Systems biology-guided understanding of white-rot fungi for biotechnological applications: A review

Manufacturing energy and greenhouse gas emissions associated with plastics consumption

(2021) Scott R. Nicholson et al.   Joule

Advances in enzymatic oxyfunctionalization of aliphatic compounds

(2021) Carmen Aranda et al.   BIOTECHNOLOGY ADVANCES

Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay

(2021) Hayat Hage et al.   ENVIRONMENTAL MICROBIOLOGY

Intracellular pathways for lignin catabolism in white-rot fungi

(2021) Carlos del Cerro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient genome editing with CRISPR/Cas9 in Pleurotus ostreatus

(2021) Tatpong Boontawon et al.   AMB Express

Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers

(2021) Hayat Hage et al.   Journal of Fungi

Anaerobic gut fungi are an untapped reservoir of natural products

(2021) Candice L. Swift et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of omics- and multi-omics-based techniques for natural product target discovery

(2021) Hong-Wei Zhang et al.   BIOMEDICINE & PHARMACOTHERAPY

Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives

(2021) Mana Iwata et al.   Scientific Reports

Techno-economic, life-cycle, and socioeconomic impact analysis of enzymatic recycling of poly(ethylene terephthalate)

(2021) Avantika Singh et al.   Joule

A Multiomic Approach to Understand How Pleurotus eryngii Transforms Non-Woody Lignocellulosic Material

(2021) Ander Peña et al.   Journal of Fungi

Overexpressing Pleurotus ostreatus rho1b results in transcriptional upregulation of the putative cellulolytic enzyme‐encoding genes observed in ccl1 disruptants

(2021) Nozomi Okuda et al.   ENVIRONMENTAL MICROBIOLOGY

The carbohydrate-active enzyme database: functions and literature

(2021) Elodie Drula et al.   NUCLEIC ACIDS RESEARCH

Application of CRISPR/Cas9 Tools for Genome Editing in the White-Rot Fungus Dichomitus squalens

(2021) Joanna E. Kowalczyk et al.   Biomolecules

Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus

(2020) Hans Kristian Mattila et al.   Biotechnology for Biofuels

Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches

(2020) Ronald P. de Vries et al.   TRENDS IN MICROBIOLOGY

Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440

(2020) Davinia Salvachúa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic biology based construction of biological activity-related library of fungal decalin-containing diterpenoid pyrones

(2020) Kento Tsukada et al.   Nature Communications

Lignin Monomers from beyond the Canonical Monolignol Biosynthetic Pathway: Another Brick in the Wall

(2020) José C. del Río et al.   ACS Sustainable Chemistry & Engineering

Transcriptional shifts in delignification‐defective mutants of the white‐rot fungus Pleurotus ostreatus

(2020) Hongli Wu et al.   FEBS LETTERS

Comparative characterization of extracellular enzymes secreted by Phanerochaete chrysosporium during solid-state and submerged fermentation

(2020) Jiawen Liu et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Opinion: We need better data about the environmental persistence of plastic goods

(2020) Collin P. Ward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glucose counteracts wood-dependent induction of lignocellulolytic enzyme secretion in monokaryon and dikaryon submerged cultures of the white-rot basidiomycete Pleurotus ostreatus

(2020) Manuel Alfaro et al.   Scientific Reports

Insight into Depolymerization Mechanism of Bacterial Laccase for Lignin

(2020) Daochen Zhu et al.   ACS Sustainable Chemistry & Engineering

Using Wood Rot Phenotypes to Illuminate the “Gray” Among Decomposer Fungi

(2020) Jonathan S. Schilling et al.   Frontiers in Microbiology

The Secretome of Phanerochaete chrysosporium and Trametes versicolor Grown in Microcrystalline Cellulose and Use of the Enzymes for Hydrolysis of Lignocellulosic Materials

(2020) Angela S. Machado et al.   Frontiers in Bioengineering and Biotechnology

Fungal mycelium classified in different material families based on glycerol treatment

(2020) Freek V. W. Appels et al.   Communications Biology

Mini review: Advances in understanding regulation of cellulase enzyme in white-rot basidiomycetes

(2020) Eyalira J. Okal et al.   MICROBIAL PATHOGENESIS

Predicted growth in plastic waste exceeds efforts to mitigate plastic pollution

(2020) Stephanie B. Borrelle et al.   SCIENCE

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

(2020) Shingo Miyauchi et al.   Nature Communications

Comparative secretome of white‐rot fungi reveals co‐regulated carbohydrate‐active enzymes associated with selective ligninolysis of ramie stalks

(2020) Chunliang Xie et al.   Microbial Biotechnology

Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity

(2020) Francisco J Ruiz-Dueñas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Omics in Systems Biology: Current Progress and Future Outlook

(2020) Timothy D. Veenstra   PROTEOMICS

De novo transcriptome assembly and protein profiling of copper-induced lignocellulolytic fungus Ganoderma lucidum MDU-7 reveals genes involved in lignocellulose degradation and terpenoid biosynthetic pathways

(2019) Kavish Kumar Jain et al.   GENOMICS

A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi

(2019) Ronnie J.M. Lubbers et al.   BIOTECHNOLOGY ADVANCES

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi

(2019) Mari Mäkinen et al.   BMC GENOMICS

The amazing potential of fungi: 50 ways we can exploit fungi industrially

(2019) Kevin D. Hyde et al.   FUNGAL DIVERSITY

The White-Rot Basidiomycete Dichomitus squalens Shows Highly Specific Transcriptional Response to Lignocellulose-Related Aromatic Compounds

(2019) Joanna E. Kowalczyk et al.   Frontiers in Bioengineering and Biotechnology

Glucose-Mediated Repression of Plant Biomass Utilization in the White-Rot Fungus Dichomitus squalens

(2019) Paul Daly et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A review on biopolymer production via lignin valorization

(2019) J. Rajesh Banu et al.   BIORESOURCE TECHNOLOGY

CRISPR-Cas9 assisted functional gene editing in the mushroom Ganoderma lucidum

(2019) Ping-An Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Extracellular vesicles of human pathogenic fungi

(2019) Ewa Bielska et al.   CURRENT OPINION IN MICROBIOLOGY

Status of filamentous fungi in integrated biorefineries

(2019) D. Troiano et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Proteomic researches for lignocellulose-degrading enzymes: A mini-review

(2018) Hongliang Guo et al.   BIORESOURCE TECHNOLOGY

Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analyses

(2018) Xing Qin et al.   Biotechnology for Biofuels

Bright Side of Lignin Depolymerization: Toward New Platform Chemicals

(2018) Zhuohua Sun et al.   CHEMICAL REVIEWS

Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading

(2018) W. Schutyser et al.   CHEMICAL SOCIETY REVIEWS

Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes

(2018) Mao Peng et al.   FUNGAL GENETICS AND BIOLOGY

Temporal transcriptome analysis of the white-rot fungus Obba rivulosa shows expression of a constitutive set of plant cell wall degradation targeted genes during growth on solid spruce wood

(2018) Mila Marinović et al.   FUNGAL GENETICS AND BIOLOGY

Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses

(2018) Shuai Zhou et al.   PLoS One

The biomass distribution on Earth

(2018) Yinon M. Bar-On et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coupling Secretomics with Enzyme Activities To Compare the Temporal Processes of Wood Metabolism among White and Brown Rot Fungi

(2018) Gerald N. Presley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effects of cre1 modification in the white-rot fungus Pleurotus ostreatus PC9: altering substrate preference during biological pretreatment

(2018) Shahar Yoav et al.   Biotechnology for Biofuels

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass

(2018) Shingo Miyauchi et al.   Biotechnology for Biofuels

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

(2018) Paul Daly et al.   ENVIRONMENTAL MICROBIOLOGY

Hydrophobin gene deletion and environmental growth conditions impact mechanical properties of mycelium by affecting the density of the material

(2018) Freek V. W. Appels et al.   Scientific Reports

Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce

(2018) E. Jurak et al.   BMC GENOMICS

Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities

(2018) Richard H. Baltz   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Fungal secondary metabolism: regulation, function and drug discovery

(2018) Nancy P. Keller   NATURE REVIEWS MICROBIOLOGY

Fabrication factors influencing mechanical, moisture- and water-related properties of mycelium-based composites

(2018) Freek V.W. Appels et al.   MATERIALS & DESIGN

The potential of cottonseed hull as biorefinery substrate after biopretreatment by Pleurotus ostreatus and the mechanism analysis based on comparative proteomics

(2018) Qiuyun Xiao et al.   INDUSTRIAL CROPS AND PRODUCTS

The molecular response of the white-rot fungus D ichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses

(2017) Johanna Rytioja et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

(2017) Naofumi Kamimura et al.   Environmental Microbiology Reports

Differential Proteomic Profiles of Pleurotus ostreatus in Response to Lignocellulosic Components Provide Insights into Divergent Adaptive Mechanisms

(2017) Qiuyun Xiao et al.   Frontiers in Microbiology

The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown

(2017) Shingo Miyauchi et al.   PLoS One

Paving the Way for Lignin Valorisation: Recent Advances in Bioengineering, Biorefining and Catalysis

(2016) Roberto Rinaldi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Progress in Top-Down Proteomics and the Analysis of Proteoforms

(2016) Timothy K. Toby et al.   Annual Review of Analytical Chemistry

A secretomic view of woody and nonwoody lignocellulose degradation by Pleurotus ostreatus

(2016) Elena Fernández-Fueyo et al.   Biotechnology for Biofuels

Comparative analysis of the secretomes of Schizophyllum commune and other wood-decay basidiomycetes during solid-state fermentation reveals its unique lignocellulose-degrading enzyme system

(2016) Ning Zhu et al.   Biotechnology for Biofuels

Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose

(2016) Jaana Kuuskeri et al.   Biotechnology for Biofuels

Extracellular proteins of Trametes hirsuta st. 072 induced by copper ions and a lignocellulose substrate

(2016) Daria V. Vasina et al.   BMC MICROBIOLOGY

Opportunities and challenges in biological lignin valorization

(2016) Gregg T Beckham et al.   CURRENT OPINION IN BIOTECHNOLOGY

Lignin depolymerization by fungal secretomes and a microbial sink

(2016) Davinia Salvachúa et al.   GREEN CHEMISTRY

Counting on natural products for drug design

(2016) Tiago Rodrigues et al.   Nature Chemistry

Review of solid state fermentation for lignocellulolytic enzyme production: challenges for environmental applications

(2016) Alicia A. Mansour et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Review of solid state fermentation for lignocellulolytic enzyme production: challenges for environmental applications

(2016) Alicia A. Mansour et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation

(2016) Lianfu Chen et al.   PLoS One

Basidiomycete DyPs: Genomic diversity, structural–functional aspects, reaction mechanism and environmental significance

(2015) Dolores Linde et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Enhanced degradation of softwood versus hardwood by the white-rot fungus Pycnoporus coccineus

(2015) Marie Couturier et al.   Biotechnology for Biofuels

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities

(2015) László G. Nagy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plastic waste inputs from land into the ocean

(2015) J. R. Jambeck et al.   SCIENCE

Synthetic biology of fungal natural products

(2015) Derek J. Mattern et al.   Frontiers in Microbiology

Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporiopsis subvermispora during Growth on Aspen Wood Reveal This Organism's Strategy for Degrading Lignocellulose

(2014) Chiaki Hori et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptomic Responses of Phanerochaete chrysosporium to Oak Acetonic Extracts: Focus on a New Glutathione Transferase

(2014) Anne Thuillier et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Understanding lignin biodegradation for the improved utilization of plant biomass in modern biorefineries

(2014) Susana Camarero et al.   Biofuels Bioproducts & Biorefining-Biofpr

The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown

(2014) Anthony Levasseur et al.   BMC GENOMICS

Ligninolytic peroxidase gene expression by Pleurotus ostreatus : Differential regulation in lignocellulose medium and effect of temperature and pH

(2014) Elena Fernández-Fueyo et al.   FUNGAL GENETICS AND BIOLOGY

Comparative analysis of secretomes in basidiomycete fungi

(2014) Manuel Alfaro et al.   Journal of Proteomics

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

(2014) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lignin Valorization: Improving Lignin Processing in the Biorefinery

(2014) A. J. Ragauskas et al.   SCIENCE

Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood

(2014) Chiaki Hori et al.   PLoS Genetics

Characterization of a Novel Dye-Decolorizing Peroxidase (DyP)-Type Enzyme from Irpex lacteus and Its Application in Enzymatic Hydrolysis of Wheat Straw

(2013) D. Salvachua et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Differential proteomic analysis of the secretome of Irpex lacteus and other white-rot fungi during wheat straw pretreatment

(2013) Davinia Salvachúa et al.   Biotechnology for Biofuels

Versatile peroxidase as a valuable tool for generating new biomolecules by homogeneous and heterogeneous cross-linking

(2013) Davinia Salvachúa et al.   ENZYME AND MICROBIAL TECHNOLOGY

Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay

(2013) Chiaki Hori et al.   MYCOLOGIA

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

(2012) Hitoshi Suzuki et al.   BMC GENOMICS

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

(2012) E. Fernandez-Fueyo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species

(2011) Amber Vanden Wymelenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reactivity of bacterial and fungal laccases with lignin under alkaline conditions

(2011) Raquel Moya et al.   BIORESOURCE TECHNOLOGY

Fungal pretreatment: An alternative in second-generation ethanol from wheat straw

(2011) Davinia Salvachúa et al.   BIORESOURCE TECHNOLOGY

Recent progress in consolidated bioprocessing

(2011) Daniel G Olson et al.   CURRENT OPINION IN BIOTECHNOLOGY

iTRAQ-based quantitative secretome analysis of Phanerochaete chrysosporium

(2011) Arulmani Manavalan et al.   Journal of Proteomics

Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals

(2011) Shishir P.S. Chundawat et al.   Annual Review of Chemical and Biomolecular Engineering

Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium

(2010) A. Vanden Wymelenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Proteomic characterization of lignocellulose-degrading enzymes secreted by Phanerochaete carnosa grown on spruce and microcrystalline cellulose

(2010) Sonam Mahajan et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

New and classic families of secreted fungal heme peroxidases

(2010) Martin Hofrichter et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Cytochrome P450 enzymes in the fungal kingdom

(2010) B. Črešnar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Laccases and their natural mediators: Biotechnological tools for sustainable eco-friendly processes

(2010) Ana I. Cañas et al.   BIOTECHNOLOGY ADVANCES

Genome sequence of the model mushroom Schizophyllum commune

(2010) Robin A Ohm et al.   NATURE BIOTECHNOLOGY

Transcriptome and Secretome Analyses of Phanerochaete chrysosporium Reveal Complex Patterns of Gene Expression

(2009) A. Vanden Wymelenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pretreatment technologies for an efficient bioethanol production process based on enzymatic hydrolysis: A review

(2009) P. Alvira et al.   BIORESOURCE TECHNOLOGY

Recent developments in biodegradation of industrial pollutants by white rot fungi and their enzyme system

(2008) Muhammad Asgher et al.   BIODEGRADATION

Proteomic and Metabolomic Analyses of the White-Rot FungusPhanerochaete chrysosporiumExposed to Exogenous Benzoic Acid

(2008) Fumiko Matsuzaki et al.   JOURNAL OF PROTEOME RESEARCH