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

Schmid J, Müller-Hagen D, Bekel T, Funk L, Stahl U, Sieber V, Meyer V (2010)
BMC Genomics 11(1): 329.

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Background The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 -> 3)-[beta]-linked glucose with a (1 -> 6)-(beta)-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.
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BMC Genomics
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11
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329
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Schmid J, Müller-Hagen D, Bekel T, et al. Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics. 2010;11(1):329.
Schmid, J., Müller-Hagen, D., Bekel, T., Funk, L., Stahl, U., Sieber, V., & Meyer, V. (2010). Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics, 11(1), 329. doi:10.1186/1471-2164-11-329
Schmid, J., Müller-Hagen, D., Bekel, T., Funk, L., Stahl, U., Sieber, V., and Meyer, V. (2010). Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics 11, 329.
Schmid, J., et al., 2010. Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics, 11(1), p 329.
J. Schmid, et al., “Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii”, BMC Genomics, vol. 11, 2010, pp. 329.
Schmid, J., Müller-Hagen, D., Bekel, T., Funk, L., Stahl, U., Sieber, V., Meyer, V.: Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii. BMC Genomics. 11, 329 (2010).
Schmid, Jochen, Müller-Hagen, Dirk, Bekel, Thomas, Funk, Laura, Stahl, Ulf, Sieber, Volker, and Meyer, Vera. “Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii”. BMC Genomics 11.1 (2010): 329.
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PMID: 26528259
Peroxidase gene discovery from the horseradish transcriptome.
Näätsaari L, Krainer FW, Schubert M, Glieder A, Thallinger GG., BMC Genomics 15(), 2014
PMID: 24666710
Differences in gene expression within a striking phenotypic mosaic Eucalyptus tree that varies in susceptibility to herbivory.
Padovan A, Lanfear R, Keszei A, Foley WJ, Külheim C., BMC Plant Biol 13(), 2013
PMID: 23421644
Tracking nickel-adaptive biomarkers in Pisolithus albus from New Caledonia using a transcriptomic approach.
Majorel C, Hannibal L, Soupe ME, Carriconde F, Ducousso M, Lebrun M, Jourand P., Mol Ecol 21(9), 2012
PMID: 22429322
The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus.
Ewen-Campen B, Shaner N, Panfilio KA, Suzuki Y, Roth S, Extavour CG., BMC Genomics 12(), 2011
PMID: 21266083
Scleroglucan: biosynthesis, production and application of a versatile hydrocolloid.
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PMID: 21732244
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PMID: 20950480

53 References

Daten bereitgestellt von Europe PubMed Central.

Notes on the parasitology of Sclerotium rolfsii
AUTHOR UNKNOWN, 1928
Corticium rolfsii
AUTHOR UNKNOWN, 1974
Collection and determination of root and stem rot pathogens
AUTHOR UNKNOWN, 1996
Scleroglucan
AUTHOR UNKNOWN, 1993
Exocellular, microbial polysaccharides.
Sandford PA., Adv Carbohydr Chem Biochem 36(), 1979
PMID: 380276
Influence of nonionic surfactant on aggregation state of scleroglucan in aqueous solution.
El Ouriaghli T, Francois J, Sarazin D, Truong DN., Carbohydrate polymers. 17(4), 1992
PMID: IND20374667
Scleroglucan: Fermentative Production, Downstream Processing and Applications
AUTHOR UNKNOWN, 2007
A new polysaccharidic gel matrix for drug delivery: preparation and mechanical properties.
Coviello T, Alhaique F, Parisi C, Matricardi P, Bocchinfuso G, Grassi M., J Control Release 102(3), 2005
PMID: 15681086
A new scleroglucan/borax hydrogel: swelling and drug release studies.
Coviello T, Grassi M, Palleschi A, Bocchinfuso G, Coluzzi G, Banishoeib F, Alhaique F., Int J Pharm 289(1-2), 2004
PMID: 15652203
Scleroglucan
AUTHOR UNKNOWN, 2002
Microbial polysaccharides-a comparison with eukaryotic polymers
AUTHOR UNKNOWN, 1989
Structure and assembly of epiglucan, the extracellular (1-->3;1-->6)-beta-glucan produced by the fungus Epicoccum nigrum strain F19.
Schmid F, Stone BA, Brownlee RT, McDougall BM, Seviour RJ., Carbohydr. Res. 341(3), 2005
PMID: 16359651
Biosynthesis of the [beta]--glucan of Sclerotium rolfsii sacc. Direction of chain propagation and the insertion of the branch residues
AUTHOR UNKNOWN, 1969
High scleroglucan production by Sclerotium rolfsii: Influence of medium composition
AUTHOR UNKNOWN, 1998
Influence of carbon source and pH on oxalate accumulation in culture filtrates of S. rolfsii
AUTHOR UNKNOWN, 1965
Scleroglucan and oxalic acid formation by Sclerotium glucanicum in sucrose supplemented fermentation
AUTHOR UNKNOWN, 1994

AUTHOR UNKNOWN, 1998
Scleroglucan.
Wang Y, McNeil B., Crit. Rev. Biotechnol. 16(3), 1996
PMID: 8856961
Repression of oxalic acid biosynthesis in the unsterile scleroglucan production process with Sclerotium rolfsii ATCC 15205
AUTHOR UNKNOWN, 2000
Enhanced production of scleroglucan by Sclerotium rolfsii MTCC 2156 by use of metabolic precursors.
Survase SA, Saudagar PS, Singhal RS., Bioresour. Technol. 98(2), 2006
PMID: 16806909
Use of complex media for the production of scleroglucan by Sclerotium rolfsii MTCC 2156.
Survase SA, Saudagar PS, Singhal RS., Bioresour. Technol. 98(7), 2006
PMID: 16822667
Oxalate production by fungi: its role in pathogenicity and ecology in the soil environment
AUTHOR UNKNOWN, 1996
Low molecular weight chelators and phenolic compounds isolated from wood decay fungi and their role in the fungal biodegradation of wood
AUTHOR UNKNOWN, 1995
A physiological role for oxalic acid biosynthesis in the wood-rotting basidiomycete Fomitopsis palustris.
Munir E, Yoon JJ, Tokimatsu T, Hattori T, Shimada M., Proc. Natl. Acad. Sci. U.S.A. 98(20), 2001
PMID: 11553780
Possible biochemical roles of oxalic acid as a low molecular weight compound involved in brown-rot and white-rot wood decays
AUTHOR UNKNOWN, 2007
Induction of polygalacturonase and the formation of oxalic acid by pectin in brown-rot fungi.
Green FIII, Clausen CA, Kuster TA, Highley TL., World J. Microbiol. Biotechnol. 11(5), 1995
PMID: IND20518631
Hydrolysis of bordered pits during colonization of conifers by brown-rot decay
AUTHOR UNKNOWN, 1995
Anion channel activity is necessary to induce ethylene synthesis and programmed cell death in response to oxalic acid.
Errakhi R, Meimoun P, Lehner A, Vidal G, Briand J, Corbineau F, Rona JP, Bouteau F., J. Exp. Bot. 59(11), 2008
PMID: 18612171
Toxic and signalling effects of oxalic acid: Oxalic acid-Natural born killer or natural born protector?
Lehner A, Meimoun P, Errakhi R, Madiona K, Barakate M, Bouteau F., Plant Signal Behav 3(9), 2008
PMID: 19704845
Oxalic acid is an elicitor of plant programmed cell death during Sclerotinia sclerotiorum disease development.
Kim KS, Min JY, Dickman MB., Mol. Plant Microbe Interact. 21(5), 2008
PMID: 18393620
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Kuster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Puhler A, Stoye J, Goesmann A., J. Biotechnol. 140(1-2), 2009
PMID: 19297685
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Evidence for a cytoplasmic pathway of oxalate biosynthesis in Aspergillus niger
AUTHOR UNKNOWN, 1988
Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi.
Han Y, Joosten HJ, Niu W, Zhao Z, Mariano PS, McCalman M, van Kan J, Schaap PJ, Dunaway-Mariano D., J. Biol. Chem. 282(13), 2007
PMID: 17244616
Production of calcium oxalate crystals by the basidiomycete Moniliophthora perniciosa, the causal agent of witches' broom disease of Cacao.
Rio MC, de Oliveira BV, de Tomazella DP, Silva JA, Pereira GA., Curr. Microbiol. 56(4), 2008
PMID: 18172716
Oxalic acid biosynthesis by Sclerotium rolfsii
AUTHOR UNKNOWN, 1968
Transcriptional control of nitric oxide reductase gene (CYP55) in the fungal denitrifier Fusarium oxysporum.
Takaya N, Uchimura H, Lai Y, Shoun H., Biosci. Biotechnol. Biochem. 66(5), 2002
PMID: 12092813
Nitrate reductase-formate dehydrogenase couple involved in the fungal denitrification by Fusarium oxysporum.
Uchimura H, Enjoji H, Seki T, Taguchi A, Takaya N, Shoun H., J. Biochem. 131(4), 2002
PMID: 11926996
Cloning and sequencing of two Ceriporiopsis subvermispora bicupin oxalate oxidase allelic isoforms: implications for the reaction specificity of oxalate oxidases and decarboxylases.
Escutia MR, Bowater L, Edwards A, Bottrill AR, Burrell MR, Polanco R, Vicuna R, Bornemann S., Appl. Environ. Microbiol. 71(7), 2005
PMID: 16000768
Cloning and characterization of the 5'-flanking region of the oxalate decarboxylase gene from Flammulina velutipes.
Azam M, Kesarwani M, Chakraborty S, Natarajan K, Datta A., Biochem. J. 367(Pt 1), 2002
PMID: 12020349
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.
Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M, Mewes HW., Nucleic Acids Res. 32(18), 2004
PMID: 15486203
Effects of salt stress on carbohydrate metabolism in desert soil alga Microcoleus vaginatus Gom
AUTHOR UNKNOWN, 2006
The correlation between salt tolerance and extracellular polysaccharide production in Rhizobium
AUTHOR UNKNOWN, 1997
Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease.
Chirgwin JM, Przybyla AE, MacDonald RJ, Rutter WJ., Biochemistry 18(24), 1979
PMID: 518835
Germin, a protein marker of early plant development, is an oxalate oxidase.
Lane BG, Dunwell JM, Ray JA, Schmitt MR, Cuming AC., J. Biol. Chem. 268(17), 1993
PMID: 8509360
Oxalate decarboxylase in the brown-rot wood decay fungus Postia placenta
AUTHOR UNKNOWN, 1995
Transformation of Aspergillus nidulans by using a trpC plasmid.
Yelton MM, Hamer JE, Timberlake WE., Proc. Natl. Acad. Sci. U.S.A. 81(5), 1984
PMID: 6324193

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