ArticleMicrobial biotechnology2011
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.
Article in Microbial biotechnology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade-off between secondary and primary metabolism.Microbial biotechnology · 2024Article
- SynergisticMicrobiome research reports · 2024Review
- Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members.BMC microbiology · 2023Article
- Altered Promoter and G-Box Binding Factor forInternational journal of molecular sciences · 2019Article
- CcpA-Dependent Carbon Catabolite Repression Regulates Fructooligosaccharides Metabolism inFrontiers in microbiology · 2018Article
- Stress Physiology of Lactic Acid Bacteria.Microbiology and molecular biology reviews : MMBR · 2016Review
- Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches.Scientific reports · 2016Article
- Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation.Microbial cell factories · 2013Article
- Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.BMC genomics · 2013Article
- Lactobacillus plantarum and Lactobacillus buchneri as expression systems: evaluation of different origins of replication for the design of suitable shuttle vectors.Molecular biotechnology · 2012Article
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- Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.Journal of bacteriology · 2012Article
- Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer.Microbial cell factories · 2011Review
- Systems solutions by lactic acid bacteria: from paradigms to practice.Microbial cell factories · 2011Review
- Lactic acid bacteria: life after genomics.Microbial biotechnology · 2011Article
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5 authors.
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Abstract
Gene regulatory networks can be reconstructed by combining transcriptome data from many different experiments to elucidate relations between the activity of certain transcription factors and the genes they control. To obtain insight in the regulatory network of Lactobacillus plantarum, microarray transcriptome data from more than 70 different experimental conditions were combined and the expression profiles of the transcriptional units (TUs) were compared. The TUs that displayed correlated expression were used to identify putative cis-regulatory elements by searching the upstream regions of the TUs for conserved motifs. Predicted motifs were extended and refined by searching for motifs in the upstream regions of additional TUs with correlated expression. In this way, cis-acting elements were identified for 41 regulons consisting of at least four TUs (correlation > 0.7). This set of regulons included the known regulons of CtsR and LexA, but also several novel ones encompassing genes with coherent biological functions. Visualization of the regulons and their connections revealed a highly interconnected regulatory network. This network contains several subnetworks that encompass genes of correlated biological function, such as sugar and energy metabolism, nitrogen metabolism and stress response.
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