ArticlePloS one2014
Structural properties of prokaryotic promoter regions correlate with functional features.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 32 citations in OpenAlex.
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- CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis inFrontiers in microbiology · 2020Article
- Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.FEMS microbiology reviews · 2019Review
- Toward a Universal Structural and Energetic Model for Prokaryotic Promoters.Biophysical journal · 2018Article
- Article
- Autoregulation of the Streptococcus mutans SloR Metalloregulator Is Constitutive and Driven by an Independent Promoter.Journal of bacteriology · 2018Article
- Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy.Scientific reports · 2018Article
- Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks.PloS one · 2017Article
- A portable expression resource for engineering cross-species genetic circuits and pathways.Nature communications · 2015Article
- Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.Nucleic acids research · 2015Article
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The structural properties of the DNA molecule are known to play a critical role in transcription. In this paper, the structural profiles of promoter regions were studied within the context of their diversity and their function for eleven prokaryotic species; Escherichia coli, Klebsiella pneumoniae, Salmonella Typhimurium, Pseudomonas auroginosa, Geobacter sulfurreducens Helicobacter pylori, Chlamydophila pneumoniae, Synechocystis sp., Synechoccocus elongates, Bacillus anthracis, and the archaea Sulfolobus solfataricus. The main anchor point for these promoter regions were transcription start sites identified through high-throughput experiments or collected within large curated databases. Prokaryotic promoter regions were found to be less stable and less flexible than the genomic mean across all studied species. However, direct comparison between species revealed differences in their structural profiles that can not solely be explained by the difference in genomic GC content. In addition, comparison with functional data revealed that there are patterns in the promoter structural profiles that can be linked to specific functional loci, such as sigma factor regulation or transcription factor binding. Interestingly, a novel structural element clearly visible near the transcription start site was found in genes associated with essential cellular functions and growth in several species. Our analyses reveals the great diversity in promoter structural profiles both between and within prokaryotic species. We observed relationships between structural diversity and functional features that are interesting prospects for further research to yet uncharacterized functional loci defined by DNA structural properties.
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