Comparative genomic analysis of T-box regulatory systems in bacteria

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 Tbox 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 (d-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.

T-box-mediated control of the anabolic proline biosynthetic genes of Bacillus subtilis

“…Although proline-responsive T-box systems are predicted to occur widely in Gram-positive bacteria (Gutiérrez-Preciado et al, 2009;Vitreschak et al, 2008;Wels et al, 2008), the data reported here on the regulation of the proBA and proI genes of B. subtilis provide, to the best of our knowledge, the first experimental proof for the functionality of a proline-responsive T-box system in any micro-organism.…”

“…T-box systems are widespread in Gram-positive bacteria, and are sensory and regulatory devices that prevent wasteful overproduction and overaccumulation of amino acids (Green et al, 2010;Gutiérrez-Preciado et al, 2009;Vitreschak et al, 2008;Wels et al, 2008;Winkler, 2007). Tbox systems are RNA-based regulatory switches (Henkin, 2008) that are used in many Gram-positive microorganisms to regulate the expression of aminoacyl-tRNA synthetase genes and of genes involved in amino acid biosynthesis and uptake (Green et al, 2010;Gutiérrez-Preciado et al, 2009;Winkler, 2007).…”

“…T-box-controlled genes typically possess very long 59-untranslated mRNA segments that function as tRNAresponsive riboswitch elements and which can fold into mutually exclusive terminator or antiterminator secondary structures (Green et al, 2010;Gutiérrez-Preciado et al, 2009;Henkin, 2008;Vitreschak et al, 2008;Wels et al, 2008;Winkler, 2007). The amino acid specificity of a given T-box system is conferred through a single codon, the specifier (Grundy & Henkin, 1993), which is present in the 59-untranslated region of each T-box-controlled gene (Foy et al, 2010;Green et al, 2010;Gutiérrez-Preciado et al, 2009;Henkin, 2008;Vitreschak et al, 2008;Wels et al, 2008).…”

“…The amino acid specificity of a given T-box system is conferred through a single codon, the specifier (Grundy & Henkin, 1993), which is present in the 59-untranslated region of each T-box-controlled gene (Foy et al, 2010;Green et al, 2010;Gutiérrez-Preciado et al, 2009;Henkin, 2008;Vitreschak et al, 2008;Wels et al, 2008). The decision between premature termination of transcription and transcription of the full-length gene is made through the combined interactions of the anti-codon of an uncharged cognate tRNA with the specifier codon and the highly conserved 59-NCCA-39 sequence in the acceptor stem of the non-acylated tRNA with a conserved 59-UGGN-39 sequence in the T-box.…”

Celebrating wobble decoding: Half a century and still much is new

“…82 The tRNA Gly UCC is also predicted to bind to the 5′-GGA-3′ Specifier codon in Bacillus and Staphylococcus species glycyl T-box riboswitches. 83 …”