Comparative genomic analysis of T-box regulatory systems in bacteria

Alexey G. Vitreschak, Andrei A. Mironov, Vassily A. Lyubetsky, Mikhail S. Gelfand

Research output: Contribution to journalArticlepeer-review

103 Citations (Scopus)

Abstract

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 (δ-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. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish
Pages (from-to)717-735
Number of pages19
JournalRNA
Volume14
Issue number4
DOIs
Publication statusPublished - Apr 2008
Externally publishedYes

Keywords

  • Amino acid biosynthesis and transport
  • Antitermination
  • Bacteria
  • Comparative genomics
  • Regulatory 5′-UTR mRNAs
  • T-box

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