PERFORM Publications

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Title		Authors	PubMed ID
1	Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses	Steindorff AS; Aguilar-Pontes MV; Robinson AJ; Andreopoulos B; LaButti K; Kuo A; Mondo S; Riley R; Otillar R; Haridas S; Lipzen A; Grimwood J; Schmutz J; Clum A; Reid ID; Moisan MC; Butler G; Nguyen TTM; Dewar K; Conant G; Drula E; Henrissat B; Hansel C; Singer S; Hutchinson MI; de Vries RP; Natvig DO; Powell AJ; Tsang A; Grigoriev IV;	39266695 CSFG
2	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
3	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
4	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
5	Screening of novel fungal Carbohydrate Esterase family 1 enzymes identifies three novel dual feruloyl/acetyl xylan esterases	Dilokpimol A; Verkerk B; Li X; Bellemare A; Lavallee M; Frommhagen M; Nørmølle Underlin E; Kabel MA; Powlowski J; Tsang A; de Vries RP;	35187647 CSFG
6	The chimeric GaaR-XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger	Kun RS; Garrigues S; Di Falco M; Tsang A; de Vries RP;	34236481 CSFG
7	Blocking utilization of major plant biomass polysaccharides leads Aspergillus niger towards utilization of minor components	Kun RS; Garrigues S; Di Falco M; Tsang A; de Vries RP;	34114741 CSFG
8	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
9	Evidence for ligninolytic activity of the ascomycete fungus Podospora anserina.	van Erven G, Kleijn AF, Patyshakuliyeva A, Di Falco M, Tsang A, de Vries RP, van Berkel WJH, Kabel MA	32322305 CSFG
10	Evolutionary adaptation of Aspergillus niger for increased ferulic acid tolerance.	Lubbers RJM, Liwanag AJ, Peng M, Dilokpimol A, Benoit-Gelber I, de Vries RP	31674709 CSFG
11	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
12	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
13	Secretion of small proteins is species-specific within Aspergillus sp.	Valette N, Benoit-Gelber I, Falco MD, Wiebenga A, de Vries RP, Gelhaye E, Morel-Rouhier M	27153937 CSFG
14	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
15	The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger.	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	28417461 CSFG
16	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
17	Introduction: Overview of Fungal Genomics.	de Vries RP, Grigoriev IV, Tsang A	29876804 CSFG
18	Evolutionary Adaptation to Generate Mutants.	de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I	29876815 BIOLOGY
19	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
20	The obligate alkalophilic soda-lake fungus Sodiomyces alkalinus has shifted to a protein diet.	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 EN, de Vries RP, van Kan JAL, Grigoriev IV, Debets AJM	30368956 CSFG
21	The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.	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	30425417 CSFG
22	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
23	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
24	Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.	de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, Dos Santos RA, Damásio AR, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus	28196534 NA

Title:	The molecular response of the white-rot fungus Dichomitus squalens to wood and non-woody biomass as examined by transcriptome and exoproteome analyses.
Authors:	Rytioja J, Hildén K, Di Falco M, Zhou M, Aguilar-Pontes MV, Sietiö OM, Tsang A, de Vries RP, Mäkelä MR
Link:	https://www.ncbi.nlm.nih.gov/pubmed/28028889?dopt=Abstract
DOI:	10.1111/1462-2920.13652
Publication:	Environmental microbiology
Keywords:
PMID:	28028889	Category:	Environ Microbiol	Date Added:	2019-06-07
Dept Affiliation:	CSFG 1 Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland. 2 Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, Utrecht, 3584, CT, The Netherlands. 3 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC H4B 1R6, Canada.

Description:

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

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

Abstract

The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi, (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate. The transcriptome and exoproteome of D. squalens were analyzed after cultivation on two natural substrates, aspen and spruce wood, and two non-woody substrates, wheat bran and cotton seed hulls. D. squalens produced ligninolytic enzymes mainly at the early time point of the wood cultures, indicating the need to degrade lignin to get access to wood polysaccharides. Surprisingly, the response of the fungus to the non-woody polysaccharides was nearly as good a match to the substrate composition as observed for the wood polysaccharides. This indicates that D. squalens has preserved its ability to efficiently degrade plant biomass types not present in its natural habitat.

PMID: 28028889 [PubMed - indexed for MEDLINE]

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