Schmid J.,TU Munich |
Schmid J.,TU Berlin |
Muller-Hagen D.,TU Berlin |
Muller-Hagen D.,PolyPhag GmbH |
And 7 more authors.
BMC Genomics | Year: 2010
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. © 2010 Schmid et al; licensee BioMed Central Ltd.
Lerchner J.,TU Bergakademie Freiberg |
Mueller-Hagen D.,Polyphag GmbH |
Roehr H.,Polyphag GmbH |
Wolf A.,TU Bergakademie Freiberg |
And 4 more authors.
Journal of Thermal Analysis and Calorimetry | Year: 2011
Rapid detection of antibiotic resistances of clinical bacterial strains would allow an early selective antibiotic therapy and a faster intervention and implementation of infection control measurements. In clinical practice, however, conventional antibiotic susceptibility tests of bacteria often need 24 h until the results are obtained. The metabolic heat production of bacteria is an excellent possibility to record their physiological activities and could therefore be used for a rapid discrimination of bacterial strains which are resistant or non-resistant to antibiotics and also to lytic bacteriophages, respectively. Unfortunately, conventional calorimeters suffer from need of comparably large volumes of bacterial suspensions are characterised by slow operation and high costs which restrict their application in clinical laboratories. The present paper demonstrates that a new type of calorimeters developed on silicon-chip technology enables the detection of antibiotic resistances on a minute-timescale. For this reasons, a prototype chip calorimeter was used which sensitivity is 20 nW related to the heat production of about 10 4 bacteria. For a clear discrimination of antibiotic resistance about 10 5 bacteria are required. The antibiotic resistances and susceptibilities of different strains of Staphylococcus aureus to cefoxitin and the sensitivities of S. aureus DSM 18421 and E. coli DSM 498 to a mixture of two bacteriophages were studied. Comparing the heat productions of cultures incubated with antibiotics or bacteriophages to those without these antibacterial preparations enabled a clear discrimination of resistant and non-resistant strains already after totally 2 h. © Akadémiai Kiadó, Budapest, Hungary 2011.