ArticleRNA (New York, N.Y.)2008
Comparative genomic analysis of T-box regulatory systems in bacteria.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
88 citing papers in PubMed, 1 synthesis or guideline pooled it, 133 citations in OpenAlex.
- Evolution of transcriptional regulation of histidine metabolism in Gram-positive bacteria.BMC genomics · 2022Pooled it
- tRNA-dependent conformational dynamics and folding coordinate translational regulation by a full-length T-box riboswitch.Nature communications · 2025Article
- Variation in phylogenetic tendencies of contiguous riboswitches.Microbial genomics · 2025Article
- Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.RNA (New York, N.Y.) · 2024Article
- Translational T-box riboswitches bind tRNA by modulating conformational flexibility.Nature communications · 2024Article
- Valine aminoacyl-tRNA synthetase promotes therapy resistance in melanoma.Nature cell biology · 2024Article
- Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.Nature communications · 2023Article
- A Riboswitch-Driven Era of New Antibacterials.Antibiotics (Basel, Switzerland) · 2022Review
- Streptococcus suis TrpX is part of a tryptophan uptake system, and its expression is regulated by a T-box regulatory element.Scientific reports · 2022Article
- Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action.Nucleic acids research · 2022Article
- Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions.Non-coding RNA · 2021Review
- Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay.Nucleic acids research · 2021Article
- TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs.Nucleic acids research · 2021Article
- A New Promising Anti-Infective Agent Inhibits Biofilm Growth by Targeting Simultaneously a Conserved RNA Function That Controls Multiple Genes.Antibiotics (Basel, Switzerland) · 2021Article
- Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea.Journal of bacteriology · 2020Article
- Unboxing the T-box riboswitches-A glimpse into multivalent and multimodal RNA-RNA interactions.Wiley interdisciplinary reviews. RNA · 2020Review
- Article
- A SAM-I riboswitch with the ability to sense and respond to uncharged initiator tRNA.Nature communications · 2020Article
- An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch.Nature chemical biology · 2020Article
- A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium.Nature communications · 2020Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
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 (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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.