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.)Wang’s 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.
What does this mean? I warn you, I hated geometry and algebra, but this sounds interesting.
Carolyn
If you look at your soap bubble picture, you will see numerous pentagons, especially one layer in from the edges. And if you try to visually follow the rows they don't have the same neatness as honecombs.
If it's the same force So why don't the honeycombs look more like the bubbles around the edges of the combs.
Plus don't the bees build the honeycombs one layer at a time. I don't see how the comb would have the opportunity to reorganize itself into a honeycomb shape the way you are suggesting.
Source>>>>>
Extensive personal observation.
The capped end is hemispherical
Do you have a cite for that?
I'm interested iin the stimulus (or stimuli) for the transition from hexagonal prism to tetrahedral pyramid.
If you look at your soap bubble picture, you will see numerous pentagons, especially one layer in from the edges. And if you try to visually follow the rows they don't have the same neatness as honecombs.
If it's the same force So why don't the honeycombs look more like the bubbles around the edges of the combs.
Plus don't the bees build the honeycombs one layer at a time. I don't see how the comb would have the opportunity to reorganize itself into a honeycomb shape the way you are suggesting.
Ichneumon explained that quite nicely in his reply to you:
Similarly, the "dome" on each one will be the "approximately 35% of the length of the side of the hexagon", as you decribe it, which "results in a local minimum on the area". It's just the way the surface tension forces work out, the molecules don't have to "do calculus". And neither do the bees.
Exactly how did you know that, hmmm?
Memo to self: have office swept for electronic devices again.
The bees do no calculus. The combs grow like crystals-once an initial hexagon is created the bees simply replicate that shape and size. The original hexagon is an optimum shape programmed through instinctive behavior.
http://www.ars.usda.gov/ar/archive/may97/beecells0597.htm
-snip-
"The scientists did this by installing in the hive sheets of starter cells that are smaller than those typically used by beekeepers. Commercially managed honey bees use these starter cells as a blueprint for building their honeycomb. With wax they manufacture themselves, they form thousands of cells to create the many floors of the honeycomb. The smaller the starter cells, the smaller the cells the bees themselves construct."
bump for later
I did a lot better in engineering mechanics than in biochem, so this explanation works for me.
Like the old maps of Africa that said "there be monsters here"
Exactly. Complete with the implication of "Don't go there"
I don't assume the bees do calculus but your use of the word "programmed" is appropriate. I don't believe it's an evolved instinct.
The bees build the original hexagon shape. And while they can be coaxed to build smaller hexagons through the use of a starter row, I doubt they can be coaxed to build anything other than hexagons.
Just because there is a mathematical way to solve a problem does not mean that every solution to that problem was done mathematically.
Using calculus you can determine the flight path of a ball thrown to you and calculate the intercept point, but that's not how people catch objects in flight.
Fascinating Professor. I have never seen the evolutionary tree for bacteria, but say, does it represent ALL known types? Or just the ones under discussion? Where's gonorrhea, streptococcus, nitrogen-fixing soil bacteria, etc. on the tree? I was under the impression that cyanobacteria had been assigned their own separate kingdom.
A plain jane timer eliminates such nasty things as division by 6 or 60, and other nasty details of man's struggle to discover best how to keep track of time and the seasons.
Well, I should hope that someone along the chain of this story had the minimal smarts to tell the difference.
And we wonder why our children can't seem to learn?
SMASH!!!!! AYYYYYYYY!!! You killed my long lost grandpa!!!
They seem to have omitted most of the Proteobacteria for which 16S sequences are known, probably because there are so many. But those would include the organisms you mention.
I was under the impression that cyanobacteria had been assigned their own separate kingdom.
The paper suggests an origin of kaiB 2300 million years ago. That would be after the cyanobacteria diverged from the others, which don't have kaiB. So the cyanobacteria have had a separate lineage for around 2.5 by, which is old enough to give them a kingdom, IMHO.
I know. I answered him.
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