Daejeon (South Korea): DNA is widely recognized as the blueprint for life, and it is required for an organism to assist biological functions. DNA may be damaged by a variety of circumstances, including radical metabolites, radiation, and some toxic compounds. Because DNA is a two-stranded molecule, any one or both strands can be damaged. When one of the two strands of DNA is damaged or broken, a single-strand break (SSB) occurs. These are very minor damages that can be quickly repaired by specialized enzymes that seal the break and restore the DNA molecule's integrity. A double-strand break (DSB), on the other hand, occurs when both strands of DNA are broken. These are the most severe types of DNA damage, with the potential to cause genetic alterations or cell death. Cells preserve genomic integrity by having many repair mechanisms for DSBs. Among the several DSB repair processes, homologous recombination repair (HR) is a highly accurate and error-free technique that employs the undamaged sister chromatid as a template to repair DSBs. However, DNA repair through polymerase theta-mediated end-joining (TMEJ) might result in the loss of some genetic material and the development of mutations. To maintain genomic integrity, it is critical to select the optimal DSB repair method. But How do cells select the right repair process? And what kinds of proteins are involved in the selection process? Led by Professor MYUNG Kyungjae, Director of the Center of Genomic Integrity (CGI) within the Institute for Basic Science (IBS), the research teams of Professor LEE Ja Yil at Ulsan National Institute of Science and Technology, and Professor OH Jung-Min at Pusan National University have discovered that repair proteins involved in DSB repair, mismatch repair, and TMEJ are closely related and interact with each other during DSB repair process.  There are various repair mechanisms in our cells, each tailored to the type of DNA damage. For instance, DSBs are repaired by DSB repair proteins, while improperly paired DNA bases are repaired by mismatch repair proteins. Until now, most researchers thought that a specific type of DNA damage is only repaired by its corresponding DNA repair mechanism. However, this study revealed that repair proteins previously thought to be responsible for different repair mechanisms can interact with each other to recognize damaged sites and select an appropriate repair mechanism. Specifically, it was revealed that MSH2-MSH3, a DNA mismatch repair protein, actually plays a crucial role in the DSB repair process. The researchers observed the recruitment of fluorescent protein-labeled MSH2-MSH3 protein to the site of DSBs and revealed that this movement occurs through binding with the chromatin remodeling protein called SMARCAD1. The binding of MSH2-MSH3 to DSBs facilitates the recruitment of EXO1 (exonuclease 1) for long-range resection of damaged DNA. After the long-range resection, the damaged DNA is repaired through error-free HR. Furthermore, it was discovered that the binding of MSH2-MSH3 inhibits the access of POLth, which mediates a more error-prone TMEJ pathway, thereby preventing mutations that may occur during DSB repair. Director Myung said, "This research has revealed a new function of the mismatch repair protein MSH2-MSH3 in regulating DSB repair," adding, "The repair proteins that have been believed so far to act independently in the mismatch repair, double-stranded break repair, and TMEJ repair pathways are now shown to closely interact each other for proper maintenance of genomic integrity." (ANI)

DNA is widely recognized as the blueprint for life, and it is required for an organism to assist biological functions

Study reveals how cells select DNA damage repair pathways

Washington: Lead author Carolyn Elya, a postdoctoral researcher in the Department of Organismic and Evolutionary Biology at Harvard, describes the molecular and cellular mechanisms underlying the ability of the parasitic fungus Entomophthora muscae (E. muscae) to influence the behaviour of fruit flies in a new study published in eLife. In a paper that was published in eLife in 2018, Elya provided the first description of the altered behaviour, known as summiting. Elya, a doctoral student at the University of California (UC) Berkeley, used rotting fruit as bait to catch wild fruit flies as she researched the bacteria that fruit flies carry. When she later checked to see if she had managed to catch any, she discovered zombie flies with an intriguing stance and an abdomen banding pattern. Elya was able to confirm the hypothesised cause, E. muscae, through the extraction and sequencing of DNA. Summiting occurs at sunset when the infected flies climb to an elevated location and extend their proboscises to the surface. A sticky droplet that emerges from the proboscis adheres the fly to the surface right before the wings raise up and away from the body and the flies die. "The climbing is very important as it positions the fly in an advantageous location for the fungus to spread to the most possible hosts," says Elya. "The fungus jumps to the new host by forming very specialized and temporary structures that burst through the fly's skin and shoots spores into the environment that are only good for a handful of hours. It's a fleeting process, so an advantageous position is everything to survival." While at UC Berkeley, Elya developed a laboratory model she refers to as the Entomophthora muscae-Drosophila melanogaster 'zombie fly' system using the wild fungal isolate she found in her backyard. With this system, Elya could continuously infect fruit flies - a laboratory staple, as well as culture the fungus independently of the fly host in media thought to mimic the internal environment of the fly.  Summiting has appeared several times in scientific literature, but studies had only been observations of dead house flies. No one had ever observed how flies behave in their last hours of life. Elya set out to fill this knowledge gap of what happens when flies summit by developing a high-throughput behavioural assay to automatically track hundreds of infected flies. While using this platform to monitor the behaviour of flies becoming zombies, she encountered a surprise. "We found that summiting is not about climbing," said Elya, "it's actually this burst of locomotor activity that starts about two and a half hours before the flies die." With this discovery, Elya and co-authors paired her system to create on-demand zombie flies with the lab's powerful fruit fly genetic toolkit. With these and the author's new behaviour assay, they could identify genes and neurons required for flies to summit. "Overall, we found the flies' hormonal axes were mediating summiting behaviour. When we silenced these neurons the flies were really bad at summiting," Elya says. These neurons send projections to a neurohemal organ that produces the juvenile hormone, a hormone conserved in insects. "We think the fungus is actually driving the activity of these neurons in order to drive the release of this hormone, which is causing the flies to have this burst of locomotor activity." Elya and co-authors were then able to collect a behavioural dataset consisting of hundreds of infected flies, which they then used to train a computer to identify flies as they are summiting. This classifier tool enabled the team to discover that fungal cells invade the fly's brains in an organized way, occupying specific regions of the brain during summiting. Interestingly, the team also discovered that the flies' blood-brain barrier is compromised when exposed to the fungus. Normally the neurons are protected from the blood that's circulating through the fly's body. The breakdown of the blood-brain barrier has important consequences for what the neurons are being exposed to, potentially allowing things that are circulating in the blood to interact with neurons in the brain, thus providing a route for modulating neural activity. "We think this could be important for the way that the fungus is driving behavioural changes," Elya said, "and we actually found that you can pull blood from flies that are doing the summiting behaviour, put it into naive flies and drive some of this increased locomotion. So we've shown that there's at least the partial ability to recapitulate this summiting behaviour just by transferring fly blood." Elya says that these experiments show some blood-borne factors can drive summiting behaviour, though it's not yet clear what the identity of these factors is or who produces them (the fungus or the fly). (ANI)

Lead author Carolyn Elya, a postdoctoral researcher in the Department of Organismic 

Study examines the intentional enslavement of zombie flies by puppeteer fungus

California: Plants form relationships with microorganisms in the soil where they grow. For example, legumes benefit from a symbiotic connection with microorganisms that reside in nodules in their roots and "fix" nitrogen in the atmosphere so that it is accessible for bean development. But, in general, are microbes beneficial to plants? Or does competition for plant access across strains reduce the function the bacteria finally provide? Experiments were put up by a team of scientists from the University of California, Riverside, to address these issues and better understand the competitive process. Acmispon strigosus, a native California plant with nodules, and a collection of eight suitable nitrogen-fixing bacterial strains were utilised by the researchers. They infected several plants with each of the eight strains in order to directly test their capacity to infect and benefit the plants. They next infected additional plants with pairs of bacterial strains to evaluate each strain's competitive capacity and the influence on plant performance. The researchers discovered that competition between types of helpful bacteria in the soil reduces the service provided by the bacteria to their hosts. “More specifically, we found interstrain competition that occurs in the soil before the bacteria infect the plant causes fewer of the bacteria to colonize the plant, resulting in the plant gaining smaller benefits in the end,” said Joel Sachs, a professor of evolution, ecology, and organismal biology, who led the research team. “To understand symbiosis, we often use sterile conditions where one strain of bacteria is ‘inoculated’ or introduced into an otherwise sterile host. Our experiments show that making that system slightly more complex — simply by using two bacterial strains at a time — fundamentally shifts the balance of benefits that the hosts receive, reshaping our understanding of how symbiosis works.” Study results appear in the journal Current Biology. Sachs explained that a core challenge in agriculture is leveraging the services that microbes can provide to crops by promoting growth in a sustainable way, without the environmental costs of chemical fertilizers. His lab studies rhizobia — bacteria that promote plant growth. Rhizobial competition is a longstanding problem for sustainable agriculture. Rhizobia form root nodules on legumes, within which the bacteria fix nitrogen for the plant in exchange for carbon from photosynthesis. Growers have long sought to leverage rhizobia to sustainably fertilize staple legume crops such as soybean, peanuts, peas, and green beans.  “One might think using rhizobia as inoculants should allow growers to minimize the use of chemical nitrogen, which is environmentally damaging,” said Sachs, who chairs the Department of Evolution, Ecology, and Organismal Biology. “But such rhizobial inoculation is rarely successful. When growers inoculate their crops with high-quality rhizobia — strains that fix a lot of nitrogen — these ‘elite’ strains get outcompeted by indigenous rhizobia that are already in the soil and provide little or no benefit to hosts.” In their experiments, Sachs and his colleagues used bacterial strains whose genomes they had already sequenced. They also characterized the strains, which ranged from highly beneficial to ineffective at nitrogen fixation, to know exactly how beneficial they were to the target plant species. The researchers sequenced the contents of more than 1,100 nodules, each of which was from a plant that was inoculated with one of 28 different strain combinations. Next, the researchers developed mathematical models to predict how much benefit co-inoculated plants would gain based on expectations from plants that were “clonally infected” (infected with one strain). This allowed the researchers to calculate the growth deficit that was specifically caused by interstrain competition. “Our models showed that co-inoculated plants got much lower benefits from symbiosis than what could be expected from the clonal infections,” said Arafat Rahman, a former graduate student in Sachs’ lab and the first author of the research paper. “While beneficial bacteria work well in the lab, they get out-competed in the natural environment. Ultimately, we want to find a strain of bacteria — or a set of them — that gives maximum benefit to the host plant and is competitive against bacterial strains that are already in the soil.” Sachs explained that to discover and develop a bacterial strain that is highly beneficial to plants, scientists need to conduct experiments under very clean conditions.  “Ultimately, we want to use beneficial bacteria in agriculture,” he said. “To identify these bacteria, we would, typically, add one bacterial strain to a plant in the lab and show that the plant grows much better with the strain than without. In the field, however, that plant is covered in microbes, complicating the story. In our experiments, we advanced from using one strain to a pair of strains to see what impact that has on plant growth. Interestingly, with just two strains, many of our predictions fell apart.” Rahman stressed that while experiments are needed to ascertain how beneficial a bacterial strain is, experiments that test how competitive the strain is against a panel of other bacterial strains are also needed. “Both steps are crucial,” he said. “Our work found some of the best strains can be highly beneficial to plant growth but as soon as you pair them with any other strain, that benefit is greatly reduced. Further, it is important to know at which stage the interstrain competition takes place: before the bacteria interact with the plant or after? Our work suggests it’s the former and provides a useful guide to designing future experiments aimed at discovering strains that are better for delivery in crops.” Sachs said that in a lot of current experimental designs the focus is on the benefit to plants.  “It’s important, however, to keep in mind that bacteria are shaped by natural selection,” he said. “Some of them may be highly competitive in entering the nodule to infect the plant but not be very beneficial to the plant and that could be a trait that wins out in nature. If we are to leverage microbial communities for the services they can provide to plants and animals, we need to understand interstrain dynamics in these communities.” According to Sachs and Rahman, sustainable growth practices need to be a critical aspect of new agriculture to feed a growing population on a limited resource base.  “This will require moving past polluting methods such as adding huge amounts of chemical nitrogen to soil,” Sachs said. “Understanding how to efficiently deliver beneficial microbes to a target host is a central challenge in medicine, agriculture, and livestock science. By revealing that interstrain dynamics can reduce the benefits of symbiosis, our work has opened new avenues of research to improve sustainable agricultural practices.” —ANI

Plants form relationships with microorganisms in the soil where they grow. For example

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Study reveals how cells select DNA damage repair pathways

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Study reveals how cells select DNA damage repair pathways

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