Now We Know How Sleeping Bacteria Return to Life

A research team from Harvard Medical School (HMS) provides new answers for the long-standing question of how dormant bacterial spores “return to life”. Their study, published in Science, could carry implications for disease prevention.

A molecular alarm clock for bacteria

To cope against harsh environmental conditions such as UV, radiation or chemical exposure, some species of bacteria seek refuge by forming spores that create a defensive armoring around the cell. The spores’ metabolic and respiratory activity is minimal, making this form of bacteria the most “dormant type”. Energy is conserved while the bacteria “wait out” the harsh conditions, until one day the spores detect specific nutrients in their environment that relight the bacteria’s metabolic fire. Picture a molecular alarm clock, if you will.

The defence mechanism itself was first identified over 150 years ago, and the molecule responsible for detecting nutrients in the environment was described almost 50 years ago. But how the molecular alarm clock delivers the “wake-up” signal has remained a mystery; that is until microbiology Professor David Rudner and colleagues at the Blavatnik Institute at HMS set their sights on solving the conundrum, with some help from artificial intelligence (AI). In Rudner’s words, this research continuously evolved from the off, thanks to a team of diverse scientists and their unique perspectives working together in tandem.

Dr. Yongqiang Gao, a research fellow in the Rudner lab was studying the commonly found microbe Bacillus subtilis, which also happens to be the cousin of the bacterium behind anthrax – a disease that can be fatal to humans and livestock.

Gao genetically engineered genes from other bacteria that form spores into B. subtilis. He wanted to understand whether the “mismatched” proteins would affect germination, the process whereby a bacterium becomes an actively growing cell. Unexpectedly Gao discovered that, if genes were inserted from a distant relative of the bacterium, B. subtilis spores would “flawlessly reawaken”. Former colleague Dr. Lior Artzi suggested that the sensor required for bacteria to “reawaken” could act like a closed gate which, upon encountering a nutrient, sugar or amino acid, opens and allows ions to flow through. This would mean that the proteins from a relative of B. subtilis needn’t interact directly with wild-type proteins, but could instead just detect changes in the electric state of the spore.

While the receptor protein didn’t carry any characteristics of an ion channel, Artzi suggested that the sensor could simply be one part of a whole. In other words, there may be many copies of the subunit working collaboratively as part of a complex structure. That’s when AI entered the picture. Dr. Jeremy Amon used an AI tool that can predict complex protein structures. The program predicted that the receptor subunit forms a five-unit ring (a pentamer), which has a channel running directly through the center, just as Artzi suggested.

Opening the gate to awakened bacteria

The researchers tested the AI-generated model working alongside Dr. Fernando Ramírez-Guadiana and members of Professor Andrew Kruse and Associate Professor Deborah Marks’ laboratory, all at HMS. When the scientists engineered spores that had altered receptor subunits that they predicted could widen the membrane channel, they found the spores “resurrected” without nutrient signals. When the membrane channel was engineered to be narrower, spores failed to awaken. The structure of the complex, therefore, is key to whether the gate is in an “open” or “stuck” state whether the bacteria remained dormant.

“The thing that I love about science is when you make a discovery and suddenly all these disparate observations that don’t make sense suddenly fall into place,” Rudner says. “It’s like you’re working on a puzzle, and you find where one piece goes and suddenly you can fit six more pieces very quickly.”

Help in fight against harmful or deadly bacteria

Beyond the satisfaction of helping to solve a longstanding mystery in microbiology, the research team emphasize that this knowledge could help us fight against harmful or deadly bacteria, like anthrax, that are known to enter dormancy for long periods of time.

Bacteria can use dormancy to protect themselves against sterilization in food processing, thereby increasing the risk of foodborne diseases, associated healthcare implications and economic costs. Rudner and colleagues suggest that understanding how spores reawaken from dormancy in more granular detail could help scientists to trigger their “waking up” prematurely. By doing so, the bacteria could be sterilized, or germination could be blocked, preventing them from growing and reproducing. 

This article is a rework of a press release issued by Harvard Medical School. Material has been edited for length and content.