In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding

Fauzi, Hamid; Jack, Karen D.; Hines, Jennifer V.

doi:10.1093/nar/gki546

Cited by 18 publications

(11 citation statements)

References 30 publications

(65 reference statements)

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“…The bound uncharged tRNA stabilizes the antiterminator hairpin, which in turn prevents formation of the terminator and allows the gene to be expressed (Fig. 1A); the structural and kinetic details of this process are now understood in considerable detail (Luo et al 1998;Pelchat and Lapointe 1999;Grundy et al 2000;van de Guchte et al 2001;Grundy and Henkin 2004;Fauzi et al 2005;Yousef et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of T-box regulatory systems in bacteria

Vitreschak

Миронов²,

Lyubetsky³

et al. 2008

RNA

121

223

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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.

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Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of T-box regulatory systems in bacteria

Vitreschak

Миронов²,

Lyubetsky³

et al. 2008

RNA

121

223

View full text Add to dashboard Cite

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“…The importance of tRNA structural features beyond the acceptor end has also been observed in in vitro selection studies with partially randomized tRNA where the predominant sequences selected to bind antiterminator model RNAs were those that retained significant elements of the tRNA tertiary fold (32). In vivo data also support this concept as in vivo antitermination was abolished when significant mutations (i.e.…”

Section: Discussionmentioning

confidence: 86%

T Box Riboswitch Antiterminator Affinity Modulated by tRNA Structural Elements

et al. 2007

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A unique RNA-RNA interaction occurs between uncharged tRNA and the untranslated mRNA leader region of bacterial T box genes. The interaction results in activation of a transcriptional antitermination molecular switch (riboswitch) by stabilizing an antiterminator RNA element and precluding formation of a competing transcriptional terminator RNA element. The stabilization requires the base pairing of cognate tRNA acceptor end nucleotides with the antiterminator. To develop an appropriate model system for detailed structural studies and to screen for small molecule disruption of this important RNA-RNA interaction, steady-state fluorescence measurements of antiterminator model RNAs were used to determine the dissociation constant for model tRNA binding. The antiterminator-binding affinity for the full, minihelix, microhelix, and tetramer tRNA models differed by orders of magnitude. In addition, not all of the tRNA models exhibited functionally relevant binding specificity. The results from these experiments highlight the importance of looking beyond the level of known base pairing interactions when designing functionally relevant models of riboswitch systems.

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“…The authors demonstrated the formation of an ALIL complex using RNase footprinting. Recently a study aiming at identifying the determi- nants of the interaction between tRNA and the tyrST box antiterminator of Bacillus subtilis led to the unanticipated selection of aptamers that generate ALIL associations (Fauzi et al, 2005). In this complex a seven base pair loop-loop helix could be formed.…”

Section: Apical Loop-internal Loop Interactionsmentioning

confidence: 99%