Vítor Martins dos Santos

Division of MicrobiologyNational 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 Centers25.000 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

ElevatorAileronThrottle

Desired Altitude Aircraft Altitude

Functional Parts Plant

In biological systems, modular control features are hardly known.

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

Time

Infla

m. C

ytok

ines

healthy

variable disease states

variable response to treatment

E.g. Virtual experiment:

The experimental observation is that M. tubercolosis activates the glyoxylateshunt upon infection to switch to lipid metabolism

SPE IVIG

C OO-

Benzoa te 1-carboxy-1,2-cis-dihydroxy-cyclohexa-3,5 -diene

C OO-

OHOH

NA DH 2 NA D

O2+

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:

E4P

X5PGLC

G6P

F6P

FDP

T3P2

3PG

13PDG

T3P1

2PG

PEP

PYR

AcCoA

SuccCoA

SUCC

AKG

ICIT

CIT

FUM

MAL

OA

RL5P

R5P

S7P

D6PGL D6PGC

ACTP

ATP

NADPHNADH FADH

Qh2+

H

pgi1

fba

tpiAgapA

pgk

gpmA

eno

pykAppsAaceE

zwfpgl gnd

rpiA

talBtktA1tktA2

gltA

acnA icdA

sucA

sucCmdh

AC

purT1

pta

ppc

cyoA

pnt1A

sdhA2nuoA

atpA

O2

acspoxB

aceA

eda

2KD6PGedd

maeB

oad

sdhA1fumA

CO2

Pirpe

pckA

glk1

fbp

glcB

AMPATP

2 ADP

adk1

pflA

: unique to PAO1

: unique to KT2440

proteins

Xyl XYZLTEGFJQKIH

 

XylS

a

XylS

i

70

XylS

h

Xyl UWCMABN 

PU

IHF

Pm

  S

Ps1

54

HU

XylRa

xylene

Pr

XylRi

3MB

Genetic circuit

Logic circuit

Inputs Outputs P

r

NORAND OR

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, 3000...

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 2006Broader and more intensive joint work on these subjects beyond PROBACTYSExploration of joint funding possibilities for clearly defined projects (DFG, DAAD, Chinese Ministries??)