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A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi.

Lubbers RJM, Dilokpimol A, Visser J, Mäkelä MR, Hildén KS, de Vries RP.

Biotechnol Adv. 2019 May 7. pii: S0734-9750(19)30077-1. doi: 10.1016/j.biotechadv.2019.05.002. [Epub ahead of print] Review.


Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens.

Casado López S, Peng M, Daly P, Andreopoulos B, Pangilinan J, Lipzen A, Riley R, Ahrendt S, Ng V, Barry K, Daum C, Grigoriev IV, Hildén KS, Mäkelä MR, de Vries RP.

Microbiol Resour Announc. 2019 May 2;8(18). pii: e00264-19. doi: 10.1128/MRA.00264-19.


Developments and opportunities in fungal strain engineering for the production of novel enzymes and enzyme cocktails for plant biomass degradation.

Kun RS, Gomes ACS, Hildén KS, Salazar Cerezo S, Mäkelä MR, de Vries RP.

Biotechnol Adv. 2019 Feb 27:107361. doi: 10.1016/j.biotechadv.2019.02.017. [Epub ahead of print] Review.


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.

N Biotechnol. 2019 Jul 25;51:57-66. doi: 10.1016/j.nbt.2019.02.005. Epub 2019 Feb 20.


Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales).

Urquhart AS, Mondo SJ, Mäkelä MR, Hane JK, Wiebenga A, He G, Mihaltcheva S, Pangilinan J, Lipzen A, Barry K, de Vries RP, Grigoriev IV, Idnurm A.

Front Microbiol. 2018 Dec 13;9:3058. doi: 10.3389/fmicb.2018.03058. eCollection 2018.


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.

Stud Mycol. 2018 Sep;91:79-99. doi: 10.1016/j.simyco.2018.09.001. Epub 2018 Oct 29.


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.

Nat Genet. 2018 Dec;50(12):1688-1695. doi: 10.1038/s41588-018-0246-1. Epub 2018 Oct 22.


Selective Cleavage of Lignin β-O-4 Aryl Ether Bond by β-Etherase of the White-Rot Fungus Dichomitus squalens.

Marinović M, Nousiainen P, Dilokpimol A, Kontro J, Moore R, Sipilä J, de Vries RP, Mäkelä MR, Hildén K.

ACS Sustain Chem Eng. 2018 Mar 5;6(3):2878-2882. doi: 10.1021/acssuschemeng.7b03619. Epub 2018 Jan 25.


Dichomitus squalens partially tailors its molecular responses to the composition of solid wood.

Daly P, López SC, Peng M, Lancefield CS, Purvine SO, Kim YM, Zink EM, Dohnalkova A, Singan VR, Lipzen A, Dilworth D, Wang M, Ng V, Robinson E, Orr G, Baker SE, Bruijnincx PCA, Hildén KS, Grigoriev IV, Mäkelä MR, de Vries RP.

Environ Microbiol. 2018 Nov;20(11):4141-4156. doi: 10.1111/1462-2920.14416. Epub 2018 Oct 18.


Efficient Extraction Method for High Quality Fungal RNA from Complex Lignocellulosic Substrates.

Mäkelä MR, Hildén K.

Methods Mol Biol. 2018;1775:69-73. doi: 10.1007/978-1-4939-7804-5_6.


In Silico Analysis of Putative Sugar Transporter Genes in Aspergillus niger Using Phylogeny and Comparative Transcriptomics.

Peng M, Aguilar-Pontes MV, de Vries RP, Mäkelä MR.

Front Microbiol. 2018 May 18;9:1045. doi: 10.3389/fmicb.2018.01045. eCollection 2018.


The fungus Aspergillus niger consumes sugars in a sequential manner that is not mediated by the carbon catabolite repressor CreA.

Mäkelä MR, Aguilar-Pontes MV, van Rossen-Uffink D, Peng M, de Vries RP.

Sci Rep. 2018 Apr 27;8(1):6655. doi: 10.1038/s41598-018-25152-x.


Characterization of a feruloyl esterase from Aspergillus terreus facilitates the division of fungal enzymes from Carbohydrate Esterase family 1 of the carbohydrate-active enzymes (CAZy) database.

Mäkelä MR, Dilokpimol A, Koskela SM, Kuuskeri J, de Vries RP, Hildén K.

Microb Biotechnol. 2018 Sep;11(5):869-880. doi: 10.1111/1751-7915.13273. Epub 2018 Apr 26.


Draft Genome Sequence of the Basidiomycete White-Rot Fungus Phlebia centrifuga.

Mäkelä MR, Peng M, Granchi Z, Chin-A-Woeng T, Hegi R, van Pelt SI, Ahrendt S, Riley R, Hainaut M, Henrissat B, Grigoriev IV, de Vries RP, Hildén KS.

Genome Announc. 2018 Apr 5;6(14). pii: e01414-17. doi: 10.1128/genomeA.01414-17.


Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens.

Casado López S, Peng M, Issak TY, Daly P, de Vries RP, Mäkelä MR.

Appl Environ Microbiol. 2018 May 17;84(11). pii: e00403-18. doi: 10.1128/AEM.00403-18. Print 2018 Jun 1.


The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates.

Pontes MVA, Patyshakuliyeva A, Post H, Jurak E, Hildén K, Altelaar M, Heck A, Kabel MA, de Vries RP, Mäkelä MR.

Fungal Genet Biol. 2018 Mar;112:12-20. doi: 10.1016/j.fgb.2017.12.004. Epub 2017 Dec 22.


Fungal feruloyl esterases: Functional validation of genome mining based enzyme discovery including uncharacterized subfamilies.

Dilokpimol A, Mäkelä MR, Varriale S, Zhou M, Cerullo G, Gidijala L, Hinkka H, Brás JLA, Jütten P, Piechot A, Verhaert R, Hildén KS, Faraco V, de Vries RP.

N Biotechnol. 2018 Mar 25;41:9-14. doi: 10.1016/j.nbt.2017.11.004. Epub 2017 Nov 23.


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

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

BMC Genomics. 2017 Nov 23;18(1):900. doi: 10.1186/s12864-017-4164-x.


Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization.

Dilokpimol A, Mäkelä MR, Cerullo G, Zhou M, Varriale S, Gidijala L, Brás JLA, Jütten P, Piechot A, Verhaert R, Faraco V, Hilden KS, de Vries RP.

N Biotechnol. 2018 Jan 25;40(Pt B):282-287. doi: 10.1016/j.nbt.2017.10.003. Epub 2017 Oct 16.


Genetic transformation of the white-rot fungus Dichomitus squalens using a new commercial protoplasting cocktail.

Daly P, Slaghek GG, Casado López S, Wiebenga A, Hilden KS, de Vries RP, Mäkelä MR.

J Microbiol Methods. 2017 Dec;143:38-43. doi: 10.1016/j.mimet.2017.10.001. Epub 2017 Oct 4.


Functional diversity in Dichomitus squalens monokaryons.

Casado López S, Theelen B, Manserra S, Issak TY, Rytioja J, Mäkelä MR, de Vries RP.

IMA Fungus. 2017 Jun;8(1):17-25. doi: 10.5598/imafungus.2017.08.01.02. Epub 2017 Mar 8.


Comparative analysis of basidiomycete transcriptomes reveals a core set of expressed genes encoding plant biomass degrading enzymes.

Peng M, Aguilar-Pontes MV, Hainaut M, Henrissat B, Hildén K, Mäkelä MR, de Vries RP.

Fungal Genet Biol. 2018 Mar;112:40-46. doi: 10.1016/j.fgb.2017.08.001. Epub 2017 Aug 10.


Temporal transcriptome analysis of the white-rot fungus Obba rivulosa shows expression of a constitutive set of plant cell wall degradation targeted genes during growth on solid spruce wood.

Marinović M, Aguilar-Pontes MV, Zhou M, Miettinen O, de Vries RP, Mäkelä MR, Hildén K.

Fungal Genet Biol. 2018 Mar;112:47-54. doi: 10.1016/j.fgb.2017.07.004. Epub 2017 Jul 25.


Occurrence and function of enzymes for lignocellulose degradation in commercial Agaricus bisporus cultivation.

Kabel MA, Jurak E, Mäkelä MR, de Vries RP.

Appl Microbiol Biotechnol. 2017 Jun;101(11):4363-4369. doi: 10.1007/s00253-017-8294-5. Epub 2017 May 2. Review.


Expanding the feruloyl esterase gene family of Aspergillus niger by characterization of a feruloyl esterase, FaeC.

Dilokpimol A, Mäkelä MR, Mansouri S, Belova O, Waterstraat M, Bunzel M, de Vries RP, Hildén KS.

N Biotechnol. 2017 Jul 25;37(Pt B):200-209. doi: 10.1016/j.nbt.2017.02.007. Epub 2017 Mar 8.


Genome Sequence of the Basidiomycete White-Rot Fungus Trametes pubescens FBCC735.

Granchi Z, Peng M, Chi-A-Woeng T, de Vries RP, Hildén K, Mäkelä MR.

Genome Announc. 2017 Feb 23;5(8). pii: e01643-16. doi: 10.1128/genomeA.01643-16.


The draft genome sequence of the ascomycete fungus Penicillium subrubescens reveals a highly enriched content of plant biomass related CAZymes compared to related fungi.

Peng M, Dilokpimol A, Mäkelä MR, Hildén K, Bervoets S, Riley R, Grigoriev IV, Hainaut M, Henrissat B, de Vries RP, Granchi Z.

J Biotechnol. 2017 Mar 20;246:1-3. doi: 10.1016/j.jbiotec.2017.02.012. Epub 2017 Feb 16.


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 A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AF, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JV, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV.

Genome Biol. 2017 Feb 14;18(1):28. doi: 10.1186/s13059-017-1151-0.


Cultivation of Podospora anserina on soybean hulls results in an efficient enzyme cocktail for plant biomass hydrolysis.

Mäkelä MR, Bouzid O, Robl D, Post H, Peng M, Heck A, Altelaar M, de Vries RP.

N Biotechnol. 2017 Jul 25;37(Pt B):162-171. doi: 10.1016/j.nbt.2017.02.002. Epub 2017 Feb 7.


Fungal Ligninolytic Enzymes and Their Applications.

Mäkelä MR, Bredeweg EL, Magnuson JK, Baker SE, de Vries RP, Hildén K.

Microbiol Spectr. 2016 Dec;4(6). doi: 10.1128/microbiolspec.FUNK-0017-2016. Review.


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.

Environ Microbiol. 2017 Mar;19(3):1237-1250. doi: 10.1111/1462-2920.13652. Epub 2017 Jan 23.


Diversity of fungal feruloyl esterases: updated phylogenetic classification, properties, and industrial applications.

Dilokpimol A, Mäkelä MR, Aguilar-Pontes MV, Benoit-Gelber I, Hildén KS, de Vries RP.

Biotechnol Biofuels. 2016 Oct 28;9:231. eCollection 2016. Review.


Penicillium subrubescens is a promising alternative for Aspergillus niger in enzymatic plant biomass saccharification.

Mäkelä MR, Mansouri S, Wiebenga A, Rytioja J, de Vries RP, Hildén KS.

N Biotechnol. 2016 Dec 25;33(6):834-841. doi: 10.1016/j.nbt.2016.07.014. Epub 2016 Jul 25.


Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2.

Miettinen O, Riley R, Barry K, Cullen D, de Vries RP, Hainaut M, Hatakka A, Henrissat B, Hildén K, Kuo R, LaButti K, Lipzen A, Mäkelä MR, Sandor L, Spatafora JW, Grigoriev IV, Hibbett DS.

Genome Announc. 2016 Sep 15;4(5). pii: e00976-16. doi: 10.1128/genomeA.00976-16.


Saccharification of Lignocelluloses by Carbohydrate Active Enzymes of the White Rot Fungus Dichomitus squalens.

Rytioja J, Hildén K, Mäkinen S, Vehmaanperä J, Hatakka A, Mäkelä MR.

PLoS One. 2015 Dec 14;10(12):e0145166. doi: 10.1371/journal.pone.0145166. eCollection 2015.


Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota).

Kuuskeri J, Mäkelä MR, Isotalo J, Oksanen I, Lundell T.

BMC Microbiol. 2015 Oct 19;15:217. doi: 10.1186/s12866-015-0538-x.


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.

Biotechnol Biofuels. 2015 Aug 1;8:107. doi: 10.1186/s13068-015-0285-0. eCollection 2015.


Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle.

Patyshakuliyeva A, Post H, Zhou M, Jurak E, Heck AJ, Hildén KS, Kabel MA, Mäkelä MR, Altelaar MA, de Vries RP.

Environ Microbiol. 2015 Aug;17(8):3098-109. doi: 10.1111/1462-2920.12967. Epub 2015 Aug 4.


Aromatic metabolism of filamentous fungi in relation to the presence of aromatic compounds in plant biomass.

Mäkelä MR, Marinović M, Nousiainen P, Liwanag AJ, Benoit I, Sipilä J, Hatakka A, de Vries RP, Hildén KS.

Adv Appl Microbiol. 2015;91:63-137. doi: 10.1016/bs.aambs.2014.12.001. Epub 2015 Feb 24. Review.


Plant-polysaccharide-degrading enzymes from Basidiomycetes.

Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR.

Microbiol Mol Biol Rev. 2014 Dec;78(4):614-49. doi: 10.1128/MMBR.00035-14. Review.


Plant biomass degradation by fungi.

Mäkelä MR, Donofrio N, de Vries RP.

Fungal Genet Biol. 2014 Nov;72:2-9. doi: 10.1016/j.fgb.2014.08.010. Epub 2014 Sep 3.


An improved and reproducible protocol for the extraction of high quality fungal RNA from plant biomass substrates.

Patyshakuliyeva A, Mäkelä MR, Sietiö OM, de Vries RP, Hildén KS.

Fungal Genet Biol. 2014 Nov;72:201-206. doi: 10.1016/j.fgb.2014.06.001. Epub 2014 Jun 18.


Carbohydrate-binding modules of fungal cellulases: occurrence in nature, function, and relevance in industrial biomass conversion.

Várnai A, Mäkelä MR, Djajadi DT, Rahikainen J, Hatakka A, Viikari L.

Adv Appl Microbiol. 2014;88:103-65. doi: 10.1016/B978-0-12-800260-5.00004-8. Review.


Biochemical and molecular characterization of an atypical manganese peroxidase of the litter-decomposing fungus Agrocybe praecox.

Hildén K, Mäkelä MR, Steffen KT, Hofrichter M, Hatakka A, Archer DB, Lundell TK.

Fungal Genet Biol. 2014 Nov;72:131-136. doi: 10.1016/j.fgb.2014.03.002. Epub 2014 Mar 20.


Oxalate-metabolising genes of the white-rot fungus Dichomitus squalens are differentially induced on wood and at high proton concentration.

Mäkelä MR, Sietiö OM, de Vries RP, Timonen S, Hildén K.

PLoS One. 2014 Feb 5;9(2):e87959. doi: 10.1371/journal.pone.0087959. eCollection 2014.


Transcriptional analysis of selected cellulose-acting enzymes encoding genes of the white-rot fungus Dichomitus squalens on spruce wood and microcrystalline cellulose.

Rytioja J, Hildén K, Hatakka A, Mäkelä MR.

Fungal Genet Biol. 2014 Nov;72:91-98. doi: 10.1016/j.fgb.2013.12.008. Epub 2014 Jan 3.


Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus.

Patyshakuliyeva A, Jurak E, Kohler A, Baker A, Battaglia E, de Bruijn W, Burton KS, Challen MP, Coutinho PM, Eastwood DC, Gruben BS, Mäkelä MR, Martin F, Nadal M, van den Brink J, Wiebenga A, Zhou M, Henrissat B, Kabel M, Gruppen H, de Vries RP.

BMC Genomics. 2013 Sep 30;14:663. doi: 10.1186/1471-2164-14-663.


Agaricus bisporus and related Agaricus species on lignocellulose: production of manganese peroxidase and multicopper oxidases.

Hildén K, Mäkelä MR, Lankinen P, Lundell T.

Fungal Genet Biol. 2013 Jun;55:32-41. doi: 10.1016/j.fgb.2013.02.002. Epub 2013 Feb 21.


Effect of copper, nutrient nitrogen, and wood-supplement on the production of lignin-modifying enzymes by the white-rot fungus Phlebia radiata.

Mäkelä MR, Lundell T, Hatakka A, Hildén K.

Fungal Biol. 2013 Jan;117(1):62-70. doi: 10.1016/j.funbio.2012.11.006. Epub 2012 Dec 13.


Heterologous expression and structural characterization of two low pH laccases from a biopulping white-rot fungus Physisporinus rivulosus.

Hildén K, Mäkelä MR, Lundell T, Kuuskeri J, Chernykh A, Golovleva L, Archer DB, Hatakka A.

Appl Microbiol Biotechnol. 2013 Feb;97(4):1589-99. doi: 10.1007/s00253-012-4011-6. Epub 2012 Apr 12.


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