Innovation: Set Of Ready-­to-use Metagenomic Libraries For Enzyme Selection And Ready To Use Clones Encoding Enzymes Of Interests

Last update: 29.08.2013
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Keywords: 
metagenomics, clone libraries
MAGICPAH aims to explore, understand and exploit the catalytic activities of microbial communities involved in the degradation of persistent PAHs. It will integrate (meta-) genomic studies with in-situ activity assessment based on stable isotope probing particularly in complex matrices of different terrestrial and marine environments.
PAH degradation under various conditions of bioavailability will be assessed as to improve rational exploitation of the catalytic properties of bacteria for the treatment and prevention of PAH pollution. We will generate a knowledge base not only on the microbial catabolome for biodegradation of PAHs in various impacted environmental settings based on genome gazing, retrieval and characterization of specific enzymes but also on systems related bioavailability of contaminant mixtures.

MAGICPAH takes into account the tremendous undiscovered meta-genomic resources by the direct retrieval from genome/meta-genome libraries and consequent characterization of enzymes through activity screens. These screens will include a high-end functional small-molecule fluorescence screening platform and will allow us to directly access novel metabolic reactions followed by their rational exploitation for bio-catalysis and the re-construction of biodegradation networks. Results from (meta-) genomic approaches will be correlated with microbial in situ activity assessments, specifically dedicated to identifying key players and key reactions involved in anaerobic PAH metabolism.

Key processes for PAH metabolism particularly in marine and composting environments and the kinetics of aerobic degradation of PAH under different conditions of bioavailability will be assessed in model systems, the rational manipulation of which will allow us to deduce correlations between system performance and genomic blueprint. The results will be used to improve treatments of PAH-contaminated sites.

PROJECT GOALS:

The main objectives of MAGICPAH in the context of the above are:

i) to generate a knowledge base of the microbial aerobic catabolome with particular relevance to biodegradation of PAHs in various impacted environmental settings

ii) to develop concepts to quantify in situ degradation of PAH employing combined hydrogen and carbon stable isotope analysis

iii) to identify key players and key reactions involved in anaerobic PAH metabolism

iv) to achieve a detailed understanding on key processes for PAH metabolism in marine and composting environments

v) to develop methods to predict the ultimate fate and the kinetics of aerobic degradation of PAH under different conditions of bioavailability

vi) to isolate and sequence novel key players in PAH metabolism to understand the genomic basis of niche specificities that allow microbes to thrive and function in extreme PAH impacted environments

vii) to investigate the potential synergistic links between environmental biotechnology and medical biotechnology by assessing novel biocatalysts for their use in new biocatalytic processes.

viii) to integrate detailed catabolome and reactome information through bioinformatic techniques to re-construct metabolic networks

ix) to apply gathered information to improve the treatment performance of PAH contaminated sites
One of the main limitations of introducing enzymes to the industry is that from the whole set of enzymes available, only a limited number of them have been experimentally characterized, and among them a minority have been shown to possess characteristics likely needed for industrial operations. In this respect, useful features such as broad substrate specificity complemented with high activity levels under a wide range of thermal and pH conditions and salt concentrations, stability in organic solvents and enantio-­? and stereoselectivity, are widely used for defining the potential application of enzymes in biotechnology settings; however, not all characterized enzymes matches these criteria and for this reason investigations related to the identification of enzymes of interest by culture-­? independent methods, namely metagenomic methods, is widely appreciated.

By those methods, genes coding enzymes of interest can be screened from various environments including soils, compost piles, landfill leachate, bioreactors and activated sludges, marine water and sediment samples (including tidal flat sediments, deep sea and water column) and freshwater samples (including drinking water, pond water, rivers and hot springs), to cite some
TThe MAGICPAH Consortium gets ready a set of 24 ready-­?to-­?use clone expression libraries, which can be targeted, for enzyme screening. The total number of available clones is 300,000.

They include:
• 8 phage-­?clone libraries
• 16 fosmid-­?clone libraries

The origin of the libraries is DNA of microbial communities from:
• 14 distinct marine samples
• 10 distinct terrestrial samples

The MAGICPAH Consortium gets ready a set of 1200 clones containing enzyme of interest. They include those encoding the following activities:
• Rieske non-­?heme iron oxygenases
• Laccases
• Extradiol dioxygenases
• Esterases and lipases
• meta-­?cleavage product (MCP) hydrolases
• Glycosyl hydrolases

? The clones available are ready?to-­use in the form of separate individual clones or pool of clones. This may help designing the most appropriate screening platform.
? In deep and/or preliminary biochemical data are available for all clones encoding activities of interest.
? The targets with relevant biotechnologically-­?relevant characteristics are identified. Features such as relevance for biotechnology processes (i.e. production of enantiomerss), salt-­? tolerance, temperature and pH optima and substrate profile are available.
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This innovation is the result of the project

Title: Molecular Approaches And Metagenomic Investigations For Optimizing Clean-Up Of PAH Contaminated Sites

Acronym: 
MAGICPAH

Runtime: 
01.04.2010 to 31.03.2014

Status: 
completed project

Organisations and people involved in this eco-innovation.

Please click on an entry to view all contact details.

HELMHOLTZ-ZENTRUM FUER INFEKTIONSFORSCHUNG GMBH

(Germany)

Role in project: Project Coordination

Contact person: Dr. CHHATWAL G. Singh

Website: http://www.helmholtz-hzi.de

Phone: +495316181 4400

Contact

AARHUS UNIVERSITET

(Denmark)

Contact person: Ms. VILSTRUP Britt Sønberg

Website: http://www.au.dk

Phone: +45-46301337

Contact

AECOM CZ SRO

(Czech Republic)

Contact person: SPISKOVA Vendulka

Phone: +420-283090643

Contact

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS

Field: Scientific research and development (Spain)

Contact person: Mr. ABAD RUIZ Carlos Manuel

Website: http://www.csic.es

Phone: +34-915668852

Contact

BANGOR UNIVERSITY

(United Kingdom)

Contact person: Ms. DAVEY Christine

Website: http://www.bangor.ac.uk

Phone: +44-12483-82136

Contact

COMMISSARIAT A L ENERGIE ATOMIQUE ET AUX ENERGIES ALTERNATIVES

(France)

Contact person: Mr. COPIN Régis

Phone: +33-160872506

Contact

CONSIGLIO NAZIONALE DELLE RICERCHE

(Italy)

Contact person: Ms. IRRERA Gaetana

Website: http://www.cnr.it

Phone: +39-090669003

Contact

CORPORACION CORPOGEN

(Colombia)

Contact person: Mr. DIAZ Luis Fernando

Website: http://www.corpogen.org

Phone: +57-18050102

Contact

DANMARKS TEKNISKE UNIVERSITET

(Denmark)

Contact person: Ms. RASMUSSEN Birte Kastrup

Website: http://www.dtu.dk

Phone: +45-45251687

Contact

HELMHOLTZ-ZENTRUM FUER UMWELTFORSCHUNG GMBH - UFZ

(Germany)

Contact person: Ms. SCHMIDT Annette

Website: http://www.ufz.de

Phone: +49-3412351663

Contact

SYNDIAL SPA - ATTIVITA DIVERSIFICATE

(Italy)

Contact person: Dr. TROVATO Giovanni

Website: http://www.syndial.it

Phone: +39-252032755

Contact

THE GOVERNING COUNCIL OF THE UNIVERSITY OF TORONTO

(Canada)

Contact person: Dr. SAVCHENKO Alexei

Phone: +1-4169784013

Contact

UNIVERSITAET LEIPZIG

(Germany)

Contact person: Mr. FUCHS Gerhard

Website: http://www.uni-leipzig.de

Phone: +49-3419735012

Contact