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J. Biol. Chem., Vol. 278, Issue 34, 31988-31997, August 22, 2003

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Transcriptional Regulation of Biomass-degrading Enzymes in the Filamentous Fungus Trichoderma reesei^*,

Pamela K. Foreman , Doug Brown , Lydia Dankmeyer, Ralph Dean , Stephen Diener , Nigel S. Dunn-Coleman, Frits Goedegebuur, Thomas D. Houfek , George J. England, Aaron S. Kelley, Hendrik J. Meerman, Thomas Mitchell , Colin Mitchinson, Heather A. Olivares, Pauline J. M. Teunissen, Jian Yao and Michael Ward

From the Genencor International, Inc., Palo Alto, California 94304 and the Fungal Genomics Laboratory, North Carolina State University, Raleigh, North Carolina 27695-7251

The filamentous fungus Trichoderma reesei produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones. Among the sequences whose predicted gene products had significant similarity to known proteins, 12 were identified that encode previously unknown enzymes that likely function in biomass degradation. Microarrays were used to query the expression levels of each of the sequences under different conditions known to induce cellulolytic enzyme synthesis. Most of the genes encoding known and putative biomass-degrading enzymes were transcriptionally co-regulated. Moreover, despite the fact that several of these enzymes are not thought to degrade cellulase directly, they were coordinately overexpressed in a cellulase overproducing strain. A variety of additional sequences whose function could not be ascribed using the limited sequence available displayed analogous behavior and may also play a role in biomass degradation or in the synthesis of biomass-degrading enzymes. Sequences exhibiting additional regulatory patterns were observed that might reflect roles in regulation of cellulase biosynthesis. However, genes whose products are involved in protein processing and secretion were not highly regulated during cellulase induction.

View larger version (50K): [in this window] [in a new window]   FIG. 2. Genome-wide regulation of gene expression by sophorose. A, samples and microarrays are as described in Fig. 1B. The indicated genes were clustered according to the log ratio: expression with sophorose relative to glycerol alone in RLP-37 (column 1), expression with sophorose relative to glycerol alone in QM6a (column 2), and the relative expression levels in RLP-37 relative to QM6a when both strains were grown in the presence of sophorose (column 3). The mean log ratios among replicate microarrays from triplicate cultures were determined and are displayed according to the color bar below. B, clustered data from the entire data set. Columns are as in A. C, the data shown in Fig. 2B was filtered to obtain the sets of ESTs with a log ratio of 0.3 or more in each of the experiments. The sets were compared to identify ESTs that were common and distinct among the sets. Numbers refer to the number of ESTs in the set. Superscripts are used to identify the sets, the full content of which are available in the Supplemental Material. D, the data shown in Fig. 2B were filtered to obtain the sets of ESTs displaying a log ratio of –0.3 or less in each of the experiments. The sets were compared as in C.

View larger version (17K): [in this window] [in a new window]   FIG. 4. Regulation of ESTs encoding putative components of the protein processing and secretion apparatus. A, list of ESTs containing ORFs with significant sequence similarity to S. cerevisiae gene products involved in protein processing and secretion was compiled. This list was compared with the sets of genes induced with log ratio 0.3 or more by lactose (as in Fig. 3) or by sophorose (as in Fig. 2) in QM6a. B, a similar analysis was performed for the sets of genes induced by 2-fold or more in RLP-37.

Received for publication, May 7, 2003 , and in revised form, June 3, 2003.

The nucleotide sequence(s) reported in this paper has been submitted to the GenBank^TM/EBI Data Bank with accession number(s) CB895227–CB909713.

^* This work was supported in part by a subcontract from the Office of Biomass Program of the Department of Energy Office of Energy Efficiency and Renewable Energy. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains sequence alignments for the predicted gene products and data sets for Figs. 2 and 4.

To whom correspondence should be addressed: Genencor International, 925 Page Mill Rd., Palo Alto, CA 94304. Tel.: 650-846-7635; Fax: 650-621-7817; E-mail: Pforeman{at}genencor.com.

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