Keyword search (4,163 papers available)

"Mäkelä MR" Authored Publications:

Title Authors PubMed ID
1 The Sugar Metabolic Model of Aspergillus niger Can Only Be Reliably Transferred to Fungi of Its Phylum Li J; Chroumpi T; Garrigues S; Kun RS; Meng J; Salazar-Cerezo S; Aguilar-Pontes MV; Zhang Y; Tejomurthula S; Lipzen A; Ng V; Clendinen CS; Tolic N; Grigoriev IV; Tsang A; Mäkelä MR; Snel B; Peng M; de Vries RP; 36547648
BIOLOGY
2 Comparative Analysis of Enzyme Production Patterns of Lignocellulose Degradation of Two White Rot Fungi: Obba rivulosa and Gelatoporia subvermispora Marinovíc M; Di Falco M; Aguilar Pontes MV; Gorzsás A; Tsang A; de Vries RP; Mäkelä MR; Hildén K; 35892327
CSFG
3 Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity Venegas FA; Koutaniemi S; Langeveld SMJ; Bellemare A; Chong SL; Dilokpimol A; Lowden MJ; Hilden KS; Leyva-Illades JF; Mäkelä MR; My Pham TT; Peng M; Hancock MA; Zheng Y; Tsang A; Tenkanen M; Powlowski J; de Vries RP; 35405333
CSFG
4 Penicillium subrubescens adapts its enzyme production to the composition of plant biomass. Dilokpimol A, Peng M, Di Falco M, Chin A Woeng T, Hegi RMW, Granchi Z, Tsang A, Hildén KS, Mäkelä MR, de Vries RP 32408196
CSFG
5 Glucose-mediated repression of plant biomass utilization in the white-rot fungus Dichomitus squalens. Daly P, Peng M, Di Falco M, Lipzen A, Wang M, Ng V, Grigoriev IV, Tsang A, Mäkelä MR, de Vries RP 31585998
CSFG
6 Closely related fungi employ diverse enzymatic strategies to degrade plant biomass. 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, Houbraken J, Barboza LAJ, Levasseur A, Majoor E, Mäkelä MR, Narang HM, Trejo-Aguilar B, van den Brink J, vanKuyk PA, Wiebenga A, McKie V, McCleary B, Tsang A, Henrissat B, de Vries RP 26236396
CSFG
7 The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses. Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR 28028889
CSFG
8 Expression-based clustering of CAZyme-encoding genes of Aspergillus niger. Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP 29169319
CSFG
9 Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri. 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 30349117
CSFG
10 Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli Mäkelä MR; DiFalco M; McDonnell E; Nguyen TTM; Wiebenga A; Hildén K; Peng M; Grigoriev IV; Tsang A; de Vries RP; 30487660
CSFG
11 The presence of trace components significantly broadens the molecular response of Aspergillus niger to guar gum. Coconi Linares N, Di Falco M, Benoit-Gelber I, Gruben BS, Peng M, Tsang A, Mäkelä MR, de Vries RP 30797054
CSFG

 

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
Publication:Nature genetics
Keywords:
PMID:30349117 Category:Nat Genet Date Added:2019-06-07
Dept Affiliation: CSFG
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]




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