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Small RNA mediates genetic parental conflict in seed endosperm
December 19, 2017

CAMBRIDGE, MA–When it comes to gene expression in the endosperm of seeds, gene provenance matters. In this specialized tissue, plants actively strive to keep the expression of genes inherited from the mother versus the father in balance, according to Whitehead Institute scientists.

The endosperm, the starchy part of a seed that envelopes and nourishes the developing embryo, comprises two-thirds of the calories in a typical human diet. It is the meat of a coconut and the sweet part of the corn on the cob we eat.  In a paper published online December 19 in the journal Cell Reports, Whitehead Member Mary Gehring, first author and former Gehring graduate student Robert Erdmann, and colleagues reveal that the endosperm is also the site where the plant must actively orchestrate a delicate balance between expression of genes inherited from the mother and those of the father.  If this critical balance errs toward one parent or the other, seeds can be too small or even abort.

Unlike most plant cells, which have two copies of the genome, cells within the endosperm have three copies: one inherited from the father, and two inherited from the mother. This ratio is established when a sperm cell in the fertilizing pollen grain fuses with the central cell associated with the egg cell in a flower’s ovule. Unlike most cells, the central cell has two nuclei, so when the sperm’s nucleus merges with the central cell, the resulting endosperm is triploid.

 The 2-to-1 ratio of maternal to paternal gene expression is crucial, and deviation can have dire consequences:  If maternal gene expression is too high, the seeds are too small; if paternal gene expression is too high, the seeds abort. Although plant biologists have known the importance of this ratio for seed viability, the balance was assumed to be passively maintained for the majority of genes.  Previously, Gehring determined that a subset of genes expressed in the endosperm are imprinted—their expression is inherited from their parent. But what about the remaining majority of the genome?

Now Gehring and colleagues have discovered a role for small RNAs—snippets of RNA that interfere with and can reduce gene expression—in actively maintaining this 2-to-1 balance in those genes that are not imprinted.  This the first time scientists have documented small RNAs maintaining such a ratio. Using Arabadopsis thaliana and Arabadopsis lyrata plants, Gehring and her lab determined that these small RNAs tamp down the expression of maternally inherited genes. When the enzyme that creates the small RNAs is mutated, fewer small RNAs are produced, and the plant’s carefully balanced gene expression is thrown off. The resulting seeds have excessive maternal gene expression. To understand the significance of this elevated maternal gene expression, Satyaki Rajavasireddy, a postdoctoral researcher in Gehring’s lab and an author of the Cell Reports paper, turned to plants with seeds that abort  because they have additional copies of paternal genes. When these plants with extra paternal DNA had their small-RNA-producing enzyme mutated, the outcome was striking: The seeds were rescued and developed to maturity.

Although the research analyzed this phenomenon in A. thaliana and A. lyrata, Gehring expects it to be a widespread manifestation of the tug-of-war between maternal and paternal genetic contributions.

“Maintaining this maternal/paternal balance is crucial for seed development, including in crop plants,” says Gehring, who is also an associate professor of biology at Massachusetts Institute of Technology.  “We’ve looked at two species that are separated by 10 million years of evolution, and I anticipate we will find this mechanism in other species as well.”

This work was supported by the National Science Foundation (NSF CAREER grant 1453459).

Written by Nicole Giese Rura
* * *
Mary Gehring’s primary affiliation is with Whitehead Institute for Biomedical Research, where her laboratory is located and all her research is conducted. She is also an associate professor of biology at Massachusetts Institute of Technology.
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Full Citation:
“A small RNA pathway mediates allelic dosage in endosperm”
Cell Reports, online December 19, 2017.
Robert M. Erdmann (1,2), P.R. V. Satyaki (1), Maja Klosinska (1), Mary Gehring (1,2).
1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142 USA
2. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
The need to know

Driven by curiosity, former auto mechanic Ryan Kohn now pursues a PhD in biology.

Bridget E. Begg | Office of Graduate Education
December 18, 2017

The name of Ryan Kohn’s son, Jayden, is tattooed in Hindi on his left outer forearm. Other tattoos on his inner arms declare “Respect” and “Loyalty.” A Latin phrase balances the tableau on his right outer forearm: “Many fear their reputation. Few their conscience.”

Kohn may stand out in the corporate milieu of Kendall Square, but he feels home at MIT. “No one has ever judged me,” he says. “For as rigorous scientifically and academically as MIT is, it can be such a laid-back place. I’ve always felt included, if I wanted to be.”

Kohn, now a PhD candidate in the Jacks Lab at MIT’s Koch Institute for Integrative Cancer Research, has overcome a challenging adolescence, colored by economic difficulties and punctuated by personal loss. These hardships developed in him a resilient curiosity that made an unexpected cultural match between MIT and Kohn, a father and former mechanic from Boyertown, Pennsylvania.

Compelled to seek answers

After being placed in an alternative high school outside of Philadelphia for insubordination, Kohn graduated with a 1.8 GPA. His son was born three years later, while Kohn worked for six and a half years as a mechanic and manager at a Dodge dealership. After losing his job during the Great Recession, he decided to go back to school, attending his local community college on a premed track before transferring to Kutztown University after two years.

Kohn attributes some of his troubled youth to early tragedy. His older sister, Nicole, died from sepsis when she was a senior in college, just 10 days after 9/11; on the morning of her funeral, Kohn’s grandfather passed away from colon cancer. Kohn felt compelled to understand why and how these illnesses happened to his loved ones, and found himself spending his time googling the immune system, the inflammatory response, and cancer.

This habit remained with him. Kohn recalls scouring the internet again and again to understand illness when it arose near him, from his own son’s immunoglobulin A deficiency to the early-onset multiple sclerosis of a friend. Though he admits he did not yet have the core scientific knowledge to fully grasp what he read at the time, Kohn says he needed, deeply, to try.

At Kutztown University, Kohn met his undergraduate mentor Angelika Antoni, a professor who taught both oncology and immunology. According to Kohn, Antoni constantly encouraged him to pursue his curiosity despite the college’s lack of laboratory resources. In fact, Antoni paid for laboratory reagents with her own credit card, while Kohn wrote his own grants and subscribed to well-known biology journals out of his own pocket because journal access was not available through Kutztown.

These challenges shaped Kohn as an experimental biologist, requiring him to precisely understand the mechanisms of experimental techniques in order to reconstruct them in the most creative and inexpensive ways possible. Perhaps most importantly, this small-college experience cultivated Kohn’s persistent curiosity.

Diving into cancer research

In his current position at the Jacks Lab, Kohn studies cancer immunotherapy, the use of a cancer patient’s own immune system to fight cancer cells. To do this, Kohn uses a mouse model of lung cancer that mimics the natural development of human cancer: Mutations identical to those found in many human cancers are triggered in the mouse, causing a tumor to arise that originates from the mouse’s own cells. These mice, like human cancer patients, have an immune system that can recognize the cancer as aberrant. Kohn’s work focuses modifying mouse immune cells to identify and attack a tumor.

Kohn is excited by the translational potential of his work, but also eagerly defends basic research at MIT when he encounters skepticism about its practicality in his conservative hometown.

Kohn often draws on metaphors in these types of conversations. He may leverage car talk, for example, to explain why there will never be a single cure for cancer: “So your ‘check engine’ light always presents the same way … but there’s literally a multitude of different things that can [cause] it. It could be a loose gas cap for the evaporative emissions system that set it off, it could be a misfire because of a bad spark plug, it could be a catalytic converter.”

Likewise, cancer can be caused by many possible biological errors that lead to an overgrowth of cells, Kohn explains. “So just like there will never be a cure for ‘check engine light,’ there will never be a [single] cure for cancer.”

Perhaps unsurprisingly, Kohn embraces the scientific freedom of the research in his lab. His advisor, Tyler Jacks, director of the Koch Institute, an HHMI investigator, and a David H. Koch Professor of Biology at MIT, is frequently in high demand, but Kohn says he has felt fully supported in his work — including in the bold ideas and unconventional projects he undertakes in his free time.

Jacks remains accessible despite his busy schedule, according to Kohn, and his emphasis on mentorship has inspired the postdocs in the lab to mentor the graduate students. The Jacks Lab also enjoys a thriving social environment. Kohn regularly attends casual weekend parties held by his labmates, and every other year Jacks organizes a cross-campus themed scavenger hunt for which the whole lab dresses in elaborate costumes.

“Real conversations about ideas”

Outside of lab, Kohn calls himself a homebody and prefers to relax after a full day, often with a beer and a movie. He spends much of this down time with his partner Ruthlyn, whether they are exploring the Boston area or talking with friends and colleagues at local pubs.

Kohn speaks about these conversations with genuine excitement: “You meet so many different people, every religion, every gender identity, every country, every language, and you just meet these people and you get to have these cool conversations … these real conversations about ideas. Because that’s really what you want, right?”

He enthusiastically notes that, in contrast to his largely homogenous hometown, more than 200 countries are represented at MIT. Kohn says the diversity and ideals of MIT reflect his own worldview.

Despite his deep sense of belonging on campus, leaving home did lay an exceptional burden on Kohn: Twelve-year-old Jayden remains in Pennsylvania with his mother, over 300 miles away.

Kohn speaks about his son with immense pride, describing Jayden as not only an extremely talented baseball player, but as a positive, energetic, and deeply mature young person. Kohn recounts with admiration, and a trace of relief, that despite the difficulty of the distance, Jayden said his father’s coming to MIT was the right thing to do.

As for his own parents, Kohn finally feels that all the headaches he has given them over the years have been worthwhile. His intense desire for knowledge has driven him through many obstacles, connected him with like minds from all over the world, and still shows no signs of waning.

Kohn has a reputation in his lab for asking questions, big and small. Asked if he’s ever afraid to admit what he doesn’t know, he says no: “I want to know … and that’s really what it comes down to.”

Epigenetic rheostat helps uncover how gene regulation is inherited and maintained
December 14, 2017

While our genome contains a vast repertoire of genes that are responsible for virtually all of the cellular and developmental processes life requires, it is the complex dance of regulating their expression that is vital for genetic programs to be executed successfully. Genes must be turned on and off at appropriate times or, in some cases, never turned on or off at all.

Methylation—the addition of chemical tags to DNA—typically reduces the expression of methylated genes. In many cases, DNA methylation can be thought of as roadblocks on a gene. The more methylated a gene is, the less likely it is that it will be active. Such genetic demarcations are critical to ensure that genes involved in particular stages of development are active at the right time, for example. Methylation is essential for proper cellular function, and its dysregulation is associated with diseases, such as cancer in humans. Despite its importance, little is known about how critical methylation patterns are inherited or maintained. Whitehead Institute Member Mary Gehring and her lab have identified a mechanism important for maintaining methylation, that when disrupted, results in the demethylation of large sections of the Arabidopsis plant’s genome. Their work is described this week in the journal Nature Communications.

Using an unusual gene in the plant Arabidopsis, Gehring is teasing apart the mechanisms that underpin methylation. By breaking this unique gene’s “circuit,” Gehring and Ben Williams, a postdoctoral researcher in her lab, have gained important insights into how methylation is maintained, including a surprising finding that previously erased methylation can be restored under certain circumstances.

In order to better understand methylation’s heritability, Gehring and Williams looked closely at an anomaly, the ROS1 gene in Arabidopsis plants, which encodes a protein that removes methylation from its own gene as well as others. Previously, Gehring and Williams had determined that ROS1 methylation actually functions in the complete opposite way from the existing paradigm—unlike most genes, when a short section of this gene is methylated, the gene is actually activated instead of inactivated. Conversely, if it is methylated, the gene is turned on. As a result, ROS1 can act as a rheostat for the Arabidopsis genome: As methylation increases, ROS1 turns on and begins removing methyl groups, and as methylation decreases, ROS1 shuts off and reduces its demethylating activity.

In the current research, Williams altered methylation at ROS1 so that its activity was uncoupled from methylation levels in the genome, in order to see what effects such a change would have on methylation throughout the entire genome. When he analyzed the plants’ methylation, it was haywire. Methylation was lost throughout the genome and progressively decreased in subsequent generations, except in a particular part of the genome called the heterochromatin—genomic areas that are strongly repressed. Interestingly, Williams found that, despite the alteration of the ROS1regulatory circuit, these heterochromatic sections of the genome actually regain their methylation and approach full methylation by the fourth generation— the same time point by which the rest of the genome has lost much of its methylation .

The researchers determined that the ROS1 circuit they uncovered is important for methylation homeostasis because it causes heritable loss of methylation when disrupted.  And yet methylation returns at some locations, albeit not immediately, suggesting that Arabidopsis enlists multiple mechanisms to maintain methylation homeostasis. Gehring and Williams are intrigued by that delay in remethylation and are working to identify its cause as well as other mechanisms that may also be at work regulating this critical process.

This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health (R01GM112851).

Written by Nicole Giese Rura
* * *
Mary Gehring’s primary affiliation is with Whitehead Institute for Biomedical Research, where her laboratory is located and all her research is conducted. She is also an associate professor of biology at Massachusetts Institute of Technology.
* * *
Full Citation:
“Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit”
Nature Communications, December 14, 2017.
Ben P. Williams (1) and Mary Gehring (1,2).
1. Whitehead Institute for Biomedical Research, Cambridge, MA 02142
2. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
Jacqueline Lees

Education

  • PhD, 1990, University of London
  • BSc, 1986, Biochemistry, University of York

Research Summary

We identify the proteins and pathways involved in tumorigenicity — establishing their mechanism of action in both normal and tumor cells. To do so, we use a combination of molecular and cellular analyses, mutant mouse models and genetic screens in zebrafish.

Michael T. Hemann

Education

  • PhD, 2001, Johns Hopkins University
  • BS, 1993, Molecular Biology and Biochemistry, Wesleyan University

Research Summary

Many human cancers do not respond to chemotherapy, and often times those that initially respond eventually acquire drug resistance. Our lab uses high-throughput screening technology — combined with murine stem reconstitution and tumor transplantation systems — to investigate the genetic basis for this resistance. Our goal is to identify novel cancer drug targets, as well as strategies for tailoring existing cancer therapies to target the vulnerabilities associated with specific malignancies.

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
Celebrating a decade of interdisciplinary microbiology

The Microbiology Graduate PhD Program spans 50 labs across 10 departments and divisions, offering a broad approach to microbial science and engineering.

Raleigh McElvery | Department of Biology
December 12, 2017

Ten years ago, MIT launched the Microbiology Graduate PhD Program. Today, it boasts 28 alumni and 33 current students, and offers a broad, interdisciplinary approach to microbial science and engineering. Between five and eight trainees enroll each year and can choose among more than 50 labs spanning 10 departments and divisions — from biology and biological engineering to chemical engineering and physics.

Many diverse disciplines are rooted in microbiology. Basic scientists use microorganisms as model systems to understand fundamental biological processes. Engineers leverage microorganisms to create new manufacturing processes and energy sources. Even ecologists, biomedical researchers, and earth scientists dedicate their careers to investigating the role of microbes in our ecosystems, on our bodies, and on our planet. In sum, the study of microbiology permeates so many research areas that no single department at MIT could house them all.

The idea for an interdisciplinary microbiology program first came to Alan Grossman, head of the Department of Biology, while he was recovering from a heart transplant back in 2006.

“There were people scattered all over MIT who were doing microbial science and engineering, but there was no mechanism to connect them or give students outside those departments easy access to the labs,” Grossman says. “I began by talking to a few faculty members in order to gauge general interest, before pitching it to a handful of department heads and forming a committee. Everyone was very excited about it, and it really grew from the ground up.”

The Committee on Graduate Programs approved his proposal in May 2007, and the first cohort of eight students began in the fall of 2008. Martin Polz, co-director since 2015 and professor of civil and environmental engineering, sat on Grossman’s initial committee.

“MIT’s program is unique from most other microbiology programs because it’s so interdisciplinary,” Polz says. “Many microbiology programs across the country are associated with medical schools and focused primarily on pathogenesis. The students who apply here really appreciate the breadth of our program, and it has become a fixture at MIT over the years.”

Kristala Prather, co-director since 2013 and professor of chemical engineering, said the program also provides an opportunity to bring life scientists and engineers together to tackle research questions.

“I find there is a difference in the way engineers and scientists approach research problems,” Prather says. “Each approach has rigor, but having both perspectives breeds a richer set of discussions than just hearing from one discipline alone.”

During the past 10 years, Prather has watched a thriving and diverse community unite, spurred by a common interest in the microbial world.

Nathaniel Chu, who matriculated in 2014, said the program allows him to sample different disciplines while still maintaining a close affiliation with his advisor’s home department, Biological Engineering. As part of Eric Alm’s lab, Chu studies the interaction between the gut microbiome and immune system, and how imbalances in that delicate relationship can trigger conditions such as Type 2 diabetes, obesity, and inflammatory bowel disease.

“The program provides flexibility to explore your research interests, and my advisor has given me a lot of space to conceive and manage my own projects,” Chu says. “I’ve been able to interact with a diverse set of individuals within the microbiology circle, including clinical partners, immunologists, geneticists, bioinformaticians, and computational biologists.”

Jacquin Niles, incoming co-director, was a junior faculty member in Department of Biological Engineering when Grossman first proposed the idea. He says the students — past and present — are the heart of the program.

“A lot has changed over the 10 years the program has been in existence, but the caliber of students has remained consistent,” Niles says. “If I had to emphasize any particular aspect of the program, the students would be numbers one, two, and three. Each generation has been exceptional, and they are all very much on top of their research game.”

Michael Laub, co-director from 2012 to 2015 and professor of biology, adds that the early students deserve much credit for the program’s success. “They took a chance on a brand-new initiative, and as a result we ended up attracting ambitious, risk-taking, and creative folks who really paved the way for current students,” he says.

Alumni pursue a variety of careers, ranging from academia to industry. Some join existing institutions or companies. Others start their own.

Mark Smith PhD ’14 was a member of the second graduating class. Like Chu, he was one of Alm’s advisees, studying networks of gene exchange within the human microbiome, and building statistical models to determine the role of environment in various gut-related diseases. Smith went on to co-found a nonprofit organization known as OpenBiome, harnessing the microbiome to cure recurrent Clostridium difficile infections. In 2016, he co-founded another company, Finch Therapeutics Group, focused on scaling and commercializing clinical treatments for diseases rooted in the microbiome. In 2017, he was named to the Forbes 30 Under 30 list for science.

“OpenBiome and Finch Therapeutics were really a translation of the initial work that was done through the microbiology program, and a step toward developing those tools to improve human health,” Smith says. “The program taught me the foundational work I’ve come to rely on in almost every aspect of my job today.”

Like Smith, Jacob Rubens PhD ’16 aims to apply his training at MIT to help develop new products. After working in Timothy Lu’s lab — straddling the realms of biological engineering and electrical engineering — Rubens joined Flagship Pioneering, a company that starts, funds, and runs breakthrough biotechnology startups in Cambridge, Massachusetts. Rubens was also named to the Forbes 30 Under 30 list for science in 2017.

During the six years that Rubens was at MIT, he watched the microbiology cohort grow from roughly 20 to a force permeating more labs across campus than he could count.

“It’s heartwarming to see people bringing a microbiological perspective into all these different spaces, and influencing cutting-edge research across the Institute,” he says. “As a microbiology student, you become an integrator and synthesizer of many different viewpoints, and a node to foster cross-talk between disciplines.”

As Niles prepares to assume the role of co-director in July 2018 and usher in the program’s second decade, he intends to maintain its integrity and structure.

“The program has matured into what it is today thanks to a lot of previous, careful thought,” he says. “The students have indicated that there is a lot of value in the structure that we’ve refined over the years, and so my goal is to continue that positive momentum.”

Douglas Lauffenburger

Education

  • PhD, 1979, University of Minnesota
  • BS, 1975, Chemical Engineering, University of Illinois, Urbana-Champaign

Research Summary

The Lauffenburger laboratory emphasizes integration of experimental and mathematical/computational analysis approaches, toward development and validation of predictive models for physiologically-relevant behavior in terms of underlying molecular and molecular network properties. Our work has been recognized as providing contributions fostering the interface of bioengineering, quantitative cell biology, and systems biology. Our main focus has been on fundamental aspects of cell dysregulation, complemented by translational efforts in identifying and testing new therapeutic ideas. Applications addressed have chiefly resided in various types of cancer (including breast, colon, lung, and pancreatic cancers along with leukemias and lymphomas), inflammatory pathologies (such as endometriosis, Crohn’s disease, colitis, rheumatoid arthritis, and Alzheimer’s disease), and the immune system (mainly for vaccines against pathogens such as HIV, malaria, and tuberculosis). We have increasingly emphasized complex tissue contexts, including mouse models, human subjects, and tissue-engineered micro-physiological systems platforms in association with outstanding collaborators. From our laboratory have come more than 100 doctoral and postdoctoral trainees. Many hold faculty positions at academic institutions in the USA, Canada, and Europe; others have gone on to research positions in biotechnology and pharmaceutical companies; and others yet have moved into policy and government agency careers.

Awards

  • Bernard M. Gordon Prize for Innovation in Engineering and Technology Education, National Academy of Engineering, 2021
  • American Association for the Advancement of Science, Member, 2019
  • American Academy of Arts and Sciences, Fellow, 2001
  • John Simon Guggenheim Memorial Foundation, Guggenheim Fellowship, 1989
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.