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.
Just a lightning bolt hitting some primordial ooze, nothing to see here...
Here's a good one to ping.
Sounds like the babelfish: Proof of God proves there is not God. ;^>
"Rotary Clock Discovered in Bacteria"
We Toastmasters demand equal time with a Toastmasters' clock.
The atheists' "living jelly" ping.
They later evolved into digital clocks, but until they evolved solar panels, the batteries died quickly and they kept flashing 12:00.
Oh, and until they evolved separate knobs for the volume control, they kept oversleeping.
Msut be a real pain to reset something so small for daylight savings time :-)
I still haven't seen a satisfactory explantion for the pointed tetrahedral apex in the honeycomb where the displacement is approximately 35% of the length of the side of the hexagon (this results in a local minimum on the area). Bees doing calculus just doesn't cut it for me.
FReepmail me if you want on or off my health and science ping list.
Wonder how this could apply to big, complex multicellular life forms, like ourselves, fr'instance.
Can someone interpret this in plain english?
This is going to be good example material the next time my stepson comes home late. "You lost track of time?!?! Even BACTERIA can keep time!"
This is my final proof that Intelligent Design is real science. Clearly, the bacteria were designed by intelligent beings from outer space who, in turn, are very simple, but super intelligent silicone-based life-forms living in a superconducting sea powered by high intensity magnetic fields. They have no moving parts and are therefore simple enough to have evolved from nonliving things. It's not the creation that evolved; it was the creator.
Prove me wrong scientifically.
I suppose this is a Wankel enzyme.
Good question. I see the earths living ecosystem as a bunch of stuff all made from the same leggo set. Discovering something about a small thing made from just a few thousand bricks (like bacteria) could give us a better understanding of things made from significantly more bricks, and brick types.
Or it could be because this was published only two years ago. The problem with making generalizations outside one's field is that someone who is a little more familiar with the literature will generally come along and shoot it all down.
Oh, BTW, hi everyone!
Abstract: Origin and evolution of circadian clock genes in prokaryotes.
Dvornyk V, Vinogradova O, Nevo E.
Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
Regulation of physiological functions with approximate daily periodicity, or circadian rhythms, is a characteristic feature of eukaryotes. Until recently, cyanobacteria were the only prokaryotes reported to possess circadian rhythmicity. It is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Using sequence data of approximately 70 complete prokaryotic genomes from the various public depositories, we show here that the kai genes and their homologs have quite a different evolutionary history and occur in Archaea and Proteobacteria as well. Among the three genes, kaiC is evolutionarily the oldest, and kaiA is the youngest and likely evolved only in cyanobacteria. Our data suggest that the prokaryotic circadian pacemakers have evolved in parallel with the geological history of the earth, and that natural selection, multiple lateral transfers, and gene duplications and losses have been the major factors shaping their evolution.
Explain to me how bees do calculus.
September 24, 2004
Martin Egli, Ph.D., and colleagues including Carl H. Johnson, Ph.D., recently solved the structure (shown on screen) of a biological clock protein in a blue-green algae. Photo by Daniel Dubois
by Leigh MacMillan
If youve ever suffered jet lag while traveling, you can blame your circadian clock. These molecular timepieces synchronize our sleep-wake cycles and a host of other physiological routines with the external environments daily rhythm.
Out-of-sync clocks cause jet lag, make shift work difficult, and have been linked to sleep disorders, some forms of depression, and even cancer.
A flurry of recent research findings is now advancing our understanding of circadian clocks and could ultimately lead to novel treatments for clock-related disorders. Vanderbilt investigators Martin Egli, Ph.D., associate professor of Biochemistry, and Carl H. Johnson, Ph.D., professor of Biological Sciences, teamed to solve the structure of a clock protein in cyanobacteria, more commonly known as blue-green algae.
Blue-green algae are the simplest organism known to have biological clocks. As in higher organisms, like human beings, the clocks in cyanobacteria regulate gene expression, cyclically turning genes on and off. Three proteins KaiA, KaiB, and KaiC, named after the Japanese word for cycle are the key components of the cyanobacterial clock; without any one of them, the clock does not keep time.
Egli and Johnson published the crystal structure a kind of molecular snapshot of KaiC last month in Molecular Cell and reported additional features of the protein this week in the Proceedings of the National Academy of Sciences.
Though the proteins that make up the gears and springs of the circadian clock in cyanobacteria differ from those that form the human clock, the fundamental biochemistry of clock function may be conserved, the investigators said.
Hopefully some of the basic principles that we uncover at the biochemical level [in cyanobacteria] will guide the research in the mammalian systems, Johnson said.
Other investigators have published structures of KaiA and KaiB in recent months, putting the field in a position to tackle complex questions of clock function, Egli said. Theres been this culmination of five years worth of work, all in a matter of months. Its a really exciting time.
The KaiC structure is already providing hints to its biochemical operations, but the investigators stressed that the work is still in an early stage.
Even though weve learned things from the structure, Egli said, the big question still is: what are the underlying biochemical mechanisms that allow organisms to control their rhythms so precisely?
Six KaiC molecules appear to group together, into a ring-like structure that looks something like a mechanical gear oddly appropriate, given its function as the core of the timepiece. KaiA and KaiB associate with the KaiC ring depending on a biochemical reaction called phosphorylation. Egli and Johnsons work has identified three phosphorylation sites on KaiC; mutation of any of these sites turns off the clock.
The KaiC structure reveals unexpected evolutionary relationships to proteins that manufacture the energy molecule ATP and to DNA pumps. What these similarities mean is still anyones best guess, Egli said. But armed with the structures of all three Kai proteins, investigators are poised to make progress at solving how the cyanobacterial clock keeps time.
I think there must be some unusual mechanism, Egli said.
In addition to potentially offering new avenues for treating some sleep disorders and forms of depression, clock research raises questions about timing of medication dosing. There may be optimum times of day for hitting a particular target, depending on the cycling of genes on and off. Other groups are investigating whether the timing of chemotherapy, for example, can reduce side effects and enhance efficacy, Egli said.
Circadian clocks, the researchers said, are increasingly being recognized as fundamental to biology.
The emerging idea is that the organism is basically a clock shop that everything is oscillating, Johnson said. The function of the brain then, specifically certain parts of the brain, is to keep all of that organized and synchronized. The brain acts as a pacemaker for all of the other clocks in all of the other cells in the body, even in your big toe.
The research was supported by the National Institutes of Health, the National Science Foundation, and a VUMC Intramural Discovery Grant.
Yeah, but us eukaryotes got digital clocks! Virii, OTOH use sundials.
Howdy, stranger ;^)
Sounds like the assembly instructions that came with the last barbecue I bought.
A person who disdains ID might find a simple object such as a toaster. He never thinks it assembled itself or evolved from it's parts or the raw materials that they are made from.
The same person looks at the simplest creatures and plants, made up of millions of cells which all have different and perfectly coordinated purposes and somehow concludes it was all a big coincidence.
Fairly interesting to contemplate.
Don't you love the way that the 'a priori' commitment to evolution interprets observations. Similarities are instantly assumed to be evolutionary relationships. Even as they admit to not having a clue.
Local minima (or maxima, depending) occur naturally all the time, just due to the way that various forces or processes interact. For example, soap bubbles are spherical -- minimizing the surface area for the volume of air included -- because that's what happens when the surface tension at every point pulls surrounding portions of the bubble surface towards each other. Because the surface is "trying" to contract, it quickly results in a spherical shape where all the forces equalize (because the curvature is equal at all points).
A somewhat more complex manifestation of the same thing (also in soap bubbles) results in something very much like the bee's honeycombing -- whenever three soap bubbles are stuck together, there results a point between them where three planar bubble surfaces are exactly 120 degrees apart from each other (like the "joints" of a hexagonal array or honeycomb). Get enough bubbles of roughly equal size on the surface of something, and they'll naturally form a "honeycomb" configuration:
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.
A lot of things that may look like "design" or "structure" often turn out to be the result of simpler processes when you take the time to learn about them. The same goes for a lot of the biological mechanisms, which is why the usual creationist method of "looks fancy to me, *must* be designed" just doesn't hold water. Especially when natural processes like evolution are *proven* producers of amazingly "clever" results, including some that are still beyond human understanding.
LOL!!!!. I know what you mean. EASY TO ASSEMBLE my bare pasty white rump!
I believe in ID, but I am an "old-earthist." Heretical as it may be, I imaging God experimenting with a chemistry set (picture the Far Side cartoon, "God as a young boy makes his first chicken," with God holding a smoking test tube and surrounded by smoke and floating feathers).
Back in my day they did. We didn't have any of that fancy "surface tension" kids nowadays do.
Well, you'll have to explain to me how a detailed analysis of the kai genes across a large number of species of cyanobacteria, proteobacteria, and archaei, showing that their interrelationships have the form of a tree, and how that tree has a very similar structure to the tree obtained by examining relationships between the genes for a completely different molecule, the 16S RNA, is a 'just-so' story.
To help you, here are the two trees. Enjoy.
It's terrible. Astronomers make the same mistake when new phenomena are not attributed to the flatulance of Woton. In fact, astronomers are so biased they don't even consider the possibility.
Your jump from soap bubbles to bees is missing a few steps. Where, exactly, is the surface tension force "working out", as you put it, in the bees constructing their honey combs?
Well, my immediate question, being a pastor, I have this one family who is late every week,so if i give them this bacteria clock will they get to the church ontime??heh!!
Truth is so boring.
Creationists misrepresenting science ping.
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.