+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs

Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs

Microbial Biotechnology 4(3): 333-344

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.

Please choose payment method:

(PDF emailed within 0-6 h: $19.90)

Accession: 055413110

Download citation: RISBibTeXText

PMID: 21375715

DOI: 10.1111/j.1751-7915.2010.00217.x

Related references

Unraveling the regulatory network of Lactobacillus plantarum WCFS1. 2007

The impact of Lactobacillus plantarum WCFS1 teichoic acid D-alanylation on the generation of effector and regulatory T-cells in healthy mice. Plos one 8(4): E63099, 2013

Differential Gene Expression by Lactobacillus plantarum Wcfs1 in Response to Phenolic Compounds Reveals New Genes Involved in Tannin Degradation. Applied and Environmental Microbiology 83(7): e03387-16, 2017

Identification of Regulatory Network Motifs from Gene Expression Data. Journal of Mathematical Modelling and Algorithms in Operations Research 9(3): 233-245, 2010

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. Bmc Genomics 9: 145, 2008

Sequence and expression of the gene encoding the respiratory nitrous-oxide reductase from Paracoccus denitrificans. New and conserved structural and regulatory motifs. European Journal of Biochemistry 218(1): 49-57, 1993

Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions. Bmc Systems Biology 8: 26, 2014

Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids. Development 145(24):, 2018

Mobile group II intron based gene targeting in Lactobacillus plantarum WCFS1. Journal of Basic Microbiology 56(10): 1107-1116, 2016

Chitinase from Bacillus licheniformis DSM13: expression in Lactobacillus plantarum WCFS1 and biochemical characterisation. Protein Expression and Purification 81(2): 166-174, 2012

The Construction of Regulatory Network for Insulin-Mediated Genes by Integrating Methods Based on Transcription Factor Binding Motifs and Gene Expression Variations. Genomics and Informatics 13(3): 76-80, 2015

Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data. Frontiers in Microbiology 7: 275, 2016

Gene regulatory networks reused to build novel traits: co-option of an eye-related gene regulatory network in eye-like organs and red wing patches on insect wings is suggested by optix expression. Bioessays 34(3): 181-186, 2012

The gene encoding plantaricin A, a bacteriocin from Lactobacillus plantarum C11, is located on the same transcription unit as an agr-like regulatory system. Applied and Environmental Microbiology 60(1): 160-166, 1994

Reconstruction of the regulatory network of Geobacter sulfurreducens from gene expression data and sequence analysis. 2005