synbio

Playing Lego with Terpene Biosynthesis

by Laura Drummond

The smell of orange, lemon and grapefruit, the fresh scent of pine trees during a walk in the forest. The taste of mint in toothpastes, the camphor in pain-relief sprays and even the bitter notes of hops in certain types of beer. Terpenes are more present in our lives than we account for, and yet most of us do not know them by name.

 Terpenes are a class of organic compounds, produced by many different types of organisms, but mostly by plants. They are responsible for severalvolatile aroma compounds that we know, but are also involved in the formation larger molecules likecarotenoids and cholesterol, as well as some very important pharmaceuticals like the anti-malarial drug artemisinin and the anti-cancer medicine taxol.

 When it comes to their biosynthesis, terpenoids always form from two universal precursors: IPP (isopentenyl pyrophosphate) and DMAPP (dimethylallyl pyrophosphate), which are isomers from each other. These two molecules have 5 carbon atomseach, and therefore moleculesdownstream normally have a multiple of 5 carbon atoms in their structures. Terpene biosynthesis is modular, with precursors of fixed size and an almost constant count of carbon atoms, which increases in blocks of five as molecules get bigger

Biosynthesis of terpenoids. The pathways have been conceptually separated into four modules. Image:  Vavitsas et al 2018  (CC BY 4.0)

Biosynthesis of terpenoids. The pathways have been conceptually separated into four modules. Image: Vavitsas et al 2018 (CC BY 4.0)

Isopentenyl pyrophosphate (IPP), the universal precursor of Terpenes, and the different precursor molecules that can be formed using a newly discovered methyltransferase.

Isopentenyl pyrophosphate (IPP), the universal precursor of Terpenes, and the different precursor molecules that can be formed using a newly discovered methyltransferase.

In our recent paper, published in ACS synthetic biology, we found a way to challenge this ‘multiples of 5’ rule. We discovered an enzyme, hidden in the genome of Streptomyces monomycini, which is able to add one or two methyl groups (CH3) to the universal precursor of terpenes IPP, creating precursors with 6 or 7 carbon atoms in their structure. The discovery brings an additional piece for the biosynthetical pathway of these compounds, which is highly modular and resembles a game of lego. We also demonstrated the formation of larger molecules, with added methyl groups, showing that natural enzymes from the pathway can accept the different versions of IPP, taking advantage of their promiscuity.

 The findings open new possibilities for the biosynthesis of compounds so far unknown, by the addition of a new piece to the lego-like terpene biosynthetical pathway.

 

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 Laura Drummond is a PhD student at the Industrial Biotechnology Department of DECHEMA Research Institute in Frankfurt, Germany. She has a BSc in Biological Sciences from the University of Sao Paulo and a MSc in Entomology from the Luiz de Queiroz College of Agriculture in Brazil.

Twitter:  @drumm34

Linkedin: https://www.linkedin.com/in/laura-drummond-dechema/

The First Synthetic Biology Conference in Cyprus

AfteriGEM, the University of Nicosia, The Cyprus Institute of Neurology and Genetics, the Cyprus School of Molecular Medicine and the European University of Cyprus joined together to make the first SynBio Conference in Cyprus reality on the 29th and 30th of March, 2019. The conference scope was dedicated to the advancement of synthetic biology, education, and the development of an open community

by Thea Chrysostomou

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Synthetic biology as an emerging interdisciplinary field that focuses on the design and creation of new biological components, as well as the reprogramming of already existing biological systems to function as optimized entities, served as a catalyst and started the national and academic conversation on the possible benefits it can bring to the island. This conference helped us understand the benefits and implications of this encounter between technology and biology, and how SynBio can add value to all aspects of Cyprus and global society in medicine, technology, research, education, environment, economy, agriculture and even art.

Results are so far promising; new biological parts and systems such as tumor-seeking microbes for cancer treatment and photosynthetic systems for fuel production are only the beginning of a series of in-progress developments which have the potential to positively reshape everyday life. 

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Through panel discussions and talks of 25 speakers from around the world, this event gave the Cypriot scientific and business ecosystem the opportunity to push the boundaries of synthetic biology and through the starting line of this movement - the intersection between biology and technology - in the island as well.

After the introduction for the conference in the local TV by the former minister of health, Dr. Stavros Malas and Thea Chrysostomou (EU iGEM Ambassador), the first day of the conference started with Thea and Representatives of Ministry of Health and Ministry of Education addressing the audience, followed by panel discussions.

Dr. Tuck Seng Wong from the University of Sheffield in UK, Dr. Lital Alfonta from the Ben Gurion University in Israel, Dr. Vassily Hadjimanikatis from Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland, Dr. Konstantinos Vavitsas from the University of Queensland, Australia, and Dr. Kostas Mathiopoulos from the University of Thessaly gave us some insights on SynBio communities and iGEM teams regionally, their experiences, educational hubs and what could be some differentiating factors to bring constituents such as academia, research, industry, government involvement for the ecosystem of Cyprus to thrive on this field and be part of this movement.

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Meagan Lizarazo, the Vice President of the iGEM foundation gave a very interesting talk on the history of iGEM and SynBio, vision for the future, startups, success stories in a global level (eg. PvP Biologics, Bluepha).

Prof. Lital Alfonta talked more about her research on “Genetic Code expansion for improved electron transfer”, Prof. Philippos Patsalis about his company NIPD Genetics on “Non-invasive Genetic Tests for Reproductive Medicine and Oncology”, Dr. Yiannis Sarigiannis on “Synthetic Biology as a useful tool in antimicrobial drug discovery”, Dr. George M. Spyrou on “ Systems Bioinformatics and Network Rewiring towards Precision Medicine”,  Dr Margarita Zachariou on “Computational Modelling of Brain/Neural Plasticity”, Dr. Vasiliki Gkretsi on “Targeting metastasis: could Ras Suppressor-1 be the key?”Dr. Kyriaki Michailidou “Large Scale genomics association studies in breast cancer”, Dr. Tuck Seng Wong on “Biological carbon dioxide capture and utilization(bioCCU)”, DR. Vasilly Hatzimanikatis on “What do we need from nature’s chemical toolbox for Synthetic Metabolism?”, Dr. Kostas Mathiopoulos on “Enginnering insects for pest control” and Dr Konstantinos Vavitsas on “ Driving synthetic Biology on with sunlight”.

We also had some after iGEMers and current iGEM teams presenting their experience in iGEM, how it shaped their career, what effect it has on their lives being part of this ecostystem and their research projects. Yiannis Ntekas from the National Technical University of Athens from iGEM 2018 talked about “Toehold switch enabled viral detection via routine glucose monitoring technology”, Fran Quero from the Complutense Univeristy of Madrid, iGEM 2018 and 2019 talked about “ From DIYBio to iGEM. The Spanish example.” Alexis Casas and Antoine Levrier from Bettencourt iGEM team 2018 in Paris on “Cell- free expression platforms enable ne possibilitis at iGEM and beyond”. Chris Graham from the University of Nottingham, iGEM 2017 on “Synthetic Biology in UK, a biological key and how iGEM changes a young scientist’s perspective”. Athina Milona and Thodori Kontogiannis represented iGEM Thessaly 2019 on “ Spot the iGEM impact; a Greek aspect of a worldwide phenomenon”. Dimitrios Michailidis from the University of Sheffield talked about Life after University. My colleague Will Wright talked about afteriGEM and entrepreneurial opportunities in iGEM and Thomas Landrain on his startups: La Paillasse, PILI, and cJOGL.

It is my conviction that the projects presented during this conference have made all of us wealthier in knowledge, ideas, and inspiration.

It is my conviction that the projects presented during this conference have made all of us wealthier in knowledge, ideas, and inspiration.

iGEM Cyprus will participate in 2020 as a research team representing the island in Boston with all the major Unis in the country involved.

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Thea Chrysostomou is currently working for the iGEM Foundation as the European Ambassador. At the same time she is continuing her research on Machine Learning and Biophysics in Paris. She has graduated from the University of Sheffield as a Biomedical Scientist.

Young PIs in action: Interview with Arren Bar-Even

For the next instalment of our young PI series, we interview Arren Bar-Even from the Max Planck Institute (Potsdam-Golm)

Kostas Vavitsas: You are working on redesigning carbon fixation and photosynthetic reactions. Do you think that we can we really improve photosynthesis?

Arren Bar-Even: That is a good question, and the answer is not very clear. There are indications that modifications in both the light and dark reactions can increase certain aspects of photosynthetic efficiency. For example, if we tamper with photorespiration, productivity can increase in crop plants, as reported recently by South et al.

The real problem is that generally we can not transfer observations and insights from one organism to the other, or even from one condition to the other. The main issue is that we don’t really know the precise metabolic and physiological mechanisms. Again in the example by South et al, they claim that the increase in crop productivity is due to the local increase in carbon dioxide. But every model we have run disagrees with this as the full oxidation of glycolate is highly counterproductive, so the reasoning for the observed increase in productivity upon expression of the pathway might be different than the one suggested.

Generally speaking, the high complexity of plants - as compared for example to bacteria - make them behave in an almost chaotic manner upon modification, that is, small modifications can have a substantial impact that is very difficult to predict. This makes many of the observed results difficult to interpret or repeat.

KV: Modern research is interdisciplinary. Do you think the way Universities and research institutes are structured facilitates this kind of research?

ABE: My first answer would be no. My research approach is dependent on close inteartion between biotic and an abiotic systems. Hence, I’m involved in multiple collaborations with chemists. I established this on my own without institutional support.

I think collaborative research is not built into the system. That is especially true within the Max Planck Society, where every Institute focuses on a very narrow research field. Universities might be a bit different, as they harbour multiple departments. However, people tend to stay in their field and within their comfort zone.

I must admit that I don’t know how this can be improved in a systematic manner. But I encourage researchers to seek interdisciplinary collaborations and not focus only on their day-to-day research and short-term outcomes. The benefits might be long-term, but keep in mind that such collaborations can substantially contribute to your research.

KV: How was the transition from a PhD student to a PI? Was it as you had imagined it?

ABE: The transitions was actually as I had imagined it. There was a lot of work and the amount of stress definitely increased. But in a way it is “my” fault, as I decided to run a big lab and multiple ambitious research goals. I could have stayed small, but I chose otherwise. What I maybe didn’t expect is the extent by which such continuous work erodes you over time.  

KV: What was your biggest professional challenge?

BE: I would say the biggest challenges come from the research itself. I set ambitious goals and they are not easy to accomplish. Besides research, I would say the workload. There is always a huge amount of stuff to do and issues to deal with.

KV: What is the one most important piece of advice you would give to an Early Career Researcher in synthetic biology?

ABE: Generally speaking, you need to find the right balance between identifying and focusing on one or few research fields in which you can become the expert and spreading out to avoid being dependent on the success of a single project. Finding this balance is tricky...


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Arren Bar-Even completed his Bachelor studies at the Technion, Israeli institute of technology, as part of the excellence program. He completed his Masters studies in the Weizmann Institute of Science (Israel) in Bioinformatics. At 2012 received his PhD from the Weizmann Institute of Science in Biochemistry. In 2015, he established the “Systems and Synthetic Metabolism” lab at the Max Planck Institute of Molecular Plant Physiology as an Independent Research Group Leader.

The answers were edited for length and clarity

Young PIs in action: Interview with Pierre Crozet

For the next blog in our Young PI series, we interview Pierre Crozet from Sorbonne Université in Paris, Frence.


Kostas Vavitsas: What is the biotechnological and synthetic biology potential of microalgae, and why did you choose to work in this area?

Pierre Crozet: As you work in the field, you have a few answers of your own, but I will try to answer with a twist. I want to work on photosynthetic organisms, for all the advantages you can imagine. There is a strong focus on the community on plants for agriculture, but in photosynthetic algae you can do more. Chlamydomonas has a bigger potential to answer biological questions and do synthetic biology. So plants can provide food, and algae could do anything else.

And here is the twist. I come from an Arabidopsis research background; Arabidopsis is easy to work with but slow to grow. Transitioning to algae was great! The algae synbio community is still small and the European GMO legislation is not very helpful, but we’re getting there. See for example the strong algae research by ExxonMobil; I think that practical applications are coming soon!


KV: How was the transition from postdoc to Associate Professor? Was it as you had imagined it?

PC: No, it was totally different. I have to note that technically I am not a PI, in the French system an Associate Professor is normally not a group leader. However, I have a significantly higher level of independence as I am the leader of my projects and already co-supervising a PhD student.

Well, for the first year in my new position I didn’t even touch a pipette. I had to do admin, write grants, teaching, teaching, and teaching. There is a lot of hidden administration work that PhD students and postdocs never see. So the nature of my job has changed.

But not all changes are bad. The interaction with the society is different, you are no longer a postdoc and people start contacting you – like you guys did – to draw on your expertise. For example, I am at the scientific advisory board of a startup biotech company named Neoplants, a position I think I wouldn’t have without being an Associate Professor.


KV:You emphatically mentioned teaching as a major part of your work routine. Do you find it a hindrance to your research role?

PC: Look, I love teaching. I never pictured myself in any other role other than professor. I wouldn’t exchange this position with anything else – maybe a full Professor position!

I really value the time I spend with the students. But teaching has more to it: administration work, marking essays and exams, preparing lecturing content… I could do with less of that.

Teaching has some benefits to the teacher. It forces you to see outside the box, and gives an incentive to improve your knowledge, especially when you are teaching something you feel unqualified for. For example, I had to train engineers in food and feed industry. As the subject was not within my immediate field of expertise, I had to become competent.

Last but not least, teaching makes you feel that you are making a difference to your students’ lives. You interact with them, you help them make a career, and some of them might choose to join in your lab for projects or research positions.


KV: And speaking of mentorship, what is the one most important piece of advice you would give to an Early Career Researcher in synthetic biology?

PC: Do what you like! This is the only important thing, do it for real and never give up!

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Pierre is interested in the molecular mechanisms allowing Plants to adapt to stresses. One of the major integrators of these environmental cues is the SnRK1 complex that allows maintenance of energy homeostasis. He studied its complex post-translational regulations that allow specific signal transduction during both his PhD at Université Paris-Sud, France, with Martine Thomas and Jean Vidal, and his postdoc at Instituto Gulbenkian de Ciência, Portugal, with Elena Baena-Gonzalez.

Since 2016, he shifted towards Synthetic Biology of carbon fixation in Chlamydomonas aiming at making this alga a better chassis to study the Calvin-Benson Cycle regulation through synthesis. He joined the team of Stéphane Lemaire and was appointed Assistant Professor in 2017 at Sorbonne Université to continue his work on developing Synthetic Biology in microalgae.


The answers were edited for length and clarity.

Young PIs in action: Interview with Ángel Goñi Moreno


Despite the numerous career option a PhD graduate has, many of us aspire to stay in Academia and become independent researchers. It is a difficult path that comes with many challenges. We therefore decide to ask fresh Principal Investigators about their experience and their words of wisdom in this aspect. Our first interviewee is a former Steering Committee member, Ángel Goñi Moreno, who leads his research group at Newcastle University.


Kostas Vavitsas: How did you find the transition from a postdoc do a PI?

Ángel Goñi Moreno: It was not trivial transition. Being a PI is a totally different type of job, and I wasn’t trained for it (I guess nobody is). So all of a sudden I had new responsibilities, new activities to take care of. For instance, I had to write project proposals, recruit people or manage a team - tasks that I did for the first time. Although challenging, it was a very exciting time. Starting your own laboratory allows you to choose which scientific questions you will prioritise. Who wouldn’t like that? Establishing collaborations is also a part of the job that I’m enjoying a lot. Anyway, I was very independent during my postdocs, so this did feel like the natural next step.

Kostas: What was the biggest professional challenge you had to overcome? What is the importance of mentoring in your career?


Ángel: The most important professional challenge is to get the first grant in. I firstly applied to a ERC Starting Grant, which I didn’t get. I then applied to the EPSRC First Grant, and I was successful at that. At this point, I felt a lot more comfortable with what I was doing. I’ve never had a “mentor” as such, so I can’t tell. However, I’ve had very good advisors during my postdocs, so I tried to copy as much as I could. Also I asked for help whenever I needed it, which was indeed very useful. By asking for help you also find out who is actually willing to help and try to build on them during those first steps.


Kostas: Do you find synthetic biologists to be computer literate? How can we better integrate information technology in common synbio practice?

Ángel: Nobody can be an expert in all the (sub)fields within synbio. There are few computer scientists, if that is what you ask. And it is a pity, because the understanding of biology from an information science standpoint can in fact be fundamental to the field. We should definitely encourage computer scientist to join in. This is not only to provide the tools and methods needed to get the most of measurements and predictions (via models), but also to provide a novel conceptual framework for the engineering (programming?) of living systems. Coming back to your question, the best way is to just do it. For instance, if your laboratory is 100% experimental, bring some theoreticians on board.

Kostas: What is the one most important piece of advice you would give to an early career researcher in synthetic biology?

Ángel: Do not (always) follow the mainstream synbio research. Try to focus on the research questions you are confortable with and then bring them into the field. Not specific to synbio, but a general advice to early career researchers: be honest and open. Never pretend you know something you don’t. Never pretend your work is better than that of your colleagues. Always try to communicate your thoughts and plans to your peers. Share. Ask for help whenever you need it. It is important to remember that the people in your team work *with* you, not *for* you. By the same token, you don’t work *for* anyone (watch out!). Last, but not least, keep an eye on your life-work balance in order not to overcommit yourself. 

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Ángel Goñi Moreno is a Lecturer in Synthetic Biology at Newcastle University (UK); PI at the Interdisciplinary Computing and Complex Biosystems (ICOS) research group and Editor of the Synthetic Biology Open Language (SBOL). He was born in Madrid (Spain) on the 6th of August, 1983. In 2001 he started studying Computer Engineering at the Technical University of Madrid (UPM), Spain. After getting the degree he joined the Natural Computing Group at UPM and started researching in the fields of DNA Computing and Synthetic Biology. In 2010 he learned the first Ph.D. to be undertaken in Synthetic Biology at UPM. I also held a M. Sc. degree in Artificial Intelligence. After UPM he joined Martyn Amos’ group at Manchester Metropolitan University (UK) as a postdoc. When finished that position, in early 2013, he came back to Madrid to join the Victor de Lorenzo's lab which is part of the Systems Biology Program at CNB-CSIC (Centro Nacional de Biotecnología - National Center for Biotechnology). During the summer of 2016 he moved to Newcastle where he is at the moment.