READ ON IGB'S WEBSITE Many of the drugs we utilize in modern medicine are naturally produced by microbes. Penicillin, an antibiotic derived from certain molds, is one of the most notable natural products due to its recognition as one of the biggest advances in medicine and human health. As DNA sequencing has become cheaper and faster, scientists now have access to hundreds of thousands of microbial genomes and the natural products they produce. However, Doug Mitchell (MMG), the John and Margaret Witt Professor of Chemistry at University of Illinois, says this pales in comparison to the number of compounds these organisms have the capacity to make using the genetic pathways they possess. “This is just the tip of the iceberg,” said Mitchell. “There’s a disparity in what we know today in terms of known molecules versus what nature has the capacity to produce. Like 100 to one at least.” One group of natural products that has become a popular source of antibiotics are called ribosomally synthesized and post-translationally modified peptides, or simply, “RiPPs.” Traditional methods for accessing RiPPs are slow, and involve taking genes one by one and putting them into a model organism, like E. coli, to see what compound it produces. However, in a new paper resulting from a massive collaborative effort at the Carl R. Woese Institute for Genomic Biology, researchers were able to discover and characterize new RiPPs at an unprecedented speed and scale using the Illinois Biological Foundry for Advanced Biomanufacturing. iBioFAB is a laboratory automation system which can evaluate and assemble multiple synthetic gene pathways from hundreds of genes at once, something that would traditionally take many researchers and much more time to accomplish. This project features a collaboration between Mitchell’s lab, the lab of Huimin Zhao (BSD/GSE leader/CABBI/CGD/MMG), the Steven L. Miller Chair of chemical and biomolecular engineering, and the lab of Wilfred van der Donk (MMG), Richard E. Heckert Endowed Chair in Chemistry and Howard Hughes Medical Institute Investigator. The three co-first authors, Alex Battiste, fourth year PhD student in the Mitchell lab, Chengyou Shi, fifth year PhD candidate in the Zhao lab, and Richard Ayikpoe, a postdoc in the van der Donk lab, described how they each led a part of the project in their respective labs. Shi’s team ordered synthetic genes and then assembled them into candidate pathways, or gene clusters, using iBioFAB integrated with a genome mining program called RODEO. Then, different classes of the gene clusters were given to Battiste and Ayikpoe’s teams to test which pathways were functional and likely to produce new RiPPs in E. coli. Any structures of RiPPs that showed antibiotic activities were characterized in detail by Ayikpoe’s team. The high-throughput technology allowed for 96 pathways comprised of about 400 genes to be tested at once, with the production of 30 new compounds. “Compared with traditional RiPP discovery methods, our platform is scalable and high-throughput in many aspects, from the biosynthetic gene cluster identification, the cloning, the production, and detection and characterization,” said Shi. “This, I would say, is the first such platform for large scale RiPP discovery.” Out of the new compounds discovered, three were found to have antibacterial properties. When tested against Klebsiella pneumoniae, which are highly virulent antibiotic-resistant bacteria, the newly discovered antibacterial RiPPs were found to be effective at killing the dangerous bacteria. The researchers say this could be a new avenue for discovering compounds that are effective against bacteria that are resistant to current antibiotic drugs. “We found three RiPPs that have antimicrobial properties against pathogens that are known to be involved in hospital acquired infections, including Klebsiella,” said Ayikpoe. “This research shows that by using this platform to extend the number of biosynthetic gene clusters that we can screen at once, we are more likely to discover anti-microbial compounds that could have therapeutic properties.” The team says the goal of the paper is two-fold: to demonstrate the ability of the high-throughput technology to quickly construct and test gene clusters for new RiPPs, but also to emphasize the kind of large-scale collaborative projects that are made possible within the IGB. “There's no way that any one of our labs could have done all of this on their own. The IGB has provided the crucible for this kind of interdisciplinary research,” Mitchell said. Battiste described how the IGB inspires collaborative projects like this one naturally through its design. “The IGB makes it very easy to just talk to people when you see them all the time in your theme, which lowers the barrier for starting projects with them,” Battiste said. “Everyone in the MMG theme works on similar stuff even if we’re from different labs. So we all have different types of expertise but they mesh well together, and you get to learn about the types of techniques they’re using. It's been one of my favorite parts of working here, the sense of camaraderie amongst all of the people on the team.” To highlight the spirit of collaboration embodied by their paper, the labs are working with the Department of Chemistry to create a video to showcase both their research and all that the IGB offers to empower projects like these, and to hopefully inspire more of them. The video is set to release soon to accompany the publication of the paper in Nature Communications. All three co-first authors described how their education, research, and job prospects have benefitted greatly from their time at the IGB, highlighting that it is both the people and the technology together that make IGB a great place to conduct research. “The collaborative atmosphere that the IGB offers in diversity and growth, both in terms of science and social life, is really remarkable.” said Ayikpoe. This research was supported by funding from NIH.
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The Carl R. Woese Institute for Genomic Biology has hosted numerous research centers over the years, fostering collaboration between researchers at the IGB and external partners, including those of academic, governmental, and industrial nature. The IGB’s centers often work together with multiple institutions and companies, producing interdisciplinary research that is then translated into real-world solutions. Here, we discuss the centers both past and current that the IGB has hosted over the last 15 years. The Big Data to Knowledge Center of Excellence The human genome is massive, totaling about 3 billion nucleotides long. Though our sequencing technology has advanced considerably in recent years, it still falls short in its capability to analyze such large quantities of genomic data quickly and accurately. The need for an advanced platform that could generate, interpret, and apply genomic data spawned the creation of BD2K, established in 2016 with funding from NIH. The focus of this center was to get computer software up to the scale of genomic data, and create a platform with an intuitive user interface, integrated analytical methods involving data mining and machine learning, and an open access design such that it be a “knowledge network” of community genomic data sets. The platform, called The Knowledge Engine for Genomics, contained data for not just human genomics, but animals and plants as well, which were used to create patient-specific treatments for disease, modify microbes for agriculture and human health, and improve efficiency of plant and animal agriculture. Center of Advanced Bioenergy and Bioproducts Innovation The human population is expected to reach 8 billion by 2023, and with this population growth comes the need for more efficient agriculture to grow enough food, and more sustainable sources of fuel to power the world. To help with this problem, CABBI was established in 2017 with funding from the U.S. Department of Energy as part of a widescale collaboration with multiple universities across the county. CABBI seeks to create a new generation of bioenergy crops, biofuels, and bioproducts, that are sustainable, resilient, and cost-effective. The crops that are developed by researchers at CABBI can produce valuable chemicals such as biodiesel, organic acids, and alcohol, that work to reduce use of fossil fuels and dependence on non-sustainable sources for these chemicals. The crops are also engineering to produce higher yields, helping to sustainably feed both people and livestock. The Center for Nutrition, Learning, and Memory Diets vary tremendously across the human population and throughout our lives, yet the effects that nutrition has on our brain function and development are still unclear. This was the inspiration for CNLM, established in 2011 in partnership with Abbott Nutrition, as the first interdisciplinary center for studying the impact of nutrition on brain cognition. Using leading-edge brain imaging and supercomputing technologies, CNLM researchers explored the mechanisms underlying nutritional enhancement of learning and memory, and used this data to create reliable tests for measuring how learning and memory changed depending on nutrition and age. CNLM also hosted an annual research competition that awarded novel multi-disciplinary research on the intersection between nutrition and cognition. Center for Genomic Diagnostics Methods for testing for some diseases in humans can be invasive, expensive, and time consuming. Furthermore, treatments for certain diseases, like cancer, often only work for some patients. Ideally, there would be a way to reliably test for biomarkers of disease and create patient-specific treatments based on the results. This is where the CGD comes in. Originally the Omics Nanotechnology for Cancer Precision Medicine theme, the CGD grew out of this theme through a partnership with the Grainer College of Engineering in 2020. This center is currently developing non-invasive genomic “liquid biopsies” which measure micro-RNAs in the blood of patients, allowing for quick, easy, and reliable testing for certain diseases. Their goal is to make this test easy to take at home, such that a patient can use a finger stick to collect a drop of blood, put it in a cartridge, and send it in the mail to be analyzed by a lab. The CGD also hopes to use blood-based diagnostics of biomarkers to create more individualized treatments for patients based on their needs. Recently CGD has developed a technique called Photonic Resonator Interferometric Scattering Microscopy, which can be used to count virus loads in real time at a low cost. The center is working to integrate PRISM technology with other virus testing, like that for COVID-19, to create rapid diagnostic tests to monitor viral load in patients with these diseases. Genome Scale Engineering Center In recent years, metabolic engineering involving microorganisms has been used to produce much of the biofuels and chemicals that we use. Usually, these efforts focus on baker’s yeast or other model organisms. Increasing the diversity of microorganisms we use can offer advantages for biomanufacturing and may even lead to discovery of new compounds. However, the time and effort needed to explore and manipulate the genes of new models microorganisms is extensive. The goal of GSE, created in 2018 with funding from the Department of Energy, is to develop genome scale engineering tools that allow for rapid testing of microorganisms for new industrial compounds. By integrating genomic engineering tools with metabolic analyses and computational modeling, the center will accelerate the “design-build-test” cycle of microorganism testing, and engineer emerging yeast models to produce valuable fuels and chemicals as part of DOE’s renewable energy mission. Catherine and Don Kleinmuntz Center for Genomics in Business and Society The Kleinmuntz Center was established in 2019 by Catherine and Don Kleinmuntz as an intersection between business and science. The center provides opportunities for scientists to engage with businesses and develop their research into something both innovative and commercial. The Kleinmuntz center hosts the Young Innovator Program yearly, through which a cohort of graduate students learn about professional development, and design a project to create something to provide economic and social impact, such as new healthcare or industrial products. The center also offers the Mikashi Awards, which provides funding for projects at the IGB that are innovative and marketable. Researchers explore gene interactions in influenza to help improve accuracy of flu vaccines10/6/2022 READ ON IGB'S WEBSITE The influenza virus, which causes the flu, is a major public health issue, infecting millions of people and estimated to cost $10 billion in direct medical costs in the United States each year. Like most viruses, influenza mutates rapidly as it spreads, making it difficult to vaccinate against every possible strain. Every year there is a massive effort to determine which strains will likely be the most prevalent, in order to make a vaccine that offers the best protection for that season. Chris Brooke, an associate professor of microbiology (left) with lead author and graduate student Tongyu Liu “It’s a super high-stakes guessing game. We're basically sitting here trying to guess what variants might pop up next. I think that emphasizes just how critical it is to better understand the fundamental rules that govern the evolution of viruses and how they escape from our immune systems,” said Chris Brooke (IGOH), an associate professor of microbiology at the University of Illinois Urbana-Champaign.
Brooke explained that most research efforts for influenza vaccination focus on evolutionary potential of the surface protein hemagglutinin because this is the main protein our immune system targets. HA binds to receptors on the surface of our cells, allowing the influenza virus to enter and start replicating. However, another surface protein called neuraminidase has been largely overlooked. NA is important for later in the virus life cycle, when it destroys the receptors originally used for entry, cleaving the cell and releasing the virions inside. HA and NA are highly functionally involved with each other, despite their opposing actions, because they are both necessary for the virus to infect cells and spread. In a new paper published in Cell Host & Microbe, Brooke’s team explored how changes in NA activity affected the evolutionary potential of HA. To do this, they used a wildtype influenza strain, along with two strains identical to the wildtype except for a mutation that reduced NA activity. Next, in collaboration with Nicholas Wu (IGOH/MMG), an assistant professor of biochemistry at Illinois, the team used a process called deep mutational scanning to essentially create a library of HA mutated versions of their three strains of influenza. The researchers could then measure HA activity and fitness across the mutated virus strains. “This is a high-throughput method for introducing every possible amino acid substitution into a given region of interest, and then measuring the effects of those substitutions on relative fitness,” said Brooke. “We can then quantify fitness effects of specific substitutions depending on the NA gene they were paired with.” Through this process, Brooke’s team determined that virus strains with reduced NA activity had higher mutational tolerance in changes in HA. In other words, when the influenza strains with lower NA receptor binding were paired with mutations that also decreased HA receptor binding, they largely showed no decrease in fitness, compared to the wildtype strain, which often did have decreased fitness. Brooke explained that this is likely due to the opposing functions of HA and NA, where the former works to break into the cell, and the latter works to escape the cell. “If NA has a substitution that decreases its activity, we see compensatory substitutions in HA that lower its relative activity as well, bringing them back into balance. If only one of them goes up or down, the cell becomes out of balance and this decreases the overall fitness. And so, you'll see a compensatory substitution to bring it back into the optimal range.” “I think we were all surprised to see that,” said Tongyu Liu, a graduate student in Brooke’s lab and lead author on the paper. “The textbook view of mutations is that they are mostly deleterious. But here in our experiment, we demonstrated that the interaction between HA and NA could reshape the fitness effect of mutations, from mostly deleterious to primarily neutral.” The researchers also grew the same strains with reduced NA activity in the presence of neutralizing antibodies that target HA to see what mutations would arise. The experiment essentially mimics what happens in the body, when immune cells target and attack the HA protein of influenza cells to clear an infection. By looking at what HA variants are selected to evolve in this environment, the researchers found more evidence that the pathways that HA evolution takes to escape immune pressure are highly contingent on NA function. The evolution of HA is mainly studied in isolation from other genes in influenza vaccine research, but Brooke says this data demonstrates the need to look at the interactions between HA and genes for other proteins, like NA, to better predict how HA will evolve depending on mutations in these other genes across strains. The hope is that this research will be used to improve accuracy for predicting future predominant genotypes and create vaccines against these strains. “Every year we try and pick which of the many different co-circulating flu strains to target with the next year's vaccine, and if we don't pick correctly, that leads to more severe infections and deaths,” Brooke said. “So it's really important to understand the rules that govern the evolution of the virus so that we can better predict the specific pathways it'll take.” This research is supported by the National Institute of Allergy and Infectious Diseases and the Roy J. Carver Charitable Trust. https://doi.org/10.1016/j.chom.2022.09.003 |