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QLK3-2002-02056
Gene mining of metagenomes for novel enzymes and therapeutics (Gemini) |
| Type of Project | Shared Cost Research |
| Contract No | QLK3-2002-02056 |
| Total Cost | |
| EC Contribution | 2,744,773 EUR |
| Start Date | 01-11-2002 |
| Duration | 48 Months |
Abstract
Microbial diversity is a key element in the search for new, valuable compounds such as enzymes with novel properties for industrial applications or which may lead to new or modified antimicrobials. Only a limited number of micro-organisms from the environment can be cultured. Therefore, this project will exploit the vast genetic potential of the unexploited metagenome in a culture-independent process using functional genomics, PCR-based screens and in silico gene mining. Expression of selected target proteins in industrially important hosts to give economically relevant yields will be investigated. Altogether, the project will combine the enormous potential of biodiversity with cutting edge screening technology, molecular biology and bioinformatics to develop products with high biotechnological or pharmaceutical value.
Objectives
The microbial diversity has been explored as an inexhaustible source for new valuable products for many years based on microbial isolation and culturing. Since one has realised that only a small number of micro-organisms can be cultured, a new approach has emerged to explore this biodiversity, based on the concept of cloning the metagenome to access the collective genomes of the environmental microflora.
The overall goal of this project, therefore, is to obtain new enzymes with interesting characteristics applicable in industry or that may give rise to new antimicrobials. This will be achieved through mining the genomes of environmental micro-organisms present in samples of diverse origin without culturing them. The proposal also aims to deliver a much clearer picture of the biodiversity of the microflora in different environments.
Activities
The consortium will develop a technology platform that will enable exploration of genetic diversity from non-cultured micro-organisms collected directly from diverse habitats at world-wide locations, as a source of new valuable compounds. Of special interest are hydrolytic enzymes or enzymes involved in the production of potent antimicrobials. Expected results will be obtained through a number of well-defined work packages in consecutive steps, starting with the construction of a series of ratified, high-quality libraries from genomic DNA of non-cultured micro-organisms. Improved purification protocols need to be developed to avoid extraneous contaminants in high Mr DNA samples without excessive size reduction thus allowing the construction of representative metagenomic libraries in suitable vectors.
Improved, high-throughput screening methods will be developed to screen the resultant colonies directly by function for the production of plant cell wall degrading enzymes, for enzymes that are at the basis for new or modified antimicrobials or that confer antibiotic resistance or are involved in heavy metal tolerance. The different libraries will also be screened by sequence-based techniques to identify clones with potentially novel forms of genes of biotechnological relevance. The central part of this proposal is the expression and, where relevant, the secretion in Bacillus and Streptomyces of the enzyme proteins cloned from natural samples of uncultured micro-organisms. To address the biodiversity in the samples by identifying and sequencing 16S rRNA genes together with neighbouring, subgenomic DNA, new bioinformatic tools will be developed.
Deliverables
Expected results are a further ratification of the metagenomic approach as a very powerful tool to mine important, novel genes among the gene pool of the unculturable microflora. Identified genes will encode hydrolytic enzymes of industrial interest or proteins leading to new and improved antimicrobial drugs. Engineered, industrially relevant micro-organisms will produce the proteins in significant amounts. Bioinformatics analysis of large subgenomic regions will be informative for biodiversity.
Contacts
Coordinator
Participant
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