Skip to comments.Rotary Clock Discovered in Bacteria
Posted on 05/18/2005 11:23:17 AM PDT by DannyTN
Rotary Clock Discovered in Bacteria
What could be more mechanical than a mechanical clock?
A biochemist has discovered one in the simplest of organisms, one-celled cyanobacteria. Examining the three complex protein components of its circadian clock, he thinks he has hit on a model that explains its structure and function: it rotates to keep time. Though it keeps good time, this clock is only about 10 billionths of a meter tall.
Scientists have known the parts of the cyanobacterial clock. They are named KaiA, KaiB, and KaiC. Jimin Wang of the Department of Molecular Biophysics and Biochemistry at Yale, publishing in Structure,1 has found an elegant solution to how the parts interact. He was inspired by the similarity of these parts to those in ATP synthase (see 04/30/2005 entry), a universal enzyme known as a rotary motor. Though structurally different, the Kai proteins appear to operate as another rotary motor this time, a clock.
We learned last time (see 09/15/2004 entry) that the parts interact in some way in sync with the diurnal cycle, but the mechanism was still a black box. Wang found that the KaiC part, a six-sided hexagonal cylinder, has a central cavity where the KaiA part can fit when it undergoes an activation that changes its shape, somewhat like unfolding scissors. Like a key, it fits into the central shaft and turns. The KaiB part, like a wing nut, fastens on KaiB at the bottom of the KaiC carousel. For every 120ö turn of the spindle, phosphate groups attach to the outside of the carousel, till KaiC is fully saturated, or phosphorylated. This apparently happens to multiple Kai complexes during the night.
How does this keep time? When unphosphorylated, KaiC affects the expression of genes. During the night, when complexed with the other two parts, it is repressed from acting, effectively shutting down the cell for the night. Apparently many of these complexes form and dissociate each cycle. As the complexes break up in the morning, expression resumes, and the cell wakes up. When KaiC separates from the other parts, it is destroyed, stopping its repression of genes and stimulating the creation of more KaiC. In summary, he says, the Kai complexes are a rotary clock for phosphorylation, which sets the destruction pace of the night-dominant Kai complexes and timely releases KaiA. The system sets up a day-night oscillation feedback loop that allows the bacterium keep in sync with the time of day.
Wang shares the surprise that a bacterium could have a clock that persists longer than the cell-division cycle. This means that the act of cell division does not break the clock:
The discovery of a bacterial clock unexpectedly breaks the paradigm of biological clocks, because rapid cell division and chromosome duplication in bacteria occur within one circadian period (Kondo et al., 1994 and Kondo et al., 1997). In fact, these cyanobacterial oscillators in individual cells have a strong temporal stability with a correlation time of several months. (Emphasis added in all quotes.)Wangs article has elegant diagrams of the parts and how they precisely fit together. In his model, the KaiC carousel resembles the hexagonal F1 motor of ATP synthase, and the KaiA key that fits into the central shaft resembles the camshaft. KaiB, in turn, acts like the inhibitor in ATP synthase. The close relationship between the two systems may well extend beyond their structural similarity, he suggests in conclusion, because the rhythmic photosynthesis-dependent ATP generation is an important process under the Kai circadian regulation.
Need we tell readers what we are about to say? There is no mention of evolution in this paper. The inverse law of Darwinese stands: the more detailed the discussion of cellular complexity, the less the tendency to mention evolution.
This is wonderful stuff. The cell is alive with wheels, gears, motors, monorails, winches, ratchets and clocks. Paley would be pleased.
I imagine God in this context as someone who uses different techniques to achieve his ends. Evolution may be one of them.
When someone tosses you a ball, do you do calculus to determine where your hand should be in order to catch the ball? Yeah, didn't think so.
I note that, like so many significant papers nowadays, it was not researched in the United States.
Pressures from surrounding cells drives the formation of the hexagonal honey comb. There is nothing supernatural about it at all.
No, if they weren't late, they'd probably be bringing a lot more bacterial clocks with them to church. Better to let them be late and just be glad they are there at all.
Ever catch a ball?
Do you do caclulus to figure it out?
That is essentially what I am saying.
Not only is it an efficient structure, it is the most efficient structure. It is straight forward to use calculus to calculate how "high" the point has to be in order to minimize the surface area of a pointed tetrahedral apex. It turns out that bees set the point height exactly to the value calculus tells us it needs to be to minimize the wax used.
That doesn't even make sense.
I type too slowly.
I am not talking about the fact that they are hexagons. I am talking about the other end. The pointed tetrahedral apex.
(of course who would Buy an illogical clock)
You kidding? Molecular cladistics is likely to be illegal in Kansas in the near future.
....Bees doing calculus just doesn't cut it for me.....
Have you ever listened to their conversations? That would be interesting and until we can understand bees, there's no hope of conversing with extraterrestials.
The other end of the wax cell is spherical and lacks the symmetry, indicating some bees have more than others in the head.
Individual bees can't do calculus - they just do what they're programmed to do. However, evolution can do calculus. If a more efficient structure causes more bee genes to be passed on, eventually evolution will select for the genes that cause the bees to build the most efficient structure - in effect, finding the point at which the slope of the efficiency with respect to each independent structural variable is zero.
Does water have to "do calculus" to form a sphere in a drop? Do you have to "do calculus" to throw a ball over the plate, or hit a moving target with a stone?
Bees that wasted energy making inefficient honeycombs lost out to bees that made them right.
Welcome back! We figured you were on one of your "black ops" projects a la A Beautiful Mind.
No, if the new definition of science goes through, it will be simple:
"This is very complex, I can't understand it. God did it."