Deviant by Design, Part 2 (of 2)

Deviant by Design, Part 2 (of 2)

Study Suggests that Nonuniversal Genetic Codes May Be Good Designs

Last week I made the point that the forces of nature–in addition to corroding national treasures like the Statue of Liberty–also appear to have degraded biochemical treasures like the highly optimized universal genetic code, causing it to yield deviant (or nonuniversal) codes.

(The universal genetic code consists of the set of rules that the cell’s machinery uses to relay the information stored in DNA to the information expressed functionally in proteins. Because of its role, the genetic code resides at the very heart of life’s chemistry. It could be argued that the genetic code is life’s most foundational system and that it defines biochemistry.)

Nonuniversal codes are best understood as deviants of the universal code. Typically, the rules of these deviants are almost identical to the universal genetic code, with only a few minor exceptions. Presumably these alternate codes evolved from the universal code through a microevolutionary process at the biochemical level. Under highly special circumstances, some of the code’s rules can change in a limited manner. For example, careful study reveals that changes in the deviations always occur in relatively small genomes, such as mitochondrial genomes, and involve either: (1) rule assignments that have a minimal, low frequency impact in that particular genome; or (2) rule assignments that tell the cell’s machinery when the information found in DNA comes to an end.

A few weeks ago I pointed out that our creation model allows for optimal designs–once created–to degrade as a consequence of the Second Law of Thermodynamics. It’s possible to understand the nonuniversal genetic codes as a “degraded” version of the optimized universal ones.

Although nonuniversal codes can be accounted for through evolutionary degradation, new research indicates that at least some of them could reflect a Creator’s intention. These deviants appear to be well-suited for the specific biochemical context in which they occur.

To appreciate this new insight, it’s helpful to explain a few details about the structure of the universal code and the nonuniversal variants. As already noted, the cell’s machinery uses the genetic code to translate information harbored in DNA into a format that can be utilized to synthesize proteins. DNA consists of chain-like molecules known as polynucleotides. Two polynucleotide chains align in an antiparallel fashion to form a DNA molecule. (The two strands are arranged parallel to one another with the starting point of one strand located next to the ending point of the other strand, and vice versa.) The paired polynucleotide chains twist around each other, creating the well-known DNA double helix. The cell’s machinery forms polynucleotide chains by linking together four different subunit molecules called nucleotides. The four nucleotides used to build DNA chains are adenosine, guanosine, cytidine, and thymidine, familiarly known as A, G, C, and T, respectively.

Each sequence of nucleotides in the DNA strands specifies a sequence of amino acids in protein chains. The cell employs twenty different amino acids to make proteins. In principle, the twenty amino acids can link up in any of the possible amino acid combinations and sequences to form a protein. They possess a variety of chemical and physical properties. Because of their variable properties, each amino acid sequence imparts the protein chain with a unique chemical and physical profile along its length. The profile determines how the chain folds in three-dimensional space and, in turn, its function.

Three grouped nucleotides that specify the twenty amino acids comprise the genetic code. The nucleotide triplets, or “codons,” represent the fundamental units of the genetic code. Sixty-four codons make up the genetic code. Because the genetic code only needs to encode twenty amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, some amino acids can be specified by up to six different codons. Others are specified by only one codon.

This table shows the universal genetic code. It lists the sixty four codons and their corresponding amino acids. For example, the coding triplets AUA, AUC, and AUU all signify the amino acid isoleucine.

In 1979, researchers studying genes in human mitochondria discovered the first variant of the universal genetic code. (Mitochondria are bean-shaped organelles that play an important role in harvesting energy for the cell’s operations. They possess a small circular piece of DNA that encodes some of the proteins needed to carry out their functions.) Instead of specifying isoleucine, AUA denoted methionine. It’s possible to understand this change as a result of microevolutionary events, but new research indicates a rationale for this deviant of the universal genetic code. This arrangement provides proteins with protection against oxidative damage in the harsh environment of mitochondria.

The energy metabolism in mitochondria generates reactive oxygen species as a by-product. These compounds are chemically corrosive materials that can damage the fragile molecules that reside in mitochondria. In addition to being incorporated into proteins, methionine plays a role as an antioxidant. Methionine reacts with reactive oxygen species. In the process it gets converted to methionine sulfoxide, consuming the harmful oxygen derivatives. An enzyme, methionine sulfoxide reductase back-converts methionine sulfoxide to methionine.

Interestingly, the physicochemical properties of methionine are similar to those of isoleucine. Because of the deviant code, methionines replace isoleucine residues in all of the proteins residing in mitochondria encoded by the mitochondrial genome.

Due to the close similarity in the properties of these two amino acids, these substitutions have minimal impact on protein structure and function. But they do have a profound effect on the structural stability of the proteins in the oxidative environment of mitochondria. By reacting with reactive oxygen species, the incorporated methionines protect mitochondrial proteins from oxidative damage. When this occurs, the methionine residues get converted to methionine sulfoxide and then back-converted to methionine by methionine sulfoxide reductase. If isoleucine, instead of methionine, were used in these proteins then they would not be afforded protection.

Even though the deviant codes of the mitochondrial genomes may be suboptimal, this loss of optimality (at least in mitochondria) represents a trade-off that allows for more robust proteins.

As I discussed a few weeks ago, what may be interpreted as a bad design in nature often turns out to be a good design when more is learned about the system. This seems to be the case for at least some of the nonuniversal genetic codes. And this advance sets up the expectation that perhaps other deviants may well turn out to be good designs as well. If so, these alternate codes can be interpreted as the intentional work of the Creator.

Part 1 | Part 2