GN/ Dynamics of DNA replication ‘licensing’ revealed
Genetics biweekly vol.20, 17th January — 31st January
TL;DR
- A new study has illuminated an important process that occurs during cell division and is a likely source of DNA damage under some circumstances, including cancer.
- Researchers show how a DNA-binding protein can search the entire genome for its target sequence without getting held up on the way. The result contradicts our current understanding of gene regulation — the genetic code affects how often the proteins bind, but not for how long.
- The scientists who discovered all-female termite colonies have now ascertained how they came to exist. In doing so, they revealed how these powerful females potentially threaten other termites, as well as homeowners.
- A protein that masterminds the way DNA is wrapped within chromosomes has a major role in the healthy functioning of blood stem cells, which produce all blood cells in the body, according to a new study.
- An international research team has established a link between gut microbiota and chronic inflammatory diseases such as arthritis. The team has discovered that a protein naturally present in the gut acts on the microbiota and causes the formation of molecules that exacerbate the symptoms of these diseases.
- Even at high concentrations, antibiotics won’t kill all bacteria. There are always a few survivors, even in a bacterial population that is genetically identical. Scientists have discovered that these survivors share a common feature: they accumulate acid in their cells.
- New research into how viral proteins interact and can be disabled holds promise to help plants defend themselves against viruses — and ultimately prevent crop losses. The study found that viral proteins interact with each other to help a virus hijack its host plant and complete its life cycle. When some of these viral proteins were disabled, the researchers found that the virus could not move from cell to cell.
- In a new study of the Zika virus, scientists have discovered a key mechanism used by the virus to evade the antiviral response of the cell it is attacking. This finding contributes to a better understanding of how viruses infect cells, overcome immune barriers and replicate — information that is essential for fighting them.
- Researchers conducted single-cell gene expression analysis to uncover the effects of manipulation of the sensory cell regulator POU IV in the protovertebrate Ciona intestinalis. Alteration of POU IV expression led to the induction of cells with characteristics of multiple sensory cell types and cells that express a gene expression profile that has not been previously observed in Ciona intestinalis. The activation of upstream POU IV regulators Foxg and Neurogenin was identified as a possible mechanism underlying the unusual sensory cell development.
- Popular belief has been that small dogs, such as Pomeranians and Chihuahuas, exist because once dogs were domesticated, humans wanted small, cute companions. But researchers now identify a genetic mutation in a growth hormone-regulating gene that corresponds to small body size in dogs that was present in wolves over 50,000 years ago, long before domestication.
- 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
The consequences of differential origin licensing dynamics in distinct chromatin environments
by Liu Mei, Katarzyna M Kedziora, Eun-Ah Song, Jeremy E Purvis, Jeanette Gowen Cook in Nucleic Acids Research
A new study from scientists at the UNC School of Medicine has illuminated an important process that occurs during cell division and is a likely source of DNA damage under some circumstances, including cancer.
The scientists devised a sophisticated experimental platform for studying the process called “origin licensing.” Cells use this process to regulate, or “license” the replication of their genomes during cell division.
The researchers revealed for the first time the dynamics of this process. They showed in particular how these dynamics differ — and bring different risks of DNA damage during replication — in the two basic states of genomic DNA, the “euchromatin” state which is relatively loose and open for gene activity, and the “heterochromatin” state which is wound more tightly to silence gene activity.
“Our findings may help explain, for example, why certain portions of the genome are relatively susceptible to DNA damage during replication in some cancer cells,” said study senior author Jean Cook, PhD, professor of biochemistry and biophysics at the UNC School of Medicine and member of the UNC Lineberger Comprehensive Cancer Center.
Origin licensing occurs in the initial, preparatory phase of cell replication, known as the G1 phase. It involves sets of special enzymes that attach to the DNA in chromosomes at various locations where DNA-copying is to originate. The enzymes essentially license the copying of DNA so that cells don’t copy their genomes more than once.
Cook and other scientists have described in prior studies the basic process of origin licensing, and have identified proteins that make it happen. But this study, for the first time, revealed in detail how the process unfolds over time in cells as they prepare for cell division. Study first author Liu Mei, PhD, a postdoctoral fellow in the Cook laboratory, combined still and time-lapse microscopic imaging techniques to accomplish this feat.
“What Liu did was incredibly painstaking and meticulous, a technical tour de force,” Cook said.
As an initial demonstration of her experimental platform, Mei compared the origin licensing process, with its loading of licensing enzymes, in the two main states of the genome — euchromatin and heterochromatin. She found an important difference.
“Essentially heterochromatin — more compacted DNA — loads these licensing enzymes relatively late compared to what we observe in the more open euchromatin,” Mei said.
This finding hinted, at least, that in dividing cells with an abnormally shortened G1 phase, the more compacted DNA in the cell genome might never be fully licensed for replication, potentially resulting in large mutations during replication and even cell death. Confirming this possibility, the researchers found that when they artificially shortened the G1 phase in test cells, there was significantly more under-replication and DNA damage in heterochromatin regions of the cells’ genomes, compared to the euchromatin regions.
Cells can have a shortened G1 phase for different reasons, including due to cancer. Thus the study suggests that the “genomic instability” or tendency to develop more mutations of some cancer types, as well as the genomic locations of that instability, might be explained in part by faulty origin licensing.
The study also establishes the researchers’ experimental platform as a tool for further studies of origin licensing dynamics and genomic instability, studies that might someday yield new strategies against cancers, for example.
Sequence specificity in DNA binding is mainly governed by association
by Emil Marklund, Guanzhong Mao, Jinwen Yuan, Spartak Zikrin, Eldar Abdurakhmanov, Sebastian Deindl, Johan Elf in Science
Researchers at Uppsala University show how a DNA-binding protein can search the entire genome for its target sequence without getting held up on the way. The result contradicts our current understanding of gene regulation — the genetic code affects how often the proteins bind, but not for how long.
Over an organism’s lifetime, its genome changes very little. What does change, constantly, are which proteins the cell produces in response to damage, changes in the environment, or stages in the reproductive cycle. The protein production is regulated by DNA-binding proteins that have evolved the ability to turn different genes on or off. Because the environment can change quickly, rapid adaptation is key. The DNA-binding proteins must find the correct DNA code among millions of base pairs, and do so fast.
When DNA-binding proteins search the genetic code for their target sequence, they slide along the DNA helix to speed up the process. When they finally find the right spot, they stay there; the interaction with the “correct” sequence prevents them from sliding along. This mechanism has been widely accepted to describe the search process. It is an appealing hypothesis, yes, but it presents an annoying problem — the DNA code is full of “almost correct” sequences. If the time a protein resides on a particular DNA motif was determined by the sequence, the searching proteins would constantly linger on sequences that resembled their target.
“If the textbook explanation was correct, the DNA-binding proteins would get stuck all the time off target. Gene regulation would be very ineffective, but we know from previous studies that this is not the case. Our favorite protein, LacI, finds its target sequence among 4.6 million base pairs in a matter of minutes,” says Emil Marklund, one of the researchers behind the discovery.
In an attempt to resolve this paradox, the researchers allowed the DNA-binding protein LacI to slide back and forth on thousands of different DNA sequences mounted on a microchip. A fluorescent molecule was attached to the LacI protein and made it possible to measure how fast LacI adhered to the different sequences and how quickly it was released. The result was striking. Contradicting previous assumptions, the DNA sequence had little effect on how long LacI remained bound to the DNA. However, it was much more likely that the sliding LacI was held up briefly when the sequence was similar to the target sequence. In other words, DNA-binding proteins often leave also the sequence they are intended to regulate, but at the target site, they all but always make a very short journey before finding their way back again. On the macroscopic time scale, this looks like a stable interaction.
“Our result, that DNA-binding proteins bind often rather than protractedly, explains how LacI can slide on the DNA sequence in search of its target without getting held up unnecessarily. LacI regulates the uptake of lactose in bacteria, but is of course just an example. The hundreds of different transcription factors that regulate our own genes likely act according to a similar principle,” says Johan Elf, Professor at the Department of Cell and Molecular Biology at Uppsala University and the national research infrastructure SciLifeLab.
Enhanced heterozygosity from male meiotic chromosome chains is superseded by hybrid female asexuality in termites
by Toshihisa Yashiro, Yi-Kai Tea, Cara Van Der Wal, Tomonari Nozaki, Nobuaki Mizumoto, Simon Hellemans, Kenji Matsuura, Nathan Lo in Proceedings of the National Academy of Sciences
Four years ago, entomologists at the University of Sydney discovered the existence of all-female, forest-dwelling drywood termite colonies in Japan. Now, they have determined how they evolved, and the implications of insect ‘girl power’ for established termite species (hint: they’re bad).
Their new research shows all-female colonies of drywood termites (Glyptotermes nakajimai) developed through unwitting human-assisted hybridisation some time in the last century. Females from one lineage mated with males from another, as one lineage was unknowingly moved from a smaller island to mainland Japan, likely via boat. Their hybrid offspring are more genetically diverse, and likely to be more robust.
In addition to stronger offspring, the all-female colonies can clone themselves and do not require a male to procreate, resulting in double the amount of breeding. According to the researchers, this is bad news for the incumbent, non-hybrid species, which can be outcompeted by its hybrid relatives.
It’s also potentially bad news for property owners. Drywood termites, as their name suggests, do not require moist conditions to burrow into and eat wooden beams, walls, floors or furniture, and are commonly moved around the world by trade, opening the door to hybridisation events. Once an infestation occurs, it can be difficult to eradicate, potentially leading to structural damage to a building, or even collapse.
Professor Nathan Lo, who led the study with University of Sydney Postdoctoral Fellow Toshihisa Yashiro, said his findings have implications for biosecurity: “Our study highlights the importance of making sure termites from overseas are not permitted to establish themselves. If they were to hybridise with local termites, it might lead to even nastier lineages of termites for homeowners to deal with.”
Aside from discerning how the female colonies evolved, the researchers also studied several drywood termitecolonies with males and females, which contained a quirk: the sperm of males consisted of either 15 Y or 15 X chromosomes, out of a total of 17. In most species, including humans, male sperm have only a single Y or X chromosome (out of 23, in the case of humans).
“It’s really weird,” said Professor Lo, who posits that this occurred out of necessity. “Termite offspring can inherit nests from their parents, saving them the trouble of venturing into the dangers of the outside world, burrowing into wood, and creating their own nests. The problem with nest inheritance is that it results in a lot of inbreeding — sisters mate with brothers, and offspring may even mate with parents.
“As a solution, male termites probably evolved to have multiple Y chromosomes, making them harbour more genetic diversity than females. So, even if a sister and brother mate, they can produce viable offspring.”
The researchers say that this chromosomal pattern is found in some other organisms, including plants and huntsman spiders, but not usually to the extremes found in drywood termites.
Histone variant H3.3 maintains adult haematopoietic stem cell homeostasis by enforcing chromatin adaptability
by Peipei Guo, Ying Liu, Fuqiang Geng, Andrew W. Daman, Xiaoyu Liu, Liangwen Zhong, Arjun Ravishankar, Raphael Lis, José Gabriel Barcia Durán, Tomer Itkin, Fanying Tang, Tuo Zhang, Jenny Xiang, Koji Shido, Bi-sen Ding, Duancheng Wen, Steven Z. Josefowicz, Shahin Rafii in Nature Cell Biology
A protein that masterminds the way DNA is wrapped within chromosomes has a major role in the healthy functioning of blood stem cells, which produce all blood cells in the body, according to a new study from researchers at Weill Cornell Medicine.
The protein, known as histone H3.3, organizes the spool-like structures around which DNA is wrapped in plants, animals and most other organisms. Histones enable DNA to be tightly compacted, and serve as platforms for small chemical modifications — known as epigenetic modifications — that can loosen or tighten the wrapped DNA to control local gene activity.
The study examined H3.3’s role in blood stem cells, also known as hematopoietic stem cells (HSCs), that are a major focus of efforts to develop stem-cell-based medicine. Normally most HSCs stay in a stem-like, uncommitted state where they can survive long-term, slowly self-renewing, while some HSCs mature or “differentiate” to produce all the different lineage-specific blood cell types. The study found that H3.3 is crucial for both processes; deleting the protein from HSCs led to reduced HSC survival, an imbalance in the types of blood cell produced by the HSCs and other abnormalities.
“How hematopoietic stem cells coordinate their self-renewal and differentiation into various blood cell types in a balanced way has been a mystery to a great extent, but this study helps us understand those processes much better at the molecular level and gives us many new clues to pursue in further investigations,” said study co-senior author Dr. Shahin Rafii, director of the Ansary Stem Cell Institute, chief of the Division of Regenerative Medicine and the Arthur B. Belfer Professor in Genetic Medicine at Weill Cornell Medicine.
The study was a collaboration that also included co-first and co-senior authors Dr. Ying Liu and Dr. Peipei Guo, who are senior instructors in the Rafii Laboratory; co-senior author Dr. Duancheng Wen, assistant professor of reproductive medicine research in obstetrics and gynecology; and co-author Dr. Steven Josefowicz, assistant professor of pathology and laboratory medicine and a member of the Sandra and Edward Meyer Cancer Center, all of Weill Cornell Medicine.
HSCs are among the most studied stem cells because of their importance in health and disease, and their potential in regenerative medicine. A single HSC can give rise to all blood cell types, from red blood cells and platelets to T cells, B cells and pathogen-engulfing macrophages. A more precise understanding of how HSCs work could lead to many applications including lab-grown blood for transfusions, and better HSC transplants for cancer patients. In addition, understanding how HSCs, upon acquiring aberrant mutations, give rise to leukemias could lead to development of new therapies for these often-refractory malignant diseases.
H3.3 also has been a major focus of interest for biologists in recent years, as evidence of its importance in HSCs and other stem cells — and its role in various cancers when mutated — has mounted. But just what histone H3.3 does in HSCs, and in other cell types where it appears, has been far from clear.
“Added to the complexity of this project, is that two different genes (H3.3A and H3.3B) code for the same H3.3 protein. Therefore, we had to painstakingly delete both genes in mice by genetic engineering, a herculean task that required a great deal of genetic manipulation of stem cells,” Dr. Wen said.
“Our powerful mouse model allows inducible and complete deletion of the H3.3 protein in all organs, or specific types of organs, at selected developmental stage of a mouse,” said Dr. Liu, who is also a research associate in Dr. Rafii’s lab. “Employing this approach, we showed that H3.3’s absence in adulthood primarily causes a depletion of the long-term, self-renewing HSCs on which future blood-cell production depends. At the same time, affected HSCs differentiated into mature blood cell types with an abnormal skew or bias towards certain types of white blood cell, including granulocytes and macrophages.
“Most importantly, we found evidence that H3.3 has its effects on HSCs in part by anchoring several key epigenetic marks at developmental genes and endogenous retroviruses (ERVs),” she added, “which are remnants of viruses that once inscribed themselves into our distant evolutionary ancestors’ DNA.”
“One intriguing observation was that H3.3’s deletion caused the loss of epigenetic marks that normally suppress ERVs, which led in turn to the activation of an inflammatory response in affected cells, and then drove the cells’ skewed production of blood cell types — a skew that is similar to what is seen in some leukemias,” said Dr. Guo, who is also a research associate in Dr. Rafii’s laboratory.
“H3.3 appears to be acting as a master regulator of self-renewal and differentiation in HSCs — which is wild, and hints at a very broad potential as a therapeutic target someday,” said co-author Andrew Daman, a Weill Cornell Graduate School of Medical Sciences doctoral candidate in the Josefowicz lab.
“Our take-home message is that normal blood cell development requires the proper epigenetic regulation provided by H3.3,” Dr. Liu said.
The team now plans further studies, in HSCs and other cell types, to understand in more detail how H3.3 exerts its effects and what happens when it is absent. More importantly, developing approaches to monitor the H3.3 command of the epigenetic landscape could enable them to more effectively increase blood production. “Finally, our team is investigating how H3.3 controls the function of the nurturing niche cells, such as blood vessels that orchestrate stem cell self-renewal and possibly block the emergence of malignancies such as leukemias,” said Dr. Rafii, who is also a member of the Meyer Cancer Center.
Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids
by Plassais et al.in Current Biology
Popular belief has been that small dogs, such as Pomeranians and Chihuahuas, exist because once dogs were domesticated, humans wanted small, cute companions. But the researchers at the National Institutes of Health (NIH) identify a genetic mutation in a growth hormone-regulating gene that corresponds to small body size in dogs that was present in wolves over 50,000 years ago, long before domestication.
The search for this mutation had been ongoing at the NIH for over a decade, but researchers didn’t find it until Jocelyn Plassais, a postdoc in geneticist Elaine Ostrander’s lab, suggested that they search for sequences around the gene that were positioned backwards and confirm if any were present in other canids and ancient DNA. With this approach, their team found a reverse form of the insulin-like growth factor 1 (IGF1) gene with variants that correlated to dog body size. “We looked at 200 breeds, and it held up beautifully,” says Ostrander.
The researchers then collaborated with evolutionary biologists Greger Larson at Oxford University and Laurent Franz at Ludwig Maximilian University to look through ancient wolf DNA to see when the IGF-1 mutation first showed up. Scientists have theorized that dogs started out large and became smaller about 20,000 years ago, when they were domesticated, but this discovery presents the possibility of a new evolutionary narrative.
Indeed, when the team looked at the DNA of a 54,000-year-old Siberian wolf (Canis lupus campestris) they found that it, too, possessed the growth hormone mutation. “It’s as though Nature had kept it tucked in her back pocket for tens of thousands of years until it was needed,” says Ostrander.
The finding holds not just for dogs and wolves, but also for coyotes, jackals, African hunting dogs, and other members of the family of animals referred to as canids. “This is tying together so much about canine domestication and body size, and the things that we think are very modern are actually very ancient,” says Ostrander.
Ostrander and her team plan to continue to investigate the genes that regulate body size in dogs. “One of the things that is pretty cool about dogs is that because they have evolved so recently there aren’t actually a lot of body size genes,” she says. Canids have only 25 known genes that regulate body size, compared to several hundred in humans. “I really want to understand the whole continuum — from Chihuahuas to Great Danes,” says Ostrander.
The interaction of secreted phospholipase A2-IIA with the microbiota alters its lipidome and promotes inflammation
by Etienne Doré, Charles Joly-Beauparlant, Satoshi Morozumi, et al. in JCI Insight
An international research team has established a link between gut microbiota and chronic inflammatory diseases such as arthritis. The team led by Éric Boilard of Université Laval has discovered that a protein naturally present in the gut acts on the microbiota and causes the formation of molecules that exacerbate the symptoms of these diseases.
The protein in question, phospholipase A2-IIA, was discovered several years ago in the fluid that surrounds the joints of people with arthritis according to Dr. Boilard, a professor in the Faculty of Medicine at Université Laval and a researcher at CHU de Québec-Université Laval Research Centre. The protein was subsequently detected elsewhere in the body, notably in the gut where it is produced in abundance.
“It took a long time before we realized that it exhibits antibacterial activity,” said Dr. Boilard. “The protein interacts little with the membrane of human cells, but it has high affinity for bacterial membranes. It binds to these membranes and splits them, releasing small molecules such as fatty acids.”
To study the effect of this protein on gut microbiota, researchers used a line of transgenic mice. “These mice have the human gene that codes for phospholipase A2-IIA,” explained the researcher. “As they age, they spontaneously develop manifestations of chronic systemic inflammation.”
Experiments on these mice revealed that phospholipase alters the profile of bacterial lipids that end up in the gut. “By releasing fatty acids from the bacterial membranes, the protein produces proinflammatory lipids that exacerbate chronic inflammation and increase the severity of arthritis symptoms in these mice,” summed up Dr. Boilard.
In another article, Japanese researchers led by Makoto Murakami of the University of Tokyo demonstrated that the action of phospholipase on the gut microbiota of mice also affects psoriasis, another inflammatory disease, as well as skin cancer. “Three years ago, we realized that our respective teams were on the same track,” said Dr. Boilard. “We agreed to work together to shed light on this new lead.”
These breakthroughs could have therapeutic implications, he says. “The work of both teams suggests that local inhibition of phospholipase may alleviate the inflammatory process that exacerbates certain diseases. It also suggests that blocking the bacterial proinflammatory lipids produced in the gut by this protein could reduce symptoms in people with systemic inflammatory diseases. The next step in our work is to test these ideas in patients with arthritis.”
Mutations in respiratory complex I promote antibiotic persistence through alterations in intracellular acidity and protein synthesis
by Bram Van den Bergh, Hannah Schramke, Joran Elie Michiels, Tom E. P. Kimkes, Jakub Leszek Radzikowski, Johannes Schimpf, Silke R. Vedelaar, Sabrina Burschel, Liselot Dewachter, Nikola Lončar, Alexander Schmidt, Tim Meijer, Maarten Fauvart, Thorsten Friedrich, Jan Michiels, Matthias Heinemann in Nature Communications
Even at high concentrations, antibiotics won’t kill all bacteria. There are always a few survivors, even in a bacterial population that is genetically identical. Scientists at the KU Leuven (Belgium) and the University of Groningen (the Netherlands) discovered that these survivors share a common feature: they accumulate acid in their cells, which shuts down their protein synthesis.
Bacteria and other micro-organisms can become resistant to antimicrobials, which is a growing problem in medicine. Although new antimicrobial drugs are one solution, we can also help prevent resistance developing by adopting better treatment regimens using existing antimicrobials. But the very first step in the development of resistance is not very well understood, explains Bram Van den Bergh, postdoc at the Center for Microbiology at VIB — KU Leuven (Belgium): ‘Cells have to survive an initial antibiotic treatment before they become resistant to future treatments. I wanted to understand why these cells survive.’
In previous work, Van den Bergh noted that in clonal cultures of bacteria (where all cells are genetically identical), there are always a few cells that survive a treatment with antibiotics. ‘Maybe one in a thousand cells, or even only one in a hundred thousand, will survive. We cultured these survivors and treated them again, to evolve bacteria in the lab that are more antibiotic-tolerant.’ After only a few days of this directed evolution via treatment and recovery, already up to 50% of all cells would survive the antibiotics.
In the current work, genetic analysis showed that these survivors share mutations in one crucial cellular system: Respiratory Complex I. This is a vital part in the machinery that drives energy production in bacteria and beyond. Specifically, the mutations blocked the ability of this complex to pump protons out of the cells. This can lead to serious heartburn, as the cells can’t get rid of accumulating acid.
‘We wondered how this could lead to increased survival’, explains Van den Bergh. The solution started partially by chance during a meeting at a conference in Switzerland between his supervisor Jan Michiels and Matthias Heinemann, a specialist in cell metabolism and professor of molecular systems biology at the University of Groningen. Michiels gave a talk on cellular acidification, Heinemann presented data that showed that a problem in metabolism can lead to tolerance against antibiotics. The two scientists concluded they were studying the same phenomenon but from different perspectives.
This was in 2018 and it took a lot of lab work from several researchers to connect their observations and determine how cells escape the lethal effects of antibiotics. Heinemann: ‘Any metabolic disturbance will lead to increased acidity inside the cells. When the Respiratory Complex I can’t pump the protons out, the acidity will continue to increase. Eventually, this leads to a full shutdown of all protein-based processes and of the synthesis of new proteins. This renders the used antibiotics useless, as their mechanism of action is interference with protein synthesis.’
This is how the hyper tolerant mutants evolved in the lab survived treatment. Once the antibiotics were removed and the metabolic problem was restored, acidity was reduced and the cells rebooted. Van den Bergh: ‘We didn’t explore how they then acquire resistance, but there are different pathways that may lead to this, like an increase in mutation rate caused by stress, or simply a numbers game: more cells survive and the needed treatment time prolongs, so the chances increases that one of these cells picks up resistance.’ The discovery could help fight antibiotic resistance, for example, by adding existing drugs that reduce acidity in cells.
Heinemann and Van den Bergh believe there is still more to discover about these tolerance mechanisms. Van den Bergh: ‘We have evolved many other hyper tolerant mutants with different mutations, most of them in transport systems for ions or charged molecules. I would like to find out more about those and how the transport and balance of ions affect antibiotic tolerance’.
Identification and Functional Analysis of Four RNA Silencing Suppressors in Begomovirus Croton Yellow Vein Mosaic Virus
by Ying Zhai, Anirban Roy, Hao Peng, Daniel L. Mullendore, Gurpreet Kaur, Bikash Mandal, Sunil Kumar Mukherjee, Hanu R. Pappu in Frontiers in Plant Science
New research, led by Washington State University scientists, into how viral proteins interact and can be disabled holds promise to help plants defend themselves against viruses — and ultimately prevent crop losses.
The study found that viral proteins interact with each other to help a virus hijack its host plant and complete its life cycle. When some of these viral proteins were disabled, the researchers found that the virus could not move from cell to cell. These proteins are also doing double duty, inducing disease as well.
“These silencing suppressor proteins are interacting with each other in a seamless, highly coordinated lockstep dance to help the virus in overcome host defense,” said WSU virologist Hanu Pappu, the senior author on the paper. Insights into the dynamics of these interactions could provide clues for blocking them, Pappu added.
“We are using genome editing approaches to do exactly that,” he said. “The more we understand about how these viruses bring down defensive ‘shields’ and cause disease, the better chance we have of saving plants from viral invaders.”
A silent, behind-the-scenes arms race between plants and the viruses that prey on them has been going on for millions of years. Viral diseases cost more than a billion dollars in losses annually to food, feed, and fiber crops worldwide, according to the Food and Agriculture Organization (FAO) of the United Nations.
Plants have developed a sophisticated defense system to protect themselves from infection, involving highly choregraphed cellular events that are triggered by viral attack, Pappu said. Plants use a molecular defense called RNA interference, RNAi for short, that chops incoming viral nucleic acid, preventing the virus from commandeering host cells. Viruses in turn evolved, producing molecules called ‘silencing suppressor proteins’ that can disable their hosts’ RNAi defenses.
“Star Trek’s Federation-versus-Klingons is playing out in real life,” said Pappu. “When the plant senses an attack by a virus, its ‘shields’ go up. Viruses are finding ways to lower the shields or slip through them and eventually take over the plant.”
Pappu, the Chuey Endowed Chair and Samuel H. Smith Distinguished Professor in WSU’s Department of Plant Pathology, studies viral proteins that suppress or evade plant defenses, ultimately devising ways to help plants repel pathogens. He and his team have been studying a group of pathogens called geminiviruses — among the most crop-destructive viruses in many parts of the world.
Lead author Ying Zhai, a WSU research associate, set out to identify which viral proteins are suppressing defenses and understand how these molecules interact with other viral proteins upon infection. Working with Anirban Roy and his team at the Indian Agricultural Research Institute, she examined a specific, damaging geminivirus, the Croton yellow vein mosaic virus. Ying and Roy learned where the viral silencing suppressor is located within cells, how it interacts with cells and brings on symptoms, and how it helps the virus move from cell to cell.
Using a technique called confocal microscopy, which focuses a tight beam of light on a small target area, co-author Dan Mullendore at WSU’s Franceschi Microscopy and Imaging Center studied individual viral proteins and where they localize inside host cells.
While most viruses make one protein with a specific function to defeat their host, Zhai and Roy found that this geminivirus contained not just one but four different proteins that take part in bringing down plant defenses. Using highly sensitive molecular and microscopic methods, they found that these viral proteins were interacting to help the virus. When some were disabled, the virus could not spread in the plant.
The Human STAT2 Coiled-Coil Domain Contains a Degron for Zika Virus Interferon Evasion
by Jean-Patrick Parisien, Jessica J. Lenoir, Gloria Alvarado, Curt M. Horvath in Journal of Virology
The world knows SARS-CoV-2 intimately now, but there are more than 200 virus species capable of infecting humans and causing disease. And they all want to do the same thing: invade the host cells, hijack each cell’s machinery and reproduce. The human immune response system has numerous levels of robust defense, but many invading pathogens — as we are seeing now with the omicron variant — have a way to break through.
In a new study of the Zika virus, Northwestern University scientists have discovered a key mechanism used by the virus to evade the antiviral response of the cell it is attacking. This finding contributes to a better understanding of how viruses infect cells, overcome immune barriers and replicate — information that is essential for fighting them.
Zika virus is responsible for one of the most recent viral disease outbreaks prior to SARS-CoV-2, andthere are no vaccines or drugs for Zika disease.The Northwestern research reveals how the virus suppresses interferon signaling — a key player in initiating the antiviral immune response — to gain access to the cells. Identification of this specific virus-hostinteraction offers a new target for antiviral therapeutics.
“Here we looked at a Zika virus protein known to inhibit the antiviral response,” said Curt Horvath, the paper’s corresponding author. “Interferon signaling is the cell’s immediate response to an invader. If Zika can block this first line of defense, it can replicate in the cell.”
Horvath and his lab study the ability of a virus to suppress the human antiviral response. He is professor of molecular biosciences in the Weinberg College of Arts and Sciences and professor of medicine and of microbiology-immunology at Northwestern University Feinberg School of Medicine.
“Zika is a simpler virus than SARS-CoV-2, but SARS-CoV-2 does a lot of the same things to suppress the antiviral response,” Horvath said. “SARS-CoV-2 also does much more, which is one of the reasons it’s more harmful to us. Understanding how one virus escapes or modifies the host antiviral response may help us learn about other viruses and also contribute to pandemic preparedness.”
Zika, identified in humans in 1952, is a member of Flavivirus family that includes dengue, hepatitis C, yellow fever and others. The Northwestern paper describes how Zika virus, through a protein called NS5, targets a cellular antiviral immune response mediator, STAT2, to escape detection by host cells. The virus’ NS5 protein degrades the cellular host’s STAT2 protein, effectively shutting down the cell’s protective interferon response.
STAT2 is an essential component of the interferon response and a common target of Zika, dengue and other Flaviviruses. The mechanistic machinery involved in specific STAT2 targeting in human cells is poorly understood, Horvath said. The Northwestern findings add to the growing understanding of Zika virus immune evasion, identifying the essential NS5-STAT2 interface in cell-based functional experiments.
Horvath and his team used molecular biology, biochemistry and fluorescence microscopy techniques coupled with virus infections to characterize Zika virus-mediated immune evasion and to dissect the essential components of the Zika virus-STAT2 interaction. The researchers demonstrate that an elongated region of the STAT2 protein called a “coiled-coil domain” is necessary and sufficient for interaction with the Zika virus protein NS5, which tags STAT2 for proteasome-mediated degradation.
Identification of the NS5 protein-STAT2 protein interaction provides a target for creating new ways to fight infection, including compound screening and chemical biology to develop new probes and drugs or enable the formulation of new vaccines or antibody therapeutics.
Neuronal identities derived by misexpression of the POU IV sensory determinant in a protovertebrate
by Prakriti Paul Chacha, Ryoko Horie, Takehiro G. Kusakabe, Yasunori Sasakura, Mona Singh, Takeo Horie, Michael Levine in Proceedings of the National Academy of Sciences
When baking a cake, even a small change to your recipe can have a major impact on the final product. Recently, researchers in Japan have demonstrated that a small alteration in the gene expression “recipe” of the model organism Ciona intestinalis leads to a significant change in the development of sensory cells.
In a new study, a research group led by the University of Tsukuba investigated the role of homeobox gene POU IV in the development of neural sensory cells in the protovertebrate Ciona intestinalis, a type of sea squirt that develops from a tadpole-like larva. Ciona is useful as a model system to examine changes in gene expression during development and to evaluate how gene networks affect the development of different cell types.
During development, multiple types of sensory neurons arise in Ciona, including palp sensory cells (PSCs) and bipolar tail neurons (BTNs). The specification of these cell types is thought to be regulated by POU IV, which has a similar counterpart in vertebrates called BRN3. The research team at the University of Tsukuba sought to understand the role of POU IV in the development of sensory cell types in Ciona by manipulating POU IV expression during development and evaluating the resultant changes in gene expression at the single-cell level.
“Single-cell transcriptomic analysis allowed us to look at individual cells produced within the organisms and analyze how their gene expression profiles were altered as a result of changes in POU IV expression,” explains main author Professor Takeo Horie.
The research team found that alteration of POU IV expression led to the expanded expression of sensory cells, including novel hybrid cell types that shared characteristics of both PSCs and BTNs, as well as cells that expressed a unique battery of genes that has not been observed previously in Ciona, which the researchers termed a ‘synthetic gene battery’.
“To better understand the processes underlying our observations, we explored the expression of Foxg and Neurogenin, two upstream regulators of POU IV,” says Professor Horie.
The research team’s findings indicated that misexpression of POU IV leads to the activation of Foxg and Neurogenin, which may underlie the development of the hybrid sensory cells and the expression of the synthetic gene battery. This study sheds light on the potential effects of gene manipulation during development and highlights the need for precise strategies to eliminate the induction of unwanted cell types during cellular reprogramming.
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