Vítor Martins dos Santos

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

2. Research Organizations in Germany • Universities • Helmholtz-Association (HGF) • Max-Planck-Society (MPG) • Leibniz Association (WGL) • Fraunhofer-Society (FhG) 15 Research Centers 25.000 Employees

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

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

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

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

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

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

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

10. B e n z o a t e 1 , 2 - d i o x y g e n a s e - - C O O C O O N A D H N A D O H 2 O H + O 2 1 - c a r b o x y - 1 , 2 - c i s - d i h y d r o x y - B e n z o a t e c y c l o h e x a - 3 , 5 - d i e n e (CDCD) Example: Targeted Development of Biotransformation Processes - precursor for many industrially relevant enantiopure derivatives - difficult to synthesize chemically Attractive alternative: cofactor dependent biotransformation Metabolic engineering

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

12. TOL-on-a-CHIP

13. Genetic circuit GLC E4P S7P X5P Pi glk1 rpe D6PGL D6PGC RL5P CO2 tktA1 talB zwf tktA2 G6P pgl gnd edd pgi1 rpiA 2KD6PG F6P R5P O2 AMP ATP Logic circuit fbp eda + adk1 cyoA FDP proteins H Qh 2 2 ADP ATP fba atpA T3P1 sdhA2 T3P2 nuoA tpiA gapA NADPH pnt1A NADH FADH 13PDG 70 FUM pgk xylene 3MB HU 3PG sdhA1 SUCC XylSa fumA MAL gpmA XylSi Ps1 XylRa mdh XylSh XylRi 2PG maeB glcB Xyl UWCMABN  sucC eno ppc PU Pm Xyl XYZLTEGFJQKIH OA PEP SuccCoA pckA pykA oad ppsA aceA AcCoA gltA aceE sucA IHF S PYR pta pflA CIT 54 acnA AKG ACTP icdA Pr Pr acs poxB : unique to PAO1 : unique to KT2440 purT1 ICIT AC OR NOR Inputs Outputs AND Interplay circuits of interest and genome: Aim is to have a bacterial blueprint that allows precise engineering

14. EU-NEST funded project: PROBACTYS: Programmable Bacterial Catalysts Our Goal is: 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

15. The global work strategy • 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.

16. Beijing Genomics Institutec & James Watson Hangzhou Genomics Institute of the Chinese Academy of Sciences 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, 3000...

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

18. 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??)