Bacterial cells transmit memories to offspring

Bacterial cells can "remember" brief, temporary changes to their bodies and immediate surroundings, a new Northwestern University and University of Texas-Southwestern study has found.

And, although these changes are not encoded in the cell's genetics, the cell still passes memories of them to its offspring -- for multiple generations.

Not only does this discovery challenge long-held assumptions of how the simplest organisms transmit and inherit physical traits, it also could be leveraged for new medical applications. For example, researchers could circumvent antibiotic resistance by subtly tweaking a pathogenic bacterium to render its offspring more sensitive to treatment for generations.

The study will be published Wednesday (Aug. 28) in the journal Science Advances.

"A central assumption in bacterial biology is that heritable physical characteristics are determined primarily by DNA," said Northwestern's Adilson Motter, the study's senior author. "But, from the perspective of complex systems, we know that information also can be stored at the level of the network of regulatory relationships among genes. We wanted to explore whether there are characteristics transmitted from parents to offspring that are not encoded in DNA, but rather in the regulatory network itself. We found that temporary changes to gene regulation imprint lasting changes within the network that are passed on to the offspring. In other words, the echoes of changes affecting their parents persist in the regulatory network while the DNA remains unchanged."

Motter is the Charles E. and Emma H. Morrison Professor of Physics at Northwestern's Weinberg College of Arts and Sciences and director of the Center for Network Dynamics. The study's co-first authors are postdoctoral fellow Thomas Wytock and graduate student Yi Zhao, who are both members of Motter's laboratory. The study also involves a collaboration with Kimberly Reynolds, a systems biologist at the University of Texas Southwestern Medical Center.

Learning from a model organism

Since researchers first identified the molecular underpinnings of genetic code in the 1950s, they have assumed traits are primarily -- if not exclusively -- transmitted through DNA. However, after the completion of the Human Genome Project in 2001, researchers have revisited this assumption.

Wytock cites the World War II Dutch famine as a famous example pointing to the possibility of heritable, non-genetic traits in humans. A recent study showed that the children of men, who were exposed to the famine in utero, exhibited an increased tendency to become overweight as adults. But isolating the ultimate causes for this type of non-genetic inheritance in humans has proved challenging.

"In the case of complex organisms, the challenge lies in disentangling confounding factors such as survivor bias," Motter said. "But perhaps we can isolate the causes for the simplest single-cell organisms, since we can control their environment and interrogate their genetics. If we observe something in this case, we can attribute the origin of non-genetic inheritance to a limited number of possibilities -- in particular, changes in gene regulation."

The regulatory network is analogous to a communication network that genes use to influence each other. The research team hypothesized that this network alone could hold the key to transmitting traits to offspring. To explore this hypothesis, Motter and his team turned to Escherichia coli (E. coli), a common bacterium and well-studied model organism.

"In the case of E. coli, the entire organism is a single cell," Wytock said. "It has many fewer genes than a human cell, some 4,000 genes as opposed to 20,000. It also lacks the intracellular structures known to underlie the persistence of DNA organization in yeast and the multiplicity of cell types in higher organisms.Because E. coli is a well-studied model organism, we know the organization of the gene regulatory network in some detail."

Reversible stress, irreversible change

The research team used a mathematical model of the regulatory network to simulate the temporary deactivation (and subsequent reactivation) of individual genes in E. coli. They discovered these transient perturbations can generate lasting changes, which are projected to be inherited for multiple generations. The team currently is working to validate their simulations in laboratory experiments using a variation of CRISPR that deactivates genes temporarily rather than permanently.

But if the changes are encoded in the regulatory network rather than the DNA, the research team questioned how a cell can transmit them across generations. They propose that the reversible perturbation sparks an irreversible chain reaction within the regulatory network. As one gene deactivates, it affects the gene next to it in the network. By the time the first gene is reactivated, the cascade is already in full swing because the genes can form self-sustaining circuits that become impervious to outside influences once activated.

"It's a network phenomenon," said Motter, who is an expert in the dynamic behaviors of complex systems. "Genes interact with each other. If you perturb one gene, it affects others."

Although his team is deactivating genes to test the hypothesis, Motter is clear that different types of perturbations could cause a similar effect. "We also could have changed the cell's environment," he said. "It could be the temperature, the availability of nutrients or the pH."

The study also suggests that other organisms have the necessary elements to exhibit non-genetic heritability. "In biology, it's dangerous to assume anything is universal," Motter contends. "But, intuitively, I do expect the effect to be common because E. coli'sregulatory network is similar or simpler than those found in other organisms."

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Low-cost microbe can speed biological discovery

Cornell University researchers have created a new version of a microbe to compete economically with E. coli -- a bacteria commonly used as a research tool due to its ability to synthesize proteins -- to conduct low-cost and scalable synthetic biological experiments.

As an inexpensive multiplier -- much like having a photocopier in a test tube -- the bacteria Vibrio natriegens could help labs test protein variants for creation of pharmaceuticals, synthetic fuels and sustainable compounds that battle weeds or pests.

The microbe can work effectively without costly incubators, shakers or deep freezers and can be engineered within hours.

The research publishes Feb. 13 in PNAS Nexus.

"It's really easy to produce," said lead author David Specht, a postdoctoral researcher in the laboratory ofBuz Barstow, assistant professor of biological and environmental engineering.

To study proteins for creating medical cures or fashioning fuels, researchers use a plasmid (a small piece of DNA) that acts as the instruction manual to make the molecular machine -- a protein -- of interest.

Currently, when researchers place a plasmid into E. coli, they can create many copies to test several variants.

E. coli cells help molecular biologists multiply and manipulate plasmids for protein engineering, but the process is expensive since they often purchase the bacteria from manufacturers, must keep it cold and maintain rooms of expensive equipment to sustain it. A modified E. coli, used for this purpose, is also very fragile.

"As scientists, we don't often know precisely what those regulatory or molecular sequences should be to achieve our goals," said Barstow.

"So, we must test a lot of variants, and Vibrio natriegens allows researchers to scale up that process of testing."

The microbe V. natriegens is not complicated, Specht said. "It's so simple to make that someone with limited resources -- like high school labs, home inventors or startup biological businesses -- can do it," he said.

Researcher Timothy Sheppard compared the simplicity of V. natriegens in conducting synthetic and molecular experiments to using a simple writing instrument hundreds of years old: "We've found nature's pencil for cloning and conducting synthetic biology," he said.

The process is inexpensive with V. natriegens, as it requires no capital equipment purchases and it can work at room temperature.

The cells produced from V. natriegens grow quickly: According to the paper, a transformation started at 9 a.m. yields visible colonies by 5 p.m., each filled with masses of proteins.

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First step towards synthetic CO2 fixation in living cells

Synthetic biology offers the opportunity to build biochemical pathways for the capture and conversion of carbon dioxide (CO2). Researchers at the Max-Planck-Institute for Terrestrial Microbiology have developed a synthetic biochemical cycle that directly converts CO2 into the central building block Acetyl-CoA. The researchers were able to implement each of the three cycle modules in the bacterium E.coli, which represents a major step towards realizing synthetic CO2 fixing pathways within the context of living cells.

Developing new ways for the capture and conversion of CO2 is key to tackle the climate emergency.

Synthetic biology opens avenues for designing new-to-nature CO2-fixation pathways that capture CO2 more efficiently than those developed by nature.

However, realizing those new-to-nature pathways in different in vitro and in vivo systems is still a fundamental challenge.

Now, researchers in Tobias Erb's group have designed and constructed a new synthetic CO2-fixation pathway, the so-called THETA cycle.

It contains several central metabolites as intermediates, and with the central building block, acetyl-CoA, as its output.

This characteristic makes it possible to be divided into modules and integrated into the central metabolism of E. coli.

The entire THETA cycle involves 17 biocatalysts, and was designed around the two fastest CO2-fixing enzymes known to date: crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase.

The researchers found these powerful biocatalysts in bacteria.

Although each of the carboxylases can capture CO2 more than 10 times faster than RubisCO, the CO2-fixing enzyme in chloroplasts, evolution itself has not brought these capable enzymes together in natural photosynthesis.

The THETA cycle converts two CO2 molecules into one acetyl-CoA in one cycle.

Acetyl-CoA is a central metabolite in almost all cellular metabolism and serves as the building block for a wide array of vital biomolecules, including biofuels, biomaterials, and pharmaceuticals, making it a compound of great interest in biotechnological applications.

Upon constructing the cycle in test tubes, the researchers could confirm its functionality.

Then the training began: through rational and machine learning-guided optimization over several rounds of experiments, the team was able to improve the acetyl-CoA yield by a factor of 100.

In order to test its in vivo feasibility, incorporation into the living cell should be carried out step by step.

To this end, the researchers divided the THETA cycle into three modules, each of which was successfully implemented into the bacterium E. coli. The functionality of these modules was verified through growth-coupled selection and/or isotopic labelling.

"What is special about this cycle is that it contains several intermediates that serve as central metabolites in the bacterium's metabolism. This overlap offers the opportunity to develop a modular approach for its implementation." explains Shanshan Luo, lead author of the study.

"We were able to demonstrate the functionality of the three individual modules in E. coli. However, we have not yet succeeded in closing the entire cycle so that E. coli can grow completely with CO2," she adds.

Closing the THETA cycle is still a major challenge, as all of the 17 reactions need to be synchronized with the natural metabolism of E. coli, which naturally involves hundreds to thousands of reactions.

However, demonstrating the whole cycle in vivo is not the only goal, the researcher emphasizes.

"Our cycle has the potential to become a versatile platform for producing valuable compounds directly from CO2 through extending its output molecule, acetyl-CoA." says Shanshan Luo.

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Ending a 50-year mystery, scientists reveal how bacteria can move

University of Virginia School of Medicine researchers and their collaborators have solved a decades-old mystery about how E. coli and other bacteria are able to move.

Bacteria push themselves forward by coiling long, threadlike appendages into corkscrew shapes that act as makeshift propellers. But how exactly they do this has baffled scientists, because the "propellers" are made of a single protein.

An international team led by UVA's Edward H. Egelman, PhD, a leader in the field of high-tech cryo-electron microscopy (cryo-EM), has cracked the case. The researchers used cryo-EM and advanced computer modeling to reveal what no traditional light microscope could see: the strange structure of these propellers at the level of individual atoms.

"While models have existed for 50 years for how these filaments might form such regular coiled shapes, we have now determined the structure of these filaments in atomic detail," said Egelman, of UVA's Department of Biochemistry and Molecular Genetics. "We can show that these models were wrong, and our new understanding will help pave the way for technologies that could be based upon such miniature propellers."

Blueprints for Bacteria's 'Supercoils'

Different bacteria have one or many appendages known as a flagellum, or, in the plural, flagella. A flagellum is made of thousands of subunits, but all these subunits are exactly the same. You might think that such a tail would be straight, or at best a bit flexible, but that would leave the bacteria unable to move. That's because such shapes can't generate thrust. It takes a rotating, corkscrew-like propeller to push a bacterium forward. Scientists call the formation of this shape "supercoiling," and now, after more than 50 years, they understand how bacteria do it.

Using cryo-EM, Egelman and his team found that the protein that makes up the flagellum can exist in 11 different states. It is the precise mixture of these states that causes the corkscrew shape to form.

It has been known that the propeller in bacteria is quite different than similar propellers used by hearty one-celled organisms called archaea. Archaea are found in some of the most extreme environments on Earth, such as in nearly boiling pools of acid, the very bottom of the ocean and in petroleum deposits deep in the ground.

Egelman and colleagues used cryo-EM to examine the flagella of one form of archaea, Saccharolobus islandicus, and found that the protein forming its flagellum exists in 10 different states. While the details were quite different than what the researchers saw in bacteria, the result was the same, with the filaments forming regular corkscrews. They conclude that this is an example of "convergent evolution" -- when nature arrives at similar solutions via very different means. This shows that even though bacteria and archaea's propellers are similar in form and function, the organisms evolved those traits independently.

"As with birds, bats and bees, which have all independently evolved wings for flying, the evolution of bacteria and archaea has converged on a similar solution for swimming in both," said Egelman, whose prior imaging work saw him inducted into the National Academy of Sciences, one of the highest honors a scientist can receive. "Since these biological structures emerged on Earth billions of years ago, the 50 years that it has taken to understand them may not seem that long."

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Futuristic coating for hospital fabrics and activewear kills COVID virus and E. coli

UBC researchers have developed an inexpensive, non-toxic coating for almost any fabric that decreases the infectivity of the virus that causes COVID-19 by up to 90 per cent.

And in the future, you might be able to spray it on fabric yourself.

"When you're walking into a hospital, you want to know that pillow you're putting your head onto is clean," says lead author Taylor Wright, a doctoral student in the department of chemistry. "This coating could take a little bit of the worry off frontline workers to have Personal Protection Equipment with antimicrobial properties."

Researchers soaked fabric in a solution of a bacteria-killing polymer which contains a molecule that releases sterilizing forms of oxygen when light shines on it. They then used an ultraviolet (UV) light to turn this solution to a solid, fixing the coating to the fabric. "This coating has both passive and active antimicrobial properties, killing microbes immediately upon contact, which is then amped up when sunlight hits the cloth," says senior author Dr. Michael Wolf (he/him), a professor of chemistry.

Both components are safe for human use, and the entire process takes about one hour at room temperature, says Wright. It also makes the fabric hydrophobic, meaning microbes are less likely to stick to the cloth, and doesn't seem to affect the strength of the fabric.

In addition, the coating can be used on almost any fabric, including cotton, polyester, denim, and silk, with applications in hospital fabrics, masks, and activewear. Whereas other such technologies can involve chemical waste, high energy use, or expensive equipment, the UBC method is relatively easy and affordable, says Wright. "All we need is a beaker and a light bulb. I'm fairly certain I could do the whole process on a stove."

To test the coating's bug-killing properties, the researchers bathed treated fabric in bacterial soups of Escherichia coli (E. coli) andMethicillin-resistant Staphylococcus aureus (MRSA), both major sources of hospital-acquired infections. They found there were 85 per cent of viable E. coli bacteria remaining after 30 minutes, which fell to three per cent when the treated cloth was exposed to green light for the same amount of time. Similarly, 95 per cent of viable MRSA bacteria remained, dropping to 35 per cent under green light. No bacteria remained after four hours.

Given that sunlight or fluorescent lights have a lesser percentage of green, the team expects similar but less intense results for fabric exposed to those light sources, says Wright. "Particularly in the Pacific Northwest, it's not always a sunny day. So, at all times you're going to have that layer of passive protection and when you need that extra layer of protection, you can step into a lit room, or place the fabric in a room with a green light bulb -- which can be found for about $35 online."

The researchers also looked into whether the coating reduced the infectivity of SARS-CoV-2, the virus causing COVID-19 by bathing treated fabric in a solution of the virus particles and then adding that solution to living cells to see if they could infect them. They found the passive properties weren't effective against the virus, but when treated fabric was exposed to green light for two hours, there was up to 90 per cent decrease in the infectivity of SARS-CoV-2. "In other words, only one tenth of the amount of virus signal was detected on cells infected with the UV-fabric and light treated virus," says co-author Dr. François Jean (he/him), professor of virology at UBC. The efficacy of the new fabric against SARS-CoV-2 was demonstrated by Dr. Jean's team at UBC FINDER, the state-of-the-art level three biocontainment facility founded by Dr. Jean in 2010.

The team found they needed an 18 square centimeter piece of fabric to kill microbes with material containing seven per cent weight of the active ingredient, but that increasing this to 23 per cent weight increased the effectiveness of the fabric at four times less material, says Wright.

Researchers also found that keeping the fabric under green light for more than 24 hours failed to produce the sterilizing forms of oxygen, highlighting an area for further study. This is a similar effect to the color fading on clothing after being exposed to sunlight for too long.

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