ArticleNucleic acids research2000
Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 187 citations in OpenAlex.
- Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content.Frontiers in microbiology · 2021Article
- Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria.Frontiers in microbiology · 2019Article
- Phyletic Distribution and Lineage-Specific Domain Architectures of Archaeal Two-Component Signal Transduction Systems.Journal of bacteriology · 2018Article
- Redundant ERF-VII Transcription Factors Bind to an Evolutionarily Conserved cis-Motif to Regulate Hypoxia-Responsive Gene Expression in Arabidopsis.The Plant cell · 2016Article
- Comparative genomics of pyridoxal 5'-phosphate-dependent transcription factor regulons inMicrobial genomics · 2016Article
- Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota.Journal of bacteriology · 2015Article
- GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.PloS one · 2015Article
- Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities.BMC genomics · 2014Article
- A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.Nucleic acids research · 2012Article
- A hybrid method for the exact planted (l, d) motif finding problem and its parallelization.BMC bioinformatics · 2012Article
- Comparative genomics of CytR, an unusual member of the LacI family of transcription factors.PloS one · 2012Article
- Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.PLoS genetics · 2012Article
- Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria.Journal of bacteriology · 2011Article
- Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.BMC genomics · 2011Article
- Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.Bioinformatics (Oxford, England) · 2010Article
- Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.BMC genomics · 2010Article
- RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.Nucleic acids research · 2010Article
- Reconstruction of xylose utilization pathway and regulons in Firmicutes.BMC genomics · 2010Article
- Article
- A novel class of modular transporters for vitamins in prokaryotes.Journal of bacteriology · 2009Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data on archaeal transcription regulation or by analogy with known bacterial regulons, and further analysis was performed using iterative profile searches. The information content of the candidate signals detected by this method is insufficient for reliable predictions to be made. Therefore, this approach has to be complemented by examination of evolutionary conservation in different archaeal genomes. This combined strategy resulted in the prediction of a conserved heat shock regulon in all euryarchaea, a nitrogen fixation regulon in the methanogens Methanococcus jannaschii and Methanobacterium thermoautotrophicum and an aromatic amino acid regulon in M.thermoautotrophicum. Unexpectedly, the heat shock regulatory site was detected not only for genes that encode known chaperone proteins but also for archaeal histone genes. This suggests a possible function for archaeal histones in stress-related changes in DNA condensation. In addition, comparative analysis of the genomes of three Pyrococcus species resulted in the prediction of their purine metabolism and transport regulon. The results demonstrate the feasibility of prediction of at least some transcription regulatory sites by comparing poorly characterized prokaryotic genomes, particularly when several closely related genome sequences are available.
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