title: Comparative analysis of the Trichoderma reesei transcriptome during growth on the cellulase inducing substrates wheat straw and lactose.
abstract: BACKGROUND
  Renewable lignocellulosic biomass is an advantageous resource for the production of second generation biofuels and other biorefinery products. In Middle Europe, wheat straw is one of the most abundant low-cost sources of lignocellulosic biomass. For its efficient use, an efficient mix of cellulases and hemicellulases is required. In this paper, we investigated how cellulase production by T. reesei on wheat straw compares to that on lactose, the only soluble and also cheap inducing carbon source for enzyme production.
  
  
  RESULTS
  We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30% of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair, iron homeostatis and autophagy. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60% of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional.
  
  
  CONCLUSIONS
  Our data reveal several major differences in the transcriptome between wheat straw and lactose which may be related to the higher enzyme formation on the former and their further investigation could lead to the development of methods for increasing enzyme production on lactose.
authors.affiliation: Austrian Centre of Industrial Biotechnology (ACIB) GmBH c/o Institute of Chemical Engineering, University of Technology of Vienna, Gumpendorferstraβe 1a, Vienna A-1060, Austria. ckubicek@mail.zserv.tuwien.ac.at.
authors.forename: Robert
authors.initials: R
authors.lastname: Bischof
authors.forename: Lukas
authors.initials: L
authors.lastname: Fourtis
authors.forename: Andreas
authors.initials: A
authors.lastname: Limbeck
authors.forename: Christian
authors.initials: C
authors.lastname: Gamauf
authors.forename: Bernhard
authors.initials: B
authors.lastname: Seiboth
authors.forename: Christian P
authors.initials: CP
authors.lastname: Kubicek
references.citation: Environ Microbiol Rep. 2013 Aug;5(4):511-7
references.pmid: 23864564
references.citation: Nucleic Acids Res. 2002 May 1;30(9):e36
references.pmid: 11972351
references.citation: Annu Rev Phytopathol. 2011;49:369-90
references.pmid: 21568704
references.citation: J Ind Microbiol Biotechnol. 2011 Apr;38(4):541-55
references.pmid: 20711629
references.citation: Autophagy. 2013 Apr;9(4):538-49
references.pmid: 23380892
references.citation: Mol Biol Cell. 2008 Feb;19(2):668-81
references.pmid: 18077553
references.citation: Mol Microbiol. 2007 Oct;66(2):279-90
references.pmid: 17854405
references.citation: Antioxid Redox Signal. 2011 May 15;14(10):1989-2001
references.pmid: 21194379
references.citation: Eukaryot Cell. 2006 Dec;5(12):2128-37
references.pmid: 17056741
references.citation: Semin Cell Dev Biol. 2010 Sep;21(7):664-70
references.pmid: 20359542
references.citation: Fungal Genet Biol. 2008 Apr;45(4):436-45
references.pmid: 17920314
references.citation: Bioresour Technol. 2010 Jul;101(13):4744-53
references.pmid: 20031394
references.citation: J Biol Chem. 1996 Oct 11;271(41):25624-9
references.pmid: 8810338
references.citation: Microb Cell Fact. 2012 Oct 04;11:134
references.pmid: 23035824
references.citation: Eukaryot Cell. 2011 Nov;10(11):1527-35
references.pmid: 21890820
references.citation: Nucleic Acids Res. 2004 Oct 14;32(18):5539-45
references.pmid: 15486203
references.citation: Appl Environ Microbiol. 1985 Nov;50(5):1137-43
references.pmid: 4091550
references.citation: Appl Microbiol Biotechnol. 2009 Nov;85(1):141-54
references.pmid: 19777228
references.citation: Fungal Genet Biol. 2009 Aug;46(8):564-74
references.pmid: 19393758
references.citation: Fungal Genet Biol. 2012 Dec;49(12):987-95
references.pmid: 23063954
references.citation: FEBS Lett. 2007 Aug 21;581(21):3915-20
references.pmid: 17662982
references.citation: PLoS One. 2013 May 08;8(5):e62631
references.pmid: 23690947
references.citation: FEMS Microbiol Rev. 2005 Sep;29(4):719-39
references.pmid: 16102600
references.citation: FEMS Microbiol Lett. 2012 Dec;337(1):1-9
references.pmid: 22924408
references.citation: Proc Natl Acad Sci U S A. 2012 May 8;109(19):7397-402
references.pmid: 22532664
references.citation: Mol Microbiol. 2009 Oct;74(2):480-96
references.pmid: 19775249
references.citation: Appl Microbiol Biotechnol. 2010 Jul;87(3):787-99
references.pmid: 20461510
references.citation: Appl Environ Microbiol. 2013 Jan;79(1):18-31
references.pmid: 23064341
references.citation: Antioxid Redox Signal. 2011 Jun;14(11):2271-87
references.pmid: 20712412
references.citation: Eukaryot Cell. 2013 Mar;12(3):390-8
references.pmid: 23291620
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W119-27
references.pmid: 18495751
references.citation: Eukaryot Cell. 2009 Dec;8(12):1837-44
references.pmid: 19801419
references.citation: Eukaryot Cell. 2012 Apr;11(4):482-93
references.pmid: 22345350
references.citation: FEBS J. 2005 Nov;272(22):5923-39
references.pmid: 16279955
references.citation: Appl Environ Microbiol. 2011 May;77(9):3009-16
references.pmid: 21421791
references.citation: J Biotechnol. 2010 Jan 1;145(1):30-7
references.pmid: 19861137
references.citation: Nat Cell Biol. 2007 Oct;9(10):1102-9
references.pmid: 17909521
references.citation: Mol Biol Cell. 2005 May;16(5):2544-53
references.pmid: 15743910
references.citation: Appl Microbiol Biotechnol. 2013 Sep;97(18):8205-18
references.pmid: 23700238
references.citation: Nat Biotechnol. 2008 May;26(5):553-60
references.pmid: 18454138
references.citation: J Biol Chem. 2001 Jun 29;276(26):24309-14
references.pmid: 11304525
references.citation: J Biotechnol. 2001 Apr 27;87(1):43-57
references.pmid: 11267698
references.citation: BMC Genomics. 2011 Dec 19;12:613
references.pmid: 22182583