Research Area: Microbiology
“Organs-on-a-chip” system sheds light on how bacteria in the human digestive tract may influence neurological diseases.
Anne Trafton | MIT News Office
January 29, 2021
In many ways, our brain and our digestive tract are deeply connected. Feeling nervous may lead to physical pain in the stomach, while hunger signals from the gut make us feel irritable. Recent studies have even suggested that the bacteria living in our gut can influence some neurological diseases.
Modeling these complex interactions in animals such as mice is difficult to do, because their physiology is very different from humans’. To help researchers better understa nd the gut-brain axis, MIT researchers have developed an “organs-on-a-chip” system that replicates interactions between the brain, liver, and colon.
Using that system, the researchers were able to model the influence that microbes living in the gut have on both healthy brain tissue and tissue samples derived from patients with Parkinson’s disease. They found that short-chain fatty acids, which are produced by microbes in the gut and are transported to the brain, can have very different effects on healthy and diseased brain cells.
“While short-chain fatty acids are largely beneficial to human health, we observed that under certain conditions they can further exacerbate certain brain pathologies, such as protein misfolding and neuronal death, related to Parkinson’s disease,” says Martin Trapecar, an MIT postdoc and the lead author of the study.
Linda Griffith, the School of Engineering Professor of Teaching Innovation and a professor of biological engineering and mechanical engineering, and Rudolf Jaenisch, an MIT professor of biology and a member of MIT’s Whitehead Institute for Medical Research, are the senior authors of the paper, which appears today in Science Advances.
The gut-brain connection
For several years, Griffith’s lab has been developing microphysiological systems — small devices that can be used to grow engineered tissue models of different organs, connected by microfluidic channels. In some cases, these models can offer more accurate information on human disease than animal models can, Griffith says.
In a paper published last year, Griffith and Trapecar used a microphysiological system to model interactions between the liver and the colon. In that study, they found that short-chain fatty acids (SCFAs), molecules produced by microbes in the gut, can worsen autoimmune inflammation associated with ulcerative colitis under certain conditions. SCFAs, which include butyrate, propionate, and acetate, can also have beneficial effects on tissues, including increased immune tolerance, and they account for about 10 percent of the energy that we get from food.
In the new study, the MIT team decided to add the brain and circulating immune cells to their multiorgan system. The brain has many interactions with the digestive tract, which can occur via the enteric nervous system or through the circulation of immune cells, nutrients, and hormones between organs.
Several years ago, Sarkis Mazmanian, a professor of microbiology at Caltech, discovered a connection between SCFAs and Parkinson’s disease in mice. He showed that SCFAs, which are produced by bacteria as they consume undigested fiber in the gut, sped up the progression of the disease, while mice raised in a germ-free environment were slower to develop the disease.
Griffith and Trapecar decided to further explore Mazmanian’s findings, using their microphysiological model. To do that, they teamed up with Jaenisch’s lab at the Whitehead Institute. Jaenisch had previously developed a way to transform fibroblast cells from Parkinson’s patients into pluripotent stem cells, which can then be induced to differentiate into different types of brain cells — neurons, astrocytes, and microglia.
More than 80 percent of Parkinson’s cases cannot be linked to a specific gene mutation, but the rest do have a genetic cause. The cells that the MIT researchers used for their Parkinson’s model carry a mutation that causes accumulation of a protein called alpha synuclein, which damages neurons and causes inflammation in brain cells. Jaenisch’s lab has also generated brain cells that have this mutation corrected but are otherwise genetically identical and from the same patient as the diseased cells.
Griffith and Trapecar first studied these two sets of brain cells in microphysiological systems that were not connected to any other tissues, and found that the Parkinson’s cells showed more inflammation than the healthy, corrected cells. The Parkinson’s cells also had impairments in their ability to metabolize lipids and cholesterol.
Opposite effects
The researchers then connected the brain cells to tissue models of the colon and liver, using channels that allow immune cells and nutrients, including SCFAs, to flow between them. They found that for healthy brain cells, being exposed to SCFAs is beneficial, and helps them to mature. However, when brain cells derived from Parkinson’s patients were exposed to SCFAs, the beneficial effects disappeared. Instead, the cells experienced higher levels of protein misfolding and cell death.
These effects were seen even when immune cells were removed from the system, leading the researchers to hypothesize that the effects are mediated by changes to lipid metabolism.
“It seems that short-chain fatty acids can be linked to neurodegenerative diseases by affecting lipid metabolism rather than directly affecting a certain immune cell population,” Trapecar says. “Now the goal for us is to try to understand this.”
The researchers also plan to model other types of neurological diseases that may be influenced by the gut microbiome. The findings offer support for the idea that human tissue models could yield information that animal models cannot, Griffith says. She is now working on a new version of the model that will include micro blood vessels connecting different tissue types, allowing researchers to study how blood flow between tissues influences them.
“We should be really pushing development of these, because it is important to start bringing more human features into our models,” Griffith says. “We have been able to start getting insights into the human condition that are hard to get from mice.”
The research was funded by DARPA, the National Institutes of Health, the National Institute of Biomedical Imaging and Bioengineering, the National Institute of Environmental Health Sciences, the Koch Institute Support (core) Grant from the National Cancer Institute, and the Army Research Office Institute for Collaborative Biotechnologies.
Raleigh McElvery
January 20, 2021
Many cells, including bacteria, are covered in a sugar-rich coating that protects their membrane and internal components. These sugars are often joined to other macromolecules, like proteins or lipids, to form glycoconjugates. The glycoconjugates that encrust bacteria help prevent them from “popping” under environmental stress, and facilitate host-pathogen interactions. Because the sugary layer perpetuates survival and virulence, researchers are looking for ways to create chinks in this microbial armor — or better yet, to prevent it from being made in the first place.
Glycoconjugates are built by many enzymes working in close succession at the cell membrane. One enzyme family, comprised of phosphoglycosyl transferases (PGTs), is responsible for catalyzing the first step in the assembly line. Of this large enzyme family, one subtype in particular stands out: “monotopic” PGTs, which are unique to bacteria and could serve as antibiotic targets. If researchers can develop drugs that inhibit monoPGTs, the sugar armor wouldn’t be built and noxious bacteria could be easier to defeat.
A new PNAS study co-authored by Professor of Biology and Chemistry, Barbara Imperiali, highlights the diversity and significance of these potential drug targets. Imperiali teamed up with graduate student Katherine O’Toole and Professor of Chemistry Karen Allen from Boston University to categorize over 38,000 different monoPGTs, compiling this information into the first database of its kind.
“We’ve taken an enzyme family that was once considered quirky and insignificant, and demonstrated that it’s actually very prevalent,” Imperiali says. “Hopefully the database will help us better understand these enzymes, their molecular pathways, and the human pathogens they support.”
Imperiali and her colleagues used sequence analysis of known monoPGTs to define a “signature” amino acid sequence. They leveraged this signature to identify the entire superfamily of monoPGTs amidst the 63,152 sequences downloaded from an online portal, which they then clustered into closely-related subtypes. The researchers also created a family tree, which included over 100 monoPGTs from diverse bacterial species. Imperiali hopes others will take advantage of this new information to pinpoint monoPGTs in pathogens of interest, and explore similarities and differences in related microbes and their enzymes.
The researchers’ analyses also revealed strange, new proteins that appeared to include two enzymes in one — a monoPGT fused to one of the other enzymes that typically play a separate role in the same sugar-modifying pathway. “It’s essentially one protein with two functions,” Imperiali explains. These fusion enzymes could reveal which enzymes “talk” to one another and work sequentially during the glycoconjugate-building process, she adds, revealing the complicated chain of events that creates the bacterial sugar shield.
The team even found cases where one monoPGT was fused to a member of a different PGT family — polytopic PGTs (polyPGTs). MonoPGTs and polyPGTs are involved in different pathways that each build glycoconjugates, so having a dual-function protein could allow cells to easily switch between mechanisms. Bacterial cells lack the organizational compartments that human and other eukaryotic cells have, so perhaps these fusion enzymes help exert control and order at different points in the cell cycle, Imperiali speculates. At the moment, though, the hybrid PGTs remain an evolutionary mystery.
While some researchers parse these ancient puzzles, others may use the database to inspire new drugs to combat antibiotic resistance. “At the end of the day,” Imperiali says, “we’ve shed light on a set of enzymes that could become pivotal therapeutic targets.”
Salvador Luria is known for his research on phage genetics, but his lab’s contribution to the discovery of restriction enzymes also sparked important technological advances.
Saima Sidik
December 15, 2020
In the early 1950s, a woman named Mary Human found the first evidence of a group of proteins called restriction enzymes — a discovery that would reverberate throughout the research community for decades. But many important discoveries, from penicillin to medical X-rays, are inspired by a messy fluke rather than carefully reasoned logic, and Human’s discovery was no different.
Fortunately, Human’s boss was a jovial scientist named Salvador Luria, who appreciated that life’s quirks often yield the most valuable results — so much so that he wrote a 1955 Scientific American article in which he praised Human’s approach. “It often pays to do somewhat untidy experiments, provided one is aware of the element of untidiness,” he wrote.
Indeed, Luria’s life was far from being a tidy package. This Italian native fled Europe to escape Nazis, was briefly blacklisted by the NIH presumably because of his vocal opposition to American foreign policy, and suffered from depression despite his outwardly cheery appearance. But Luria’s life was also extraordinary. He earned a medical degree in Torino, Italy, but decided he preferred performing research over practicing medicine. After leaving Europe in the 1940s to escape the persecution of Jews like himself, he held professorships at three American institutions, including MIT. He was known as an insightful scientist, a kind colleague, and a thoughtful mentor, right up until his death in 1991.
A Surprising Observation in the Midwest
For much of his career, Luria applied his keen insight to phages — viruses that invade and kill bacteria. He and two collaborators won the Nobel Prize after realizing that genetic mutations in bacteria can protect them from deadly phages. But the untidy experiment Luria referred to in his Scientific American article related to a lesser-known aspect of his lab’s phage work: restriction enzymes, which cut DNA at specific places. Luria was the first person to find evidence of these critical tools, which opened a whole new field of genetic manipulation. A cascade of research spanning two decades eventually led a scientist supervised by Luria’s former research associate to win a Nobel prize for characterizing these enzymes, which catalyzed modern molecular biology.
The restriction enzyme story starts in the late 1940s, when Luria was a professor at Indiana University. He noticed that a phage called T2 didn’t seem to grow inside and kill certain mutant strains of Escherichia coli. T2 always killed the first batch of mutant E. coli, but when he tested whether a new batch of the same type of bacteria would catch the virus from the dead bacteria, the new batch didn’t succumb to the virus.
In 1950, Luria moved to the University of Illinois, Urbana, where one of his employees, a woman named Mary Human, continued to work on the T2 mystery. One day, in the midst of an experiment, Human realized she’d run out of the strain of E. coli she usually used, and this is where the experiment got a little untidy. Instead of waiting to do the experiment on another day with a healthy batch of E. coli, Human mixed phage-killed E. coli with a different type of bacteria called Shigella. T2 always seemed to act the same in Shigella as it did in E. coli, so she didn’t expect the switch to matter. But the next morning, the Shigella were dead! It seemed that T2 could only reproduce once in the particular mutant strain of E. coli that Human was studying, but when she moved T2 from these mutant E. coli to Shigella, it restored the virus’ ability to reproduce. Human and Luria concluded that something about the mutant E. coli changed the T2, and limited the kinds of bacteria in which it could grow.
At the time, Human and Luria couldn’t explain what was happening to T2 in these mutant bacteria. Luria went about his career, still carrying this mystery with him.
An explanation in Cambridge, Massachusetts
In 1958, Luria came to MIT Biology for a sabbatical. The structure of DNA had been discovered just five years earlier, and MIT needed someone who understood its implications to usher the Institute into the genomics era. Luria was renowned for his ability to predict which direction biology would move, so the Institute wanted him to fill this role. At the end of his sabbatical, Luria accepted a permanent position in MIT Biology, where he stayed for the rest of his career.
“I asked Luria if he thought it was possible to do molecular biology with animal viruses, and he said, ‘I don’t know, why don’t you find out and tell me?’” Baltimore says.In addition to being a skilled scientist, Luria was a thoughtful mentor. David Baltimore, professor at the California Institute of Technology, was one of Luria’s early mentees at MIT. At the time, most research into viruses focused on the phages that Luria studied, but Baltimore wanted to break new ground by studying viruses that infect animals. He credits Luria for encouraging him to go down this path — one that led him to become a Nobel Laureate himself.
In addition to being a skilled scientist, Luria was deeply opposed to McCarthyism and the Vietnam War, and he devoted a lot of time to political activism like writing letters, to newspaper editors as well as to other scientists, trying to gather support for his views.
Fortunately, Luria had a deputy to help him run his lab while he was revamping MIT Biology and trying to stop the war. “If you wanted to know something on a daily basis, you went to Helen Revel,” recalls Costa Georgopoulos, a professor at the University of Utah who earned his PhD in Luria’s lab in the 1960s.
Revel earned her PhD with MIT Biology’s Boris Magasanik before becoming Luria’s research associate. “Those days, women were not readily made professors, so she worked on Luria’s grants,” Georgopoulos says.
Georgopoulos describes Revel as reserved and meticulous. She didn’t advertise her skill as a scientist; she just got to work. With this attitude, she led the scientists who figured out the mystery of the mutant bacteria that changed the T2 phage.
Since Human’s fortuitously messy experiment, a lineage of phage researchers that originated in Luria’s lab had learned a lot about how bacteria and phages interact. First, Luria’s former research associate, Guiseppe Bertani, showed that phages other than T2 also behave differently in different types of bacteria. Later, Bertani’s own research associate, Werner Arber, went on to discover that bacteria can mark the DNA of phages that replicate within them. When marked phages try to enter new bacteria, the marks can signal that the phages are foreign invaders, allowing the new bacteria to kill the phages. Arber and two of his colleagues, Daniel Nathans and Hamilton O. Smith, eventually won their own Nobel prize for their work on restriction enzymes.
Certain bacteria mark phage DNA by replacing one of the bases that make up the genetic code, called cytosine, with a modified version called 5-hydroxymethylcytosine. Revel, with help from Luria, Georgopoulos, and others, found that the T2 phage takes this system one step farther by using a bacterial enzyme to attach sugars to modified cytosines. Some mutant bacteria are unable to transfer sugars to phage cytosines, and so the phages grown in these bacteria come out “sour” instead of “sweet,” as Luria wrote. Restriction enzymes recognize these sweet-natured phages as foreign, and destroy them.
As researchers learned more about restriction enzymes, they realized that they can work in all sorts of ways. Bacteria can also mark their own DNA to prevent restriction enzymes from cutting it, allowing certain kinds of restriction enzymes to cut naked DNA sequences in the genomes of invading phages. Soon, biologists realized that restriction enzymes would let them cut any kind of DNA, not just phage genomes. This discovery had many consequences, one of which was that scientists could paste snipped DNA back together in new combinations. Many people were initially wary that combining DNA from different organisms could have unintended consequences. But by the 1980s, scientists had harnessed restriction enzymes for a whole host of safe purposes, and technologies centered around these enzymes continue to evolve.
Today, after decades of work, scientists have used restriction enzymes to study genetic variations in humans, find sequences that cause disease, identify relationships between people, and solve crimes. Scientists have used restriction enzymes to make proteins glow like jellyfish, to study the structure of DNA, and to make bacteria produce insulin.
T2 phages and their relationship to restriction enzymes are just one area of biology where Luria and his lab made profound contributions. Among his biggest achievements was recruiting and employing many forward-thinking scientists who built MIT Biology into the department it is today. In fact, as the first director of the Center for Cancer Research, Luria recruited Phillip Sharp, who would go on to win a Nobel Prize for discovering RNA splicing. Sharp joined a center that already included David Baltimore, as well as current MIT Biology professors Nancy Hopkins and Robert Weinberg, all of whom have made huge contributions to cancer research.
Scientists had just begun to elucidate the link between genetics, viruses, and cancer in the early 1970s, but Baltimore says that Luria was often the first person to jump on new applications for the techniques and thinking underlying molecular biology.
“Luria’s genius was understanding where biology was going,” says Baltimore. “At every stage, he was wondering what the next step would be.” But even geniuses need a messy fluke like Human’s now and then.
Transform your apartment into a yeast lab, and have fun doing it!
Grad Admissions Blog | Veda K.
October 22, 2020
One of the very first lessons you learn in microbiology is that while countless things can – and will – go wrong, you can almost always count on your microbes to grow. There is some strange comfort in knowing that what looks like clear liquid today will reveal countless gleaming colonies smiling up at you from your petri dish tomorrow. This radical assurance of growth transforms the many tedious tasks of lab work into an almost meditative experience. Pouring, plating, streaking — these could easily be yoga poses in the clinically sterile studio of a BSL-2 lab[1].
When the pandemic-that-shall-not-be-named abruptly separated me from my work this March, I threatened to bring the lab home. Unsurprisingly, my roommates were far from enthused at the idea of me culturing human pathogens in our garage. Somewhere in-between trying to bribe them with beer and baked goods I realized I could turn my scientific focus on an organism far more delicious than MRSA[2]: yeast!
Yeast, the tiny organism so miraculous that it was known as “godisgoode” in the days before microscopes were invented, is behind the magical transformations that give us beer, wine, sourdough, doughnuts, kombucha — you name it. In our technological times, it is tempting to relegate the study of microbes to sterile, fluorescently-lit, strictly controlled labs where the genetically engineered organisms you order off the internet live pampered lives. In quarantine in my own home, I re-discovered a centuries-old truth: yeast will appear and grow anywhere. Like any good pet, yeast are largely well-behaved and will sit, stand, and shake your hand on command. Disclaimer: they may also bubble over and stain your carpet in unsavory ways.
With a bit of intuition and a lot of patience, you too can transform any apartment into a lab to grow your pet yeast in!
The kitchen: your new bench
Sourdough: needy but delicious
Growing your own sourdough starter is a relatively low-effort process that is not only ridiculously easy, it also lends you serious kitchen clout. All you need to get started are flour, water, and the right temperature. Combine the flour and water in equal quantities in a container with quite a bit of headspace. “Feed” your starter once a day by replacing half of it by weight with a fresh water-flour mixture. Grow your starter at 68-75F. In the cold of the winter, yeast will take longer to grow and consume the complex nutrients in flour. In the summer, your starter may be so active it requires “feeding” twice a day!
A young starter with “hooch” on top
As the complex community develops in your starter, it will go from being watery (the liquid on top is actually called “hooch”, if that is any indication of its actual nature) and frankly pretty stinky to bubbly and aromatic. Your nose and eyes are your best tools for judging what bugs are living in your starter (move over, Illumina[3]!). Fuzzy and white? Probably mould! Orange and cheesey? Serratia marcescens is likely the culprit. Simply use a clean spoon to remove these offending species. The wonderful magic of your starter is that, as a living community of wild yeasts and bacteria, it will eventually fend off nastier invaders and reach a set-point of well-behaved yeast. Patience is crucial! Keep feeding, and believe in “godisgoode”.
As a microbiologist, I must admit that the process of developing a working starter far outweighed the actual bread-baking process. For those of you who are excited about baking – the starter can be used for pancakes, doughnuts, muffins, cake, almost any dessert that uses dry active yeast. When you need a break from your prolific baking streak, simply pop your starter in the freezer and it’ll be ready for the next time you get hungry!
Beer: hurry up and wait
Over our many weeks in confinement, my roommates and I have been refining our beer-tasting palates by attending Lamplighter Brewery’s virtual tasting events. The wonderful folks at lamp gave me my first introduction to how beer is made and, eager to fill my weekends with more than just existential dread, I decided to venture into brewing.
To be completely honest, I’d also been missing those $6 pitchers of High Life at the Muddy (the Muddy Charles Pub, a campus highlight).
Like baking, brewing is a process that has engendered a cult-following. Homebrewers take their craft seriously, and you can find countless blog posts and youtube videos describing everything from sanitization techniques to pitch rates (how much yeast goes in) to heated debates on hop flavor profiles. To an MIT grad student, drinking from this “firehose” of information should feel almost comfortable, if you can withstand the flashbacks to 7.51 (principles of biochemical analysis). The trick, I’ve learned, is to dive in headfirst and take in specific pieces of information only as needed.
Brewing requires a little more investment than baking. The equipment you need will likely not be lying around the house, and unfortunately cannot be repurposed for much if you find that brewing isn’t quite your thing. The good news is that there are several companies selling pre-assembled “kits” to get you started on your boozy journey. After doing some research of my own, and soliciting advice from my homebrewer friends, I went with an IPA kit that included most of the hardware I’d need.
My first (and only, so far) brew day was a 6-hour process. Like any experiment in the lab, I anxiously sanitized, scrubbed, stirred, heated and cooled alternately. The day after, I realized my hyper-aware level of caution had been superfluous – my yeast were happily bubbling away in their preferred temperature range of 68F-75F. Little did I know that they’d still be bubbling away two weeks later at 91F (!!), thanks to the heat of a Boston summer and a failed condenser in our central AC.
The garage: your new incubator / engineering lab
Once your beer has been brewed, it needs to ferment in a cool, dark place for two weeks. The only cool, dark place in our now very hot apartment is our garage, which has been taken over by my MechE roomie (hey Annie!) Annie, not constrained by a study of deadly bacteria, was uninhibited in her assembly of a mini-engineering lab in our garage, even having equipment sent directly to our apartment! My yeast and fermenting beer join her assorted selection of wires in filling the void in our hearts normally filled by our labs.
Sourdough starter fed and beer bottled, all that is left to do is wait. In between waiting for bread and booze, I like to sneak in some studying for my upcoming qualifying exams!
As we become ever more intimately acquainted with our homes and the yeast that inhabit them, I highly encourage you to experience the magic of micro-organismal life for yourself. Biting into that first slice of bread or taking your first sip of home-brewed beer is a fulfilling reminder that, but for the pardoning mercy of an only 99.99% effective clorox wipe, our sterile world would be dull and flat. Grant yourself a moment to breathe and celebrate the 0.01% of microbes that make our world wonderful — you’ll be back in the lab in no time!
[1] Biosafety level 2 (BSL-2)refers to laboratories that work with biological agents that pose a moderate health hazard
[2] Methicillin-Resistant Staphylococcus Aureus (MRSA) is a form of antibiotic resistant bacteria that causes infections
[3] Illumina is a DNA sequencing company that is well known for its technology
Eva Frederick | Whitehead Institute
September 23, 2020
The essential malaria drug artemisinin acts like a “ticking time bomb” in parasite cells — but in the half a century since the drug was introduced, malaria-causing parasites have slowly grown less and less susceptible to the treatment, threatening attempts at global control over the disease.
In a paper published September 23 in Nature Communications, Whitehead Institute Member Sebastian Lourido and colleagues use genome screening techniques in the related parasite Toxoplasma gondii (T. gondii) to identify genes that affect the parasites’ susceptibility to artemisinin. Two genes stood out in the screen: one that makes the drug more lethal, and another that helps the parasite survive the treatment.
Artemisinin is derived from the extract of sweet wormwood (Artemisia annua), and is usually used against malaria as part of a combination therapy. “Artemisinin kills malaria-causing parasites super fast—it will wipe out 90 percent of parasites within 24 hours,” says former postdoctoral researcher and co-first author Clare Harding, now a research fellow at the University of Glasgow. Once the fast-acting drug clears out the bulk of the parasites—such as Plasmodium falciparum, the culprit in the deadliest forms of malaria—from the bloodstream, the second drug finishes off the stragglers, curing the infection.
“Artemisinin works differently than most antibiotics,” Lourido said. “You can think of it as a sort of bomb that needs to be turned on in order to work.” The molecule required to light the drug’s fuse is called heme. Heme is a small molecule that facilitates several cellular functions, including electron transport and the delivery of oxygen to tissues as a component of hemoglobin. When heme molecules encounter artemisinin, they activate the drug allowing the creation of small, toxic radicals which react with proteins, lipids and metabolites inside the parasite, leading to its death.
Lourido, Harding, and co-first authors Boryana Petrova and Saima Sidik (“We were the ‘Heme Team,’” Harding said) wanted to understand what mechanisms the less susceptible parasites were using to avoid activating the “bomb”. Previously, Lourido and his lab—which focuses on apicomplexan parasites, a group which includes both Toxoplasma gondii and the malaria-causing Plasmodium falciparum—had developed a method to screen the entire genome of T. gondii to discover beneficial and harmful mutations. For a number of reasons, the screen does not work on Plasmodium parasites, but Lourido hypothesized that the related parasites’ genomes were similar enough that the method could prove helpful.
After running the screen, two genes stood out to the researchers as important factors in the parasites’ susceptibility to artemisinin treatment. One, called Tmem14c, seemed to be protecting the parasites: when the gene was disrupted in the screen, the parasites became more susceptible to treatment with artemisinin. The gene is analogous to one in red blood cells that serves as a transporter for heme and its building blocks, shuttling them in and out of the mitochondrion.
“What could be happening here is that, in the absence of Tmem14c, heme, artemisinin’s activator, collects within the mitochondria where it is being synthesized, thereby rendering the mitochondria better at activating that ticking time bomb,” Lourido said. “Having that high concentration of heme in the mitochondria is like having a flame when there is a gas leak.”
The screen also identified one mutation that led to parasites being less sensitive to artemisinin. The mutation affected a gene called DegP2, the product of which interacts with several mitochondrial proteins and appears to play a role in heme metabolism. When less DegP2 was present, the cells contained a lower amount of heme, which in turn made it less likely that the parasites would be killed by artemisinin.
Both the findings support other research suggesting that heme metabolism is crucial for artemisinin susceptibility. “It is important to consider the role of heme when combining artemisinin with other therapies,” Lourido said. “You would want to avoid combination therapy that might inadvertently suppress the level of heme within the parasite and thereby reduce susceptibility to antiparasitic agents.”
The project also showed the potential of using the Toxoplasma screening method as a model to study other related parasites. The screen confirmed findings in Toxoplasma that had previously been shown in Plasmodium, suggesting that it could be a valuable tool in studying malaria and other diseases caused by apicomplexan parasites.
“Through the amazing screens and molecular biology that you can do in Toxoplasma, we can really learn a lot about the biology of this diverse group of parasites,” Lourido said. “Defeating malaria is going to take a lot of different and creative approaches, and the fundamental research that we can do in Toxoplasma can in fact inform many of the critical clinical questions we need to answer to control this disease.”
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Written by Eva Frederick
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Harding, C., Sidik, S, and Petrova, B., et al. “Genetic screens reveal a central role for heme metabolism in artemisinin susceptibility.” Nature Communications. DOI: https://doi.org/10.1038/s41467-020-18624-0
Researchers discover new rules governing bacterial gene expression that overturn fundamental assumptions about basic biological pathways.
Raleigh McElvery
August 26, 2020
On the evolutionary tree, humans diverged from yeast roughly one billion years ago. By comparison, two seemingly similar species of bacteria, Escherichia coli and Bacillus subtilis, have been evolving apart for roughly twice as long. In other words: walking, talking bipeds are closer on the tree of life to single-celled fungus than these two bacteria are to one another. In fact, it’s becoming increasingly clear that what is true of one bacterial type may not be true of another — even when it comes down to life’s most basic biological pathways.
E. coli has served as a model organism in scientific research for over a century, and helped researchers parse many fundamental processes, including gene expression. In these bacteria, as one molecular machine, the RNA polymerase, moves along the DNA transcribing it into RNA, it is followed in close pursuit by a second molecular machine, the ribosome, which translates the RNA into proteins. This “coupled” transcription-translation helps monitor and tune RNA output, and is considered a hallmark of bacteria.
However, an interdisciplinary team of biologists and physicists recently showed that the B. subtilis bacterium employs a different set of rules. Rather than working in tandem with the ribosome, the polymerase in B. subtilis speeds ahead. This system of “runaway” transcription creates alternative rules for RNA quality control, and provides insights into the sheer diversity of bacterial species.
“Generations of researchers, including myself, were taught that coupled transcription-translation is fundamental to bacterial gene expression,” says Gene-Wei Li, an associate professor of biology and senior author of the study. “But our very precise, quantitative measurements have overturned that long-held view, and this study could be just the tip of the iceberg.”
Grace Johnson, a graduate student in the Department of Biology, and Jean-Benoît Lalanne, a graduate student in the Department of Physics, are the lead authors on the paper, which appeared in Nature on Aug. 26.
A curious clue
In 2018, Lalanne developed an experimental technique to measure the boundaries of RNA transcripts. When DNA is transcribed into RNA, the resulting transcripts are generally longer than the DNA coding sequence because they also have to include an extra bit at the end to signal the polymerase to stop. In B. subtilis, Lalanne noticed there simply wasn’t enough space between the ends of the coding sequences and the ends of the RNA transcripts — the extra code was too short for both the polymerase and the ribosome to fit at the same time. In this bacterium, coupled transcription-translation didn’t seem possible.
“It was a pretty weird observation,” Lalanne recalls. “It just didn’t square up with the accepted dogma.”
To delve further into these puzzling observations, Johnson measured the speeds of the RNA polymerase and ribosome in B. subtilis. She was surprised to find that they were moving at very different rates: the polymerase was going roughly twice as fast as the ribosome.
During coupled transcription-translation in E. coli, the ribosome is so closely associated with the RNA polymerase that it can control when transcription terminates. If the RNA encodes a “premature” signal for the polymerase to stop transcribing, the nearby ribosome can mask it and spur the polymerase on. However, if something goes awry and the ribosome is halted too far behind the polymerase, a protein called Rho can intervene to terminate transcription at these premature sites, halting the production of these presumably non-functional transcripts.
However, in B. subtilis, the ribosome is always too far behind the polymerase to exert its masking effect. Instead, Johnson found that Rho recognizes signals encoded in the RNA itself. This allows Rho to prevent production of select RNAs while ensuring it doesn’t suppress all RNAs. However, these specific signals also mean Rho likely has a more limited role in B. subtilis than it does in E. coli.
A family trait
To gauge how common runaway transcription is, Lalanne created algorithms that sifted through genomes from over 1,000 bacterial species to identify the ends of transcripts. In many cases, there was not enough space at the end of the transcripts for both the RNA polymerase and the ribosome to fit, indicating that more than 200 additional bacteria also rely on runaway transcription.
“It was striking to see just how widespread this phenomenon is,” Li says. “It raises the question: How much do we really know about these model organisms we’ve been studying for so many years?”
Carol Gross, a professor in the Department of Microbiology and Immunology at University of California San Francisco who was not involved with the study, refers to the work as a “tour de force.”
“Gene-Wei Li and colleagues show transcription-translation coupling, thought to be a foundational feature of bacterial gene regulation, is not universal,” she says. “Instead, runaway transcription leads to a host of alternative regulatory strategies, thereby opening a new frontier in our study of bacterial strategies to thrive in varied environments.”
As researchers widen their experimental radius to include more types of bacteria, they are learning more about the basic biological processes underlying these microorganisms — with implications for those that take up residence in the human body, from helpful gut microbes to noxious pathogens.
“We’re beginning to realize that bacteria can have distinct ways of regulating gene expression and responding to environmental stress,” Johnson says. “It just shows how much interesting biology is left to uncover as we study increasingly diverse bacteria.”
Citation:
“Functionally uncoupled transcription–translation in Bacillus subtilis”
Nature, online August 26, 2020, DOI: 10.1038/s41586-020-2638-5
Grace E. Johnson, Jean-Benoît Lalanne, Michelle L. Peters, and Gene-Wei Li
Top illustration: Researchers discovered a new system of transcription and translation in bacteria, where the polymerase (pink) in B. subtilis “runs away” from the ribosome (blue). Credit: Grace Johnson
Posted: 8.26.20
Emma H. Yee, Steven S. Cheng, Grant A. Knappe, and Christine A. Moomau | MIT Science Policy Review
August 25, 2020
Article Summary
Antibiotics are a vital component of global health. By killing or inhibiting the growth of bacteria, antibiotics treat infections like pneumonia, staph, and tuberculosis.By preventing infections, they enable major medical procedures such as surgeries and chemotherapy. However,bacteria are becoming increasingly resistant to current antibiotics, causing an estimated 34,000 deaths annually in the US. Left unchecked, antibiotic resistance will have major public health consequences, causing over 5 million deaths each year by 2050. Major causes of this crisis are the misuse of existing antibiotics and the slow development of new antibiotics. To incentivize responsible use, governments and institutions are initiating education programs, mandating comprehensive hospital antibiotic stewardship programs, and funding the development of rapid diagnostics. To bring new antibiotic drugs to market, the US government and other non-governmental organizations are funding scientific research toward antibiotic development.Additional incentives are being pursued to improve the commercial viability of antibiotic development and protect drug developers from the unique challenges of the antibiotic market. With diligent efforts to improve responsible use and encourage novel antibiotic drug discovery, we can decrease the global disease burden, save money, and save lives.
Antibiotics are drugs that kill or inhibit the growth of bacteria, and we have them to thank for the 25-year increase in American life expectancy in the last century[1,2]. In 1900, the three leading causes of death were bacterial infections: pneumonia, tuberculosis, and diarrhea/enteritis[3]. Penicillin, the first antibiotic, was discovered in 1928. But it was not until World War II, when wounded soldiers were more likely to die from infections than the injuries themselves, that governments realized penicillin’s life-saving potential[4]. The US government began developing and mass-producing penicillin through unprecedented public, private, and international collaborations, prompting a new era of antibiotics. Antibiotics are now used to treat a myriad of common infections like strep throat, meningitis, tuberculosis, tetanus, urinary tract infections, and food poisoning. They also enable medical procedures that otherwise create a high risk of infection, such as invasive surgery, organ transplantation, and chemotherapy[5]. However, antibiotics are not “one size fits all”; certain types of antibiotics are only effective against certain kinds of bacteria, and all antibiotics are ineffective against viruses[6].
Antibiotics kill or inhibit bacterial growth via various mechanisms of action; they might attack the protective bacterial cell wall, interfere with bacterial reproduction, or interrupt production of molecules necessary for the bacteria’s survival[7]. However, bacteria reproduce and evolve rapidly, changing over time to resist an antibiotic’s destructive mechanism of action. In fact, the more we use antibiotics, the faster bacteria evolve to resist those antibiotics. As bacteria reproduce, random DNA mutations will occur. Most random mutations have no effect on the bacteria, but sometimes a mutation will give the bacteria a special ability to resist an antibiotic—for instance, the mutation may change the cellular target of the antibiotic, or allow the bacteria to pump the drug out of the cell. When an antibiotic is used on bacteria, most of the population will die, but if any of the bacteria have one of these resistance-conferring mutations, they will survive and continue to reproduce, until the entire population is resistant[5]. The use of antibiotics therefore creates environments where bacteria with antibiotic resistance mutations are more likely to survive and reproduce, while susceptible bacteria are gradually killed off.
Figure 1: Use of an antibiotic gradually increases the prevalence of resistant bacteria. If any cell has developed characteristics allowing it to resist attack by an antibiotic, it is more likely to survive and multiply.
This means that, over time, the bacteria that cause infections in humans are more and more likely to be resistant to common antibiotics. It is important to note that bacteria develop antibiotic resistance–not people. But when people use lots of antibiotics, they change bacterial populations such that more and more bacteria are resistant to those antibiotic drugs. This illustrates the double-edged sword nature of antibiotic use: antibiotics are immensely valuable for combating countless infections and enabling medical procedures, but the more we use them, the less valuable they become.
Today, antibiotic resistance is accelerating at alarming rates. The Centers for Disease Control and Prevention (CDC) estimates there are 3 million antibiotic resistant infections in the US every year, causing at least 34,000 deaths[5]. Globally, at least 700,000 deaths occur due to resistant infections, most of which are bacterial; the actual number is likely higher due to poor reporting and surveillance[8]. The prospect of widespread antibiotic resistance threatens to bring society into a post-antibiotic age where infections are more expensive and difficult to treat. This is a threat to not only public health but also the economic stability of the healthcare system[9] and national security[10].
Figure 2:Annual global deaths due to different factors. Antimicrobial resistance (AMR) accounts for resistance from bacteria, as well as fungi, viruses, parasites, and other microbes[15].
This review will focus on medical use of antibiotics in humans in the US, but antibiotic use in animals and agriculture are also major contributors to the current crisis[6]. It is also critical to understand that combating antibiotic resistance will require global cooperative action because infection-causing bacteria spread rapidly between cities, countries, and continents. A large part of addressing antibiotic resistance in the US is assisting and coordinating with other governments, especially those in low-income countries which have the highest instances of antibiotic resistance, but the fewest resources to deal with it[11]. It is also vital to understand the causes of antibiotic resistance in the US and effective actions US institutions can take.
Misuse and Overuse of Antibiotics
Overuse of antibiotics is a major contributor to the rapid proliferation of antibiotic resistant infections. It is estimated that US doctors’ offices and emergency departments prescribe about 47 million unnecessary antibiotic courses annually, amounting to 30% of all antibiotic prescriptions[12]. Many studies show that even when illnesses do require antibiotics, prescribed time courses are significantly longer than national guidelines[13, 14].
Rapid Diagnostics and Antibiotic Prescriptions: A major cause of ubiquitous antibiotic overuse is a lack of rapid methods for diagnosing infections. Physicians rely on tests that usually take days to weeks to identify if an infection is bacterial and, if so, which antibiotics will be most effective. Waiting this long can be harmful or even fatal for patients[15]. Therefore, physicians usually prescribe broadly effective antibiotics while knowing little about the nature of the infection[15]. This can save lives, but if the infection is caused by a virus or resistant bacteria, the antibiotics will not treat the illness and will give resistant strains a chance to further multiply, leaving patients susceptible to additional infections.
With growing awareness in the last 5-10 years that appropriate antibiotic use is difficult with current diagnostics, the CDC, the National Institute of Allergy and Infectious Diseases (NIAID), and the Biomedical Advanced Research and Development Authority (BARDA) have collectively awarded hundreds of millions of dollars to state health departments, businesses, and universities to develop rapid diagnostics[16]. BARDA and NIAID also organized a $20 million prize, the Antimicrobial Resistance Diagnostic Challenge[17], and fund the global non-profit, CARB-X, which has invested $82.5 million in 55 projects worldwide for antibiotic resistance research, including diagnostics[18]. This surge in resources and funding has increased rapid diagnostic development. For example, the NIAID funded development of BioFire’s FilmArray[19], which is now an FDA-cleared diagnostic test available for purchase in the US[20]. In just an hour, it tests patient samples for several common types of bacteria, viruses, and yeast, including antibiotic resistant ones[21].
However, new diagnostic technologies have limited effectiveness when they fail to meet practical cost and resource requirements. Cepheid’s GeneXpert MTB/RIF test, for example, can diagnose tuberculosis infection and determine resistance to rifampicin, a common antibiotic for tuberculosis, in 2 hours[22]. Unfortunately, it has not been used as widely as initially expected[23], mainly because the equipment costs $17,000, not counting training and set-up costs[24]. This illustrates another major shortcoming of current diagnostic technologies: high healthcare infrastructure and cost requirements that render them inaccessible to many people.
Widespread access to rapid diagnostics is not just about fairness, it’s a necessity. Antibiotic resistance will remain a problem in the US as long as it is a problem anywhere in the country or the world due to inevitable intra- and international bacterial transmission. Many recently developed rapid diagnostics cost $100-$250 per test[25, 26]. These diagnostic innovations are promising and valuable in filling part of the gap in rapid diagnostics, but their benefits will not be felt by the majority of global hospitals and patients that cannot afford or support high cost, high tech diagnostic investments. Increasing institutional funding in the last 10 years has resulted in new rapid diagnostics for identifying and characterizing infections, a potential step towards reducing antibiotic misuse and subsequent development of antibiotic resistance. However, ensuring accessibility of technological improvements is essential in combating antibiotic resistance.
Prescribing Practices: Updating prescription standards and educating healthcare workers and patients on responsible antibiotic use is another key step in reducing antibiotic overuse. In the US, patients are often prescribed antibiotics for far longer than necessary. Two recent studies found that 70% of patients with sinus infections and 70% of adults hospitalized with pneumonia were given antibiotics for 3 or more days longer than recommended[13, 14]. Oftentimes, this stems from an out-of-date belief that longer is better in terms of preventing the development and spread of resistant bacteria. In fact, the opposite is true. Shorter courses of antibiotics lower the selective pressure for development of resistance. This was illustrated in a study of pediatric antibiotic use[27], where children prescribed 5 days of amoxicillin for the treatment of respiratory infections were less likely to carry antibiotic resistant Streptococcus pneumoniae in their nasal passage than their peers who were treated for 10 days. These children were also found to be less likely to transmit resistant bacteria to others.
In many cases, common antibiotic treatments can be shortened without affecting the outcome. A trial of pneumonia patients found that the standard 8-day course of amoxicillin can be shortened to just 3 days with equal symptom relief and fewer side effects[28]. Similarly, treatment of ventilator-associated pneumonia can be effectively shortened from 14 to 8 days[29]. In some cases, shortened antibiotic courses have actually improved patient outcomes. A reduced course for urinary tract infections from 14 days to 7 days is not only effective, it also prevents post-treatment yeast infections[30].
As scientists and clinicians become more aware of the dangers of resistance, more studies are being conducted to determine the minimum amount of antibiotic required to adequately treat infections. The Infectious Diseases Society of America has also updated their Clinical Practice Guidelines to reflect findings that shorter treatment schedules are often just as effective, are easier to comply with, and reduce development and spread of resistant bacteria[31]. Performing
minimum effective antibiotic treatment trials is costly in the short term, but necessary to safely revise guidelines and save on long-term healthcare costs.
Public misunderstanding and misinformation regarding antibiotics also contribute to their overprescription. In many clinical settings where antibiotics are not necessary, patients may believe antibiotics are the most effective treatment and push their doctors to inappropriately prescribe them. For example, patients often seek antibiotics for viral respiratory illnesses (i.e. cold and flu), despite antibiotics being ineffective against viral infections[5]. It has been demonstrated that patient expectation of antibiotics or physician perception of this desire have a significant influence on antibiotic prescription[32–34].
Table 1: Antibiotic overuse is caused largely by shortcomings in diagnostic technologies and prescribing practices, but there are many possible ways to address these challenges.
Efforts to address this issue include educational initiatives for the public and antibiotic stewardship programs for healthcare providers. One such initiative was France’s national campaign to reduce antibiotic use, launched in 2001[35]. France, Europe’s largest antibiotics consumer, sought to address the problem through physician training and a public health campaign called “Antibiotics are not automatic”. This campaign spread public awareness that overusing antibiotics leads to resistance, and, during the winter flu season, that antibiotics kill bacteria – not the viruses responsible for most respiratory infections. Concurrently with this initiative, antibiotic use in France dropped by over 25% from 2000 to 2007, highlighting the ability of public health education to change clinical outcomes. In recent years, steps have been taken both in the US and internationally to encourage responsible antibiotic use via education, updated prescribing standards, and other courses of action. In 2016, the Joint Commission on Hospital Accreditation, an organization that accredits US healthcare organizations, mandated antibiotic stewardship programs in US hospitals that participate in Medicare and Medicaid. The Joint Commission issued standards cited from the CDC’s Core Elements of Hospital Antibiotic Stewardship Programs[36], including educating staff, healthcare practitioners, patients, and their families on responsible antibiotic use and resistance, appointing a pharmacist leaders to improve hospitals’ antibiotic use, tracking and reporting antibiotic prescribing and resistance patterns, and developing protocols for specific antibiotic use cases, such as pneumonia. The number of hospitals reporting an antibiotic stewardship program that meets all the CDC’s Core Elements doubled between 2014 and 2017[37], and will likely increase further, with stewardship programs now tied to accreditation. On an international scale, the UN and CDC have pushed for global implementation of One Health responses by releasing recommendations for engaging all members of society—governments, businesses, healthcare workers, etc.—in coordinated and strategic efforts to address antibiotic resistance[8]. Comprehensive promotion of responsible antibiotic use is vital to maintaining their usefulness for as long as possible, especially given the difficulty of developing new antibiotics.
Revitalizing the Antibiotic Pipeline
While it is important that existing antibiotics are prescribed cautiously and used responsibly, all antibiotics inevitably encounter resistance[38]. Consequently, continuously developing antibiotics with novel mechanisms of action—the method that an antibiotic uses to kill bacteria—that circumvent existing resistances will remain essential. However, developing these new drugs is costly; it can take well over a decade and cost more than $2 billion, with a 90% failure rate looming over the project[38]. Clinical trials, which require large, diverse populations to demonstrate evidence of drug superiority, account for 65% of the risk-adjusted cost for developing antibiotics[15]. The difficulty of antibiotic drug development is illustrated by the 2019 FDA approval of lefamulin, which marked the first approval of an IV/orally-administered antibiotic with a novel mechanism of action in two decades[39]. Scientific challenges inhibit discovery significantly. The immediately apparent antibiotic candidates have been developed, and discovering antibiotics with new mechanisms of action is challenging. It is now thought that any new, effective antibiotics will need multiple capabilities for killing bacteria, making their discovery more complex[3]. Emerging approaches in antibiotic discovery such as deep learning algorithms are promising technologies to solve these scientific challenges, but are far from bringing new antibiotics to patients[40].
In addition to scientific obstacles, the economics of antibiotic development have reduced innovation and output. The free market is failing to meet society’s antibiotic needs via multiple pathways[41]. Traditional sales-based models, in which revenue is directly proportional to the volume of sales, are antagonistic towards society’s goal of sustainable antibiotic use[2]. Evidence of the current system’s failure is the drastic decrease in antibiotic research programs[3] and the sparse output of new [2]. To address these challenges, policymakers are crucial actors; they can facilitate fertile economic conditions using a combination of 1) “push” policies to galvanize antibiotic discovery and development efforts and 2) “pull” policies to create profitable
economic conditions, incentivizing industry to work in this area. Simultaneously, these policies must be supplemented by sufficient regulations to ensure sustainable and equitable usage, broadly maximizing overall societal benefits.
Push Policies: Push policies drive companies to conduct antibiotic research and clinical trials[42] by providing monetary resources to antibiotic developers. Push policies are realized via grants and pipeline coordinators. Government grants allow both academia and industry to investigate antibiotic candidates and conduct clinical trials. Pipeline coordinators are agencies that ensure governmental funding is distributed efficiently across development stages. Coordinators are essential to ensuring equitable funding distribution across antibiotic candidates and identifying gaps and needs in the antibiotic pipeline from basic research through production. These vehicles have broad precedents and have demonstrated effectiveness at stimulating early stage scientific research. Current estimates show $550 million is spent annually on push spending, though some recommendations show that this number should be $800 million to fully meet the demand for antibiotic research[42]. However, push policies and spending do not completely address the major economic issues.
Figure 3:A combination of push and pull policies are necessary to generate conditions to revitalize the antibiotic pipeline. Currently, only push policies are implemented. Pull policies can de-link an antibiotic’s development from its economic success, which is projected to increase the development rate of antibiotics that society needs.
Pull Policies: The primary goal of push policies is to jump start research and development in antibiotic discovery, but issues remain with the current market structure for antibiotics. This is illustrated by the fact that companies are failing after bringing important antibiotics to market. For instance, the biopharmaceutical company Achaogen successfully developed the antibiotic plazomicin in 2018, but filed for bankruptcy the following year due to insufficient profits from plazomicin[43]. Why would a company that successfully brings a new antibiotic to market fail? Antibiotics are generally prescribed for short periods of time (usually under two weeks), modern health policies support reducing or delaying the use of new antibiotics, and the market lifetime of antibiotics is reduced due to the inevitable development of resistance[44].Overall, these realities minimize sales of the new antibiotic and thus the profits of the developing company. In response, policymakers have proposed pull policies to de-link the sales of the new antibiotic to the economic reward given to the developers, improving the economic viability of developing new antibiotics. These pull policies are supported by the Infectious Diseases Society of America[45]. By de-linking sales from economic reward, the revenue from a new antibiotic is not purely based on the sales volume of that antibiotic. For example, a market entry reward (MER) — a large monetary sum given to developers of novel antibiotics upon successful drug approval — can be used to partially or fully de-link the number of sales from the economic reward. Multiple groups, such as the Boston Consulting Group, have estimated that a $1 billion MER per antibiotic is sufficient, suggesting that this award amount would lead to twenty novel antibiotics for society over the next three decades[42, 46].
An important supplement to any MER policy is the antibiotic susceptibility bonus (ASB)[47]. The ASB rewards companies that develop antibiotics that are effective over long periods of time. As an antibiotic remains effective against target bacteria, companies receive monetary awards. This policy helps better align all stakeholders’ (companies, patients, hospitals, insurance networks) interests towards generating and maintaining effective antibiotics. Companies will no longer have an incentive to oversell antibiotics, as they will receive more money the longer their drug is effective. This supplemental policy could safeguard MERs against abuse, and incentivize the development of antibiotics that act in society’s best interest: to develop effective treatments for long periods of time.
Another potential pull policy is the long-term supply continuity model (LSCM)[42], which addresses how companies respond once market exclusivity for a drug ends due to patent expiration. Suppliers may respond to loss of market exclusivity by either manufacturing fewer units in the case of a modest market or by increasing sales through marketing and promotion. Both actions are detrimental to public health in the case of an antibiotic, either promoting antibiotic overuse or making it harder for people who need the antibiotic to get it. The LSCM addresses this by having a country or group of countries make an agreement with manufacturers to produce a predetermined amount of the respective antibiotic for a specified price. This model to generate a predictable supply of an antibiotic acts as a pull mechanism by making the market for novel, essential antibiotics more sustainable for manufacturers.
Pull policies also have some downsides. For one, pull policies only reward successful antibiotic discovery campaigns; the inherent risk in developing these drugs may still dissuade companies. Also, while push policies have been validated with real world results, pull policies have not been evaluated as extensively. To encourage companies to work in this area, push policies, as well as pull policies, are needed to lower the risk of failed discovery programs. To develop the new drugs that society needs, companies need funding to start research and development and economic incentives to take the drugs to market.
Conclusion Proliferation of antibiotic resistance in bacteria is a major public health problem that is only accelerating. This crisis is caused by overuse of existing antibiotic drugs and lagging development of new ones. To address the former, many US and international institutions are working to improve current diagnostic practices and adopt standards for responsible antibiotic use. Increasing funding for rapid diagnostics R&D, initiating educational programs, and mandating the adoption of comprehensive hospital antibiotic stewardship programs are possible ways to reduce antibiotic overuse. To encourage the development of novel antibiotic drugs, many organizations have also subsidized research and development in this area. Additional incentives are being pursued to improve the commercial viability of antibiotic development and protect drug developers from the risks of the antibiotic market. Antibiotic resistance is a major global health crisis, but with efforts to improve responsible use and end the almost 40-year drought of novel antibiotic drug discovery[48], we can take steps to prevent the next public health emergency. 4“The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no warrants shall issue, but upon probable cause supported by oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.”
Acknowledgements
We thank Erika Madrian for her input in shaping the manuscript.
Citation
Yee, E. H., Cheng, S. S., Knappe, G. A. & Moomau, C. A. Antibiotic resistance: How to prevent the next public health emergency. MIT Science Policy Review 1, 10-17 (2020).
Researchers determine how much of an enzyme is ‘just enough’ to keep a cell healthy and growing.
Raleigh McElvery
July 28, 2020
What ratio of ingredients makes a healthy cell? Researchers know which components are required for proper function, but they’re still working to understand what happens when there’s too much of one protein or not enough of another. As a graduate student in Gene-Wei Li’s lab, Darren Parker PhD ’20 spent years tweaking the recipe for a bacterial cell, adding more or less of one enzyme, aminoacyl-tRNA synthetase (aaRS). He wanted to know: How much aaRS is “just right” for bacterial cells? His findings were published in Cell Systems on July 28.
tRNAs, or transfer RNAs, carry amino acids to the ribosome to help produce proteins. But first, aaRSs must “charge” the tRNAs by attaching an amino acid to them. In doing so, aaRSs not only help the cell make proteins and grow; they also ensure the levels of “uncharged” tRNAs lacking amino acids don’t rise too high, as too many of them can trigger stress responses that slow cell growth. Parker and his collaborators predicted that tinkering with aaRS levels would uncover one of two possible scenarios. Perhaps cells tune their aaRS production to minimize the amount of uncharged tRNAs present. Alternatively, aaRS production could be dictated by the rate of protein synthesis necessary for cell growth — even if that means accumulating uncharged tRNAs.
The researchers determined the latter was true: cells make “just enough” aaRSs to optimize protein production and cell growth. This delicate balance was easily upset when too few aaRSs were produced, cueing the stress responses to kick in and slow growth. Although excess aaRSs reduced the amount of uncharged tRNA, it also hindered cell growth. The researchers determined that the cellular circuits in charge of controlling and sensing tRNA charging are collectively tuned to optimize bacterial growth.
“These results demonstrate that cells have delicately balanced the costs and benefits of producing their proteins,” Parker says. “Understanding the driving forces behind protein production is important for better understanding disease processes, and engineering cells to perform new functions.”