Mighty Mitochondria Conduct Energy Exquisitely

None of us could live without mitochondria.  These are the power centers ubiquitous in eukaryotic cells.  They contain molecular machines in factories whose jobs are to generate and conduct electrical currents.  The currents run turbines that packetize the energy in molecules of ATP, which are then used by most processes in the cell.  New discoveries continue to fascinate scientists with how mitochondria work.  Some scientists use their energy to find ways Darwinian evolution could build the machinery of life.

Background.  The energy source for animals is food; for plants, the sun.  Since animals eat plants, or eat other animals that ate plants, sunlight is the ultimate energy source.  In the chloroplasts of plants, sunlight energy is captured to produce energy-rich molecules, including glucose.  Mitochondria have inner and outer membranes.  The inner membranes are folded into protrusions called cristae that increase their surface area.  With the help of transporter machines, the mitochondrion takes in molecules (glucose, pyruvate, and NADH) from the cytosol into its outer and inner membranes into the interior where, with the aid of oxygen and a large number of enzymes and cofactors, electrons are transferred to oxygen through five complexes of machines.  The first three, called NADH dehydrogenase (Complex I), cytochrome c reductase, and cytochrome c oxidase, provide an “electron transport chain” that is used to pump protons into the space between the mitochondrion’s inner and outer membranes.  The protons return through the inner membrane via the fifth machine, the turbine-like rotary motor ATP synthase (see CMI), which uses the proton motive force generated by the other machines to synthase ATP.  Although cells can generate ATP without oxygen (anaerobic respiration), producing it through the mitochondrial machinery is much more efficient.  On a busy day you produce approximately your body’s weight in ATP.  This entry will look at some of the recent discoveries about the machinery of mitochondria.

1. Machine spacing:  An abstract on PNAS (8/29/2011, 10.1073/pnas.1107819108) described what new images of mitochondria using single particle cryoelectron tomography revealed.  Dudkina et al. could see how Complexes I, III, and IV are organized in mitochondria from cow hearts.  The spacing affects how the complexes interact.  “Surprisingly,” the Dutch and Swiss scientists said, “the distance between cytochrome c binding sites of complexes III₂ and IV is about 10 nm.”  Ten nanometers is quite a bit at this scale.  Fortunately, there is a molecular glue – fat – that keeps them in place: “Modeling indicates a loose interaction between the three complexes and provides evidence that lipids are gluing them at the interfaces.”
2. Architectural machines:  PhysOrg reported on research at the University of Freiburg in Germany that identified another large machine whose job is to keep the inner and outer membranes from detaching.  “The researchers identified a huge molecular machine made up of six different membrane proteins required for attaching the cristae to the envelope of the mitochondria in the unicellular model organism baker’s yeast,” the article said.  “The data show that the defects in the protein complex trigger the detachment of the cristae, which in turn results in significant growth disturbances in the cell.”  Science Daily’s coverage called the structures produced by these machines the “supporting pillars of the structure of cellular power plants”.
3. Power plant placement:  Current Biology summarized a finding about how mitochondria are placed along the cell’s highway system.  “In fission yeast, microtubules control mitochondrial position by a mechanism that is dependent on microtubule dynamics but not motor proteins,” Liza A. Pon wrote in the Sept 13 issue of Current Biology (21:7, 10.1016/j.cub.2011.07.035). “A new study now reveals the molecular basis for this novel mechanism of organelle movement.”  In essence, mitochondria do not ride the rail cars (dynein and kinesin) like other organelles; they fasten to the tracks which shorten and stretch to put them where needed.  “This binding results in the uniform distribution of mitochondria as elongated tubular structures by two mechanisms: first, microtubule bundles serve as a scaffold to maintain the position of the organelle; and second, elongation of microtubules results in extension of mitochondria toward the cell tip.”  Another reason for the unusual mode of distribution may be to ensure that mitochondria (which divide by their own mechanism, with their own DNA) end up correctly in the daughter cells after cell division.
4. Mitochondrial division:  “New research from the University of California, Davis, and the University of Colorado at Boulder puts an unexpected twist on how mitochondria, the energy-generating structures within cells, divide,” an article on PhysOrg began.  The researchers found that “mitochondrial division overwhelmingly occurred at points where the two structures, mitochondria and ER [endoplasmic reticulum], touched.”  Why is that?  “Their study indicates that ER tubules first squeeze the mitochondrion, then dynamin-related proteins assemble on the surface to complete the job.”  They called this finding that “transforms our view of cell organization” a “paradigm shift in cell biology.”  Proper controls on mitochondrial division are vital.  “Defects in mitochondria have been linked to a wide range of degenerative conditions and diseases, including diabetes, cardiovascular disease and stroke.”
5. Mitochondrial genome:  Since mitochondria are approximately bacteria-sized, and contain their own DNA which they replicate with their own machinery, evolutionists believe that at some time in the history of life the first eukaryote engulfed a free-living bacterium and developed a symbiotic relationship with it.  Whether this theory of “endosymbiosis” is defensible is a question for another time (see 6/09/2006), but PhysOrg did have some news about the machine that transcribes mitochondrial DNA, “mitochondrial RNA polymerase” (an analogue of the RNA polymerase in the nucleus).  Scientists at the Ludwig-Maximilians-Universitat Munchen were able to image the 3-D structure of this molecular machine in atomic detail.  They found similarities to the RNA polymerases found in phages (viruses that attack bacteria) and speculated those as the source of mitochondrial RNA polymerase.  But they also found that this machine is not a lone ranger: “In particular, the structure explains why two other protein factors are necessary to enable the RNA polymerase to bind at the right site on the DNA, and to transcribe the genetic information from this location,” one of the scientists said.  Interestingly, one of the machine complexes (Complex II) gets its genes from the cell nucleus.  The mitochondrial genome is passed on through the female.
6. Why you’re so tired:  Science Daily reported on work from McMaster University that may explain some couch potatoes.  They may be missing genes that generate mitochondria.  Mice with defects in the AMPK gene had fewer mitochondria and less energy.  Professor Gregory Steinberg explained, “When you exercise you get more mitochondria growing in your muscle. If you don’t exercise, the number of mitochondria goes down. By removing these genes we identified the key regulator of the mitochondria is the enzyme AMPK.”  It’s not an excuse, of course; you can increase your mitochondrial count through exercise.

How did this all evolve?  “The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not,” wrote a team of three scientists from Alaska and Canada in a paper entitled, “Positive Darwinian Selection in the Piston That Powers Proton Pumps in Complex I of the Mitochondria of Pacific Salmon” (PLoS ONE 6[9]: e24127. doi:10.1371/journal.pone.0024127).  So they decided to address the question.  Readers might remember the amazing discovery that Complex I uses a piston-rod mechanism to pump protons in the electron transport chain (7/6/2010, 9/22/2010).  Now, Garvin, Bielawski and Gharrett looked for evidence of positive Darwinian selection for these pistons in salmon, but is their answer just a fish story?  In a sense, yes; they only looked for evolution within one kind of fish: “These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon.”  They did not attempt to explain where the pistons came from in the first place; they only discussed slight changes in the amino acid sequences in the proteins for part of Complex I between salmon species, which they attributed to “positive selection” (natural selection acting for a positive change in function, or innovation). 

In passing, they pointed out some interesting facts about mitochondria.  Mitochondrial genes tend to accumulate mutations faster than nuclear genes.  “The rate difference was previously thought to be due to the lack a proof reading activity by the mitochondrial DNA polymerase… but recent work suggests the replication machinery does indeed proof read,” they said.  “A current theory posits that free radicals or reactive oxygen species, which are a byproduct of superoxide production by complexes of the oxidative phosphorylation system, damage the mitochondrial DNA (mtDNA) and produce a higher mutation rate.”

Bad mutations, they admitted, have disastrous consequences on human health, but then they assumed the converse: “It follows that other mutations may have beneficial effects on metabolism and thereby positively affect fitness.”  That's a logical fallacy; other mutations might simply be neutral.  Just because some brickbats harm computers, it doesn't follow that other brickbats will have beneficial effects.  They offered some weak empirical evidence to try to back that statement up – evidence they admitted is countered by other evidence.   So did they find evidence for positive Darwinian selection?  Is there a new function or improvement of function in salmon due to mutations in the mitochondrial DNA?  (Remember, they were only looking at the piston arm in Complex I of a five-machine system.)  Not really.  They used models, Bayesian analysis and phylogenetic methods to see if mutations differed from what would be expected if purely random or due to neutral drift, and if non-synonymous substitutions outnumbered synonymous substitutions (a synonymous substitution yields the same amino acid).  Then they tried to see if the mutations occurred in functionally important parts of the Complex I piston arm they were studying.  Of the seven candidate substitutions they found, only two were long-term, they said.  They also pointed out that their study was only the third of its kind (looking for positive selection in the mitochondrial genome).

In their Discussion section, they put their best foot forward.  “We observed that changes in the piston arm and, consequently, proton pumping, may have influenced fitness during the evolution of Pacific salmon species.”  But they didn't tell the fish they were better off thanks to Darwin.  The mutations might do something: “it is likely that the positively selected mutations influence the electrochemical gradient, which is comprised of both a voltage potential and a difference in pH,” they suggested, but they were not ready to say that it actually helped the salmon get more energy, avoid reactive oxygen species, live longer, or anything else.  In fact, any connection between these seven mutations and a functional benefit to the fish had to be shuttled off to the future: “When a higher resolution structure becomes available, it should be possible to determine which of the specific amino acids in the ND5 piston arm interact with which proton pumps and the nature of the changes in the interactions that result at the sites under positive selection,” they concluded.  “This might provide information to determine if the piston arm is more tightly or loosely coupled to the pumps and therefore if pumping is made more or less efficient by the amino acid substitutions.”  So very little was actually learned by this evolutionary exercise.  In fact, they stated outright, “It is not possible to correlate the selected amino acid sites with Pacific salmon life-history at this point.”  To do that, someone would have to do field studies: “Empirical studies that established functional differences among species would make this connection possible.”  Maybe someone could take the salmon under controlled conditions and compare their oxidative output.  Even so, they are still all salmon, and they seem to get along quite well in their habitats. [Note: even creationists can accept diversification of salmon from an original created kind, so their findings, even if they did support positive selection, would not differentiate between creation and evolution.]

The kicker is in the last two paragraphs.  Despite their boast that “Our discovery of positive selection in a protein that is central to energy metabolism establishes an explicit connection between molecular evolution, protein function, and respiration,” they had just let the cat out of the bag in the prior paragraph: “Our SCA identified potentially important regions within the ND5 protein with respect to the sites under selection. However, this may have been simple phylogenetic signal, and we were not able to identify specific sites that were coupled to the positively selected sites with any certainty.”

Doggone; we just read that whole paper for nothing?  This is like government waste: lots of verbiage, lots of paper, with little to show for it.  They generated pages of models, Bayesian analysis, sequence comparisons, and at the end, out popped seven mutations that they couldn’t tie to any improvement for the salmon, other than that they didn’t get proof-read out.  Then they tell us that they couldn’t say anything for certain! 

All the while, the wonders of mitochondria and of salmon were staring them in the face.  Pacific salmon turn their food into energy through a complex series of molecular machines inside an organelle containing genetic information that is transcribed, copied and proof-read by other molecular machines.  ATP synthase, the last machine in the respiratory chain, is a marvelous rotary engine that is irreducibly complex, pumping out ATP like gangbusters all the time (see CMI).  Then the fish take this ATP energy and “smell” their way up miles of river, leaping up waterfalls with all that chemical energy, to find the exact spot where their parents spawned them in prior years.  Those wonders scream “design!” – but choosing to ignore it, the Darwinists, focused on a few base pairs in one enzyme of the machine, look for tiny bits of wee changes that might vindicate Charlie against the mountain of evidence against him.  Pity is hardly a sufficient emotion for these ingrates.  We hope other scientists will use their brain ATP for nobler pursuits.