Another Problem Bacteria Have to Worry About, and How They Solve It Effectively
Evolution News & Views
In 1665, the Dutch physicist Christiaan Huygens put two pendulum clocks next to each other. To his surprise, after half an hour or so, they started swinging in sync (actually, anti-sync, in opposite directions). No matter where he put them, or how off-sync they started, it happened over and over. This phenomenon, called phase locking, has been confirmed in many different situations, including heart cells that twitch together, fireflies that fire together, and moons that synchronize their spin with their orbital velocity.
In 2002, Nature reported that the "350 year mystery" of Huygen's clocks had just been solved. If there is just the right amount of energy transfer between two oscillators, experiments showed, they will begin oscillating in sync. More recent articles, such as in Scientific Reports and Live Science (2015), and again by different scientists in Scientific Reports this year, claim again that the 350-year mystery has just been solved. These announcements suggest that the intriguing phenomenon is still not fully understood.
Synchronization can have good or bad biological consequences. Jonatan Peña Ramirez (co-author of the 2016 paper in Scientific Reports) says in Live Science:
"Something similar happens in living organisms," Peña said. "For instance, inside the human body, there are several biological rhythms -- respiration, heartbeat and blood perfusion, just to mention a few of them. It has been found that when some of these rhythms synchronize with each other, the energy consumption is minimal; hence, in this case, the onset of synchronization is beneficial. On the other hand, synchronization can also be dangerous or detrimental; it is widely accepted that the process of seizure generation is closely associated with abnormal synchronization of neurons." [Emphasis added.]
Too bad nobody warned bacteria about this. Since their first appearance on earth, these "simple" microbes confronted a deleterious synchronization problem. On one hand, they need a reliable biological clock that keeps sync with 24-hour day/night cycles. On the other hand, they have to divide on a regular basis. The two cycles are close enough in time to create a phase-locking situation. If not mitigated, the cell cycle could force the circadian clock to lose accurate time. Somehow, though, the bacteria are able to keep the two cycles from interfering.
Now, Dutch scientists, appropriately, have discovered the mechanisms bacteria use to avoid phase locking. Publishing in PNAS, they point out that it is no easy trick to escape the forces of physics:
Huygens famously showed that two mechanically connected clocks tend to tick in synchrony. We uncovered a generic mechanism that can similarly phase-lock two rhythmic systems present in many living cells: the cell cycle and the circadian clock. DNA replication during the cell cycle causes protein synthesis rates to show sharp, periodic jumps that can entrain the clock. To faithfully keep time in the face of these disturbances, circadian clocks must incorporate specific insulating mechanisms. We argue that, in cyanobacteria, the presence of multiple, identical chromosome copies and the clock's core protein-modification oscillator together play this role. Our results shed new light on the complex factors that constrain the design of biological clocks.
You can imagine the problem. Picture yourself as a conductor trying to keep a steady beat before a school band, while outside some machinery is emitting loud periodic sounds off of your rhythm. It would be tempting to synchronize your downbeats with the machinery. One way to protect your beat from outside influences would be to install heavier insulation in the walls to mask the sound.
The problem is worse for the cyanobacterium S. elongatus used in the research, because both rhythms are "intricately intertwined," they point out. The circadian clock keeps a steady rhythm by transcribing and phosphorylating 3 proteins, KaiA, KaiB, and KaiC, calibrated by day-night cycles and other environmental cues. Interrupting this rhythm periodically, the process of mitosis copies all the DNA, sending surges of protein, including the clock proteins, into the mix as the cell prepares to divide. For the clock, this "can dramatically alter its behavior and impair its function."
Think about it; the circadian clocks in both daughter cells must keep time through all this construction work without losing a beat. They do this with "specific insulating mechanisms," the paper says, employing not just one, but two complex methods:
We argue that the cyanobacterium Synechococcus elongatus has evolved two features that protect its clock from such disturbances, both of which are needed to fully insulate it from the cell cycle and give it its observed robustness: a phosphorylation-based protein modification oscillator, together with its accompanying push-pull read-out circuit that responds primarily to the ratios of different phosphoform concentrations, makes the clock less susceptible to perturbations in protein synthesis; the presence of multiple, asynchronously replicating copies of the same chromosome diminishes the effect of replicating any single copy of a gene.
Graphs in the paper show how pulse waves get damped by these mechanisms, so that the cell cycle's rhythms are effectively insulated from the circadian clock. And they're right; it is complex. The bacterium uses a transcription-translation cycle (TTC) and a protein-phosphorylation cycle (PPC) to weaken the coupling between the cell cycle and the clock. Another enzyme, RpaA, which communicates the clock output to downstream genes, is effectively insulated from the cell cycle by the TTC and PPC. Independently, the bacterium also uses multiple chromosome copies to insulate the clock from protein surges:
The presence of multiple chromosome copies has a still more striking effect: If the cell has four copies after division (rather than only one), as can often be the case in S. elongatus, and if these are replicated one after the other, then the dose of the clock genes changes much more gradually, and cell-cycle effects are almost completely lost. Thus, S. elongatus may have evolved to carry multiple, identical chromosome copies in part to insulate its circadian clock from its DNA replication cycles.
ID advocates know not to choke on the phrase "may have evolved." What else could they say? That this multi-part protective mechanism was intelligently designed? One sympathizes with the authors' plight. Omitting the obligatory word "evolved" could likely have disqualified the paper from publication. Take comfort in the fact that design received equal mention with evolution. For example,
We propose that cyanobacterial clocks have evolved specific features that can mitigate this effect. More broadly, this generically strong coupling to the cell cycle implies important constraints on the design of biological timekeepers if they are to remain accurate in dividing cells....
Our analysis thus highlights an important constraint on the design of circadian clocks in organisms from bacteria to humans.
Something had to be aware of this problem long before Huygens discovered it in 1665, and had to come up with insulating mechanisms to prevent it. Was it natural selection? Unlikely; the cell needed multiple methods to solve this one type of crisis. It needed to build a TTC, a PPC, and allow for multiple chromosome copies timed to replicate in series. That's three complex systems for one solution. Without all these methods working together, the circadian clock would likely drift, resulting in dramatically altered behavior and impaired function. Was that the work of sheer dumb luck that "may have evolved" that way?
The researchers write, "Our results shed new light on the complex factors that constrain the design of biological clocks." Light on design is a beautiful thing.
Want a list of previous articles about circadian clocks at Evolution News? Here you go.
