Ancient molecules help bacteria sort out genetic activity

DNA has a twig problem. Thousands of times longer than the cell that contains it, this intricate string of As, Ts, Gs and Cs must fold itself into a compact package. But the thin double-spiral molecule can not attach itself in any way, so that it does not become terribly attached. In addition, the cell needs certain segments of the strand – specific genes – to remain available for protein-making machinery while others are hidden and shut down. It’s like playing Tetris with a tangled ball of yarn.

Nuclear “eukaryotic” cells, the type found in humans, plants and animals, rely on complex interactions between chemical tags and specialized proteins to provide instructions on which genes to activate and when – a system called epigenetics. For decades, researchers believed that epigenetic regulation was unique to eukaryotic cells and lacked simpler ones, such as bacteria. But a number of recent findings have challenged that idea.

“Bacteria are much more sophisticated than anyone realized,” said David Low, a microbiologist at the University of California, Santa Barbara.

New studies by biochemists Ursula Jakob and Peter Freddolino at the University of Michigan reveal that interactions between DNA-binding proteins and an ancient molecule called polyphosphate help turn on and off the bacteria’s genes on a large scale. Not only do these findings tell researchers more about the basic biology of such organisms, but they can also help researchers fine-tune genetically modified bacteria for biotechnology – and even contribute to new antibiotics.

“Bacteria carry around the seeds of their own destruction, and we may be able to remove the oppression that remains [those seeds] down, says Freddolino.

Eukaryotic cells have long been known to use several layers of regulation, which control which genes are active and how much of a given protein each one makes. Bacterial DNA, on the other hand, was usually portrayed in textbooks as a long piece of inert string waiting to be transcribed. That idea began to be revived in 1994, when Low discovered that a chemical label called a methyl group could block transcription in bacteria – something researchers thought was exclusive to eukaryotic cells.

More similarities have emerged over the years. For example, eukaryotic cells attach chemical tags and proteins called histones to hide parts of the genome. Last year, Freddolino’s laboratory showed that bacteria use an analogous strategy: the researchers identified 200 regions in Escherichia coli by which are silenced by chemical tags and structures called nucleoid-associated proteins (NAPs).

For a recent study in EMBO JournalFreddolino showed that NAPs functioned similarly to silence specific sections of the bacterial genome in distantly related species E coli and Bacillus subtilis. NAP acts as a position around which a portion of DNA is wound, making it physically impossible for the cell’s protein-making machinery to access genes in that portion. This effect is extremely important for bacteria: it allows them to seal pieces of external DNA and viruses that have wedged themselves into the bacterial genome, and it allows them to wallow in genes that are rarely used when they are not needed.

However, NAPs do not work alone. To determine what causes them to turn off parts of DNA, Freddolino and Jakob turned their attention to polyphosphate. This molecule was used for energy storage of the earth’s early life and has developed a variety of functions in cells. In 2020, Jakob found that mutant E coli the inability to synthesize polyphosphate showed more activity in genes that were absorbed outside the cell – and that this activity plays a key role in cell death from DNA damage.

Recently, in The progress of science, Jakob and Freddolino showed that negatively charged polyphosphate binds to positively charged NAPs using a process called liquid-liquid phase separation, in which ultra-dense protein groups condense into droplets. As more and more polyphosphate attaches to the NAPs, the normally dispersed structure of polyphosphate, NAPs and DNA becomes organized. Just as oil droplets can form in a well-mixed vinaigrette, droplets of protein, DNA and polyphosphate can solidify in bacterial cells – and this blocks parts of the genome from transcription. The process requires no additional auxiliary proteins, and it can be reversed as polyphosphate levels fall.

These studies are a big step in understanding bacterial epigenetics, says biochemist Remus Dame at the University of Leiden, who was not involved in any of the studies. “There is good reason to believe that the global structure in which these genes are embedded dictates how active they are,” he says. “This is really something very new – and very hot – that means we have to look at our system of interests differently.”

Freddolino says that when his biotechnology-focused colleagues first found out about these results, they began using this knowledge to insert engineered genes into spots along the bacterial genome that optimize protein production. The process, he says, has since gone from “keep your fingers crossed and hope for the best” to a sound strategy that works almost every time.

At the Massachusetts Institute of Technology, biochemist Peter Dedon is investigating how researchers can make new antibiotics using these mechanisms. Work from his lab (and others around the world) shows that bacteria turn genes on and off to help infect hosts – and to resist antibiotics. Dedon imagines a small molecule that can disrupt this process and keep a bacterium’s infection-raising properties or antibiotic resistance genes off; another option would be to interfere with the ability of polyphosphate to bind to NAP. This would not kill bacteria directly, but it would make them less capable of causing disease and more susceptible to attacks by the immune system. “There’s a lot of potential there,” Dedon said. “There is a whole new world of antibiotic targets.”

Bacterial epigenetics is an excellent focus for antibiotic development, says Jakob, because its mechanisms are shared between many bacterial species – but use fundamentally different proteins than eukaryotic cells do. This means that researchers can specifically target bacterial proteins and avoid disrupting the body’s own epigenetic processes, says Jakob: “It is a way to prevent diseases without having to kill the cell.”

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