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PubMed Publications| Keyword search (4,163 papers available) |  |
"De Vries RP" Authored Publications:
| 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 chimeric GaaR-XlnR transcription factor induces pectinolytic activities in the presence of D-xylose in Aspergillus niger | ||||
| Authors: | Kun RS, Garrigues S, Di Falco M, Tsang A, de Vries RP | ||||
| Link: | https://pubmed.ncbi.nlm.nih.gov/34236481/ | ||||
| DOI: | 10.1007/s00253-021-11428-2 | ||||
| Publication: | Applied microbiology and biotechnology | ||||
| Keywords: | Aspergillus niger; CRISPR/Cas9; Chimeric transcription factor; D-xylose; Pectinases; | ||||
| PMID: | 34236481 | Category: | Date Added: | 2021-07-08 | |
| Dept Affiliation: |
CSFG
1 Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. 2 Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada. 3 Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands. r.devries@wi.knaw.nl. |
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Description: |
Aspergillus niger is a filamentous fungus well known for its ability to produce a wide variety of pectinolytic enzymes, which have many applications in the industry. The transcriptional activator GaaR is induced by 2-keto-3-deoxy-L-galactonate, a compound derived from D-galacturonic acid, and plays a major role in the regulation of pectinolytic genes. The requirement for inducer molecules can be a limiting factor for the production of enzymes. Therefore, the generation of chimeric transcription factors able to activate the expression of pectinolytic genes by using underutilized agricultural residues would be highly valuable for industrial applications. In this study, we used the CRISPR/Cas9 system to generate three chimeric GaaR-XlnR transcription factors expressed by the xlnR promoter by swapping the N-terminal region of the xylanolytic regulator XlnR to that of the GaaR in A. niger. As a test case, we constructed a PpgaX-hph reporter strain to evaluate the alteration of transcription factor specificity in the chimeric mutants. Our results showed that the chimeric GaaR-XlnR transcription factor was induced in the presence of D-xylose. Additionally, we generated a constitutively active GaaR-XlnR V756F version of the most efficient chimeric transcription factor to better assess its activity. Proteomics analysis confirmed the production of several pectinolytic enzymes by ?gaaR mutants carrying the chimeric transcription factor. This correlates with the improved release of D-galacturonic acid from pectin by the GaaR-XlnR V756F mutant, as well as by the increased L-arabinose release from the pectin side chains by both chimeric mutants under inducing condition, which is required for efficient degradation of pectin. KEY POINTS: • Chimeric transcription factors were generated by on-site mutations using CRISPR/Cas9. • PpgaX-hph reporter strain allowed for the screening of functional GaaR-XlnR mutants. • Chimeric GaaR-XlnR induced pectinolytic activities in the presence of D-xylose. |
