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Creating efficient cell factories

Synthetic biology is a new approach to improving the performance of industrial microorganisms on a larger scale by designing and building in new functionalities. Flagship 6 of BE-Basic will focus in the coming years on increasing the production and excretion of compounds and improving the cell robustness through membrane engineering.

Prof. Bert Poolman of the University of Groningen: ‘Within the Synthetic Biology Flagship, we aim to improve some of today’s most important production organisms – namely the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli – so that they are better equipped to produce all sorts of compounds.’ Synthetic biology is especially suited to reprogram metabolic pathways and give the cell new functionalities. ‘We can build on existing knowledge of the cell machinery of these two production organisms, so there’s a good chance that we can be successful and take large steps forward in building efficient cell factories.’ Scientists from the universities of Groningen, Delft, Wageningen and Utrecht together with their industrial project partner DSM are collaborating on the engineering of metabolic pathways for amino acid production and the performance of membrane functions

Membrane mysteries

A major part of the programme is dedicated to the cell membrane (the outer shell of a cell), primarily in order to get it to excrete more of the substances the cell produces. Poolman: ‘You could say that biological cells are designed to take up substances from their surroundings, but not to excrete their products. For a more efficient production we have to persuade them to excrete solutes by, for instance, reversing the transport reactions.’ In the coming years, Poolman’s research group will focus on this, while Delft scientists try to improve the production of amino acids inside the cell. Most products that are of interest for a bio-based economy – such as alcohols for biofuels, or fatty acids – are toxic to cells because they dissolve well in the cell membrane. Poolman: ‘In practice, this means that the cell membrane is disrupted, and that is usually detrimental to the cell factory. But if you can change the membrane properties in such a way that the products hardly dissolve, you will have gained a lot. For instance, butanol at a concentration lower than 1% is already lethal to E.coli, but there are cells that can tolerate much higher concentrations. We aim to find out how they do this and we will evolve E. coli to become more tolerant to this type of solvent.’

Making robust cells

One approach is a computational method. Cell membranes are exposed to a large library of different compounds to determine the basis of their toxic effect. Poolman: ‘Then we determine whether the toxic effect can be reduced by changing the lipid composition of the membrane. If you find that a certain lipid composition performs better in the computer, then you have a lead for making the corresponding changes in the cell.’ This requires the insertion and expression of the genes for the corresponding pathways into E. coli. This approach will be a joint effort by research groups at Groningen and Wageningen. ‘Groups in Utrecht that are experienced in lipid analysis and engineering will find out what the differences are in evolved industrial strains, and use this information to rationally engineer the membrane system. We hope that a comparative study with different strains will provide a clue as to why these organisms can cope with toxic cell products.’ Most of the technologies that the consortium is going to develop will be generic. Poolman: ‘Our first goal is to make cells that are more robust; the actual application can be added later. For now, the proof-of-principle is the most important.’

Started

January 2010

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  • Delft University of Technology
  • BioDetection Systems B.V.
  • Bioclear earth
  • Food & Biobased Research
  • VU University Amsterdam
  • Netherlands Institute of Ecology (NIOO-KNAW)
  • Corbion Purac
  • Utrecht University
  • Maastricht University
  • Synthon
  • DSM
  • Microdish BV
  • Wageningen UR
  • AkzoNobel
  • Deltares
  • MESA+ Institute for Nanotechnology
  • University of Amsterdam
  • University of Groningen
  • Radboud University Nijmegen
  • TU Dortmund
  • Karlsruhe Institute of Technology
  • Microlife Solutions
  • Essent New Energy B.V.
  • Amyris, Inc.
  • Imperial College London
  • ClearDetections
  • Soil Cares Research
  • Dyadic
  • Friesland Campina
  • Delft Advanced Biorenewables
  • Basidiofactory
  • Chr. Hansen
  • NIZO food research B.V.
  • Tertium
  • Stichting Natuur en Milieu
  • ECN
  • Leiden University
  • Platform Bio-Energie
  • CSK Food Enrichment
  • Bioprocess Pilot Facility
  • SkyNRG
  • Zirk Technology
  • Procede Group
  • ChainCraft
  • Deltalinqs
  • GEVO
  • Sweco
  • Proteonic
  • Goodfuels
  • Groen Agro Control