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

dc.contributor.authorSchmid, Jochen
dc.contributor.authorMüller-Hagen, Dirk
dc.contributor.authorBekel, Thomas
dc.contributor.authorFunk, Laura
dc.contributor.authorStahl, Ulf
dc.contributor.authorSieber, Volker
dc.contributor.authorMeyer, Vera
dc.date.accessioned2018-05-03T11:28:59Z
dc.date.available2018-05-03T11:28:59Z
dc.date.issued2010-05-26
dc.description.abstractBackground 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.en
dc.description.sponsorshipBMBF, 0313397, Verbundprojekt: Entwicklung von Verfahren zur Herstellung mikrobieller Exopolysacchariden als wasserlösliche Verdicker auf Basis nachwachsender Rohstoffeen
dc.identifier.issn1471-2164
dc.identifier.urihttps://depositonce.tu-berlin.de//handle/11303/7741
dc.identifier.urihttp://dx.doi.org/10.14279/depositonce-6919
dc.language.isoenen
dc.rights.urihttps://creativecommons.org/licenses/by/2.0/en
dc.subject.ddc570 Biowissenschaften; Biologiede
dc.subject.otherOxalateen
dc.subject.otherFormate Dehydrogenaseen
dc.subject.otherOxalate Oxidaseen
dc.subject.otherFlammulina Velutipesen
dc.subject.otherOxalate Decarboxylaseen
dc.titleTranscriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsiien
dc.typeArticleen
dc.type.versionpublishedVersionen
dcterms.bibliographicCitation.articlenumber329en
dcterms.bibliographicCitation.doi10.1186/1471-2164-11-329en
dcterms.bibliographicCitation.journaltitleBMC Genomicsen
dcterms.bibliographicCitation.originalpublishernameBioMed Centralen
dcterms.bibliographicCitation.originalpublisherplaceLondonen
dcterms.bibliographicCitation.volume11en
tub.accessrights.dnbfreeen
tub.affiliationFak. 3 Prozesswissenschaften>Inst. Biotechnologie>FG Angewandte und Molekulare Mikrobiologiede
tub.affiliation.facultyFak. 3 Prozesswissenschaftende
tub.affiliation.groupFG Angewandte und Molekulare Mikrobiologiede
tub.affiliation.instituteInst. Biotechnologiede
tub.publisher.universityorinstitutionTechnische Universität Berlinen
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