mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support

Strasser, Kimchi-Audrey; McDonnell, Erin; Nyaga, Carol; Wu, Min; Wu, Sherry Y.; Almeida, Hayda; Meurs, Marie-Jean; Kosseim, Leila; Powlowski, Justin; Butler, Gregory; Tsang, Adrian

doi:10.1093/database/bav008

Cited by 29 publications

(18 citation statements)

References 18 publications

(23 reference statements)

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“…2017 ). Discrepancies between the two analyses were further examined using Blastp against annotated databases including UniProtKB and mycoCLAP ( Murphy et al., 2011 , Strasser et al., 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Mäkelä¹,

DiFalco²,

McDonnell³

et al. 2018

Studies in Mycology

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We classified the genes encoding carbohydrate-active enzymes (CAZymes) in 17 sequenced genomes representing 16 evolutionarily diverse Aspergillus species. We performed a phylogenetic analysis of the encoding enzymes, along with experimentally characterized CAZymes, to assign molecular function to the Aspergilli CAZyme families and subfamilies. Genome content analysis revealed that the numbers of CAZy genes per CAZy family related to plant biomass degradation follow closely the taxonomic distance between the species. On the other hand, growth analysis showed almost no correlation between the number of CAZyme genes and the efficiency in polysaccharide utilization. The exception is A. clavatus where a reduced number of pectinolytic enzymes can be correlated with poor growth on pectin. To gain detailed information on the enzymes used by Aspergilli to breakdown complex biomass, we conducted exoproteome analysis by mass spectrometry. These results showed that Aspergilli produce many different enzymes mixtures in the presence of sugar beet pulp and wheat bran. Despite the diverse enzyme mixtures produced, species of section Nigri, A. aculeatus, A. nidulans and A. terreus, produce mixtures of enzymes with activities that are capable of digesting all the major polysaccharides in the available substrates, suggesting that they are capable of degrading all the polysaccharides present simultaneously. For the other Aspergilli, typically the enzymes produced are targeted to a subset of polysaccharides present, suggesting that they can digest only a subset of polysaccharides at a given time.

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Section: Methodsmentioning

confidence: 99%

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Mäkelä¹,

DiFalco²,

McDonnell³

et al. 2018

Studies in Mycology

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“…The high levels of β-xylosidase secretion found when A. nidulans was cultivated on beechwood xylan provided evidence that this enzyme was highly important for biomass degradation [4]. β-Xylosidases have been detected in various prokaryotes and eukaryotes, but, according to the mycoCLAP database [26, 27], only 11 eukaryotic GH3 β-xylosidases have been characterized. Among them, four β-xylosidases have been expressed in hosts such as Aspergillus spp.…”

Section: Discussionmentioning

confidence: 99%

Redesigning N-glycosylation sites in a GH3 β-xylosidase improves the enzymatic efficiency

Rubio

Terrasan

Contesini

et al. 2019

Biotechnol Biofuels

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Backgroundβ-Xylosidases are glycoside hydrolases (GHs) that cleave xylooligosaccharides and/or xylobiose into shorter oligosaccharides and xylose. Aspergillus nidulans is an established genetic model and good source of carbohydrate-active enzymes (CAZymes). Most fungal enzymes are N-glycosylated, which influences their secretion, stability, activity, signalization, and protease protection. A greater understanding of the N-glycosylation process would contribute to better address the current bottlenecks in obtaining high secretion yields of fungal proteins for industrial applications.ResultsIn this study, BxlB—a highly secreted GH3 β-xylosidase from A. nidulans, presenting high activity and several N-glycosylation sites—was selected for N-glycosylation engineering. Several glycomutants were designed to investigate the influence of N-glycans on BxlB secretion and function. The non-glycosylated mutant (BxlBnon-glyc) showed similar levels of enzyme secretion and activity compared to the wild-type (BxlBwt), while a partially glycosylated mutant (BxlBN1;5;7) exhibited increased activity. Additionally, there was no enzyme secretion in the mutant in which the N-glycosylation context was changed by the introduction of four new N-glycosylation sites (BxlBCC), despite the high transcript levels. BxlBwt, BxlBnon-glyc, and BxlBN1;5;7 formed similar secondary structures, though the mutants had lower melting temperatures compared to the wild type. Six additional glycomutants were designed based on BxlBN1;5;7, to better understand its increased activity. Among them, the two glycomutants which maintained only two N-glycosylation sites each (BxlBN1;5 and BxlBN5;7) showed improved catalytic efficiency, whereas the other four mutants’ catalytic efficiencies were reduced. The N-glycosylation site N5 is important for improved BxlB catalytic efficiency, but needs to be complemented by N1 and/or N7. Molecular dynamics simulations of BxlBnon-glyc and BxlBN1;5 reveals that the mobility pattern of structural elements in the vicinity of the catalytic pocket changes upon N1 and N5 N-glycosylation sites, enhancing substrate binding properties which may underlie the observed differences in catalytic efficiency between BxlBnon-glyc and BxlBN1;5.ConclusionsThis study demonstrates the influence of N-glycosylation on A. nidulans BxlB production and function, reinforcing that protein glycoengineering is a promising tool for enhancing thermal stability, secretion, and enzymatic activity. Our report may also support biotechnological applications for N-glycosylation modification of other CAZymes.

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“…Lignocellulose genes are most important for degradation (Yin et al, 2012 ; Strasser et al, 2015 ). Here, we identified 70% lignocellulose genes of all CAZymes, which is more than those found in the previous proteomic analysis (Gao et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis

et al. 2018

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The molecular mechanism underlying the elimination of algal cells by fungal mycelia has not been fully understood. Here, we applied transcriptomic analysis to investigate the gene expression and regulation at time courses of Trametes versicolor F21a during the algicidal process. The obtained results showed that a total of 193, 332, 545, and 742 differentially expressed genes were identified at 0, 6, 12, and 30 h during the algicidal process, respectively. The gene ontology terms were enriched into glucan 1,4-α-glucosidase activity, hydrolase activity, lipase activity, and endopeptidase activity. The KEGG pathways were enriched in degradation and metabolism pathways including Glycolysis/Gluconeogenesis, Pyruvate metabolism, the Biosynthesis of amino acids, etc. The total expression levels of all Carbohydrate-Active enZYmes (CAZyme) genes for the saccharide metabolism were increased by two folds relative to the control. AA5, GH18, GH5, GH79, GH128, and PL8 were the top six significantly up-regulated modules among 43 detected CAZyme modules. Four available homologous decomposition enzymes of other species could partially inhibit the growth of algal cells. The facts suggest that the algicidal mode of T. versicolor F21a might be associated with decomposition enzymes and several metabolic pathways. The obtained results provide a new candidate way to control algal bloom by application of decomposition enzymes in the future.

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mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support

Cited by 29 publications

References 18 publications

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli

Redesigning N-glycosylation sites in a GH3 β-xylosidase improves the enzymatic efficiency

The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis

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