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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
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
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
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
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 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:Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.
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,  Kogle ME,  Strasser K,  McDonnell E,  Barry K,  Clum A,  Chen C,  LaButti K,  Haridas S,  Nolan M,  Sandor L,  Kuo A,  Lipzen A,  Hainaut M,  Drula E,  Tsang A,  Magnuson JK,  Henrissat B,  Wiebenga A,  Simmons BA,  Mäkelä MR,  de Vries RP,  Grigoriev IV,  Mortensen UH,  Baker SE,  Andersen MR
Link:https://www.ncbi.nlm.nih.gov/pubmed/30349117?dopt=Abstract
DOI:10.1038/s41588-018-0246-1
Category:Nat Genet
PMID:30349117
Dept Affiliation: GENOMICS
1 Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
2 US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
3 Amyris, Inc., Emeryville, CA, USA.
4 US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA.
5 Sandia National Laboratory, Livermore, CA, USA.
6 Chemical and Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
7 Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada.
8 Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 7257, Aix-Marseille University, Marseille, France.
9 Institut National de la Recherche Agronomique, USC 1408 Architecture et Fonction des Macromolécules Biologiques, Marseille, France.
10 Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
11 Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.
12 Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
13 Department of Microbiology, University of Helsinki, Helsinki, Finland.
14 Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
15 US Department of Energy Joint BioEnergy Institute, Emeryville, CA, USA. scott.baker@pnnl.gov.
16 Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. scott.baker@pnnl.gov.
17 Department of Biotechnology and Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark. mr@bio.dtu.dk.

Description:

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.

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, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR

Abstract

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.

PMID: 30349117 [PubMed - indexed for MEDLINE]