New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria.

The tryptophan operon of Bacillus subtilis serves as an excellent model for investigating transcription regulation in Gram-positive bacteria. In this article, we extend this knowledge by analyzing the predicted regulatory regions in the trp operons of other fully sequenced Gram-positive bacteria. Interestingly, it appears that in eight of the organisms examined, transcription of the trp operon appears to be regulated by tandem T-box elements. These regulatory elements have recently been described in the trp operons of two bacterial species. Single T-box elements are commonly found in Gram-positive bacteria in operons encoding aminoacyl tRNA synthetases and proteins performing other functions. Different regulatory mechanisms appear to be associated with variations of trp gene organization within the trp operon.

Elucidating metabolic pathways and digging for genes of unknown function in microbial communities: the riboswitch approach.

In the current post-genomic era, only 3% of all genes have been annotated based on experimental evidence. Even though functions can readily be predicted for many genes, 25% of these are likely to be wrong. The most widely used methods for function prediction rely on sequence similarity, which might be misleading in many cases. Other methods such as genomic context or phylogenetic profiles have been developed to increase gene annotation accuracy; nevertheless these are only efficient when complete genome sequences are available. Here we propose a new approach based on riboswitch identification. Riboswitches are highly conserved regulators of gene expression located in the 5' untranslated region of certain genes. When transcribed they adopt three-dimensional structures that recognize their ligands with great affinity and specificity. This specificity is a key issue for our method, allowing functional assignment with great accuracy.