Research Area: Biochemistry, Biophysics, and Structural Biology

3 Questions: Brady Weissbourd on a new model of nervous system form, function, and evolution

Developing a new neuroscience model is no small feat. New faculty member Brady Weissbourd has risen to the challenge in order to study nervous system evolution, development, regeneration, and function.

Lillian Eden | Department of Biology
April 26, 2023

How does animal behavior emerge from networks of connected neurons?  How are these incredible nervous systems and behaviors actually generated by evolution? Are there principles shared by all nervous systems or is evolution constantly innovating? What did the first nervous system look like that gave rise to the incredible diversity of life that we see around us?

Combining the study of animal behavior with studies of nervous system form, function, and evolution, Brady Weissbourd, a new faculty member in the Department of Biology and investigator in The Picower Institute for Learning and Memory, uses the tiny, transparent jellyfish Clytia hemisphaerica, a new neuroscience model.

Q: In your work, you developed a new model organism for neuroscience research, the transparent jellyfish Clytia hemisphaerica. How do these jellyfish answer questions about neuroscience, the nervous system, and evolution in ways that other models cannot?

A: First, I believe in the importance of more broadly understanding the natural world and diversifying the organisms that we deeply study. One reason is to find experimentally tractable organisms to identify generalizable biological principles – for example, we understand the basis of how neurons “fire” from studies of the squid giant axon. Another reason is that transformative breakthroughs have come from identifying evolutionary innovations that already exist in nature – for example, green fluorescent protein (GFP, from jellyfish) or CRISPR (from bacteria). In both ways, this jellyfish is a valuable complement to existing models.

I have always been interested in the intersection of two types of problems: how nervous systems generate our behaviors; and how these incredible systems were actually created by evolution.

On the systems neuroscience side, ever since working on the serotonin system during my PhD I have been fascinated by the problem of how animals control all of their behaviors simultaneously in a flexible and context-dependent manner, and how behavioral choices depend not just on incoming stimuli but on how those stimuli interact with constantly changing states of the nervous system and body. These are extremely complex and difficult problems, with the particular challenge of interactions across scales, from chemical signaling and dynamic cell biology to neural networks and behavior.

To address these questions, I wanted to move into a model organism with exceptional experimental tractability.

There have been exciting breakthroughs in imaging techniques for neuroscience, including these incredible ways in which we can actually watch and manipulate neuronal activity in a living animal. So, the first thing I wanted was a small and transparent organism that would allow for this kind of optical approach. These jellyfish are a few millimeters in diameter and perfectly transparent, with interesting behaviors but relatively compact nervous systems. They have thousands of neurons where we have billions, which also puts them at a nice intermediate complexity compared to other transparent models that are widely used – for example, C. elegans have 302 neurons and larval zebrafish have something like 100,000 in the brain alone. These features will allow us to look at the activity of the whole nervous system in behaving animals to try to understand how that activity gives rise to behaviors and how that activity itself arises from networks of neurons.

On the evolution side of our work, we are interested in the origins of nervous systems, what the first nervous systems looked like, and broadly what the options are for how nervous systems are organized and functioning: to what extent there are principles versus interesting and potentially useful innovations, and if there are principles, whether those are optimal or somehow constrained by evolution. Our last common ancestor with jellyfish and their relatives (the cnidarians) was something similar to the first nervous system, so by comparing what we find in cnidarians with work in other models we can make inferences about the origins and early evolution of nervous systems. As we further explore these highly divergent animals, we are also finding exciting evolutionary innovations: specifically, they have incredible capabilities for regenerating their nervous systems. In the future, it will be exciting to better understand how these neural networks are organized to allow for such robustness.

Q: What work is required to develop a new organism as a model, and why did you choose this particular species of jellyfish?

A: If you’re choosing a new animal model, it’s not just about whether it has the right features for the questions you want to ask, but also whether it technically lets you do the right experiments. The model we’re using was first developed by a research group in France, who spent many years doing the really hard work of figuring out how to culture the whole life cycle in the lab, injecting eggs, and developing other key resources. For me, the big question was whether we’d be able to use the genetic tools that I was describing earlier for looking at neural activity. Working closely with collaborators in France, our first step was figuring out how to insert things into the jellyfish genome. If we couldn’t figure that out, I was going to switch back to working with mice. It took us about two years of troubleshooting, but now we can routinely generate genetically modified jellyfish in the lab.

Switching to a new animal model is tough – I have a mouse neuroscience background and joined a postdoc lab that used mice and flies; I was the only person working with jellyfish but had no experience. For example, building an aquaculture system and figuring out how to keep jellyfish healthy is not trivial, particularly now that we’re trying to do genetics. One of my goals is now to optimize and simplify this whole process so that when other labs want to start working with jellyfish we have a simple aquaculture platform to get them started, even if they have no experience.

In addition to the fact that these things are tiny and transparent, the main reason that we chose this particular species is because it has an amazing life cycle that makes it an exciting laboratory animal.

They have separate sexes that spawn daily with the fertilized eggs developing into larvae that then metamorphose into polyps. We grow these polyps on microscope slides, where they form colonies that are thought to be immortal. These colonies are then constantly releasing jellyfish, which are all genetically identical “clones” that can be used for experiments. That means that once you create a genetically modified strain, like a transgenic line or a knockout, you can keep it forever as a polyp colony – and since the animals are so small, we can culture them in large numbers in the lab.

There’s still a huge amount of foundational work to do, like characterizing their behavioral repertoire and nervous system organization. It’s shocking how little we know about the basics of jellyfish biology – particularly considering that they kill more people per year than sharks and stingrays combined – and the more we look into it the more questions there are.

Q: What drew you to a faculty position at MIT?

A: I wanted to be in a department that does fundamental research, is enthusiastic about basic science, is open-minded, and is very diverse in what people work on and think about. My goal is also to be able to ultimately link mechanisms at the molecular and cellular level to organismal behavior, which is something that MIT Biology is particularly strong at doing. It’s been an exciting first few months! MIT Biology is such an amazing place to do science and it’s been wonderful how enthusiastic and supportive everyone in the department has been.

I was additionally drawn to MIT by the broader community and have already found it so easy to start collaborations with people in neuroscience, engineering, and math. I’m also thrilled to have recently become a member of The Picower Institute for Learning and Memory, which further enables these collaborations in a way that I believe will be transformational for the work in my lab.

It’s a new lab. It’s a new organism. There isn’t a huge, well-established field that is taking these approaches. There’s so much we don’t know, and so much that we have to establish from scratch. My goal is for my lab to have a sense of adventure and fun, and I’m really excited to be doing that here in MIT Biology.

3 Questions: Sara Prescott on the brain-body connection

New faculty member Sara Prescott investigates how sensory input from within the body control mammalian physiology and behavior.

Lillian Eden | Department of Biology
April 26, 2023

Many of our body’s most important functions occur without our conscious knowledge, such as digestion, heartbeat, and breathing. These vital functions depend on the signals generated by the “interoceptive nervous system,” which enables the brain to monitor our internal organs and trigger responses that sometimes save our lives. One second you are breathing normally as you eat your salad and the next, when a vinegar-soaked crouton enters your throat, you are coughing or swallowing to protect and clear your airway. We know our bodies are sensitive to cues like irritants, but we still have a lot to learn about how the interoceptive system works to meet our physiological needs, keep organs safe and healthy, and affect our behavior. We can also learn how chronic insults may lead to organ dysfunction and use what we learn to create therapeutic interventions.

Focusing on the airway, Sara Prescott, a new faculty member in the Department of Biology and Investigator in The Picower Institute for Learning and Memory, seeks to understand the ways our nervous systems detect and respond to stimuli in health and disease.

Q: You’re interested in interoceptive biology. What makes the nervous system of mice a good model for doing that?

A: Our flagship system is the mammalian airway. We use a mouse model and modern molecular neuroscience tools to manipulate various neural pathways and observe what the effects are on respiratory function and animal health.

Neuroscience and mouse work have a reputation for being a little challenging and intense, but I think this is also where we can ask really important questions that are useful for our everyday lives — and the only place where we can fully recapitulate the complexity of nervous system signaling all the way down to our organs, back to our brain, and back to our organs.

It’s a very fun place to do science with lots of open questions.

One of the core discoveries from my postdoctoral work was focusing on the vagus nerve as a major body-to-brain conduit, as it innervates our lungs, heart and gastrointestinal tract. We found that there were about 40 different subtypes of sensory neurons within this small nerve, which is really a remarkable amount of diversity and reflects the massive sensory space within the body. About a dozen of those vagal neurons project to the airways.

We identified a rare neuron type specifically responsible for triggering protective responses like coughing when water or acid entered the airway. We also discovered a separate population of neurons that make us feel and act sick when we get a flu infection. The field now knows what four to five vagal populations of neurons are actually sensing in the airways, but the remaining populations are still a mystery to us; we don’t know what those populations of sensory neurons are detecting, what their anatomy is, and what reflex effects those neurons are evoking.

Looking ahead, there are many exciting directions for the interoceptive biology field. For example, there’s been a lot of focus on characterizing the circuits underlying acute motor reflexes, like rapid responses to visceral stimuli on the timescale of minutes to hours. But we don’t have a lot of information about what happens when these circuits are activated over long periods of time. For example, respiratory tract infections often last for weeks or longer. We know that the airways undergo changes in composition when they’re exposed to different types of infection or stress to better accommodate future threats. One of the hypotheses we’re testing is that chronically activating neural circuits may drive changes in organ composition. We have this idea, which we’re calling reflexive remodeling: neurons may be communicating with stem cells and progenitor cells in the periphery to drive adaptive remodeling responses.

We have the genetic, molecular and circuit scale tools to explore this pheno­­­menon in mice. In parallel, we’re also setting up some in vitro models of the mouse airway mucosa to expedite receptor screening and to explore basic mechanisms of neuron-epithelium crosstalk. We hope this will inform our understanding of how the airway surface senses and responds to different types of irritants or damage. 

Q: Why is understanding the peripheral nervous system important, and what parts of your background are you drawing on for your current research?

A: The lab focuses on really trying to explore the body-brain connection. 

People often think that our mind exists in a vacuum, but in reality, our nervous system is heavily integrated with the rest of the body, and those neural interfaces are important, both for taking information from our body or environment and turning it into an internal representation of the world, and, in reverse, being able to process that information and being able to enact changes throughout the body. That includes things like autonomic reflexes, basic functions of the body like breathing, blood-gas regulation, digestion, and heart rate.

I’ve integrated both my graduate training and postdoctoral training into thinking about biology across multiple scales.

Graduate school for me was quite focused on deep molecular mechanism questions, particularly gene regulation, so I feel like that has been very useful for me in my general approach to neuroscience because I take a very molecular angle to all of this.

It also showed me the power of in vitro models as reductionist tools to explore fundamental aspects of cell biology. During my postdoc, I focused on larger, emergent phenotypes. We were able to manipulate specific circuits and see very impressive behavioral responses in animals. You could stimulate about 100 neurons in a mouse and see that their breathing would just stop until you remove the stimulation, and then the breathing would return to normal.

Both of those experiences inform how we approach a problem in my research. We need to understand how these circuits work, not just their connectivity at the anatomical level but what is driving their changes in sensitivity over time, the receptor expression programs that affect how they sense and signal, how these circuits emerge during development, and their gene expression.

There are still s­o many foundational questions that haven’t been answered that there’s enough to do in the mouse for quite some time.

Q: This all sounds fascinating. Where does it lead?

A: Human health has been my north star for a long time and I’ve taken a long, wandering path to find particular areas where I can scratch whatever intellectual itch that I have.

I originally thought I would be a doctor and then realized that I felt like I could have a more lasting impact by discovering fundamental truths about how our bodies work. I think there are a number of chronic diseases in which autonomic imbalance is actually a huge clinical component of the disorder.

We have a lot of interest in some of these very common airway remodeling diseases, like chronic obstructive pulmonary disorder—COPD—asthma, and potentially lung cancer. We want to ask questions like how autonomic circuits are altered in disease contexts, and when neurons actually drive features of disease. 

Perhaps this research will help us come up with better molecular, cellular or tissue engineering approaches to improve the outcomes for a variety of autonomic diseases. 

It’s very easy for me to imagine how one day not too far from now we can turn these findings into something actionable for human health.

Paying it forward

When she’s not analyzing data about her favorite biomolecule, senior Sherry Nyeo focuses on improving the undergraduate experience at MIT.

Phie Jacobs | School of Science
January 31, 2023

Since arriving at MIT in fall 2019, senior Sherry Nyeo has conducted groundbreaking work in multiple labs on campus, acted as a mentor to countless other students, and made a lasting mark on the Institute community. But despite her well-earned bragging rights, Nyeo isn’t one to boast. Instead, she takes every opportunity to express just how grateful she is to the professors, alumni, and fellow students who have helped and inspired her during her time at MIT. “I like helping people if I can,” says Nyeo, who is majoring in computer science and molecular biology, “because I got helped so much.”

Nyeo’s passion for science began when she applied for the Selective Science Program at Tainan First Senior High School, widely considered one of the most prestigious high schools in Taiwan. “Preparing for that process made me realize that biology was pretty cool,” she recalls.

When Nyeo was 16, her family moved from Taiwan to Colorado, where she continued to cultivate her interest in STEM. Although she excelled at biology, she initially struggled to master computer science. “[Programming] was really hard for me,” she says. “It was a completely different way of thinking.” When she arrived at MIT, she decided to pursue a degree in computer science precisely because she knew she would find it challenging and because she appreciates how vital data analysis is to the field of biology. After all, she says, when you’re working at the scale of cells and molecules, “you need a lot of data to describe what’s going on.”

In the winter of her first year at MIT, Nyeo began doing hands-on research in laboratories on campus through the Undergraduate Research Opportunities Program (UROP). Her work in the lab of Whitehead Fellow Silvi Rouskin sparked an enduring interest in RNA, which she has come to regard as her “favorite biomolecule.”

Nyeo’s work in the Rouskin lab focused on alternative RNA structures and the roles they play in human and viral biology. While DNA mostly exists as a double helix, RNA can fold itself into a huge variety of structures in order to fulfill different functions. During her time as a student researcher, Nyeo has demonstrated a similar ability to adapt to different circumstances. When MIT campus members evacuated due to the Covid-19 pandemic in March 2020, and her UROP became entirely remote, she treated her time away from the lab as an opportunity to explore the computational side of research. Her work was subsequently included in a Nature Communications paper on the SARS-CoV-2 genome, on which she is listed as a co-author.

Since returning to campus, Nyeo has often worked in multiple labs simultaneously, conducting innovative research while also juggling classes, internships, and several demanding extracurriculars. Through it all, she has continued to pursue her fascination with RNA, a tiny, somewhat unassuming molecule that nonetheless has a massive impact on practically every aspect of our biology. Nyeo, who has shown herself to be equally multifaceted, seems especially well-suited to the study of this remarkable biomolecule.

Although Nyeo’s work in the life sciences keeps her busy, she finds time to nurture a diverse set of other passions. She took a class on experimental ethics, is working on an original screenplay, and has even picked up a minor in German. Since her sophomore year, she has also been a part of the New Engineering Education Transformation (NEET) program, which provides students with multidisciplinary interests the opportunity to collaborate across departments. Through NEET, currently directed by professor of biological engineering Mark Bathe, Nyeo has been able to pursue her interest in bioengineering research and connect to a vast community of students and professors. Most recently, she has been working within the Bathe BioNano Lab to use DNA to engineer new materials at the nanometer scale.

Nyeo hopes to put her skills to use by pursuing a career in biotechnology. She is currently minoring in management and dreams of one day starting her own company. But she doesn’t want to leave academia behind just yet and has begun working on applications for PhD programs in biology. “I originally came in thinking that I would just go straight into the biotech industry,” Nyeo explains. “And then I realized that I don’t dislike research and that I actually enjoy it.”

As part of her current work in the lab of professor of biology David Bartel, Nyeo investigates how viral infection affects RNA metabolism, and she often finds herself using her computational skills to help postdocs with their data analysis. In fact, one of the things Nyeo has most enjoyed about working as a student researcher is the opportunity to join a network of people who provide one another with support and guidance.

Nyeo’s willingness to help others is perhaps the aspect of her personality that best suits her to the study of RNA. Over the past few decades, researchers have discovered an increasingly large number of therapeutic uses for RNA, including cancer immunotherapy and vaccine development. In the summer of 2022, Nyeo worked as an intern at Eli Lilly and Company, where she helped identify potential targets for RNA therapeutics. She may continue to explore this area of research when she eventually enters the biotech industry. In the meantime, however, she’s finding ways to help people closer to home.

Since her first year, Nyeo has been a part of the MIT Biotech Group. When she first joined, the group had a fairly small undergraduate presence, and most events were geared toward graduate students and postdocs. Nyeo immediately dedicated herself to making the group more welcoming for undergraduates. As the director of the Undergraduate Initiative and later the undergraduate student president, she was a leading architect of a new seminar series in which MIT alumni came to campus to teach undergraduates about biotechnology. “There are a lot of technical terms associated with [biotech],” Nyeo explains. “If you just come in as an undergrad, not knowing what’s happening, that can be a bit daunting.”

Between her research in the Bartel lab and her work with NEET and the MIT Biotech Group, Nyeo doesn’t have a lot of free time, but she dedicates most of it to making MIT a friendlier environment for new students. She promotes research opportunities as a UROP panelist and has worked as an associate advisor since her junior year. She helps first-year students choose and register for classes, works with faculty advisors, and provides moral support to students who are feeling overwhelmed with options. “When I came [to MIT], I also didn’t know what I wanted to do,” Nyeo explains. “Upperclassmen helped me a lot with that process, and I want to pay it forward.”

Uncovering how cells control their protein output

Gene-Wei Li investigates the rules that cells use to maintain the correct ratio of the proteins they need to survive.

Anne Trafton | MIT News Office
January 4, 2023

A typical bacterial genome contains more than 4,000 genes, which encode all of the proteins that the cells need to survive. How do cells know just how much of each protein they need for their everyday functions?

Gene-Wei Li, an MIT associate professor of biology, is trying to answer that question. A physicist by training, he uses genome-wide measurements and biophysical modeling to quantify cells’ protein production and discover how cells achieve such precise control of those quantities.

Using those techniques, Li has found that cells appear to strictly control the ratios of proteins that they produce, and that these ratios are consistent across cell types and across species.

“Coming from a physics background, it’s surprising to me that these cells have evolved to be really precise in making the right amount of their proteins,” Li says. “That observation was enabled by the fact that we are able to design measurements with a precision that matches what is actually happening in biology.”

From physics to biology

Li’s parents — his father, a marine biologist who teaches at a university in Taiwan, and his mother, a plant biologist who now runs a science camp for high school students — passed their affinity for science on to Li, who was born in San Diego while his parents were graduate students there.

The family returned to Taiwan when Li was 2 years old, and Li soon became interested in math and physics. In Taiwan, students choose their college major while still in high school, so he decided to study physics at National Tsinghua University.

While in college, Li was drawn to optical physics and spectroscopy. He went to Harvard University for graduate school, where after his first year, he started working in a lab that works on single-molecule imaging of biological systems.

“I realized there are a lot of really exciting fields at the boundary between disciplines. It’s something that we didn’t have in Taiwan, where the departments are very strict that physics is physics, and biology is biology,” Li says. “Biology is a lot messier than physics, and I had some hesitancy, but I was happy to see that biology does have rules that you can observe.”

For his PhD research, Li used single-molecule imaging to study proteins called transcription factors — specifically, how quickly they can bind to DNA and initiate the copying of DNA into RNA. Though he had never taken a class in biology, he began to learn more about it and decided to do a postdoc at the University of California at San Francisco, where he worked in the lab of Jonathan Weissman, a professor of cellular and molecular pharmacology.

Weissman, who is now a professor of biology at MIT, also trained as a physicist before turning to biology. In Weissman’s lab, Li developed techniques for studying gene expression in bacterial cells, using high-throughput DNA sequencing. In 2015, Li joined the faculty at MIT, where his lab began to work on tools that could be used to measure gene expression in cells.

When genes are expressed in cells, the DNA is first copied into RNA, which carries the genetic instructions to ribosomes, where proteins are assembled. Li’s lab has developed ways to measure protein synthesis rates in cells, along with the amount of RNA that is transcribed from different genes. Together, these tools can yield precise measurements of how much a particular gene is expressed in a given cell.

“We had the qualitative tools before, but now we can really have quantitative information and learn how much protein is made and how important those protein levels are to the cell,” Li says.

Precise control

Using these tools, Li and his students have discovered that different species of bacteria can have different strategies for making proteins. In E. coli, transcription of DNA and translation of RNA into proteins had long been known to be a coupled process, meaning that after RNA is produced, ribosomes immediately translate it into protein.

Many researchers assumed that this would be true for all bacteria, but in a 2020 study, Li found that Bacillus subtilis and hundreds of other bacterial species use a different strategy.

“A lot of other species have what we call runaway transcription, where the transcription happens really fast and the proteins don’t get made at the same time. And because of this uncoupling, these species have very different mechanisms of regulating their gene expression,” Li says.

Li’s lab has also found that across species, cells make the same proportions of certain proteins that work together. Many cellular processes, such as breaking down sugar and storing its energy as ATP, are coordinated by enzymes that perform a series of reactions in a specified sequence.

“Evolution, it turns out, gives us the same proportion of those enzymes, whether in E. coli or other bacteria or in eukaryotic cells,” Li says. “There are apparently rules and principles for designing these pathways that we didn’t know of before.”

Mutations that cause too much or too little of a protein to be produced can cause a variety of human diseases. Li now plans to investigate how the genome encodes the rules governing the correct quantities of each protein, by measuring how changes to genetic and regulatory sequences affect gene expression at each step of the process — from initiation of transcription to protein assembly.

“The next level that we’re trying to focus on is: How is that information stored in the genome?” he says. “You can easily read off protein sequences from a genome, but it’s still impossible to tell how much protein is going to be made. That’s the next chapter.”

The Interview: MIT President Sally Kornbluth

The incoming queen of Kendall Square talks Smoots, "cancel culture," and how to get more young women into STEM.

Jonathan Soroff | Boston Magazine
December 20, 2022

With renewed concerns about diversity, affordability, and censorship on campus—to say nothing about the future of space exploration and renewable energy—there’s a lot going on at MIT these days. For recently named president Sally Kornbluth, who is moving to the Bay State from North Carolina, where she’d served as provost at Duke University since 2014, it means the chance to shape one of the world’s most prestigious universities at a time of momentous change.

We caught up with her to discuss all of that, plus Smoots, the Sox, and how she plans to navigate the academic waters north of the Charles when she officially takes her post on January 1.

What do you anticipate being the best perk of your new job?

I’m a scientist by training, and I haven’t had a lab for some time. So I can live vicariously through the work of others, in a way, and really enjoy the discoveries that they’re making. I expect to learn about a lot of exciting projects, findings, discoveries, and inventions that I can help enable or support in a way that I could never do in my own work. I think it’s going to be like a candy store for the intellectually curious.

What percentage of what goes on academically or in research at MIT do you think will be comprehensible to you since—for most of us—the answer is zero?

Well, I’ll certainly understand what’s going on in the biology department, deeply. A lot of my colleagues, I follow their work. I have some understanding of what’s going on in engineering—although I’m not an engineer—particularly in the biomedical or biological engineering space. And, you know, I’ve closely followed a lot of different disciplines in my work as provost. I’m excited by what’s going on in the arts at MIT, the social sciences, and the humanities. A big part of the MIT ethos and culture is to try to make the work really accessible to others because it’s important to people’s lives on this planet. So, either I will understand it and help to translate it, or my faculty and colleagues will help translate it for me.

First thing you’ll do when you walk in the door?

The first thing I’ve got to do is get a map. I have never seen such a confusing welter of buildings that are numbered in a seemingly crazy manner. And then, honestly, just really get out there and meet everybody: the students, the faculty, the staff. It’s really going to be an exciting moment to get to know all these new people and all their exciting work.

So, offhand, do you know MIT’s Latin motto?

I believe it’s “Mind and hand.”

Yes! “Mens et Manus.” Well done. What do you think are the things you’ll miss most about North Carolina, and what are you most looking forward to in moving to New England?

I’ve been here [in North Carolina] a long time. I’m going to miss all my friends and colleagues. You know, my kids grew up here, there’s people here that I’ve known for years. Also, the weather’s pretty mild here. But it’s funny. I was up at MIT last weekend, and I was walking around with friends, and something really struck me, which is you don’t realize how much the foliage, plants, and trees that you were used to seeing growing up make you feel at home. I grew up in northern New Jersey, and I went to school at Williams College. I was with a friend who’s also from the Northeast, and she reached out and touched this shrub. She said, “You remember this?” I said, “Yes. I haven’t seen it in years.” I’m kind of excited about going back to this environment that’s so familiar.

But probably less excited about a long winter?

Well, I just bought myself a nice warm coat.

This next question is extremely important: Are you a sports fan, and if so, are you ready to swear fealty to Red Sox Nation, Patriots Nation, and Celtics Nation?

It’s so funny. I was thinking about that because when I was growing up, and my father would be watching sports on television, I’d say, “Dad, who are you rooting for?” And he’d say, “Nobody. I just find the game interesting.” I like watching sporting events, but I must admit, I’m not rabid for one team or another. I will be rooting for the MIT Engineers. But I have to say, I’ve gotten emails from people saying, “Don’t you dare root for the Red Sox!” Maybe I’ll maintain my neutrality for a bit, but then I might get sucked in.

But I assume you’ll always have a warm spot for the Blue Devils?

Yeah, of course. Plus, I have an extensive wardrobe of Duke stuff.

In a nutshell, what do you see as MIT’s greatest strength?

Honestly, it’s the ingenuity and brilliance of the faculty and students. If you believe that higher education is the talent development game, you can’t be anyplace better than MIT to help do that. It’s just brilliant people doing what they do best, and it’s amazing to me the amount of mind-bending work going on there.

Here’s another gotcha question: Do you know what a Smoot is?

I do. I know because my son is a graduate student at MIT, and we were walking across the bridge, like a year or two ago, and he explained it to my husband and me.

Are you prepared for, and what do you think of, the incredibly elaborate pranks MIT students are famous for, like taking apart and reassembling a police car on top of the dome?

I have to admit that I find those kinds of things incredibly amusing. I remember hearing about pranks like that throughout my career. My favorite was a sign on an elevator that said, “Elevator has now become voice activated. Please loudly announce the floor you wish to go to.” And there were all these people yelling, “Fourth floor!” It was hilarious. So, I’m familiar with them, and I think it’ll be fun.

On a more serious note, you’re joining a heavily female executive team: board chair, chancellor, provost, dean of science. Do you think that has particular significance?

I think we’ve reached a point, or I hope that we have, where we’re selecting the top talent and tapping into the full range of human talent. I think all of the leaders at MIT, and I hope I’m included, have been selected for their skills. It’s wonderful that they’re also women, but I believe that it’s a really strong team. My husband always says he thinks women should run the world.

How do we, as a society, get more young girls interested and involved with math and science?

One way is that I do think the presence of more women in these areas provides more role models, and it behooves women who have had success in these areas to reach down the pipeline and help others have the same success. The other thing is to have low barriers to entry into these areas. Because in some areas, girls may not have been traditionally encouraged to jump in. Girls, as well as boys, should be able to gravitate to their true interests and talent and not have to scale a wall to get into certain areas.

At this point, you’ve served in an administrative role for nearly nine years. Do you think you could go back to teaching an undergraduate course in your field of biology, or has that ship sailed?

I’d have to do a lot of reading, a lot of catch-up. But the basic skill set is still there. Could I understand what I read and learn to think about ways to teach it effectively? I think so. To go back and run a lab from scratch? That would be a bigger mountain to climb than teaching a course.

Any thoughts about the affirmative action question facing the Supreme Court?

Well, obviously, we’ll see how this plays out, and certainly, MIT will follow the law, whatever that is. But I think the bottom line is that institutions really, really benefit from a diversity of perspectives and a diversity of backgrounds, and regardless of the outcome of the Supreme Court decision, it’s going to be important for a place like MIT to still be able to hear truly diverse voices. A diverse team just comes up with much better ideas and discoveries. It’s not an echo chamber.

Do you think that in academics and society, too much emphasis is placed on sort of “brand name” schools?

There are many, many, many institutions in this country where you can get a fabulous education. So, do I divide the world in that way? Not necessarily. That said, what’s exciting to me about MIT and other institutions you might name is the high concentration of fabulous scholars. There are some institutions that can offer students exposure to that kind of scholarship as part of their experience.

Your predecessor had to navigate censorship and “cancel culture” on campus. How do you intend to handle that?

You’ve got to foster a culture where freedom of speech is strongly supported, even if that speech is maybe something someone doesn’t want to hear. That’s fine, as long as it doesn’t incite violence and doesn’t target individuals. That said, it can be difficult because people feel that words can hurt them. They don’t like to hear things they don’t want to hear. But I believe it’s the role of an educational institution to expose students to ideas or positions that they might not have otherwise entertained or heard.

Will it be weird to be president of a university where your son is a Ph.D. candidate?

[Laughs.] You might ask him that. I hope it won’t be weird for him. For me, it’s delightful because I’ll get to see him more often. And I’m not going to show up at his lab with a batch of cookies.

Thoughts on the idea of making tuition free to all?

You know, I can’t speak to that for MIT now, but I will say this: 85 percent of MIT graduates leave debt-free. There is a very robust financial aid program that’s both need-blind admissions-based and meeting the full needs of students financially. MIT is, no doubt, in a very privileged position in this way to have the resources to do that, but I don’t think that an MIT education is where these problems currently reside.

You were the chair of the trustees for the Duke Kunshan University partnership. China is so demonized these days; do you see it as an ally or a threat?

Well, let me just say up front that the partnership was really meant to bring liberal, American-style education to China, so it was not a deeply political play, nor was it a heavily research-based program. China is a place to approach with some balance. The open exchange of ideas has really fueled science, taking advantage of brilliant ideas from all over the world. But you have to balance that with national security threats and risks, which are very real. And greater minds than mine are grappling with that. I don’t demonize it as a country, but there are certainly thorny issues that have to be navigated.

What are your hobbies or pastimes?

I have two dogs that I like to walk all the time. People will see them walking around campus. I like to read. I have to admit that I like to watch those British mysteries. In fact, given the number I’ve watched, it’s surprising there’s a person left alive in the British Isles. I like to ride my bike. I like to hike. And during the pandemic, I took up needlepoint and felt flower making, which is a little odd. Some sort of latent craftiness that I never knew I had.

Any desire for a Nobel Prize?

No. I’ve never done anything that would merit a Nobel Prize. But I hope to be able to create, continue to create, I should say, fertile ground for future Nobel Prize winners.

 

New tool can assist with identifying carbohydrate-binding proteins

Groundbreaking research can help alleviate the challenges affiliated with studying carbohydrates.

Danielle Doughty | Department of Chemistry
December 19, 2022

One of the major obstacles that those conducting research on carbohydrates are constantly working to overcome is the limited array of tools available to decipher the role of sugars. As a workaround, most researchers utilize lectins (sugar-binding proteins) isolated from plants or fungi, but they are large, with weak binding, and they are limited in their specificity and in the scope of sugars that they detect. In a new study published in ACS Chemical Biology, researchers in Professor Barbara Imperiali’s group have developed a platform to address this shortcoming.

“The challenge with polymers of carbohydrates is that their biosynthesis is not template driven,” said Imperiali, the senior author of the study, and a Professor in the Departments of Chemistry and Biology. “Biology, medicine, and biotechnology have been fueled by technological advancements for proteins and nucleic acids. The carbohydrate field lags terribly behind, and is desperately seeking tools.”

Identifying carbohydrate-binding proteins

Biosynthesizing carbohydrates requires every link between individual sugar molecules to be made by a particular enzyme, and, there’s no ready way to decipher the structures and sequences of complex carbohydrates. Antibodies to carbohydrates can be generated,  but doing so is challenging, expensive, and results in a molecule that is far larger than what is really needed for the research. An ideal resource for this field plagued with limited mechanisms would be discovery of binding proteins, of limited size, that recognize small chunks of carbohydrates to piece together a structure by using those binders, or methods to detect and identify particular carbohydrates within complicated structures.

To achieve their breakthrough, the authors of this study used directed evolution and clever screen design to identify carbohydrate-binding proteins from proteins that have absolutely no ability to bind carbohydrates at all.  Their findings lay the groundwork for identifying carbohydrate-binding proteins with diverse and programmable specificity.

Streamlining for collaboration

This exciting breakthrough will allow researchers to go after a user-defined sugar target without being limited by what a lectin does, or challenged by the abilities of generating antibodies. These results could serve to inspire future collaborations with engineering communities to maximize the efficiency of glycobiology’s yeast surface display pipeline. As it is, this pipeline works well for proteins, but sugars are far more difficult targets and require the pipeline to be modified.

In terms of future applications, the potential for this innovation ranges from diagnostic to, in the longer term, therapeutic, and paves the way for collaborations with researchers at MIT and beyond. Chemistry Professor Laura Kiessling’s research group works with Mycobacterium tuberculosis (Mtb), which has an unusual cell wall composition with unique, distinct, and exclusive sugars. Using this method, a binder could potentially be evolved to that particular feature on Mtb. Chemical Engineering Professor Hadley Sikes develops paper-based diagnostic tools where the binding partner for a particular epitope or marker is laid down, and with the use of this discovery, in the longer term, a lateral flow assay device could be developed.

Laying the groundwork for future solutions

In cancer, certain sugars are over-represented on cell surfaces, so theoretically, researchers can utilize this finding, which is also amenable to labeling, to develop a tool out of the evolved glycan binder for detection.

This discovery also stands to contribute significantly to improving cell imaging. Researchers can modify binders with a fluorophore using a simple ligation strategy, and can then choose the best fluorophore for tissue or cell imaging. The Kiessling group, for example, could apply small protein binders labeled with fluorophore to detect bacterial sugars to initiate fluorescence-activated cell sorting to probe a complex mixture of microbes. This could in turn be used to determine how a patient’s microbiome has been disturbed. It also has the potential to screen the microbiome of a patient’s mouth or their upper or lower gastrointestinal tract to read out the imbalance within the community using these types of reagents. In the more distant future, the binders could potentially have therapeutic purposes like clearing the gastrointestinal tract or mouth of a particular bacterium based on the sugars that the bacterium displays.

A career in biochemistry unfolds

In an MIT summer research program, Rita Anoh learned about molecular machines and the value of collaborations.

Sarah Costello | School of Science
November 1, 2022

Rita Anoh’s first exposure to college-level research was not something she recognized as a path she could follow. While in high school, the daughter of Anoh’s Advanced Placement biology teacher presented a poster to her class about what she was working on in graduate school. “At the time, actually, it did not click to me what she was presenting,” Anoh laughs. “Because I didn’t know that you could do research as such, I just didn’t put it together.”

Instead, Anoh traces the start of her journey to science back to her childhood in Ghana, where she enjoyed spending summers assisting in a health clinic run by her grandmother, a nurse. Anoh especially loved the problem-solving and teamwork involved. “Every time, people would leave like, ‘Problem solved!’ or ‘Oh, my problem is not solved, but I know where to go next.’”

Anoh’s enthusiasm for finding solutions to complex problems shifted from medicine to research when she arrived as an undergraduate at Mount Saint Mary’s University (The Mount) in Maryland, and later as a participant in the 2022 Bernard S. and Sophie G. Gould MIT Summer Research Program in Biology (BSG-MSRP-Bio).

As a first-year majoring in biology at The Mount, Anoh applied to a summer research program with the encouragement of Patrick Lombardi, assistant professor of chemistry. She earned an internship to work in his lab exploring how DNA damage in cells is detected and repaired. Then, the summer following her sophomore year, she participated in the Caltech WAVE Fellows program in the lab of Douglas Rees, the Roscoe Gilkey Dickinson Professor of Chemistry, focusing on the structures and mechanisms of complex metalloproteins and integral membrane proteins. Anoh was also awarded a Barry M. Goldwater Scholarship for students intending to pursue research careers in natural science, mathematics, and engineering. “I was the first sophomore to receive at my school, so that was very exciting,” adds Anoh.

“It’s been a blast”

Eager to continue building her science skills and experience a new city, Anoh quickly accepted an offer to join the BSG-MSRP-Bio program at MIT this past summer.

Anoh spent 10 weeks in the lab of assistant professor of biology Joey Davis, whose lab works to uncover how cells construct and degrade complex molecular machines rapidly and efficiently. Anoh also worked with Robert Sauer, the Salvador E. Luria Professor of Biology at MIT, who studies the relationship between protein structure, function, sequence, and folding.

“It’s been a blast,” says Anoh.

Specifically, her project centered on a complex in the cell that helps oversee proteolysis, or the breakdown of proteins into peptides, or strings of amino acids, and further into amino acids for recycling by the cell. Called ClpXP, this molecular machine is made up of two substructures: ClpX and ClpP. First, ClpX identifies and unfolds peptide sequences in the protein substrate to be broken down; then ClpP breaks the unfolded peptides down into smaller fragments.

In her research, Anoh looked at the degradation of a protein RseA by ClpXP bound to another piece of molecular machinery called SspB. This “adapter protein” delivers the targeted protein to ClpXP to begin breaking it down. By degrading RseA, ClpXP plays an essential role in the signaling pathway in bacteria allowing the bacterial cell to respond to stress. Along with her mentor, she examined samples under a cryo‐electron microscope (Cryo-EM) at MIT.nano and collected data to determine its 3D map, shedding light on how ClpXP with the help of SspB breaks down proteins within a cell.

In addition to her gain of technical and research skills, one of Anoh’s takeaways from her summer at MIT was “how collaborative and dynamic science is in general,” she says, especially with mentors such as Alireza Ghanbarpour, a joint postdoc in the Davis and Sauer labs.

“During her time at our lab, she became friends with everyone,” says Ghanbarpour, who mentored Anoh and another undergraduate student whom Anoh befriended. “Rita developed a great relationship with her and, on many occasions, helped her with her project.”

Anoh attended group meetings, lab retreats, and conferences. In MSRP seminars, she heard from MIT researchers about their own experiences solving problems using advice from fellow scientists.

“I talk to my peers about what we’re all doing, and how different people at the same lab work together, or how different labs work together,” Anoh says. “I’ve learned different ways to achieve the same goal.”

Ghanbarpour also assisted Anoh in deepening her understanding of the material beyond the bench. Passionate about structural biology and biochemistry, he provided explanations and connected Anoh with materials to expand her knowledge of relevant researchers and concepts. “I was learning not just stuff in the lab but actually the meaning of what I was doing, so that was pretty cool,” she says.

Now in her senior year back at The Mount, Anoh intends to keep an open mind. An open mind, after all, is why she acted on her professor’s suggestion when she was a first-year student to apply to the program that set her on her current path to a research career. Without a doubt, though, Anoh says she plans to pursue a PhD in biochemistry and mentor young researchers like herself along the way.

Ankur Jain Named as Pew Scholar in Biomedical Sciences
Merrill Meadow | Whitehead Institute
June 13, 2022

The Pew Charitable Trusts has selected Whitehead Institute Member Ankur Jain to be a 2022 Pew Scholar in the Biomedical Sciences. The Pew program provides funding to young investigators of outstanding promise who work in areas of science relevant to the advancement of human health.

Jain, who joined the Whitehead Institute faculty in 2019, is one of 22 scientists selected to receive this year’s honor, chosen from among 197 nominations submitted by leading U.S. academic and research institutions. “I am grateful to the Pew Trusts for funding our work, and thrilled to be a part of the Pew community,” says Jain, who is also an assistant professor of biology and the Thomas D. and Virginia W. Cabot Career Development Professor at Massachusetts Institute of Technology.

The Pew award will provide research support for the next four years, enabling him to study the role of evolutionarily ancient metabolites called polyamines, which are essential for cell growth and survival.

“Polyamine concentrations within cells are carefully regulated, and disruptions in polyamine production are known to be associated with conditions ranging from cancer and aging to neurological disorders such as Parkinson’s disease” Jain explains. “But, despite being studied for more than a century, the specific role polyamines play in both healthy and diseased cells remains obscure. This is due, in part, to a lack of technologies effective in probing polyamines.”

Jain’s lab will harness the cell’s own polyamine detection machinery to build new tools to inspect polyamines. Those tools will allow his team to measure and track polyamines in individual cells, study how cells maintain their polyamine content, and explore how changing polyamine levels affect cellular functions. “Ultimately, this work could provide the basis for novel strategies for treating cancer or promoting healthy aging,” Jain observes.

Previously, Jain received a 2017 NIH Pathway to Independence Award and was named a 2019 Packard Fellow for Science and Engineering. He is the third current Whitehead Member to be named a Pew Scholar, following in the steps of Mary Gehring (2010) and Jing-Ke Weng (2014). Former Whitehead Fellow Fernando Camargo, now professor of stem cell and regenerative biology at Harvard University, also became a Pew Scholar in 2010.

Launched in 1985, the Pew Scholars in the Biomedical Sciences program supports top U.S. scientists at the assistant professor level and has, since inception, provided nearly 1000 young investigators with  funding for research projects that, though seemingly risky, have the potential to benefit human health. Pew Scholars are selected by a national advisory committee of eminent scientists, who evaluate candidates on the basis of proven creativity.

More information about Jain’s selection, the 2022 class of Pew Scholars, and the Pew Scholars program is available here.

Researchers biosynthesize anti-cancer compound found in venomous Australian tree
Eva Frederick | Whitehead Institute
April 20, 2022

The Australian stinging tree (Dendrocnide moroides) is a plant that many people avoid at all costs. The tree, which is a member of the nettle family, is covered in thin silicon needles laced with one of nature’s most excruciating toxins, a compound called moroidin. “It’s notorious for causing extreme pain, which lingers for a very long time,” said Whitehead Institute Member Jing-Ke Weng.

There’s another side to moroidin, though; in addition to causing pain, the compound binds to cells’ cytoskeletons, preventing them from dividing, which makes moroidin a promising candidate for chemotherapy drugs.

Harvesting enough of the chemical to study has proven difficult, for obvious reasons. Now, in a paper published April 19 in the Journal of the American Chemical Society, Weng, who is also an associate professor of biology at the Massachusetts Institute of Technology (MIT) and former postdoc Roland Kersten, now an assistant professor at the University of Michigan College of Pharmacy, present the first published method to biosynthesize moroidin within the tissues of harmless plants such as tobacco, facilitating research on the compound’s utility for cancer treatments.

Taking a leaf out of plants’ book to create peptides

Moroidin is a bicyclic peptide — a type of molecule made up of building blocks called amino acids and circularized to contain two connected rings. For synthetic chemists, moroidin has proved nearly impossible to synthesize due to its complex chemical structure. Weng and Kersten wanted to dig deeper into what methods the plants were using to create this molecule.

In plant cells, cyclic peptides are made from specific precursor proteins synthesized by the ribosome, the macromolecular machine that produces proteins by translating messenger RNAs. After leaving the ribosome, these precursor proteins are further processed by other enzymes in the cell to give rise to the final cyclic peptides. In 2018, Weng and Kersten had elucidated the biosynthetic mechanism of another type of plant peptides called lyciumins, first found in the goji berry plant, which gave them some insight into how post-translational modifications might play a role in creating different types of plant peptide chemistry. “We learned a lot about the principal elements of this system by studying lyciumins,” said Weng.

When they began to look into how moroidin was synthesized, the researchers found a few other plants, such as Kerria japonica and Celosia argentea, also produce peptides with similar chemistry to moroidin. “That really gave us the very critical insight that this is a new class of peptides,” Weng said.

Weng and Kersten previously learned that the BURP domain, which is part of the precursor proteins for lyciumins and several other plant cyclic peptides, catalyzes key reactions involved in the peptide ring formation. They found that the BURP domain was present in the precursor proteins for moroidins in Kerria japonica, and seemed to be essential for creating the two-ring structure of the molecules. The BURP domain creates ring chemistry when in the presence of copper, and when the researchers incubated the moroidin precursor protein with copper chloride in the lab together with other downstream proteolytic enzymes, they were able to create moroidin-like peptides.

With this information, they were able to produce a variety of moroidin analogs in tobacco plants by transgenically expressing the moroidin precursor gene of Kerria japonica and varying the core motif sequence corresponding to moroidin peptides. “We show that you can produce the same moroidin chemistry in a different host plant,” Weng said. “Tobacco itself is easier to be farmed on a large scale, and we also think in the future we can derive a plant cell line from the existing tobacco cell lines that we put in the moroidin precursor peptide, then we can use the cell line to produce the molecule, which really enables us to scale up for medicine production.”

Future use of moroidin

Moroidin’s anti-cancer property is due, at least in part, to the compound’s unique structure that allows it to bind to a protein called tubulin. Tubulin forms a skeletal system for living cells, and provides the means by which cells separate their chromosomes as they prepare to divide. Currently, two existing anti-cancer drugs, vincristine and paclitaxel, work by binding tubulin. These two compounds are derived from plants as well (the Madagascar periwinkle and Pacific yew tree, respectively).

In their new work, Weng and Kersten synthesized a moroidin analog called celogentin C. They tested its anti-cancer activity against a human lung cancer cell line, and found that the compound was toxic to the cancer cells. Their new study also suggests potentially new anti-cancer mechanisms specific to this lung cancer cell line in addition to tubulin inhibition.

In the past, researchers have run into issues when trying to create effective drugs from peptides. “There are two major challenges for peptides as medicine,” Weng said. “For one thing they are not very stable in vivo, and for another they are not very bioavailable and don’t readily pass the membrane of a cell.”

But cyclic peptides like moroidin and its analogs are a bit different. “These peptides essentially evolve to be drug-like,” Weng said. “In the case of the Australian stinging tree, the peptides are present because the plants want to deter any animals that want to eat the leaves. So over millions of years of evolution these plants eventually figured out a way to construct these specific cyclic peptides that are stable, bioavailable and can get to the animal that is trying to eat the plants.”

It’s likely that the painful reaction that occurs when moroidin enters the body through a sting from the tree would not be an issue in traditional methods of administering chemotherapy. “The pain is really caused if you get injections of the compound into the skin,” Weng said. “If you take it orally or intravenously, your body will most likely not sense the pain.”

Somewhat counterintuitively, the compound could also be used as a pain reliever. “If something causes pain, you can sometimes use that as an anti-pain medicine,” Weng said. “You could essentially exhaust the pain receptors, or if you alter the structure a little bit, you could turn an agonist into an antagonist and potentially block the pain.”

On a more fundamental level, moroidin could help researchers study pain receptors. “We don’t know exactly why being stung by the stinging tree produces that enormous amount of pain, and there may be additional pain receptors people haven’t identified,” Weng said. “Being able to synthesize moroidin provides a chemical probe that allows us to study this unknown pain perception in humans.”

In the future, the researchers hope to create analogs of moroidin to study, and hopefully create an optimal version for use in cancer therapy. “We want to generate a library of moroidin-like peptides,” Weng said. “We’ve done this for lyciumins, and since the initial moroidins are anti-tubulin molecules, we can use this system to find an improved version that binds to tubulin even tighter and contains other pharmacological properties making it suitable to be used as a therapeutic.

Directing evolution in search of a better plastic-degrading enzyme

Graduate student En Ze Linda Zhong-Johnson is creating new methods to measure and enhance enzyme activity — which she hopes will help restore a plastic-choked world.

Grace van Deelen
April 21, 2022

After graduating with her undergraduate degree in molecular genetics from the University of Toronto in 2016, En Ze Linda Zhong-Johnson celebrated with a trip to Alaska. There, she saw a pristine landscape unlike the plastic-littered shores of the Toronto waterfront. “What I saw up there was so different from what I saw in the city,” Zhong-Johnson says. “I realized there shouldn’t be all this waste floating everywhere, in our water, in our environment. It’s not natural.”

As a trained biologist, Zhong-Johnson began to think about the problem of plastic pollution from a biological perspective. One solution, she thought, could be biological recycling: a process by which living organisms break down materials, using digestion or other metabolic processes to turn these materials into smaller pieces or new compounds. Composting, for example, is a type of biological recycling — microbes in the soil break down discarded food, speeding up the decomposition process. Zhong-Johnson wondered if there were any organisms on Earth that could use the carbon in polyethylene terephthalate (PET), a common plastic used in water bottle and food packaging, as an energy source.

Earlier that same year, Japanese scientists discovered that a bacterium, Ideonella sakaiensis, could do just that by producing enzymes that could break down PET. The two main PET-degrading enzymes, referred to as IsPETase and IsMHETase, are able to turn PET into two chemical compounds, terephthalic acid and ethylene glycol, which I. sakaiensis can use for food.

The discovery of these enzymes opened up many new questions and possible applications that scientists have continued to work on since. However, because there was — and still is — much to learn about PET-degrading enzymes, they are still not widely used to recycle consumer products. Zhong-Johnson figured that, in graduate school, she could build on the existing IsPETase research and help to accelerate their use at recycling facilities. Specifically, she wanted to engineer the enzyme to work faster at lower temperatures, and study how, fundamentally, the enzymes worked on the surface of PET plastic to degrade it.

“I hopped on the excitement train, along with the rest of the world,” she says.

A better enzyme

After receiving her acceptance to MIT to complete her PhD, Zhong-Johnson approached various professors, pitching her idea to speed up IsPETase activity. Christopher Voigt, the Daniel I. C. Wang Professor of Biological Engineering, and Anthony Sinskey, professor of biology, were interested, and formed a co-advisorship to support Zhong-Johnson’s project. Sinskey, in particular, was impressed by her idea to help solve the world’s plastic problem with PET-degrading enzymes.

Woman pipetting in lab
Zhong-Johnson screens for enzyme variants with improved activity. Credit: Grace van Deelen

“Plastic pollution is a big problem,” he says, “and that’s the kind of problem my lab likes to tackle.” Plus, he says, he feels “committed to helping graduate students who want to apply their science and technology learnings to the environment.”

While the idea of a plastic-degrading enzyme seems like a panacea, the enzyme’s practical applications have been limited by its biology. The wild-type IsPETase is a mesophilic enzyme, meaning the structure of the enzyme is only stable around ambient temperatures, and the enzyme loses its activity above that threshold. This restriction on temperature limits the number and types of facilities that can use IsPETase, as well as the rate of the enzyme reaction, and drives up the cost of their use.

However, Zhong-Johnson thinks that, with combined approaches of biological and chemical engineering, it’s possible to scale up the use of the enzymes by increasing their stability and activity. For example, an enzyme that’s highly active at lower temperatures could work in unheated facilities, or even be sprinkled directly into landfills or oceans to degrade plastic waste — a process called bioremediation. Increasing the activity of the enzyme at ambient temperatures could also expand the possible applications.

“Most of the environments where plastic is present are not above 50 degrees Celsius,” said Zhong-Johnson. “If we can increase enzyme activity at lower temperatures, that’s really interesting for bioremediation purposes.”

Now a fifth-year graduate student, Zhong-Johnson has honed her project, and is focusing on increasing the activity of IsPETase. To do so, she’s using directed evolution — creating random mutations in the IsPETase gene, and selecting for IsPETase variants that digest PET faster. When they do, she combines the beneficial mutations and uses that as template for the next round of library generation, to improve the enzyme even further. The evolution is “directed” because Zhong-Johnson herself, rather than nature, is picking out which gene sequences of enzyme proceed through to the next round of random mutagenesis, and which don’t. Her ultimate goal is to create a more efficient and hardier enzyme that will, hopefully, work faster at ambient temperatures.

A better protocol

Just as Zhong-Johnson was beginning her project, she ran into an obstacle: There wasn’t a standard way to measure whether her experiments were successful. In particular, no immediately applicable method existed to measure enzyme kinetics for IsPETases on solid substrates like plastic bottles and other plasticware. That was a problem for Zhong-Johnson because understanding enzyme activity was a crucial part of how she selected her enzymes in the directed evolution process.

Usually, enzyme activity is measured via product accumulation: When enzymes metabolize a substance, they create a new substance in return, called a product. Measuring the amount of product created by an enzyme after a certain amount of time gives the researcher a snapshot of that enzyme’s activity.

There are two problems with the product accumulation method, though. First, it is usually done using liquid or soluble substrates. In other words, the material that the enzyme is targeting is dissolved, like sugar dissolved in water. Then, the enzyme is added to that liquid concoction and mixed evenly throughout. However, the substrate Zhong-Johnson wanted to use — PET — was not soluble but solid, meaning it could not be evenly distributed like a soluble substrate. Second, the product accumulation measurement methods available were only practical for measuring less than a handful of timepoints for a few enzyme or substrate concentrations. As a result, many in the field opted to measure a single time point, late in the enzyme reaction, which doesn’t provide an indication of how an enzyme’s rate of digestion actually changes over the course of time — something that can be measured through kinetic measurements.

Taking kinetic measurements would help researchers like Zhong-Johnson illustrate the full pattern of enzyme activity and answer questions like: When is the enzyme most active? Does most product accumulation happen at the beginning of the reaction or the end? How does temperature impact the rate of these reactions over time? To answer these questions, she realized she would have to develop the method herself. 

Through a serendipitous discussion with a group of chemical engineering undergraduate students that Zhong-Johnson was mentoring, she came up with a solution, which she published in a 2021 paper in Scientific Reports. The undergraduates brought to her attention many factors that she had overlooked about the enzyme, and she says she would not have realized the importance of kinetic measurements if it weren’t for the fact that she was trying to design an experiment that the undergraduates could perform over the course of three hours.

The paper outlined a new way to measure enzyme activity, which Zhong-Johnson calls “the bulk absorbance method.” Instead of measuring the final product accumulation at very late time points, the bulk absorbance method involves taking multiple kinetic measurements at early time intervals during the experiment. This technique informs Zhong-Johnson’s directed evolution approach: If she can find which enzymes are most active at low temperatures, she can select the best possible enzyme for the next round of analyses. She hasn’t yet engineered an enzyme she’s completely happy with, but she’s gotten much closer to her ultimate goal.

Solving big problems together

Zhong-Johnson’s discoveries have been made possible by the collaboration between her and her two co-advisors, Voigt and Sinskey, who have supported her independence throughout her five years at MIT.

Man and woman smile by whiteboard
Zhong-Johnson and her advisor, professor Anthony Sinskey, in his office. Credit: Grace van Deelen

When she first started her graduate work, neither Voigt nor Sinskey had expertise in enzyme biochemistry involving solid substrates: Sinkey’s lab focuses on bacterial metabolism, while Voigt’s lab focuses on genetic engineering (though Voigt did have experience with directed evolution research). Additionally, Zhong-Johnson’s path to her project was rather unconventional. Most grad students do not come to potential advisors proposing entire dissertations, which posed a unique challenge for Zhong-Johnson.

Despite not having specific expertise in enzyme biochemistry involving solid substrates, Voigt and Sinskey have supported Zhong-Johnson in other ways: by helping her to develop critical thinking skills and connecting her to other people in her field, such as potential collaborators, who can help her project thrive in the future. Zhong-Johnson has supplemented her MIT experience by having enzyme experts as part of her dissertation committee as well.

Sinskey says that, in the future — once Zhong-Johnson has engineered the ideal enzyme — they would like to partner with industry, and work on making the enzyme into a product that waste companies might use to recycle plastic. Additionally, Sinskey says, the plastic problem and the IsPETase solution raise so many interesting questions that Zhong-Johnson’s project will probably live on in the Voigt and Sinskey labs even after she graduates. He’d like to see other graduate students working to understand the enzyme’s activity and progressing the directed evolution that Zhong-Johnson started.

Zhong-Johnson is already working on understanding the specifics of how IsPETase act on PET. “How does it eat a hole in a plastic bottle? How does it move along and make the hole bigger as it moves through the process? Does it jump around? Or does it keep degrading a single polymer chain until its completely broken down? We just don’t know the answers yet,” says Sinskey.

But Zhong-Johnson is up to the task. “My graduate students have to have three skills, in my opinion,” Sinskey says. “One, they have to be intelligent. Two, they have to be energetic, and three, they have to be of high integrity, in research and behavior.” Zhong-Johnson, he says, has all three qualities.