Innovative Enterprise Week 2019

Over the course of three days – 19, 20 and 21st of June 2019 – the conference focused on topics and challenges for the next EU Research and Innovation Programme (2021-2027) – Horizon Europe as well as on the European Innovation Council, a very powerful instrument foreseen to strongly support European “breakthrough innovators”. The event was co-organised by the European Commission, through DG CONNECT and DG RTD, together with the Romanian Presidency of the Council of the European Union. The aim was to debate about how to bridge the gap from idea to investable project, how to support breakthrough innovations and the scale-up potential with high risk for private investors. Our partner IN was there with a booth in the exhibition area to promote the innovation proposed by the FutureAgriculture approach.

Metabolic Engineering in Plants: From Design Concepts to Applications

The Plant Metabolic Engineering GRC was held for the first time in Europe, at the Renaissance Tuscany, Il Ciocco, Italy between June 16th and June 21st, 2019. The objective was to build stronger networks between those working on plant metabolic engineering in the USA, Europe and Asia. The meeting provides an exemplar ground for innovative research networks to blossom thanks to a collegial atmosphere, deep discussion sessions, and informal gatherings. Personnel from MPI-TM was there to represent the project FutureAgriculture.

EMBL Conference Biological Solutions for the Global CO2 Challenge

The conference, hosted in Heidelberg (June, 3-4), covered the entire chain of innovation, from the laboratory to the field implementation: approaches that make optimal use of the evolutionarily optimized biological systems, like algae and plants, as well as novel synthetic biology solutions for CO2 fixation and conversion to value-added chemicals. The role of fundamental molecular biology in catalyzing innovation was one of the main focus areas for discussion. Partners from MPI-TM attended the event with posters and talks.

See them growing!

Evogene is currently growing and testing the FutureAgriculture plants in its greenhouses under two conditions (normal and drought) with the final aim of validating their growth-advantage.

To evaluate the pathways in vivo, scientists at Evogene have established a set of molecular and phenotypic experiments.  Molecular parameters are tested to ensure the presence of the FutureAgriculture pathway inside the plant’s DNA and its correct expression. Phenotypic parameters are monitored to check the health and growth of the plant, e.g its general appearance, the efficiency of the photosynthetic systems, the biomass, etc.

The results obtained from previous stages of FutureAgriculture were essential for the selection and optimization of potential pathways to be inserted into higher plants. However, higher plants are more complex and differ from the bacteria used until now (E. coli and cyanobacteria). The preceding tests gave a general direction as for what to expect in the engineered plants; therefore, the whole Consortium is eager to see them growing.

Gene transfer into plants: exploiting a pathogenic machinery

In FutureAgriculture, Evogene is responsible for the pathway implementation in higher plants and phenotype characterization. First, they have selected the best sequences to implement the new pathways in vivo based on the results obtained by the other FutureAgriculture partners in silico and in vitro.

Then, in order to insert the necessary components into plants, Evogene takes advantage of the pathogenic machinery of Agrobacterium tumefaciens (A. tumefaciens). In nature, A. tumefaciens is a bacterium responsible for the crown gall disease in many dicot plants: a small segment of its plasmid DNA moves from the bacterium cell into the plant genome and causes the disease. Scientists have succeeded in deactivating the pathogenic machinery and use it to insert desired DNA pieces into dicot plants instead, and later into monocot plants too. The sophisticated machinery of A. tumefaciens is the basis of many scientific studies carried out today in plants as well as of Evogene’s ability at FutureAgriculture to transfer the new metabolic pathway genes into the model plants.

 

The long-standing experience of Evogene with plant transformation has allowed them to precisely calibrate many parameters, thus mitigating potential difficulties. In the case of B. distachyon, Evogene has even developed unique proprietary transformation protocols for high throughput gene screening.

Nevertheless, some unexpected challenges can still occur during the process. Sometimes even if the gene is correctly transferred into the plant and enters its genome, it doesn’t get expressed, meaning that the plant has silenced it for some unknown reasons. Other difficulties are related to low transformation rates, but internal know-how helps to solve them.

Even if no obstacles arise during the process, it still takes several months from the initial transformation to the first results on the pathway performance in planta. The process takes more time in B. distachyon (up to one year), comparing to A. thaliana (up to six months), due to the transformation method.

Model plants can take us one step closer to better yield productive crop plants.

In FutureAgriculture, Evogene has chosen to work with two different model plants; Arabidopsis thaliana (A. thaliana) and Brachypodium distachyon (B. distachyon). Together they represent two major types of crop plants: A. thaliana is a model for widespread dicot crops like soybean, tomato, potato, lentil and peanut; whereas, B. distachyon for important monocot crops such as rice, corn, wheat, barley and oat.

Similarly, to animal models, model plants are an ideal ground for testing initial hypothesis rapidly and with high certainty. Compared to crop plants, they are characterized with shorter life cycles, smaller-sized plants and a simpler genome; all features that speed up and simplify the scientific process. Indeed, working with model plants allows scientists to perform a large number of experiments at a relatively low cost while gaining valuable knowledge and process understanding before moving to more complex crop plants.

Another powerful tool of A. thaliana and B. distachyon, is their known genetics. A. thaliana was the first plant genome to be fully sequenced (and the third multicellular organism). Ten years later, in 2010, the genome of B. distachyon – double of the size of A.thaliana’s genome – has been sequenced and published. The knowledge of the plant DNA is a fundamental prerequisite for the success of the FutureAgriculture project as it encodes useful information on the metabolic pathways. The pathways selected in FutureAgriculture are composed both from bacteria genetically modified enzymes as well as plant native ones. Without knowing the enzymes involved in the native network of the plant, it would have been almost impossible to establish a new pathway there. Through new discoveries and insights from the model plants we can take one step closer to better yield productive crop plants.

Workshop at the ICT Day – “Mind the Gap”

We’ve concluded 2018 with the exciting networking event MIND THE GAP, organized by our partner IN S.r.l at the last ICT Day in Vienna, Austria, on 4 December 2018. The goal was to find a common language between science and business to foster innovation.

The hot topics of our panel discussion were about the common struggles of scientists approaching business, the role of venture capitalists in this ecosystem, the best strategies to bridge the gap between early-stage disruptive technologies and the creation of successful start-ups.

Four speakers were invited to confront significant questions:
VIOREL PECA, Head of Unit Future Emerging Technologies – DG CONNECT, European Commission;
LORENZO MORETTI Associate and Venture Capital Investor Invitalia Ventures SGR;
HAROLD P. DE VLADAR CEO of Ribbon Biolabs and Synthetic Biologist;
ANDREA ZORZETTO Managing Partner, Italy Plug & Play

Sustainability: where are we today? The view of Patrik Jones.

Patrik Jones is the group leader of the Microbial Metabolic Engineering lab at the Imperial College London. His lab aims at engineering metabolic solution to convert CO2 into biomass and other sustainable chemicals that can replace less sustainable products. We asked him to share his point of view on sustainability.

“A major problem in sustainability today is that we still rely on fossil fuels for most of our human activities. A major leap will only happen if we fully replace fossil fuels with alternatives that match different points of view: the financial feasibility, the long-term sustainability for the environment, the energetic return and the efficient use of resources.

As of today, fossil fuels are still the cheapest option compared to biofuels from cyanobacteria or other microorganisms. The production of biofuels is technically feasible but not financially competitive. In some cases, it also competes for valuable resources, such as agricultural land, water and nutrients, and therefore, we need to carefully design future biofuel production systems so that they can be sustainable in all dimensions, incl. financial, energetic and environmental.

As a palliative, commercial biotechnology is currently focused on the production of other more valuable products for which no cheap alternatives exist e.g. fragrances, food additives, pharmaceuticals, etc.

But, the real problem, the fossil fuels, remains. We have got used to low fuel price tag as it doesn’t include the indirect costs of fuel production and consumption on society and on the environment. To quantify in money the impact of pollution and climate change on society it’s hard but if we don’t, we lose the other side of the coin.”

FURTHER READINGS:

Factfulness- Hans Rosling

Climate change and the 75% problem – gatesnotes.com – Bill Gates

The real cost of energy – Nature – Erica Gies

IMF: ‘True cost’ of fossil fuels is $5.3 trillion a year – pri.org – Adam Wernick

The challenges of introducing the synthetic pathway into cyanbacteria

Introducing new genes into cyanobacteria is quicker than into plants but not as quick as one might expect. For example, the bacteria E. coli can be transformed overnight. The same process for cyanobacteria takes up to 1 month, instead. Its timing is extended because cyanobacteria are polyploid – they have multiple copies of their genome – and a process called segregation needs to happen to ensure that the new DNA propagates in all the copies.

Further care is needed when introducing a complex pathway in cyanobacteria: “We can’t introduce all the necessary genes at once, as there are too many,” explains Patrik, “Therefore, we do it in a stepwise manner: we start from a group of enzymes that operates at the end of the pathway and move forward”. This trick avoids the production of potentially harmful intermediates that otherwise could impair cell growth. “After one month of waiting, there are still chances that the strain rejects the new DNA and we might have to start all-over” warns Patrik, “Still, this method is way faster than the several months needed to generate an engineered plant”.

Evaluate the synthetic photorespiration pathways in vivo

FutureAgriculture uses cyanobacteria to evaluate the in vivo behaviour of the synthetic photorespiration pathways. Their quick life-cycle and simpler compartmentalisation make cyanobacteria an ideal model organism to work with before moving into plants.

At the laboratory of Patrik Jones at the Imperial College London, scientists evaluate the pathways in a very comprehensive way, addressing their impact on carbon fluxes, metabolism and cell growth: “We study the carbon flux by following the journey inside the cell of carbon atoms taken up during photosynthesis. The CO2 absorbed by the cell contains the carbon isotope 13C, distinguishable in our analytical machines over time. After only 20 seconds we are ready to follow the isotope through its metabolic steps in the natural and synthetic pathway.”

The technique is not trivial as the resulting data need an elaborate computational analysis to be interpreted correctly. But it helps to assess if and how the synthetic pathways are replacing the natural photorespiration pathways, and it might even provide some answers on the role of natural photorespiration.

Cyanobacteria: who are they?

Who would have known that a tiny unnoticeable organism as a bacterium would be the father of photosynthesis? Plants have taken their ability to convert solar energy into chemical energy from cyanobacterial-like organisms, which ultimately became the chloroplasts in plant cells. Today, cyanobacteria, sometimes referred to as prokaryotic algae, live in a wide variety of environments: moist soils, seawater and lakes, and they still retain the ability to perform photosynthesis. Actually, their efficiency per area of land is even higher than plants.

Like plants, cyanobacteria carry out the detoxifying process called photorespiration to recycle 2-phosphoglycolate (2PG), the toxic side-product of carbon fixation. Unlike plants, they have not one but three photorespiration pathways. “This is quite surprising,” explains Patrik Jones from the Imperial College London, “Cyanobacteria have already a carbon concertation mechanism that elevates the amount of CO2 near the active site of Rubisco.” This strategy should minimize the need for photorespiration, since, if Rubisco has better access to CO2, the production of 2PG is lowered. “It is commonly thought that photorespiration is negligible in cyanobacteria. However, when cyanobacteria lose the ability to carry it out, their growth is impaired.” Indeed, as part of the FA studies, the Jones group is also trying to further our understanding of photorespiration in cyanobacteria.

Patrik’s lab uses cyanobacteria as a tool to evaluate the synthetic pathways developed within the FutureAgriculture project and that have been designed to increase the yield of crop plants. “If we could improve the growth of cyanobacteria as well, this would also have positive consequences, as we might even rely directly on them for food” suggests Patrik. “They are extremely good in making proteins: in some strains, proteins account for more than 50% of their dry weight. Few food-sources can boast such a high protein content.” Actually, we already eat cyanobacteria – one example for all, the super-food Spirulina. Get ready, soon cyanobacteria might be part of our diet.

4th Applied Synthetic Biology in Europe

The 4th Applied Synthetic Biology in Europe took place from 24th to 26th of October 2018 in Toulouse. The wealth of applied synthetic biology research was explored, covering diverse product and application areas and utilizing biological systems from bacteria through yeast to plants and mammalian cells. Partners from MPI-MP were there to present the work developed within FutureAgriculture.

EUSynBioS Symposium

The third EUSynBioS Symposium was organized in the biotech hub in Toulouse, France bringing together the young European synthetic biology community. The symposium took place in October 2018 right before the main conference “4th Applied Synthetic Biology in Europe”. Our Phd Student, Armin Kibin from MPI-MP, was there to represent the project.

 

New Scientist Live 2018

FutureAgriculture was at the New Scientist Live 2018 –  an award-winning, mind-blowing festival of ideas and discoveries for everyone curious about science and why it matters. For 4 days in September, more than 120 speakers and 100 exhibitors come together in one venue to create an unrivalled atmosphere and energy, packed with thought-provoking talks, ground-breaking discoveries, interactive experiences, workshops, and performances. We were at our stand in the Earth zone with a puzzle game about the role of photorespiration in plants and the fun activity “Smell the Future” organized by our partners from Imperial College London.  We got so many enthusiastic feedback about the project, thanks to all of you that came to visit us.

 

GASB II Conference

The German Association of Synthetic Biology GASB II Conference took place in Berlin in 2018 (. After a successful GASB I conference with more than 100 participants, 26 scientific talks, a panel discussion, and a poster session, GASB II continued in a similar fashion. Partners from MPI-MP attended the event.

CPSC PhD Summer School on Synthetic Biology 2018

Our PhD student, Armin, from MPI-MP, attended the summer course  “Synthetic Biology: From Pro- to Eukaryotic Systems (SynBioSys)”. The course aimed at a well-rounded presentation of synthetic biology through the discussion of selected topics across the DNA-RNA-protein-metabolite spectrum. The academic discussions were complemented by a discussion on intellectual property rights and a visit to the local industry. The course was organized by the Copenhagen Plant Science Centre from 20 August – 24 August 2018.

The 1st European Conference for Photosynthesis Research

ePS-1, organized under the auspices of the International Society for Photosynthesis Research, is held in Uppsala, Sweden during the last week of June. ePS-1 covers all aspects of photosynthesis, from genetics and molecular mechanisms, to crop yields, artificial photosynthesis and solar fuels. Our partner Jan Zarzycki was invited to give a talk at the  Metabolism and Metabolic Engineering session.

Canada Protein Engineering Conference 2018

The third edition of the Protein Engineering Canada (PEC) Conference was held at the University of British Columbia (Vancouver, BC, Canada) between June 17-20, 2018. The goals of the PEC Conference are to bring together leading experts in the fields of protein engineering, evolution and design, and structural and synthetic biology, to present their latest findings and develop a strong network throughout Canada and abroad. Among the invited speakers Dan Tawfik, our partner in FutureAgriculture.

Annual Conference 2018 of the Association for General and Applied Microbiology

The Annual conference of the Association for General and Applied Microbiology (VAAM) is an innovative and internationally recognized platform for all microbiology fields that promotes the scientific exchange and cooperation between its members.  The spectrum of presentations and discussions on the meeting includes biodegradation, fungal biology, synthetic microbiology and many more. The MPI-TM team was present at the meeting to provide an insight into their current research work for FutureAgriculture.

INTERVIEW TO TOBIAS ERB ON THE FUTURE OF… SYN BIO!

The National Academy of Sciences in Germany have selected artificial photosynthesis as one of the key technologies to keep an eye on. Tobias Erb was part of the working group that aimed at evaluating the state-of-the-art of this technology and its future perspectives. We asked him to summarize this experience for us.

T: Over the last two years, I was part of the group of experts, coming from different disciples (biology, physics, chemistry, material sciences, etc), that analysed the state of the art of the artificial photosynthesis for the German Academy of Sciences. The field is actually vast, it includes projects like Future Agriculture, in which synthetic biology is used to improve the natural photosynthesis, and others that try to mimic the basic principles of photosynthesis by combining chemical catalysts with photovoltaic elements.

We have been asked to imagine what we could achieve with this technology in the next ten, twenty, and thirty years, respectively, and what it will require to move the field forward.  We all agreed that synthetic biology is an important technology in developing synthetic photosynthesis. There is an innovative and disruptive potential in synthetic biology and thus it is important to keep the vision up and going. Some projects are very risky, like FA, as there is no sure outcome. However, you need to push the limits of technologies and see what it is achievable –  that’s why national and Europe projects are fundamental to keep the disciple up and running.

What is so disruptive about synthetic biology now?

T: In Synthetic Biology, we build something new by recombining biological parts. We can implement very refined and rational changes to build something that Nature has not invented yet, following our intuition. The evolution of the discipline doesn’t differ from what happened in other fields too. Chemistry, for example, started by studying the building blocks of matter i.e. elements, atoms etc. Then it moved forward to synthetize new compounds using the same building blocks. And that’s how we ended up with modern textiles, colours, drugs – and an entire range of new materials that are non-natural but commonly used.

That’s exactly what it is happening now in biology: we started by studying the building blocks of the biological material: enzyme, cells, DNA, etc. Now we can use them to synthetize something new with the additional advantage that biological materials are self-optimizing and environmentally sustainable compared to chemistry.

What the future holds for synthetic biology?

T: The market potential for synthetic biology is estimated at around 38 billion euros for 2020; it will be a key technology in the near future and there is no way to skip this. Nowadays you can look up gene sequences in public databases, use modeling software to make predictions how this gene will perform in the context of a cell and you can order the gene for little more than 100 euros online. Prices will probably drop even more and it’s going to be easier and cheaper to use this technology.

At this point we are witnessing the merge between information technology and biology – as scientists, we aim at developing future technologies but citizens and policymakers are the ones that will decide if and how these technologies should be used. This is still an ongoing process because we need to make sure that the technology is feasible, safe and accepted by people. For that, we need to openly communicate throughout the entire process. It’s important that citizens realize that they are part of the decision process and that scientists are listening to the needs and fears of people. Facts and evidence work well in science but to create a fruitful discussion between science and society the best strategy is listening.

High-throughput improvements

So far, to improve enzyme efficiency only the active site has been taken into account. However, parts that are far away from the active site can still affect the reaction. The further away from the active site, the less predictable it is what will happen by modifying that part and therefore the rational thinking alone won’t help much anymore. The FutureAgriculture team is now using high-throughput mutagenesis to expand the modifications and cover the entire structure of the enzyme.

Lately, some 10.000 variants of the same enzyme have been created and are currently analysed thanks to a novel high throughput method established in collaboration with external partners in Bordeaux that are not part of the consortium. The method consists in creating very small droplets, in the order of 50 picoliters, containing several thousand copies of a modified enzyme. The enzyme activity in the droplets is then tested very quickly with lasers: 200 droplets are processed per second – which means that in only 5 minutes 60.000 enzyme variants can be tested!

This droplet screening method developed some years ago, relies mainly on sensitive instruments with custom setups adapted to each system. To that end the partners at MPI-TM teamed up with Jean-Christoph Baret at the University of Bordeaux who is an expert in placing the enzymes in small droplets, sorting the good drops from the bad ones and assaying the enzyme activity.

As explains Tobias Erb “Among the variants that we are currently testing we are hoping to find a faster and more specific variant of the key-enzyme of the carbon positive pathway, a new CO2 fixing enzyme.  Once we find an improved version, we are going to test it again in the in vitro metabolism and hopefully, it will improve the plant metabolism even more.“

Building a winning team of enzymes

Once identified the best enzymes, it’s time to study them in their context: the carbon positive CO2 fixation pathway. “We want to make sure the enzyme can work well as a team. It’s like in football, you might have great individual players but to score you need a good teamwork, too. Sometimes it makes sense to take out one of the best players and substitute with another option because it interacts better with the rest of the team” explains Tobias Erb (MPI-MP).

To test the interplay of the individual enzymes, the CO2 fixation pathway is first recreated in vitro: a small vessel containing all the ingredients necessary to the pathway i.e. the individual enzymes, the chemical energy (ATP) and its reducing equivalents (NADPH), other cofactors that help the enzyme to exert its function, and a buffer that mimics the cell environment.

The pathway performance is then quantified by measuring the variations in the concentration of the ingredients. This is done by using highly sensitive mass spectrometers that can accurately quantify the amounts of substrates, intermediates and other metabolites for all the reactions that are happening in the vessel.

The team of FutureAgriculture has already tested in vitro the effect of the newly designed pathway onto the CO2 fixing-machinery of the plant. The outcome was extremely encouraging as the pathway showed a beneficial effect on the plant metabolism. This is the very first proof of principle that the pathway is able to improve plant metabolism in the lab condition, and that the pathway if transplanted in vivo has the potential to positively affect plant growth.

Making enzymes more efficient

“It’s not enough to find an enzyme that can perform a reaction; the enzyme needs to be sufficiently active too” explains Tobias Erb, group leader and director of the MPI-TM in Marburg.
That’s why the partners at the Weizmann Institute and MPI-TM have worked hard to improve the identified enzymes and make them more efficient.

The method used by Erb’s lab starts by looking at the crystal structure of the enzyme – a 3D dimensional model with the position of the atoms. On that model point mutations can be made, usually by modifying the amino acids in active site – where the reaction takes place – to have a positive effect on the enzyme’s efficiency. The changes are not random but according to the scientist’s chemical logic and rational thinking. Two outcomes are important to be achieved:

  • A fast enzyme: The faster the enzymes the higher will be the impact on plant growth. If the speed of the enzyme reactions is high then the metabolism of the plant will be very active and can operate with high CO2 fixation efficiency. Thanks to the computer modelling of the photosynthesis developed by the partner at MPI-MP (LINK), the threshold of activity that needs to be reached to ensure high efficiency is well-known.
  • An accurate enzyme: The enzyme needs also to be as accurate as possible, which means that it should not have side-reactions. Such side-reaction might be toxic or slow down the metabolism and ultimately affect the plant growth negatively.

Once a set of mutation is decided, the mutations are implemented on the enzyme and their performance is tested in the lab. In Tobias Erb’s words “we try to make sure that the modelling is actually happening, that it becomes real” and therefore there is a lot of trial and error and back and forth, from the model to the experiments. Following this process, the FutureAgriculture team has found all the efficient enzymes necessary to complete a new pathway – the so-called “carbon positive pathway” – that should stimulate CO2 fixation in the plant and increase growth yield. Now it’s time to see how the individual enzymes work together.

2018 Otto Bayer Award goes to Dr. Tobias Erb

Our partner, Tobias Erb from the Max Planck Institute for Terrestrial Microbiology have been awarded the prestigious Otto Bayer Award for his outstanding contributions in the field of “Synthetic biology, especially the application on artificial photosynthesis”.  Part of this research is contributing to FutureAgriculture –  the group of Tobias Erb is responsible for the in vitro tests of the enzymes. You can read more in the official press release.

The official video to be released soon

We are currently collaborating with MedioMix to create the official video for FutureAgriculture! The first shooting day was at the MPI-MP in Potsdam – it has been a long day among laboratories, greenhouses and finding the right location for interviews. The official video for FutureAgriculture will be released soon, in the meantime, you can check our other videos on the dedicated YouTube Channel.

1948 Unbound @ HKW, Berlin

Unleashing the technical present / Nov 30 – Dec 02. Researchers & artists met for this experimental conference in order to explore the meaning and implications of the technosphere. Arren Bar-Even was invited to the SEEDS session – watch the full performance here.

12