METAEXPLORE

Metagenomics for bioexploration - Tools and application

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 Obiettivo del progetto (Objective)

'This proposal will (further) develop and apply metagenomics tools to access the enzymatic potential borne in the cryptic biota of selected natural habitats, in particular target soil-related and aquatic ones. In the light of the environmental relevance of chitins and lignins (as natural compounds recalcitrant to degradation) and halogenated aliphatic and aromatic compounds (anthropogenic recalcitrant compounds), the enzymatic activities that we will target are functions able to degrade these compounds. A database of gene functions will be established and maintained. Next to its great relevance to environmental biotechnology including bioremediation, a spin-off of the work will be the discovery of novel biocatalytic functions of industrial relevance. We will in particular address the catabolic potential that is encoded by the mobilome, the collective pool of mobile genetic elements in the microbiota. We will further apply high-throughput (454-based) sequencing to rapidly unravel the metabolic complement in this mobile gene pool. The project brings together a suite of 15 contractors across Europe, encompassing 21 laboratories spread over 11 copuntries and including 4 SMEs. Most of the partners are renowned laboratories which have vast experience in metagenomics of environmental samples, biotechnology, enzymology, bioinformatics, the mobilome, waste management and bioremediation and enzyme production.'

Introduzione (Teaser)

Certain natural and synthetic compounds are resistant to degradation by natural enzymes. Scientists have conducted comprehensive genetic screening of aquatic and terrestrial organisms to find and design the appropriate enzymes for the recalcitrant molecules.

Descrizione progetto (Article)

Bioremediation has been used successfully for oil spills, chlorinated solvents and pesticides, but many compounds are resistant to degradation (recalcitrant). Using genetic material from the EU-funded project 'Metagenomics for bioexploration - Tools and application' (http://www.rug.nl/research/metaexplore/ (METAEXPLORE)) has helped to develop a wide range of improved enzymes.

In particular, the researchers focused on the naturally recalcitrant molecules chitin and lignin. Anthropogenic-sourced materials include halogenated and organic compounds as well as xenobiotic compounds foreign to biological systems, herbicides for example.

Following pre-screening of a large number of terrestrial and aquatic habitats with specially developed tools, the team cloned and sequenced promising enzymes from selected environments. A total of nine metagenomic libraries were produced from selected environmental habitats. A software platform (MetaSAMS) with search routines, genomic mapping and tools for comparative analysis of metagenomics data has been successfully developed. All data warehouses contain functional genes and operons to provide genetic resources for future explorations.

Derived from industrial demand, these collections were screened for improved enzymes, including novel chitinases, laccases/ligninases, and aerobic and anaerobic dehalogenases. Another target was the beta-amino transferring enzyme family involved in the production of a wide range of pharmaceuticals.

A large proportion of the gene sequences coding for the enzymes are housed on the mobile genetic element of microbes, the mobilome. After characterisation of structure and function and expression in suitable hosts, the researchers extended their activities of the cream of the enzymes for use in industry using directed evolution.

METAEXPLORE deliverables are expected to have an important impact on sustainability and EU environmental goals. Alternative raw materials are needed for the future supply of energy and chemicals. Recalcitrant waste materials like lignin and chitin contain various building blocks for chemical production. Disposal of waste is expensive and creates numerous environmental and public health challenges.

Bioremediation not only helps keep nature clean in a natural way, it is also a low-energy process for decontamination of water and soil. Availability of novel biocatalysts is an important pillar of sustainability given the innumerable industrial reactions based on catalysis.