Let's start by reviewing some basic facts about codons.
Look at the standard genetic code (right). Notice that for some amino acids there are several codons. For example, There are four different codons for alanine (A): GCT (GCU), GCC, GCA, and GCG. These are called "synonymous" codons.
A lot of mutations in coding regions will change one codon into another without changing the amino acid encoded by the mRNA. These are presumably neutral mutations, since they occur frequently in populations and in comparisons between species. What this means is that it mostly doesn't matter which codons are being used.
It's important to keep in mind that there are 50 different tRNAs in most cells and most of them are expressed from multiple copies of their respective genes. There are about 500 tRNA genes in the human genome [Wikipedia: Transfer RNA]. There are many copies of the gene for the alanyl-tRNA with the IGC anticodon but there are also different alanyl-tRNAs with UGC, GGC, and CGC anticodons. The same variation is seen with synonymous codons for the other amino acids.
If you have lots of tRNAs for a particular codon then that codon is going to be translated relatively quickly during protein synthesis. (The rate of protein synthesis is about 20 amino acids per second.) Similarly, if there's a codon that can only be recognized by one of the minor tRNAs then synthesis will be slower. Normally this different isn't significant but there are times when it makes a difference.
Codon usage bias]. An example for Escherichia coli is shown on the left. (Codon bias can also be due to mutation bias and overall GC content of the genome.)
Note that the preferred alanine codon is GCG and the least preferred codon is GCU. This is a reflection of the fact that highly expressed genes tend to use GCG because there are more tRNAS for that codon. Keep in mind that there's only a three-fold difference because for most genes the GCU codon works just fine.
All this has been well known for decades. There have even been studies that measure the translation rate for different codons. I was able to dig from my files a paper that dates back to 1991 (Sørensen and Pedersen, 1991). Those authors showed that the GAA codon for glutamate (E) was translated at 21.6 codons per second while the GAG codon was only translated at 6.4 codons per second.
Long-held assumptions about "silent" genetic mutations have been torn down, challenging a fundamental evolutionary theory.
March 2007I blogged about this back in 2007 when I criticized an article in the now-defunct SEED magazine [Silent Mutations and Neutral Theory]. A reporter for SEED, Lindsay Bothwick, got all excited when a paper was published showing that rare codons slowed the rate of translation and this slow down could be detrimental because it leads to misfolding of the protein.
According to Lindsay Bothwick, this result conflicts with the idea that synonomous codons are "neutral." That was ridiculous back in 2007 and it's still ridiculous. We've known for decades that in some genes there are preferred codons. (But in most genes, it doesn't matter.) Most synonymous mutations are neutral, but some aren't.
Now there's another paper with the same result but a slight twist. D'Onofrio and Abel (2014) have shown that some bacterial genes have translational pause sites that assist protein folding. The idea is that pausing at some of the less preferred codons might actually be beneficial because it allows time for protein folding. There's nothing remarkable about this paper. It's pretty much confirming what we already knew.
Paper Finds Functional Reasons For "Redundant" Codons, Fulfilling a Prediction from Intelligent Design.
A new peer-reviewed paper in the journal Frontiers in Genetics, "Redundancy of the genetic code enables translational pausing," finds that so-called "redundant" codons may actually serve important functions in the genome. Redundant (also called "degenerate") codons are those triplets of nucleotides that encode the same amino acid. For example, in the genetic code, the codons GGU, GGC, GGA, and GGG all encode the amino acid glycine. While it has been shown (see here) that such redundancy is actually optimized to minimize the impact of mutations resulting in amino acid changes, it is generally assumed that synonymous codons are functionally equivalent. They just encode the same amino acid, and that's it.Gee, I wonder where Casey Luskin was when I started teaching this stuff to undergraduates back in 1982? That was years before the modern Intelligent Design Movement produced the Wedge Document. Did he make his prediction before there ever was a "theory of intelligent design"?
Well, think again. The theory of intelligent design predicts that living organisms will be rich in information, and thus it encourages us to seek out new sources of functionally important information in the genome. This new paper fulfills an ID prediction by finding that synonymous codons can lead to different rates of translation that can ultimately impact protein folding and function.
I suppose anything is possible if you believe in gods.
But most of this (below) is not possible (or true) ...
It's this sort of sophisticated, information-rich control that is expected by intelligent design, in contrast to Darwinian biology which fails to anticipate it. On the contrary, Darwinian advocates publish mountains of papers banking upon the unquestioned assumption that there is no important, functional reason for the existence of "redundant" or "degenerate" features. Slowly but surely, the data are turning the tide in the evolution debate.Do you still wonder why I call them "IDiots"?
D'Onofrio, D.J. and Abel, D.L. (2014) Redundancy of the genetic code enables translational pausing. Frontiers in Genetics, May 20, 2014. [doi: 10.3389/fgene.2014.00140]
Sørensen, M.A. and Pedersen, S. (1991) Absolute in Vivo Translation Rates of Individual Codons in Excherichia coli: The Two Glutamic Acid Codons GAA and GAG Are Translated with a Threefold Difference in Rate. J. Mol. Biol. 222:265-280.