Keyword search (3,619 papers available)


Penicillium subrubescens adapts its enzyme production to the composition of plant biomass.

Author(s): Dilokpimol A, Peng M, Di Falco M, Chin A Woeng T, Hegi RMW, Granchi Z, Tsang A, Hildén KS, Mäkelä MR, de Vries RP

Bioresour Technol. 2020 May 05;311:123477 Authors: Dilokpimol A, Peng M, Di Falco M, Chin A Woeng T, Hegi RMW, Granchi Z, Tsang A, Hildén KS, Mäkelä MR, de Vries RP

Article GUID: 32408196
Evidence for ligninolytic activity of the ascomycete fungus Podospora anserina.

Author(s): van Erven G, Kleijn AF, Patyshakuliyeva A, Di Falco M, Tsang A, de Vries RP, van Berkel WJH, Kabel MA

Biotechnol Biofuels. 2020;13:75 Authors: van Erven G, Kleijn AF, Patyshakuliyeva A, Di Falco M, Tsang A, de Vries RP, van Berkel WJH, Kabel MA

Article GUID: 32322305
Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance.

Author(s): Lubbers RJM, Liwanag AJ, Peng M, Dilokpimol A, Benoit-Gelber I, de Vries RP

J Appl Microbiol. 2019 Nov 01;: Authors: Lubbers RJM, Liwanag AJ, Peng M, Dilokpimol A, Benoit-Gelber I, de Vries RP

Article GUID: 31674709
Glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens.

Author(s): Daly P, Peng M, Di Falco M, Lipzen A, Wang M, Ng V, Grigoriev IV, Tsang A, Mäkelä MR, de Vries RP

Appl Environ Microbiol. 2019 Oct 04;: Authors: Daly P, Peng M, Di Falco M, Lipzen A, Wang M, Ng V, Grigoriev IV, Tsang A, Mäkelä MR, de Vries RP

Article GUID: 31585998
Closely related fungi employ diverse enzymatic strategies to degrade plant biomass.

Author(s): Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, Bouzid O, Brouwer CPJM, El-Bushari HBO, Coutinho PM, Gruben BS, Hild...

Biotechnol Biofuels. 2015;8:107 Authors: Benoit I, Culleton H, Zhou M, DiFalco M, Aguilar-Osorio G, Battaglia E, Bouzid O, Brouwer CPJM, El-Bushari HBO, Coutinho PM, Gruben BS, Hildén KS, Hou...

Article GUID: 26236396
Secretion of small proteins is species-specific within Aspergillus sp.

Author(s): Valette N, Benoit-Gelber I, Falco MD, Wiebenga A, de Vries RP, Gelhaye E, Morel-Rouhier M

Microb Biotechnol. 2017 03;10(2):323-329 Authors: Valette N, Benoit-Gelber I, Falco MD, Wiebenga A, de Vries RP, Gelhaye E, Morel-Rouhier M

Article GUID: 27153937
The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses.

Author(s): Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR

Environ Microbiol. 2017 03;19(3):1237-1250 Authors: Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR

Article GUID: 28028889
The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger.

Author(s): Alazi E, Khosravi C, Homan TG, du Pré S, Arentshorst M, Di Falco M, Pham TTM, Peng M, Aguilar-Pontes MV, Visser J, Tsang A, de Vries RP, Ram AFJ

FEBS Lett. 2017 05;591(10):1408-1418 Authors: Alazi E, Khosravi C, Homan TG, du Pré S, Arentshorst M, Di Falco M, Pham TTM, Peng M, Aguilar-Pontes MV, Visser J, Tsang A, de Vries RP, Ram AFJ

Article GUID: 28417461
Expression-based clustering of CAZyme-encoding genes of Aspergillus niger.

Author(s): Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP

BMC Genomics. 2017 Nov 23;18(1):900 Authors: Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP

Article GUID: 29169319
Introduction: Overview of Fungal Genomics.

Author(s): de Vries RP, Grigoriev IV, Tsang A

Methods Mol Biol. 2018;1775:1-7 Authors: de Vries RP, Grigoriev IV, Tsang A

Article GUID: 29876804
Evolutionary Adaptation to Generate Mutants.

Author(s): de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I

Methods Mol Biol. 2018;1775:133-137 Authors: de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I

Article GUID: 29876815
Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.

Author(s): Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, ...

Nat Genet. 2018 12;50(12):1688-1695 Authors: Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, K...

Article GUID: 30349117
The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.

Author(s): Grum-Grzhimaylo AA, Falkoski DL, van den Heuvel J, Valero-Jiménez CA, Min B, Choi IG, Lipzen A, Daum CG, Aanen DK, Tsang A, Henrissat B, Bil...

Mol Ecol. 2018 12;27(23):4808-4819 Authors: Grum-Grzhimaylo AA, Falkoski DL, van den Heuvel J, Valero-Jiménez CA, Min B, Choi IG, Lipzen A, Daum CG, Aanen DK, Tsang A, Henrissat B, Bilanenko ...

Article GUID: 30368956
The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.

Author(s): Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR,...

Stud Mycol. 2018 Sep;91:61-78 Authors: Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR, Tsang A, de Vrie...

Article GUID: 30425417
The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum.

Author(s): Coconi Linares N, Di Falco M, Benoit-Gelber I, Gruben BS, Peng M, Tsang A, Mäkelä MR, de Vries RP

N Biotechnol. 2019 Jul 25;51:57-66 Authors: Coconi Linares N, Di Falco M, Benoit-Gelber I, Gruben BS, Peng M, Tsang A, Mäkelä MR, de Vries RP

Article GUID: 30797054
Title:The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.
Authors:Aguilar-Pontes MV,  Brandl J,  McDonnell E,  Strasser K,  Nguyen TTM,  Riley R,  Mondo S,  Salamov A,  Nybo JL,  Vesth TC,  Grigoriev IV,  Andersen MR,  Tsang A,  de Vries RP
Link:https://www.ncbi.nlm.nih.gov/pubmed/30425417?dopt=Abstract
DOI:10.1016/j.simyco.2018.10.001
Category:Stud Mycol
PMID:30425417
Dept Affiliation: GENOMICS
1 Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
2 Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.
3 Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kongens Lyngby, Denmark.
4 Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada.
5 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.

Description:

The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.

Stud Mycol. 2018 Sep;91:61-78

Authors: Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR, Tsang A, de Vries RP

Abstract

The fungal kingdom is too large to be discovered exclusively by classical genetics. The access to omics data opens a new opportunity to study the diversity within the fungal kingdom and how adaptation to new environments shapes fungal metabolism. Genomes are the foundation of modern science but their quality is crucial when analysing omics data. In this study, we demonstrate how one gold-standard genome can improve functional prediction across closely related species to be able to identify key enzymes, reactions and pathways with the focus on primary carbon metabolism. Based on this approach we identified alternative genes encoding various steps of the different sugar catabolic pathways, and as such provided leads for functional studies into this topic. We also revealed significant diversity with respect to genome content, although this did not always correlate to the ability of the species to use the corresponding sugar as a carbon source.

PMID: 30425417 [PubMed]