Science AMA Series: I am Dr. Ioannis Pavlidis, a junior group leader in the University of Kassel, Germany. Our group of Biotechnology focuses on Enzyme Technology and Development of Biocatalytic Applications. Anyone interested on the topics is welcome to AMA!

Abstract

Nature provides us with a wide toolbox of enzymes as biocatalysts, we just need to refine them in order to fit to our process. I am a biologist by training, but thoughout my academic career I always seeked to combine different fields. For instance, good knowledge of chemistry is required, as in many cases biocatalysis needs to compete to established chemical processes in industry in order to be transfered to the production. Our recent publication in Nature Chemistry (http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.2578.html) is such an example, where we developed enzymes that can produce pharmaceutical interesting building blocks in an environmentally friendly way. At the moment my group is working on another group of enzymes, the methyltransferases, which could be of significant industrial interest, especially in the fields of food and pharma industry. Our research focuses combines the fields of biochemistry, molecular biology, bioinformatics, organic chemistry and more. Everyone that is interested in these topics is welcome to join our discussion, on the 17th of August at 14:00 CET (8 am ET) . I'll be there to answer all your questions, so AMA!

I just graduated with a degree in biochemistry and molecular biology, so I'm very interested in your work! What current biotechnology research do you think will have the most impact within the next 5-10 years?

Sjmman

Really interesting background you have there. I am just a biologist by training. These topics are evolving really fast and predictions are really high-risk. What draws my interest is of course the alternative applications of the CRISPR-Cas systems, and the personalized medicine. More targeted, more accurate solutions with less unwanted side effects (hopefully). The future will only reveal the impact and application of these techniques, but I foresee great potency.


My undergrad was in biology and biochemistry, and I'm doing a PhD right now in molec/cell biology. Could you expand upon your answer regarding alternative applications of CRISPR? There's the obvious genetic changes that could be brought about with that particular method, were you referring to something else?

ComputerPlayerOne

You are absolutely right. The CRISPR obvious application has to do with the genetic modification. However, it could be used also otherwise, as for instance to label specific areas in the genome, or to regulate. As long as we have the tools to identify and modify the DNA, the way to be used can vary. Don't even forget the original role of this system, which is a defensive mechanism. Can we use the system (or other similar systems) in these aforementioned ways? It only needs to be proven. But I would not stick only to the obvious application.


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You sound like you have a Cypriot name. Has that helped or held you back in your studies/career?

yourunconscious

I am a Greek citizen and I studied in Greece, although Cypriots have similar if not the same surnames. I do not think that my nationality affected somehow my career. At this level the CV plays more significant role than where you come from. Especially in Natural Sciences you just need to speak English. However, it is interesting to see the differences of various educational systems (i.e. the Greek and the German). Everything has its pros and cons.

Edit: To be absolutely correct, the only way that my nationality played a role was on my first post-doc year, because I got a Marie Curie position. For these positions the researchers need to move between countries. And as the position was offered in Germany, I shouldn't be German. But it would be no difference if I were French or Italian I suppose.


If I have a potentially awesome idea for an enzyme but my degree is in neuroscience. I was wondering what it might take to get into a lab and work on something or what should I do to try and turn this into a product?

neilarmstrong13

Our age is a multidisciplinary era. You should not be afraid of shifting topics. Actually I would suggest that you do so, to get more experiences from different fields and to combine several techniques. I find the most interesting science happens, in my humble opinion, where fields meet. To be honest, when I was in high school, I did not want to hear about chemistry and wanted to become a physicists. Then I studied biology, I took a taste of biophysics and here I am again in chemistry. I would suggest that you should contact a laboratory active on the field and explore the opportunities. In any case, enzymes are also involved in neurobiology, so there can be a bridging project that can make the transition easier.


Eli5 what is Biocatalysis and the research you are doing ( I have a basic understanding about biochemistry in general. Not my major, just interested)

mitomeen

Biocatalysis is the field of transforming a substance to another one, with the use of biological molecules. Usually we use proteins that have this activity (catalytic activity), called enzymes. What we are doing in my group is to try to provide interesting products (like drugs, food additives or other chemicals of interests) with enzymes. To do so, we need to make the enzymes working under desired conditions. Of course the native enzymes (the ones in nature) are not designed for the specific process, for this reason we modify them (with means of protein engineering, medium engineering or immobilization), in order to increase their efficiency and yield the desired product. The field becomes interesting especially for expensive products which can be produced from wastes (so we speak about valorization of the wastes, and not only bioremedation), or in the case that the specificity is important. You see, that is the main benefit of enzymes compared to chemical catalysis; it can be highly selective.


Hello I am a current biology major in Texas! I am taking an interest in molecular and microbiology. By allowing more control of our biological processes could this potentially be used for patients in hospitals, who have disorders that cause them to not be able to produce correct enzymes? Or could it be used to help patients with auto-immune diseases? I'm very curious as to see what this field of research can bring!

twallace313

I am not really sure what you are meaning by "allowing more control of our biological processes", and my field in not the application of enzymes in medicine. But already a huge amount of therapeutic proteins are used. A nice story is the development of the insulin; how we started from the porcine insulin and now different variants of the human version are already offered (for instance for slower or faster activity). Now, if we go a step further from the proteins and move on to enzymes, this is really interesting. However, we have several topics to consider: how to deliver the enzyme locally on all affected cells? Is the enzyme stable? Would it have side-effects if it is located in wrong tissue? You see, all our cells share the same genome, but the differentiation of the tissues bring the regulation of the proteome in each cell. The metabolism in a cell is really amazing and by changing one flow in all these pathways a whole cascade may be initiated which we cannot predict. So, combined with the genetic engineering there could be some specific advances on the medical field, but it requires years of research and test phases before they are really applied (not to mention the ethical side of the genome editing on humans).


How does somebody "develop" an enzyme? Are you modifying the sequence of naturally occurring enzymes, or coming up with novel mechanisms from scratch? Also, I'm curious about your process for evaluating the enzymes. I imagine you express the enzyme in culture, purify the enzyme, then test for activity? Do you consider the feasibility of purification in your research, given how important that is for industrial applications?

Thanks for doing the AMA, Dr. Pavlidis!

Dombey_And_Son

Really interesting question. Well, there is no simple solution. There are several enzyme sources. One way is to get an enzyme you know and try to modify it to meet your requirements. If you do not have an enzyme that makes the job, you can maybe search in databases. Many genome projects offer genetic data and gene sequences, where we do not know what the encoded proteins do. Searching with homologue sequences, then you can identify totally new enzymes that were not previously characterized. A last possibility is to develop de novo an enzyme. If you have a good understanding of the catalytic mechanism of the desired enzyme, you can design the active site (the geometry of the compounds to be converted and the participating amino acid, so to say). Once you find the proper geometry, you can try to find a protein scaffold that you could "import" the amino acids in the right positions. This approach usually provides a small initial activity, where further evolution of the enzyme is needed - but it is ideal for new activities that were not reported earlier.


How does somebody "develop" an enzyme? Are you modifying the sequence of naturally occurring enzymes, or coming up with novel mechanisms from scratch? Also, I'm curious about your process for evaluating the enzymes. I imagine you express the enzyme in culture, purify the enzyme, then test for activity? Do you consider the feasibility of purification in your research, given how important that is for industrial applications?

Thanks for doing the AMA, Dr. Pavlidis!

Dombey_And_Son

I forgot to reply on the second part of the question. Yes, we express the proteins and we test the activity. Depending the amount of mutants we have different approaches. If there are only a few we purify the proteins and we characterize them properly. If there are libraries of thousand variants, we need fast assays. Now, we need to consider if the metabolism of the expression system (the cell where we express our enzyme) interferes with the assay or not. If not, we can use whole cell assays - for instance plate assays or selection pressure. But there is no unique answer, and you always need to check the specific problem / assay. Concerning the purification in a final application, the answer is simple; the cheaper / simpler the better. If you can use whole cells and the cells do not use the product as carbon source for instance, or they do not convert it otherwise, then you can use whole cells. But the mass transfer limitations need to be considered (can the substrate and product pass the cell membrane easily?). If you have such problems, then a purification can be considered - but there are different types of purification that lead to different purities with different costs. For instance we developed a treatment to reduce the background of NAD(P)H dependent enzymes in E. coli, so that we can measure NADH dependent activity of our desired enzyme without purification. Before that this was not possible, as many of the host enzymes would use the same cofactor and you would have a huge background.


Is there potential for biotechnology to improve camera sensor technology? For example, the sensors inside a DSLR. It is impossible to capture a photograph with the quality of the human eye with a full frame complimentary mental oxide semiconductor sensor. I wonder what role nature could play in micromanaging colour, sharpness, and contrast if integrated in the sensor. Like manipulating existing natural process and reactions to restructure the way we use light and optics to capture what we see. For example, the colour and texture changing capabilities of cuttlefish skin, or algae that glows in certain conditions.

Do you think theres hope for biology in camera technology?

(Only asking to entertain the thought)

Kubrick007

Wow, this is way out of my field, but really interesting question. Enzymes are used already in biosensors in order to lower the detection limit and maximize the signal to noise ratio. There are even some enzymes that undergo structural changes in the presence of light. However, to be able to improve colour, sharpness or contrast in a camera? I am not sure how to do that, at least now in the digital technology - with the films exposure it could be different. What we see with our eyes is the result of a really complicated organ, with several protein and enzymes involved, not to mention the complicated structure of the tissues involved. What I could maybe see as possible is in the near-IR photography (where all enzymes absorb) - but then the photos are sharper anyway, without the use of enzymes. I am sorry, I cannot think some application right now - but I'll think about it :)


Sorry for the late question. I have recently been thinking about apparently non-enzymatic structural proteins like crescentin, a cytoskeletal protein which patterns curvature in bacterial cells.

The jury is out on exactly how these proteins work (perhaps they act mechanically, perhaps they sterically hinder or localize the function of other enzymes), but it always remains possible that they have cryptic catalytic properties. Since the biochemistry is complicated (number of potential targets, amount of biochemical "space" to consider), how can we ever exclude this hypothesis?

Also, do you feel that, in the absence of known enzymatic function, higher-order definitions of "mechanism" should replace the standard "molecular mechanism" we normally search for? E.g., If crescentin is indeed not an enzyme, perhaps searching for a "cellular mechanism" makes more sense than a "molecular mechanism"?

subito_lucres

The quest to find the enzymatic reaction, a protein may catalyse is similar to looking to all the sand grains. There are just too many to screen them! You could potentially exclude the existence of specific structural motifs (for instance binding pockets for NADH or other cofactors), or catalytic mechanisms (like the catalytic triad of hydrolases (like Ser-His-Asp/Glu for hydrolases), but you will never be sure that there is no other catalytic activity. If you need to disprove catalytic activity, then I would start from that: disproving motives that coordinate cofactors, metal ions or known geometries of amino acids of catalytic mechanisms. You need however to consider the fact that several structural proteins have also a promiscuous catalytic activity. These proteins are called "moonlighting proteins".

Considering the terminology, you are probably right; if these proteins make supermolecular structures, then the term molecular mechanism may not be appropriate.


How many years are we from having the know-how to make enzymes from custom sequences that are able to do a function we desire them to?

ngserdna

There are already some works where the did it. Well, not starting from the sequence, but starting from the geometry of the active site. If you want, you can check the work on the Kemp eliminase, it is a nice example on the field. However, we need some more time to have a high success rate between what we design in silico (in a computer) and what really happens in our test tube. At this moment, softwares cannot predict the solubility of the proteins and many mutants suggested from such softwares result as insoluble protein aggregates. To my opinion, this is a results that we simplify the process and we only look on the first cluster of interactions of the amino acids. If we could have a system where we could monitor all interactions, then maybe we could increase accuracy. But probably with the current capacities of CPUs, such a computer would run an experiment for months.


Aaa I see.. So from what I understand that protein engineering is just a trial and error and see which dna works best ? And medium engineering also the same but with the enviroment changes. So how does an enviroment ie the solution itself changes its own cataclytic efficiency ?

mitomeen

Well, the protein engineering has two major "schools". The rational design and the directed evolution. If you do not know anything about your enzyme, you make random mutations and you should have a nice way to prove the activity quite fast. But if you have the 3D structure, you can make rational design of the mutations needed and then target really the positions needed. Of course there are several methods in between, where they combine these two approaches. For the medium engineering, you need also to consider the thermodynamics of your reaction and also the solubility of your compounds in the solvent. A classic example is the synthesis of esters. If you use a hydrolase in water, it will break an ester in an alcohol and a fatty acid. But if you use the same enzyme in organic solvent, then there is not water available for the hydrolysis and the synthesis of ester can take place from the respective alcohol and fatty acid.


This is maybe a little out of your area of expertise, and I'm just a lay person, but I had this thought running through my head for a little while now.

In short, the staple crops, that by far take up most of agricultural area and cause most environmental problems, are all either starch or fat producers.

What I always asked myself is, why has no one developed heavy starch and fat producing algae/cyanobacteria cultures? Diverse cultures that have red and green pigment for maximum light spectrum use. That replicate in low populations and store fat or starch in high populations until they die.

In such cultures you could than scrape starch from the ground or scoop oil from the top of the tank. And this can then be used either directly or as raw material for all kinds of processing and fermentation.

So in my uneducated ignorance, I see tremendous economical, environmental and social reasons to have such cultures. And for the same reason I also don't see too great technical problems, since all the traits I have described, i.e. fat and starch production etc. are all traits that widely occur in many different micro-oganisms in nature already.

And since such cultures would be grown in closed managed systems, there is also not this political hassle about introducing gene-manipulated organisms into the wild.

Continuous production with no growing seasons ...

Someone's got to start the project to create lab grown instant ramen noodles, where the starch and the oil and the binding proteins come from algae cultures.

imbecile

Actually there are several engineering microalgae that can produce up to 50% (or even more, I am not updated) of their mass as oil (for instance Nanochloropsis). These algae are used for biodiesel production. The problem I see in this case is the cost of the setup of such a bioreactor. You need a high surface area, so all algae can reach to the sunlight (you do not want to spend energy with lamps). You can google "photobioreactor" or "algae bioreactor" to see photos of such systems even in the open environment. But I think that the cost of building and maintaining such a system is not viable.


What is the process that is involved in catabolic and anabolic reactions and how is this sped up manually?

Sxrcastic

Catabolism is the breaking down of complex molecules to simpler ones, either to gain energy, or to use the simpler ones as building blocks for biomacromolecules later. Anabolism is exactly this step: the building of complex molecules out of simpler ones. There is not a process that combines both, they are more of less complimentary. In the cells enzymes involved either in anabolic or catabolic pathways are strictly regulated from their substrates and products, or even from other regulators (molecules that can affect their activity). Usually the end product of a pathway works as an inhibitor in one of the steps. If you remove this product, then the reaction / process will be forced always to this direction. Can you please be more specific with your question?


What's a Greek doing in Germany? Not good science jobs in Greece at the moment?

YTsetsekos

I studied and got my PhD in Greece. After that I moved to Germany for my post-doc, in the frame of the mobility that is needed for an academic career. After 4 years post-doc, I applied for this position and I was offered the job of a junior group leader. At the same time, I was rejected from a University in Greece as an assistant professor (I was the second best candidate according to the final decision), so I think it has to do more with where the opportunity is provided and nothing to do with the Greek crisis. But I assume that the conditions under which research is performed in Greece were significantly worsened since I finished my PhD.


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