Why is this important? How intricate molecular machines evolve is largely unknown. Today’s research shows novelties arising from simpler ancestors – but not byDarwin’s natural selection. Now, no one knows how it happens.
Molecular “machines” work in all animal cells (including humans); bacteria and plants have them too. Gears, axles and crankshafts (their equivalents) are perfectly shaped molecules (thousands of atoms may constitute one molecule). Motors made of molecules propel microscopic creatures. Shuttles transport materials among cellular factories. Pores screen molecules through cell walls. Pumps expel poisons (e.g. chemotherapies from cancer cells!).
The pump that is today’s subject is imaged at the end of this entry. A few other machines are at: www.ks.uiuc.edu/Highlights/?section=2004
How can we know how these things came to be, when their ancestors are extinct?
In fact, a few ancestors of modern machines are known. This helps. Chronological age and structural similarity show their evolution, sort of like knowing that tempus from Julius Caesar’s language is the ancestor of temps (French), tiempo (Spanish) and time. But these proofs are few, and molecular clockworks are numerous. To show how more of them came to be is a delight of science.
Today’s research does that, and adds an enticing mystery, too.
The research studied a pump that flushes electrically charged atoms out of cells. All animals and plants have them. One pump component is a ring (sort of like a ball-bearing housing for the pump’s spinning rotor). Two varieties of protein hook together to make the ring. The 2-protein ring works in all cell types, except one. The exception is a fungus cell; 800 million years ago, it evolved a more complicated 3-protein ring for its pump. The researchers asked: How could this evolve and persist, when 2-protein-rings succeed in all other cells?
At the molecular level, “gene duplication” was how the 3-protein ring arose. Cells divide when, for instance, an embryo’s first cell is proliferating into a whole organ. At each division, daughter cells may make an extra copy of a gene. This is common. At first, each duplicate gene produces the same protein. But genes that were twins originally may mutate differently in later generations. When descendants are no longer identical, they make different proteins.
That’s what happened here. A daughter cell duplicated one gene of the normal 2-protein ring. The duplicate’s mutations eventually constructed a novel, third protein, but (surprisingly) that protein still worked in the pump’s ring. For reasons unknown (see below), this 3-protein novelty became the norm for this fungus cell 800 million years ago.
The researchers asked: was it really true that ancient ancestors, 800 million years ago, had 2-protein rings? Yes, which they ingeniously proved by genetically manipulating modern fungus cells to construct ancient versions with 2-protein ring pumps. These ancestral “machines” worked; they functioned as well as modern, 3-protein-rings do. This shows that an ancestral 2-protein pump “worked,” and was the ancestor of today’s 3-protein version.
(How did they know the structure of the ancient proteins? They deduced it from the structures of 139 similar proteins today. (The analogy, again, is to Latin’s tempus, and today’s temps, tiempo and time. Evolution is deduced from gradual changes over time.))
The researchers’ last finding is the enticing mystery. The 3-protein ring mutation wasn’t an improvement. Cells with 3-protein rings didn’t live longer or reproduce more copiously than 2-protein ones. The mutation was neutral. So why did a more complicated gene duplication that brought no benefits become the norm in fungus cells for 800 million years?
Evolutionary theory doesn’t know. Darwinism posits that mutations (such as 3-proteins from 2-proteins) survive because of their advantages. Mutants survive longer or reproduce more copiously: that’s the theory. But not here. Here, there was no advantage.
The researchers caution: this is one example. Others aren’t yet known. But it is a fascinating instance of evolution occurring, by means unknown, in one of nature’s most ubiquitous and complicated cellular machines.
E. Finnigan et al., Evolution of increased complexity in a molecular machine, 481 Nature 360-364 (January 19, 2012); W.F. Doolittle, A ratchet for protein complexity, ibid, 270-271.
Here are pictorial representations of the pump described in today’s entry. Fig. 1 pictures protein components like carved machine parts. The 3-protein “ring” consists of blue wedges labeled c, c’ and c”.
Image link: sackler.tufts.edu/…/Michael-Forgac
Proteins are not, obviously, blue wedges. Nor are tan ellipses the real appearance of the proteins labeled A and B. Figure 2’s diagrams, below, get closer to cells’ real complexity:
http://www.nature.com/emboj/journal/v28/n23/fig_tab/emboj2009310a_F1.html
Here, curlique tangles represent long protein molecules whose atoms bond in ribbon-like sheets. The left-hand view looks downward into the channel between Fig. 1’s tan ellipses. The right-hand view tilts the pump. Fig. 2’s pale green and mauve ellipses represent the same pump components as Figure 1’s tan ellipses A and B.
Also amazing: the proteins signified by Fig. 1’s tan ellipses whirl. Fig. 1’s “D” and “d” are their protein axle, and the ring of c, c’ and c” is like the axle’s ball bearing housing. (“Cytoplasm” is the interior of the cell.)