Vítor Martins dos Santos Division of Microbiology National Centre for Biotechnology Research (GBF), Germany NEST Pathfinder project on Synthetic Biology PROBACTYS: Programmable Bacterial Catalysts

Research Organizations in Germany Universities Helmholtz-Association (HGF) Max-Planck-Society (MPG) Leibniz Association (WGL) Fraunhofer-Society (FhG) 15 Research Centers Employees

600 Employees 200 Scientists 100 PhD students Yearly Budget: 40 Mill. € (plus 15 Mill. € External) 6 Divisions The GBF

HGF office in Beijing (Head: Mr. He Hong)

GBF Long-term Objectives and Goals Understand basic mechanisms of infection and immunity Develop new vaccines, anti-infectives and immunotherapies

How do we specifically capitalise on this wealth of knowledge and how do we translate it into relevant biotechnological & biomedical applications? Engineering challenge: Exponetial increase in genome sequencing and post-genomic research

Understanding Biology by Reverse Engineering Control: Aircraft Analogy Sensor Controller Feed-Forward Actuators Elevator Aileron Throttle Desired Altitude Aircraft Altitude Functional Parts Plant In biological systems, modular control features are hardly known.

A microbial blueprint: E.g. Central Carbon Pathways:

healthy variable disease states variable response to treatment E.g. Virtual experiment: The experimental observation is that M. tubercolosis activates the glyoxylate shunt upon infection to switch to lipid metabolism SPE IVIG

COO - Benzoate 1-carboxy-1,2-cis-dihydroxy- cyclohexa-3,5-diene COO - OH OH NADH 2 NAD O 2 + Benzoate 1,2-dioxygenase (CDCD) - difficult to synthesize chemically - precursor for many industrially relevant enantiopure derivatives Example: Targeted Development of Biotransformation Processes Attractive alternative: cofactor dependent biotransformation Metabolic engineering

But, this reaction is part of a complex metabolic network and is under control of various interconnected regulatory loops In biological systems, these modular control features are hardly known and blueprints are basically nonexistent

TOL-on-a-CHIP

Interplay circuits of interest and genome: proteins Aim is to have a bacterial blueprint that allows precise engineering

To construct a functioning, streamlined bacterial cell devoid of part (ideally most) of its genome and endowed with a series of highly coordinated, newly assembled genetic circuits for the biotransformation of a range of chloroaromatics into high added value compounds that would include circuits for synchronized behaviour, noise minimisation, low-temperature biocatalysis, among others. By achieving such constructs as a proof-of-principle, it aims at establishing a solid, rational framework for the engineering of cells that can effectively and efficiently perform specific functions of biotechnological, environmental or medical interest EU-NEST funded project: PROBACTYS: Programmable Bacterial Catalysts Our Goal is:

The global work strategy 1)Establishment, standardization and inventory of computational and experimental strategies and platform; 2) Genome minimization (random ; directed),automation 3) Engineering the different genetic circuits of choice (Biotransformation parts list etc.); 5) Assessment of the interplay of constructed circuits with the template genome, intensive computational biology 6) Use of the model framework and constructed cells for the production of high-added value products from halogenated aromatics.

1% human genome Rice genome Chicken genome Pig genome Silk worm genome & various other 6th largest genome sequecing centre in the world Many Prizes including Nikkei Asia Prize for Science in 2003 Dawning 4000, Beijing Genomics Institutec & James Watson Hangzhou Genomics Institute of the Chinese Academy of Sciences

Setting up Strategic Collaborations with Beijing Genomics Institute and James Watson Hangzhou Genomics Institute of the Chinese Academy of Sciences

Collaborative activities with the BGI Current and past: BGI full partner in STREP project on Synthetic Biology (NEST-Pathfinder) BGI full Partner in STREP project proposal in NEST ADVENTURE Visit to the BJI Beijing & Hangzhou January 2006: Meeting with EU Minister Councellor for Research in Beijing Meeting at Sino-German Science Foundation Bilateral agreements, preparative collaborative work undergoing on Computational, Automation and Sequencing aspects Planned: Sino-German Workshop on Synthetic Biology in Hangzhou, October 2006 Broader and more intensive joint work on these subjects beyond PROBACTYS Exploration of joint funding possibilities for clearly defined projects (DFG, DAAD, Chinese Ministries??)