Evolution of Complexity in ATPase

How does complexity evolve?  ATPase is a really complicated molecular machine, and how one aspect of its complexity evolved has now been figured out.

Few molecular machines are as complicated as the ATPase, which forms ATP (the “battery” at powers many function in the cell) from ADP, phosphate, and a protein gradient.  ATPase consists of an 8-parted, vaguely windmill-like structure that sticks into the cytoplasm, with a wheel-like 6-parted unit anchored in the cell membrane.  Protons move through membrane via the wheel and that ends what I know about how the ATP is made, but that’s not the point.

Finnigan et al. (2012) explored the history of a change in the 6-parted wheel-like part.  In most eukaryotes (living things with complex cells), this wheel consists of 1 unit we’ll call A and 5 units we’ll call B.  They’re arranged as ABBBBB, with the last B attached to the other side of A.  In fungi, the wheel consists of 1 unit of A, 4 units of C, and 1 unit of D.

The researchers convincingly demonstrate that units C and D evolved from B via a gene duplication event that occurred about 800 million years ago.  Subsequently, several mutation occurred in each gene.  One mutation changed 1 amino acid in what became C and made it able to attach only to A at one side and B at the other.  A change in one amino acid in what became A allowed it to attach to A on side and B on the other, but didn’t allow it to attach to the other side of A.  To complete the ring, therefore, it was now necessary to have ACDDDD (with D attached to the other side of A, making a ring).  Thus the complex ABBBBB ring became the even more complex ACDDDD ring.

The most impressive part of this to me was how the authors casually state, “we introduced historical mutations into [one part] by directed mutagenesis” and then tested whether mutations produced functional ATPase’s in live yeast.  It’s amazing what humans can do with genetics now.

Finnigan, G. C., V. Hanson-Smith, T. H. Stevens, and J. W. Thornton.  2012.  Evolution of increased complexity in a molecular machine.  Nature 481: 360-364.  doi: 10.1038/nature10724.

Is the actual genetic code the best of all possible codes?

Is our genetic code the best of all possible codes? A 2000 article concludes that maybe it is, depending on what “best” and “possible” mean in this context. Although the article goes well beyond my expertise, I attempt to explain.

The genetic code in question is DNA’s “language” of 3-base-pair-long codons, each specifying an amino acid for building proteins.

What would the “best” genetic code be? The authors hypothesize that the best code might be the one that produces the fewest faulty proteins if a mutation changes one of the base pairs in the codon. In this code, a change in DNA would either produce specify the same codon or a physiochemically similar one. But how do we measure amino acid physiochemical similarity? There are several plausible possibilities. The authors test a few. The actual genetic code scores extremely well on one, and they go with that, hopefully not circularly.

How does one measure how good a code is at inserting the same or similar amino acids after point mutations? There are several ways to measure that, too. Authors choose one for reasons that are probably plausible, though I wouldn’t know. Along the way they explain that people using other methods found that there could be many better codes only because they used the wrong method.

Now that they have defined “best” and “similar”, what is “possible”?  The authors briefly explain what random assignment of amino acids to codons would produce a LOT of errors and choose “possible” to mean either “arangements that remain synonymous codon block structure [of real DNA] for all variants” or organized according to a plausible hypothesis of evolution of the code.  Thus they have two different sets data to analyze.

After solving a last problem – how to measure optimality – the authors are ready to report their results.

Results and conclusions:  The code is adaptive and apparently the result of selection for minimizing protein errors after mutation errors. Its apparent excellence is not a result of the analytical methods used. Its excellence is not a result of optimizing treatment of a few extreme amino acids, but of how it treats the entire set. The code is not a result of stereochemic limitations. If the possibilities are restricted to those considered evolutionarily likely and if a realistic transition bias is included, the code is 95-100% optimized. It is possible that no better code could develop under these restrictions.

Under any assumptions, the actual code is extremely good and equally good or better codes are extremely rare. Nonetheless, there theoretically can be a few better codes. Most of these probably can’t evolve given plausible evolutionary starting points for the code. Only under evolutionarily plausible restrictions may the actual code be the best of all possible codes.

Source: Freeland, Stephen J., Robin D. Knight, Laura F. Landweber, and Laurence D. Hurst. 2000. Early Fixation of an Optimal Genetic Code. Molecular Biology and Evolution 17(4): 551-518. DOI: 10.1093/oxfordjournals.molbev.a026331

What are commercial Sheep Fescue cultivars?

Most Sheep Fescue sold commercially is not Festuca ovina, though much of it is labeld as such. These commercial fescues could all have been included in F. ovina when Hackel’s broad concept fo this species was accepted, but that hasn’t been true for the last 60 or more years. So what are commercial Sheep Fescues?

As horticulturalists became aware of that Festuca ovina was broken up taxonomicly, most recognized two species of bunch-forming fine-leaved fescues. The bluish ones were called Sheep Fescue, F. ovina, and the green ones were called Hard Fescue, F. trachyphylla. Actually, nearly all commercial Sheep and Hard Fescues are F. trachyphylla, a widely distributed European grass.

Before I go on discuss the commercial fescues that aren’t F. trachyphylla, I should mention a problem with the scientific name F. trachyphylla itself. The name F. trachyphylla was published twice for different species. Normally, the first publication is the only one that counts. In this case, the name was first used for a South American fescue. That would normally make it unavailable for the European species. However, there was an error in this first publication and some people argue that the name was therefore available to be used for the European grass. If that is true, this grass should be called F. trachyphylla. If the mistake was trivial, however, we have to call it something else. If so, it should be called. F. brevipila. Probably. There are some people who think that this commercial fescue should be considered the same as the wild F. longifolia of Great Britain. If that is true, the much earlier name F. longifolia should be used for our commercial Sheep and Hard Fescues, but other botanists argue vehemently against this. Personally, I use the name F. trachyphylla because Stephen Darbyshire, a recent authority in the group, thinks it’s the right name and I don’t care.

Are there any “Sheep Fescue” that aren’t F. trachyphylla? Yes. I know two and suspect that others are coming into use recently.

Quatro Sheep Fescue, developed for golf courses, is real F. ovina. (Yes, it’s green; don’t let that bother you.)

Covar Sheep Fescue is F. valesiaca, developed from Turkish seeds. Covar is very tolerant of dry conditions. It is widely planted on roadsides in eastern Oregon and is sometimes planted for pasture renovation. I expect more cultivars to be developed from drought-tolerant F. valesiaca. Covar tends to spread slowly into surrounding habitat. Vegetatively, it looks a lot like F. idahoensis, but it can survive on dry, sunny, south-facing slopes where F. idahoensis would die. When fertile, Covar has much more dense inflorescences than F. idahoensis.

As a “handy” wasy to tell them apart, Covar is diploid, the F. trachyphylla cultivars are hexaploid, and I believe Quatro is tetraploid.

Sheep Fescue, not native to North America

Sheep Fescue (Festuca ovina) is not native to North America. Here’s a little history.

Festuca ovina was originally described about 250 yearas ago from Scandinavian specimens. In 1880, European grass expert Hackel wrote an influential monograph on fescues. He worked to show the differences among fescues while at the same time recognizing their similarities. He placed most of the fine-leaved fescues within a few variable “species.”

One of those species was Festuca ovina, Sheep Fescue. Within Sheep Fescue Hackel included fine-leaved bunchgrass fescues from Europe, Asia, and North America. These fescues varied in structure and ecology. Hackel recognized these variation as subspecies, varieties, and subvarieties of F. ovina. Although all “F. ovina” shared the overall look, the subtaxa differ in habitat as well as leaf structure, awn length, lemma length, leaf color, and a host of other details.  Also, many of these forms fail to produce fertile offspring when crossed.  Hackel’s F. ovina species concept was gradually rejected as overly broad.

As botanists and agronomists became more familiar with the fescues, they began separating the more distinct units as species in their own right. At one time, Festuca ovina included such North American fescues as Idaho Fescue (F. idahoensis), Roemer’s Fescue (F. roemeri), Western Fescue (F. occidentalis), Rocky Mountain Fescue (F. saximontana), Alpine Fescue (F. brachyphylla), and Tiny Fescue (F. minutiflora). However, these fescues differ greatly in ecology and their structural differences are real though easily overlooked. By 1969 when Hitchcock et al. published Vascular Plants of the Pacific Northwest, only a few alpine and arctic fescues remained within what was left of the broad Festuca ovina concept.

Since then, further surgery has been performed on the Festuca ovina species concept. Now, the name Festuca ovina is restricted to an arctic/alpine bunchgrass of northern Europe. It is not native to North America.