Synthetic biologists make their mark in EU

Synthetic biologists from the University of Groningen play an important role in two of the three large grants awarded in this field under the EU’s Seventh Framework Programme (FP7). Oscar Kuipers and Matthias Heinemann will each receive EUR 1 million. Heinemann’s proposal took first place and Kuipers’ came second.

New peptides, new antibiotics

Professor of Molecular Genetics Oscar Kuipers is participating in the SYNPEPTIDE programme, the aim of which is to produce synthetic peptides, with a special emphasis on creating novel antibiotics. Kuipers: ‘In the last 20 years or so no really new antibiotics have been developed. As bacteria become resistant to the existing antibiotics, we may reach a point where many infections are untreatable.’

The European consortium of which Kuipers is a member will use different techniques to try to develop novel synthetic peptides (short proteins). Peptides are normally a combination of 20 different amino acids. Kuipers: ‘These are the naturally occurring amino acids, but there are many more, and these can also be incorporated into a peptide.’ Such ‘unnatural’ amino acids can be used to make these novel peptides.

Kuipers’ group will focus on a second approach: the modification of natural and new-to-nature peptides. ‘We can change them at will, so that they form rings in the peptide structure.’ These ‘lanthipeptides’ are more resistant to degradation, but they may also exhibit novel antimicrobial activity.

Kuipers is building on research he performed decades ago in the food industry on the antimicrobial peptide nisin. ‘This peptide is used as a food preservative, but modified versions of it are potential antibiotics.’

Kuipers will receive around EUR 1 million for his part of the SYNPEPTIDE project. ‘We will have several postdocs working on it over four years.’ A biotech company from Groningen, Lanthio Pharma, is also participating. ‘They specialize in modifying bioactive peptides with lanthionine bridges.’

Two research groups from ETH Zürich will lead the project, but after them Kuipers’ group is the largest. ‘The Zürich team have a very good screening tool to evaluate antimicrobial peptides’, Kuipers explains. ‘We can screen millions of modified peptides in a very short time.’

Kuipers’ group will also transfer gene clusters from sponge microbiota that produce potentially interesting antimicrobial peptides to bacteria. ‘We will add these clusters to Lactococus lactis, our workhorse, and make new variants of the sponge-microbiota genes.’

The strength of the European proposal is that it aims to make and screen modified peptides on a very large scale. But the road from an interesting lead compound to a tried-and-tested new antibiotic is a long one, Kuipers warns: ‘It takes about ten to twenty years to get from a promising compound to the market’.

Taming evolution

‘We’re making cells produce what we want, using the power of evolution.’ This is University of Groningen synthetic biologist Matthias Heinemann ’s brief summary of the EU project he is working on. Like his colleague Oscar Kuipers, he will also receive EUR 1 million, this time for his role in PROMYS, as the project is known.

‘Microorganisms can produce useful compounds’, is how he begins his more detailed explanation. ‘But if you find one that makes what you want, you have to engineer it to make it more productive, and adapt it to do so in industrial fermenters.’ These steps are quite laborious, which is why Heinemann and his co-workers have opted for a different approach.

‘Once we have a microorganism that makes a useful product, we will generate a lot of different mutants carrying an engineered synthetic selection system that will “reward” those mutants that have high concentrations of the desired compound or “punish” those mutants that are performing badly.’

The proposed system uses what are known as riboswitches . These are strands of RNA which can recognize a ligand. Once it is bound to such a product, the riboswitch responds in a specially engineered way to give the cell a growth advantage

In this way, bacteria that produce the right content are selected during growth. To select cells that produce lots of the wanted product at high rates, Heinemann will develop a ‘metabolic flux’ selection. ‘We have recently proposed that cells can actually measure the metabolic rate in certain pathways and respond to it.’ Heinemann wants to exploit these flux-sensing mechanisms to tell him which cells make the desired product at a high rate.

Once everything works, bacteria fitted with synthetic selection systems will generate offspring that produce a specific compound at high rates. ‘We therefore harness evolution to engineer the right pathways we need. The advantage of this system is that you only have to grow a large bank of mutant bacteria, and the right cells get selected automatically.’ Of course, evolution is also a risk factor. ‘The cells could evolve in such a way that they circumvent the selection process.’

The project won first place in the synthetic biology call. What makes it so special? Heinemann: ‘We proposed a highly innovative approach, which at the same time has high potential for high impact. That is a rare combination.’

From berry to bacteria

Oscar Kuipers is involved in a second European project, the BACHBerry consortium, which will try to isolate the genes that make healthy organic molecules in different types of berries. ‘There are a host of compounds in berries, such as tannins or polyphenols, that have a proven effect on our health’, Kuipers explains. It is difficult to extract these compounds from the berries in a pure form, and it takes a long time and a lot of space to grow them.

Which is why the project aims to isolate the genes that are responsible for the production of these compounds. ‘We will isolate the gene clusters that make up the entire metabolic pathway and transfer this to a “cell factory”, a bacterium that will express the genes and make the compound.’ It will require quite a bit of tinkering to make plant genes work properly in a microorganism.

This is not all, however; the process will also make it possible to check the plant genomes for ‘hidden’ gene clusters that are not active under normal circumstances. ‘If you simply look at the compounds a plant makes, you could miss gene products that respond to, for example, stress. By looking at the genome, we can recognize potentially interesting gene clusters.’ This FP7 project, which was not part of the Synthetic Biology call, will secure Kuipers’ group about EUR 300,000.