Study shows how circadian clocks help bacteria adapt to changing daylight

Nearly all organisms have internal timing systems that help them manage biological processes in response to daily cycles of light and dark. Cyanobacteria, a common group of bacteria that produce oxygen by photosynthesis, have two different kinds of timers: one, a typical, free-running circadian clock that oscillates continuously, and another that runs for a preset amount of time, like an hourglass.

There is a long-running debate among scientists about why these two different kinds of timers exist. Circadian clocks can maintain themselves over a long period of time under constant laboratory conditions, but constant conditions don’t occur in nature. Days are longer and shorter in different seasons, and weather or environmental conditions impact how much light the bacteria might receive on a given day.

New research from the University of Chicago pits the two different timers against each other and shows that while they both perform the same in a consistent light-dark cycle, a free-running clock can adapt to changing periods of light, whereas the hourglass model gets out of sync. The self-sustaining timer likely helped these bacteria adapt to environments further from the equator, where day lengths vary across the seasons.

“We found that if you have a balanced day with 12 hours of light, 12 hours of dark, like if you're at the equator, the output of the two systems is almost indistinguishable. But suppose it’s like the middle of winter in Chicago when the day is much shorter, that’s when the output of these two systems becomes very different,” said Michael Rust, PhD, Professor of Molecular Genetics and Cell Biology and senior author of the study, which was published in Current Biology.

Comparing two types of timers

The results also mapped neatly onto the geographic range of different cyanobacteria species. Those at higher latitudes have free-running clock systems exclusively, and those with an hourglass are found only near the equator. Rust and his colleagues studied a common freshwater bacterium called Synechococcus elongatus, which has a free-running clock to maintain part of its metabolism. The rhythm is controlled by a cluster of three genes named kaiABC, which are present in most cyanobacteria except for one group of marine species called Prochlorococcus, which is missing the first of these genes, kaiA. Importantly, Prochlorococcus also has an hourglass timer.

Rust and his team wanted to engineer a version of S. elongatus that was also missing kaiA to see if that converted it into using an hourglass timer. That didn’t work, but further genetic work showed that Prochlorococcus also had a slightly different version of kaiC. When the researchers created another version of S. elongatus with a ProchlorococcuskaiC, it created an hourglass timer.

“That allowed us to say that in the same organism, we can have either the natural oscillator function, or we can import this hourglass function from its distant relatives,” Rust said. “We thought it was neat that you don't have to make too many changes to go from one to the other.”

Now, able to compare how the two types of timers work in the same species, the researchers tested the effects of different day lengths. The bacteria express genes differently at different times of day, so they were able to measure different levels of expression throughout the changing periods. When dark-light cycles were equal, the two timers performed the same. But as the light periods grew longer, the hourglass system got out of sync.

Just like an hourglass made with sand, the bacterial hourglass runs for a preset amount of time, every time, before it stops. Imagine a timer that is set to activate genes that provide UV protection six hours after sunrise. That works great for a 12-hour day when the sun rises at 6:00 a.m., to catch the highest sun at noon. But as the day lengthens to 15 or 18 hours, that timer will keep activating genes six hours after sunrise, too soon for the true midpoint later in the day.

In contrast, the researchers saw that bacteria with the free-running clocks were able to change their cycles in response to changing periods of light. “In a sense, the clock can remember what the conditions of the past few days were like and adjust itself. So, if it's a summer day, it can shift itself to turn on gene expression maybe nine hours after sunrise instead of six,” Rust said.

Adapting to the modern world

This flexibility has helped cyanobacteria with clock-based systems thrive in environments with variable day lengths, further from the equator. Prochlorococcus is one of the most abundant photosynthetic organisms in the ocean, and a major participant in the carbon cycle. Some scientists speculate that since they thrive in warmer waters near the equator, they may be able to expand their range with global warming as well, increasing their oxygen production. But this new study shows that fitness may be based more on light than temperature.

Rust says the study gives other food for thought about the modern age we live in. “I think it's underappreciated how time-dependent biology is in general. We have our own clock systems that evolved to get inputs from the cycle of the sun rising and the sun setting, changing in different seasons,” he said.

“Now, in the last 150 years, we've basically transitioned to living in dim boxes all the time, not really exposed to the sun in consistent intervals. So, I think really understanding how these systems function when you change the environmental input dramatically from what they evolved under, is an important and challenging problem for understanding our own health.”

The study, “The free-running property of circadian clocks is needed to tolerate changing photoperiods,” was supported by the National Institutes of Health and National Science Foundation. Additional authors include Andrew F. Schober, Caroline Holmes, and Stephanie Palmer from UChicago.