Michael Gilchrist

UTK ecology and evolutionary biology

Protein translation is a universal biological process that occurs in all living organisms.

The instructions a cell uses for making a particular protein are encoded within an organism’s genome. The genome itself is made up of long strings of nucleotides, which join together to form double helix DNA molecules. The genes consist of long strings of nucleotides within a DNA molecule.

Somewhat surprisingly, only four different nucleotide molecules are used to encode the instructions held within a gene—adenine (A), guanine (G), cytosine (C), and thymine (T). As a result, genes encode their information in triplets of nucleotides called codons. Since there are four types of nucleotides (A, T, G, or C) and three nucleotides in a codon, the genetic code consists of 64 different codons (4x4x4=64). However, cells only use 20 different types of amino acids. As a result, the genetic code is inherently redundant with some amino acids having as many as six different codon choices.

Curiously, says JDRD team leader Michael Gilchrist, even though multiple codons can be translated into the same amino acid, they are not all used with the same frequency.

"Highly expressed genes seem to be quite picky (anthropomorphically speaking) about which codon they use to put an amino acid into the protein. In contrast, genes with low expression are not nearly so picky.

"People have seen this pattern for a long time and speculated about its cause. Our goal is to make quantitative inferences about how often a gene is expressed based on how picky it is in its choice of codons," Gilchrist says.

JDRD Project: Integrating models of protein translation and gene fixation with experimental data in the archaeal system: Ignicoccus-Nanoarchaeum; LDRD Project: A systems biology approach to study metabolic and energetic interdependencies in the Ignicoccus-Nanoarchaeum system, Mircea Podar.

An evolutionary biologist, Gilchrist turned to computing power to pull information out of the data. He and LDRD companion project leader, Mircea Podar, are developing computational tools to identify the subtle codon preferences within specific genes and to calculate how often, on average, each gene is expressed during an organism’s life cycle.

"If you know the biological roles these genes play, then knowing how often they’re expressed will tell you how important those different biochemical pathways are to the organism," says Gilchrist, "which should give you a clue about the organism’s life cycle."