Article
Green & Sustainable Science & Technology
Sangita Dixit, Kalpana Sahoo, Mahendra Gaur, Rajesh Kumar Sahoo, Suchanda Dey, Vijai Kumar Gupta, Enketeswara Subudhi
Summary: This study explores enzymes in a carbohydrate-contaminated unique environment at Deulajhari hot spring using a multi-omics approach. The study identifies a diverse range of potential lignocellulose-digesting enzymes and highlights their significant potential in industrial-scale biofuel production.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2023)
Article
Biotechnology & Applied Microbiology
Douglas Antonio Alvaredo Paixao, Geizecler Tomazetto, Victoria Ramos Sodre, Thiago A. Goncalves, Cristiane Akemi Uchima, Fernanda Buchli, Thabata Maria Alvarez, Gabriela Felix Persinoti, Marcio Jose da Silva, Juliano Bragatto, Marcelo Vizona Liberato, Joao Paulo L. Franco Cairo, Adriana Franco Paes Leme, Fabio Marcio Squina
Summary: The study used an enrichment process and integrative omics approaches to identify new lignocellulose-degrading enzymes, revealing that the lignocellulolytic-enriched mangrove microbial community can efficiently degrade sugarcane bagasse and harbor a large number of CAZyme sequences, including cellulases and hemicellulases.
ENZYME AND MICROBIAL TECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Claire E. Anderson, Jiwei Zhang, Lye Meng Markillie, Hugh D. Mitchell, William B. Chrisler, Matthew J. Gaffrey, Galya Orr, Jonathan S. Schilling
Summary: Earth's aboveground terrestrial biomass is primarily wood, and fungi dominate wood decomposition. This study focused on a common brown rot-type fungus, Rhodonia placenta, and revealed its pathway for extracting sugars from wood lignin. The researchers used high-resolution transcriptome sequencing to uncover that many genes previously assumed to be constitutively expressed were actually turned off before being upregulated during the decay process. Additionally, they found that the benzoquinone reductase gene was activated in the early stages of decay and quickly downregulated, indicating its key role in initiating brown rot.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Retraction
Biotechnology & Applied Microbiology
Baojun Wu, Jill Gaskell, Benjamin W. Held, Cristina Toapanta, Thu V. Vuong, Steven Ahrendt, Anna Lipzen, Jiwei Zhang, Jonathan S. Schilling, Emma Master, Igor V. Grigoriev, Robert A. Blanchette, Dan Cullen, David S. Hibbett
Summary: The study found that Fomitopsis pinicola is able to adjust gene expression across different substrate species and culture conditions, involving various enzymes related to wood decay.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Janne Wallenius, Jussi Kontro, Christina Lyra, Jaana Kuuskeri, Xing Wan, Mika A. Kahkonen, Irshad Baig, Paul C. J. Kamer, Jussi Sipila, Miia R. Makela, Paula Nousiainen, Kristiina Hilden
Summary: By mutating the substrate-binding site of fungal laccases, the oxidation capacity of the enzyme was improved, with the rOrLcc2-D206N variant showing particular promise for lignin-related applications. This variant exhibited significant structural changes and oxidation capabilities when used with redox mediators, suggesting its potential for efficient lignin valorization.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Microbiology
Zichen Zhang, Aabid Manzoor Shah, Hassan Mohamed, Yao Zhang, Nino Tsiklauri, Yuanda Song
Summary: Cerrena unicolor is a basidiomycete with high lignocellulose degrading ability. The genome sequence of C. unicolor SP02 was reported in this study, revealing its potential application in lignocellulosic biomass conversion. The genetic basis and molecular mechanisms for lignocellulosic degradation were explored, providing insights for industrial biotechnology.
Article
Plant Sciences
Rong Liu, Xue Lv, Xiaohua Wang, Li Yang, Jun Cao, Ya Dai, Wang Wu, Yu Wu
Summary: Wheat, a major food crop, is significantly affected by stripe rust fungus. This study investigated the gene and metabolite expression in R88 (resistant) and CY12 (susceptible) during Pst-CYR34 infection. The results showed that Pst infection promotes the synthesis of phenolic compounds, and the key enzyme gene TaPAL contributes to wheat's resistance to Pst. Metabolome analysis also revealed the significant impact of Pst on lignin synthesis. These findings help understand the regulatory networks of wheat-Pst interactions and facilitate durable resistance breeding in wheat.
FRONTIERS IN PLANT SCIENCE
(2023)
Proceedings Paper
Forestry
Simang Champramary, Boris Indic, Laszlo Kredics, Gyorgy Sipos
Summary: Armillaria species may play a dominant role in lignocellulose degradation and assertive invasive, pathogenic activities in forest communities.
10TH HARDWOOD CONFERENCE PROCEEDINGS 2022
(2022)
Review
Biotechnology & Applied Microbiology
David Ribeaucourt, Bastien Bissaro, Fanny Lambert, Mickael Lafond, Jean-Guy Berrin
Summary: This review explores the potential and challenges of producing fatty aldehydes using biotechnologies, focusing on the three main classes of enzymes involved in the catalytic reactions. It highlights the importance of developing biotechnology-based solutions in the flavors and fragrances industry.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Ecology
Lisa K. Mahdi, Shingo Miyauchi, Charles Uhlmann, Ruben Garrido-Oter, Gregor Langen, Stephan Wawra, Yulong Niu, Rui Guan, Senga Robertson-Albertyn, Davide Bulgarelli, Jane E. Parker, Alga Zuccaro
Summary: Plant root-associated bacteria can protect against pathogen infections, while root endophytic fungi combined with core bacterial members provide synergistic protection. The early growth promotion benefits of these interactions are dependent on the host and microbiota composition, and are associated with modulation of microbial effectors and carbohydrate-active enzymes instead of extensive host transcriptional reprogramming.
Article
Plant Sciences
Feng Zhang, Aurore Labourel, Mireille Haon, Minna Kemppainen, Emilie Da Silva Machado, Nicolas Brouilly, Claire Veneault-Fourrey, Annegret Kohler, Marie-Noelle Rosso, Alejandro Pardo, Bernard Henrissat, Jean-Guy Berrin, Francis Martin
Summary: This study characterizes the biochemical properties of the symbiosis-induced polygalacturonase LbGH28A in the ectomycorrhizal fungus Laccaria bicolor and confirms its key role in symbiosis. The enzyme is involved in the formation of the Hartig net and is an important determinant for successful symbiotic colonization.
Article
Plant Sciences
Brian Looney, Shingo Miyauchi, Emmanuelle Morin, Elodie Drula, Pierre Emmanuel Courty, Annegret Kohler, Alan Kuo, Kurt LaButti, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, William Andreopoulos, Guifen He, Jenifer Johnson, Matt Nolan, Andrew Tritt, Kerrie W. Barry, Igor Grigoriev, Laszlo G. Nagy, David Hibbett, Bernard Henrissat, P. Brandon Matheny, Jesse Labbe, Francis M. Martin
Summary: In this study, the researchers identified genomic signatures of the transition to ectomycorrhizal habit within the Russulaceae family. They found that the genomes of ectomycorrhizal Russulaceae species have a loss of genes for plant cell wall-degrading enzymes, an expansion of genome size through increased transposable element content, a reduction in secondary metabolism clusters, and an association of small secreted proteins with transposable element 'nests'. Some plant cell wall-degrading enzyme genes have been retained or expanded in a species-specific manner. The genome of a saprotrophic member of Russulaceae also showed some characteristics of ectomycorrhizal genomes. Functional specialization in ectomycorrhizal decomposition may drive diversification. Accelerated gene evolution predates the evolution of the ectomycorrhizal habit, suggesting that changes in genome architecture and gene content may be necessary for the evolutionary switch.
Article
Plant Sciences
Gang Wu, Shingo Miyauchi, Emmanuelle Morin, Alan Kuo, Elodie Drula, Torda Varga, Annegret Kohler, Bang Feng, Yang Cao, Anna Lipzen, Christopher Daum, Hope Hundley, Jasmyn Pangilinan, Jenifer Johnson, Kerrie Barry, Kurt LaButti, Vivian Ng, Steven Ahrendt, Byoungnam Min, In-Geol Choi, Hongjae Park, Jonathan M. Plett, Jon Magnuson, Joseph W. Spatafora, Laszlo G. Nagy, Bernard Henrissat, Igor V. Grigoriev, Zhu-Liang Yang, Jianping Xu, Francis M. Martin
Summary: This study compared the genomes of 21 ectomycorrhizal species within Boletales with their saprotrophic brown-rot relatives, revealing that symbiotic boletes have become functionally diverse over their evolutionary history with reduced plant cell-wall-degrading enzymes but distinct sets of enzymes. Additionally, the study showed that transposable element proliferation contributed to the higher evolutionary rate of certain genes, while the loss of secreted CAZymes was related to DNA decay rather than TE activity. These findings provide new insights into the mechanisms influencing the evolutionary diversification of symbiotic boletes.
Article
Plant Sciences
Annie Lebreton, Nianwu Tang, Alan Kuo, Kurt LaButti, William Andreopoulos, Elodie Drula, Shingo Miyauchi, Kerrie Barry, Alicia Clum, Anna Lipzen, Daniel Mousain, Vivian Ng, Ran Wang, Yucheng Dai, Bernard Henrissat, Igor V. Grigoriev, Alexis Guerin-Laguette, Fuqiang Yu, Francis M. Martin
Summary: This study sequenced and compared the genomes of seven species of milk-cap fungi with different host specificity. The size of milk-cap genomes was larger due to the accumulation of transposable elements and duplication of dispensable genes. These fungi have a limited number of genes coding for plant cell wall-degrading enzymes, but retain genes involved in microbial cell wall degradation. They also showed an expansion of protease genes and genes coding for small secreted proteins and lectins, which may be related to host specificity.
Article
Biotechnology & Applied Microbiology
Jean-Lou Reyre, Sacha Grisel, Mireille Haon, David Navarro, David Ropartz, Sophie Le Gall, Eric Record, Giuliano Sciara, Olivier Tranquet, Jean-Guy Berrin, Bastien Bissaro
Summary: Filamentous fungi, such as Ustilago maydis, play a key role in regulating various processes on Earth. They secrete carbohydrate-active enzymes (CAZymes) to modify and degrade carbohydrates. In this study, researchers analyzed the secretome of U. maydis and identified several CAZymes involved in the modification of the fungal cell wall components. They characterized two new CAZymes and found a potential biocatalytic cascade. These findings provide insights into the role of CAZymes in fungi and highlight the need for further research in this area.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Radka Koncitikova, Lisa Zuily, Emeline Lemarie, David Ribeaucourt, Safwan Saker, Mireille Haon, Harry Brumer, Victor Guallar, Jean-Guy Berrin, Mickael Lafond
Summary: This study identified key amino acid residues involved in substrate selectivity of AA5_2 enzymes towards galactose-containing saccharides using a rational site-directed mutagenesis approach, revealing the differences in substrate preferences between alcohol oxidases and galactose oxidases.
Article
Plant Sciences
Francois Maillard, Annegret Kohler, Emmanuelle Morin, Christian Hossann, Shingo Miyauchi, Isabelle Ziegler-Devin, Dominique Gerant, Nicolas Angeli, Anna Lipzen, Keykhosrow Keymanesh, Jenifer Johnson, Kerrie Barry, Igor V. Grigoriev, Francis M. Martin, Marc Buee
Summary: This study found that certain ectomycorrhizal fungi depolymerize chitin using hydrolytic mechanisms, indicating that the degradation of exogenous chitin by ectomycorrhizal fungi might be a key functional trait of nutrient cycling in forests dominated by ectomycorrhizal fungi.
Article
Multidisciplinary Sciences
Bastien Bissaro, Sayo Kodama, Takumi Nishiuchi, Anna Maria Diaz-Rovira, Hayat Hage, David Ribeaucourt, Mireille Haon, Sacha Grisel, A. Jalila Simaan, Fred Beisson, Stephanie M. Forget, Harry Brumer, Marie-Noelle Rosso, Victor Guallar, Richard O'Connell, Mickael Lafond, Yasuyuki Kubo, Jean-Guy Berrin
Summary: Global food security is at risk due to fungal phytopathogens that damage crop production. A pair of alcohol oxidase-peroxidase enzymes has been found to be crucial for the pathogenicity of these pathogens, aiding in the penetration of plant cuticles. These enzymes play a role in oxidizing plant cuticular long-chain alcohols into aldehydes and are involved in the transcriptional regulation of genes necessary for host penetration. The discovery of these infection-specific metalloenzymes opens up new possibilities for understanding the role of wax-derived compounds and designing oxidase-specific inhibitors for crop protection.
Article
Biochemistry & Molecular Biology
Izumi Yotsui, Hidenori Matsui, Shingo Miyauchi, Hidekazu Iwakawa, Katharina Melkonian, Titus Schlueter, Santiago Michavila, Takehiko Kanazawa, Yuko Nomura, Sara Christina Stolze, Hyung-Woo Jeon, Yijia Yan, Anne Harzen, Shigeo S. Sugano, Makoto Shirakawa, Ryuichi Nishihama, Yasunori Ichihashi, Selena Gimenez Ibanez, Ken Shirasu, Takashi Ueda, Takayuki Kohchi, Hirofumi Nakagami
Summary: This study reveals the mechanism of PTI in M. polymorpha and its importance in bryophytes. The researchers identified four lysin motif (LysM)-domain-containing receptor homologs in M. polymorpha, and found that two of them are responsible for sensing bacterial and fungal components and triggering immune responses. Phosphoproteomic analysis of M. polymorpha treated with chitin also identified potential regulatory proteins. This study provides insights into the basic framework of PTI in M. polymorpha and highlights conserved elements and new aspects of pattern-triggered immunity in land plants.
Article
Chemistry, Multidisciplinary
Eden Kaddouch, Maria E. Cleveland, David Navarro, Sacha Grisel, Mireille Haon, Harry Brumer, Mickael Lafond, Jean-Guy Berrin, Bastien Bissaro
Summary: This study presents a simple method for direct measurement of galactose oxidase (GalOx) activity by identifying galactosylated oxidized products using high-performance anion-exchange chromatography coupled to pulsed amperometric detection (HPAEC-PAD). The results showed that this method is more sensitive than other methods.
Article
Chemistry, Analytical
Elena Piersanti, Claudio Righetti, David Ribeaucourt, A. Jalila Simaan, Yasmina Mekmouche, Mickael Lafond, Jean-Guy Berrin, Thierry Tron, Mehdi Yemloul
Summary: 1D H-1 NMR spectroscopy is commonly used for monitoring enzymatic activity through the evolution of substrate and product spectra. A simple analytical method using MaxQ NMR and NUS acquisition procedure allows for rapid characterization of reaction mixtures involving enzymatic complexes, providing valuable insights into enzyme affinity for different compounds in the mixture. Combining MaxQ and diffusion experiments results in improved resolution and simplified spectra.
Article
Biotechnology & Applied Microbiology
Nicholas G. S. McGregor, Casper de Boer, Mikhaaeel Santos, Mireille Haon, David Navarro, Sybrin Schroder, Jean-Guy Berrin, Herman S. Overkleeft, Gideon J. Davies
Summary: This study demonstrates that ABP-Cel can be used to analyze endo-beta-glucanase secreted by different fungi, revealing significant dynamics and unique enzyme fingerprints associated with each species substrate combination. Chemical proteomic analysis identifies significant arsenals of cellulases secreted by each fungal species during growth on lignocellulosic biomass. Recombinant production and characterization of a collection of probe-reactive enzymes from GH5, GH10, and GH12 confirm that ABP-Cel shows broad selectivity towards enzymes with endo-beta-glucanase activity.
BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS
(2022)
