Guiding the Blind Watchmaker again

Both mitochondria and chloroplasts have ribosomes, as we would expect from the endosymbiotic theory. During the history of plants, the gene rps13 was moved to the nucleus. It codes for the chloroplast ribosomal protein S13. Yet early on, a gene duplication occurred in the nucleus, giving us two versions of the gene: nucp rps13, that is sent to the chloroplast, while the other encodes a mitochondria-imported RPS13 (numit rps13).

In other words, after gene duplication, one of the chloroplast ribosomal proteins evolved to become a mitochondrial ribosomal protein. So what if we compared the sequence of numit rps13 to standard mitochondrial rps13?

Researchers found 16 sites where the amino acids in those sites had changed from the original chloroplast version to become residues commonly seen in the mitochondrial proteins. The figure below maps those sites in two different bacterial versions of the ribosomal protein (since we have the three dimensional structures of these proteins) and as you can see, the changes are evenly dispersed throughout the protein:

Red regions and plus signs indicate relative positions of positively selected sites. Green regions and asterisks indicate relative positions of amino acids in numit Rps13 in at least one rosid species that have mutated to the amino acid present in mt rps13 genes. From reference below.

So what does all this mean?

According to the researchers:

Because numit rps13 was derived from nucp rps13 and encodes a RPS13 protein that functions in the mitochondria, we were interested in determining if the numit RPS13 has become more like the mt RPS13 amino acid sequence.

And conclude:

The sixteen amino acids in one or more rosid species that have changed to the amino acid present in mt RPS13 indicate that numit RPS13 is becoming more like mt RPS13. We propose that this is a type of convergent sequence evolution of numit rps13 that possibly improves the function of numit RPS13 in the ribosome.

In other words, the blind watchmaker is reinventing the mitochondrial protein S13. But how can it do so if it is blind? The answer is obvious – the blind watchmaker is being led by a seeing eye dog again. In this case, the seeing eye dog is the chloroplast S13 protein fold which provides the framework, and the mitochondrial ribosome, which will interact with the S13 protein. Together, these structures serve as bait to fish out the appropriate amino acids at the appropriate positions for crafting the mitochondrial versions of S13.

This is just another example where natural selection is being guided by the intrinsic structures and design of the cell.

1. Liu and Adams BMC Evolutionary Biology 2008 8:25

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