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Volume 2
     

Gene mining of metagenomes for novel enzymes and therapeutics (Gemini)

   
Project

QLK3-2002-02056

Cell factory area

3.3.4

EU Contribution

2,744,773 Euro

Duration

48 months

Type

RS

Starting date

01 November 2002

Keywords
antimicrobials
hydrolitic enzymes
Mr DNA
RRNA
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.

DESCRIPTION OF THE WORK

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 to constructing 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.

CONSORTIUM
COORDINATOR
 
Jozef Anné
Microbiology and Immunology, lab. Bacteriology
Katholieke Universiteit Leuven
3000 Leuven, Belgium
Tel: +32-16-337 371
Fax: +32-16-337 340
Jozef.anne@rega.kuleuven.ac.be
 
PARTNERS
 
Harry Flint
Microbial Genetics Group
Rowett Research Institute
Aberdeen AB21 9SB, United Kingdom
Tel: +44-1224-716 651
Fax: +44-1224-716 687
h.flint@rri.sari.ac.uk

Andreas Vente
Combinature BioPharm AG
13125 Berlin, Germany
Tel: +49-30-9489 4050 • Fax:49-30-9489 4051
Vente@combinature.com

Anastassios Economou
Department of Unicellular organisms
Institute of Molecular Biology and Biotechnology
71110 Iraklio-Crete, Greece
Tel: +30-810-391 167
Fax: +30-810-391 166
aeconomo@imbb.forth.gr

Thomas Schäfer
Bacterial Discovery
Novozymes A/S
2880 Bagsvaerd Denmark
Tel: +45-4442 6444
Fax: +45-4442 7828
tsch@novozymes.com

Andrew W. B. Johnston
School of Biological Sciences
University of East Anglia
Norwich NR4 7TJ, United Kingdom
Tel: +44-1603-592 264
Fax: +44 -1603-592 250
a.johnston@uea.ac.uk

Wolfgang Streit
Institüt für Mikrobiologie und Genetik
Georg-August-Universität Göttingen
37077 Göttingen, Germany
Tel: +49-55-139 3775
Fax: +49-55-139 3793
wstreit@gwdg.de

Francisco Rodríguez-Valera
Department of Microbiology
Universidad Miguel Hernandez de Elche
03550 San Juan, Spain
Tel: +34-96-591 9451 • Fax 34-96-591 9457
frvalera@umh.es