Research Area: Biochemistry, Biophysics, and Structural Biology

Sizing up cancer

Graduate student Zhaoqi Li investigates how cancer cells grow by harnessing exceptional chemical reactions

Justin Chen
January 11, 2018

Cancer cells use extreme measures to fuel their growth. In fact, researchers like Zhaoqi Li, a third-year graduate student, witness chemical reactions in these cells that would be impossible in the context of normal cells. In a petri dish, normal cells stop dividing once they cover the bottom of the dish and fit neatly together like mosaic tiles. In contrast, cancer cells continue to proliferate and pile haphazardly into small mounds. Within the human body, this abnormal growth — when combined with the spread of cancer cells throughout the body — interferes with organ function and causes death.

Li, a member of Professor Matthew Vander Heiden’s lab located in the Koch Institute, studies cancer metabolism. His work describes the chemical reactions cancer cells use to create energy and materials to make new cells such as membranes, proteins, and DNA. By tracking the flow of nutrients through cancer cells, Li and his labmates are learning how such cells change their metabolism to stimulate growth. These insights will help scientists develop new ways to treat the disease.

Cell metabolism comprises all the chemical reactions occurring in the cell, but researchers are particularly interested in a few reactions that aren’t required by normal cells but are critical for cancer growth. Stopping these reactions with drugs would disrupt the metabolism of cancer cells and hinder tumor development.

“Even though many people may not think of metabolism as a treatment target for cancer, this strategy has been used unwittingly for a long time,” Li says. “Many chemotherapies, such as antifolates, were originally used by doctors without knowing exactly how they worked. Since then, we’ve discovered that those treatments target metabolic pathways. By understanding the details of cancer metabolism we are hoping to design drugs in a more rational way.”

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Li might never have joined the Vander Heiden lab or studied cancer metabolism were it not for the unique structure of graduate training at MIT.

During their first year at MIT, graduate students are required to take four classes. Unlike their counterparts at many other PhD programs, they do not work in laboratories until their second semester. This allows students to focus initially on coursework — covering biochemistry, genetics, and research methodology — designed to build a foundation of knowledge. As a result, students discover new interests and develop the confidence to move out of their comfort zones. When it comes time to select a lab, they can choose from 56 spread across six locations, spanning a wide breadth of biological research.

Li could study how the brain forms memories, interpret X-rays to deduce protein structure, or even build miniature organs for drug testing. Before making his decision, he rotated in three laboratories. During each month-long rotation, he performed a small project allowing him to experience the culture of the lab and learn more about its research.

“The first two labs I visited were studying topics I was familiar with and thought were interesting,” he says. “But when I visited the Vander Heiden lab it was so different and caught me off guard. That’s why I eventually joined, even though I had never imagined myself working in a metabolism lab before.”

Diagram showing a metabolism pathway
Cellular metabolism is comprised of a network of interconnected biochemical reactions resembling a subway system. Zhaoqi Li compares normal and diseased cells to determine the differences in the way nutrients travel through this network. Credit: Justin Chen

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Although he is new to the community of researchers specializing in metabolism, Li has long known that he wanted to interact with the world through science. As an immigrant who moved from China to southern Tennessee at the age of six, Li struggled to learn English and began to view science as a universal language that transcended culture.

“My parents were also non-native speakers and the English as a Second Language classes in my elementary school were geared towards Spanish speakers, so I had a really hard time,” Li says. “I joke that the only reason I passed the first grade was because I was good at math.”

Li’s contrasting relationship with science and English continued as an undergraduate at Columbia University. There he majored in biochemistry and also studied literature of the Western Canon to fulfill his general degree requirements.

“I took four semesters worth of classes that started with Plato and ended with Virginia Woolf,” he says, “It was an eye-opening experience, but I never really loved it. I found biology more intuitive because it doesn’t rely on being familiar with a specific cultural lens. Most every society in the world values the scientific method to some extent.”

Li began working in a lab during his sophomore year at Columbia. To his surprise, he was mentored by a professor who valued his input and encouraged creative thinking. Li’s supervisor also introduced him to basic science — a type of research driven not by the desire to find a specific answer or cure, but by curiosity and the need to better understand the natural world.

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During his second semester rotation at MIT, Li searched for similarly open-minded environments, and was attracted to cancer metabolism because the field was relatively young.

“In other more established areas of biology, if you have a question someone has probably answered it in some capacity,” Li says. “The Vander Heiden lab was using new techniques so there was a lot of space to explore. Many questions I asked — even during my initial rotation —  didn’t have an answer, which was exciting.”

The great challenge confronting the metabolism field is translating decades’ worth of research on enzymes — proteins that manage chemical reactions — from the test tube to the cell and human body. By studying enzymes individually in the controlled setting of test tubes, researchers have documented almost all the chemical reactions that occur in the cell. When combined, these reactions look like a giant subway map where each stop, indicated by a dot, is a different molecule, and the line between stops represents a chemical reaction where atoms are added or subtracted. Some pathways are a straight line but others have nodes or intersections where a molecule can take part in several different reactions. Other pathways are circular where the molecule that starts the pathway is remade at the end so that the line circles back on itself.

Despite the ability to study chemical reactions in a test tube, scientists have struggled to understand what is actually happening in the complex environment of cells, which coordinate millions of reactions that not only affect each other, but are also influenced by outside stresses like nutrient deprivation.

To Li, using the metabolism map to figure out what chemical reactions are occurring and how atoms are moving through the cell is like using a subway map to track how people are traveling through a city.

“The map describes all the possible routes people could take,” Li says, “but you have to track the passengers to figure out where they are actually going. You could imagine people commuting into the city during the week and going to entirely different places on the weekend. There are a lot of different patterns of movement that you can’t infer just from looking at a map.”

To analyze what chemical reactions are occurring in the cell, Li utilizes cutting edge technology to track carbon atoms — an essential element that is required to build all components of the cell. By tagging carbon with an extra neutron, Li makes the experimentally altered atom heavier and distinguishable from naturally occurring carbon in the cell. Feeding cells nutrients like glucose made with heavy carbons allows Li to compare how molecules are broken down and used by normal and cancerous cells.

Person at lab instrument with sample“Returning to the subway map analogy, this labeling technique is similar to not only being inside the subway, but also giving everyone in Downtown Boston a red shirt,” Li says. “After 12 hours, we can look at the rest of the city. If we see a lot of red shirts in Allston, we would know that this particular route is really popular.”

In the case of glucose, Li and his labmates observed that normal cells break down the sugar to release energy and heavy carbons in the form of carbon dioxide. In contrast, cancer cells alter their metabolism so that the heavy carbons originally found in glucose are used to build new parts of the cells that are required for cancer cells to grow, such as membranes, DNA, and proteins.

Li’s observations demonstrate how cancer cells sustain abnormal growth by accumulating carbon. For his thesis project, Li has chosen to investigate one of the main tricks cancer cells use to hoard carbon atoms: a process known as carbon fixation. This type of chemical reaction, originally studied in plants performing photosynthesis, attaches carbon dioxide to other molecules. Li’s initial findings suggest that a protein, Malic Enzyme 1, helps cancer cells use carbon dioxide to build components required for growing and dividing.

“This is surprising,” he says, “because the textbook version of this enzyme actually catalyzes the reverse reaction in normal cells where carbon dioxide is removed from molecules.  Malic Enzyme 1 is an example of how cancer performs remarkable chemical reactions — who would have thought that cancer cells use carbon like plants do?”

Li is at the beginning stages of his research, and can’t predict where his project will take him. His current goal is to determine how cancer cells react when they are missing Malic Enzyme 1. Such loss could slow growth, but Li will have to perform experiments to be sure, since cancer is a resourceful and elusive target.

Like a detour rerouting travelers around a closed metro stop, cancer cells may further contort their metabolism, taking advantage of little-used or still unidentified chemical reactions to maintain growth. In the face of such adaptability, Li and his labmates believe the best course of action is to be as curious as possible to understand as much as they can about how cancer works. Working together, they discuss confounding results, adjust hypotheses, and design new experiments.

“It’s really encouraging to be part of Matt’s lab and the Koch Institute in general where researchers take a basic science approach,” Li says. “We try to keep an open mind because there’s probably no single thing that cancer cells depend on. Everyone’s work builds together to form a cumulative understanding.”

Photo credit: Raleigh McElvery
Combatting chemotherapy resistance

Graduate student Faye-Marie Vassel investigates a protein that helps cells tolerate DNA damage, sharing her expertise with budding scientists to further STEM education

Raleigh McElvery
December 8, 2017

Combatting chemotherapy resistance

Person with long, dark hair and lab coat stares into microscope.

Graduate student Faye-Marie Vassel investigates a protein that helps cells tolerate DNA damage, sharing her expertise with budding scientists to further STEM education

Raleigh McElvery

 

Faye-Marie Vassel has a protein. Well, as a living entity, technically she has many, but just one she affectionately refers to as her own. “My protein, REV7.” And it makes sense — if you were hard at work characterizing a single protein for all six years of your graduate career, you’d be pretty attached, too. Plus, the stakes are high. REV7, which aids in DNA damage repair, could ultimately provide insight into ways to combat chemotherapy resistance.

Although Vassel’s mother trained as an OB/GYN in Russia before moving to the U.S., serving as what Vassel describes as a “quiet” scientific role model, Vassel spent her early childhood emulating her father, a social worker, and engrossed in the social sciences. She intended to one day work in science policy — until high school when she joined an after-school program at the American Museum of Natural History in New York City, and discovered an additional interest.

Here, Vassel took a series of molecular biology classes and met her first female research mentor, a postdoctoral fellow at Rockefeller University, who encouraged her to participate in another, more advanced science program funded by the National Science Foundation.

“I initially had my doubts, but just having that support changed everything,” Vassel says. “That was my first time doing research of any kind, and I got a sense of the sheer diversity of potential research projects. That’s also when I heard there was something called biophysics.”

From that point on, Vassel was hooked. As an undergraduate at Stony Brook University, she initially declared a major in physics before switching to biochemistry. Later, when it came time to select a graduate school, she was split between MIT and the University of California, Berkeley. As she recalls, MIT’s graduate preview weekend made all the difference.

“I had the chance to stay with biology students and speak with professors,” she says. “The whole experience made the department seem personal, and demystified the graduate school process by making it more tangible.”

She proposed a joint position between two labs: Graham Walker’s lab, based in Building 68, and Michael Hemann’s lab situated in the Koch Institute for Integrative Cancer Research. Walker’s lab focuses on microbiology, DNA repair, and antibiotic resistance, while Hemann’s lab investigates chemotherapy resistance in hopes of improving cancer therapies. After stumbling upon one of their joint papers, Vassel decided she’d like to combine the two.

“It’s invaluable to have both perspectives,” she says. “Mike’s lab just celebrated its 10th anniversary, while Graham‘s just had its 35th. It’s been interesting seeing the different ways they approach their respective research questions, because they were trained in such different scientific eras.”

Although Vassel is currently the only student formally working in both labs, the collaboration between Walker and Hemann, aimed at combatting chemotherapy resistance, has been ongoing.

Frontline chemotherapies, including one anticancer agent called cisplatin, kill cancer cells by damaging their DNA and preventing them from synthesizing new genetic material. Just how sensitive cancer cells are to cisplatin — and therefore how effective the treatment is — depends on whether the cell can repair the damage and bypass DNA-damage induced cell death. In some cases, cells increase production of “translesion polymerases,” which are specialized DNA polymerases that can help cells tolerate certain kinds of DNA damage by synthesizing across from damaged DNA or DNA bound to a carcinogen.

Vassel’s protein, REV7, is a structural subunit of one key translesion polymerase, and its expression is deregulated in many different cancer cells. As Vassel suggests, if one aspect of these translesion polymerases — say, the REV7 subunit — could be altered to hinder repair, then perhaps cancer-ridden cells could regain drug sensitivity.

Thanks to recently-developed CRISPR-Cas9 gene editing techniques, Vassel has removed REV7 entirely from drug resistant lung cancer cells, and watched as cisplatin sensitivity was restored. She also conducted rescue experiments, adding REV7 back into cell lines lacking the protein to see whether those cells become resistant to the drug once again. Most recently, she has been working in murine models to see whether REV7 has similar effects in a living system.

If her hypothesis is correct, REV7 would be a powerful target for drug development. Treatments that inhibit REV7, she explains, could be used in tandem with frontline chemotherapies like cisplatin to prevent resistance.

Since her foray into biology at the American Museum of Natural History almost a decade ago, Vassel has maintained her passion for science outreach. During her time at MIT, she has served as a math tutor for middle schoolers in the Cambridge public school system. She also volunteered as a science and math mentor for high school students, as part of a dual athletic and academic program founded by MIT.

As Vassel wraps up her final year of graduate studies, she is torn between completing an academic postdoc and indulging her early interest in science education policy.

“Growing up in New York City, it was not lost on me that — despite the city’s wonderful diversity — people from historically underserved groups were still missing from many science-related positions,” Vassel says. “It got me thinking about the dire need for policymakers to improve curricula to make science more inclusive of all life experiences. There’s this idea that science is apolitical when it’s really not, and that mindset can have detrimental effects on equity and diversity in science.”

Photo credit: Raleigh McElvery
Biologists’ new peptide could fight many cancers

Drug that targets a key cancer protein could combat leukemia and other types of cancer.

Anne Trafton | MIT News Office
January 15, 2018

MIT biologists have designed a new peptide that can disrupt a key protein that many types of cancers, including some forms of lymphoma, leukemia, and breast cancer, need to survive.

The new peptide targets a protein called Mcl-1, which helps cancer cells avoid the cellular suicide that is usually induced by DNA damage. By blocking Mcl-1, the peptide can force cancer cells to undergo programmed cell death.

“Some cancer cells are very dependent on Mcl-1, which is the last line of defense keeping the cell from dying. It’s a very attractive target,” says Amy Keating, an MIT professor of biology and one of the senior authors of the study.

Peptides, or small protein fragments, are often too unstable to use as drugs, but in this study, the researchers also developed a way to stabilize the molecules and help them get into target cells.

Loren Walensky, a professor of pediatrics at Harvard Medical School and a physician at Dana-Farber Cancer Institute, is also a senior author of the study, which appears in the Proceedings of the National Academy of Sciences the week of Jan. 15. Researchers in the lab of Anthony Letai, an associate professor of medicine at Harvard Medical School and Dana-Farber, were also involved in the study, and the paper’s lead author is MIT postdoc Raheleh Rezaei Araghi.

A promising target

Mcl-1 belongs to a family of five proteins that play roles in controlling programmed cell death, or apoptosis. Each of these proteins has been found to be overactive in different types of cancer. These proteins form what is called an “apoptotic blockade,” meaning that cells cannot undergo apoptosis, even when they experience DNA damage that would normally trigger cell death. This allows cancer cells to survive and proliferate unchecked, and appears to be an important way that cells become resistant to chemotherapy drugs that damage DNA.

“Cancer cells have many strategies to stay alive, and Mcl-1 is an important factor for a lot of acute myeloid leukemias and lymphomas and some solid tissue cancers like breast cancers. Expression of Mcl-1 is upregulated in many cancers, and it was seen to be upregulated as a resistance factor to chemotherapies,” Keating says.

Many pharmaceutical companies have tried to develop drugs that target Mcl-1, but this has been difficult because the interaction between Mcl-1 and its target protein occurs in a long stretch of 20 to 25 amino acids, which is difficult to block with the small molecules typically used as drugs.

Peptide drugs, on the other hand, can be designed to bind tightly with Mcl-1, preventing it from interacting with its natural binding partner in the cell. Keating’s lab spent many years designing peptides that would bind to the section of Mcl-1 involved in this interaction — but not to other members of the protein family.

Once they came up with some promising candidates, they encountered another obstacle, which is the difficulty of getting peptides to enter cells.

“We were exploring ways of developing peptides that bind selectively, and we were very successful at that, but then we confronted the problem that our short, 23-residue peptides are not promising therapeutic candidates primarily because they cannot get into cells,” Keating says.

To try to overcome this, she teamed up with Walensky’s lab, which had previously shown that “stapling” these small peptides can make them more stable and help them get into cells. These staples, which consist of hydrocarbons that form crosslinks within the peptides, can induce normally floppy proteins to assume a more stable helical structure.

Keating and colleagues created about 40 variants of their Mcl-1-blocking peptides, with staples in different positions. By testing all of these, they identified one location in the peptide where putting a staple not only improves the molecule’s stability and helps it get into cells, but also makes it bind even more tightly to Mcl-1.

“The original goal of the staple was to get the peptide into the cell, but it turns out the staple can also enhance the binding and enhance the specificity,” Keating says. “We weren’t expecting that.”

Killing cancer cells

The researchers tested their top two Mcl-1 inhibitors in cancer cells that are dependent on Mcl-1 for survival. They found that the inhibitors were able to kill these cancer cells on their own, without any additional drugs. They also found that the Mcl-1 inhibitors were very selective and did not kill cells that rely on other members of the protein family.

Keating says that more testing is needed to determine how effective the drugs might be in combating specific cancers, whether the drugs would be most effective in combination with others or on their own, and whether they should be used as first-line drugs or when cancers become resistant to other drugs.

“Our goal has been to do enough proof-of-principle that people will accept that stapled peptides can get into cells and act on important targets. The question now is whether there might be any animal studies done with our peptide that would provide further validation,” she says.

Joshua Kritzer, an associate professor of chemistry at Tufts University, says the study offers evidence that the stapled peptide approach is worth pursuing and could lead to new drugs that interfere with specific protein interactions.

“There have been a lot of biologists and biochemists studying essential interactions of proteins, with the justification that with more understanding of them, we would be able to develop drugs that inhibit them. This work now shows a direct line from biochemical and biophysical understanding of protein interactions to an inhibitor,” says Kritzer, who was not involved in the research.

Keating’s lab is also designing peptides that could interfere with other relatives of Mcl-1, including one called Bfl-1, which has been less studied than the other members of the family but is also involved in blocking apoptosis.

The research was funded by the Koch Institute Dana-Farber Bridge Project and the National Institutes of Health.

Harnessing nature’s riches
December 19, 2017

Cambridge, MA – Researchers at Whitehead Institute have reconstructed the full suite of biochemical steps required to make salidroside, a plant-derived compound widely used in traditional medicine to combat depression and fatigue and boost immunity and memory. Their new study, which appears online this week in the journal Molecular Plant, resolves some long-standing questions about how this compound is manufactured by a type of high-altitude plant, known commonly as golden root. This work not only paves a path toward large-scale synthetic efforts—thereby protecting plants already in danger of extinction—but also provides a model for dissecting the biochemical synthesis of a host of natural products, which represent a treasure trove for modern medical discoveries.

“By cracking open the natural synthesis of this compound, known as salidroside, we have helped eliminate a major bottleneck in the broader development of plant-derived natural products into pharmaceuticals,” says Jing-Ke Weng, the senior author of the paper, a Member of Whitehead Institute, and an assistant professor of biology at Massachusetts Institute of Technology. “We simply can’t rely on the native plants as the sole sources of these biologically important molecules.”

Golden root, also called Tibetan ginseng, typically grows in high-altitude, arctic environments, such as Tibet. It is well known in Eastern cultures for its medicinal properties and produces a variety of chemical substances, particularly salidroside, which have garnered interest in the biomedical research community for their potential therapeutic effects.

“People have tried to farm golden root, but the medicinal value is much lower because the plants make much less salidroside when cultivated outside of their normal habitat,” says Weng.

That means collecting enough salidroside to fuel scientific studies is largely impossible, without risking the viability of these plants and their surroundings. So Weng and his team, including first author Michael Torrens-Spence, set out to find a better way. “If we can figure out how plants make these high-value natural products, then we can devise sustainable engineering approaches to recreate such molecules—we won’t have to destroy nature in order to harness its riches,” says Torrens-Spence, a postdoctoral researcher in Weng’s laboratory.

Torrens-Spence and his colleagues used a systematic multi-omics approach to characterize various tissues from a three-month-old, greenhouse-grown golden root plant. By correlating the active genes with the abundance of key metabolites between various tissue types, the researchers created a massive biochemical catalog of the plant’s tissues.

The researchers then mined these data and matched the likely biochemical precursors of salidroside with the candidate genes (and their corresponding enzymes) responsible for those compounds’ synthesis. This approach allowed Weng and his team to create a kind of draft blueprint of how salidroside is made in nature.

To test the validity of this draft blueprint—and the molecular players from the golden root plant that comprise it—the scientists turned to two well-studied laboratory organisms: the baker’s yeast Saccharomyces cerevisiae and the tobacco plant Nicotiana benthamiana. Normally, these organisms do not make salidroside. But if the researchers’ model was correct, by inserting the candidate genes involved in salidroside synthesis Weng and his colleagues should be able to bestow that special property upon them.

That is precisely what the researchers did. Using three key enzymes they identified through their “-omics” approach, including 4HPAAS (4-hydroxyphenylacetaldehyde synthase), 4HPAR (4-hydroxyphenylacetaldehyde reductase), and T8GT (tyrosol:UDP-glucose 8-O-glucosyltransferase), they engineered yeast and tobacco plants with the capacity to make salidroside. Notably, this biochemical pathway for synthesizing salidroside involves three enzymes, rather than four, as had previously been proposed.

“This is an exciting proof-of-principle for how we can systematically unlock the biochemistry behind a range of intriguing plant-derived natural products,” says Weng. “With this capability, we can accelerate biomedical studies of these unique compounds as well as their potential therapeutic development.”

Written by Nicole Davis
* * *
Jing-Ke Weng’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at Massachusetts Institute of Technology.
* * *
Full citation:
“Complete pathway elucidation and heterologous reconstitution of Rhodiola salidroside biosynthesis”
Molecular Plant, online December 19, 2017. DOI: 10.1016/j.molp.2017.12.007
Michael P. Torrens-Spence (1), Tomáš Pluskal (1), Fu-Shuang Li (1), Valentina Carballo (1) and Jing-Ke Weng (1,2).
1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Tania A. Baker

Education

  • PhD, 1988, Stanford University
  • BS, 1983, Biochemistry, University of Wisconsin-Madison

Research Summary

Our goal is to understand the mechanisms and regulation behind AAA+ unfoldases and macromolecular machines from the “Clp/Hsp100 family” of protein unfolding enzymes. We study these biological catalysts using biochemistry, structural biology, molecular biology, genetics, and single molecule biophysics.

No longer accepting students.

Awards

  • Margaret MacVicar Faculty Fellow, 2008-2018
  • National Academy of Sciences, Member, 2007
  • American Academy of Arts and Sciences, Fellow, 2005
  • Howard Hughes Medical Institute, HHMI Investigator, 1994
Matthew Vander Heiden

Education

  • PhD, 2000, University of Chicago; MD, 2002, University of Chicago
  • SB, 1994, Biological Chemistry, University of Chicago

Research Summary

We study the biochemical pathways cells use and how they are regulated to meet the metabolic requirements of cells in different physiological situations. We focus on the role of metabolism in cancer, particularly how metabolic pathways support cell proliferation. We aim to translate our understanding of cancer cell metabolism into novel cancer therapies.

Awards

  • National Academy of Medicine, 2024
  • Howard Hughes Medical Institute Faculty Scholar, 2016
  • SU2C Innovative Research Grant Recipient, 2016
Researchers establish long-sought source of ocean methane

An abundant enzyme in marine microbes may be responsible for production of the greenhouse gas.

Anne Trafton | MIT News Office
December 7, 2017

Industrial and agricultural activities produce large amounts of methane, a greenhouse gas that contributes to global warming. Many bacteria also produce methane as a byproduct of their metabolism. Some of this naturally released methane comes from the ocean, a phenomenon that has long puzzled scientists because there are no known methane-producing organisms living near the ocean’s surface.

A team of researchers from MIT and the University of Illinois at Urbana-Champaign has made a discovery that could help to answer this “ocean methane paradox.” First, they identified the structure of an enzyme that can produce a compound that is known to be converted to methane. Then, they used that information to show that this enzyme exists in some of the most abundant marine microbes. They believe that this compound is likely the source of methane gas being released into the atmosphere above the ocean.

Ocean-produced methane represents around 4 percent of the total that’s discharged into the atmosphere, and a better understanding of where this methane is coming from could help scientists better account for its role in climate change, the researchers say.

“Understanding the global carbon cycle is really important, especially when talking about climate change,” says Catherine Drennan, an MIT professor of chemistry and biology and Howard Hughes Medical Institute Investigator. “Where is methane really coming from? How is it being used? Understanding nature’s flux is important information to have in all of those discussions.”

Drennan and Wilfred van der Donk, a professor of chemistry at the University of Illinois at Urbana-Champaign, are the senior authors of the paper, which appears in the Dec. 7 online edition of Science. Lead authors are David Born, a graduate student at MIT and Harvard University, and Emily Ulrich, a graduate student at the University of Illinois at Urbana-Champaign.

Solving the mystery

Many bacteria produce methane as a byproduct of their metabolism, but most of these bacteria live in oxygen-poor environments such as the deep ocean or the digestive tract of animals — not near the ocean’s surface.

Several years ago, van der Donk and University of Illinois colleague William Metcalf found a possible clue to the mystery of ocean methane: They discovered a microbial enzyme that produces a compound called methylphosphonate, which can become methane when a phosphate molecule is cleaved from it. This enzyme was found in a microbe called Nitrosopumilus maritimus, which lives near the ocean surface, but the enzyme was not readily identified in other ocean microbes as one would have expected it to be.

Van der Donk’s team knew the genetic sequence of the enzyme, known as methylphosphonate synthase (MPnS), which allowed them to search for other versions of it in the genomes of other microbes. However, every time they found a potential match, the enzyme turned out to be a related enzyme called hydroxyethylphosphonate dioxygenase (HEPD), which generates a product that is very similar to methylphosphonate but cannot be cleaved to produce methane.

Van der Donk asked Drennan, an expert in determining chemical structures of proteins, if she could try to reveal the structure of MPnS, in hopes that it would help them find more variants of the enzyme in other bacteria.

To find the structure, the MIT team used X-ray crystallography, which they performed in a special chamber with no oxygen. They knew that the enzyme requires oxygen to catalyze the production of methylphosphonate, so by eliminating oxygen they were able to get snapshots of the enzyme as it bound to the necessary reaction partners but before it performed the reaction.

The researchers compared the crystallography data from MPnS with the related HEPD enzyme and found one small but critical difference. In the active site of both enzymes (the part of the protein that catalyzes chemical reactions), there is an amino acid called glutamine. In MPnS, this glutamine molecule binds to iron, a necessary cofactor for the production of methylphosphonate. The glutamine is fixed in an iron-binding orientation by the bulky amino acid isoleucine, which is directly below the glutamine in MPnS. However, in HEPD, the isoleucine is replaced by glycine, and the glutamine is free to rearrange so that it is no longer bound to iron.

“We were looking for differences that would lead to different products, and that was the only difference that we saw,” Born says. Furthermore, the researchers found that changing the glycine in HEPD to isoleucine was sufficient to convert the enzyme to an MPnS.

An abundant enzyme

By searching databases of genetic sequences from thousands of microbes, the researchers found hundreds of enzymes with the same structural configuration seen in their original MPnS enzyme. Furthermore, all of these were found in microbes that live in the ocean, and one was found in a strain of an extremely abundant ocean microbe known as Pelagibacter ubique.

“This exciting result builds on previous, related studies showing that the metabolism of the methylphosphonate can lead to the formation of methane in the oxygenated ocean. Since methane is a potent greenhouse gas with poorly understood sources and sinks in the surface ocean, the results of this study will serve to facilitate a more comprehensive understanding of the methylphosphonate cycle in nature,” says David Karl, a professor of oceanography at the University of Hawaii, who was not involved in the research.

It is still unknown what function the MPnS enzyme and its product serve in ocean bacteria. Methylphosphonates are believed to be incorporated into fatty molecules called phosphonolipids, which are similar to the phospholipids that make up cell membranes.

“The function of these phosphonolipids is not well-established, although they’ve been known to be around for decades. That’s a really interesting question to ask,” Born says. “Now we know they’re being produced in large quantities, especially in the ocean, but we don’t actually know what they do or how they benefit the organism at all.”

Another key question is how the production of methane by these organisms is influenced by environmental conditions in the ocean, including temperature and pollution such as fertilizer runoff.

“We know that methylphosphonate cleavage occurs when microbes are starved for phosphorus, but we need to figure out what nutrients are connected to this, and how is that connected to the pH of the ocean, and how is it connected to temperature of the ocean,” Drennan says. “We need all of that information to be able to think about what we’re doing, so we can make intelligent decisions about protecting the oceans.”

The research was funded by the National Institutes of Health and the Howard Hughes Medical Institute.

Rethinking transcription factors and gene expression

Study shows that, like proteins, genomes must fold appropriately to function properly and that some transcription factors provide the structural support.

Nicole Giese Rura | Whitehead Institute
December 7, 2017

Transcription — the reading of a segment of DNA into an RNA template for protein synthesis — is fundamental for nearly all cellular processes, including growth, responding to stimuli, and reproduction. Now, Whitehead Institute researchers have upended our understanding of how transcription is controlled and the role of transcription factors in the process.

The paradigm shift, described in an article online on Dec. 7 in the journal Cell, hinges on a small protein that plays a key role in genome structure and gives us new insights into how changes in the control of transcription and gene expression can lead to disease.

Transcription has several important players that must all be in the right place at the right time: the transcription machinery, transcription factors, promoters, and enhancers.  According to the existing model, transcription factors are proteins that bind to enhancer regions of the genome and recruit the transcription machinery to the promoter DNA regions, which then initiate the genes’ transcription.

“We’ve always assumed that the role of transcription factors was to recruit the transcription machinery to genes to turn them on or turn them off,” says Richard Young, a Whitehead Insistute member and professor of biology at MIT. “But we never imagined that the transcription factors we’ve studied for three decades actually contribute to the genome’s structure. And as a consequence, they regulate genes. So we now look at genomes like proteins: They have to fold up appropriately in order to control genes.”

Scientists have known that the genome’s structure — how it bends and folds — is essential for efficiently compressing two meters of DNA into each human cell, which is the equivalent of packing a strand ten football fields long into a space the size of a marble. Yet until recently, researchers have not had the tools necessary to appreciate this architecture’s importance in fine control of gene expression or study the genome’s structure at sites ready for transcription.

In 2014, Young and his lab determined that portions of the genome reside in loop-based structures, creating insulated neighborhoods that bring enhancers, promoters, and genes into close proximity. Each loop is tied at the top by a pair of molecules, called CTCF, that are bound together. This structure is essential for proper gene control: If the loop structure is broken, gene expression is altered, and cells can become diseased or die.

In the current research, Young along with co-first authors Abraham Weintraub and Charles Li took a closer look at a protein that is well known but not well understood: Yin Yang 1 (YY1). Hundreds of scientific papers have linked YY1 dysfunction to diseases such as viral infections, cancer, and arthritis, and yet the studies produced seemingly contradictory observations of YY1’s function.

According to Young and colleagues, YY1 is a unique transcription factor that occupies both enhancers and promoters, is essential for cell survival, and is found in almost every cell type in humans and mice. Like CTCF, YY1 can also pair with itself and bind to DNA to form loops that enhance DNA transcription.

“YY1 is expressed broadly, and it is necessary for establishing enhancer-promoter loops in multiple cell types,” says Weintraub. “That’s its job, not recruiting the transcription apparatus. When the structure created by YY1 is removed, the genome is no longer folded properly, gene control is lost and transcription of the affected genes is significantly diminished, which can cause dysfunction.”

This model of YY1’s function could account for its association with a number of disparate diseases. Earlier this year, scientists reported YY1 syndrome — a genetic syndrome causing cognitive disabilities in people with mutations in their YY1 gene.

According to Young, YY1 is probably not the only transcription factor with this loop-forming role, and his lab will be searching for additional factors with similar functions.

“YY1 is most likely just the first one, and there are probably a bunch of collaborators that have similar roles,” says Young. “Instead of the classic function that we thought these transcription factors had — interacting with the transcription apparatus and giving instructions on how much or how little of a gene’s transcript to produce — they are bringing together regulatory elements with the gene. The whole job of these transcription factors is just making structure. We are realizing that the things that form physical structures are much more important than we had appreciated.”

The researchers’ work was supported by the National Institutes of Health, the Ludwig Graduate Fellowship funds, the National Science Foundation, the American Cancer Society, a Margaret and Herman Sokol Postdoctoral Award, the Damon Runyon Cancer Research Foundation, and the Cancer Research Institute. The Whitehead Institute has filed a patent application based on this study.

Laurie A. Boyer

Education

  • PhD, 2001, University of Massachusetts Medical School
  • BS, 1990, Biomedical Science, Framingham State University

Research Summary

We investigate how complex circuits of genes are regulated to produce robust developmental outcomes particularly during heart development. A main focus is to determine how DNA is packaged into chromatin, and how ATP-dependent chromatin remodelers modify this packaging to control lineage commitment. We are now applying these principles to develop methods to stimulate repair of damaged cardiac tissue (e.g., regeneration). Our ability to combine genomic, genetic, biochemical, and cell biological approaches both in vitro and in vivo as well as ongoing efforts to use tissue engineering to model the 3D architecture of the heart will ultimately allow us to gain a systems level and quantitative understanding of the regulatory circuits that promote normal heart development and how faulty regulation can lead to disease.

Awards

  • Medicine by Design Distinguished Lecture, 2017
  • Cardiovascular Rising Star Distinguished Lecture, 2017
  • American Heart Association Innovative Research Award, 2013
  • Irvin and Helen Sizer Career Development Award, 2012
  • Smith Family Award for Excellence in Biomedical Science, 2009
  • Massachusetts Life Sciences Center New Investigator Award, 2008
  • Pew Scholars Award in the Biomedical Sciences, 2008
  • Honorary Doctorate, Framingham State College, 2007
  • The Scientific American World’s 50 Top Leaders in Research, Business or Policy, 2006
Michael B. Yaffe

Education

  • PhD, 1987, Case Western Reserve University; MD, 1989, Case Western Reserve University
  • BS, 1981, Chemistry with Concentration in Solid-State and Polymer Physics, Cornell University

Research Summary

Our goal is to understand how signaling pathways are integrated at the molecular and systems levels to control cellular responses. We have two main focuses: First, we study signaling pathways and networks that control cell cycle progression and DNA damage responses in cancer and cancer therapy. Second, we examine the cross-talk between inflammation, cytokine signaling and cancer. Much of our work focuses on how modular protein domains and kinases work together to build molecular signaling circuits, and how this information can be used to design synergistic drug combinations for the personalized treatment of human disease.

Awards

  • MacVicar Faculty Fellow, 2021
  • Fellow, Association of American Physicians, 2021
  • Teaching with Digital Technology Award, 2018