ArticlePloS one2012
Genome context as a predictive tool for identifying regulatory targets of the TetR family transcriptional regulators.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 71 citations in OpenAlex.
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- The TetR-like regulator Sco4385 and Crp-like regulator Sco3571 modulate heterologous production of antibiotics inApplied and environmental microbiology · 2025Article
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- Effect of Precursors and Their Regulators on the Biosynthesis of Antibiotics inMolecules (Basel, Switzerland) · 2024Review
- Systematic investigation of TetR-family transcriptional regulators and their roles on lignocellulosic inhibitor acetate tolerance inFrontiers in bioengineering and biotechnology · 2024Article
- Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.Nature communications · 2023Article
- Enhancement of acarbose production by genetic engineering and fed-batch fermentation strategy in Actinoplanes sp. SIPI12-34.Microbial cell factories · 2022Article
- Involvement of the SCO3366 efflux pump from S. coelicolor in rifampicin resistance and its regulation by a TetR regulator.Applied microbiology and biotechnology · 2022Article
- MadR mediates acyl CoA-dependent regulation of mycolic acid desaturation in mycobacteria.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Cloning and identification of a new repressor of 3,17β-Hydroxysteroid dehydrogenase of Comamonas testosteroni.Molecular biology reports · 2021Article
- A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters.Annual review of biochemistry · 2021Review
- Acinetobacter baylyi regulates type IV pilus synthesis by employing two extension motors and a motor protein inhibitor.Nature communications · 2021Article
- Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites.Nucleic acids research · 2020Article
- A genome-wide approach for identification and characterisation of metabolite-inducible systems.Nature communications · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
TetR family transcriptional regulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA. We explore predicted target gene product identity and intergenic separation to see which either correlates with a direct regulatory relationship. While intergenic separation is a critical factor in regulatory prediction the identity of the putative target gene product is not. Our data suggest that those TFRs that are <200 bp from their divergently oriented neighbors are most likely to regulate them. These target genes include membrane proteins (26% of which 22% are probable membrane-associated pumps), enzymes (60%), other proteins such as transcriptional regulators (1%), and proteins having no predictive sequence motifs (13%). In addition to establishing a solid foundation for identifying targets for TFRs of unknown function, our analysis demonstrates a much greater diversity of TFR-regulated biochemical functions.
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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.