GN/ Scientists hijack bacteria to ease drug manufacturing
Genetics biweekly vol.32, 29th June — 13th July
TL;DR
- For more affordable, sustainable drug options than we have today, the medication we take to treat high blood pressure, pain or memory loss may one day come from engineered bacteria, cultured in a vat like yogurt. And thanks to a new bacterial tool, the process of improving drug manufacturing in bacterial cells may be coming sooner than we thought.
- Researchers have captured images of an auto-antibody bound to a nerve cell surface receptor, revealing the physical mechanism behind a neurological autoimmune disease. The findings could lead to new ways to diagnose and treat autoimmune conditions, the study authors said.
- After almost two decades of synchrotron experiments, scientists have captured a clear picture of a cell’s nuclear pores, which are the doors and windows through which critical material in your body flows in and out of the cell’s nucleus. These findings could lead to new treatments of certain cancers, autoimmune diseases and heart conditions.
- Bioscientists learn to trigger ‘silent’ gene clusters in bacteria that could be rich sources of new antibiotic candidates.
- Chemists discovered how the epidermal growth factor receptor changes its shape when it binds to its target, and how those changes trigger cells to grow and proliferate.
- A discovery could offer new methods for treating HIV, while uncovering the innate immune system’s role in other diseases.
- Using four unrelated strains of the microscopic nematode C. elegans originating from different parts of the world, a group of worm biologists have developed a model system to study individual differences in metabolism. This advancement represents a potentially important step toward ‘personalized’ or ‘precision’ medicine, a relatively new discipline that tailors dietary advice and disease treatment to an individual’s own genome sequence.
- Scientists discovered that hepatitis A viral replication requires specific interactions between the human protein ZCCHC14 and a group of enzymes called TENT4 poly(A) polymerases, and they used a molecule to stop replication at a key step, making it impossible for the virus to infect liver cells.
- Scientists have identified more than 1,500 genetic differences between migratory and non-migratory hoverflies.
- Genome engineering using CRISPR offers novel solutions for controlling invasive alien species, but its efficiency for eradicating harmful vertebrates is yet to be tested. In a new study, researchers confirm that genetic biocontrols could rapidly eradicate animals like rats, mice and rabbits. Others — like cats and foxes — would, however, take a lot longer.
- And more!
Overview
Genetic technology is defined as the term which includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do and how DNA can be modified to add, remove or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
- The valuation of the genetic engineering market is projected to escalate to USD 6.90 MN by the end of 2027.
- Global Genetic Engineering Market is projected to grow at 12.48% CAGR during the assessment period (2017–2027).
- North America holds the largest share in the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
- Another research provider, MarketsandMarkets, forecasts the genome editing, genome engineering market to grow from USD 3.19 billion in 2017 to USD 6.28 billion by 2022, at a compounded annual growth rate (CAGR) of 14.5% during the forecast period. The key factors propelling market growth are rising government funding and growth in the number of genomics projects, high prevalence of infectious diseases (like COVID-19) and cancer, technological advancements, increasing production of genetically modified (GM) crops, and growing application areas of genomics.
Latest News & Research
Using fungible biosensors to evolve improved alkaloid biosyntheses
by Simon d’Oelsnitz, Wantae Kim, Nathaniel T. Burkholder, Kamyab Javanmardi, Ross Thyer, Yan Zhang, Hal S. Alper, Andrew D. Ellington in Nature Chemical Biology
For more affordable, sustainable drug options than we have today, the medication we take to treat high blood pressure, pain or memory loss may one day come from engineered bacteria, cultured in a vat like yogurt. And thanks to a new bacterial tool developed by scientists at The University of Texas at Austin, the process of improving drug manufacturing in bacterial cells may be coming sooner than we thought.
For decades, researchers have been eyeing ways to make drug manufacturing more affordable and sustainable than pharmaceutical makers’ current processes, many of which depend on either plant crops or petroleum. Using bacteria has been suggested as a good organic alternative, but detecting and optimizing the production of therapeutic molecules is difficult and time-consuming, requiring months at a stretch. In a new paper, the UT Austin team introduces a biosensor system, derived from E. coli bacteria, that can be adapted to detect all kinds of therapeutic compounds accurately and in mere hours.
“We’re figuring out how to give bacteria ‘senses,’ similar to olfactory receptors or taste receptors, and use them for detection of the various compounds they might make,” said Andrew Ellington, a professor of molecular biosciences and corresponding author on the paper.
Many of the medicines we take are made with ingredients extracted from plants (think, for example, morphine, the narcotic painkiller that comes from poppies, or galantamine, a drug treatment for dementia that comes from daffodils). Extracting drugs from these plants is complicated and resource-intensive, requiring water and acreage to grow the crops. Supply chains are easily disrupted. And crops can be damaged by floods, fires and drought. Deriving similar therapeutic components using synthetic chemistry brings problems, too, since the process depends on petroleum and petroleum-based products linked to waste and expense.
Enter the humble bacteria, a cheap, efficient and sustainable alternative. The genetic code of bacteria can be easily manipulated to become factories for drug production. In a process called biosynthesis, the bacteria’s biological systems are harnessed to produce specific molecules as part of the natural cellular process. And bacteria can replicate at high speed. All they need to do the job is sugar.
Unfortunately, manufacturers have not had a way to quickly analyze different strains of engineered bacteria to identify the ones capable of producing quantities of a desired drug at commercial volumes — until now. Accurately analyzing the thousands of engineered strains on the way to a good producer can take weeks or months with current technology, but only a day with the new biosensors.
“There are currently no biosensors for most plant metabolites,” said Simon d’Oelsnitz, a research scientist in the Department of Molecular Biosciences and first author on the paper. “With this technique, it should be possible to create biosensors for a wide range of medicines.”
The biosensors developed by d’Oelsnitz, Ellington and colleagues quickly and accurately determine the amount of a given molecule that a strain of bacteria is producing. The team developed the biosensors for several types of common drugs, such as cough suppressants and vasodilators, which are used to treat muscle spasms. Molecular images of the biosensors taken by X-ray crystallographers Wantae Kim and Yan Jessie Zhang show exactly how they tightly grab onto their partner drug. When the drug is detected by the biosensor, it glows. Additionally, the team engineered their own bacteria to produce a compound found in several FDA-approved drugs and used the biosensors to analyze product output, in essence showing how industry might adopt biosensors to quickly optimize chemical manufacturing.
“While this is not the first biosensor,” d’Oelsnitz said, “this technique allows them to be developed faster and more efficiently. In turn, that opens the door to more medicines being produced using biosynthesis.”
Structural mechanisms of GABAA receptor autoimmune encephalitis
by Colleen M. Noviello, Jakob Kreye, Jinfeng Teng, Harald Prüss, Ryan E. Hibbs in Cell
Using UT Southwestern’s Cryo-Electron Microscopy Facility, researchers for the first time have captured images of an autoantibody bound to a nerve cell surface receptor, revealing the physical mechanism behind a neurological autoimmune disease. The findings could lead to new ways to diagnose and treat autoimmune conditions, the study authors said.
“We’re entering a new era of understanding how autoimmune disease works in the central nervous system,” said Colleen M. Noviello, Ph.D., Assistant Professor of Neuroscience at UTSW who specializes in obtaining cryo-electron microscopy (cryo-EM) images down to an atomic level of resolution. Dr. Noviello co-led the study with Ryan Hibbs, Ph.D., Associate Professor of Neuroscience and Biophysics, an Effie Marie Cain Scholar in Medical Research, and an Investigator in the Peter O’Donnell Jr. Brain Institute and Harald Prüss of Universitätsmedizin Berlin.
Researchers have studied autoimmune diseases — a class of conditions in which the immune system attacks healthy parts of the body — for decades. However, the first autoimmune disease targeting a neuronal receptor protein was discovered just 15 years ago, Dr. Noviello explained. Since then, researchers have reported the existence of a handful of other diseases that fall into this category. These include autoimmune encephalitis, a condition characterized by the sudden onset of severe symptoms including psychosis, seizures, movement disorders, impaired consciousness, and problems with the autonomic nervous system, which controls involuntary bodily functions.
Researchers in Germany recently identified a patient, then 8 years old, whose autoimmune encephalitis appeared to be caused by antibodies that attack the GABAA receptor, a protein that sits on the surface of synapses — specialized structures that connect brain cells. This receptor’s role is to inhibit neuronal firing, balancing the electrical signals prompted by excitatory receptors to maintain healthy signaling between nerve cells.
After confirming that two kinds of antibodies derived from this young patient’s immune cells readily bound to the GABAA receptor, Drs. Noviello, Hibbs, and their colleagues in the Hibbs lab performed cryo-EM — a technique that freezes proteins in place to get high-resolution microscopic images — for each antibody bound to the receptor. UTSW’s cryo-EM facility, opened in 2016 with support from the Cancer Prevention and Research Institute of Texas (CPRIT), provides 3D images of biological molecules up to atomic resolution.
The images show that, both together and separately, the antibodies prevent the GABAA receptor from inhibiting neuronal signaling, causing neurons to become too electrically excited and leading to brain inflammation, cell death, and seizures characteristic of autoimmune encephalitis. Screening for these antibodies could lead to better diagnosis of this condition, said Dr. Noviello; likewise, finding ways to block the interaction between these antibodies and their target could lead to better ways to treat it.
Architecture of the linker-scaffold in the nuclear pore
by Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches, Christopher J. Bley, Karsten Thierbach, Bonnie Brown, Si Nie, George W. Mobbs, Taylor A. Stevens, Xiaoyu Liu, Giovani Pinton Tomaleri, Lucas Schaus, André Hoelz in Science
Your body is made of close to 100 trillion cells that keep you healthy and alive. Each cell has billions of parts of its own, all of them working in tandem to keep life’s processes moving.
One vital component of a cell is called a nuclear pore, which acts like the doors and windows in a house — they allow important things, like RNA and proteins, to enter and exit a cell’s nucleus. Without nuclear pores, your cells, and everything else in your body, would shut down. Until now, scientists have not seen exactly how nuclear pores are built and how their many parts function.
Enter a team of researchers from the California Institute of Technology (Caltech), led by André Hoelz, professor of chemistry and biochemistry and faculty scholar of the Howard Hughes Medical Institute (HHMI). After almost two decades of persistence, researchers successfully mapped the atomic structure of the nuclear pore complex (NPC) by determining the structures of its many components and fitting them together. Seeing how the NPC fits together in cells furthers our understanding about how cells work and will potentially lead to new treatments for certain cancers, autoimmune and neurodegenerative diseases, and certain heart conditions.
Unraveling the NPC took time because it’s not a simple puzzle like the ones that wait in pieces in a box. It contains more than 1,000 individual proteins, and it can take scientists years to map a single one before they can even begin to put them together. The entire process is akin to a gigantic three-dimensional jigsaw puzzle, but one that is made from pieces so tiny that you cannot see them with your naked eyes or even with the best light microscope.
To make this milestone possible, the Caltech team turned to high-energy X-rays generated by the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s (DOE) SLAC National Accelerator Laboratory, the Advanced Photon Source at the DOE’s Argonne National Laboratory, and National Synchrotron Light Source II at the DOE’s Brookhaven National Laboratory. In many experiments over the years, they zapped crystallized NPC protein samples with X-ray light, illuminating the samples’ atomic structure and overall shape. They published their findings this month in two papers. The first paper reported the architecture of the face that lies at the outside of the nucleus, and the second paper revealed how the many pieces of the NPC are held together by “glue” proteins.
“X-ray crystallography provided atomic details of the individual protein components,” Aina Cohen, SLAC senior scientist, said. “As technologies have been improving, including at SLAC’s SSRL, researchers have been able to see the nuclear pore complex in clearer ways, so that they could fit the different proteins together to complete this complex puzzle.”
Without SSRL’s upgraded technology over the years, such as its microfocus capabilities and a pixel array detector (PAD), installed in 2009, the research could not have happened, Hoelz said. SSRL had one of the country’s first PADs, and the detector generated much better X-ray diffraction data than previously possible, helping the Caltech researchers map the NPC’s protein structures. Determining the crystal structure of a large six-protein piece and identifying its arrangement in the nuclear pore in 2015 showed that, with patience and diligence, the researchers could eventually provide a complete picture of the entire NPC.
“SSRL was the facility where most of the initial structural work occurred due to the ample access we had through Caltech’s Molecular Observatory, an X-ray crystallography facility with access to SSRL’s Beam Line 12–2,” Hoelz said. “This regular access allowed for the systematic improvement of various aspects of the X-ray diffraction experiments, which allowed us to solve even the most challenging nucleoporin structure determination problems. We had multiple structures that we worked on for over a decade before we solved them.”
The completed human NPC puzzle will provide a framework on which a lot of important experiments can now be done, said Christopher Bley, a senior postdoctoral scholar research associate in chemistry at Caltech and also co-first author of the studies.
“We have this composite structure now, and it enables and informs future experiments on NPC function, or even diseases,” Bley said. “There are a lot of mutations in the NPC that are associated with terrible diseases, and knowing where they are in the structure and how they come together can help design the next set of experiments to try and answer the questions of what these mutations are doing.”
Having determined the human NPC structure, scientists can now focus on working out the molecular basis for various enigmatic functions of NPCs, such as how mRNA gets exported, the underlying causes for the many NPC-associated diseases, and the targeting of NPC function by many viruses, including SARS-CoV-2 and monkeypox virus, with the goal of developing novel therapies, Hoelz said.
Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces
by Andrea Ameruoso, Maria Claudia Villegas Kcam, Katherine Piper Cohen, James Chappell in Nucleic Acids Research
Silents are potentially golden in the search for antibiotics to slow the ongoing crisis of resistance in the treatment of disease.
Rice University bioscientists have designed novel on and off switches to control the “silent” genes in a strain of bacteria. Their strategy could boost the perpetual search for new antibiotics. The researchers customized CRISPR tools to control the expression of genes in Streptomyces bacteria that, in nature, are only expressed when necessary. Until now, those genes have been challenging for synthetic biologists to access.
“As labs started to sequence the genomes of these organisms that were known to produce one or a few antibiotics, we realized that the pathways responsible for the production of antibiotic and other molecules of interest are much more abundant than previously thought,” said James Chappell, an assistant professor of biosciences whose lab studies bacteria and ways to engineer them.
“Each Streptomyces strain is now predicted to be able to produce up to 40 different molecules of interest, including antibiotics, on average,” he said.
The work led by Chappell and graduate student Andrea Ameruoso may allow labs to quickly develop libraries of possible antibiotics to test on pathogens. Significantly, they said that while CRISPR-Cas9 has been used to create a platform to activate genes in organisms like Escherichia coli, this is the first time it’s been applied to Streptomyces.
“Bacteria such as Streptomyces have evolved to only produce antibiotics when they need to, in natural environments like soil,” Chappell explained. “When we grow them in the lab, it’s an artificial environment and very different to how they naturally grow, so sets of genes are silenced.
“They’re a kind of genetic dark matter,” he said. “We can’t isolate the chemicals they express to perform a functional screen.”
The lab’s new strategy eliminates the time-consuming task of exposing their proof-of-concept bacteria, S. venezuelae, the source of the common antibiotic chloramphenicol, to potential triggers for gene expression. “Andrea’s technology adds synthetic regulators into the cell to artificially stimulate or repress the expression of these pathways,” Chappell said.
“Now we just need one protein and one small piece of RNA and we can go wherever we want to directly repress or activate a given target,” Ameruoso added.
The emergence of CRISPR technology, which adapts bacterial immune system mechanisms to locate specific genes along a strand of DNA, simplified access to the previously hidden gene clusters, he said.
“Streptomyces is a genus of bacteria that encompasses up to 500 species, and each species can have between 20 and 40 of these clusters of genes able to produce antibiotics or other molecules of interest,” Ameruoso said. “So once we figure out a way to scale up our technology, it can be incredibly powerful.”
Chappell said it’s a simple matter to design CRISPR to bind to different DNA sequences. “We exploit that for gene expression control,” he said. “If we want to do this in a bunch of different species on a bunch of different pathways, it should in theory be possible. So this paper lays the foundation for a new type of approach.”
Ameruoso said he’s working on a fluorescent technique to observe the activation of clusters in real time. “The main challenge is that observing the depths of the activation of a cluster relies on the purification of the molecule from the extracts we generate,” he said. “That’s a low-throughput process that requires a lot of work. We want to develop a reporter to observe a fluorescent signal when a pathway is being activated.”
The researchers noted the process could be used to manufacture molecules for antifungal and anticancer agents or for agriculture. “We focus on antibiotics because at some point in history, we’ve observed that they kill microbes,” Chappell said. “But that’s not necessarily what they evolved for, because they’re also frequently used as communication signals between cells. So there are many potential uses.”
He said the study demonstrates an important new approach to the activation of silent pathways. “The vision for the next generation of the work is to go big,” he said. “We showed it works on a single silent pathway. Now let’s do it on the 40 pathways in this one species, and then let’s do it on thousands of microbes. “The power of CRISPR-Cas9 is that it’s really scalable for that,” Chappell said.
Ligand-induced transmembrane conformational coupling in monomeric EGFR
by Shwetha Srinivasan, Raju Regmi, Xingcheng Lin, Courtney A. Dreyer, Xuyan Chen, Steven D. Quinn, Wei He, Matthew A. Coleman, Kermit L. Carraway, Bin Zhang, Gabriela S. Schlau-Cohen in Nature Communications
Receptors found on cell surfaces bind to hormones, proteins, and other molecules, helping cells respond to their environment. MIT chemists have now discovered how one of these receptors changes its shape when it binds to its target, and how those changes trigger cells to grow and proliferate.
This receptor, known as epidermal growth factor receptor (EGFR), is overexpressed in many types of cancer and is the target of several cancer drugs. These drugs often work well at first, but tumors can become resistant to them. Understanding the mechanism of these receptors better may help researchers design drugs that can evade that resistance, says Gabriela Schlau-Cohen, an associate professor of chemistry at MIT. Schlau-Cohen and Bin Zhang, the Pfizer-Laubach Career Development Assistant Professor of Chemistry, are the senior authors of the study. The paper’s lead authors are MIT graduate student Shwetha Srinivasan and former MIT postdoc Raju Regmi.
“Thinking about more general mechanisms to target EGFR is an exciting new direction, and gives you a new avenue to think about possible therapies that may not evolve resistance as easily,” she says.
The EGF receptor is one of many receptors that help control cell growth. Found on most types of mammalian epithelial cells, which line body surfaces and organs, it can respond to several types of growth factors in addition to EGF. Some types of cancer, especially lung cancer and glioblastoma, overexpress the EGF receptor, which can lead to uncontrolled growth.
Like most cell receptors, the EGFR spans the cell membrane. An extracellular region of the receptor interacts with its target molecule (also called a ligand); a transmembrane section is embedded within the membrane; and an intracellular section interacts with cellular machinery that controls growth pathways. The extracellular portion of the receptor has been analyzed in detail, but the transmembrane and intracellular sections have been difficult to study because they are more disordered and can’t be crystallized.
About five years ago, Schlau-Cohen set out to try to learn more about those lesser-known structures. Her team embedded the proteins in a special type of self-assembling membrane called a nanodisc, which mimics the cell membrane. Then, she used single molecule FRET (fluorescence resonance energy transfer) to study how the conformation of the receptor changes when it binds to EGF.
FRET is commonly used to measure tiny distances between two fluorescent molecules. The researchers labeled the nanodisc membrane and the end of the intracellular tail of the protein with two different fluorophores, which allowed them to measure the distance between the protein tail and the cell membrane, under a variety of circumstances.
To their surprise, the researchers found that EGF binding led to a major change in the conformation of the receptor. Most models of receptor signaling involve interaction of multiple transmembrane helices to bring about large-scale conformational changes, but the EGF receptor, which has only a single helical segment within the membrane, appears to undergo such a change without interacting with other receptor molecules.
“The idea of a single alpha helix being able to transduce such a large conformational rearrangement was really surprising to us,” Schlau-Cohen says.
To learn more about how this shape change would affect the receptor’s function, Schlau-Cohen’s lab teamed up with Zhang, whose lab does computer simulations of molecular interactions. This kind of modeling, known as molecular dynamics, can model how a molecular system changes over time. The modeling showed that when the receptor binds to EGF, the extracellular segment of the receptor stands up vertically, and when the receptor is not bound, it lies flat against the cell membrane. Similar to a hinge closing, when the receptor falls flat, it tilts the transmembrane segment and pulls the intracellular segment closer to the membrane. This blocks the intracellular region of the protein from being able to interact with the machinery needed to launch cell growth. EGF binding makes those regions more available, helping to activate growth signaling pathways.
The researchers also used their model to discover that positively charged amino acids in the intracellular segment, near the cell membrane, are key to these interactions. When the researchers mutated those amino acids, switching them from charged to neutral, ligand binding no longer activated the receptor.
“There’s a nice consistency we can see between the simulation and experiment,” Zhang says. “With the molecular dynamics simulations, we can figure out what are the amino acids that are essential for the coupling, and quantify the role of different amino acids. Then Gabriela showed that those predictions turned out to be correct.”
The researchers also found that cetuximab, a drug that binds to the EGF receptor, prevents this conformational change from occurring. Cetuximab has shown some success in treating patients with colorectal or head and neck cancer, but tumors can become resistant to it. Learning more about the mechanism of how EGFR responds to different ligands could help researchers to design drugs that might be less likely to lead to resistance, the researchers say.
Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA
by Sunnie M. Yoh, João I. Mamede, Derrick Lau, Narae Ahn, et al in Molecular Cell
Human immunodeficiency virus 1, more commonly known as HIV-1, is known for its uncanny ability to evade the immune system. Scientists at Scripps Research and collaborators have now uncovered how our innate immune system — the body’s first line of quick defense in attacking foreign invaders — detects HIV-1, even when the virus is present in very small amounts.
The findings reveal the two-step molecular strategy that jolts the innate immune response into action when exposed to HIV-1. This discovery could impact drug development for HIV treatments and vaccines, as well as shape our understanding of how the innate immune response is implicated in other areas — including neurodegenerative disorders such as Alzheimer’s.
“This research delineates how the immune system can recognize a very cryptic virus, and then activate the downstream cascade that leads to immunological activation,” says Sumit Chanda, PhD, professor in the Department of Immunology and Microbiology. “From a therapeutic potential perspective, these findings open up new avenues for vaccines and adjuvants that mimic the immune response and offer additional solutions for preventing HIV infection.”
The innate immune system is activated before the adaptive immune system, which is the body’s secondary line of defense that involves more specialized functions, such as generating antibodies. One of the innate immune system’s primary responsibilities is recognizing between “self” (our own proteins and genetic material) and foreign elements (such as viruses or other pathogens). Cyclic GMP-AMP synthase (cGAS) is a key signaling protein in the innate immune system that senses DNA floating in a cell. If cGAS does detect a foreign presence, it activates a molecular pathway to fight off the invader. However, because HIV-1 is an RNA virus, it produces very little DNA — so little, in fact, that scientists have not understood how cGAS and the innate immune system are able to detect it and distinguish it from our own DNA.
Scripps Research scientists discovered that the innate immune system requires a two-step security check for it to activate against HIV-1. The first step involves an essential protein — polyglutamine binding protein 1 (PQBP1) — recognizing the HIV-1 outer shell as soon as it enters the cell and before it can replicate. PQBP1 then coats and decorates the virus, acting as an alert signal to summon cGAS. Once the viral shell begins to disassemble, cGAS activates additional immune-related pathways against the virus.
The researchers were initially surprised to find that two steps are required for innate immune activation against HIV-1, as most other DNA-encoding viruses only activate cGAS in one step. This is a similar concept to technologies that use two-factor authentication, such as requiring users to enter a password and then respond to a confirmation email. This two-part mechanism also opens the door to vaccination approaches that can exploit the immune cascade that is initiated before the virus can start to replicate in the host cell, after PQBP1 has decorated the molecule.
“While the adaptive immune system has been a main focus for HIV research and vaccine development, our discoveries clearly show the critical role the innate immune response plays in detecting the virus,” says Sunnie Yoh, PhD, first author of the study and senior staff scientist in Chanda’s lab. “In modulating the narrow window in this two-step process — after PQBP1 has decorated the viral capsid, and before the virus is able to insert itself into the host genome and replicate — there is the potential to develop novel adjuvanted vaccine strategies against HIV-1.”
By shedding light on the workings of the innate immune system, these findings also illuminate how our bodies respond to other autoimmune or neurodegenerative inflammatory diseases. For example, PQBP1 has been shown to interact with tau — the protein that becomes dysregulated in Alzheimer’s disease — and activate the same inflammatory cGAS pathway. The researchers will continue to investigate how the innate immune system is involved in disease onset and progression, as well as how it distinguishes between self and foreign cells.
C. elegans as a model for inter-individual variation in metabolism
by Bennett W. Fox, Olga Ponomarova, Yong-Uk Lee, Gaotian Zhang, Gabrielle E. Giese, Melissa Walker, Nicole M. Roberto, Huimin Na, Pedro R. Rodrigues, Brian J. Curtis, Aiden R. Kolodziej, Timothy A. Crombie, Stefan Zdraljevic, L. Safak Yilmaz, Erik C. Andersen, Frank C. Schroeder, Albertha J. M. Walhout in Nature
Using four unrelated strains of the microscopic nematode C. elegans originating from different parts of the world, a group of worm biologists have developed a model system to study individual differences in metabolism. The use of C. elegans, a widely studied model organism, allowed the team to study the unique and complex interplay between genetics, diet, microbiota and other environmental factors that can affect fundamental metabolic processes in different individuals. This advancement represents a potentially important step toward “personalized” or “precision” medicine, a relatively new discipline that tailors dietary advice and disease treatment to an individual’s own genome sequence.
The research, by Marian Walhout, PhD, the Maroun Semaan Chair in Biomedical Research and chair and professor of systems biology at UMass Chan Medical School and collaborators Erik Andersen, PhD, from Northwestern University and Frank Schroeder, PhD, from Cornell University, identifies a novel metabolic condition linked to variation in the hphd-1 gene of a strain of C. elegans found on the Big Island in Hawaii. The strain, known as DL238, has an abnormal accumulation and secretion of the metabolite 3-hydroxypropionate (3HP). Moreover, this strain was found to generate a set of novel metabolites that have 3HP conjugated to several amino acids. These novel metabolites are not found in the laboratory strain that has been used for decades to make seminal biological discoveries. By conjugating 3HP to amino acids, DL238 is removing 3HP, which is toxic at high concentrations.
“This work provides an important step toward the development of metabolic network models that capture individual-specific differences of metabolism and more closely represent the diversity that is found over entire species,” said Walhout. “Employing this system, we can begin studying interindividual metabolism and the unique interplay of metabolites, diets and environments on an individual level.”
When the human genome was sequenced, clinical researchers envisioned an era when our personal genomic information could be used to tailor medical treatments to fit the needs of each individual, explained Walhout. Despite the completion of the Human Genome Project in 2003, and advancements in genomics and deep sequencing technologies, personalized medicine remains more promise than reality.
Part of the challenge in developing personalized medicine is that our DNA makes up only a portion of human health; an individual’s diet and environment both profoundly impact metabolic processes. And because no two individuals have the same exact diet, unraveling the complex interplay of genetics, diet and environment and connecting these to variations in metabolism is cumbersome. In addition to sequencing individual genomes, scientists would need to replicate metabolic measurements in people of the same age and gender, who ideally would also consume the same exact diet and experience identical environments.
To address this challenge, Walhout, a leader in metabolism and gene expression research, teamed up with Dr. Andersen, an expert in quantitative genetics, and Dr. Schroeder, a chemist, to develop a comparative system for studying interindividual variations in metabolism. The group designed a system where environmental conditions and diet were constant among “individuals” with variable genomes, much like our genomes vary from person-to-person. To do this, the four separate strains of C. elegans with completely sequenced genomes — including the standard laboratory strain, two from Hawaii and another from Taiwan — were grown under identical conditions: each strain was grown at the same time in the same incubator and were fed the same diet.
“Each strain represents an individual,” said Olga Ponomarova, PhD, a postdoctoral researcher in the Walhout lab and co-author of the study. “We collected about 100,000 animals from each strain and because they are all grown in the same conditions, given the same diet and have the same genome, it’s possible to explore how genetic differences among the four strains impact metabolism. It’s like comparing four different people.”
At its core, metabolism is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food into energy for cellular processes; the conversion of food to building blocks for proteins, such as lipids, nucleic acids and some carbohydrates; and the elimination of wastes generated by these two processes.
A series of experiments including gas chromatography-mass spectrometry, high performance liquid chromatography-mass spectrometry, and metabolic network analysis were performed and analyzed to identify possible differences and variations in metabolites between the four strains. As a result, more than 20,000 likely metabolites, the small molecules that collectively carry out metabolism, were detected, most of which remain unknown.
When researchers compared the presence of metabolites between the four strains, they found more than 200 metabolites that were highly specific to one of the strains. One metabolite, 3HP, was found in exceptionally high abundance in the DL238 strain from Hawaii. Past studies by the Walhout lab have shown that high 3HP levels are found in nematodes whose diet are low in vitamin B12. These studies showed that 3HP is formed during propionate breakdown via a B12-independent metabolic route, or shunt. 3-HP is then metabolized by the HPHD-1 enzyme and ultimately converted into acetyl-CoA.
In the current study, researchers were able to trace the abundance of 3HP molecules in the DL238 strain to a variation in the hphd-1 gene, which allows 3HP to accumulate. To compensate for the excess 3HP, the DL238 C. elegans developed a mechanism for “shunting” the excess molecule out of the animal cells by cojoining 3HP with amino acids. This keeps the 3HP molecule from building to toxic levels and may be an adaptation to changing nutrient conditions, according to Walhout, who referred to the system as “a shunt within a shunt.”
The study shows the power of moving toward a pan-species metabolic network model for deep biological investigations. “We’re just starting to scratch the surface,” said Walhout. “Our study only uses four strains, but the next step is to see what we find when we look at 100 different strains. Or what happens when we use the same strain but vary the diets.
“We’ve put together a really robust model for measuring metabolic variation between individuals,” said Walhout. “What made this possible, more than anything, is our unique, multidisciplinary collaboration. It’s the expertise that each lab brought to this project that enabled this discovery.”
The ZCCHC14/TENT4 complex is required for hepatitis A virus RNA synthesis
by You Li, Ichiro Misumi, Tomoyuki Shiota, Lu Sun, et al in Proceedings of the National Academy of Sciences
The viral replication cycle is crucial for a virus to spread inside the body and cause disease. Focusing on that cycle in the hepatitis A virus (HAV), UNC School of Medicine scientists discovered that replication requires specific interactions between the human protein ZCCHC14 and a group of enzymes called TENT4 poly(A) polymerases. They also found that the oral compound RG7834 stopped replication at a key step, making it impossible for the virus to infect liver cells.
These findings are the first to demonstrate an effective drug treatment against HAV in an animal model of the disease. “Our research demonstrates that targeting this protein complex with an orally delivered, small-molecule therapeutic halts viral replication and reverses liver inflammation in a mouse model of hepatitis A, providing proof-of-principle for antiviral therapy and the means to stop the spread of hepatitis A in outbreak settings,” said senior author Stanley M. Lemon, MD, professor in the UNC Department of Medicine and UNC Department of Microbiology & Immunology, and member of the UNC Institute for Global Health and Infectious Diseases.
Lemon, who in the 1970s and 80s was part of a Walter Reed Army Medical Center research team that developed the first inactivated HAV vaccine administered to humans, said research on HAV tapered off after the vaccine became widely available in the mid-1990s. Cases plummeted in the 2000s as vaccination rates skyrocketed. Researchers turned their attention to hepatitis B and C viruses, both of which are very different from HAV and cause chronic disease. “It’s like comparing apples to turnips,” Lemon said. “The only similarity is that they all cause inflammation of the liver.” HAV is not even part of the same virus family as hepatitis B and C viruses.
Hepatitis A outbreaks have been on the rise since 2016, even though the HAV vaccine is very effective. Not everyone gets vaccinated, Lemon pointed out, and HAV can exist for long periods of time in the environment — such as on our hands and in food and water — resulting in more than 44,000 cases, 27,000 hospitalizations and 400 deaths in the United States since 2016, according to the CDC.
Several outbreaks have occurred over the past several years, including in San Diego in 2017 driven largely by homelessness and illicit drug use, causing severe illness in about 600 people and killing 20. In 2022, there was a small outbreak linked to organic strawberries in multiple states, leading to about a dozen hospitalizations. Another outbreak in 2019 was linked to fresh blackberries. Globally, tens of millions of HAV infections occur each year. Symptoms include fever, abdominal pain, jaundice, nausea, and loss of appetite and sense of taste. Once sick, there is no treatment.
In 2013, Lemon and colleagues discovered that the hepatitis A virus changes dramatically inside the human liver. The virus hijacks bits of cell membrane as it leaves liver cells, cloaking itself from antibodies that would have otherwise quarantined the virus before it spread widely through the blood stream. This work provided insight into how much researchers had yet to learn about this virus that was discovered 50 years ago and has likely caused disease dating back to ancient times.
A few years ago, researchers found that hepatitis B virus required TENT4A/B for its replication. Meanwhile, Lemon’s lab led experiments to search for human proteins that HAV needs in order to replicate, and they found ZCCHC14 — a particular protein that interacts with zinc and binds to RNA.
“This was the tipping point for this current study,” Lemon said. “We found ZCCHC14 binds very specifically to a certain part of HAV’s RNA, the molecule that contains the virus’s genetic information. And as a result of that binding, the virus is able to recruit TENT4 from the human cell.”
In normal human biology, TENT4 is part of an RNA-modification process during cell growth. Essentially, HAV hijacks TENT4 and uses it to replicate its own genome. This work suggested that stopping TENT4 recruitment could stop viral replication and limit disease. Lemon’s lab then tested the compound RG7834, which had previously been shown to actively block Hepatitis B virus by targeting TENT4. The researchers detailed the precise effects of oral RG7834 on HAV in liver and feces and how the virus’s ability to cause liver injury is dramatically diminished in mice that had been genetically modified to develop HAV infection and disease. The research suggests the compound was safe at the dose used in this research and the acute timeframe of the study.
“This compound is a long way from human use,” Lemon said, “But it points the path to an effective way to treat a disease for which we have no treatment at all.”
The pharmaceutical company Hoffmann-La Roche developed RG7834 for use against chronic hepatitis B infections and tested it in humans in a phase 1 trial, but animal studies suggested it may be too toxic for use over long periods of time.
“The treatment for Hepatitis A would be short term,” Lemon said, “and, more importantly, our group and others are working on compounds that would hit the same target without toxic effects.”
Genome‐wide transcriptomic changes reveal the genetic pathways involved in insect migration
by Toby Doyle, Eva Jimenez‐Guri, Will L. S. Hawkes, Richard Massy, Federica Mantica, Jon Permanyer, Luca Cozzuto, Toni Hermoso Pulido, Tobias Baril, Alex Hayward, Manuel Irimia, Jason W. Chapman, Chris Bass, Karl R. Wotton in Molecular Ecology
Scientists have identified more than 1,500 genetic differences between migratory and non-migratory hoverflies.
A team led by the University of Exeter captured migrating insects as they flew through a mountain pass, and sequenced active genes to identify which determine migratory behaviour. This genetic information was then compared to that of non-migrating summer hoverflies.
“We identified 1,543 genes whose activity levels were different in the migrants,” said lead author Toby Doyle, of the Centre for Ecology and Conservation on Exeter’s Penryn Campus in Cornwall. “What really struck us though was the remarkable range of roles these genes play.
“Migration is energetically very demanding, so finding genes for metabolism was no surprise but we also identified genes with roles in muscle structure and function, hormonal regulation of physiology, immunity, stress resistance, flight and feeding behaviour, sensory perception and for increasing longevity.”
Each autumn, billions of migratory hoverflies leave northern Europe and make a long-distance journey south. Their journey takes them through the Pyrenees where they become concentrated through high mountain passes.
“It is an amazing spectacle to witness, an endless stream of hundreds of thousands of individuals through a 30-metre pass,” said Dr Karl Wotton.
When the researchers started ordering these genes by function, they discovered suites of genes were being activated in concert: insulin signalling for longevity, pathways for immunity, and those leading to octopamine production, the insect equivalent of the fight or flight hormone adrenaline, for long-distance flight.
“These pathways have been integrated into migratory hoverflies and modified by evolution to allow for long-distance movement,” Dr Wotton said.
The work provides a powerful genomic resource and theoretical framework to direct future studies into the evolution of migration.
Dr Wotton added: “It is an exciting time to be studying the genetics of migration. “Our research has already indicated several genes that have previously been associated with migration in butterflies, suggesting the existence of a shared ‘migratory gene package’ that controls migration across multiple animals.”
Scalability of genetic biocontrols for eradicating invasive alien mammals
by Aysegul Birand, Phillip Cassey, Joshua V. Ross, Paul Q. Thomas, Thomas A. A. Prowse in NeoBiota
Invasive alien mammals can have catastrophic impacts on native flora and fauna, causing species extinctions and driving profound environmental change. Classical control methods such as poison baiting, trapping, or hunting are currently not feasible on a large scale, which is why researchers are looking for alternatives.
CRISPR-based genome engineering is often seen as a “silver bullet” for pest control. Despite the increasing interest in the development of this technology for invasive mammals like mice, rats, rabbits, feral cats, and foxes, studies have so far only focused on mice.
Scientists have been pondering whether genome editing technologies could help eradicate larger mammals, and if so, how long it would take. In order to address these questions, a team of researchers from the University of Adelaide developed a mathematical model able to simulate the impact of gene drives on mammal populations at a landscape scale. Their study is the first to estimate the time it would take to eradicate long-lived alien mammals.
Using CRISPR-Cas9 technology, the simulated gene drive relies on “molecular scissors” inserted into the Y-chromosome that target and slice up the X-chromosome at the right time during meiosis, so that only Y-chromosome carrying sperms are functional and can successfully fertilize the egg. In this way, the drive carrying males should only produce sons that also carry the molecular scissors on their Y-chromosome. Over multiple generations, females will become rarer and produce fewer offspring; as a result, the population size will fall.
This “X-shredder” drive has been successfully developed and demonstrated to suppress cage populations of malaria-carrying mosquitos, but has not yet been developed in mammals. The model shows that the X-shredder drive could potentially achieve landscape-scale eradication of mice, rats, rabbits, feral cats, and red foxes, but the probability of success and the time it would take to eradicate them vary greatly.
The researchers investigated the ability of the X-shredder drive to eradicate a population of 200,000 individuals of each species. “CRISPR-based gene drives offer novel solutions for controlling invasive alien species, which could ultimately extend eradication efforts to continental scales,” they concluded. The method could be effective in small-sized pests, such as rodents and rabbits. The expected time to eradication is 18 years for mice, 19 years for rats, and 48 years for rabbits, with 90% population suppression achieved in around half those times. However, the results suggest that gene drives are not a one-size-fits-all solution: they might not be so useful in larger species like cats and foxes.
“The probability of eradicating feral cats with gene drives is identical to flipping a coin, 50/50; and provided that the coin lands on the right side, it would take about 140 years to get rid of them,” says Dr. Aysegul Birand, part of the research team. “The probability of eradication is higher for foxes, but the wait is even longer.”
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