Publications (14) View all
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Article: Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB).
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ABSTRACT: Modular biosynthetic clusters are responsible for the synthesis of many important pharmaceutical products. They include polyketide synthases (PKS clusters), non-ribosomal synthetases (NRPS clusters), and mixed clusters (containing both PKS and NRPS modules). The ClustScan database (CSDB) contains highly annotated descriptions of 170 clusters. The database has a hierarchical organization, which allows easy extraction of DNA and protein sequences of polypeptides, modules, and domains as well as an organization of the annotation so as to be able to predict the product chemistry to view it or export it in a standard SMILES format. The recombinant ClustScan database contains information about predicted recombinants between PKS clusters. The recombinants are generated by modeling homologous recombination and are associated with annotation and prediction of product chemistry automatically generated by the model. The database contains over 20,000 recombinants and is a resource for in silico approaches to detecting promising new compounds. Methods are available to construct the corresponding recombinants in the laboratory.Journal of Industrial Microbiology 03/2013; · 1.80 Impact Factor -
Dataset: 2012 Starcevic et al
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Article: Annotation of modular PKS and NRPS gene clusters in the genome of Streptomyces tsukubaensis NRRL18488.
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ABSTRACT: The high G+C-content and large genome size make sequencing and assembly of Streptomyces genomes more difficult than for those of other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). Analysing such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs and sequencing errors can introduce apparent frame shifts in the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats that may cause assembly errors. The genome sequence of Streptomyces tsukubaensis NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. 4 PKS clusters and 6 NRPS clusters were identified. Contigs containing cluster sequences were analysed in detail using the ClustScan program, which suggested the order and orientation of the contigs. Sequencing of appropriate PCR products confirmed the ordering and allowed correction of apparent frame shifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. Analysis of one PKS cluster showed that it should produce a bafilomycin-like compound and RT-PCR was used to show that the cluster was transcribed.Applied and environmental microbiology 09/2012; · 3.69 Impact Factor -
Article: Recombinatorial biosynthesis of polyketides.
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ABSTRACT: Modular polyketide synthases (PKSs) from Streptomyces and related genera of bacteria produce many important pharmaceuticals. A program called CompGen was developed to carry out in silico homologous recombination between gene clusters encoding PKSs and determine whether recombinants have cluster architectures compatible with the production of polyketides. The chemical structure of recombinant polyketides was also predicted. In silico recombination was carried out for 47 well-characterised clusters. The predicted recombinants would produce 11,796 different polyketide structures. The molecular weights and average degree of reduction of the chemical structures are dispersed around the parental structures indicating that they are likely to include pharmaceutically interesting compounds. The details of the recombinants and the chemical structures were entered in a database called r-CSDB. The virtual compound library is a useful resource for computer-aided drug design and chemoinformatics strategies for finding pharmaceutically relevant chemical entities. A strategy to construct recombinant Streptomyces strains to produce these polyketides is described and the critical steps of mobilizing large biosynthetic clusters and producing new linear cloning vectors are illustrated by experimental data.Journal of Industrial Microbiology 03/2012; 39(3):503-11. · 1.80 Impact Factor -
Article: A profile of an endosymbiont-enriched fraction of the coral Stylophora pistillata reveals proteins relevant to microbial-host interactions.
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ABSTRACT: This study examines the response of Symbiodinium sp. endosymbionts from the coral Stylophora pistillata to moderate levels of thermal "bleaching" stress, with and without trace metal limitation. Using quantitative high throughput proteomics, we identified 8098 MS/MS events relating to individual peptides from the endosymbiont-enriched fraction, including 109 peptides meeting stringent criteria for quantification, of which only 26 showed significant change in our experimental treatments; 12 of 26 increased expression in response to thermal stress with little difference affected by iron limitation. Surprisingly, there were no significant increases in antioxidant or heat stress proteins; those induced to higher expression were generally involved in protein biosynthesis. An outstanding exception was a massive 114-fold increase of a viral replication protein indicating that thermal stress may substantially increase viral load and thereby contribute to the etiology of coral bleaching and disease. In the absence of a sequenced genome for Symbiodinium or other photosymbiotic dinoflagellate, this proteome reveals a plethora of proteins potentially involved in microbial-host interactions. This includes photosystem proteins, DNA repair enzymes, antioxidant enzymes, metabolic redox enzymes, heat shock proteins, globin hemoproteins, proteins of nitrogen metabolism, and a wide range of viral proteins associated with these endosymbiont-enriched samples. Also present were 21 unusual peptide/protein toxins thought to originate from either microbial consorts or from contamination by coral nematocysts. Of particular interest are the proteins of apoptosis, vesicular transport, and endo/exocytosis, which are discussed in context of the cellular processes of coral bleaching. Notably, the protein complement provides evidence that, rather than being expelled by the host, stressed endosymbionts may mediate their own departure.Molecular & Cellular Proteomics 02/2012; 11(6):M111.015487. · 7.40 Impact Factor
