PERFORM Publications

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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:	Expression-based clustering of CAZyme-encoding genes of Aspergillus niger.
Authors:	Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP
Link:	https://www.ncbi.nlm.nih.gov/pubmed/29169319?dopt=Abstract
DOI:	10.1186/s12864-017-4164-x
Publication:	BMC genomics
Keywords:	AmyR; AraR; Aspergillus niger; CAZy genes; GalX; Plant biomass degradation; RhaR; Transcriptional regulators; XlnR;
PMID:	29169319	Category:	BMC Genomics	Date Added:	2019-06-07
Dept Affiliation:	CSFG 1 Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. 2 Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands. 3 Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. 4 Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland. 5 Current affiliation: ATGM, Avans University of Applied Sciences, Lovensdijkstraat 61-63, 4818, AJ, Breda, The Netherlands. 6 Current affiliation: Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada. 7 Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. r.devries@westerdijkinstitute.nl. 8 Microbiology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands. r.devries@westerdijkinstitute.nl. 9 Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. r.devries@westerdijkinstitute.nl.

Description:

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger.

BMC Genomics. 2017 Nov 23;18(1):900

Authors: Gruben BS, Mäkelä MR, Kowalczyk JE, Zhou M, Benoit-Gelber I, De Vries RP

Abstract

BACKGROUND: The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ?xlnR, ?araR, ?amyR, ?rhaR and ?galX that were grown on their specific inducing compounds.

RESULTS: The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far.

CONCLUSIONS: Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes.

PMID: 29169319 [PubMed - indexed for MEDLINE]

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