title: Construction and verification of the transcriptional regulatory response network of Streptococcus mutans upon treatment with the biofilm inhibitor carolacton.
abstract: BACKGROUND
  Carolacton is a newly identified secondary metabolite causing altered cell morphology and death of Streptococcus mutans biofilm cells. To unravel key regulators mediating these effects, the transcriptional regulatory response network of S. mutans biofilms upon carolacton treatment was constructed and analyzed. A systems biological approach integrating time-resolved transcriptomic data, reverse engineering, transcription factor binding sites, and experimental validation was carried out.
  
  
  RESULTS
  The co-expression response network constructed from transcriptomic data using the reverse engineering algorithm called the Trend Correlation method consisted of 8284 gene pairs. The regulatory response network inferred by superimposing transcription factor binding site information into the co-expression network comprised 329 putative transcriptional regulatory interactions and could be classified into 27 sub-networks each co-regulated by a transcription factor. These sub-networks were significantly enriched with genes sharing common functions. The regulatory response network displayed global hierarchy and network motifs as observed in model organisms. The sub-networks modulated by the pyrimidine biosynthesis regulator PyrR, the glutamine synthetase repressor GlnR, the cysteine metabolism regulator CysR, global regulators CcpA and CodY and the two component system response regulators VicR and MbrC among others could putatively be related to the physiological effect of carolacton. The predicted interactions from the regulatory network between MbrC, known to be involved in cell envelope stress response, and the murMN-SMU_718c genes encoding peptidoglycan biosynthetic enzymes were experimentally confirmed using Electro Mobility Shift Assays. Furthermore, gene deletion mutants of five predicted key regulators from the response networks were constructed and their sensitivities towards carolacton were investigated. Deletion of cysR, the node having the highest connectivity among the regulators chosen from the regulatory network, resulted in a mutant which was insensitive to carolacton thus demonstrating not only the essentiality of cysR for the response of S. mutans biofilms to carolacton but also the relevance of the predicted network.
  
  
  CONCLUSIONS
  The network approach used in this study revealed important regulators and interactions as part of the response mechanisms of S. mutans biofilm cells to carolacton. It also opens a door for further studies into novel drug targets against streptococci.
authors.forename: Padhmanand
authors.initials: P
authors.lastname: Sudhakar
authors.forename: Michael
authors.initials: M
authors.lastname: Reck
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Feng Q
authors.initials: FQ
authors.lastname: He
authors.forename: Irene
authors.initials: I
authors.lastname: Wagner-Döbler
authors.affiliation: Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, 21073 Hamburg, Germany. iwd@helmholtz-hzi.de.
authors.forename: Irene W
authors.initials: IW
authors.lastname: Dobler
authors.forename: An-Ping
authors.initials: AP
authors.lastname: Zeng
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D018441:Biofilms / Q000187:drug effects*; D003545:Cysteine / Q000378:metabolism; D053263:Gene Regulatory Networks / Q000187:drug effects; D008040:Genetic Linkage; D016680:Genome, Bacterial; D005973:Glutamine / Q000378:metabolism; D018942:Macrolides / Q000494:pharmacology*; D008969:Molecular Sequence Data; D011743:Pyrimidines / Q000378:metabolism; D016415:Sequence Alignment; D013295:Streptococcus mutans / Q000235:genetics / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D018942:Macrolides; D011743:Pyrimidines; D014157:Transcription Factors; C553423:carolacton; D005973:Glutamine; D003545:Cysteine; C030986:pyrimidine