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Applied and Environmental Microbiology, June 2009, p. 4058-4068, Vol. 75, No. 12
0099-2240/09/$08.00+0     doi:10.1128/AEM.00314-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Transcriptome and Secretome Analyses of Phanerochaete chrysosporium Reveal Complex Patterns of Gene Expression ^,

Amber Vanden Wymelenberg,¹ Jill Gaskell,² Mike Mozuch,² Phil Kersten,² Grzegorz Sabat,³ Diego Martinez,⁴ and Dan Cullen^2*

Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706,¹ U.S. Forest Service, Forest Products Laboratory, Madison, Wisconsin 53726,² Genetics and Biotechnology Center, University of Wisconsin, Madison, Wisconsin 53706,³ University of New Mexico, Albuquerque, New Mexico 87131⁴

Received 8 February 2009/ Accepted 5 April 2009

The wood decay basidiomycete Phanerochaete chrysosporium was grown under standard ligninolytic or cellulolytic conditions and subjected to whole-genome expression microarray analysis and liquid chromatography-tandem mass spectrometry of extracellular proteins. A total of 545 genes were flagged on the basis of significant changes in transcript accumulation and/or peptide sequences of the secreted proteins. Under nitrogen or carbon limitation, lignin and manganese peroxidase expression increased relative to nutrient replete medium. Various extracellular oxidases were also secreted in these media, supporting a physiological connection based on peroxide generation. Numerous genes presumed to be involved in mobilizing and recycling nitrogen were expressed under nitrogen limitation, and among these were several secreted glutamic acid proteases not previously observed. In medium containing microcrystalline cellulose as the sole carbon source, numerous genes encoding carbohydrate-active enzymes were upregulated. Among these were six members of the glycoside hydrolase family 61, as well as several polysaccharide lyases and carbohydrate esterases. Presenting a daunting challenge for future research, more than 190 upregulated genes are predicted to encode proteins of unknown function. Of these hypothetical proteins, approximately one-third featured predicted secretion signals, and 54 encoded proteins detected in extracellular filtrates. Our results affirm the importance of certain oxidative enzymes and, underscoring the complexity of lignocellulose degradation, also support an important role for many new proteins of unknown function.

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* Corresponding author. Mailing address: Forest Products Laboratory, One Gifford Pinchot Drive, Madison, WI 53726. Phone: (608) 231-9468. Fax: (608) 231-9262. E-mail: dcullen{at}facstaff.wisc.edu

Published ahead of print on 17 April 2009.

Supplemental material for this article may be found at http://aem.asm.org/.

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Applied and Environmental Microbiology, June 2009, p. 4058-4068, Vol. 75, No. 12
0099-2240/09/$08.00+0     doi:10.1128/AEM.00314-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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