ArticleBMC genomics2008
An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 42 citations in OpenAlex.
- Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.RNA (New York, N.Y.) · 2024Article
- 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
- BrnQ-Type Branched-Chain Amino Acid Transporters Influence Bacillus anthracis Growth and Virulence.mBio · 2022Article
- TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs.Nucleic acids research · 2021Article
- Small-Molecule Antibiotics Inhibiting tRNA-Regulated Gene Expression Is a Viable Strategy for Targeting Gram-Positive Bacteria.Antimicrobial agents and chemotherapy · 2020Article
- Systematic engineering of branch chain amino acid supply modules for the enhanced production of bacitracin fromMetabolic engineering communications · 2020Article
- Resistance to serine in Bacillus subtilis: identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism.Environmental microbiology · 2020Article
- A riboswitch gives rise to multi-generational phenotypic heterogeneity in an auxotrophic bacterium.Nature communications · 2020Article
- Enhancement of precursor amino acid supplies for improving bacitracin production by activation of branched chain amino acid transporter BrnQ and deletion of its regulator geneSynthetic and systems biotechnology · 2018Article
- Transcriptional Regulation of Cysteine and Methionine Metabolism inFrontiers in microbiology · 2018Article
- Direct modulation of T-box riboswitch-controlled transcription by protein synthesis inhibitors.Nucleic acids research · 2017Article
- Capture and Release of tRNA by the T-Loop Receptor in the Function of the T-Box Riboswitch.Biochemistry · 2017Article
- A glyS T-box riboswitch with species-specific structural features responding to both proteinogenic and nonproteinogenic tRNAGly isoacceptors.RNA (New York, N.Y.) · 2015Article
- Role of branched-chain amino acid transport in Bacillus subtilis CodY activity.Journal of bacteriology · 2015Article
- The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand.Biochimica et biophysica acta · 2014Review
- Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.BMC genomics · 2013Article
- Two-codon T-box riboswitch binding two tRNAs.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Stress responses of the industrial workhorse Bacillus licheniformis to osmotic challenges.PloS one · 2013Article
- Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria.Journal of bacteriology · 2012Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundT-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so-called specifier codon and can in principle be used to guide the functional annotation of the genes controlled via the T-box anti-termination mechanism.
resultsHidden Markov Models were defined to search the T-box regulatory element and were applied to all completed prokaryotic genomes. The vast majority of the genes found downstream of the retrieved elements encoded functionalities related to transport and synthesis of amino acids and the charging of tRNA. This is completely in line with findings reported in literature and with the proposed biological role of the regulatory element. For several species, the functional annotation of a large number of genes encoding proteins involved in amino acid transport could be improved significantly on basis of the amino acid specificity of the identified T-boxes. In addition, these annotations could be extrapolated to a larger number of orthologous systems in other species. Analysis of T-box distribution confirmed that the element is restricted predominantly to species of the phylum Firmicutes. Furthermore, it appeared that the distribution was highly species specific and that in the case of amino acid transport some boxes seemed to "pop-up" only recently.
conclusionWe have demonstrated that the identification of the molecular specificity of a regulatory element can be of great help in solving notoriously difficult annotation issues, e.g. by defining the substrate specificity of genes encoding amino acid transporters on basis of the amino acid specificity of the regulatory T-box. Furthermore, our analysis of the species-dependency of the occurrence of specific T-boxes indicated that these regulatory elements propagate in a semi-independent way from the genes that they control.
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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.