TARPOL

Targeting environmental pollution with engineered microbial systems à la carte

Acronym: TARPOL

Coordinator

Prof. Andrés Moya, Universitat de Valencia - Estudi General (UVEG) (Spain)

Contact Person

Dr. Andrés Moya
Instituto Cavanilles de Biodiversidad y Biología Evolutiva
Universitat de València
Apartado Postal 22085
46071 - Valencia, Spain
e-mail: andres.moya[at]uv.es
tel:(+34) 96 354 3480

Partners

Universitat de Valencia - Estudi General (UVEG) (Spain)
Helmholtz-Zentrum fuer Infektionsforschung GmbH (HZI) (Germany)
Consejo Superior de Investigaciones Científicas (CSIC) (Spain)
Institut Pasteur (IP) (France)
Universidad Politécnica de Valencia (UPVLC) (Spain)
Université de Lausanne (UNIL) (Switzerland)
Universita’ degli Studi di Milano (UMIL) (Italy)
Geneart GmbH (GA) (Germany)
Centre National de la Recherche Scientifique (CNRS) (France)
Universita’ Ca’foscardi di Venezia (UNIVE) (Italy)
Biological Research Centre (BRC HAS) (Hungary)
Fundación Centro Nacional de Investigaciones Oncologicas Carlos III (CNIO) (Spain)
Commissariat a L’energie atomique (CEA) (France)
Organisation for International Dialogue and Conflict Management (IDC) (Austria)
Centre National de la Recherche Scientifique (CNRS-ENS) (France)
Eidgenöessische Technische Hochschule Zuerich (ETH-Zurich) (Switzerland)
The Imperial College of Science, Technology and Medicine (IMPERIAL) (United Kingdom)
Bauer Umwelr GmbH (BU) (Germany)

Project Description

Synthetic Biology deals with the rational combination of biological properties with central elements of engineering design. We argue that by merging the genetic tool box already available with disciplines such as electrical, mechanical, or chemical engineering and computer sciences, there is an extraordinary opportunity to take a fresh approach to longstanding environmental pollution problems through a vigorous application of modelling techniques and organizing the development of novel biological (e.g. catalytic) systems along a hierarchical architecture with defined and standardized interfaces. However, this endeavour faces 3 major bottlenecks that this Coordination Action attempts to overcome: [i] The scientific and technical communities of european contributors to the application of SB to environmental issues (i.e., Environmental Biotechnologists, Bioinformaticians and experts on the Origin-of-Life subject) have so far failed to recognise their latent capacity to shape a fresh discipline at their very interface, [ii] The new field still misses a comprehensive language and a shared conceptual frame for description of minimally functional biological parts (specifically dealing with catalytic properties and regulatory circuits) and [iii] The development of the SB field touches upon social sensitivities related to recreating life-in-the-test-tube, which threats with a re-enactment of the controversy on GMOs and thus it worries off the needed industrial ease in the field. To tackle all these challenges, TARPOL proposes a dynamic 2-year programme of activities, run by a large collection of stakeholders in the field and aimed at coordinating the so far fragmented efforts to direct this emerging discipline into the most industrially beneficial and socially viable directions.

Publications

V Barbe, S Cruveiller, F Kunst, P Lenoble, G Meurice, A Sekowska, D Vallenet, TZ Wang, I Moszer, C Médigue, A Danchin
From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later
Microbiology (2009) 155: 1758-1775    

This article describes the re-sequencing of the Bacillus subtilis genome. It is dedicated to the memory of Frank Kunst, who was instrumental in the whole B. subtilis genome project, victim of an unjust law which forces active scientists to retire, without any consideration for their contribution to creation and diffusion of knowledge.

Cet article rapporte le reséquençage du génome de Bacillus subtilis. Il est dédié à la mémoire de Frank Kunst, sans qui le projet n'aurait jamais pu être mené à son terme en 1997. Frank Kunst a été victime d'une loi inique qui force les chercheurs encore actifs à cesser leur activité sans aucune considération de l'apport qu'ils peuvent avoir à la création et la diffusion du savoir.

In memoriam Frank Kunst, let us remember that, when the article reporting the first complete sequencing of the genome appeared in 1997, Chet Raymo, for the Boston Globe wrote (january 5th, 1998): Beauty bare on the spiral staircase […] « Euclid alone has looked on Beauty bare, » wrote the poet Edna St. Vincent Millay. Here, in this exquisite geometrical molecule [DNA], we look on Beauty bare. I felt the same response recently when I looked at a schematic map of the complete genome (genetic material) of the bacterium Bacillus subtilis in the journal Nature. […] I was looking at the gene map for Bacillus subtilis in the college library, with the 8-page foldout spread across a table. Several students stopped to look over my shoulder, curious as to what the colorful chart might be. « This is the blueprint for making a living organism, » I said. I started to provide a more complete explanation, but fell silent. The map spoke for itself. Elegant. Simple. Unfathomably profound. Beauty bare.

A Danchin
Cells need safety valves
Bioessays (2009) 31: 769-773 

In Escherichia coli, the role of lacA, the third gene of the lactose operon, has remained an enigma. I suggest that its role is the consequence of the need for cells to have safety valves that protect them from the osmotic effect created by their permeases. Safety valves allow them to cope with the buildup of osmotic pressure under accidental transient conditions. Multidrug resistance (MDR) efflux, thus named because of our anthropocentrism, is ubiquitous. Yet, the formation of simple leaks would result in futile influx/efflux cycles. Versatile modification enzymes with low sensitivity solve the problem if the modified metabolite is the one exported by MDR permeases. This may account for the pervasive presence of acetyltransferases, such as LacA, associated to acetyl-metabolite exporters. This scenario of constraints imposed by efficient influx of metabolites provides us with a model that should be followed when constructing synthetic cells

A Danchin
Information of the chassis and information of the program in synthetic cells
Syst Synth Biol (2009) 3(1-4):125-134 

A Danchin
Myopic selection of novel information drives evolution
Curr Opin Biotechnol (2009) 20: 504-508 

MF Liu, S Cescau, U Mechold, J Wang, D Cohen, A Danchin, HJ Boulouis, F Biville
Identification of a new nanoRNase in Bartonella
Microbiology (2012) 158: 886-895