Bacterial pathogens build antibiotic-resistant 'bunkers' using filament scaffolds

Researchers have discovered and characterized at the atomic level a mechanism that enables bacterial pathogens—including hospital bacteria Acinetobacter baumannii and Pseudomonas aeruginosa—to assemble antibiotic-resistant three-dimensional (3D) biofilms. These findings open a new avenue for developing therapies against multidrug-resistant bacterial infections by targeting the biofilm assembly. The work is published in the journal Nature Communications.

Many pathogenic bacteria form 3D biofilms to protect themselves from the immune system, antibiotic treatments, and drying on environmental surfaces. Some of the most problematic hospital bacteria, such as multidrug-resistant A. baumannii and P. aeruginosa, use specialized hair-like filaments called adhesive pili to attach to tissues or abiotic surfaces. After attaching, the bacteria then grow into thick 3D biofilms consisting of multiple layers of bacteria. This process is also mediated by adhesive pili, but until now it has been unclear how they prevent the growing 3D biofilm from falling apart.

Using a combination of advanced electron microscopy methods, the researchers at the MediCity Research Laboratory of the University of Turku in Finland, led by S. Jusélius Senior Researcher Anton Zavialov, discovered that adhesive Csu pili from neighboring A. baumannii bacteria attach to each other in an antiparallel manner. These pili rapidly assemble into flat sheets that link bacteria together and shield them from hostile environments.

"Impressively, Csu pili can self-assemble into huge, complex networks connecting hundreds of bacterial cells," says Dr. Zavialov.

The team demonstrated that Csu pili can form at least two types of flat structures and resolved them at a near-atomic resolution.

"Cryo-electron microscopy methods are developing very rapidly. To obtain the first model, I initially developed a manual approach, and only later did we apply computational tools to solve these exceptionally large assemblies in 3D," explains first author Doctoral Researcher Henri Malmi.

The researchers also found that the pilus network becomes embedded in a less defined matrix composed of polysaccharides and DNA secreted by the bacteria.

"This final structure somewhat resembles reinforced concrete: the pili act like steel bars, while polysaccharides and DNA form the concrete. In this way, the bacteria effectively hide in a bunker," adds Dr. Zavialov.

The team is now focused on developing inhibitors that target the connections between pili. Such inhibitors could be used in combination therapies to prevent 3D biofilm assembly and help antibiotics eliminate the pathogens more effectively.

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Why do microbes team up? A new model explains nutrient sharing in fluctuating environments

 Depending on others for something you need may feel like a risky proposition—and perhaps a human one. It is actually a survival strategy found in the microbial world, and far more frequently than one might expect. Discovering why is key to understanding how microbes form stable communities across medical, industrial, and ecological settings.

A new study by bioengineering professor Sergei Maslov (CAIM co-leader), computational scientist Ashish George, and biology professor Tong Wang explores why interdependence can be such a winning move for microbial communities. Their work, published in Cell Systems, demonstrated that a mathematical model of how bacteria produce and share resources accurately predicted the outcome of experiments with living E. coli strains.

The researchers' collaboration began during their time as colleagues at the Carl R. Woese Institute for Genomic Biology at the University of Illinois Urbana-Champaign. George continued the collaboration in his position at the Broad Institute; Wang, in his appointment at Purdue University. Maslov, who led the study, remains at Illinois and is an affiliate member of the National Institute for Theory and Mathematics in Biology.

"Microbes rarely live in isolation. They actually live in communities just like humans," Wang said to explain their inspiration for embarking on the study. "We wanted to establish a mathematical model to try to capture how they trade essential nutrients, and eventually what kind of community they will be able to assemble due to their cooperative interactions."

Maslov and Wang focused in particular on auxotrophs—microbes that are missing the capability to make one or several essential nutrients, often amino acids, which they must instead absorb from their environment. Auxotrophy seems—at first glance—like a weakness. The cell's survival is dependent upon its surroundings, and most often its neighbors. Yet auxotrophs are not a rare occurrence; they are commonly found in microbial communities.

"Previous studies seem to show that when a community has more auxotrophic species, it seems to be more stable, and these communities are actually pretty prevalent," Wang said. "So another reason why we want to establish this type of model is to answer: Why are there so many auxotrophic species, and what's their connection with ecological stability?"

Other research groups have explored—through laboratory experiments and a mathematical model only based on pairwise species–species interactions—how auxotrophs can remain a functioning part of communities by focusing on how two types of auxotrophs might pair up, each one supplying a resource the other needs. The experimental dynamic is intriguing, but the model can't fully portray microbial cooperation accurately, failing to predict how interdependencies develop across a whole community of 14 members with many different nutrients to share or consume.

The research team wanted a mathematical model that could describe in numbers how the interplay across a whole community of multiple types of microbes might develop. Based on the established model, they derived two key ecological principles.

"One principle is that we have to balance all the fluxes. Let's make sure that everything that is being generated, all the amino acids being generated by the community, is consumed by somebody in the community, so nothing is left," Maslov said. "The second one is, let's make sure that for every species, there is actually something that limits its growth, because if nothing is limiting your growth, you will be growing exponentially and eventually you will take over ... so we explored in this model how we can simultaneously balance fluxes, and make sure that all the species have their unique limiting resource and they can all coexist because they are fighting for different things."

Their model's results showed how the presence of auxotrophs can make a community more stable in the face of environmental fluctuations, because collectively, their network of interdependent production and consumption is more self-sufficient. In addition, once a group has formed, it is difficult for other microbes to "invade" unless their own nutrient requirements fit into the established group dynamic.

To test their model, the researchers applied their model to predict the outcome of a past study from another group that combined 14 lab-created auxotroph strains of E. coli. In that study, four strains survived to form a stable community. The present model was able to correctly predict the identities of three of the four strains, a marked improvement over past modeling efforts.

From here, Tong and Maslov plan to apply the new modeling approach to a variety of real-world conditions, such as understanding the communities of bacteria and other microbes that live in and on our bodies and impact our health.

"We would like to study community assembly and try to explain some of the patterns of the human gut microbiome, why some species tend to sort of coexist together," Tong said. "Maybe they are complementary to each other regarding the generation of different amino acids, or even include other essential resources like vitamins. That's actually one of the applications we can imagine."

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Electrochemical signals can reshape bacterial protein patterns, boosting electron transfer

 Sometimes, transporting electrons from one cell to another is a team effort. In electroactive bacteria, that team is a group of proteins that shepherds electrons forward, passing them along like a relay baton, so they can penetrate the thick cell envelope comprising multiple layers of membranes that otherwise are not electroconductive. But how these proteins collaborate to achieve this has not been clear.

Cornell researchers have discovered this electron transfer is mediated by CymA proteins' ability to synchronize and form a biomolecular condensate in the inner membrane—something that had not been previously observed in electroactive bacteria. The researchers then demonstrated for the first time that by applying an electrochemical signal to the bacteria, they could manipulate the spatial pattern of the proteins and spur the extracellular process.

The technique could eventually find applications in biotechnologies such as microbial energy conversion, in which electrons need to be shuttled to other cells or electrodes. The findings were published in Nature Communications. The lead author is former postdoctoral researcher Youngchan Park, now an assistant professor at Indiana University.

The project was led by Peng Chen, the Peter J.W. Debye Professor of Chemistry in the College of Arts and Sciences. It grew out of a collaboration with co-author Buz Barstow, Ph.D. '09, assistant professor of biological and environmental engineering in the College of Agriculture and Life Sciences, that explored how electroactive bacteria interact with semiconducting materials.

That research inspired Chen to delve further into extracellular electron transport in bacteria—specifically Shewanella oneidensis, the most well-known and extensively studied microbe used for electron transport. As a so-called Gram-negative bacteria, S. oneidensis has inner and outer membranes, connected by a kind of buffer zone of periplasm. Those stacked layers are a structural advantage, protecting the bacteria in unfriendly environments—for example, ones rife with heavy metals or antibiotics. However, the membranes, which mostly consist of insulating fatty lipids, aren't electroconductive.

"Electrons have to go through the cell envelope: the inner membrane, outer membrane and the periplasmic space," Chen said. "Now, electron transfer in biology, of course, doesn't just go through solutions. Electrons do not swim through water. Otherwise, they would get short-circuited."

But both membranes and the periplasm contain a secret asset: proteins. Using photoelectrochemistry-fluorescence microscopy, the researchers determined that during extracellular electron transfer, CymA proteins in the inner membrane reorganize in a confined region and drive their electron-transfer partners to do the same in the periplasm.

This type of condensate is a well-documented phenomenon in bacteria and many other types of cells, playing a role in metabolic enzymatic reactions and gene regulation, but it was not known to be important for electron transfer and hadn't been observed in electroactive bacteria, Chen said. The researchers were able to induce the formation of CymA condensate by applying electrochemical signals, which allowed them to quantify the spatiotemporal dynamics of protein reorganization at the single-cell level.

"Many people have applied electrical signals to bacteria, but we discovered that by applying an electrochemical signal to the cell, it can change the spatial pattern of the protein," Chen said. "The pattern initially is homogeneous, and then you condense it. The electrical signal—basically, the electron transfer—will drive the change of a spatial pattern. That's a new thing."

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Nuclear speckles play a key role in the progression of viral infection, research reveals

 Herpes simplex virus type 1 (HSV-1) infection dramatically remodels the host cell's nuclear structures. Infection leads to the formation of viral replication compartments and to chromatin marginalization to the nuclear periphery. Joint research by the Universities of Jyväskylä (Finland) and Bar-Ilan (Israel) reveals that viral infection also alters the structure of nuclear speckles, which are essential for messenger RNA processing.

The study was published in the Proceedings of the National Academy of Sciences.

"Nuclear speckles are dynamic, membraneless nuclear bodies that primarily function as sites for the storage, assembly, and modification of factors involved in gene expression. Both cellular and viral messenger RNAs are processed in nuclear speckles. The disassembly of nuclear speckles severely limits the export of viral messenger RNAs from the nucleus," explains Research Director Maija Vihinen-Ranta from the University of Jyväskylä.

The research indicates that nuclear speckles function as intermediate hubs for the modification of viral messenger RNAs, thereby highlighting their essential role in viral messenger RNA processing and nuclear export pathways. Without them, viruses cannot function normally, and infection cannot progress.

"A better understanding of how viruses interact with host cells and exploit their cellular machinery can help us develop new ways to treat and prevent viral diseases," says Vihinen-Ranta.

The study was conducted in cooperation with Professor Shav-Tal's research group, Bar-Ilan University (Israel).

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A survival strategy inside stressed cells: Ribosomes in pairs

 Ribosomes, the cell's protein-making factories, consume large amounts of energy as they build the proteins that keep cells alive and functioning. When cells experience stress—such as lack of nutrients or sudden drops in temperature—they quickly switch into survival mode. New research from the Schuman Lab at the Max Planck Institute for Brain Research in Frankfurt now reveals an unexpected way cells manage this transition: by pairing up inactive ribosomes using a ribosomal RNA link. This RNA-based mechanism reveals a previously unknown role for ribosomal RNA in the cellular stress response. The new study is published in Science.

Ribosomes are large molecular machines made of protein and RNA that build all proteins in the cell. Because protein production is extremely energy-intensive, cells rapidly reduce protein synthesis when stressed. It has long been known that bacterial cells pair their inactive ribosomes into so-called "hibernating disomes"; however, such structures had not previously been identified in animal cells.

An unexpected role for ribosomal RNA during cellular stress

Using advanced imaging techniques, Erin Schuman and her team at the Department of Synaptic Plasticity at the Max Planck Institute for Brain Research in Frankfurt discovered that stressed animal cells—including neurons—assemble inactive ribosomes into tightly linked pairs, known as disomes. These ribosome pairs are not accidental collisions or artifacts, but a regulated and reversible response to stress.

"Surprisingly, the two ribosomes are not held together by proteins, as is common in bacteria. Instead, the connection is made by a specific piece of ribosomal RNA called an expansion segment," explains one of the lead authors, postdoctoral researcher, Andre Schwarz.

Expansion segments are long, flexible RNA "tentacles" that protrude from ribosomes and have grown larger over the course of evolution. Although they are a prominent feature of animal ribosomes, their functions have only just started to emerge. This study now shows that one particular expansion segment, called "31b," is both necessary and sufficient to link ribosomes together during stress.

At the molecular level, the expansion segment forms a precise RNA-RNA interaction—a so-called "kissing loop"—in which identical RNA loops bind each other through complementary sequences. Disrupting this interaction prevents disome formation, stunts cellular growth, and makes cells more sensitive to stress.

Seeing ribosomes inside cells

A key strength of the study was the ability to visualize ribosomes directly inside intact cells using cryogenic electron tomography (Cryo-ET). Cryo-ET is a powerful 3D imaging technique that uses an electron microscope to see inside frozen biological samples (cells, organelles, molecules) with very high resolution. This approach allowed the team to visualize ribosomes in their native environment and resolve how they re-organize during stress.

The study combined an unusually broad range of techniques, including cell biology, biochemistry, yeast and mammalian cell genetic engineering, and high-resolution structural imaging.

"One major challenge was manipulating ribosomal RNA, which is encoded by hundreds to thousands of nearly identical gene copies in animal genomes. We overcame this hurdle by engineering hybrid ribosomes in yeast and by introducing small RNA molecules that specifically disrupted ribosome pairing in animal cells," says Mara Mueller, graduate student in the Schuman Lab and co-first author of the study.

A new view of translation control

"Our findings uncover a previously unknown mechanism by which animal cells regulate protein synthesis during stress—one that relies on RNA structure. The study reveals a new function for ribosomal RNA expansion segments which have been rather mysterious," says Erin Schuman.

By temporarily storing ribosomes in inactive pairs, cells protect these costly machines and enable rapid recovery once favorable conditions return. The discovery opens new avenues for understanding how cells adapt to stress and how ribosome organization contributes to health and disease.

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Stronger scents and healthier crops: Unlocking plants' hidden potential through precision gene editing

Scientists have long sought to understand why some plants are fragrant powerhouses while others remain subtle. Now, a research team from the Hebrew University of Jerusalem has cracked a genetic "bottleneck," using precision gene editing to boost the scent of flowers and the nutritional profile of vegetables. The paper is published in the International Journal of Molecular Sciences.

The study, led by Dr. Oded Skaliter and Prof. Alexander Vainstein from the Institute of Plant Sciences and Genetics in Agriculture at the Hebrew University of Jerusalem, focused on a specific enzyme called HMGR. This enzyme acts as a biological gatekeeper for the production of terpenoids, the largest group of natural compounds in plants. Terpenoids are responsible for everything from plant defense, the sweet smell of a rose, the striking colors of fruits, to the medicinal properties of anti-malarial drugs.

Breaking the genetic brake In nature, plants have a built-in system to prevent themselves from overproducing certain metabolites. The HMGR enzyme has a specific regulatory domain that acts like a metabolic brake. When the plant senses it has enough terpenoids, this domain shuts down HMGR to stop terpenoids production and save energy.

Using a virus-based CRISPR/Cas9 system, the researchers targeted this regulatory region in petunias and lettuce. By subtly editing the genetic code rather than completely knocking out the gene, they were able to disable the "brake" without harming the plant's health.

"These results establish a transgene-free strategy to enhance the production of natural compounds, like volatiles and pigments," said Prof. Alexander Vainstein. "Our work provides a framework for developing resilient, nutrient-enriched crops that can meet both agricultural and consumer needs."

The results were striking. The edited petunias did not just smell stronger; they were more vigorous, and grew larger flowers.

A surprising connection

One of the most unexpected findings was that editing the terpenoid pathway also boosted a completely different group of metabolites called phenylpropanoids. These compounds are responsible for the spicy and floral notes in many scents, such as the smell of almonds or cloves.

"We found that the induced mutations alleviated the negative feedback regulation of the enzyme," explained Dr. Oded Skaliter. "This reveals a complex layer of interaction between metabolic pathways, showing how we can use precision breeding to improve the sensory qualities of plants."

By analyzing the plant's internal chemistry, the team discovered that the genetic edit caused a "carbon shift." Because the terpenoid pathway was working more efficiently, the plant began producing more raw carbon, which then flowed into other scent- and health-related pathways.

From better flowers to healthy salads

The researchers applied the same logic to lettuce, a crop known for its crunch but often criticized for its low nutritional density. The edited lettuce showed increased levels of sesquiterpenes and apocarotenoids, which contribute to flavor and antioxidant activity.

This "transgene-free" strategy is particularly important for the future of agriculture. Because the final plants do not contain foreign DNA, they offer a precise alternative for metabolic engineering that may gain better consumer acceptance than traditional GMOs.

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Hidden insect diversity in grass shoots threatened by mowing

When it comes to biodiversity, researchers and the public tend to focus on large-scale patterns. This overlooks a hidden but precious diversity: small, inconspicuous wasps, midges, flies, beetles and other insects that live in plants. These tiny creatures are actually very common, as shown by a team of researchers at the University of Göttingen and the Hungarian HUN-REN Center for Ecological Research.

The researchers measured, dissected and searched for insects in over 23,000 shoots of grass. They found 255 species of insects in 10 perennial grass species, which last year-round, but not a single one in five annual, short-lived grass species. The longer the shoots of the perennial grass species, the higher the diversity of insects found in them.

Around a third of the insect species feed directly on the grass. The remaining species, mostly wasps, live parasitically on the insects that feed on plants. Almost two-thirds of insects specialize in grasses, half of them even in specific grass species.

The conclusion is that areas of grassland should not be mown for several years: stable insect populations need undisturbed refuges with intact shoots of grass. The results are published in Basic and Applied Ecology.

The team studied ubiquitous grasses that occur in large populations in many regions. These included five annual species such as black grass and wind grass, and 10 longer-lasting species such as cat grass and couch grass. In autumn and winter, the researchers collected all insects from the shoots and classified them according to their respective species.

They raised the larvae in the laboratory so that they could be clearly identified. They then analyzed the "food web"—the multiple food chains—between the grasses, the plant-eating insects and the parasitic wasps that are their predators.

This revealed the diversity of insects hidden in shoots of grass. Eighty-three of the species found are plant-eaters such as grass flies and gall midges. The remaining 172 species are their natural enemies: tiny parasitic wasps whose larvae develop on or inside a host and attack and ultimately often kill it.

On average, each perennial grass species is home to 12 plant-eating insect species that are attacked by 30 species of parasitic wasps. According to the data, perennial grass species with longer shoots attract more insects. This is explained by the fact that they are more visible and productive host plants with a more diverse food supply.

The difficulty in predicting when and where short-lived annual grasses will grow seems to be the reason why only a few insects have evolved to specialize in them.

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