Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-6919
Main Title: Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii
Author(s): Schmid, Jochen
Müller-Hagen, Dirk
Bekel, Thomas
Funk, Laura
Stahl, Ulf
Sieber, Volker
Meyer, Vera
Type: Article
Language Code: en
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.
URI: https://depositonce.tu-berlin.de//handle/11303/7741
http://dx.doi.org/10.14279/depositonce-6919
Issue Date: 26-May-2010
Date Available: 3-May-2018
DDC Class: 570 Biowissenschaften; Biologie
Subject(s): Oxalate
Formate Dehydrogenase
Oxalate Oxidase
Flammulina Velutipes
Oxalate Decarboxylase
Sponsor/Funder: BMBF, 0313397, Verbundprojekt: Entwicklung von Verfahren zur Herstellung mikrobieller Exopolysacchariden als wasserlösliche Verdicker auf Basis nachwachsender Rohstoffe
License: https://creativecommons.org/licenses/by/2.0/
Journal Title: BMC Genomics
Publisher: BioMed Central
Publisher Place: London
Volume: 11
Article Number: 329
Publisher DOI: 10.1186/1471-2164-11-329
ISSN: 1471-2164
Appears in Collections:FG Angewandte und Molekulare Mikrobiologie » Publications

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