The Experts below are selected from a list of 1419 Experts worldwide ranked by ideXlab platform

Otto Miettinen - One of the best experts on this subject based on the ideXlab platform.

  • a revised family level classification of the Polyporales basidiomycota
    Fungal Biology, 2017
    Co-Authors: Alfredo Justo, Otto Miettinen, Daniel L. Lindner, Karen K. Nakasone, Elisabet Sjökvist, Dimitrios Floudas, Beatriz Ortizsantana, Tuomo Niemela, Karlhenrik Larsson, Leif Ryvarden
    Abstract:

    Polyporales is strongly supported as a clade of Agaricomycetes, but the lack of a consensus higher-level classification within the group is a barrier to further taxonomic revision. We amplified nrLSU, nrITS, and rpb1 genes across the Polyporales, with a special focus on the latter. We combined the new sequences with molecular data generated during the PolyPEET project and performed Maximum Likelihood and Bayesian phylogenetic analyses. Analyses of our final 3-gene dataset (292 Polyporales taxa) provide a phylogenetic overview of the order that we translate here into a formal family-level classification. Eighteen clades are assigned a family name, including three families described as new (Cerrenaceae fam. nov., Gelatoporiaceae fam. nov., Panaceae fam. nov.) and fifteen others (Dacryobolaceae, Fomitopsidaceae, Grifolaceae, Hyphodermataceae, Incrustoporiaceae, Irpicaceae, Ischnodermataceae, Laetiporaceae, Meripilaceae, Meruliaceae, Phanerochaetaceae, Podoscyphaceae, Polyporaceae, Sparassidaceae, Steccherinaceae). Three clades are given informal names (/hypochnicium,/climacocystis and/fibroporia + amyloporia). Four taxa (Candelabrochete africana, Mycoleptodonoides vassiljevae, Auriporia aurea, and Tyromyces merulinus) cannot be assigned to a family within the Polyporales. The classification proposed here provides a framework for further taxonomic revision and will facilitate communication among applied and basic scientists. A survey of morphological, anatomical, physiological, and genetic traits confirms the plasticity of characters previously emphasized in taxonomy of Polyporales.

  • Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2.
    Genome Announcements, 2016
    Co-Authors: Otto Miettinen, Matthieu Hainaut, Robert Riley, Kerrie Barry, Daniel Cullen, Bernard Henrissat, Annele Hatakka, Ronald P. De Vries, Kristiina Hildén
    Abstract:

    We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.

  • comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores Polyporales basidiomycota
    Cladistics, 2012
    Co-Authors: Otto Miettinen, Elisabet Sjökvist, Ellen Larsson, Karlhenrik Larsson
    Abstract:

    The phylogeny of the poroid and hydnoid genera Antrodiella, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2, and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer than 15 new genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within the Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinum is shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within the Steccherinaceae. © The Willi Hennig Society 2011.

  • Sidera, a new genus in Hymenochaetales with poroid and hydnoid species
    Mycological Progress, 2011
    Co-Authors: Otto Miettinen, Karlhenrik Larsson
    Abstract:

    A new genus, Sidera (Hymenochaetales), is described to accommodate the dimitic polypores Skeletocutis lenis and S. vulgaris , the monomitic polypore Ceriporiopsis lowei , and the monomitic, hydnoid Athelopsis lunata . The genus is characterised by white-rot, whitish resupinate fruiting bodies, crystal rosettes on specialised hyphae, and allantoid spores. Cinereomyces (Polyporales) is confirmed to be a good genus including C. lindbladii , separate from Diplomitoporus as defined by its type species D. flavescens and the closely related D. crustulinus . Fabisporus is a taxonomic synonym of Diplomitoporus . Poriodontia subvinosa belongs to the Hymenochaetales.

David S Hibbett - One of the best experts on this subject based on the ideXlab platform.

  • Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12
    Genomics Data, 2017
    Co-Authors: Jill Gaskell, Monika Schmoll, Diego Martinez, Phil Kersten, David S Hibbett, Luis Larrondo, Paulo Canessa, Christian Kubicek, Angel Martinez, Jagjit Yadav
    Abstract:

    We report the genome of Postia (Rhodonia) placenta MAD-SB12, a homokaryotic wood decay fungus (Basidiomycota, Polyporales). Intensively studied as a representative brown rot decayer, the gene complement is consistent with the rapid depolymerization of cellulose but not lignin.

  • Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay
    Mycologia, 2013
    Co-Authors: Chiaki Hori, Jill Gaskell, David S Hibbett, Bernard Henrissat, Kiyohiko Igarashi, Masahiro Samejima, Dan Cullen
    Abstract:

    To degrade the polysaccharides, wood- decay fungi secrete a variety of glycoside hydrolases (GHs) and carbohydrate esterases (CEs) classified into various sequence-based families of carbohydrate- active enzymes (CAZys) and their appended carbohy- drate-binding modules (CBM). Oxidative enzymes, such as cellobiose dehydrogenase (CDH) and lytic polysaccharide monooxygenase (LPMO, formerly GH61), also have been implicated in cellulose degradation. To examine polysaccharide-degrading potential between white- and brown-rot fungi, we performed genomewide analysis of CAZys and these oxidative enzymes in 11 Polyporales, including recently sequenced monokaryotic strains of Bjerkan- dera adusta, Ganoderma sp. and Phlebia brevispora. Furthermore, we conducted comparative secretome analysis of seven Polyporales grown on wood culture. As a result, it was found that genes encoding cellulases belonging to families GH6, GH7, GH9 and carbohydrate-binding module family CBM1 are lacking in genomes of brown-rot Polyporales. In addition, the presence of CDH and the expansion of LPMO were observed only in white-rot genomes. Indeed, GH6, GH7, CDH and LPMO peptides were identified only in white-rot polypores. Genes encod- ing aldose 1-epimerase (ALE), previously detected with CDH and cellulases in the culture filtrates, also were identified in white-rot genomes, suggesting a physiological connection between ALE, CDH, cellu- lase and possibly LPMO. For hemicellulose degrada- tion, genes and peptides corresponding to GH74 xyloglucanase, GH10 endo-xylanase, GH79 b-glucu- ronidase, CE1 acetyl xylan esterase and CE15 glucur- onoyl methylesterase were significantly increased in white-rot genomes compared to brown-rot genomes. Overall, relative to brown-rot Polyporales, white-rot Polyporales maintain greater enzymatic diversity

  • Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes
    Mycologia, 2013
    Co-Authors: Francisco J. Ruiz-dueñas, David S Hibbett, Taina Lundell, Dimitris Floudas, László Nagy, José María Barrasa, Angel T Martinez
    Abstract:

    The genomes of three representative Poly- porales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species repre- senting the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequencedB. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)- oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.

  • Short title: Peroxidase genes in Polyporales genomes Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes
    2013
    Co-Authors: Francisco J. Ruiz-dueñas, Dimitrios Floudas, Taina Lundell, László Nagy, José María Barrasa, Ramiro De Maeztu, Ciencias Ambientales, Carretera De Barcelona, David S Hibbett
    Abstract:

    The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was

  • A phylogenetic overview of the Agaricomycotina.
    Mycologia, 2006
    Co-Authors: David S Hibbett
    Abstract:

    The Agaricomycotina contains about one- third of the described species of Fungi, including mushrooms, jelly fungi and basidiomycetous yeasts. Recent phylogenetic analyses by P. Matheny and colleagues combining nuclear rRNA genes with the protein-coding genes rpb1, rpb2 and tef1 support the division of Agaricomycotina into Tremellomycetes, Dacrymycetes and Agaricomycetes. There is strong support for the monophyly of the Tremellomycetes, and its position as the sister group of the rest of the Agaricomycotina. Dacrymycetes and Agaricomycetes also are supported strongly, and together they form a clade that is equivalent to the Hymenomycetidae of Swann and Taylor. The deepest nodes in the Agaricomycetes, which are supported only by Bayes- ian measures of confidence, suggest that the Sebaci- nales, Cantharellales and Auriculariales are among the most ancient lineages. For the first time, the Polyporales are strongly supported as monophyletic and are placed as the sister group of the Thelepho- rales. The Agaricales, Boletales and Atheliales are united as the Agaricomycetidae, and the Russulales might be its sister group. There are still some problematical nodes that will require more loci to be resolved. Phylogenomics has promise for recon- structing these difficult backbone nodes, but current genome projects are limited mostly to the Agaricales, Boletales and Polyporales. Genome sequences from other major lineages, especially the early diverging clades, are needed to resolve the most ancient nodes and to assess deep homology in ecological characters

Nils Hallenberg - One of the best experts on this subject based on the ideXlab platform.

  • The white-rotting genus Phanerochaete is polyphyletic and distributed throughout the phleboid clade of the Polyporales (Basidiomycota)
    Fungal Diversity, 2010
    Co-Authors: Henrik R. Nilsson, Chengtao Chen, Nils Hallenberg
    Abstract:

    The genus Phanerochaete (Polyporales, Basidiomycota) has traditionally been delimited based on the gross morphology of the fruiting body and on the nature of the hyphal structure, cystidia, and spores. However, several recent studies based on molecular data indicate that the genus is polyphyletic as presently circumscribed, although most of its species are found in the phlebioid clade of the Polyporales . To further our understanding of the genus, 54 new sequences from the large subunit of the nuclear ribosomal DNA of 45 previously unsequenced Phanerochaete species were obtained and analyzed jointly with a large selection of taxa in the phlebioid clade. The results show that there is a well-supported Phanerochaete core group that includes the type species Phanerochaete velutina (the currently accepted name of the generic type, Thelephora alnea ). Representatives of a few satellite genera, including Hjortstamia , Phlebiopsis , and Rhizochaete , are found in the immediate topological vicinity of Phanerochaete . Outside the core group but still within the phlebioid clade are several taxa that have been referred to as members of Phanerochaete by some authors but that are here assigned to at least five different monophyletic clades. Phanerochaete viticola is found in the Hymenochaetales and is shown to have phylogenetic affinities to the partially symbiotic Rickenellaceae . A new genus, Ginnsia , is erected for this species, and the new combinations Ginnsia viticola , Hjortstamia brunneocystidiata , H. laxa , and Phlebiopsis lamprocystidiata are proposed. A denser taxon and gene sampling in the phleboid clade will be needed to settle the precise taxonomic affiliation of many of the species presently referred to as Phanerochaete , and numerous nomenclatural changes are doubtlessly looming on the horizon.

  • the white rotting genus phanerochaete is polyphyletic and distributed throughout the phleboid clade of the Polyporales basidiomycota
    Fungal Diversity, 2010
    Co-Authors: Shenghua Wu, Henrik Nilsson, Chengtao Chen, Shiyi Yu, Nils Hallenberg
    Abstract:

    The genus Phanerochaete (Polyporales, Basidiomycota) has traditionally been delimited based on the gross morphology of the fruiting body and on the nature of the hyphal structure, cystidia, and spores. However, several recent studies based on molecular data indicate that the genus is polyphyletic as presently circumscribed, although most of its species are found in the phlebioid clade of the Polyporales. To further our understanding of the genus, 54 new sequences from the large subunit of the nuclear ribosomal DNA of 45 previously unsequenced Phanerochaete species were obtained and analyzed jointly with a large selection of taxa in the phlebioid clade. The results show that there is a well-supported Phanerochaete core group that includes the type species Phanerochaete velutina (the currently accepted name of the generic type, Thelephora alnea). Representatives of a few satellite genera, including Hjortstamia, Phlebiopsis, and Rhizochaete, are found in the immediate topological vicinity of Phanerochaete.

  • Pseudolagarobasidium (Basidiomycota): on the reinstatement of a genus of parasitic, saprophytic, and endophytic resupinate fungi
    Botany, 2008
    Co-Authors: Nils Hallenberg, Martin Rybergm. Ryberg, R. Henrik Nilsson, Alan R. Wood, Sheng-hua Wus.-h. Wu
    Abstract:

    The small resupinate genus Pseudolagarobasidium (Polyporales, Basidiomycota) presently comprises less than five species, all of which were described from tropical to subtropical regions, and two of which are root parasites on leguminous trees. The genus has recently been synonymized with Radulodon on morphological grounds, and the present study evaluates this proposal in a molecular context. Pseudolagarobasidium was found to constitute a well supported, monophyletic group excluding Radulodon and this synonymy is rejected. The ecological range of the genus spans saprotrophy to parasitism, and this study presents evidence that at least one lineage in Pseudolagarobasidium is endophytic in the cacao tree (Theobroma cacao L.).

Angel T Martinez - One of the best experts on this subject based on the ideXlab platform.

  • peroxidase evolution in white rot fungi follows wood lignin evolution in plants
    Proceedings of the National Academy of Sciences of the United States of America, 2019
    Co-Authors: Ivan Ayusofernandez, Jorge Rencoret, Ana Gutierrez, Francisco J Ruizduenas, Angel T Martinez
    Abstract:

    A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k2app and k3app) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limiting k3app). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral “tryptophanless” enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.

  • Evolutionary convergence in lignin-degrading enzymes
    Proceedings of the National Academy of Sciences of the United States of America, 2018
    Co-Authors: Iván Ayuso-fernández, Francisco J. Ruiz-dueñas, Angel T Martinez
    Abstract:

    The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.

  • Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date
    Biotechnology for Biofuels, 2017
    Co-Authors: Iván Ayuso-fernández, Angel T Martinez, Francisco J. Ruiz-dueñas
    Abstract:

    Background Floudas et al. ( Science 336: 1715) established that lignin-degrading fungi appeared at the end of Carboniferous period associated with the production of the first ligninolytic peroxidases. Here, the subsequent evolution of these enzymes in Polyporales, where most wood-rotting fungi are included, is experimentally recreated using genomic information. Results With this purpose, we analyzed the evolutionary pathway leading to the most efficient lignin-degrading peroxidases characterizing Polyporales species. After sequence reconstruction from 113 genes of ten sequenced genomes, the main enzyme intermediates were resurrected and characterized. Biochemical changes were analyzed together with predicted sequences and structures, to understand how these enzymes acquired the ability to degrade lignin and how this ability changed with time. The most probable first peroxidase in Polyporales would be a manganese peroxidase (Mn^3+ oxidizing phenolic lignin) that did not change substantially until the appearance of an exposed tryptophan (oxidizing nonphenolic lignin) originating an ancestral versatile peroxidase. Later, a quick evolution, with loss of the Mn^2+-binding site, generated the first lignin peroxidase that evolved to the extant form by improving the catalytic efficiency. Increased stability at acidic pH, which strongly increases the oxidizing power of these enzymes, was observed paralleling the appearance of the exposed catalytic tryptophan. Conclusions We show how the change in peroxidase catalytic activities meant an evolutionary exploration for more efficient ways of lignin degradation by fungi, a key step for carbon recycling in land ecosystems. The study provides ancestral enzymes with a potential biotechnological interest for the sustainable production of fuels and chemicals in a biomass-based economy.

  • Experimental recreation of the evolution of lignin-degrading enzymes from the Jurassic to date
    Biotechnology for biofuels, 2017
    Co-Authors: Iván Ayuso-fernández, Angel T Martinez, Francisco J. Ruiz-dueñas
    Abstract:

    Background Floudas et al. (Science 336: 1715) established that lignin-degrading fungi appeared at the end of Carboniferous period associated with the production of the first ligninolytic peroxidases. Here, the subsequent evolution of these enzymes in Polyporales, where most wood-rotting fungi are included, is experimentally recreated using genomic information.

  • Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes
    Mycologia, 2013
    Co-Authors: Francisco J. Ruiz-dueñas, David S Hibbett, Taina Lundell, Dimitris Floudas, László Nagy, José María Barrasa, Angel T Martinez
    Abstract:

    The genomes of three representative Poly- porales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species repre- senting the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequencedB. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)- oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.

Taina Lundell - One of the best experts on this subject based on the ideXlab platform.

  • Polyporales brown rot species fomitopsis pinicola enzyme activity profiles oxalic acid production and fe3 reducing metabolite secretion
    Applied and Environmental Microbiology, 2018
    Co-Authors: Firoz Shah, Tuulia Mali, Taina Lundell
    Abstract:

    Basidiomycota fungi in the order Polyporales are specified to decomposition of dead wood and woody debris and thereby are crucial players in the degradation of organic matter and cycling of carbon in the forest ecosystems. Polyporales wood-decaying species comprise both white rot and brown rot fungi, based on their mode of wood decay. While the white rot fungi are able to attack and decompose all the lignocellulose biopolymers, the brown rot species mainly cause the destruction of wood polysaccharides, with minor modification of the lignin units. The biochemical mechanism of brown rot decay of wood is still unclear and has been proposed to include a combination of nonenzymatic oxidation reactions and carbohydrate-active enzymes. Therefore, a linking approach is needed to dissect the fungal brown rot processes. We studied the brown rot Polyporales species Fomitopsis pinicola by following mycelial growth and enzyme activity patterns and generating metabolites together with Fenton-promoting Fe3+-reducing activity for 3 months in submerged cultures supplemented with spruce wood. Enzyme activities to degrade hemicellulose, cellulose, proteins, and chitin were produced by three Finnish isolates of F. pinicola Substantial secretion of oxalic acid and a decrease in pH were notable. Aromatic compounds and metabolites were observed to accumulate in the fungal cultures, with some metabolites having Fe3+-reducing activity. Thus, F. pinicola demonstrates a pattern of strong mycelial growth leading to the active production of carbohydrate- and protein-active enzymes, together with the promotion of Fenton biochemistry. Our findings point to fungal species-level "fine-tuning" and variations in the biochemical reactions leading to the brown rot type of wood decay.IMPORTANCEFomitopsis pinicola is a common fungal species in boreal and temperate forests in the Northern Hemisphere encountered as a wood-colonizing saprotroph and tree pathogen, causing a severe brown rot type of wood degradation. However, its lignocellulose-decomposing mechanisms have remained undiscovered. Our approach was to explore both the enzymatic activities and nonenzymatic Fenton reaction-promoting activities (Fe3+ reduction and metabolite production) by cultivating three isolates of F. pinicola in wood-supplemented cultures. Our findings on the simultaneous production of versatile enzyme activities, including those of endoglucanase, xylanase, β-glucosidase, chitinase, and acid peptidase, together with generation of low pH, accumulation of oxalic acid, and Fe3+-reducing metabolites, increase the variations of fungal brown rot decay mechanisms. Furthermore, these findings will aid us in revealing the wood decay proteomic, transcriptomic, and metabolic activities of this ecologically important forest fungal species.

  • Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes
    Mycologia, 2013
    Co-Authors: Francisco J. Ruiz-dueñas, David S Hibbett, Taina Lundell, Dimitris Floudas, László Nagy, José María Barrasa, Angel T Martinez
    Abstract:

    The genomes of three representative Poly- porales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was completed by analyzing the heme-peroxidase genes in the already available genomes of seven more Polyporales species repre- senting the antrodia, gelatoporia, core polyporoid and phlebioid clades. The study confirms the absence of ligninolytic peroxidase genes from the manganese peroxidase (MnP), lignin peroxidase (LiP) and versatile peroxidase (VP) families, in the brown-rot fungal genomes (all of them from the antrodia clade), which include only a limited number of predicted low redox-potential generic peroxidase (GP) genes. When members of the heme-thiolate peroxidase (HTP) and dye-decolorizing peroxidase (DyP) superfamilies (up to a total of 64 genes) also are considered, the newly sequencedB. adusta appears as the Polyporales species with the highest number of peroxidase genes due to the high expansion of both the ligninolytic peroxidase and DyP (super)families. The evolutionary relationships of the 111 genes for class-II peroxidases (from the GP, MnP, VP, LiP families) in the 10 Polyporales genomes is discussed including the existence of different MnP subfamilies and of a large and homogeneous LiP cluster, while different VPs mainly cluster with short MnPs. Finally, ancestral state reconstructions showed that a putative MnP gene, derived from a primitive GP that incorporated the Mn(II)-oxidation site, is the precursor of all the class-II ligninolytic peroxidases. Incorporation of an exposed tryptophan residue involved in oxidative degradation of lignin in a short MnP apparently resulted in evolution of the first VP. One of these ancient VPs might have lost the Mn(II)- oxidation site being at the origin of all the LiP enzymes, which are found only in species of the order Polyporales.

  • Short title: Peroxidase genes in Polyporales genomes Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes
    2013
    Co-Authors: Francisco J. Ruiz-dueñas, Dimitrios Floudas, Taina Lundell, László Nagy, José María Barrasa, Ramiro De Maeztu, Ciencias Ambientales, Carretera De Barcelona, David S Hibbett
    Abstract:

    The genomes of three representative Polyporales (Bjerkandera adusta, Phlebia brevispora and a member of the Ganoderma lucidum complex) were sequenced to expand our knowledge on the diversity of ligninolytic and related peroxidase genes in this Basidiomycota order that includes most wood-rotting fungi. The survey was