Identification of attenuation and antitermination regulation in prokaryotes

Many operons of biochemical pathways in bacterial genomes are regulated by processes called attenuation and antitermination. Though the specific mechanism can be quite different, attenuation and antitermination in these operons have in common the termination of transcription by a RNA 'terminator' fold upstream of the first gene in the operon. In the past, detecting regulation by attenuation or antitermination has often been a long process of experimental trial and error, on a case by case basis. We report here the prediction of over 290 upstream regions of genes with attenuation or antitermination regulation structures in the completed genomes of Bacillis subtilis and Escherichia coli for which extensive experimental studies have been done on attenuation and antitermination regulation. These predictions are based on a computational method devised from characteristics of known terminator fold candidates and benchmark regions of entire genomes. We extend this methodology to 24 additional complete genomes and are thus able to give a more complete picture of attenuation and antitermination regulation in bacteria

Evolution of tuf genes: ancient duplication, differential loss and gene conversion

The tuf gene of eubacteria, encoding the EF-tu elongation factor, was duplicated early in the evolution of the taxon. Phylogenetic and genomic location analysis of 20 complete eubacterial genomes suggests that this ancient duplication has been differentially lost and maintained in eubacteria

Gene context conservation of a higher order than operons

Operons, co-transcribed and co-regulated contiguous sets of genes, are poorly conserved over short periods of evolutionary time. The gene order, gene content and regulatory mechanisms of operons can be very different, even in closely related species. Here, we present several lines of evidence which suggest that, although an operon and its individual genes and regulatory structures are rearranged when comparing the genomes of different species, this rearrangement is a conservative process. Genomic rearrangements invariably maintain individual genes in very specific functional and regulatory contexts. We call this conserved context an uber-operon