Aventis Announces Complete Genome Sequence of Saccharopolyspora Erythraea in Cooperation with MWG Biotech.

Business Editors/Health/Medical Writers/High-Tech Writers

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EBERSBERG, Germany--(BUSINESS WIRE)--March 8, 2004

Aventis Bulk S.p.A., the Italian consociate of the pharmaceutical company Aventis S.A., has successfully sequenced the whole genome of Saccharopolyspora erythraea. The strain is an industrial overproducer of erythromycin antibiotic. The work was carried out in collaboration with MWG Biotech AG, Ebersberg, Germany, which undertook the sequencing work. The project was undertaken as part of a major research program "New technologies for the study of antibiotic producing microorganisms" supported by the Italian Ministry of Research (MIUR), in order to reliance the pharmaceutical research and development activities in Italy.

Within a wider collaboration agreement with the Italian CNR (National Research Council) and other academic institutions, Aventis Bulk commissioned to MWG Biotech A.G. the sequence of the whole S. erythraea genome. The complete genomic sequence will form the basis for innovative approaches in strain development methodologies. The whole sequence is property of Aventis Bulk.

Sequencing and Annotation of Saccharopolyspora erythraea

The complete sequence of S. erythraea was derived from 256 canonically ordered cosmid clones representing a circular genome of 8.2 Megabases.The sequence information of S. erythraea was determined using a cosmid-to-cosmid walking approach. First a cosmid library was generated and cosmid end sequences up to 20fold physical coverage of the genome were produced. Afterwards, randomly selected cosmids, the so called seed clones, were sequenced up to publication quality. These seed clones served as starting points in a cosmid walking approach in which adjacent cosmid clones were identified using cosmid end sequences. Using this procedure enabled rapid sequencing while avoiding the problems associated with repetitive DNA elements known to complicate whole genome shot gun approaches. The sequence information of the microorganism comprises 8,212,111 base pairs and a GC content of 71%.The project revealed that the sequenced strain seems to harbor a circular genome.

Two programs were used in parallel for gene finding. Critica (by J. Badger) identified 7,008 ORFs whereas Glimmer2 (from TIGR) yielded 9,544 ORFs. 2,679 of all ORFs identified are identical, while the others either just differ in length or are completely different. Quite a number of predicted ORFs show overlaps and, interestingly, other , large regions do not have any gene predictions. This might have potential technical (GC content) or biological implications. An intelligent combination of both sets resulted in a final number of 8,007 ORFs.

The predicted genes where translated into proteins using the general bacterial translation table. Subsequently these proteins were matched against the protein database PIR-NREF. As cutoff for matches a 50% homology on a minimum of 100 amino acids was set. Moreover, not only identical amino acids but also similar amino acids were regarded as homologous.

Interestingly, only 63% (5,066) of the ORFs had a homologous sequence in a related species. 44% of these have homologues in Streptomycetes, 19% in Mycobacteria , next in line being Corynebacteria sp. (4%) and various Rhizobiales (5%).

Functional annotation of ORFs without significant similarity to sequences stored in public databases was performed using InterProScan (European Bioinformatic Centre). In this way, additional 901 ORFs were functionally annotated. 25% of the ORFs could not be allocated to a putative function, neither with InterProScan nor by homology search. Additionally, 49 tRNAs and 12 rRNAs in four clusters were identified.

The percentage of homology found in erythromycin cluster vs the wild erythromycin strain already published was 83%. Many deletion areas where detected in the erythromycin cluster of the high potency strain in comparison with the published wild sequence.

MWG Biotech is the world leading company in microbial genome sequencing and the bioinformatic analysis associated with it. The Company's special focus is on supplying solutions for the continually increasing demand for genome sequence comparisons of pathogen bacteria or production strains with the respective strains of origin. Information generated from these processes, from genome restructuring to the identification of individual mutations, will give decisive insight into the genetic modifications of the organisms of interest, with the target of improving productivity resp. product yield and increasing process efficiency. This approach is increasingly used for the industrial production of amino acids, vitamins and lead structures for medical applications. Additional information at www.the-mwg.com.