Dataset Information

Comparative genomics reveals high biological diversity and specific adaptations in the fungal genus Aspergillus

ABSTRACT: The project compares the genomes of multiple Aspergillus species. In particular, the genes involved in the degradation of plant-derived biomass have been analyzed. As well, the extracellular proteins produced by the fungi during the utilization of sugar beet pulp and wheat bran were examined by LC-MS/MS. Results show that closely related species can deploy different enzyme mixtures in the hydrolysis of plant-derived biomass. These results imply that efficient hydrolysis of biomass can be achieved by combining enzyme mixtures from two or more fungi.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Aspergillus Wentii Aspergillus Foetidus Var. Acidus Aspergillus Versicolor Aspergillus Zonatus Aspergillus Aculeatus Atcc 16872 Aspergillus Carbonarius Item 5010 Aspergillus Tubingensis Aspergillus Brasiliensis Aspergillus Sydowii

TISSUE(S): Fungal Cell

SUBMITTER: Marcos Di Falco

LAB HEAD: Ronald de Vries

PROVIDER: PXD005563 | Pride | 2018-10-26

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 81

Publications

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

de Vries Ronald P RP Riley Robert R Wiebenga Ad A Aguilar-Osorio Guillermo G Amillis Sotiris S Uchima Cristiane Akemi CA Anderluh Gregor G Asadollahi Mojtaba M Askin Marion M Barry Kerrie K Battaglia Evy E Bayram Özgür Ö Benocci Tiziano T Braus-Stromeyer Susanna A SA Caldana Camila C Cánovas David D Cerqueira Gustavo C GC Chen Fusheng F Chen Wanping W Choi Cindy C Clum Alicia A Dos Santos Renato Augusto Corrêa RA Damásio André Ricardo de Lima AR Diallinas George G Emri Tamás T Fekete Erzsébet E Flipphi Michel M Freyberg Susanne S Gallo Antonia A Gournas Christos C Habgood Rob R Hainaut Matthieu M Harispe María Laura ML Henrissat Bernard B Hildén Kristiina S KS Hope Ryan R Hossain Abeer A Karabika Eugenia E Karaffa Levente L Karányi Zsolt Z Kraševec Nada N Kuo Alan A Kusch Harald H LaButti Kurt K Lagendijk Ellen L EL Lapidus Alla A Levasseur Anthony A Lindquist Erika E Lipzen Anna A Logrieco Antonio F AF MacCabe Andrew A Mäkelä Miia R MR Malavazi Iran I Melin Petter P Meyer Vera V Mielnichuk Natalia N Miskei Márton M Molnár Ákos P ÁP Mulé Giuseppina G Ngan Chew Yee CY Orejas Margarita M Orosz Erzsébet E Ouedraogo Jean Paul JP Overkamp Karin M KM Park Hee-Soo HS Perrone Giancarlo G Piumi Francois F Punt Peter J PJ Ram Arthur F J AF Ramón Ana A Rauscher Stefan S Record Eric E Riaño-Pachón Diego Mauricio DM Robert Vincent V Röhrig Julian J Ruller Roberto R Salamov Asaf A Salih Nadhira S NS Samson Rob A RA Sándor Erzsébet E Sanguinetti Manuel M Schütze Tabea T Sepčić Kristina K Shelest Ekaterina E Sherlock Gavin G Sophianopoulou Vicky V Squina Fabio M FM Sun Hui H Susca Antonia A Todd Richard B RB Tsang Adrian A Unkles Shiela E SE van de Wiele Nathalie N van Rossen-Uffink Diana D Oliveira Juliana Velasco de Castro JV Vesth Tammi C TC Visser Jaap J Yu Jae-Hyuk JH Zhou Miaomiao M Andersen Mikael R MR Archer David B DB Baker Scott E SE Benoit Isabelle I Brakhage Axel A AA Braus Gerhard H GH Fischer Reinhard R Frisvad Jens C JC Goldman Gustavo H GH Houbraken Jos J Oakley Berl B Pócsi István I Scazzocchio Claudio C Seiboth Bernhard B vanKuyk Patricia A PA Wortman Jennifer J Dyer Paul S PS Grigoriev Igor V IV

Genome biology 20170214 1

<h4>Background</h4>The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.<h4>Results</h4>We have generated genome se ...[more]

PMID: 28196534

Similar Datasets

Project description:Background: Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers [GSE33852]. Results: In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. Conclusions: By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production. Six samples in total consisting of duplicate shake flask Aspergillus niger cultures from three conditions: glucose 48 h, willow 24 h, willow 24 h + glucose 5 h

Project description:Lytic polysaccharide monooxygenases (LPMOs) are oxidative enzymes found in viruses, archaea, bacteria as well as eukaryotes, such as fungi, algae and insects, actively contributing to the degradation of different polysaccharides. In Aspergillus nidulans, LPMOs from family AA9 (AnLPMO9s), along with an AA3 cellobiose dehydrogenase (AnCDH1), are co-secreted upon growth on crystalline cellulose and lignocellulosic substrates, indicating their role in the degradation of plant cell wall components. Functional analysis revealed that the three main secreted LPMO9s (AnLPMO9C, AnLPMO9F and AnLPMO9G) correspond to cellulose- active enzymes with distinct regioselectivity. Deletion and overexpression studies confirmed that the abundantly secreted AnLPMO9F is a major component of the extracellular cellulolytic system, while AnLPMO9G, less abundant in the secretome, has an important role by oxidizing crystalline fractions of cellulose. Single or double deletion of these AnLPMO9s partially impair fungal growth on sugarcane straw but not on crystalline cellulose, demonstrating the importance of LPMO9s for the saprophytic fungal lifestyle in the degradation of complex lignocellulosic substrates. Although the deletion of AnCDH1 slightly reduced the cellulolytic activity, it did not affect fungal growth indicating the existence of other electron donors to LPMOs. Additionally, double or triple knockouts of these enzymes had no accumulative deleterious effect on the cellulolytic activity nor on fungal growth, regardless of the deleted gene. The extracelllular proteomes of single deleted mutants growing in Avicel was analysed on a Q-TOF mass spectrometer and revealed an overall reduction in cellulase secretion, and some specifically some changes in the secretion of some enzymes, suggesting an adaptive mechanism adopted to compensate LPMO9s absence during cellulose degradation. Overexpression of AnLPMO9s in a cellulose-induced secretome background confirmed the importance and applicability of AnLPMO9G to improve lignocellulose saccharification.

			Action	DRS
	AA_SBP1.msf	Msf
	AA_SBP1.raw	Raw
	AA_SBP2.msf	Msf
	AA_SBP2.raw	Raw
	AA_WB1.msf	Msf