Fold usage on genomes and protein fold evolution

Abstract

We review fold usage on completed genomes to explore protein structure evolution. The patterns of presence or absence of folds on genomes gives us insights into the relationships between folds, the age of different folds and how we have arrived at the set of folds we see today. We examine the relationships between different measures which describe protein fold usage, such as the number of copies of a fold per genome, the number of families per fold, and the number of genomes a fold occurs on. We obtained these measures of fold usage by searching for the structural domains on 157 completed genome sequences from all three kingdoms of life. In our comparisons of these measures we found that bacteria have relatively more distinct folds on their genomes than archaea. Eukaryotes were found to have many more copies of a fold on their genomes. If we separate out the different fold classes, the alpha/beta class has relatively fewer distinct folds on large genomes, more copies of a fold on bacteria and more folds occurring in all three kingdoms simultaneously. These results possibly indicate that most alpha/beta folds originated earlier than other folds. The expected power law distribution is observed for copies of a fold per genome and we found a similar distribution for the number of families per fold. However, a more complicated distribution appears for fold occurrence across genomes, which strongly depends on fold class and kingdom. We also show that there is not a clear relationship between the three measures of fold usage. A fold which occurs on many genomes does not necessarily have many copies on each genome. Similarly, folds with many copies do not necessarily have many families or vice versa.