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The effects of external Mn2+ concentration on hyphal morphology and citric acid production are mediated primarily by the NRAMP-family transporter DmtA in Aspergillus niger.

Fejes B, Ouedraogo JP, Fekete E, Sándor E, Flipphi M, Soós Á, Molnár ÁP, Kovács B, Kubicek CP, Tsang A, Karaffa L.

Microb Cell Fact. 2020 Jan 30;19(1):17. doi: 10.1186/s12934-020-1286-7.


Superior cellulolytic activity of Trichoderma guizhouense on raw wheat straw.

Grujić M, Dojnov B, Potočnik I, Atanasova L, Duduk B, Srebotnik E, Druzhinina IS, Kubicek CP, Vujčić Z.

World J Microbiol Biotechnol. 2019 Nov 27;35(12):194. doi: 10.1007/s11274-019-2774-y.


Manganese Deficiency Is Required for High Itaconic Acid Production From D-Xylose in Aspergillus terreus.

Kolláth IS, Molnár ÁP, Soós Á, Fekete E, Sándor E, Kovács B, Kubicek CP, Karaffa L.

Front Microbiol. 2019 Jul 9;10:1589. doi: 10.3389/fmicb.2019.01589. eCollection 2019.


Evolution and comparative genomics of the most common Trichoderma species.

Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS.

BMC Genomics. 2019 Jun 12;20(1):485. doi: 10.1186/s12864-019-5680-7.


Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi.

Zhang J, Miao Y, Rahimi MJ, Zhu H, Steindorff A, Schiessler S, Cai F, Pang G, Chenthamara K, Xu Y, Kubicek CP, Shen Q, Druzhinina IS.

Environ Microbiol. 2019 Aug;21(8):2644-2658. doi: 10.1111/1462-2920.14575. Epub 2019 Apr 22.


Citric acid and itaconic acid accumulation: variations of the same story?

Karaffa L, Kubicek CP.

Appl Microbiol Biotechnol. 2019 Apr;103(7):2889-2902. doi: 10.1007/s00253-018-09607-9. Epub 2019 Feb 13. Review.


Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family.

Atanasova L, Dubey M, Grujić M, Gudmundsson M, Lorenz C, Sandgren M, Kubicek CP, Jensen DF, Karlsson M.

BMC Microbiol. 2018 Nov 7;18(1):178. doi: 10.1186/s12866-018-1310-9.


High oxygen tension increases itaconic acid accumulation, glucose consumption, and the expression and activity of alternative oxidase in Aspergillus terreus.

Molnár ÁP, Németh Z, Kolláth IS, Fekete E, Flipphi M, Ág N, Soós Á, Kovács B, Sándor E, Kubicek CP, Karaffa L.

Appl Microbiol Biotechnol. 2018 Oct;102(20):8799-8808. doi: 10.1007/s00253-018-9325-6. Epub 2018 Aug 24.


Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts.

Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, Rahimi MJ, Grujic M, Cai F, Pourmehdi S, Salim KA, Pretzer C, Kopchinskiy AG, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, LaButti K, Barry K, Grigoriev IV, Shen Q, Kubicek CP.

PLoS Genet. 2018 Apr 9;14(4):e1007322. doi: 10.1371/journal.pgen.1007322. eCollection 2018 Apr.


Optimization of sample preparation for intact cell mass spectrometry (matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometry) of endophytic Xylaria.

da Silva Amaral L, Rodrigues-Filho E, Kubicek CP, Herwig C, Marchetti-Deschmann M, Allmaier G.

Rapid Commun Mass Spectrom. 2018 May 30;32(10):815-823. doi: 10.1002/rcm.8098.



Przylucka A, Akcapinar GB, Bonazza K, Mello-de-Sousa TM, Mach-Aigner AR, Lobanov V, Grothe H, Kubicek CP, Reimhult E, Druzhinina IS.

Colloids Surf B Biointerfaces. 2017 Nov 1;159:913-923. doi: 10.1016/j.colsurfb.2017.08.058. Epub 2017 Sep 4.


Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12.

Gaskell J, Kersten P, Larrondo LF, Canessa P, Martinez D, Hibbett D, Schmoll M, Kubicek CP, Martinez AT, Yadav J, Master E, Magnuson JK, Yaver D, Berka R, Lail K, Chen C, LaButti K, Nolan M, Lipzen A, Aerts A, Riley R, Barry K, Henrissat B, Blanchette R, Grigoriev IV, Cullen D.

Genom Data. 2017 Aug 10;14:21-23. doi: 10.1016/j.gdata.2017.08.003. eCollection 2017 Dec. No abstract available.


A Novel Derivative of (-)mycousnine Produced by the Endophytic Fungus Mycosphaerella nawae, Exhibits High and Selective Immunosuppressive Activity on T Cells.

Wang LW, Wang JL, Chen J, Chen JJ, Shen JW, Feng XX, Kubicek CP, Lin FC, Zhang CL, Chen FY.

Front Microbiol. 2017 Jul 5;8:1251. doi: 10.3389/fmicb.2017.01251. eCollection 2017.


Genetic engineering of Trichoderma reesei cellulases and their production.

Druzhinina IS, Kubicek CP.

Microb Biotechnol. 2017 Nov;10(6):1485-1499. doi: 10.1111/1751-7915.12726. Epub 2017 May 29. Review.


The Constitutive Endopolygalacturonase TvPG2 Regulates the Induction of Plant Systemic Resistance by Trichoderma virens.

Sarrocco S, Matarese F, Baroncelli R, Vannacci G, Seidl-Seiboth V, Kubicek CP, Vergara M.

Phytopathology. 2017 May;107(5):537-544. doi: 10.1094/PHYTO-03-16-0139-R. Epub 2017 Mar 20.


HFB7 - A novel orphan hydrophobin of the Harzianum and Virens clades of Trichoderma, is involved in response to biotic and abiotic stresses.

Przylucka A, Akcapinar GB, Chenthamara K, Cai F, Grujic M, Karpenko J, Livoi M, Shen Q, Kubicek CP, Druzhinina IS.

Fungal Genet Biol. 2017 May;102:63-76. doi: 10.1016/j.fgb.2017.01.002. Epub 2017 Jan 13.


Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats.

Zhang N, Yang D, Kendall JR, Borriss R, Druzhinina IS, Kubicek CP, Shen Q, Zhang R.

Front Microbiol. 2016 Dec 20;7:2039. doi: 10.3389/fmicb.2016.02039. eCollection 2016.


Several steps of lateral gene transfer followed by events of 'birth-and-death' evolution shaped a fungal sorbicillinoid biosynthetic gene cluster.

Druzhinina IS, Kubicek EM, Kubicek CP.

BMC Evol Biol. 2016 Dec 7;16(1):269. doi: 10.1186/s12862-016-0834-6.


Two degradation strategies for overcoming the recalcitrance of natural lignocellulosic xylan by polysaccharides-binding GH10 and GH11 xylanases of filamentous fungi.

Miao Y, Li P, Li G, Liu D, Druzhinina IS, Kubicek CP, Shen Q, Zhang R.

Environ Microbiol. 2017 Mar;19(3):1054-1064. doi: 10.1111/1462-2920.13614. Epub 2017 Feb 6.


Enzymatic deconstruction of plant biomass by fungal enzymes.

Kubicek CP, Kubicek EM.

Curr Opin Chem Biol. 2016 Dec;35:51-57. doi: 10.1016/j.cbpa.2016.08.028. Epub 2016 Sep 8. Review.


Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes.

Druzhinina IS, Kubicek CP.

Adv Appl Microbiol. 2016;95:69-147. doi: 10.1016/bs.aambs.2016.02.001. Epub 2016 Mar 21. Review.


Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass.

Gupta VK, Kubicek CP, Berrin JG, Wilson DW, Couturier M, Berlin A, Filho EXF, Ezeji T.

Trends Biochem Sci. 2016 Jul;41(7):633-645. doi: 10.1016/j.tibs.2016.04.006. Epub 2016 May 17. Review.


A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness.

Druzhinina IS, Kopchinskiy AG, Kubicek EM, Kubicek CP.

Biotechnol Biofuels. 2016 Mar 29;9:75. doi: 10.1186/s13068-016-0488-z. eCollection 2016.


Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture.

de Man TJ, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SS, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3567-72. doi: 10.1073/pnas.1518501113. Epub 2016 Mar 14.


Restoration of female fertility in Trichoderma reesei QM6a provides the basis for inbreeding in this industrial cellulase producing fungus.

Linke R, Thallinger GG, Haarmann T, Eidner J, Schreiter M, Lorenz P, Seiboth B, Kubicek CP.

Biotechnol Biofuels. 2015 Sep 24;8:155. doi: 10.1186/s13068-015-0311-2. eCollection 2015.


Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.

Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP.

BMC Genomics. 2015 Sep 22;16(1):725. doi: 10.1186/s12864-015-1917-2. No abstract available.


Friend or foe: differential responses of rice to invasion by mutualistic or pathogenic fungi revealed by RNAseq and metabolite profiling.

Xu XH, Wang C, Li SX, Su ZZ, Zhou HN, Mao LJ, Feng XX, Liu PP, Chen X, Hugh Snyder J, Kubicek CP, Zhang CL, Lin FC.

Sci Rep. 2015 Sep 8;5:13624. doi: 10.1038/srep13624.


Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei.

Yang D, Pomraning K, Kopchinskiy A, Karimi Aghcheh R, Atanasova L, Chenthamara K, Baker SE, Zhang R, Shen Q, Freitag M, Kubicek CP, Druzhinina IS.

Genome Announc. 2015 Aug 13;3(4). pii: e00885-15. doi: 10.1128/genomeA.00885-15.


L-Methionine repressible promoters for tuneable gene expression in Trichoderma reesei.

Bischof RH, Horejs J, Metz B, Gamauf C, Kubicek CP, Seiboth B.

Microb Cell Fact. 2015 Aug 14;14:120. doi: 10.1186/s12934-015-0308-3.


The neutral metallopeptidase NMP1 of Trichoderma guizhouense is required for mycotrophy and self-defence.

Zhang J, Bayram Akcapinar G, Atanasova L, Rahimi MJ, Przylucka A, Yang D, Kubicek CP, Zhang R, Shen Q, Druzhinina IS.

Environ Microbiol. 2016 Feb;18(2):580-97. doi: 10.1111/1462-2920.12966. Epub 2015 Aug 17.


Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology.

Aghcheh RK, Kubicek CP.

Appl Microbiol Biotechnol. 2015 Aug;99(15):6167-81. doi: 10.1007/s00253-015-6763-2. Epub 2015 Jun 27. Review.


A deficiency of manganese ions in the presence of high sugar concentrations is the critical parameter for achieving high yields of itaconic acid by Aspergillus terreus.

Karaffa L, Díaz R, Papp B, Fekete E, Sándor E, Kubicek CP.

Appl Microbiol Biotechnol. 2015 Oct;99(19):7937-44. doi: 10.1007/s00253-015-6735-6. Epub 2015 Jun 16.


Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.

Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP.

BMC Genomics. 2015 Apr 20;16:326. doi: 10.1186/s12864-015-1526-0. Erratum in: BMC Genomics. 2015;16(1):725.


Enhanced cutinase-catalyzed hydrolysis of polyethylene terephthalate by covalent fusion to hydrophobins.

Ribitsch D, Herrero Acero E, Przylucka A, Zitzenbacher S, Marold A, Gamerith C, Tscheließnig R, Jungbauer A, Rennhofer H, Lichtenegger H, Amenitsch H, Bonazza K, Kubicek CP, Druzhinina IS, Guebitz GM.

Appl Environ Microbiol. 2015 Jun;81(11):3586-92. doi: 10.1128/AEM.04111-14. Epub 2015 Mar 20.


The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei.

Ghassemi S, Lichius A, Bidard F, Lemoine S, Rossignol MN, Herold S, Seidl-Seiboth V, Seiboth B, Espeso EA, Margeot A, Kubicek CP.

Mol Microbiol. 2015 Apr;96(2):405-18. doi: 10.1111/mmi.12944. Epub 2015 Mar 4.


Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper-producer Trichoderma reesei strain.

Poggi-Parodi D, Bidard F, Pirayre A, Portnoy T, Blugeon C, Seiboth B, Kubicek CP, Le Crom S, Margeot A.

Biotechnol Biofuels. 2014 Dec 12;7(1):173. doi: 10.1186/s13068-014-0173-z. eCollection 2014.


Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood.

Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Dueñas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutiérrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kües U, Berka RM, Martínez AT, Covert SF, Blanchette RA, Cullen D.

PLoS Genet. 2014 Dec 4;10(12):e1004759. doi: 10.1371/journal.pgen.1004759. eCollection 2014 Dec.


The VELVET A orthologue VEL1 of Trichoderma reesei regulates fungal development and is essential for cellulase gene expression.

Karimi Aghcheh R, Németh Z, Atanasova L, Fekete E, Paholcsek M, Sándor E, Aquino B, Druzhinina IS, Karaffa L, Kubicek CP.

PLoS One. 2014 Nov 11;9(11):e112799. doi: 10.1371/journal.pone.0112799. eCollection 2014.


Nucleo-cytoplasmic shuttling dynamics of the transcriptional regulators XYR1 and CRE1 under conditions of cellulase and xylanase gene expression in Trichoderma reesei.

Lichius A, Seidl-Seiboth V, Seiboth B, Kubicek CP.

Mol Microbiol. 2014 Oct 10. doi: 10.1111/mmi.12824. [Epub ahead of print]


The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte.

Xu XH, Su ZZ, Wang C, Kubicek CP, Feng XX, Mao LJ, Wang JY, Chen C, Lin FC, Zhang CL.

Sci Rep. 2014 Jul 22;4:5783. doi: 10.1038/srep05783.


Plant cell wall-degrading enzymes and their secretion in plant-pathogenic fungi.

Kubicek CP, Starr TL, Glass NL.

Annu Rev Phytopathol. 2014;52:427-51. doi: 10.1146/annurev-phyto-102313-045831. Epub 2014 Jun 16. Review.


The transcriptome of lae1 mutants of Trichoderma reesei cultivated at constant growth rates reveals new targets of LAE1 function.

Fekete E, Karaffa L, Karimi Aghcheh R, Németh Z, Fekete E, Orosz A, Paholcsek M, Stágel A, Kubicek CP.

BMC Genomics. 2014 Jun 9;15:447. doi: 10.1186/1471-2164-15-447.


The polyketide synthase gene pks4 of Trichoderma reesei provides pigmentation and stress resistance.

Atanasova L, Knox BP, Kubicek CP, Druzhinina IS, Baker SE.

Eukaryot Cell. 2013 Nov;12(11):1499-508. doi: 10.1128/EC.00103-13. Epub 2013 Sep 13.


Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose.

Bischof R, Fourtis L, Limbeck A, Gamauf C, Seiboth B, Kubicek CP.

Biotechnol Biofuels. 2013 Sep 9;6(1):127. doi: 10.1186/1754-6834-6-127.


The putative protein methyltransferase LAE1 of Trichoderma atroviride is a key regulator of asexual development and mycoparasitism.

Karimi Aghcheh R, Druzhinina IS, Kubicek CP.

PLoS One. 2013 Jun 24;8(6):e67144. doi: 10.1371/journal.pone.0067144. Print 2013.


Systems analysis of lactose metabolism in Trichoderma reesei identifies a lactose permease that is essential for cellulase induction.

Ivanova C, Bååth JA, Seiboth B, Kubicek CP.

PLoS One. 2013 May 8;8(5):e62631. doi: 10.1371/journal.pone.0062631. Print 2013.


Two novel class II hydrophobins from Trichoderma spp. stimulate enzymatic hydrolysis of poly(ethylene terephthalate) when expressed as fusion proteins.

Espino-Rammer L, Ribitsch D, Przylucka A, Marold A, Greimel KJ, Herrero Acero E, Guebitz GM, Kubicek CP, Druzhinina IS.

Appl Environ Microbiol. 2013 Jul;79(14):4230-8. doi: 10.1128/AEM.01132-13. Epub 2013 May 3.


A novel L-xylulose reductase essential for L-arabinose catabolism in Trichoderma reesei.

Metz B, Mojzita D, Herold S, Kubicek CP, Richard P, Seiboth B.

Biochemistry. 2013 Apr 9;52(14):2453-60. doi: 10.1021/bi301583u. Epub 2013 Mar 29.


Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism.

Atanasova L, Le Crom S, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS.

BMC Genomics. 2013 Feb 22;14:121. doi: 10.1186/1471-2164-14-121.


Functional analyses of Trichoderma reesei LAE1 reveal conserved and contrasting roles of this regulator.

Karimi-Aghcheh R, Bok JW, Phatale PA, Smith KM, Baker SE, Lichius A, Omann M, Zeilinger S, Seiboth B, Rhee C, Keller NP, Freitag M, Kubicek CP.

G3 (Bethesda). 2013 Feb;3(2):369-78. doi: 10.1534/g3.112.005140. Epub 2013 Feb 1.

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