AudioHelicase Special: How researchers at Whitehead Institute are building a more sustainable future

This story is part of our series, A Good Environment for Sustainability Research. Click here to see all stories in this collection. 

Making our world more sustainable to preserve it for future generations will take not just one but many solutions. Researchers at Whitehead Institute are exploring how the natural world could teach us how to improve the sustainability of how we produce food, how we make medicines, how we make products more durable, and potentially how we remove carbon from the atmosphere. In this special episode of AudioHelicase, we’ll hear from researchers at the Institute that are pursuing creative solutions to sustainability that combine a passion for making a difference with boundless curiosity for the living world.

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CONOR GEARIN, HOST: Making our world more sustainable to preserve it for future generations will take not just one but many solutions. Researchers at Whitehead Institute are exploring how the natural world could teach us how to improve the sustainability of how we produce food, how we make medicines, how we make products more durable, and potentially how we remove carbon from the atmosphere. 

I’m Conor Gearin, digital media specialist at Whitehead Institute. In this special episode of AudioHelicase, we’ll hear from researchers at the Institute that are pursuing creative solutions to sustainability that combine a passion for making a difference with boundless curiosity for the living world.

Whitehead Institute Member Jing-Ke Weng studies the natural products made by plants and animals, and how we can use the tools of biological engineering to solve problems in drug discovery and beyond. In this episode, we’ll hear from four graduate students in the Weng lab: Carly Martin on figuring out how to support crop plants’ microbiomes during climate change, Colin Kim on learning how to make medicine with fewer environmental impacts by learning from plants, and Joe Jacobowitz and Sophia Xu on how we could produce more durable coatings for metal products and even develop carbon-capturing organisms using plant-based processes.

Weng lab graduate student Carly Martin is branching out in a new direction for the lab — helping global agriculture become more sustainable.

CARLY MARTIN: I joined a plant biology lab because I think there's this great opportunity for biologists in engineering for agriculture — specifically, in adapting to climate change through agricultural engineering.

I’m excited about this project because I am deeply motivated by research that is climate-change relevant, and I think that biology and bioengineering is uniquely well-positioned to address some of the huge problems that we'll have to adapt to in a climate that has drastically changed. Specifically in the agricultural realm, I think that we'll have to engineer crops that are more robust or use crops that are more resilient in a harsh climate.

GEARIN: The consequences of climate change extend far beyond the atmosphere and weather patterns. Carly is exploring how a warming climate could affect the microbial communities that live in the soil. Plants need these soil microbes, because they provide nitrogen in a form that the plants can use.

MARTIN: We, on a molecular level, don't really understand soil biology very well, and that's something that is also very dramatically impacted by climate change. Perhaps if we had a better understanding about the relationship between soil microbiome composition and plants, perhaps we don't have to necessarily engineer the plants, but we could sort of dope in certain beneficial bacteria into those symbiotic relationships to improve crop yield and robustness.

GEARIN: The key is to figure out the ideal mix of soil microbes for supporting crops. The plants themselves may have strategies for influencing their microbial partners. Carly is investigating one potential way that plants could manage their microbes—by producing a special class of chemicals in their roots.

MARTIN: I'm right now studying this class of peptides in plants, called RIPPs. That stands for ribosomally synthesized post translationally modified peptides — kind of a mouthful. But RIPPs are a really interesting class of peptide because they're short, and they adopt these very unconventional shapes, and they have very interesting bioactive properties. They can be very heavily modified and so their bioactivity can change. Some examples are ACE inhibitors, many venoms have RIPPs, poisons. They also are used in antibiotics in some cases. 

There's not a consensus as to what they might be doing especially in plants. Our hypothesis is that they're mediating some kind of like root-microbe interaction. The root has its own microbiome. That's very well known in plants like soybean that require a symbiosis between nitrogen-fixing microbes, but all plants have a microbiome. 

GEARIN: There’s still much to learn about these small proteins that could mediate the conversation between a plant's roots and microbes in the soil around it, so Carly is taking a broad approach.

MARTIN: One thing that we're thinking about doing is just kind of doing a broad characterization of RIPPs in agriculturally relevant plants, and having a matched microbiome census for those plants. I'm very interested in just generally characterizing this really interesting class of peptides in plants.

GEARIN: Seeing if and how RIPPs affect the soil microbiome, and then how the microbiome then affects plants’ gene expression in turn, could help us better understand what soil conditions are best for growing crops.

MARTIN: Those things could potentially inform potential soil management or microbiome engineering around crop species. For my initial project, I'm focusing on soybean because that microbiome has been very well characterized, and it's very agriculturally relevant.

GEARIN: Carly wanted her project to provide information directly useful to farmers. The best way to do that, she realized, would be to call up some farmers herself and learn what challenges they’re facing.

MARTIN: I basically just emailed a bunch of farms that were local. There's this one in northern Pennsylvania, Charlann Farms. 

GEARIN: The farm provided Carly with soy plants straight from their fields.

MARTIN: It was very cool to interact with the farmer who provided me with the samples, Tim Stewart. It's kind of like a family farm and they grow many different types of produce. I have to have a good understanding of the problems that people are experiencing on the ground on due to climate change, and so that is also a really exciting thing that's beginning in my work right now, this collaboration between Charlann Farms and our lab. 

Now that I've been thinking about these problems I realize how huge they are and how big of an effort is needed in order to address them. That makes me much more invested in building teams, building collaborations, getting to know people that exist and work and are affected by this problem at many different levels.

GEARIN: Part of the teamwork we need to solve our world’s problems with sustainability is teaming up with plants themselves. Colin Kim, a graduate student in the Weng lab, is seeking to learn chemistry from the plant world.

COLIN KIM: Plants are excellent chemists. And they're able to produce these complex compounds in nature. And plants have evolved for millions of years to do this. So they use primary metabolites like amino acids or nucleic acids — a lot of these metabolites that are found commonly in organisms — and plants have evolved specialized metabolism, where they're able to use these substrates from primary metabolism to actually build on top of these molecules and create very highly complex structures that are of medicinal importance.

GEARIN: The success of plants as chemists has made them crucial to medicine. For thousands of years, people have harvested plants for the medicinal compounds they contain. But this has become a problem for many plant species with dwindling populations in the wild. In many cases, the only alternative for producing the drugs at large scales involved chemical reactions that create harmful byproducts. Neither of these approaches tend to be sustainable. Now, Colin and others in Jing-Ke Weng’s lab are looking to plants to show them a better way.

KIM: So we are trying to harness how plants are actually synthesizing these. It’s quite interesting because when we look at how biochemical reactions and biochemical transformations happen, a lot of these reactions take place in water, right, like in aqueous solutions. As opposed to organic chemical synthesis, where you're using organic solvents and it produces a lot of toxic waste to the environment. Those organic solvents, the environmental harm that it causes, it accumulates in the earth and we don't quite know how to efficiently get rid of organic solvents that we end up using. Whereas when we look into nature, nature has already optimized the setting and the solvent in the environment for these very complex biochemical reactions and biochemical transformations to take place.

GEARIN: By discovering the process through which a plant species produces a medicinal chemical, scientists could then recreate that process in a common plant species like the tobacco plant, or in a microbe like yeast. Colin’s research focuses on a plant called moonseed. 

KIM: One of the projects that I'm heavily looking into currently is to really characterize how these moonseed vines are able to synthesize this chlorinated tetracyclic-structure alkaloid, which has interesting bioactivities, including potential anti-leukemia and memory-enhancing effects. And also, it also exhibits cytotoxicity to human cultured T cells as well. And so this alkaloid is pretty complex and structured. Synthetic chemists have synthesized it, but we actually don't know how plants are naturally making these, mostly accumulated in the root tissues of these plant vines.

GEARIN: Plants have the potential to guide the development of new drugs—and how to produce them more sustainably. 

KIM: So the natural product pool is a very exciting field for drug discovery. And in fact, approximately one third of all existing pharmaceuticals today have a plant origin. So it's very exciting and still underexplored as to how plants are making these compounds. Elucidating these biosynthetic pathways will give rise to a lot of different potential methods and alternative routes to synthesizing these potential drug candidates.

GEARIN: Plants excel at creating chemicals with special properties, but they’re also inventive in how they use their tissues to protect themselves from the outside world. Weng lab graduate student Joe Jacobowitz studies how plants defend their pollen from the summer sun and winter chill.

JOSEPH JACOBOWITZ: When we're growing crops, if they become stressed at the wrong time with the growing season, like, if there's a drought, or if there's a cold snap, or a heat wave, something that can happen is the plants become sterile. And that's a problem, especially if you're growing the crops to collect the seeds, because the seeds, it's the product of fertilization, so if the plant is sterile, then you get no seeds and then you get no crop.

GEARIN: Joe has shed light on why stress can make plants sterile by studying Arabidopsis, a model plant species. His research revealed that plants require two specific genes to make the tapetum, the plant tissue that nourishes and protects pollen grains. The genes produce proteins in the tapetum that act like the mortar holding together the bricks in a wall. When the genes are knocked out, the tapetum collapses and the plant can’t make pollen.

JACOBOWITZ: And one of the things that's been observed with these stress-induced sterile crops is that the tapetum sort of swells, which is the same thing that I saw in my mutant plants of Arabidopsis. It's not really understood why the swelling happens. And I feel like my research maybe provides a little bit of insight into why it's happening, which might help us to prevent it from happening with crops.

GEARIN: These findings could prove important to raising crop plants as climate change becomes more severe and increases stress on plants. But the tapetum isn’t the only line of defense for pollen grains. The grains themselves are coated with sporopollenin, one of the toughest compounds in the living world.

JACOBOWITZ: Sporopollenin is basically like a shell that protects pollen grains, and sporopollenin is this material that is actually the toughest biopolymer that is known in nature. And it's really not well understood what makes it so much tougher than all the other polymers that organisms are making, and it's not understood how it was made. 

What Jing-Ke was interested in doing was pursuing those questions in the lab. That's what I began when I joined the lab. I spent a lot of time essentially trying to find genes that are involved in sporopollenin biosynthesis, and then from there trying to figure out what those genes are doing and how they're actually contributing to making this polymer.

GEARIN: Unlike most of the plant’s tissues, pollen has to make a perilous journey from one flower to another.

JACOBOWITZ: It has to survive harsh conditions, sometimes it gets attached to insects, sometimes it's being pushed around by wind, it's experiencing high light conditions, it's experiencing very dry conditions, and it's this really important part of the plant life cycle, because without pollen, you know, for most plants, without pollen, you're not going to get the next generation. So we think that sporopollenin is really important. It needs to be so strong because the pollen is such a vulnerable part of the plant life cycle—the strength of sporopollenin is proportional to the vulnerability of the pollen.

GEARIN: And the remarkable properties of sporopollenin could make it useful for other things, says Sophia Xu, a grad student in the Weng lab, who is exploring how plants make sporopollenin.

SOPHIA XU: This thing is extremely durable. It withstands both physical and chemical forces. Previous genetic studies have identified some of the enzymes that are involved in making sporopollenin. Since I’m interested in more in the biochemistry and enzymology side, I’m taking some of these enzymes, and now that we know what the chemical structure of sporopollenin looks like, now we can start to guess, like, this enzyme falls into this class of enzymes, so we think it might be making this modification to sporopollenin. That’s what I’ve been trying to test. 

GEARIN: A material that resists breaking down could have uses in protecting metallic products from the elements and making them last longer, reducing the need to manufacture more.

XU: One of the interesting applications that Jing-Ke likes to talk about is if you have this durable coating that can also withstand weather, it might be a useful coating for things like bikes, which are, especially in Boston winters, prone to rusting.

GEARIN: But that’s not all. If engineered plants could produce sporopollenin in large amounts, not just coating their pollen but also produced elsewhere on the plant, they could be used to store large amounts of carbon and permanently remove it from the atmosphere, explains Joe Jacobowitz.

JACOBOWITZ: There is an idea that's beginning to gain traction in plant biology in general, which is to take plants, which can sequester carbon dioxide, and use them to take carbon dioxide out of the atmosphere, and then bury it in these polymers, which are very carbon dense, essentially. It's like one of the toughest biopolymers there are, we actually have no idea how it's degraded in nature. And the more decay resistant it is, the more permanent the sequestration of the carbon dioxide is. So the idea would be to make plants that make a lot of sporopollenin.

GEARIN: The first step, says Sophia Xu, is to figure out how plants manufacture sporopollenin in their cells so that scientists can harness the process and potentially engineer carbon-capturing organisms.

XU: If we can understand what these enzymes are doing, one of the practical applications is definitely to engineer systems — not even just plants — to be able to make more sporopollenin, and do the carbon sequestration that way. 

GEARIN: To accomplish this ambitious goal, researchers in the Weng lab will work together with Whitehead Institute Member Mary Gehring, who specializes in plant molecular biology and genomics; with Whitehead Institute Member Jonathan Weissman, who will provide expertise in precision genome editing; as well as Xuanhe Zhao in MIT’s Department of Mechanical Engineering, who will guide the design and testing of biopolymers.

Working on science that can help our society become more sustainable helps deal with the anxiety caused by climate change, says Carly Martin.

MARTIN: I feel more motivated than I ever have before, because I walk outside and I experience the effects of climate change every day. It's something that is impossible to ignore when you are a biologist and have this really clear perspective about how climate change is threatening natural ecosystems—but also your own existence. Working on such a big problem is a great way to make yourself a little bit less worried about it, because at least you know that you're doing as much as you can to address it. It's incredibly rewarding and I think has honestly just been great for my own mental health, because it's a problem that is much less scary if you understand it and know that the thing you're working on might end up helping it a little bit.

GEARIN: You can learn more about sustainability research at Whitehead Institute on our website at Find past episodes of AudioHelicase and stay tuned for new ones by subscribing on Soundcloud and iTunes. Thanks for listening.



Interviews by Greta Friar and Eva Frederick. Music by Pierce Murphy (CC BY 4.0) and Chris Zabriskie (CC BY 3.0). Produced and hosted by Conor Gearin. 



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