ArticleBMC microbiology2005
Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria.
Article in BMC microbiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 51 citations in OpenAlex.
- A conserved uORF in theMicrobial genomics · 2023Article
- De novo tryptophanase-based indole production by metabolically engineered Corynebacterium glutamicum.Applied microbiology and biotechnology · 2023Article
- Production of indole by Corynebacterium glutamicum microbial cell factories for flavor and fragrance applications.Microbial cell factories · 2022Article
- Diversity and prevalence of ANTAR RNAs across actinobacteria.BMC microbiology · 2021Article
- Simulation of Folding Kinetics for Aligned RNAs.Genes · 2021Article
- Extensive Reannotation of the Genome of the Model StreptomyceteFrontiers in microbiology · 2021Article
- Ribosome reinitiation at leader peptides increases translation of bacterial proteins.Biology direct · 2016Article
- Genome-scale analysis reveals a role for NdgR in the thiol oxidative stress response in Streptomyces coelicolor.BMC genomics · 2015Article
- T box riboswitches in Actinobacteria: translational regulation via novel tRNA interactions.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum.Microbial biotechnology · 2014Review
- Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.BMC genomics · 2013Article
- Regulation of an auxiliary, antibiotic-resistant tryptophanyl-tRNA synthetase gene via ribosome-mediated transcriptional attenuation.Journal of bacteriology · 2010Article
- TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.PLoS computational biology · 2010Article
- Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation.Genome biology · 2010Article
- An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters.BMC genomics · 2008Article
- The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.RNA (New York, N.Y.) · 2008Article
- Comparative genomic analysis of T-box regulatory systems in bacteria.RNA (New York, N.Y.) · 2008Article
- A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.PLoS computational biology · 2007Article
- The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.Journal of bacteriology · 2007Article
- Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.Nucleic acids research · 2007Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFormation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria.
resultsComparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element) was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria.
conclusionThe metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns allowed for identification of ML1624 of M. leprae and its orthologs as the candidate regulatory proteins that may bind to the LEU element. T-boxes upstream of the ileS genes are unusual, as their regulatory mechanism seems to be inhibition of translation initiation via a hairpin sequestering the Shine-Dalgarno box.
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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.