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1.
Fungal Genet Biol ; 159: 103670, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35121171

RESUMEN

The current impetus towards a sustainable bio-based economy has accelerated research to better understand the mechanisms through which filamentous fungi convert plant biomass, a valuable feedstock for biotechnological applications. Several transcription factors have been reported to control the polysaccharide degradation and metabolism of the resulting sugars in fungi. However, little is known about their individual contributions, interactions and crosstalk. D-galactose is a hexose sugar present mainly in hemicellulose and pectin in plant biomass. Here, we study D-galactose conversion by Aspergillus niger and describe the involvement of the arabinanolytic and xylanolytic activators AraR and XlnR, in addition to the D-galactose-responsive regulator GalX. Our results deepen the understanding of the complexity of the filamentous fungal regulatory network for plant biomass degradation and sugar catabolism, and facilitate the generation of more efficient plant biomass-degrading strains for biotechnological applications.


Asunto(s)
Aspergillus niger , Galactosa , Aspergillus , Aspergillus niger/genética , Biomasa , Pectinas
2.
Appl Environ Microbiol ; 87(6)2021 02 26.
Artículo en Inglés | MEDLINE | ID: mdl-33397706

RESUMEN

Salicylic acid plays an important role in the plant immune response, and its degradation is therefore important for plant-pathogenic fungi. However, many nonpathogenic microorganisms can also degrade salicylic acid. In the filamentous fungus Aspergillus niger, two salicylic acid metabolic pathways have been suggested. The first pathway converts salicylic acid to catechol by a salicylate hydroxylase (ShyA). In the second pathway, salicylic acid is 3-hydroxylated to 2,3-dihydroxybenzoic acid, followed by decarboxylation to catechol by 2,3-dihydroxybenzoate decarboxylase (DhbA). A. niger cleaves the aromatic ring of catechol catalyzed by catechol 1,2-dioxygenase (CrcA) to form cis,cis-muconic acid. However, the identification and role of the genes and characterization of the enzymes involved in these pathways are lacking. In this study, we used transcriptome data of A. niger grown on salicylic acid to identify genes (shyA and crcA) involved in salicylic acid metabolism. Heterologous production in Escherichia coli followed by biochemical characterization confirmed the function of ShyA and CrcA. The combination of ShyA and CrcA demonstrated that cis,cis-muconic acid can be produced from salicylic acid. In addition, the in vivo roles of shyA, dhbA, and crcA were studied by creating A. niger deletion mutants which revealed the role of these genes in the fungal metabolism of salicylic acid.IMPORTANCE Nonrenewable petroleum sources are being depleted, and therefore, alternative sources are needed. Plant biomass is one of the most abundant renewable sources on Earth and is efficiently degraded by fungi. In order to utilize plant biomass efficiently, knowledge about the fungal metabolic pathways and the genes and enzymes involved is essential to create efficient strategies for producing valuable compounds such as cis,cis-muconic acid. cis,cis-Muconic acid is an important platform chemical that is used to synthesize nylon, polyethylene terephthalate (PET), polyurethane, resins, and lubricants. Currently, cis,cis-muconic acid is mainly produced through chemical synthesis from petroleum-based chemicals. Here, we show that two enzymes from fungi can be used to produce cis,cis-muconic acid from salicylic acid and contributes in creating alternative methods for the production of platform chemicals.


Asunto(s)
Aspergillus niger/enzimología , Proteínas Fúngicas/metabolismo , Oxigenasas de Función Mixta/metabolismo , Ácido Salicílico/metabolismo , Aspergillus niger/genética , Carboxiliasas/genética , Catecol 1,2-Dioxigenasa/genética , Proteínas Fúngicas/genética , Oxigenasas de Función Mixta/genética , Filogenia
3.
Adv Appl Microbiol ; 114: 73-109, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33934853

RESUMEN

Lignocellulosic biomass is an abundant and renewable resource, and its utilization has become the focus of research and biotechnology applications as a very promising raw material for the production of value-added compounds. Filamentous fungi play an important role in the production of various lignocellulolytic enzymes, while some of them have also been used for the production of important metabolites. However, wild type strains have limited efficiency in enzyme production or metabolic conversion, and therefore many efforts have been made to engineer improved strains. Examples of this are the manipulation of transcriptional regulators and/or promoters of enzyme-encoding genes to increase gene expression, and protein engineering to improve the biochemical characteristics of specific enzymes. This review provides and overview of the applications of filamentous fungi in lignocellulosic biomass based processes and the development and current status of various molecular engineering strategies to improve these processes.


Asunto(s)
Hongos , Lignina , Biomasa , Biotecnología , Hongos/genética
4.
Environ Microbiol ; 22(3): 1154-1166, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-31876091

RESUMEN

Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.


Asunto(s)
Adaptación Fisiológica , Aspergillus niger/metabolismo , Carbono/metabolismo , Biomasa , Hifa/metabolismo , Pectinas/metabolismo
5.
Appl Environ Microbiol ; 85(23)2019 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-31585998

RESUMEN

The extent of carbon catabolite repression (CCR) at a global level is unknown in wood-rotting fungi, which are critical to the carbon cycle and are a source of biotechnological enzymes. CCR occurs in the presence of sufficient concentrations of easily metabolizable carbon sources (e.g., glucose) and involves downregulation of the expression of genes encoding enzymes involved in the breakdown of complex carbon sources. We investigated this phenomenon in the white-rot fungus Dichomitus squalens using transcriptomics and exoproteomics. In D. squalens cultures, approximately 7% of genes were repressed in the presence of glucose compared to Avicel or xylan alone. The glucose-repressed genes included the essential components for utilization of plant biomass-carbohydrate-active enzyme (CAZyme) and carbon catabolic genes. The majority of polysaccharide-degrading CAZyme genes were repressed and included activities toward all major carbohydrate polymers present in plant cell walls, while repression of ligninolytic genes also occurred. The transcriptome-level repression of the CAZyme genes observed on the Avicel cultures was strongly supported by exoproteomics. Protease-encoding genes were generally not glucose repressed, indicating their likely dominant role in scavenging for nitrogen rather than carbon. The extent of CCR is surprising, given that D. squalens rarely experiences high free sugar concentrations in its woody environment, and it indicates that biotechnological use of D. squalens for modification of plant biomass would benefit from derepressed or constitutively CAZyme-expressing strains.IMPORTANCE White-rot fungi are critical to the carbon cycle because they can mineralize all wood components using enzymes that also have biotechnological potential. The occurrence of carbon catabolite repression (CCR) in white-rot fungi is poorly understood. Previously, CCR in wood-rotting fungi has only been demonstrated for a small number of genes. We demonstrated widespread glucose-mediated CCR of plant biomass utilization in the white-rot fungus Dichomitus squalens This indicates that the CCR mechanism has been largely retained even though wood-rotting fungi rarely experience commonly considered CCR conditions in their woody environment. The general lack of repression of genes encoding proteases along with the reduction in secreted CAZymes during CCR suggested that the retention of CCR may be connected with the need to conserve nitrogen use during growth on nitrogen-scarce wood. The widespread repression indicates that derepressed strains could be beneficial for enzyme production.


Asunto(s)
Represión Catabólica , Glucosa/metabolismo , Polyporaceae/metabolismo , Madera/microbiología
6.
Environ Microbiol ; 20(11): 4141-4156, 2018 11.
Artículo en Inglés | MEDLINE | ID: mdl-30246402

RESUMEN

White-rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed-wood forests containing both soft- and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood [guaiacyl (G) lignin and higher mannan content] and hardwood [syringyl/guaiacyl (S/G) lignin and higher xylan content] using semi-natural solid cultures. Spruce (softwood) and birch (hardwood) sticks were degraded by D. squalens as measured by oxidation of the lignins using 2D-NMR. The fungal response as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition. Mannanolytic transcripts and proteins were more abundant in spruce cultures, while a proportionally higher xylanolytic activity was detected in birch cultures. Both wood types induced manganese peroxidases to a much higher level than laccases, but higher transcript and protein levels of the manganese peroxidases were observed on the G-lignin rich spruce. Overall, the molecular responses demonstrated a stronger adaptation to the spruce rather than birch composition, possibly because D. squalens is mainly found degrading softwoods in nature, which supports the ability of the solid wood cultures to reflect the natural environment.


Asunto(s)
Basidiomycota/metabolismo , Polyporaceae/metabolismo , Madera/química , Basidiomycota/enzimología , Basidiomycota/genética , Betula/química , Betula/microbiología , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Lacasa/genética , Lacasa/metabolismo , Lignina/química , Lignina/metabolismo , Mananos/química , Mananos/metabolismo , Peroxidasas/genética , Peroxidasas/metabolismo , Picea/química , Picea/microbiología , Madera/microbiología
7.
Fungal Genet Biol ; 112: 47-54, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-28754284

RESUMEN

The basidiomycete white-rot fungus Obba rivulosa, a close relative of Gelatoporia (Ceriporiopsis) subvermispora, is an efficient degrader of softwood. The dikaryotic O. rivulosa strain T241i (FBCC949) has been shown to selectively remove lignin from spruce wood prior to depolymerization of plant cell wall polysaccharides, thus possessing potential in biotechnological applications such as pretreatment of wood in pulp and paper industry. In this work, we studied the time-course of the conversion of spruce by the genome-sequenced monokaryotic O. rivulosa strain 3A-2, which is derived from the dikaryon T241i, to get insight into transcriptome level changes during prolonged solid state cultivation. During 8-week cultivation, O. rivulosa expressed a constitutive set of genes encoding putative plant cell wall degrading enzymes. High level of expression of the genes targeted towards all plant cell wall polymers was detected at 2-week time point, after which majority of the genes showed reduced expression. This implicated non-selective degradation of lignin by the O. rivulosa monokaryon and suggests high variation between mono- and dikaryotic strains of the white-rot fungi with respect to their abilities to convert plant cell wall polymers.


Asunto(s)
Pared Celular/metabolismo , Regulación Fúngica de la Expresión Génica , Hidrolasas/biosíntesis , Células Vegetales/metabolismo , Polyporales/enzimología , Polyporales/crecimiento & desarrollo , Madera/microbiología , Perfilación de la Expresión Génica , Hidrolasas/genética , Lignina/metabolismo , Polyporales/genética
8.
Fungal Genet Biol ; 112: 40-46, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-28803908

RESUMEN

Basidiomycete fungi can degrade a wide range of plant biomass, including living and dead trees, forest litter, crops, and plant matter in soils. Understanding the process of plant biomass decay by basidiomycetes could facilitate their application in various industrial sectors such as food & feed, detergents and biofuels, and also provide new insights into their essential biological role in the global carbon cycle. The fast expansion of basidiomycete genomic and functional genomics data (e.g. transcriptomics, proteomics) has facilitated exploration of key genes and regulatory mechanisms of plant biomass degradation. In this study, we comparatively analyzed 22 transcriptome datasets from basidiomycetes related to plant biomass degradation, and identified 328 commonly induced genes and 318 repressed genes, and defined a core set of carbohydrate active enzymes (CAZymes), which was shared by most of the basidiomycete species. High conservation of these CAZymes in genomes and similar regulation pattern in transcriptomics data from lignocellulosic substrates indicate their key role in plant biomass degradation and need for their further biochemical investigation.


Asunto(s)
Basidiomycota/enzimología , Basidiomycota/genética , Hidrolasas/biosíntesis , Hidrolasas/genética , Lignina/metabolismo , Plantas/metabolismo , Transcriptoma , Basidiomycota/metabolismo , Biomasa
9.
Fungal Genet Biol ; 112: 12-20, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29277563

RESUMEN

The white button mushroom Agaricus bisporus is one of the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. bisporus strains for their potential to convert the components that are poorly utilized by the commercial strain A15. We therefore focused our analysis on the stages where the fungus is producing fruiting bodies. Growth profiling was used to identify A. bisporus strains with different abilities to use plant biomass derived polysaccharides, as well as to transport and metabolize the corresponding monomeric sugars. Six wild-type isolates with diverse growth profiles were compared for mushroom production to A15 strain in semi-commercial cultivation conditions. Transcriptome and proteome analyses of the three most interesting wild-type strains and A15 indicated that the unrelated A. bisporus strains degrade and convert plant biomass polymers in a highly similar manner. This was also supported by the chemical content of the compost during the mushroom production process. Our study therefore reveals a highly conserved physiology for unrelated strains of this species during growth in compost.


Asunto(s)
Agaricus/crecimiento & desarrollo , Agaricus/metabolismo , Compostaje , Cuerpos Fructíferos de los Hongos/crecimiento & desarrollo , Cuerpos Fructíferos de los Hongos/metabolismo , Perfilación de la Expresión Génica , Polisacáridos/metabolismo , Proteoma/análisis , Triticum/metabolismo , Triticum/microbiología
10.
Appl Environ Microbiol ; 84(11)2018 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-29572208

RESUMEN

Fungi can decompose plant biomass into small oligo- and monosaccharides to be used as carbon sources. Some of these small molecules may induce metabolic pathways and the production of extracellular enzymes targeted for degradation of plant cell wall polymers. Despite extensive studies in ascomycete fungi, little is known about the nature of inducers for the lignocellulolytic systems of basidiomycetes. In this study, we analyzed six sugars known to induce the expression of lignocellulolytic genes in ascomycetes for their role as inducers in the basidiomycete white-rot fungus Dichomitus squalens using a transcriptomic approach. This identified cellobiose and l-rhamnose as the main inducers of cellulolytic and pectinolytic genes, respectively, of D. squalens Our results also identified differences in gene expression patterns between dikaryotic and monokaryotic strains of D. squalens cultivated on plant biomass-derived monosaccharides and the disaccharide cellobiose. This suggests that despite conservation of the induction between these two genetic forms of D. squalens, the fine-tuning in the gene regulation of lignocellulose conversion is differently organized in these strains.IMPORTANCE Wood-decomposing basidiomycete fungi have a major role in the global carbon cycle and are promising candidates for lignocellulosic biorefinery applications. However, information on which components trigger enzyme production is currently lacking, which is crucial for the efficient use of these fungi in biotechnology. In this study, transcriptomes of the white-rot fungus Dichomitus squalens from plant biomass-derived monosaccharide and cellobiose cultures were studied to identify compounds that induce the expression of genes involved in plant biomass degradation.


Asunto(s)
Basidiomycota/enzimología , Basidiomycota/genética , Pared Celular/metabolismo , Proteínas Fúngicas/genética , Lignina/metabolismo , Biomasa , Celobiosa/metabolismo , Expresión Génica , Perfilación de la Expresión Génica , Células Vegetales/metabolismo , Madera/metabolismo , Madera/microbiología
11.
BMC Genomics ; 18(1): 900, 2017 Nov 23.
Artículo en Inglés | MEDLINE | ID: mdl-29169319

RESUMEN

BACKGROUND: The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. RESULTS: The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. CONCLUSIONS: Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes.


Asunto(s)
Aspergillus niger/genética , Regulación Fúngica de la Expresión Génica , Aspergillus niger/enzimología , Aspergillus niger/metabolismo , Metabolismo de los Hidratos de Carbono/genética , Análisis por Conglomerados , Proteínas Fúngicas/metabolismo , Perfilación de la Expresión Génica , Regulación Enzimológica de la Expresión Génica , Inulina/metabolismo , Mutación , Pectinas/metabolismo , Almidón/metabolismo , Sacarosa/metabolismo , Transactivadores/metabolismo
12.
Environ Microbiol ; 19(3): 1237-1250, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-28028889

RESUMEN

The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.


Asunto(s)
Proteínas Fúngicas/genética , Polyporaceae/genética , Madera/microbiología , Biomasa , Proteínas Fúngicas/metabolismo , Lignina/metabolismo , Picea/metabolismo , Picea/microbiología , Polyporaceae/crecimiento & desarrollo , Polyporaceae/aislamiento & purificación , Polyporaceae/metabolismo , Transcriptoma , Madera/metabolismo
13.
Appl Microbiol Biotechnol ; 101(11): 4363-4369, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-28466110

RESUMEN

The white button mushroom Agaricus bisporus is economically the most important commercially produced edible fungus. It is grown on carbon- and nitrogen-rich substrates, such as composted cereal straw and animal manure. The commercial mushroom production process is usually performed in buildings or tunnels under highly controlled environmental conditions. In nature, the basidiomycete A. bisporus has a significant impact on the carbon cycle in terrestrial ecosystems as a saprotrophic decayer of leaf litter. In this mini-review, the fate of the compost plant cell wall structures, xylan, cellulose and lignin, is discussed. A comparison is made from the structural changes observed to the occurrence and function of enzymes for lignocellulose degradation present, with a special focus on the extracellular enzymes produced by A. bisporus. In addition, recent advancements in whole genome level molecular studies in various growth stages of A. bisporus in compost are reviewed.


Asunto(s)
Agaricus/enzimología , Celulosa/metabolismo , Lignina/metabolismo , Xilanos/metabolismo , Agaricus/genética , Agaricus/crecimiento & desarrollo , Animales , Carbono/metabolismo , Ciclo del Carbono , Genoma Fúngico , Micelio/crecimiento & desarrollo , Nitrógeno/metabolismo , Suelo , Xilanos/química
14.
Environ Microbiol ; 17(8): 3098-109, 2015 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-26118398

RESUMEN

The economically important edible basidiomycete mushroom Agaricus bisporus thrives on decaying plant material in forests and grasslands of North America and Europe. It degrades forest litter and contributes to global carbon recycling, depolymerizing (hemi-)cellulose and lignin in plant biomass. Relatively little is known about how A. bisporus grows in the controlled environment in commercial production facilities and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were only highly expressed during the spawning stage day 16. In contrast, (hemi-)cellulolytic genes were highly expressed at the first flush, whereas low expression was observed at the second flush. The essential role for many highly expressed plant biomass degrading genes was supported by exo-proteome analysis. Our data also support a model of sequential lignocellulose degradation by wood-decaying fungi proposed in previous studies, concluding that lignin is degraded at the initial stage of growth in compost and is not modified after the spawning stage. The observed differences in gene expression involved in (hemi-)cellulose degradation between the first and second flushes could partially explain the reduction in the number of mushrooms during the second flush.


Asunto(s)
Agaricus/metabolismo , Celulosa/metabolismo , Lignina/metabolismo , Microbiología del Suelo , Suelo , Madera/metabolismo , Agaricus/enzimología , Animales , Carbono/metabolismo , Europa (Continente) , Estadios del Ciclo de Vida , Datos de Secuencia Molecular , América del Norte , Plantas/metabolismo , Proteoma/genética , Proteómica , Transcriptoma/genética
15.
BMC Microbiol ; 15: 217, 2015 Oct 19.
Artículo en Inglés | MEDLINE | ID: mdl-26482661

RESUMEN

BACKGROUND: The fungal genus Phlebia consists of a number of species that are significant in wood decay. Biotechnological potential of a few species for enzyme production and degradation of lignin and pollutants has been previously studied, when most of the species of this genus are unknown. Therefore, we carried out a wider study on biochemistry and systematics of Phlebia species. METHODS: Isolates belonging to the genus Phlebia were subjected to four-gene sequence analysis in order to clarify their phylogenetic placement at species level and evolutionary relationships of the genus among phlebioid Polyporales. rRNA-encoding (5.8S, partial LSU) and two protein-encoding gene (gapdh, rpb2) sequences were adopted for the evolutionary analysis, and ITS sequences (ITS1+5.8S+ITS2) were aligned for in-depth species-level phylogeny. The 49 fungal isolates were cultivated on semi-solid milled spruce wood medium for 21 days in order to follow their production of extracellular lignocellulose-converting oxidoreductases and carbohydrate active enzymes. RESULTS: Four-gene phylogenetic analysis confirmed the polyphyletic nature of the genus Phlebia. Ten species-level subgroups were formed, and their lignocellulose-converting enzyme activity profiles coincided with the phylogenetic grouping. The highest enzyme activities for lignin modification (manganese peroxidase activity) were obtained for Phlebia radiata group, which supports our previous studies on the enzymology and gene expression of this species on lignocellulosic substrates. CONCLUSIONS: Our study implies that there is a species-level connection of molecular systematics (genotype) to the efficiency in production of both lignocellulose-converting carbohydrate active enzymes and oxidoreductases (enzyme phenotype) on spruce wood. Thus, we may propose a similar phylogrouping approach for prediction of lignocellulose-converting enzyme phenotypes in new fungal species or genetically and biochemically less-studied isolates of the wood-decay Polyporales.


Asunto(s)
Basidiomycota/clasificación , Basidiomycota/enzimología , Lignina/metabolismo , Filogenia , Basidiomycota/genética , Basidiomycota/metabolismo , Biotransformación , Análisis por Conglomerados , Medios de Cultivo/química , ADN de Hongos/química , ADN de Hongos/genética , ADN Ribosómico/química , ADN Ribosómico/genética , ADN Espaciador Ribosómico/química , ADN Espaciador Ribosómico/genética , Gliceraldehído-3-Fosfato Deshidrogenasa (Fosforilante)/genética , Técnicas Microbiológicas , Datos de Secuencia Molecular , ARN Polimerasa II/genética , ARN Ribosómico/genética , ARN Ribosómico 5.8S/genética , Análisis de Secuencia de ADN
16.
Adv Appl Microbiol ; 91: 63-137, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-25911233

RESUMEN

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.


Asunto(s)
Hongos/fisiología , Lignina/metabolismo , Plantas/química , Biomasa , Hongos/química , Redes y Vías Metabólicas , Compuestos Orgánicos/metabolismo , Plantas/microbiología
17.
Fungal Genet Biol ; 72: 2-9, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-25192611

RESUMEN

Plant biomass degradation by fungi has implications for several fields of science. The enzyme systems employed by fungi for this are broadly used in various industrial sectors such as food & feed, pulp & paper, detergents, textile, wine, and more recently biofuels and biochemicals. In addition, the topic is highly relevant in the field of plant pathogenic fungi as they degrade plant biomass to either gain access to the plant or as carbon source, resulting in significant crop losses. Finally, fungi are the main degraders of plant biomass in nature and as such have an essential role in the global carbon cycle and ecology in general. In this review we provide a global view on the development of this research topic in saprobic ascomycetes and basidiomycetes and in plant pathogenic fungi and link this to the other papers of this special issue on plant biomass degradation by fungi.


Asunto(s)
Biomasa , Hongos/crecimiento & desarrollo , Hongos/metabolismo , Plantas/metabolismo , Plantas/microbiología , Biotransformación , Microbiología Industrial , Enfermedades de las Plantas/microbiología
18.
Fungal Genet Biol ; 72: 91-98, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24394946

RESUMEN

The recent discovery of oxidative cellulose degradation enhancing enzymes has considerably changed the traditional concept of hydrolytic cellulose degradation. The relative expression levels of ten cellulose-acting enzyme encoding genes of the white-rot fungus Dichomitus squalens were studied on solid-state spruce wood and in microcrystalline Avicel cellulose cultures. From the cellobiohydrolase encoding genes, cel7c was detected at the highest level and showed constitutive expression whereas variable transcript levels were detected for cel7a, cel7b and cel6 in the course of four-week spruce cultivation. The cellulolytic enzyme activities detected in the liquid cultures were consistent with the transcript levels. Interestingly, the selected lytic polysaccharide monooxygenase (LPMO) encoding genes were expressed in both cultures, but showed different transcription patterns on wood compared to those in submerged microcrystalline cellulose cultures. On spruce wood, higher transcript levels were detected for the lpmos carrying cellulose binding module (CBM) than for the lpmos without CBMs. In both cultures, the expression levels of the lpmo genes were generally higher than the levels of cellobiose dehydrogenase (CDH) encoding genes. Based on the results of this work, the oxidative cellulose cleaving enzymes of D. squalens have essential role in cellulose degrading machinery of the fungus.


Asunto(s)
Celulasas/biosíntesis , Celulosa/metabolismo , Perfilación de la Expresión Génica , Picea/microbiología , Polyporaceae/enzimología , Madera/metabolismo , Celulasas/genética , ADN de Hongos/química , ADN de Hongos/genética , Datos de Secuencia Molecular , Polyporaceae/genética , Análisis de Secuencia de ADN , Madera/microbiología
19.
Fungal Genet Biol ; 72: 201-206, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24951842

RESUMEN

Isolation of high quantity and quality RNA is a crucial step in the detection of meaningful gene expression data. Obtaining intact fungal RNA from complex lignocellulosic substrates is often difficult, producing low integrity RNA which perform poorly in downstream applications. In this study we developed an RNA extraction method using CsCl centrifugation procedure, modified from previous reports and adapted for isolation of RNA from plant biomass. This method provided high level of integrity and good quantity of RNA which were suitable for reliable analyses of gene expression and produced consistent and reproducible results.


Asunto(s)
Biomasa , Centrifugación por Gradiente de Densidad/métodos , Biología Molecular/métodos , Plantas/microbiología , ARN de Hongos/aislamiento & purificación , Perfilación de la Expresión Génica/métodos
20.
Fungal Genet Biol ; 72: 131-136, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24657475

RESUMEN

Agrocybe praecox is a litter-decomposing Basidiomycota species of the order Agaricales, and is frequently found in forests and open woodlands. A. praecox grows in leaf-litter and the upper soil and is able to colonize bark mulch and wood chips. It produces extracellular manganese peroxidase (MnP) activities and mineralizes synthetic lignin. In this study, the A. praecox MnP1 isozyme was purified, cloned and enzymatically characterized. The enzyme catalysed the oxidation of Mn(2+) to Mn(3+), which is the specific reaction for manganese-dependent class II heme-peroxidases, in the presence of malonate as chelator with an activity maximum at pH 4.5; detectable activity was observed even at pH 7.0. The coding sequence of the mnp1 gene demonstrates a short-type of MnP protein with a slightly modified Mn(2+) binding site. Thus, A. praecox MnP1 may represent a novel group of atypical short-MnP enzymes. In lignocellulose-containing cultures composed of cereal bran or forest litter, transcription of mnp1 gene was followed by quantitative real-time RT-PCR. On spruce needle litter, mnp1 expression was more abundant than on leaf litter after three weeks cultivation. However, the expression was constitutive in wheat and rye bran cultures. Our data show that the atypical MnP of A. praecox is able to catalyse Mn(2+) oxidation, which suggests its involvement in lignocellulose decay by this litter-decomposer.


Asunto(s)
Agrocybe/enzimología , Peroxidasas/genética , Peroxidasas/metabolismo , Agrocybe/genética , Agrocybe/metabolismo , Clonación Molecular , ADN de Hongos/química , ADN de Hongos/genética , Fibras de la Dieta/metabolismo , Fibras de la Dieta/microbiología , Estabilidad de Enzimas , Expresión Génica , Perfilación de la Expresión Génica , Concentración de Iones de Hidrógeno , Manganeso/metabolismo , Datos de Secuencia Molecular , Oxidación-Reducción , Peroxidasas/química , Peroxidasas/aislamiento & purificación , Hojas de la Planta/metabolismo , Hojas de la Planta/microbiología , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Análisis de Secuencia de ADN
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