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RNA (2008), 14:717-735. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 RNA Society.
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Comparative genomic analysis of T-box regulatory systems in bacteria

Alexey G. Vitreschak1, Andrei A. Mironov1,2,3, Vassily A. Lyubetsky1, and Mikhail S. Gelfand1,2

1 Institute for Information Transmission Problems (The Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia
2 Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
3 State Scientific Center GosNIIGenetika, Moscow 117545, Russia

T-box antitermination is one of the main mechanisms of regulation of genes involved in amino acid metabolism in Gram-positive bacteria. T-box regulatory sites consist of conserved sequence and RNA secondary structure elements. Using a set of known T-box sites, we constructed the common pattern and used it to scan available bacterial genomes. New T-boxes were found in various Gram-positive bacteria, some Gram-negative bacteria ({delta}-proteobacteria), and some other bacterial groups (Deinococcales/Thermales, Chloroflexi, Dictyoglomi). The majority of T-box-regulated genes encode aminoacyl-tRNA synthetases. Two other groups of T-box-regulated genes are amino acid biosynthetic genes and transporters, as well as genes with unknown function. Analysis of candidate T-box sites resulted in new functional annotations. We assigned the amino acid specificity to a large number of candidate amino acid transporters and a possible function to amino acid biosynthesis genes. We then studied the evolution of the T-boxes. Analysis of the constructed phylogenetic trees demonstrated that in addition to the normal evolution consistent with the evolution of regulated genes, T-boxes may be duplicated, transferred to other genes, and change specificity. We observed several cases of recent T-box regulon expansion following the loss of a previously existing regulatory system, in particular, arginine regulon in Clostridium difficile and methionine regulon in Lactobacillaceae. Finally, we described a new structural class of T-boxes containing duplicated terminator–antiterminator elements and unusual reduced T-boxes regulating initiation of translation in the Actinobacteria.

Keywords: comparative genomics; amino acid biosynthesis and transport; T-box; antitermination; regulatory 5'-UTR mRNAs; bacteria

Received September 6, 2007 ; accepted December 31, 2007.


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