Bacterial cis-regulatory RNA structures

Gelfand, Mikhail S.

doi:10.1134/s0026893306040066

Cited by 7 publications

(3 citation statements)

References 121 publications

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“…Various RNA regulatory systems including riboswitches, translational attenuators, T-boxes, and RNA-binding proteins have been described in bacteria. 7 The main mechanisms involved in regulation by cis-regulatory RNAs are based on the formation of alternative mRNA structures that either terminate transcription (terminators) or inhibit initiation of translation (sequestors). Different classes of RNA elements use different mechanisms to sense the concentration of a metabolite.…”

Section: Analysis Of Rna Regulatory Elementsmentioning

confidence: 99%

“…4 include binding of a small molecule (effector), interaction with other proteins (e.g., phosphorylation), changing redox state, temperature, and other conditions. 5 Finally, various regulatory RNA structures including cis-acting metabolitesensing riboswitches, T-boxes, and attenuators 6,7 and transacting small RNAs 8 control gene expression without involvement of specific proteins. The operon is a set of adjacent genes that are transcribed as a single polycistronic mRNA.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

2007

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TFs and their TFBSs (Section 3). Finally, I discuss the likely evolutionary scenarios for bacterial regulons and the balance of conservation and flexibility in the composition of TRNs among species (Section 4). 2. Computational Methods for Identification of Regulatory Motifs 2.1. Structure, Function, and Representation of Transcription Factor Binding Sites 2.1.1. Position of TFBSs in Promoter Regions-TFs regulate gene expression via specific binding to DNA sequences (or operators) located in promoter regions. The DNAbinding affinity and activity of TFs could be modulated by various signals including interaction with small ligands or covalent modification (e.g., phosphorylation by a specific sensor kinase). When a TF binds to an operator, it can either activate or repress transcription initiation. 30 In bacteria, there are TFs that act solely as repressors or as activators, whereas some other TFs have a dual regulatory role in gene expression. Positive or negative effects of such dual TFs depend on the position of the operator site within the target promoter region. Most repressor sites are located between −60 and +60 relative to the transcriptional start site, suggesting that repression by steric hindrance of RNA polymerase binding to the promoter is the most common regulatory mechanism. 31-33 Alternatively, repressors may act by blocking transcription elongation or by looping DNA in the promoter region (Fig. 1). The degree of repression depends significantly on the operator site position relative to the promoter. 34 Analysis of the data for various negatively acting regulators shows large variability in the relative positions of operators and promoters for each regulon. This variation in the repressor site position is in contrast to the relatively fixed positions of activator sites. Activators promote gene expression by binding to an operator that is located either upstream of or adjacent to, the promoter −35 element and by recruiting RNA polymerase to the promoter by direct proteinprotein interaction (Fig. 1). For example, the global catabolic activator Crp in E. coli binds operators, which have a preference to be centered at positions −62.5, −72.5, or −92.5 at Class I promoters, or at position −41.5 at Class II promoters. 35 Some activators (e.g., those from the MerR family) bind at or near to the promoter elements and alter the conformation of the promoter to allow its interaction with RNA polymerase. 30 2.1.2. Structure of TFBSs-The size of a single TFBS usually varies between ~ 12 to 30 nt, the most common length being 16-20 nt. Since TF proteins often recognize and bind to DNA as homodimers or homo-multimeric protein complexes, the TFBSs usually possess an intrinsic symmetry. Cooperative binding of transcription factors to DNA plays an important role in regulating gene expression, ensuring a sigmoid response to the concentration of effector. Inverted repeats (palindromes) and direct repeats are the most common structures of TFBSs. Some homo-multimeric TFs cooperatively bind more complex TFBSs composed of b...

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Section: Analysis Of Rna Regulatory Elementsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

2007

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“…While the most common regulatory mechanism seems to be regulation of transcription by DNA-binding proteins (van Nimwegen 2003;Rodionov 2007), there are other important mechanisms, in particular, regulation of transcription (by premature termination) and translation (by interference with initiation) via formation of alternative RNA structures in 59-untranslated gene regions (Henkin and Yanofsky 2002;Gutierrez-Preciado et al 2005;Merino and Yanofsky 2005;Gelfand 2006;Weinberg et al 2007). One particular set of genes that are frequently regulated by RNA-mediated mechanisms are the genes involved in metabolism of amino acids.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of T-box regulatory systems in bacteria

Vitreschak

Миронов²,

Lyubetsky³

et al. 2008

RNA

124

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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The LysR-type transcriptional regulator (LTTR) AlsR indirectly regulates expression of the Bacillus subtilis bdhA gene encoding 2,3-butanediol dehydrogenase

Oliveira

Nicholson

2013

Appl Microbiol Biotechnol

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Bacillus subtilis ferments pyruvate to 2,3-butanediol via α-acetolactate synthase, α-acetolactate decarboxylase, and butanediol dehydrogenase (BDH), encoded by the alsSD operon and the unlinked monocistronic bdhA gene, respectively. Upstream and divergent from alsSD is the alsR gene that encodes AlsR, a member of the LysR-type transcriptional regulator family. AlsR directly stimulates alsSD transcription by binding to characteristic sites preceding the alsS promoter, but its effect on bdhA expression was unknown. The effect of AlsR on bdhA expression was assessed in a wild-type strain and a congenic strain carrying an alsR::spc knockout mutation by measuring: (a) expression of a transcriptional bdhA-lacZ fusion; (b) bdhA mRNA steady-state levels by quantitative reverse transcriptase PCR; and (c) expression of BDH enzymatic activity. Activation of bdhA expression occurred in early stationary phase, and expression was lowered, but not abolished, in the alsR::spc mutant. Mapping the transcriptional start site of bdhA by primer extension revealed a 268-nucleotide 5'-untranslated region preceding the bdhA initiation methionine codon. Transcription initiation was not reduced in the alsR::spc mutant, and by electrophoretic mobility shift assay, purified AlsR protein did not bind to the bdhA promoter region, suggesting that bdhA expression is indirectly under AlsR transcriptional control.

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Bacterial cis-regulatory RNA structures

Cited by 7 publications

References 121 publications

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria

Comparative genomic analysis of T-box regulatory systems in bacteria

The LysR-type transcriptional regulator (LTTR) AlsR indirectly regulates expression of the Bacillus subtilis bdhA gene encoding 2,3-butanediol dehydrogenase

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