Research Area: Biochemistry, Biophysics, and Structural Biology

A tough case cracked
Greta Friar | Whitehead Institute
December 17, 2018

CAMBRIDGE, Mass. — For hundreds of millions of years, plants thrived in the Earth’s oceans, safe from harsh conditions found on land, such as drought and UV radiation. Then, roughly 450 million years ago, plants found a way to make the move to land: They evolved spores—small reproductive cells—and eventually pollen grains with tough, protective outer walls that could withstand the harsh conditions in the terrestrial environment until they could germinate and grow into a plant or fertilize an ovule. A key component of the walls is sporopollenin, a durable polymer — a large molecule made up of many small subunits — that is absent in algae but remains ubiquitous in all land plants to this day.

Understanding the molecular composition of polymers found in nature is a fundamental pursuit of biology, with a long history tracing back to the early days of elucidating DNA and protein structures. However, the very toughness that makes sporopollenin so important for all land plants also makes it tough for researchers to study. It is extremely inert, resistant to reacting with other chemicals, including the ones researchers typically use to determine the structures of other plant biopolymers, such as polysaccharides, lignin, and natural rubber. Consequently, scientists have struggled for decades to figure out exactly what the sporopollenin polymer is made of. Now, in an article published in the journal Nature Plants on December 17, Whitehead Institute Member Jing-Ke Weng and first author and Weng lab postdoc Fu-Shuang Li, together with collaborators Professor Mei Hong and graduate student Pyae Phyo from the Massachusetts Institute of Technology (MIT) Department of Chemistry, have used innovative chemical degradation methods and state-of-the-art nuclear magnetic resonance (NMR) spectroscopy to determine the chemical structure of sporopollenin.

“Plants could not have colonized the land if they had not developed a way to withstand harsh environments,” says Weng, who is also an assistant professor of biology at MIT. “Sporopollenin helped make the terrestrial ecosystem as we know it possible.”

In addition to solving a longstanding puzzle in plant chemistry, identifying the structure of sporopollenin opens the door for its potential use in a host of other applications. Sporopollenin’s inertness is a desirable attribute to replicate in the development of, for example, medical implants such as stents, which prop open clogged arteries, to prevent negative interactions between the device and the body. It could also be a good model for durable paints and coatings, such as those used on boats, where its inertness would prevent reactions with compounds in the water and so protect the ship’s hull from environmental degradation.

Finding the shape and composition of sporopollenin was not a simple task. The first challenge was getting enough of the material to study, as pollen amounts that can be collected from most plants are minute. However, pollen from the pitch pine, Pinus rigida, is sold in bulk in China as a topping for rice cakes, so Weng used an unconventional sample collection method: He asked his parents in China to ship him copious quantities of pitch pine pollen.

A common approach to determine a complex plant polymer’s structure is to dissolve it in solutions with specific chemical compounds that will break it apart into smaller and smaller pieces from which the complete structure can be deduced. But since sporopollenin is inert and does not react with the researchers’ usual cadre of chemicals, figuring out how to break down the molecule was a key challenge.

In order to crack this problem — and make the sporopollenin dissolve more easily — Li used a specially designed grinder known as the high-energy ball mill to physically shear the tiny pollen coat into even finer pieces. Then he began testing different chemical mixtures to find ones that could break apart the sporopollenin polymer into more accessible fragments. The big breakthrough came when he tried a chemical degradation process called thioacidolysis, an acid catalyzed reaction with a pinch of a special sulfur-containing compound. This allowed Li to consistently break down 50% of the total sporopollenin polymer into small pieces, with the structure of each of these pieces resolved one by one.

To help complete the puzzle, the researchers collaborated with Mei Hong’s group in MIT’s Department of Chemistry and used magic-angle-spinning solid-state NMR spectroscopy, which can determine the chemical structures of insoluble compounds by having them interact with magnetic fields. This investigation narrowed the possible structures for sporopollenin. Combined with more chemical degradation tests to verify certain possibilities and eliminate others, it ultimately led to the complete structure.

With the structure of sporopollenin in hand, the researchers were then able to identify aspects of this unique polymer that make it such a good protective wall for spores and pollen.

A key finding was that sporopollenin molecules contain two types of cross-linkages, esters and acetals, that act like chemical clips, binding the chains of the molecule together. Other known plant polymers have only one main type of cross-link, and this unique characteristic likely provides the extreme chemical inertness of sporopollenin. Ester bonds are resistant to mildly acidic conditions, while acetals are resistant to basic conditions, meaning the molecule won’t break down in either type of environment in the wild or in the lab.

Other components of sporopollenin that the researchers found include multiple molecules known to provide UV protection, as well as fatty acids, which are water resistant and may protect spores and pollen from drought or other changes in water availability.

The researchers are now looking for differences in sporopollenin between species. Pine is not a flowering plant, but the majority of plants of interest to agriculture and medicine are, so Weng and Li are investigating how sporopollenin may have changed with the evolution of the flowering plants.

“Since I was a student, inspired by the magnificent discovery of the structure of DNA, I have been driven to discover the fundamental forms of things in nature,” Weng says. “It has been so rewarding to illuminate the structure of this crucial biopolymer in plants.”

This work was supported by the Pew Scholar Program in the Biomedical Sciences and the Searle Scholars Program, and the U.S. Department of Energy (# DE-SC0001090).

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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.

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Full citation:
“The molecular structure of plant sporopollenin”
Nature Plants, December 17, 2018, DOI: 10.1038/s41477-018-0330-7
Fu-Shuang Li (1), Pyae Phyo (2), Joseph Jacobowitz (1,3), Mei Hong (2), Jing-Ke Weng (1,3)
1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, United States.
2. Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.
3. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.
Engineering “capture compounds” to probe cell growth

Researchers develop a method to investigate how bacteria respond to starvation and to identify which proteins bind to what they call the “magic spot” — ppGpp.

Raleigh McElvery | Department of Biology
December 17, 2018

In 1969, scientist Michael Cashel was analyzing the compounds produced by starved bacteria when he noticed two spots appearing on his chromatogram as if by magic. Today, we know one of these “magic spots,” as researchers call them, as guanosine tetraphosphate, or ppGpp for short. We also understand that it is a signaling molecule present in virtually all bacteria, helping tune cell growth and size based on nutrient availability.

And yet, despite decades of study, precisely how ppGpp regulates bacterial growth has remained rather mysterious. Delving further requires a more comprehensive list of the molecules that ppGpp binds to exert its effects.

Now, collaborators from MIT’s departments of Biology and Chemistry have developed a method to do just that, and used their new approach to pinpoint over 50 ppGpp targets in Escherichia coli — roughly half which had not been identified previously. Many of these targets are enzymes required to produce nucleotides, the building blocks of DNA and RNA. During times when the bacteria do not have enough nutrients to grow and divide normally, the researchers propose that ppGpp prevents these enzymes from creating new nucleotides from scratch, helping cells enter a dormant state.

“With small molecules or metabolites like ppGpp, it’s been difficult historically to determine which proteins they bind,” says Michael Laub, a professor of biology, a Howard Hughes Medical Institute investigator, and the senior author of the study. “This has been an intractable problem that’s held the field back for some time, but our new approach allows you to nail down the likely targets in a matter of weeks.”

Postdoc Boyuan Wang is the first author of the study, which appeares in Nature Chemical Biology on Dec. 17.

Since ppGpp was discovered nearly 50 years ago, it has been shown to suppress DNA replication, transcription, translation, and various metabolic pathways. It puts the brakes on cell growth and allows bacteria to persist in the face of starvation, stress, and antibiotics. Its influence over numerous regulatory processes has remained somewhat of a mystery, however — after all, it doesn’t just modulate a single pathway but coordinates multiple operations simultaneously to orchestrate a mass shutdown of the cell.

In order to discern which proteins ppGpp binds to effect such widespread change, the researchers built what they call “capture compounds” that contain ppGpp, allowing them to fish out its targets from bacterial extracts. These compounds included a photoreactive crosslinker that latched tightly onto the proteins of interest in the presence of light, and a biotin handle that helped the scientists pull out the proteins to identify them. Most importantly, they were joined to ppGpp in such a way that they wouldn’t interfere with its ability to bind to its targets. This method is more efficient and accurate compared to more traditional means of distinguishing ppGpp targets, which are far more arduous and lack sensitivity.

“Our approach solves these problems because you’re no longer required to do such labor-intensive protocols in order to identify ppGpp targets — and it works even in bacteria beyond E. coli,” says Wang. “Although ppGpp is common among many bacterial species, it seems to exert its effects through different mechanisms, which complicates things. Our capture compounds provide a way to unravel this diversity, and in short order.”

Although the 56 ppGpp targets Wang identified in his screen control a myriad of cellular processes, he homed in on the enzyme PurF — which initiates the biosynthesis of purine nucleotides bearing adenine and guanine bases, also known as A and G.

When bacteria are stressed or starved, they enter a dormant state to survive. But simply curbing translation and transcription is not enough; nucleotides are still being generated and will build up if their synthesis is not put on pause. Cells can build nucleotides in one of two ways: either by salvaging existing materials or starting completely from scratch. PurF kicks off the first step in the latter process leading to the A and G nucleotides. However, when ppGpp binds to PurF, it causes the enzyme to change its shape, which prevents it from doing its job, thus reducing nucleotide production in the cell.

“This is the first time that an enzyme involved in that specific pathway or function has been identified as a ppGpp target,” Wang says. “If you limit the consumption of nucleotides but not their production, the nucleotide pool is going to explode, which isn’t good for the cell. So we’ve shown that ppGpp actually addresses this problem as well.”

In addition to PurF and other enzymes required for nucleotide production, the researchers noticed that ppGpp also binds to many GTPase enzymes involved in translation. This could indicate a failsafe mechanism slowing down translation by striking multiple, similar enzymes in an almost redundant manner in the face of starvation.

As Wang continues to refine his method, he aims to increase its specificity and ensure his capture compounds bind to the exact same proteins they would inside a live cell. He also hopes to screen for ppGpp binding proteins in other bacteria, including pathogens that rely on ppGpp to survive within their hosts and propagate conditions like tuberculosis.

“This is an exciting chemical approach to better understand the function of a long-studied conserved signaling molecule in bacteria,” says Jue Wang, professor of bacteriology at the University of Wisconsin at Madison, who was not involved with the study. “Their findings and techniques are highly relevant to many other bacteria, and will greatly improve knowledge of how bacteria use this critical signaling molecule to mediate everything from surviving in the human gut to causing disease.”

Adds Laub: “We are still discovering new nucleotide-based signaling molecules in bacteria even today, and every single one of them could eventually be derivatized in a similar way to identify their binding partners.”

This research was supported by a fellowship from the Jane Coffin Childs Memorial Fund for Medical Research and a grant from the National Institutes of Health.

Biologists discover an unusual hallmark of aging in neurons

Snippets of RNA that accumulate in brain cells could interfere with normal function.

Anne Trafton | MIT News Office
November 27, 2018

As we age, neurons in our brains can become damaged by free radicals. MIT biologists have now discovered that this type of damage, known as oxidative stress, produces an unusual pileup of short snippets of RNA in some neurons.

This RNA buildup, which the researchers believe may be a marker of neurodegenerative diseases, can reduce protein production. The researchers observed this phenomenon in both mouse and human brains, especially in a part of the brain called the striatum — a site involved in diseases such as Parkinson’s and Huntington’s.

“The brain is very metabolically active, and over time, that causes oxidative damage, but it affects some neurons more than others,” says Christopher Burge, an MIT professor of biology. “This phenomenon appears to be a previously unrecognized consequence of oxidative stress, which impacts hundreds of genes and may influence translation and RNA regulation globally.”

Burge and Myriam Heiman, the Latham Family Career Development Associate Professor of Brain and Cognitive Sciences, are the senior authors of the paper, which appears in the Nov. 27 issue of Cell Reports. Peter Sudmant, a former MIT postdoc, is the lead author of the paper, and postdoc Hyeseung Lee and former postdoc Daniel Dominguez are also authors.

A mysterious finding

For this study, the researchers used a technique developed by Heiman that allows them to isolate and sequence messenger RNA from specific types of cells. Messenger RNA carries protein-building instructions to cell organelles called ribosomes, which read the mRNA and translate the instructions into proteins by stringing together amino acids in the correct sequence.

Heiman’s technique involves tagging ribosomes from a specific type of cells with green fluorescent protein, so that when a tissue sample is analyzed, researchers can use the fluorescent tag to isolate and sequence RNA from only those cells. This allows them to determine which proteins are being produced by different types of cells.

“This is particularly useful in the nervous system where you’ve got different types of neurons and glia closely intertwined together, if you want to isolate the mRNAs from one particular cell type,” Burge says.

In separate groups of mice, the researchers tagged ribosomes from either D1 or D2 spiny projection neurons, which make up 95 percent of the neurons found in the striatum. They labeled these cells in younger mice (6 weeks old) and 2-year-old mice, which are roughly equivalent to humans in their 70s or 80s.

The researchers had planned to look for gene expression differences between those two cell types, and to explore how they were affected by age. “These two types of neurons are implicated in several neurodegenerative diseases that are aging-related, so it is important to understand how normal aging changes their cellular and molecular properties,” says Heiman, who is a member of MIT’s Picower Institute for Learning and Memory and the Broad Institute of MIT and Harvard.

To the researchers’ surprise, a mysterious result emerged — in D1 neurons from aged mice (but not neurons from young mice or D2 neurons from aged mice), they found hundreds of genes that expressed only a short fragment of the original mRNA sequence. These snippets, known as 3’ untranslated regions (UTRs), were stuck to ribosomes, preventing the ribosomes from assembling normal proteins. “While these RNAs have been observed before, the magnitude and age-associated cell-type specificity was really unprecedented,” says Sudmant.

The 3’ UTR snippets appeared to originate from about 400 genes with a wide variety of functions. Meanwhile, many other genes were totally unaffected.

“There are some genes that are completely normal, even in aged D1 neurons. There’s a gene-specific aspect to this phenomenon that is quite interesting and mysterious,” Burge says.

The findings led the researchers to explore a possible role for oxidative stress in this 3’ UTR accumulation. Neurons burn a great deal of energy, which can produce free radicals as byproducts. Unlike many other cell types, neurons do not get replaced, so they are believed to be susceptible to accumulated damage from these radicals over time.

The MIT team found that the activation of oxidative stress response pathways was higher in D1 neurons compared to D2 neurons, suggesting that they are indeed undergoing more oxidative damage. The researchers propose a model for the production of isolated 3′ UTRs involving an enzyme called ABCE1, which normally separates ribosomes from mRNA after translation is finished. This enzyme contains iron-sulfur clusters that can be damaged by free radicals, making it less effective at removing ribosomes, which then get stuck on the mRNA. This leads to cleavage of the RNA by a mechanism that operates upstream of stalled ribosomes.

“Sending neural signals takes a lot of energy,” Burge says. “Over time, that causes oxidative damage, and in our model one of the proteins that eventually gets damaged is ABCE1, and that triggers the production of 3’ UTRs.”

RNA buildup

The researchers also found the same accumulation in most parts of the human brain, including the frontal cortex, which is very metabolically active. They did not see it in most other types of human tissue, with the exception of liver tissue, which is exposed to high levels of potentially toxic molecules.

In human brain tissue, the researchers found that the amount of 3’ UTRs gradually increased with age, which fits their proposed model of gradual damage by oxidative stress. The researchers’ findings and model suggest that the production of these 3′ UTRs involves the destruction of normal mRNAs, reducing the amount of protein produced from the affected genes.  This buildup of 3′ UTRs with ribosomes stuck to them can also block ribosomes from producing other proteins.

It remains to be seen exactly what effect this would have on those neurons, Burge says, but it is possible that this kind of cellular damage could combine with genetic and environmental factors to produce a general decline in cognitive ability or even neurodegenerative conditions such as Parkinson’s disease. In future studies, the researchers hope to further explore the causes and consequences of the accumulation of 3’ UTRs.

The research was funded by the National Institutes of Health and the JPB Foundation.

The long and short of CDK12

A new study linking RNA processing to DNA repair may open new avenues to cancer therapy.

Bendta Schroeder | Koch Institute
December 3, 2018

Mutations in the BRCA1 and BRCA2 genes pose a serious risk for breast and ovarian cancer because they endanger the genomic stability of a cell by interfering with homologous recombination repair (HR), a key mechanism for accurately repairing harmful double-stranded breaks in DNA. Without the ability to use HR to fix double-stranded breaks, the cell is forced to resort to more error-prone — and thus more cancer-prone — forms of DNA repair.

The BRCA1 and BRCA2 genes are not the only genes whose mutations foster tumorigenesis by causing an inability to repair DNA double strand breaks by HR. Mutations in twenty-two genes are known to disrupt HR, giving rise to tumors with what researchers call “BRCAness” characteristics. All but one of these BRCAness genes are known to be directly involved in the HR pathway.

The one exception, CDK12, is thought to facilitate a set of different processes altogether, involving how RNA transcripts are elongated, spliced and cleaved into their mature forms. While the connection between this RNA-modulating gene to DNA repair remained poorly understood, the identification of CDK12 as a BRCAness gene piqued significant clinical interest.

The researchers who pinpointed this connection, Sara Dubbury and Paul Boutz, both work in the laboratory of Phillip Sharp, Institute Professor, professor of biology, and member of the Koch Institute for Integrative Cancer Research. In a study appearing online in Nature on Nov. 28, they describe how they discovered a previously unknown mechanism by which CDK12 enables the production of full-length RNA transcripts and that this mechanism was especially critical to maintain functional expression of the other BRCAness genes.

When the researchers knocked out expression of CDK12, mouse stem cells showed many signs of accumulating DNA damage that prevented DNA replication from going forward, classic indications of a BRCAness phenotype. To identify what roles CDK12 may play in regulating gene expression, the researchers turned to RNA sequencing to determine which genes had increased or decreased their overall expression.

To their surprise, only genes activated by p53 and early differentiation (side effects of accumulating unrepaired DNA damage and BRCAness in mouse stem cells) accounted for the lion’s share of changes to RNA transcription. However, when the researchers instead focused on the types of RNAs transcribed, they found that many genes produced unusually short transcripts when CDK12 was absent.

Not every stretch of DNA in a gene makes it into the final RNA transcript. The initial RNA from a gene often includes sections, which researchers call “introns,” that are cut out of transcript, the discovery that earned Sharp the 1993 Nobel Prize in Physiology or Medicine and the remaining sections. “Exons,” are spliced together to form a mature transcript (mRNA). Alternately, an intronic polyadenylation (IPA) site may be activated to cleave away the RNA sequence that follows it preventing intron removal and generating a prematurely shortened transcript. These processes allow the same gene to produce alternate forms of messenger RNA (mRNA), and thus be translated into different protein sequences.

Surprisingly CDK12 knockout cells produced significantly more IPA-truncated transcripts genome-wide, while full-length transcripts for the same genes were reduced. These shortened mRNAs can vary greatly in their stability, their ability to be translated into protein, and their protein function. Thus, even while a gene may be actively transcribed, its translation into functional proteins can be radically altered or depleted by IPA activation.

While this observation began to illuminate CDK12’s role in regulating mRNA processing, what remained puzzling was why CDK12 loss affected the HR pathway so disproportionately. In investigating this question, Dubbury and Boutz found that BRCAness genes were overrepresented as a group among those genes that have increased IPA activity upon CDK12 loss.

Additionally, while CDK12 suppresses IPA activity genome-wide, 13 of the other 21 BRCAness genes were found to be particularly vulnerable to CDK12 loss, in part, because they possess multiple high-sensitivity IPA sites, which have a compound effect in decreasing the total amount of full-length transcripts. Moreover, because multiple CDK12-senstive BRCAness genes operate in the same HR pathway, the researchers believe that the disruption to HR repair of double-stranded DNA breaks is amplified.

CDK12 mutations are found recurrently in prostate and ovarian cancer patients, making them an attractive diagnostic and therapeutic target for cancer. However, not enough is known about CDK12 to distinguish between true loss-of-function mutations and so-called “passenger mutations” with no functional consequence.

“The ability to identify patients with true loss-of-function mutations in CDK12 would enable clinicians to label a new cohort of patients with bona fide BRCAness tumors that could benefit from certain highly effective and targeted chemotherapeutics against BRCAness, such as PARP1 inhibitors,” says Dubbury, a former David H. Koch Fellow.

Dubbury and Boutz were able to confirm that IPA sites in key BRCAness genes were also used more frequently upon CDK12 loss in human tumor cells using RNA sequencing data from prostate and ovarian tumor patients with CDK12 mutations and by treating human prostate adenocarcinoma and ovarian carcinoma cells with a CDK12 inhibitor. This result suggests that the CDK12 mechanism observed in mouse cell lines is conserved in humans and that CDK12 mutations in human ovarian and prostate tumors may promote tumorigenesis by increasing IPA activity and thus functionally attenuating HR repair.

“These results not only give us a better understanding how CDK12 contributes to BRCAness, they also may have exciting potential impact in the clinic,” Dubbury says. “Currently available diagnostic techniques could be used to probe the usage of IPA sites found in this study to rapidly screen for patients with true loss-of-function CDK12 mutations, who would respond to BRCAness-targeted treatments.”

Paul Boutz, a research scientist in the Sharp Lab, is co-first author of the study, and has plans to follow-up many of these implications for ovarian and prostate cancer his lab at the University of Rochester School of Medicine and Dentistry.

“CDK12 provides a remarkable example of how factors that control the processing of RNA molecules can function as master regulators of gene networks, and thereby profoundly affect the physiology of both normal and cancerous cells,” he says.

Phil Sharp, the senior author on the work, says “Sara’s and Paul’s surprising discovery that CDK12 suppresses intronic polyadenylation has implications for fundamental new insights into gene structure as well as for control of cancer.”

Computer model offers more control over protein design

New approach generates a wider variety of protein sequences optimized to bind to drug targets.

Anne Trafton | MIT News Office
October 15, 2018

Designing synthetic proteins that can act as drugs for cancer or other diseases can be a tedious process: It generally involves creating a library of millions of proteins, then screening the library to find proteins that bind the correct target.

MIT biologists have now come up with a more refined approach in which they use computer modeling to predict how different protein sequences will interact with the target. This strategy generates a larger number of candidates and also offers greater control over a variety of protein traits, says Amy Keating, a professor of biology, a member of the Koch Institute, and the leader of the research team.

“Our method gives you a much bigger playing field where you can select solutions that are very different from one another and are going to have different strengths and liabilities,” she says. “Our hope is that we can provide a broader range of possible solutions to increase the throughput of those initial hits into useful, functional molecules.”

In a paper appearing in the Proceedings of the National Academy of Sciences the week of Oct. 15, Keating and her colleagues used this approach to generate several peptides that can target different members of a protein family called Bcl-2, which help to drive cancer growth.

Recent PhD recipients Justin Jenson and Vincent Xue are the lead authors of the paper. Other authors are postdoc Tirtha Mandal, former lab technician Lindsey Stretz, and former postdoc Lothar Reich.

Modeling interactions

Protein drugs, also called biopharmaceuticals, are a rapidly growing class of drugs that hold promise for treating a wide range of diseases. The usual method for identifying such drugs is to screen millions of proteins, either randomly chosen or selected by creating variants of protein sequences already shown to be promising candidates. This involves engineering viruses or yeast to produce each of the proteins, then exposing them to the target to see which ones bind the best.

“That is the standard approach: Either completely randomly, or with some prior knowledge, design a library of proteins, and then go fishing in the library to pull out the most promising members,” Keating says.

While that method works well, it usually produces proteins that are optimized for only a single trait: how well it binds to the target. It does not allow for any control over other features that could be useful, such as traits that contribute to a protein’s ability to get into cells or its tendency to provoke an immune response.

“There’s no obvious way to do that kind of thing — specify a positively charged peptide, for example — using the brute force library screening,” Keating says.

Another desirable feature is the ability to identify proteins that bind tightly to their target but not to similar targets, which helps to ensure that drugs do not have unintended side effects. The standard approach does allow researchers to do this, but the experiments become more cumbersome, Keating says.

The new strategy involves first creating a computer model that can relate peptide sequences to their binding affinity for the target protein. To create this model, the researchers first chose about 10,000 peptides, each 23 amino acids in length and helical in structure, and tested their binding to three different members of the Bcl-2 family. They intentionally chose some sequences they already knew would bind well, plus others they knew would not, so the model could incorporate data about a range of binding abilities.

From this set of data, the model can produce a “landscape” of how each peptide sequence interacts with each target. The researchers can then use the model to predict how other sequences will interact with the targets, and generate peptides that meet the desired criteria.

Using this model, the researchers produced 36 peptides that were predicted to tightly bind one family member but not the other two. All of the candidates performed extremely well when the researchers tested them experimentally, so they tried a more difficult problem: identifying proteins that bind to two of the members but not the third. Many of these proteins were also successful.

“This approach represents a shift from posing a very specific problem and then designing an experiment to solve it, to investing some work up front to generate this landscape of how sequence is related to function, capturing the landscape in a model, and then being able to explore it at will for multiple properties,” Keating says.

Sagar Khare, an associate professor of chemistry and chemical biology at Rutgers University, says the new approach is impressive in its ability to discriminate between closely related protein targets.

“Selectivity of drugs is critical for minimizing off-target effects, and often selectivity is very difficult to encode because there are so many similar-looking molecular competitors that will also bind the drug apart from the intended target. This work shows how to encode this selectivity in the design itself,” says Khare, who was not involved in the research. “Applications in the development of therapeutic peptides will almost certainly ensue.”

Selective drugs

Members of the Bcl-2 protein family play an important role in regulating programmed cell death. Dysregulation of these proteins can inhibit cell death, helping tumors to grow unchecked, so many drug companies have been working on developing drugs that target this protein family. For such drugs to be effective, it may be important for them to target just one of the proteins, because disrupting all of them could cause harmful side effects in healthy cells.

“In many cases, cancer cells seem to be using just one or two members of the family to promote cell survival,” Keating says. “In general, it is acknowledged that having a panel of selective agents would be much better than a crude tool that just knocked them all out.”

The researchers have filed for patents on the peptides they identified in this study, and they hope that they will be further tested as possible drugs. Keating’s lab is now working on applying this new modeling approach to other protein targets. This kind of modeling could be useful for not only developing potential drugs, but also generating proteins for use in agricultural or energy applications, she says.

The research was funded by the National Institute of General Medical Sciences, National Science Foundation Graduate Fellowships, and the National Institutes of Health.

How Many Evolutionary Events Can It Take To Screw in Nature’s Lightbulb?

Firefly genomics reveals independent evolution of bioluminescence in beetles

Lisa Girard | Whitehead Institute
October 16, 2018

Cambridge, MA — Researchers at Whitehead Institute and collaborators from fourteen other institutions around the world have shed light on the evolutionary origins of luciferase, the key enzyme behind the glow of fireflies and other bioluminescent beetles. By sequencing the genomes of two American and Japanese firefly species that diverged approximately 100 million years ago, along with a more evolutionarily distant bioluminescent Caribbean click beetle, the team discovered that luciferase appears to have arisen independently in fireflies and click beetles. Examining the genes flanking that encoding the luciferase gene, suggests an evolutionary path along which the luciferase gene arose from duplications and divergences of CoA ligase genes involved in fat metabolism. As described online October 16 in the journal eLife, these findings provide fundamental insights into how enzymes can evolve, potentially inform strategies to help protect bioluminescent beetles from a shifting climate and habitat, and could extend the utility of luciferase, which has also been harnessed for biomedical and agricultural research, as a laboratory tool.

Throughout much of the world, the silent flash of a firefly on a warm evening can only mean one thing-Summer has arrived. But fireflies don’t just signal summer, their glow serves as a mating signal to other fireflies, and is even a warning that they are chemically defended, having a noxious taste capable of repelling the boldest of predators.

Belying its grandeur, the chemistry of firefly bioluminescence is relatively straightforward. Their light is produced by a specialized firefly enzyme, luciferase, that breaks down a molecule called luciferin, producing light in the process. Luciferase has become a mainstay tool in the laboratory. Scientists can fuse their gene of interest to luciferase and assay for gene expression by measuring the intensity of the glow after luciferin is added.

Beyond fireflies, there are other bioluminescent beetles (despite their name, fireflies are actually beetles), including certain tropical click-beetles. Perplexingly, these diverse bioluminescent beetles use very similar luciferase enzymes and luciferin molecules, but have an unrelated anatomy of their light-producing organs (also known as lanterns), making it unclear if their bioluminescence evolved from a common luminous ancestor, or if their special glow evolved independently.

Since fireflies and bioluminescent click-beetles are not model organisms like mice or fruit flies for which there is a wealth of genetic information, Jing-Ke Weng, Whitehead Institute Member and assistant professor of biology at Massachusetts Institute of Technology (MIT), along with a  graduate student in Weng’s lab, Tim Fallon, and Cornell postdoctoral researcher, Sarah Lower, began their investigations by sequencing the genome of the American Big Dipper firefly, Photinus pyralis. Named for its distinctive swooping “J” flash , this common inhabitant of meadows and suburban lawns has been called the “All-American firefly”. Due to its abundance and ease of identification, it was also the firefly of choice for scientific study, and is the species from which luciferin and luciferase were first characterized. Wanting to start their work quickly and make their progress and data available to others in the firefly community, Whitehead Institute researchers and collaborators crowdsourced funds to sequence the Big Dipper firefly.

The Big Dipper genome sequence, they discovered, revealed interesting insights into the origin of the luciferase gene. Examining the genes flanking that encoding luciferase, they found a cluster, or tandem repeat, of fatty acid CoA ligase genes with the luciferase gene sitting in the middle of this cluster. Sequence similarity and proximity between the luciferase and fatty acid CoA ligase genes suggested an evolutionary path along which the luciferase gene was produced from tandem duplication and divergence of an ancestral fatty acid CoA ligase gene.

“When the luciferase gene was cloned, people knew it was similar to the fatty acid CoA ligase gene in sequence, and hypothesized that it must be related to that ancestry. But what we uncovered from the luciferase gene locus is a tandem repeat of five genes, four are still the fatty acid CoA ligases, but then luciferase evolved right in the middle we believe from divergence of one of these duplications,” says Weng.

The Big Dipper sequencing provided important insights into the origin of luciferase and additional factors involved in bioluminescence, but in order to gain additional insights into the evolution of bioluminescence, the researchers set out to sequence two additional species that they hoped would provide the additional context to help them triangulate on some answers.

The bioluminescent click beetle, Ignelater luminosus, is related to the firefly, but on another branch of the tree of life entirely. Instead of producing light at its tail, it has two lanterns behind its head.

“We thought that sequencing the click beetle would provide insights into the evolution of bioluminescence as well as perhaps into how these animals could acquire very similar traits in terms of their biochemistry, but not in terms of their development,” says Fallon.

The third species they selected to sequence was a Japanese aquatic firefly (Aquatica lateralis), known in Japan as the Heike firefly.  Heike and the Big Dipper diverged from one another over 100 million years ago (to give you a sense of how far this is, it is older than the evolutionary distance between humans and rodents).

The researchers analyzed genomic data from the Japanese aquatic firefly and saw a similar arrangement around the luciferase gene locus as they had in the Big Dipper genome, suggesting that luciferase arose from a common ancestral event in both firefly species. The structure around the luciferase locus in the click beetle, however, was entirely absent, suggesting that luciferase arose through a different event.  Taken together, by sequencing and analyzing data from the genomes of two firefly species that diverged approximately 100 million years ago, along with a more evolutionarily distant bioluminescent click beetle, the team discovered that luciferase appears to have evolved independently in both fireflies and click beetles.

“Having the genome allowed us to understand how the evolution of luciferase happened. Before sequencing, we knew there were five genes cloned, including luciferase, in firefly. By sequencing the genomes we actually uncovered those genomic loci where those initial gene duplication events occured,” says Lower.

In addition to the origins of luciferase, these findings also provided the researchers with insights into the evolution of the light organs.

“Since our findings suggest that luciferase originated independently in both lineages, we can infer that anything that came after luciferase, for example the light organs, or other things dependent on luciferase should also be independent,” says Fallon.

Discovering how bioluminescence arose, as well as other complex traits, can be studied now that genomic information is available. The information can also inform strategies to protect fireflies, whose populations in many parts of the world are diminishing. In addition to adding tools to help reveal a constituent parts list that could allow researchers to optimize bioluminescence as a tool, these findings reveal important insights into the evolution of bioluminescence as well as genomic evolution more broadly.

“Luciferase is a perfect example of how to build a new enzyme, duplication of a related progenitor gene followed by mutation and selection,” says Weng. “And one of the most exciting parts of this study was that by examining the evolutionary scars in the genomes we studied we could actually see it happen.”

* * *
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:
“Firefly genomes illuminate parallel origins of bioluminescence in beetles”
eLife, online on October 9, 2018. doi: 10.7554/eLife.36495
Timothy R. Fallon (1,2,*), Sarah E. Lower (3,*), Ching-Ho Chang (4) , Manabu Bessho-Uehara (5,6), Gavin J. Martin (7), Adam J. Bewick (8) , Megan Behringer (9) , Humberto J. Debat (10), Isaac Wong (4) , John C. Day (11), Anton Suvorov (7) , Christian J. Silva (4,12), Kathrin F. Stanger-Hall1 (3), David W. Hall (8) , Robert J. Schmitz (8), David R. Nelson (14), Sara M. Lewis (15), Shuji Shigenobu (16), Seth M. Bybee (7) , Amanda M. Larracuente (4), Yuichi Oba (5), and Jing-Ke Weng (1,2)
1. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.
2.Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
3. Department of Molecular Biology & Genetics, Cornell University, Ithaca, New York 14850, USA.
4. Department of Biology, University of Rochester, Rochester, New York 14627, USA.
5. Department of Environmental Biology, Chubu University, Kasugai, Aichi 487-8501, Japan.
6. Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
7. Department of Biology, Brigham Young University, Provo, Utah 84602, USA.
8. Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
9. Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona 85287, USA.
10. Center of Agronomic Research National Institute of Agricultural Technology, Córdoba, Argentina.
11. Centre for Ecology and Hydrology (CEH) Wallingford, Wallingford, Oxfordshire, UK.
12. Department of Plant Sciences, University of California Davis, Davis, California, USA.
13. Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
14. Department of Microbiology Immunology and Biochemistry, University of Tennessee  HSC, Memphis 38163, USA.
15. Department of Biology, Tufts University, Medford, Massachusetts 02155, USA.
16. NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki 444-8585, Japan.
Joining the resolution revolution

Department of Biology hosts a symposium to celebrate the launch of MIT.nano and its new Cryogenic Electron Microscopy Facility.

Raleigh McElvery | Department of Biology
October 16, 2018

It’s a time of small marvels and big ideas. Welcome to the Nano Age.

MIT’s preparations for this new era are in full swing, including the recent launch of MIT.nano, the Institute’s center for nanoscience and nanotechnology. And on the day after MIT.nano’s opening ceremonies, the Department of Biology hosted its Cryogenic Electron Microscopy (Cryo-EM) Symposium, which was co-organized by biology professor Thomas Schwartz and the director of the new facility, Edward Brignole.

“We organized the symposium to raise awareness of this new research capacity, and to celebrate the many people who worked to fund these instruments, design the space, build the suites, and set up the microscopes,” Brignole said of the Oct. 5 event. “We also wanted to bring together the various groups across MIT working on diverse technologies to improve Cryo-EM, from mathematicians, computer scientists, and electrical engineers to biologists, chemists, and biological engineers.”

The event featured pioneers leveraging Cryo-EM for various interdisciplinary applications both on campus and outside of MIT — from biology and machine learning to quantum mechanics.

The program included Ed Egelman from the University of Virginia, Mark Bathe from the MIT Department of Biological Engineering, Katya Heldwein from Tufts University’s School of Medicine, and Karl Berggren from the Department of Electrical Engineering and Computer Science. Also giving talks were computational and systems biology graduate student Tristan Bepler from MIT’s Computer Science and Artificial Intelligence Laboratory, Luke Chao from Harvard Medical School and Massachusetts General Hospital, postdoc Kuang Shen from the Whitehead Institute at MIT, and graduate student Jonathan Weed from the MIT Department of Mathematics. The talks were followed by a reception in Building 68 and guided tours of the Cryo-EM Facility.

Unlike other popular techniques for determining 3-D macromolecular structures, Cryo-EM permits researchers to visualize more diverse and complex molecular assemblies in multiple conformations. Cryo-EM is housed in precisely climate-controlled rooms in the basement of MIT.nano, built atop a 5 million pound slab of concrete to minimize vibrations. Two multimillion-dollar instruments are being installed that will enable scientists to analyze cellular machinery in near-atomic detail; the microscopes are the first instruments to be installed in MIT.nano.

As Schwartz explained to an audience of more than 100 people during his opening remarks, he and his colleagues realized they needed to bring this technology to the MIT community. Like many of the center’s other tools, they would be too costly to purchase and too onerous to maintain for a single researcher or lab.

“Microscopes are very special and expensive tools, so this endeavor turned out to be much more involved than anything else I have done during my 14 years at MIT,” he said. “But this was not an effort of one or two people, it really took a whole community. We have many people to thank today.”

Establishing the Cryogenic Electron Microscopy Facility at MIT has been a long-time dream for Catherine Drennan, a professor of chemistry and biology and a Howard Hughes Medical Institute investigator. At the symposium, Drennan spoke about her work using the microscopes to capture snapshots of enzymes in action.

She remembers it was a “happy coincidence” that the plans for MIT.nano and the Cryo-EM Facility unfolded around the same time and then merged together to become one multi-disciplinary effort. Drennan, Schwartz, and others worked closely with MIT.nano Founding Director Vladimir Bulović and Vice President for Research Maria Zuber to gain institutional support and jumpstart the project. It took six years to design and construct MIT.nano, and four to implement the Cryo-EM Facility.

“We had this vision that the Cryo-EM Facility would be a shared space that people from all around MIT would use,” Drennan said.

An anonymous donor offered $5 million to fund the first microscope, the Titan Krios, while the Arnold and Mabel Beckman Foundation contributed $2.5 million to purchase the second, the Talos Arctica.

“The Beckman Foundation is really pleased to be supporting this kind of technology,” said Anne Hultgren, the foundation’s executive director, who attended the symposium. “It was a win-win in terms of the timing and the need in the community. We are excited to be part of this effort, and to drive forward new innovations and experiments.”

The Beckman Foundation has made similar instrumentation grants to Johns Hopkins University School of Medicine, University of Pennsylvania’s Perelman School of Medicine, the University of Utah, and the University of Washington School of Medicine.

Drennan said that as the revolution in resolution continues to build, she hopes MIT’s new microscopes will bolster the resurging Cryo-EM community that’s slowly growing in and around Boston.

“Thanks to facilities like this, the Boston area went from being way behind the curve to right in front of it,” she said. “It’s an incredibly exciting time, and I can’t wait to see how we learn and grow as a research community.”

A Summer of Protein Degradation and the Beauty of Basic Science

MSRP-Bio student Elizabeth Bond worked in the Baker Lab, investigating the macromolecular machines that roam the cell and gobble up unneeded proteins.

Raleigh McElvery
September 25, 2018

Elizabeth Bond’s greatest summer accomplishment is proudly displayed as the background image on her phone. To the casual observer, it looks like columns of black blobs, but to Bond this stained protein gel signifies that, after two long weeks, she successfully isolated her protein of interest. The snapshot also underscores that she’s found her “people” — the kind who, as she describes, “will freak out with you over a great looking gel.”

A rising senior at UMass Amherst, Bond joined 18 fellow MIT Summer Research Program in Biology (MSRP-Bio) students — collaborating in labs across the biology department and various MIT-affiliated institutes for 10 weeks. Together, they attended seminars, lectures, Q&A sessions, meals, and field trips while living in dorms and bonding over science and life in general.

“You’re with a group of other college students looking towards the future, and you’re all stressing out about what comes next,” she says. “That’s amazing because you’re able to talk about your different insecurities and anxieties. You have a built-in support system that you might not get by staying at your home institution over the summer.”

Bond grew up not too far from MIT in the quiet town of Boxford, Massachusetts. Before setting foot on campus, she expected MIT to be cutthroat and competitive. Instead, she found “a bunch of nerds who are willing to help other nerds learn, make mistakes, and be human beings.” The researchers she met were supportive and eager to share their insights, scientific or otherwise. “In addition to being really interesting, these conversations helped me feel that I fit in with a group of very intelligent scientists,” she says.

As a biochemistry major, Bond appreciates basic science because it allows her to probe biological phenomena with no immediate goal other than to understand the underlying mechanisms. “Maybe 10 years down the line my research will help someone’s translational work, but right now I can pursue knowledge for its own sake,” she says. “The beauty of basic science is that you’re able to study things because they’re cool, while also contributing to the body of work your lab family began before you.”

At UMass Amherst, she serves as an undergraduate research assistant, investigating AAA+ proteases — the same protein degradation machines she studied all summer in Tania Baker’s lab, mentored by graduate student Kristin Zuromski. Back home, Bond examines these proteases in bacteria, using a combination of microbiology and computational biology. As a member of the Baker lab, she studied these macromolecular machines leveraging biochemical approaches.

She likens AAA+ proteases to Pac-Men from the classic arcade game, roaming the cell and gobbling up misfolded, excess, or unneeded proteins. One of the AAA+ proteases studied in the Baker lab is ClpAP, which is comprised of the AAA+ unfoldase ClpA and its partner peptidase ClpP. Bond’s protein of interest this summer was ClpA, a hexameric protein depicted as a cylinder with a central channel. ClpA unfolds and threads protein substrates through its channel, which contains pore loop structures that protrude from the chamber and play important roles in the function of ClpA. From there, the proteins enter ClpP, where they are degraded into small peptide fragments.

There are two types of pore loops in ClpA, D1 and D2, but their respective roles in the recognition, unfolding, and movement of proteins for degradation are not fully characterized. Bond hoped to discern their roles relative to one another.

She introduced a mutation into the gene that encodes ClpA, switching one amino acid for another in the D2 pore loop, in a region thought to be critical for recognizing proteins targeted for degradation. This mutation would, in theory, lead to a variant of ClpA where the D1 pore loop retained normal activity, but the D2 pore loop was unable to function. She used chemical crosslinking to generate a ClpA dimer variant that was half wildtype and half mutant in the D2 pore loops, and monitored the ability of the assembled hexameric AAA+ protease to function.

By observing the degradation activity of this crosslinked ClpA variant containing three active and three inactive D2 pore loops in an alternating order, she hoped to get a better sense of the role the D2 pore loops play in ClpAP protease function.

Although there is still more to be done to answer this particular question, reflecting on the summer Bond feels her project went “surprisingly well,” despite being more challenging than she initially anticipated — primarily due to multi-week protein purification experiments and performing many procedures simultaneously. She arrived with the sole intention of bolstering her biochemistry knowledge, and left with a greater appreciation for the breadth of scientific fields she could pursue.

“MSRP-Bio gave me the chance to talk with students and faculty members working in multiple branches of science,” she says. “I study bacteria, but I can learn a lot from someone researching roundworms or cancer cells, or using computational approaches to biology. Those conversations prompted me to think more critically about my own research.”

Besides feeling integrated into the tightly-knit Baker lab, her favorite aspect of the summer was the bond she formed within her MSRP-Bio cohort. In addition to freaking out over protein gels, they started their own journal club, and they discussed personal struggles, family, where they came from, and where they want to go.

“A lot of students of color who come from underrepresented groups in science, like I do, have this anxiety about not being smart enough or not fitting in,” she says. “The program allows you to bond over these shared feelings and that is part of what makes it really amazing for students who are trying to do great things, but do not often feel fully represented.”

At the beginning of the summer, Bond hadn’t fully admitted to herself that she wanted to apply to grad school. “It was easier for me to be ambiguous about what I wanted to do, because it was scary to admit that grad school was something I might actually want,” she recalls. After a summer at MIT, she’s gained the confidence to apply and state her ambitions out loud.

“My project’s been amazing and great, but now I want to have my own body of work,” she says. “It’s something I have this great urge to do — and, because of MSRP-Bio, I’m ready for it.”

Photo credit: Raleigh McElvery
Chemists discover unexpected enzyme structure

Metal cluster in enzyme that breaks down carbon dioxide can switch between two different shapes.

Anne Trafton | MIT News Office
October 2, 2018

Many microbes have an enzyme that can convert carbon dioxide to carbon monoxide. This reaction is critical for building carbon compounds and generating energy, particularly for bacteria that live in oxygen-free environments.

This enzyme is also of great interest to researchers who want to find new ways to remove greenhouse gases from the atmosphere and turn them into useful carbon-containing compounds. Current industrial methods for transforming carbon dioxide are very energy-intensive.

“There are industrial processes that do these reactions at high temperatures and high pressures, and then there’s this enzyme that can do the same thing at room temperature,” says Catherine Drennan, an MIT professor of chemistry and biology and a Howard Hughes Medical Institute Investigator. “For a long time, people have been interested in understanding how nature performs this challenging chemistry with this assembly of metals.”

Drennan and her colleagues at MIT, Brandeis University, and Aix-Marseille University in France have now discovered a unique aspect of the structure of the “C-cluster” — the collection of metal and sulfur atoms that forms the heart of the enzyme carbon monoxide dehydrogenase (CODH). Instead of forming a rigid scaffold, as had been expected, the cluster can actually change its configuration.

“It was not what we expected to see,” says Elizabeth Wittenborn, a recent MIT PhD recipient and the lead author of the study, which appears in the Oct. 2 issue of the journal eLife.

A molecular cartwheel

Metal-containing clusters such as the C-cluster perform many other critical reactions in microbes, including splitting nitrogen gas, that are difficult to replicate industrially.

Drennan began studying the structure of carbon monoxide dehydrogenase and the C-cluster about 20 years ago, soon after she started her lab at MIT. She and another research group each came up with a structure for the enzyme using X-ray crystallography, but the structures weren’t quite the same. The differences were eventually resolved and the structure of CODH was thought to be well-established.

Wittenborn took up the project a few years ago, in hopes of nailing down why the enzyme is so sensitive to inactivation by oxygen and determining how the C-cluster gets put together.

To the researchers’ surprise, their analysis revealed two distinct structures for the C-cluster. The first was an arrangement they had expected to see — a cube consisting of four sulfur atoms, three iron atoms, and a nickel atom, with a fourth iron atom connected to the cube.

In the second structure, however, the nickel atom is removed from the cube-like structure and takes the place of the fourth iron atom. The displaced iron atom binds to a nearby amino acid, cysteine, which holds it in its new location. One of the sulfur atoms also moves out of the cube. All of these movements appear to occur in unison, in a movement the researchers describe as a “molecular cartwheel.”

“The sulfur, the iron, and the nickel all move to new locations,” Drennan says. “We were really shocked. We thought we understood this enzyme, but we found it is doing this unbelievably dramatic movement that we never anticipated. Then we came up with more evidence that this is actually something that’s relevant and important — it’s not just a fluke thing but part of the design of this cluster.”

The researchers believe that this movement, which occurs upon oxygen exposure, helps to protect the cluster from completely and irreversibly falling apart in response to oxygen.

“It seems like this is a safety net, allowing the metals to get moved to locations where they’re more secure on the protein,” Drennan says.

Douglas Rees, a professor of chemistry at Caltech, described the paper as “a beautiful study of a fascinating cluster conversion process.”

“These clusters have mineral-like features and it might be thought they would be ‘as stable as a rock,’” says Rees, who was not involved in the research. “Instead, the clusters can be dynamic, which confers upon them properties that are critical to their function in a biological setting.”

Not a rigid scaffold

This is the largest metal shift that has ever been seen in any enzyme cluster, but smaller-scale rearrangements have been seen in some others, including a metal cluster found in the enzyme nitrogenase, which converts nitrogen gas to ammonia.

“In the past, people thought of these clusters as really being these rigid scaffolds, but just within the last few years there’s more and more evidence coming up that they’re not really rigid,” Drennan says.

The researchers are now trying to figure out how cells assemble these clusters. Learning more about how these clusters work, how they are assembled, and how they are affected by oxygen could help scientists who are trying to copy their action for industrial use, Drennan says. There is a great deal of interest in coming up with ways to combat greenhouse gas accumulation by, for example, converting carbon dioxide to carbon monoxide and then to acetate, which can be used as a building block for many kinds of useful carbon-containing compounds.

“It’s more complicated than people thought. If we understand it, then we have a much better chance of really mimicking the biological system,” Drennan says.

The research was funded by the National Institutes of Health and the French National Research Agency.

Detangling DNA replication

Researchers identify an essential protein that helps enzymes relax overtwisted DNA so each strand can be copied during cell division.

Raleigh McElvery | Department of Biology
September 18, 2018

DNA is a lengthy molecule — approximately 1,000-fold longer than the cell in which it resides — so it can’t be jammed in haphazardly. Rather, it must be neatly organized so proteins involved in critical processes can access the information contained in its nucleotide bases. Think of the double helix like a pair of shoe laces twisted together, coiled upon themselves again and again to make the molecule even more compact.

However, when it comes time for cell division, this supercoiled nature makes it difficult for proteins involved in DNA replication to access the strands, separate them, and copy them so one DNA molecule can become two.

Replication begins at specific regions of the chromosome where specialized proteins separate the two strands, pulling apart the double helix as you would the two shoe laces. However, this local separation actually tangles the rest of the molecule further, and without intervention creates a buildup of tension, stalling replication. Enter the enzymes known as topoisomerases, which travel ahead of the strands as they are being peeled apart, snipping them, untwisting them, and then rejoining them to relieve the tension that arises from supercoiling.

These topoisomerases are generally thought to be sufficient to allow replication to proceed. However, a team of researchers from MIT and the Duke University School of Medicine suggests the enzymes may require guidance from additional proteins, which recognize the shape characteristic of overtwisted DNA.

“We’ve known for a long time that topoisomerases are necessary for replication, but it’s never been clear if they were sufficient on their own,” says Michael Laub, an MIT professor of biology, Howard Hughes Medical Institute Investigator, and senior author of the study. “This is the first paper to identify a protein in bacteria, or eukaryotes, that is required to localize topoisomerases ahead of replication forks and to help them do what they need to do there.”

Postdoc Monica Guo ’07 and former graduate student Diane Haakonsen PhD ’16 are co-first authors of the study, which appeared online in the journal Cell on Sept. 13.

Necessary but not sufficient

Although it’s well established that topoisomerases are crucial to DNA replication, it has now becoming clear that we know relatively little about the mechanisms regulating their activity, including where and when they act to relieve supercoiling.

These enzymes fall into two groups, type I and type II, depending on how many strands of DNA they cut. The researchers focused on type II topoisomerases found in a common species of freshwater bacteria, Caulobacter crescentus. Type II topoisomerases in bacteria are of particular interest because a number of antibiotics target them in order to prevent DNA replication, treating a wide variety of microbial infections, including tuberculosis. Without topoisomerases, the bacteria can’t grow. Since these bacterial enzymes are unique, poisons directed at them won’t harm human topoisomerases.

For a long time, type II topoisomerases were generally assumed adequate on their own to manage the overtwisted supercoils that arise during replication. Although researchers working in E. coli and other, higher organisms have pinpointed additional proteins that can activate or repress these enzymes, none of these proteins were required for replication.

Such findings hinted that there might be similar interactions taking place in other organisms. In order to understand the protein factors involved in compacting Caulobacter DNA — regulating topoisomerase activity specifically — the researchers screened their bacteria for proteins that bound tightly to supercoiled DNA. From there, they honed in on one protein, GapR, which they observed was essential for DNA replication. In bacteria missing GapR, the DNA became overtwisted, replication slowed, and the bacteria eventually died.

Surprisingly, the researchers found that GapR recognized the structure of overtwisted DNA rather than specific nucleotide sequences.

“The vast majority of DNA-binding proteins localize to specific locations of the genome by recognizing a specific set of bases,” Laub says. “But GapR basically pays no attention to the actual underlying sequence — just the shape of overtwisted DNA, which uniquely arises in front of replication forks and transcription machinery.”

The crystal structure of the protein bound to DNA, solved by Duke’s Maria Schumacher, revealed that GapR recognizes the backbone of DNA (rather than the bases), forming a snug clamp that encircles the overtwisted DNA. However, when the DNA is relaxed in its standard form, it no longer fits inside the clamp. This might signify that GapR sits on DNA only at positions where topoisomerase is needed.

An exciting milestone

Although GapR appears to be required for DNA replication, it’s still not clear precisely how this protein promotes topoisomerase function to relieve supercoiling.

“In the absence of any other proteins, GapR is able to help type II topoisomerases remove positive supercoils faster, but we still don’t quite know how,” Guo says. “One idea is that GapR interacts with topoisomerases, recognizing the overtwisted DNA and recruiting the topoisomerases. Another possibility is that GapR is essentially grabbing onto the DNA and limiting the movement of the positive supercoils, so topoisomerases can target and eliminate them more quickly.”

Anthony Maxwell, a professor of biological chemistry at the John Innes Centre who was not involved with the study, says the buildup of DNA supercoils is a key problem in both bacterial replication and transcription.

“Identifying GapR and its potential role in controlling supercoiling in vivo is an exciting milestone in understanding the control of DNA topology in bacteria,” he says. “Further work will be required to show how exactly these proteins cooperate to maintain bacterial genomic integrity.”

According to Guo, the study provides insight into a fundamental process — DNA replication — and the ways topoisomerases are regulated, which could extend to eukaryotes.

“This was the first demonstration that a topoisomerase activator is required for DNA replication,” she says. “Although there’s no GapR homolog in higher organisms, there could be similar proteins that recognize the shape of the DNA and aid or position topoisomerases.”

This could open up a new field of drug research, she says, targeting activators like GapR to increase the efficacy of existing topoisomerase poisons to treat conditions like respiratory and urinary tract infections. After all, many topoisomerase inhibitors have become less effective due to antibiotic resistance. But only time will tell; there is still much to learn in order to untangle the complex process of DNA replication, along with its many twists and turns.

The research was funded by NIH grants, the HHMI International Predoctoral Fellowship, and the Jane Coffin Childs Memorial Fellowship.