecules are strategies of bacteria in their competition with fungi for nutrients. Since these strategies are often coordinated and under control of quorum sensing by the bacteria, interference with this bacterial communication system can be used as a counter-strategy by the fungi in this competition. Hydrolysis of N-acyl-homoserine lactones (HSL), a quorum sensing molecule used by Gram-negative bacteria, by fungal cultures has been demonstrated. However, the enzymes that are responsible for this activity, have not been identified. In this study, we identified and characterized two paralogous HSL hydrolyzing enzymes from the coprophilous fungus Coprinopsis cinerea. The C. cinerea HSL lactonases belong to the metallo-β-lactamase family and show sequence homology to and a similar biochemical activity as the well characterized lactonase AiiA from Bacillus thuringiensis. We show that the fungal lactonases, similar to the bacterial enzymes, are kept intracellularly and act as a sink for the bacterial quorum sensing signals both in C. cinerea and in Saccharomyces cerevisiae expressing C. cinerea lactonases, due to the ability of these signal molecules to diffuse over the fungal cell wall and plasma membrane. The two isogenes coding for the C. cinerea HSL lactonases are arranged in the genome as a tandem repeat and expressed preferentially in vegetative mycelium. The occurrence of orthologous genes in genomes of other basidiomycetes appears to correlate with a saprotrophic lifestyle.
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Affiliation(s)
- Martina Stöckli
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Ramon Sieber
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - David F Plaza
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Robin A Ohm
- Microbiology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, The Netherlands.
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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Lehmann L, Rønnest NP, Jørgensen CI, Olsson L, Stocks SM, Jørgensen HS, Hobley T. Linking hydrolysis performance to Trichoderma reesei cellulolytic enzyme profile. Biotechnol Bioeng 2015; 113:1001-10. [PMID: 26524197 DOI: 10.1002/bit.25871] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 11/07/2022]
Abstract
Trichoderma reesei expresses a large number of enzymes involved in lignocellulose hydrolysis and the mechanism of how these enzymes work together is too complex to study by traditional methods, for example, by spiking with single enzymes and monitoring hydrolysis performance. In this study, a multivariate approach, partial least squares regression, was used to see whether it could help explain the correlation between enzyme profile and hydrolysis performance. Diverse enzyme mixtures were produced by T. reesei Rut-C30 by exploiting various fermentation conditions and used for hydrolysis of washed pretreated corn stover as a measure of enzyme performance. In addition, the enzyme mixtures were analyzed by liquid chromatography-tandem mass spectrometry to identify and quantify the different proteins. A multivariate model was applied for the prediction of enzyme performance based on the combination of different proteins present in an enzyme mixture. The multivariate model was used for identification of candidate proteins that are correlated to enzyme performance on pretreated corn stover. A very large variation in hydrolysis performance was observed and this was clearly caused by the difference in fermentation conditions. Besides β-glucosidase, the multivariate model identified several xylanases, Cip1 and Cip2, as relevant proteins to study further.
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Affiliation(s)
- Linda Lehmann
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Nanna P Rønnest
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Lyngby, Denmark
| | | | - Lisbeth Olsson
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | | | | | - Timothy Hobley
- Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Conroy N, Tebble I, Lye GJ. Creation of an ultra scale-down bioreactor mimic for rapid development of lignocellulosic enzymatic hydrolysis processes. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2015; 90:1983-1990. [PMID: 27594729 PMCID: PMC4989448 DOI: 10.1002/jctb.4801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/18/2015] [Accepted: 08/18/2015] [Indexed: 06/06/2023]
Abstract
BACKGROUND Cellulosic bioethanol processes involve several steps, all of which require experimental optimisation. A significant aid to this research would be a validated ultra scale-down (USD) model that could be used to perform rapid, wide ranging screening and optimisation experiments using limited materials under process relevant conditions. RESULTS In this work, the use of 30 mL shaken conical tubes as a USD model for an enzymatic hydrolysis process is established. The approach is demonstrated for the hydrolysis of distillers' dried grains with solubles (DDGS). Results from the USD tubes closely mimic those obtained from 4 L stirred tanks, in terms of the rate, composition and concentrations of sugars released, representing an 80-fold scale reduction. The utility of the USD approach is illustrated by investigating factors that may be limiting hydrolysis yields at high solids loadings. Washing the residual solids periodically during hydrolysis allowed 100% of the available sugar to be hydrolysed using commercially available enzymes. CONCLUSION The results demonstrate that the USD system reported successfully mimics the performance of conventional stirred tanks under industrially relevant conditions. The utility of the system was confirmed through its use to investigate performance limitation using a commercially relevant feedstock. © 2015 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Neil Conroy
- ReBio Technologies LtdUnit 59 Dunsfold ParkCranleighSurreyGU6 8TBUK; The Advanced Centre for Biochemical Engineering, Department of Biochemical EngineeringUniversity College LondonGordon StreetLondonWC1H 0AHUK
| | - Ian Tebble
- ReBio Technologies Ltd Unit 59 Dunsfold Park Cranleigh Surrey GU6 8TB UK
| | - Gary J Lye
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering University College London Gordon Street London WC1H 0AH UK
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Paudel YP, Qin W. Characterization of Novel Cellulase-producing Bacteria Isolated From Rotting Wood Samples. Appl Biochem Biotechnol 2015; 177:1186-98. [DOI: 10.1007/s12010-015-1806-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/10/2015] [Indexed: 11/30/2022]
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Gaur R, Tiwari S. Isolation, production, purification and characterization of an organic-solvent-thermostable alkalophilic cellulase from Bacillus vallismortis RG-07. BMC Biotechnol 2015; 15:19. [PMID: 25886936 PMCID: PMC4377051 DOI: 10.1186/s12896-015-0129-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
Background The rising concerns about the scarcity of fossil fuels, the emission of green house gasses and air pollution by incomplete combustion of fossil fuel have also resulted in an increasing focus on the use of cellulases to perform enzymatic hydrolysis of the lignocellulosic materials for the generation of bioethanol. The aim of this study was to isolate a potential thermo-solvent tolerant cellulase producing bacterium from natural resources, and then applied for purification and characterization. The purified enzyme was to be accessible for the bioethanol production as well as industrial exploitation (discuss in our next study). Results It is the first instance when thermo-solvent tolerant cellulase producing bacterium was isolated from soil sample. The culture was identified as Bacillus vallismortis RG-07 by 16S rDNA sequence analysis. Bacillus vallismortis RG-07 reported maximum cellulase production from sugarcane baggase (4105 U ml−1) used as agro-waste carbon source. The cellulase enzyme produced by the Bacillus sp. was purified by (NH4)2SO4 precipitation, ion exchange and gel filtration chromatography, with overall recovery of 28.8%. The molecular weight of purified cellulase was 80 kDa as revealed by SDS-PAGE and activity gel analysis. The optimum temperature and pH for enzyme activity was determined as 65°C and 7.0 and it retained 95 and 75% of activity even at 95°C, and 9.0 respectively. The enzyme activity was enhanced in the presence of organic solvents (30%) n-dodecane, iso-octane, n-decane, xylene, toluene, n-haxane, n-butanol, and cyclohexane, after prolonged incubation (7 days). The enzyme activity was also stimulated by Ca2+, mercaptoethanol, Tween-60, and Sodium hypochloride whereas strongly inhibited by Hg. Kinetic analysis of purified enzyme showed the Km and Vmax to be 1.923 mg ml−1 and 769.230 μg ml−1 min−1, respectively. Conclusion The unique property of solvent-thermostable-alkalophilic, nature proves the potential candidature of this isolate for current mainstream biomass conversion into fuel and other industrial process. Electronic supplementary material The online version of this article (doi:10.1186/s12896-015-0129-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rajeeva Gaur
- Department of Microbiology (Centre of Excellence), Dr. Ram Manohar Lohia Avadh University, Faizabad, 224001, Uttar Pradesh, India.
| | - Soni Tiwari
- Department of Microbiology (Centre of Excellence), Dr. Ram Manohar Lohia Avadh University, Faizabad, 224001, Uttar Pradesh, India.
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Chaib De Mares M, Hess J, Floudas D, Lipzen A, Choi C, Kennedy M, Grigoriev IV, Pringle A. Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal Amanita. THE NEW PHYTOLOGIST 2015; 205:1552-1564. [PMID: 25407899 DOI: 10.1111/nph.13140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/24/2014] [Indexed: 06/04/2023]
Abstract
The genus Amanita encompasses both symbiotic, ectomycorrhizal fungi and asymbiotic litter decomposers; all species are derived from asymbiotic ancestors. Symbiotic species are no longer able to degrade plant cell walls. The carbohydrate esterases family 1 (CE1s) is a diverse group of enzymes involved in carbon metabolism, including decomposition and carbon storage. CE1 genes of the ectomycorrhizal A. muscaria appear diverged from all other fungal homologues, and more similar to CE1s of bacteria, suggesting a horizontal gene transfer (HGT) event. In order to test whether AmanitaCE1s were acquired horizontally, we built a phylogeny of CE1s collected from across the tree of life, and describe the evolution of CE1 genes among Amanita and relevant lineages of bacteria. CE1s of symbiotic Amanita were very different from CE1s of asymbiotic Amanita, and are more similar to bacterial CE1s. The protein structure of one CE1 gene of A. muscaria matched a depolymerase that degrades the carbon storage molecule poly((R)-3-hydroxybutyrate) (PHB). Asymbiotic Amanita do not carry sequence or structural homologues of these genes. The CE1s acquired through HGT may enable novel metabolisms, or play roles in signaling or defense. This is the first evidence for the horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal fungi.
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Affiliation(s)
- Maryam Chaib De Mares
- Department of Microbial Ecology, University of Groningen, 9747 AG, Groningen, the Netherlands
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jaqueline Hess
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biosciences, University of Oslo, 0371, Oslo, Norway
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Megan Kennedy
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anne Pringle
- Harvard Forest, 324 North Main Street, Petersham, MA, 01366, USA
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Mäkelä MR, Marinović M, Nousiainen P, Liwanag AJM, Benoit I, Sipilä J, Hatakka A, de Vries RP, Hildén KS. Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass. ADVANCES IN APPLIED MICROBIOLOGY 2015; 91:63-137. [PMID: 25911233 DOI: 10.1016/bs.aambs.2014.12.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The biological conversion of plant lignocellulose plays an essential role not only in carbon cycling in terrestrial ecosystems but also is an important part of the production of second generation biofuels and biochemicals. The presence of the recalcitrant aromatic polymer lignin is one of the major obstacles in the biofuel/biochemical production process and therefore microbial degradation of lignin is receiving a great deal of attention. Fungi are the main degraders of plant biomass, and in particular the basidiomycete white rot fungi are of major importance in converting plant aromatics due to their ability to degrade lignin. However, the aromatic monomers that are released from lignin and other aromatic compounds of plant biomass are toxic for most fungi already at low levels, and therefore conversion of these compounds to less toxic metabolites is essential for fungi. Although the release of aromatic compounds from plant biomass by fungi has been studied extensively, relatively little attention has been given to the metabolic pathways that convert the resulting aromatic monomers. In this review we provide an overview of the aromatic components of plant biomass, and their release and conversion by fungi. Finally, we will summarize the applications of fungal systems related to plant aromatics.
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Affiliation(s)
- Miia R Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mila Marinović
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Paula Nousiainen
- Department of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, Helsinki, Finland
| | - April J M Liwanag
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Jussi Sipilä
- Department of Chemistry, Laboratory of Organic Chemistry, University of Helsinki, Helsinki, Finland
| | - Annele Hatakka
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Kristiina S Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Scott F, Li M, Williams DL, Conejeros R, Hodge DB, Aroca G. Corn stover semi-mechanistic enzymatic hydrolysis model with tight parameter confidence intervals for model-based process design and optimization. BIORESOURCE TECHNOLOGY 2015; 177:255-265. [PMID: 25496946 DOI: 10.1016/j.biortech.2014.11.062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 06/04/2023]
Abstract
Uncertainty associated to the estimated values of the parameters in a model is a key piece of information for decision makers and model users. However, this information is typically not reported or the confidence intervals are too large to be useful. A semi-mechanistic model for the enzymatic saccharification of dilute acid pretreated corn stover is proposed in this work, the model is a modification of an existing one providing a statistically significant improved fit towards a set of experimental data that includes varying initial solid loadings (10-25% w/w) and the use of the pretreatment liquor and washed solids with or without supplementation of key inhibitors. A subset of 8 out of 17 parameters was identified, showing sufficiently tight confidence intervals to be used in uncertainty propagation and model analysis, without requiring interval truncation via expert judgment.
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Affiliation(s)
- Felipe Scott
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2147, Valparaíso, Chile; Bioenercel S.A. Barrio Universitario s/n, Ideaincuba building, Concepción, Chile.
| | - Muyang Li
- DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA; Department of Biosystems & Agricultural Engineering, Michigan State University, 48824 East Lansing, MI, USA
| | - Daniel L Williams
- DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA; Department of Chemical Engineering & Materials Science, Michigan State University, 48824 East Lansing, MI, USA
| | - Raúl Conejeros
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2147, Valparaíso, Chile; Bioenercel S.A. Barrio Universitario s/n, Ideaincuba building, Concepción, Chile
| | - David B Hodge
- DOE-Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA; Department of Biosystems & Agricultural Engineering, Michigan State University, 48824 East Lansing, MI, USA; Department of Chemical Engineering & Materials Science, Michigan State University, 48824 East Lansing, MI, USA; Division of Chemical Engineering, Luleå University of Technology, Luleå, Sweden
| | - Germán Aroca
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2147, Valparaíso, Chile; Bioenercel S.A. Barrio Universitario s/n, Ideaincuba building, Concepción, Chile
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31
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Greene ER, Himmel ME, Beckham GT, Tan Z. Glycosylation of Cellulases: Engineering Better Enzymes for Biofuels. Adv Carbohydr Chem Biochem 2015; 72:63-112. [PMID: 26613815 DOI: 10.1016/bs.accb.2015.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulose in plant cell walls is the largest reservoir of renewable carbon on Earth. The saccharification of cellulose from plant biomass into soluble sugars can be achieved using fungal and bacterial cellulolytic enzymes, cellulases, and further converted into fuels and chemicals. Most fungal cellulases are both N- and O-glycosylated in their native form, yet the consequences of glycosylation on activity and structure are not fully understood. Studying protein glycosylation is challenging as glycans are extremely heterogeneous, stereochemically complex, and glycosylation is not under direct genetic control. Despite these limitations, many studies have begun to unveil the role of cellulase glycosylation, especially in the industrially relevant cellobiohydrolase from Trichoderma reesei, Cel7A. Glycosylation confers many beneficial properties to cellulases including enhanced activity, thermal and proteolytic stability, and structural stabilization. However, glycosylation must be controlled carefully as such positive effects can be dampened or reversed. Encouragingly, methods for the manipulation of glycan structures have been recently reported that employ genetic tuning of glycan-active enzymes expressed from homogeneous and heterologous fungal hosts. Taken together, these studies have enabled new strategies for the exploitation of protein glycosylation for the production of enhanced cellulases for biofuel production.
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32
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Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 2014; 78:614-49. [PMID: 25428937 PMCID: PMC4248655 DOI: 10.1128/mmbr.00035-14] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer Yuzon
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment. Fungal Genet Biol 2014; 72:168-181. [DOI: 10.1016/j.fgb.2014.08.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 12/30/2022]
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34
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Ye Z, Zheng Y, Li B, Borrusch MS, Storms R, Walton JD. Enhancement of synthetic Trichoderma-based enzyme mixtures for biomass conversion with an alternative family 5 glycosyl hydrolase from Sporotrichum thermophile. PLoS One 2014; 9:e109885. [PMID: 25295862 PMCID: PMC4190410 DOI: 10.1371/journal.pone.0109885] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 09/01/2014] [Indexed: 11/24/2022] Open
Abstract
Enzymatic conversion of lignocellulosic materials to fermentable sugars is a limiting step in the production of biofuels from biomass. We show here that combining enzymes from different microbial sources is one way to identify superior enzymes. Extracts of the thermophilic fungus Sporotrichum thermophile (synonym Myceliophthora thermophila) gave synergistic release of glucose (Glc) and xylose (Xyl) from pretreated corn stover when combined with an 8-component synthetic cocktail of enzymes from Trichoderma reesei. The S. thermophile extracts were fractionated and an enhancing factor identified as endo-β1,4-glucanase (StCel5A or EG2) of subfamily 5 of Glycosyl Hydrolase family 5 (GH5_5). In multi-component optimization experiments using a standard set of enzymes and either StCel5A or the ortholog from T. reesei (TrCel5A), reactions containing StCel5A yielded more Glc and Xyl. In a five-component optimization experiment (i.e., varying four core enzymes and the source of Cel5A), the optimal proportions for TrCel5A vs. StCel5A were similar for Glc yields, but markedly different for Xyl yields. Both enzymes were active on lichenan, glucomannan, and oat β-glucan; however, StCel5A but not TrCel5A was also active on β1,4-mannan, two types of galactomannan, and β1,4-xylan. Phylogenetically, fungal enzymes in GH5_5 sorted into two clades, with StCel5A and TrCel5A belonging to different clades. Structural differences with the potential to account for the differences in performance were deduced based on the known structure of TrCel5A and a homology-based model of StCel5A, including a loop near the active site of TrCel5A and the presence of four additional Trp residues in the active cleft of StCel5A. The results indicate that superior biomass-degrading enzymes can be identified by exploring taxonomic diversity combined with assays in the context of realistic enzyme combinations and realistic substrates. Substrate range may be a key factor contributing to superior performance within GH5_5.
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Affiliation(s)
- Zhuoliang Ye
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Yun Zheng
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Quebec, Canada
| | - Bingyao Li
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Melissa S. Borrusch
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Reginald Storms
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Quebec, Canada
| | - Jonathan D. Walton
- Department of Energy Great Lakes Bioenergy Research Center and Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
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35
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Zhang Y, Xu B, Zhou W. On a novel mechanistic model for simultaneous enzymatic hydrolysis of cellulose and hemicellulose considering morphology. Biotechnol Bioeng 2014; 111:1767-81. [DOI: 10.1002/bit.25244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 02/07/2014] [Accepted: 03/19/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Yang Zhang
- Department of Chemical Engineering; Michigan Technological University; Houghton Michigan 49931
| | - Bingqian Xu
- Engineering and Nanoscale Science and Engineering Center; University of Georgia; Athens Georgia 30602
| | - Wen Zhou
- Department of Chemical Engineering; Michigan Technological University; Houghton Michigan 49931
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36
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Balestrini R, Bonfante P. Cell wall remodeling in mycorrhizal symbiosis: a way towards biotrophism. FRONTIERS IN PLANT SCIENCE 2014; 5:237. [PMID: 24926297 PMCID: PMC4044974 DOI: 10.3389/fpls.2014.00237] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 05/12/2014] [Indexed: 05/05/2023]
Abstract
Cell walls are deeply involved in the molecular talk between partners during plant and microbe interactions, and their role in mycorrhizae, i.e., the widespread symbiotic associations established between plant roots and soil fungi, has been investigated extensively. All mycorrhizal interactions achieve full symbiotic functionality through the development of an extensive contact surface between the plant and fungal cells, where signals and nutrients are exchanged. The exchange of molecules between the fungal and the plant cytoplasm takes place both through their plasma membranes and their cell walls; a functional compartment, known as the symbiotic interface, is thus defined. Among all the symbiotic interfaces, the complex intracellular interface of arbuscular mycorrhizal (AM) symbiosis has received a great deal of attention since its first description. Here, in fact, the host plasma membrane invaginates and proliferates around all the developing intracellular fungal structures, and cell wall material is laid down between this membrane and the fungal cell surface. By contrast, in ectomycorrhizae (ECM), where the fungus grows outside and between the root cells, plant and fungal cell walls are always in direct contact and form the interface between the two partners. The organization and composition of cell walls within the interface compartment is a topic that has attracted widespread attention, both in ecto- and endomycorrhizae. The aim of this review is to provide a general overview of the current knowledge on this topic by integrating morphological observations, which have illustrated cell wall features during mycorrhizal interactions, with the current data produced by genomic and transcriptomic approaches.
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Affiliation(s)
- Raffaella Balestrini
- Institute for Sustainable Plant Protection, National Research CouncilTorino, Italy
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of TorinoTorino, Italy
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Rich MK, Schorderet M, Reinhardt D. The role of the cell wall compartment in mutualistic symbioses of plants. FRONTIERS IN PLANT SCIENCE 2014; 5:238. [PMID: 24917869 PMCID: PMC4041022 DOI: 10.3389/fpls.2014.00238] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 05/12/2014] [Indexed: 05/18/2023]
Abstract
Plants engage in mutualistic interactions with microbes that improve their mineral nutrient supply. The most wide-spread symbiotic association is arbuscular mycorrhiza (AM), in which fungi of the order Glomeromycota invade roots and colonize the cellular lumen of cortical cells. The establishment of this interaction requires a dedicated molecular-genetic program and a cellular machinery of the plant host. This program is partially shared with the root nodule symbiosis (RNS), which involves prokaryotic partners collectively referred to as rhizobia. Both, AM and RNS are endosymbioses that involve intracellular accommodation of the microbial partner in the cells of the plant host. Since plant cells are surrounded by sturdy cell walls, root penetration and cell invasion requires mechanisms to overcome this barrier while maintaining the cytoplasm of the two partners separate during development of the symbiotic association. Here, we discuss the diverse functions of the cell wall compartment in establishment and functioning of plant symbioses with the emphasis on AM and RNS, and we describe the stages of the AM association between the model organisms Petunia hybrida and Rhizophagus irregularis.
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Affiliation(s)
| | | | - Didier Reinhardt
- Department of Biology, University of FribourgFribourg, Switzerland
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38
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Debeire P, Delalande F, Habrylo O, Jeltsch JM, Van Dorsselaer A, Phalip V. Enzymatic cocktails produced by Fusarium graminearum under submerged fermentation using different lignocellulosic biomasses. FEMS Microbiol Lett 2014; 355:116-23. [PMID: 24828340 DOI: 10.1111/1574-6968.12467] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/07/2014] [Accepted: 05/11/2014] [Indexed: 01/09/2023] Open
Abstract
Fusarium graminearum was grown on four lignocellulosic substrates (corn cobs, wheat bran, hop cell walls, and birchwood) and glucose as the sole carbon source. Proteomic studies performed on the resulting enzymatic cocktails highlighted a great diversity in the number and type of proteins secreted. The cell wall-degrading enzymes (CWDE) proportion varied greatly from 20% to 69%. Only one of the 57 CWDEs detected in this study was common to the five proteomes. In contrast, 35 CWDEs were specific to one proteome only. The polysaccharide-degradation activities were different depending on the cocktail and the polysaccharide used. F. graminearum strongly modifies the enzymatic cocktail it secretes as a function of the biomass used for growth.
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Affiliation(s)
- Philippe Debeire
- Institut de Chimie et Procédés pour l'Énergie, l'Environnement et la Santé (UMR 7515 Strasbourg University/CNRS), ECPM, Strasbourg Cedex 2, France
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39
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Meng F, Ma L, Ji S, Yang W, Cao B. Isolation and characterization of Bacillus subtilis strain BY-3, a thermophilic and efficient cellulase-producing bacterium on untreated plant biomass. Lett Appl Microbiol 2014; 59:306-12. [PMID: 24773580 DOI: 10.1111/lam.12276] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/24/2014] [Accepted: 04/15/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Bioconversion of biomass, particularly crop wastes, into biofuels is being developed as an alternative approach in meeting the high energy demand. In this study, a thermophilic bacterial strain BY-3 that exhibits cellulolytic potential was isolated from faecal samples of Tibetan pigs; this strain was identified as Bacillus subtilis. The strain can produce cellulase when grown on various substrates, including carboxymethyl cellulose, rice straw, corn stover, soluble starch and wheat bran. The maximum cellulase activity of the strain was up to 4·323 ± 0·065 U ml(-1) when cultivated in the medium containing corn stover (30 g l(-1) ) for 24 h. The results demonstrated that corn stover is the most suitable substrate for cellulase production by the strain BY-3. The crude cellulase of strain BY-3 was most active at pH 5·5 and 60°C, and the enzyme in acetate buffer (50 mmol l(-1) ) demonstrated a good stability at 60°C for at least 1 h. The crude cellulase exhibited a strong antibacterial activity against Staphylococcus aureus. The strain can be used in cost-efficient cellulase production for bioconversion of agricultural residual biomass into biofuels. SIGNIFICANCE AND IMPACT OF THE STUDY The increased consumption of fossil fuels has caused serious energy crisis and environmental problem. Thus, an alternative energy source is necessary. Bioconversion of biomass, particularly agricultural residuals, into value-added bioproducts, such as biofuels and chemical solvents, has received considerable attention. In this study, the newly isolated thermophilic Bacillus subtilis strain BY-3 produces cellulase efficiently with the use of untreated corn stover as a sole carbon source. This strain possesses the thermostable cellulase that is active with diverse crop wastes with a broad pH range and is a highly promising candidate for agricultural waste management.
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Affiliation(s)
- F Meng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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40
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Phillips LA, Ward V, Jones MD. Ectomycorrhizal fungi contribute to soil organic matter cycling in sub-boreal forests. THE ISME JOURNAL 2014; 8:699-713. [PMID: 24173458 PMCID: PMC3930324 DOI: 10.1038/ismej.2013.195] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/25/2013] [Accepted: 09/26/2013] [Indexed: 11/08/2022]
Abstract
Soils of northern temperate and boreal forests represent a large terrestrial carbon (C) sink. The fate of this C under elevated atmospheric CO2 and climate change is still uncertain. A fundamental knowledge gap is the extent to which ectomycorrhizal fungi (EMF) and saprotrophic fungi contribute to C cycling in the systems by soil organic matter (SOM) decomposition. In this study, we used a novel approach to generate and compare enzymatically active EMF hyphae-dominated and saprotrophic hyphae-enriched communities under field conditions. Fermentation-humus (FH)-filled mesh bags, surrounded by a sand barrier, effectively trapped EMF hyphae with a community structure comparable to that found in the surrounding FH layer, at both trophic and taxonomic levels. In contrast, over half the sequences from mesh bags with no sand barrier were identified as belonging to saprotrophic fungi. The EMF hyphae-dominated systems exhibited levels of hydrolytic and oxidative enzyme activities that were comparable to or higher than saprotroph-enriched systems. The enzymes assayed included those associated with both labile and recalcitrant SOM degradation. Our study shows that EMF hyphae are likely important contributors to current SOM turnover in sub-boreal systems. Our results also suggest that any increased EMF biomass that might result from higher below-ground C allocation by trees would not suppress C fluxes from sub-boreal soils.
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Affiliation(s)
- Lori A Phillips
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada.
- Department of Environment and Primary Industries, Biosciences Research Division, Bundoora, Victoria, Australia.
| | - Valerie Ward
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
| | - Melanie D Jones
- Department of Biology, University of British Columbia, Kelowna, British Columbia, Canada
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Inoue H, Decker SR, Taylor LE, Yano S, Sawayama S. Identification and characterization of core cellulolytic enzymes from Talaromyces cellulolyticus (formerly Acremonium cellulolyticus) critical for hydrolysis of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:151. [PMID: 25342974 PMCID: PMC4196096 DOI: 10.1186/s13068-014-0151-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/25/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Enzymatic hydrolysis of pretreated lignocellulosic biomass is an essential process for the production of fermentable sugars for industrial use. A better understanding of fungal cellulase systems will provide clues for maximizing the hydrolysis of target biomass. Talaromyces cellulolyticus is a promising fungus for cellulase production and efficient biomass hydrolysis. Several cellulolytic enzymes purified from T. cellulolyticus were characterized in earlier studies, but the core enzymes critical for hydrolysis of lignocellulosic biomass remain unknown. RESULTS Six cellulolytic enzymes critical for the hydrolysis of crystalline cellulose were purified from T. cellulolyticus culture supernatant using an enzyme assay based on synergistic hydrolysis of Avicel. The purified enzymes were identified by their substrate specificities and analyses of trypsin-digested peptide fragments and were classified into the following glycosyl hydrolase (GH) families: GH3 (β-glucosidase, Bgl3A), GH5 (endoglucanase, Cel5A), GH6 (cellobiohydrolase II, Cel6A), GH7 (cellobiohydrolase I and endoglucanase, Cel7A and Cel7B, respectively), and GH10 (xylanase, Xyl10A). Hydrolysis of dilute acid-pretreated corn stover (PCS) with mixtures of the purified enzymes showed that Cel5A, Cel7B, and Xyl10A each had synergistic effects with a mixture of Cel6A and Cel7A. Cel5A seemed to be more effective in the synergistic hydrolysis of the PCS than Cel7B. The ratio of Cel5A, Cel6A, Cel7A, and Xyl10A was statistically optimized for the hydrolysis of PCS glucan in the presence of Bgl3A. The resultant mixture achieved higher PCS glucan hydrolysis at lower enzyme loading than a culture filtrate from T. cellulolyticus or a commercial enzyme preparation, demonstrating that the five enzymes play a role as core enzymes in the hydrolysis of PCS glucan. CONCLUSIONS Core cellulolytic enzymes in the T. cellulolyticus cellulase system were identified to Cel5A, Cel6A, Cel7A, Xyl10A, and Bgl3A and characterized. The optimized mixture of these five enzymes was highly effective for the hydrolysis of PCS glucan, providing a foundation for future improvement of the T. cellulolyticus cellulase system.
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Affiliation(s)
- Hiroyuki Inoue
- />Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Stephen R Decker
- />Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401 USA
| | - Larry E Taylor
- />Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401 USA
| | - Shinichi Yano
- />Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Shigeki Sawayama
- />Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
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Kernaghan G. Functional diversity and resource partitioning in fungi associated with the fine feeder roots of forest trees. Symbiosis 2013. [DOI: 10.1007/s13199-013-0265-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kawai T, Nakazawa H, Ida N, Okada H, Ogasawara W, Morikawa Y, Kobayashi Y. A comprehensive analysis of the effects of the main component enzymes of cellulase derived from Trichoderma reesei on biomass saccharification. ACTA ACUST UNITED AC 2013; 40:805-10. [DOI: 10.1007/s10295-013-1290-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/10/2013] [Indexed: 10/26/2022]
Abstract
Abstract
The aim of this study was a comprehensive analysis of the effects of the component enzymes of cellulase derived from Trichoderma reesei strain PC-3-7 on biomass saccharification. We used cellulases with deleted CBH I, CBH II, or EG I, which contain all other component enzymes, for saccharification of differently pretreated biomasses of rice straw, Erianthus, eucalyptus, and Japanese cedar. We found that CBH I was the most effective in saccharification of all pretreated cellulosic biomasses, although the effect was weaker in saccharification of sulfuric acid- and hydrothermally pretreated rice straw than of others; CBH II was more effective for rice straw than for eucalyptus, and was the most effective at the early stages of biomass degradation; EG I had little effect on pretreated biomasses, in particular, it had no effect on steam-exploded Japanese cedar. Thus, the effects of the main component enzymes depend on the biomass source and pretreatment. These findings will likely help to improve cellulase for industrial use.
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Affiliation(s)
- Tetsushi Kawai
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
| | - Hikaru Nakazawa
- grid.260427.5 0000000106712234 Department of Bioengineering Nagaoka University of Technology 1603-1 Kamitomioka 940-2188 Nagaoka Japan
| | - Noriko Ida
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
| | - Hirofumi Okada
- grid.260427.5 0000000106712234 Department of Bioengineering Nagaoka University of Technology 1603-1 Kamitomioka 940-2188 Nagaoka Japan
| | - Wataru Ogasawara
- grid.260427.5 0000000106712234 Department of Bioengineering Nagaoka University of Technology 1603-1 Kamitomioka 940-2188 Nagaoka Japan
| | - Yasushi Morikawa
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
| | - Yoshinori Kobayashi
- Japan Bioindustry Association AIST Tsukuba Central 6, 1-1-1 Higashi 305-8566 Tsukuba Ibaraki Japan
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Davey ML, Heimdal R, Ohlson M, Kauserud H. Host- and tissue-specificity of moss-associated Galerina and Mycena determined from amplicon pyrosequencing data. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2013.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Liu G, Qin Y, Li Z, Qu Y. Development of highly efficient, low-cost lignocellulolytic enzyme systems in the post-genomic era. Biotechnol Adv 2013; 31:962-75. [PMID: 23507038 DOI: 10.1016/j.biotechadv.2013.03.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/09/2013] [Accepted: 03/10/2013] [Indexed: 11/19/2022]
Abstract
The current high cost of lignocellulolytic enzymes is a major bottleneck in the economic bioconversion of lignocellulosic biomass to fuels and chemicals. Fungal lignocellulolytic enzyme systems are secreted at high levels, making them the most promising starting points for further development of highly efficient lignocellulolytic enzyme systems. In this paper, recent advances in improvement of fungal lignocellulolytic enzyme systems are reviewed, with an emphasis on the achievements made using genomic approaches. A general strategy for lignocellulolytic enzyme system development is proposed, including the improvement of the hydrolysis efficiencies and productivities of current enzyme systems. The applications of genomic, transcriptomic and proteomic analysis methods in examining the composition of native enzyme systems, discovery of novel enzymes and synergistic proteins from natural sources, and understanding of regulatory mechanisms for lignocellulolytic enzyme biosynthesis are summarized. By combining systems biology and synthetic biology tools, engineered fungal strains are expected to produce high levels of optimized lignocellulolytic enzyme systems.
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Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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Miyauchi S, Te'o VS, Bergquist PL, Nevalainen KMH. Expression of a bacterial xylanase in Trichoderma reesei under the egl2 and cbh2 glycosyl hydrolase gene promoters. N Biotechnol 2013; 30:523-30. [PMID: 23467195 DOI: 10.1016/j.nbt.2013.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 02/24/2013] [Accepted: 02/25/2013] [Indexed: 11/17/2022]
Abstract
Expression vectors were constructed for Trichoderma reesei using the promoters, secretion signals and the modular structure of the efficiently expressed and secreted cellulase enzymes EGL2 (Cel5A) and CBH2 (Cel6A) as a prelude to establishing a platform where a gene of interest can be expressed under several promoters simultaneously. The designs featured (i) EGL2sigpro (egl2 promoter and secretion signal), (ii) EGL2cbmlin (egl2 promoter, secretion signal, EGL2 cellulose binding module and linker), (iii) CBH2sigpro (cbh2 promoter and secretion signal) and (iv) CBH2cbmlin (cbh2 promoter, secretion signal, CBH2 cellulose binding module and linker). Recombinant vectors were introduced individually into the high protein-secreting T. reesei RUT-C30 strain to generate single-promoter transformants expressing the Dictyoglomus thermophilum xynB gene that encodes a thermophilic xylanase enzyme (XynB). Ten transformants producing XynB representing each of the four different types of vectors were selected for further testing and the highest XynB production was achieved from a transformant containing 1-2copies of the EGL2cbmlin vector. Best xylanase producers did not show any particular pattern in terms of the number of gene copies and their mode of integration into the chromosomal DNA. Transformants generated with the cbmlin-type vectors produced multiple forms of XynB which were decorated with various N- and O-glycans. One of the O-glycans was identified as hexuronic acid, whose presence had not been observed previously in the glycosylation patterns of T. reesei.
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Affiliation(s)
- Shingo Miyauchi
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
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Li Z, Chen CH, Liu T, Mathrubootham V, Hegg EL, Hodge DB. Catalysis with CuII(bpy) improves alkaline hydrogen peroxide pretreatment. Biotechnol Bioeng 2012. [DOI: 10.1002/bit.24793] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Proteome-Based Profiling of Hypercellulase-Producing Strains Developed Through Interspecific Protoplast Fusion Between Aspergillus nidulans and Aspergillus tubingensis. Appl Biochem Biotechnol 2012. [DOI: 10.1007/s12010-012-9985-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Liu M, Yu H. Cocktail production of an endo-β-xylanase and a β-glucosidase from Trichoderma reesei QM 9414 in Escherichia coli. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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