Research Projects

Logos GenomEnviron and Ampere
Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 65 14

     

 


METAGENOMICS FOR BIOEXPLORATION

– TOOLS AND APPLICATION

METAEXPLORE


http://www.2020-horizon.com/METAEXPLORE-Metagenomics-for-bioexploration-tools-and-application%28METAEXPLORE%29-s11702.html

Coordinator:
J.D. van ELSAS
Funding Source:

SEVENTH FRAMEWORK PROGRAMME; THEME [#] KBBE-2007-3-3-05
ACTIVITY MINING IN METAGENOMES

Period:

2009-2013

Partners:

Rijksuniversiteit, Netherlands 
University of Copenhagen, Denmark
Sodertorn Hogskola Stockholm, Sweden 
University of Warwick, United Kingdom
Wageningen Universiteit, Netherlands
Ecole Centrale de Lyon, Université de Lyon, France
University of Bielefeld, Germany
Julius Kuhn Institut, Germany
Leuven Katholieke Universiteit, Belguim
Valtion Teknillinen Tutkimuskeskus, Finland
Universite Catholique Louvain, Belguim
University of Insubria, Italy
University of Ljubljana, Slovenia
University of La Plata, Argentina 
Bio Detection Systems, Netherlands
Whitby Seafoods Ltd, United Kingdom
INRA Dijon, France

Abstracts:

This project is driven by both industrial demand and state-of-the-art environmental metagenomics technologies. It will develop and apply advanced molecular tools that allow the cloning and sequencing of the metagenomes of microbial communities of selected soil and aquatic habitats, followed by educated activity-and sequence-based screenings for, and analyses and engineering of, target enzymatic activities. These desired activities are derived from industrial demand, and focus in particular on improved enzymes involved in the biodegradation of recalcitrant and xenobiotic molecules, including novel chitinases, ligninases, and aerobic and anaerobic dehalogenases (halogenases as a spin-off). A strong focus will be placed on the mobilome, that is, the collective pool of mobile genetic elements (MGE, including plasmids) carried by a microbial community, as there is strong evidence that the frequency of occurrence of genes encoding the desired enzymatic activities is raised in this gene pool. Selected genes/operons found to encode desired novel enzymatic functions will be analyzed at the molecular level and expressed in optimized expression vectors in suitable hosts. Subsequently, the enzymes will be characterized as to structure and function (kinetics), and used in directed evolution experiments to enhance or extend their activities to a practical level. This will pave the way towards application, however this project will not fully tackle the practical issues involved in industrial production. Finally, a database will be established that contains the collective functional genes and operons with novel activities found in the project.

Objectives:

· Consolidated methodology - Development of Consortium-wide cutting-edge
methodology that allows highly optimized use of environmental metagenomics to
search for novel biocatalytic activity useful in waste management*.
*production of chiral pharmaceuticals as a spin-off
· Novel enzymes - Production of novel enzymes with:
o chitin-degrading activities,
o lignin-degrading activities,
o dehalogenase / halogenase activities,
o ammonia lyase/epoxide hydrolase activities
· Habitat prediction - Improvement of the current understanding of the natural
prevalence and mobility of the genes encoding the selected enzymes, to allow
identification of habitats most conducive to successful exploration. Special attention
will be given to the mobilome as the carrier of such genes.
· Supporting database - Establishment of effective sequence database systems to
support screening and exploitation of the targeted enzymatic activities.

Description
of the work:

 

Deliverables:

Publications & Communications:

 

 
     

PROJECT