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Open Access Research article

Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii

Jochen Schmid12*, Dirk Müller-Hagen26, Thomas Bekel3, Laura Funk2, Ulf Stahl2, Volker Sieber14 and Vera Meyer25

Author Affiliations

1 Chair of Chemistry of Biogenic Resources, Straubing Centre of Science, Technische Universität München, Schulgasse 16, 94315 Straubing, Germany

2 Department of Microbiology and Genetics, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany

3 Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, D-33594 Bielefeld, Germany

4 Degussa Food Ingredients GmbH, Lise Meitner Str. 34, 85354 Freising, Germany

5 Molecular Microbiology and Biotechnology, Institute of Biology, Leiden University, 2333 BE Leiden, The Netherlands

6 PolyPhag GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany

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BMC Genomics 2010, 11:329  doi:10.1186/1471-2164-11-329

Published: 26 May 2010

Abstract

Background

The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 → 3)-β-linked glucose with a (1 → 6)-β-glycosyl branch on every third unit. Although the physicochemical properties of scleroglucan are well understood, almost nothing is known about the genetics of scleroglucan biosynthesis. Similarly, the biosynthetic pathway of oxalate, the main by-product during scleroglucan production, has not been elucidated yet. In order to provide a basis for genetic and metabolic engineering approaches, we studied scleroglucan and oxalate biosynthesis in S. rolfsii using different transcriptomic approaches.

Results

Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified ~800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions. From these, candidate genes were identified which could represent potential leads for targeted modification of the S. rolfsii metabolism for increased scleroglucan yields.

Conclusions

The results presented in this paper provide for the first time genomic and transcriptomic data about S. rolfsii and demonstrate the power and usefulness of combined transcriptome sequencing and comparative microarray analysis. The data obtained allowed us to predict the biosynthetic pathways of scleroglucan and oxalate synthesis and to identify important genes putatively involved in determining scleroglucan yields. Moreover, our data establish the first sequence database for S. rolfsii, which allows research into other biological processes of S. rolfsii, such as host-pathogen interaction.