Genome size and operon content.

Prokaryotic genes are often organized into operons, clusters of genes that are transcribed together. Because all genes in an operon must be transcribed in the same direction, this organization will be reflected in a tendency for nearby genes to have the same orientation. This tendency can be used to estimate the degree to which the genes in a genome are clustered into operons. Application of the technique to Escherichia coli yields results that are similar to estimates based on detailed examination of the genome and empirical knowledge about particular operons. Results for Saccharomyces cerevisiae are consistent with the near absence of polycistronic transcripts in eukaryotes. The method is easily applied to other genomes that have been sequenced and annotated. Analysis of 26 bacterial and archaeal genomes indicates that the degree of clustering varies widely among prokaryotes. Comparison of these genomes shows that those containing more genes tend to have less clustering of genes into operons. This observation may have implications concerning the evolution of operons. Copyright 2003 Elsevier Science Ltd.