Interview by Charlay Wood
Today, I had the star-struck experience of meeting Prof. Jing-Ke Weng in person! Imagine meeting someone you’ve idolized from the pages of academic journals brought to life right in front of you. It’s like bumping into your favorite movie star, but in the world of plant specialized metabolism. I’ve poured over more of his research papers than I dare admit, even eclipsing those of my own supervisor (sorry Benjy) — It was a true fan moment for me!
Jing-Ke gave a fascinating talk on acutumine biosynthesis. Afterward, I had the opportunity to discuss secondary metabolism with him directly. Here’s how it went (interview edited for brevity):
Charlay Wood: Amazing talk! I was wondering, now that you’ve found this dechloroacutumine halogenase (DAH) enzyme, are you continuing your work on the scaffold formation of acutumine? Through coexpression, perhaps?
Jing-Ke Weng: Yes, so this is work ongoing. It has turned out to be a really challenging pathway because we did a coexpression analysis, we found a few candidate genes, tested their functions, but they do not function the way we hypothesised. So we think even the alkaloid scaffold formation is different from anything we’ve known before.So now we’ve moved to knock-out and knock-down experiments and differential expression analysis to see what genes have altered regulation patterns.
CW: Do you have any tips for when you find candidate genes, and are looking to characterise the enzymes, how do you know which assays to run?
JKW: It really depends. So in this case, we knew the substrates already. It’s the dechlorinated acutumine. Sometimes getting the substrates can be tough with chemical synthesis. But we knew where to start at least.
CW: How about when it’s not known?
JKW: Yes, so for example with the flavonol synthase (the ancestor to DAH) there’s a 40% difference between the two enzymes. We stared at the sequence, at the structure, finding which regions are different. And then mutated the residues, we ended up mutating everything possible. But only recovered 2% activity. Which means there must still be mutations that actually matter a lot. It also tells us why halogenase activity is so difficult to evolve. There are over 10,000 2-oxoglutarate-oxidase sequences, and this is the only case (in plants) that is a halogenase. This means it is hard to come up with halogenase activity based on ancestral oxidase activity.
CW: This activity has been seen in bacteria though. How common is it to find an enzyme that is in bacteria and then evolves separately in plants?
JKW: I would say it’s really, really rare. We’ve worked on other cases, such as in kavalactones, the chalcone synthase is secondary metabolism that comes from a polyketide synthase common across all life for lipid biosynthesis. Aldehyde synthases coming from decarboxylases has happened many times in plant evolution, and also in insects. But I would still say that it’s extremely rare to see this.
CW: What do you think, in the field of plant natural products, is a currently undiscovered pathway that is key for the future?
JKW: In our lab, we’ve been doing “stamp collection.” Each person is working on different plant biosynthetic pathways. But I’m really looking for some breakthroughs in the way we study pathways. Ideally, to the point where we can essentially predict pathways without doing any experiment. Each plant has about 30,000 genes and 5,000 metabolites. It’s a number I think that is feasible. Reflecting 20 years ago, you had to purify the enzyme without knowing the gene and painstakingly define its activity. A single pathway could take one researcher 30 years. So using model plants, and doing knockouts and finding mutations was the way to define pathways. This was during my PhD training. Then in the last 10 years we used a multi-omics approach, using a transcriptome to find candidate genes and reconstitute the pathway in tobacco. But it’s still low-throughput. Moving forward, I hope to see ways to enhance our prediction power. For example, with AlphaFold you can predict the protein structure of all 30,000 genes in a species and with a learning model predict the reaction that is most likely to happen. So without doing any experiments that’s a very good way of finding candidate enzymes. I think that’s the next move. Ultimately, if we have strong prediction power, once you sequence a genome you should be able to predict the function of most enzymes. My lab is investigating this.
CW: Definitely! If we could do everything on a computer first before tackling the molecular biology and biochemistry, that would save us all a lot of time!
JKW: Exactly! I see this to be the theme of the next 10 years or even shorter.
CW: Last question, I know you have spin-out companies. Would you suggest someone to patent and build a company out of any novel enzyme discovery?
JKW: I’ve been practicing entrepreneurship for the last five years, and at the same time I also advise and teach a course on companies. I think I learned a lot more as a practitioner of entrepreneurship compared to 6-7 years ago. So I would say to actually do it more carefully. I wouldn’t start a company just because I found an enzyme. For a company to succeed, the science has to be really great and can translate to products and services that contain value. And has market fit! It’s easy to start a company but very difficult to make it successful. And you have to think about trade-offs. If you start this company, you’re not spending effort on an alternative idea that could be better. But you only learn this by doing this, so I think for people who are entrepreneurial by heart, I would encourage them to start something but definitely talk to people who have done it first! Just to minimise stupid mistakes!
CW: Thank you so much for your time today! It was great talking to Jing-Ke! And good luck with the move to NorthEastern!
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About the Author
Charlay Wood is currently in the final year of her PhD program at the University of York, UK, diving deep into the fascinating world of enzyme discovery in plant specialized metabolism. She was a 2023 ASPB Plant Biology Conference Correspondent. Find her on Twitter (X) @charlaywood.
good information to broaden my horizons but if there is any other information if you can let me know