ArticleNucleic acids research2006
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
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- Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation.Microbial cell factories · 2013Article
- Known and novel post-transcriptional regulatory sequences are conserved across plant families.RNA (New York, N.Y.) · 2012Article
- Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.Journal of bacteriology · 2012Article
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- Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.PloS one · 2012Article
- Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer.Microbial cell factories · 2011Review
- Short- and long-term adaptation to ethanol stress and its cross-protective consequences in Lactobacillus plantarum.Applied and environmental microbiology · 2011Article
- Unraveling networks of co-regulated genes on the sole basis of genome sequences.Nucleic acids research · 2011Article
- MotifClick: prediction of cis-regulatory binding sites via merging cliques.BMC bioinformatics · 2011Article
- Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.Microbial biotechnology · 2011Article
- Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes.BMC bioinformatics · 2010Article
- RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.Nucleic acids research · 2010Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cis-acting elements in Lactobacillus plantarum were predicted by comparative analysis of the upstream regions of conserved genes and predicted transcriptional units (TUs) in different bacterial genomes. TUs were predicted for two species sets, with different evolutionary distances to L.plantarum. TUs were designated 'cluster of orthologous transcriptional units' (COT) when >50% of the genes were orthologous in different species. Conserved DNA sequences were detected in the upstream regions of different COTs. Subsequently, conserved motifs were used to scan upstream regions of all TUs. This method revealed 18 regulatory motifs only present in lactic acid bacteria (LAB). The 18 LAB-specific candidate regulatory motifs included 13 that were not described previously. These LAB-specific different motifs were found in front of genes encoding functions varying from cold shock proteins to RNA and DNA polymerases, and many unknown functions. The best-described LAB-specific motif found was the CopR-binding site, regulating expression of copper transport ATPases. Finally, all detected motifs were used to predict co-regulated TUs (regulons) for L.plantarum, and transcriptome profiling data were analyzed to provide regulon prediction validation. It is demonstrated that phylogenetic footprinting using different species sets can identify and distinguish between general regulatory motifs and LAB-specific regulatory motifs.
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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.