metabolic engineering

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...


ABE3.jpg

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

Synthetic metabolic route allows optimal use of xylose for bio-production of chemicals

Scientists from Toulouse, France, genetically modified Escherichia coli in order to assimilate (d)-xylose and direct it towards commercially interesting compounds in a novel manner.

 

Early, this July I attended the Synthetic and Systems Biology School in Taormina, Italy. Apart from the lectures and poster sessions, selected talks from the participants were also presented. Amongst others, I distinctly remember two postdoctoral researchers, Ceren and Débora, who enthusiastically described their work about producing interesting chemicals in E. coli. I was therefore very pleased when I saw their paper published in ACS Synthetic Biology a few weeks ago.

     
  
 
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      Native (blue) and synthetic (green) (D)-xylose assimilation pathway. The chemicals of interest (pink) and the first steps of glycolysis are also noted. The green numbers represent the heterologous enzymes that were used. Figure adapted with permission from Cam et al., 2015. Copyright American Chemical Society (2015).   

 

Native (blue) and synthetic (green) (D)-xylose assimilation pathway. The chemicals of interest (pink) and the first steps of glycolysis are also noted. The green numbers represent the heterologous enzymes that were used. Figure adapted with permission from Cam et al., 2015. Copyright American Chemical Society (2015).   

This article narrates a nice metabolic engineering approach to introduce a novel (D)-xylose assimilation metabolic route in E.coli. Naturally, E.coli phosphorylates (D)-xylose at C5 and incorporates it into the main metabolism. What the designed pathway does is assimilate the (D)-xylose through C1 phosphorylation, bypassing the pentose phosphate pathway and its native regulation. The sugars can now be introduced in the glycolysis pathway and thus be used for organism growth, while the desired chemical products are produced in a more targeted manner by expressing the respective biosynthetic enzymes. The theoretical product yields were computed and compared to the native metabolism and other engineering approaches, the novel enzymes that need to be expressed were identified and characterised, and microarray experiments and metabolite analysis were carried out to study the organism’s response to the new pathway. Finally, selected chemicals were produced by dedicated strains that performed impressively in terms of yields and product concentration.

So what's missing? It would be informative to see how the strains behave and what titres can be achieved in large batch-fermentation experiments. There is a small loss of growth rate of the modified strains. Moreover, it would be interesting to optimise the strains further and to test how generic this approach is by transferring the pathway to other organisms, such as baker’s yeast. Overall, however, this research paper is an easy-to follow biotechnology story that begins with the motivation and design and reaches the desired outcome of increased product formation.


There are two take-home messages that I would like to address after reading this article. The first comes from the use of (D)-xylose as a substrate. The rationale behind it is that xylose constitutes a large proportion of the unused cellulose and hemicellulose biomass that are byproducts of bio-refinery. This is a prime example of synthetic biology employed in sustainability efforts, where a waste product is converted into commercially interesting compounds. Those formed products are currently available in industrial scale as fossil fuel byproducts and their production using E.coli is an environmentally friendlier alternative. However, the bio-sustainability argument has some pitfalls and needs to be employed carefully. A fermentation production is itself an energy consuming process. Also, the use of sugars should not directly compete with or use up agriculture resources. Nevertheless, it is my opinion that the industry needs to disengage fast from oil as a feedstock, and synthetic biology is a powerful tool that can provide novel alternatives.

A second point is the use of systems biology together with synthetic biology. Taking into account that a system cannot be simply described by the addition of its components but also requires the interactions between those parts, likewise a bioengineering approach cannot rely on the simple expression of a heterologous pathway and the optimisation of the participating enzymes. This principle is illustrated in this article, where metabolic modelling and microarray analysis that provide invaluable insights during the pathway design and the strain optimisation steps respectively. Interdisciplinary research is also present in this work, as computational science, bioinformatics, and analytical chemistry are employed together with molecular biology and biochemistry. It becomes more and more obvious that single-focus and narrow approaches are getting obsolete. The new generation of scientists needs to speak the language of and understand collaborators coming from different backgrounds. Synthetic biology, which in principle combines parts to obtain new properties and novel functions, cannot fall behind in combining different disciplines in a way that facilitates research and strengthens innovation and creativity.

 

 

Research Paper: 

Yvan Cam, Ceren Alkim, Debora Trichez, Vincent Trebosc, Amélie Vax, François Bartolo, Philippe Besse, Jean Marie François, and Thomas Walther (2015) Engineering of a Synthetic Metabolic Pathway for the Assimilation of (d)-Xylose into Value-Added Chemicals. ACS Synthetic Biology DOI: 10.1021/acssynbio.5b00103

 

Written by:

Konstantinos Vavitsas

Konstantinos is a PhD student at the University of Copenhagen, working on the photosynthetic production of high-value compounds. 

Edited by: Devang Mehta

 

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