title: Comparative systems biology analysis to study the mode of action of the isothiocyanate compound Iberin on Pseudomonas aeruginosa.
abstract: Food is now recognized as a natural resource of novel antimicrobial agents, including those that target the virulence mechanisms of bacterial pathogens. Iberin, an isothiocyanate compound from horseradish, was recently identified as a quorum-sensing inhibitor (QSI) of the bacterial pathogen Pseudomonas aeruginosa. In this study, we used a comparative systems biology approach to unravel the molecular mechanisms of the effects of iberin on QS and virulence factor expression of P. aeruginosa. Our study shows that the two systems biology methods used (i.e., RNA sequencing and proteomics) complement each other and provide a thorough overview of the impact of iberin on P. aeruginosa. RNA sequencing-based transcriptomics showed that iberin inhibits the expression of the GacA-dependent small regulatory RNAs RsmY and RsmZ; this was verified by using gfp-based transcriptional reporter fusions with the rsmY or rsmZ promoter regions. Isobaric tags for relative and absolute quantitation (iTRAQ) proteomics showed that iberin reduces the abundance of the LadS protein, an activator of GacS. Taken together, the findings suggest that the mode of QS inhibition in iberin is through downregulation of the Gac/Rsm QS network, which in turn leads to the repression of QS-regulated virulence factors, such as pyoverdine, chitinase, and protease IV. Lastly, as expected from the observed repression of small regulatory RNA synthesis, we also show that iberin effectively reduces biofilm formation. This suggests that small regulatory RNAs might serve as potential targets in the future development of therapies against pathogens that use QS for controlling virulence factor expression and assume the biofilm mode of growth in the process of causing disease.
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore School of Biological Sciences, Nanyang Technological University, Singapore.
authors.forename: Sean Yang-Yi
authors.initials: SY
authors.lastname: Tan
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore.
authors.forename: Song Lin
authors.initials: SL
authors.lastname: Chua
authors.affiliation: Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
authors.forename: Rebecca Munk
authors.initials: RM
authors.lastname: Vejborg
authors.affiliation: Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
authors.forename: Tim Holm
authors.initials: TH
authors.lastname: Jakobsen
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore Interdisciplinary Graduate School, Nanyang Technological University, Singapore.
authors.forename: Su Chuen
authors.initials: SC
authors.lastname: Chew
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore School of Biological Sciences, Nanyang Technological University, Singapore.
authors.forename: Yingying
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Nielsen
authors.affiliation: Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
authors.forename: Tim
authors.initials: T
authors.lastname: Tolker-Nielsen
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore School of Biological Sciences, Nanyang Technological University, Singapore yangliang@ntu.edu.sg.
authors.forename: Liang
authors.initials: L
authors.lastname: Yang
authors.affiliation: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore Costerton Biofilm Center, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen N, Denmark.
authors.forename: Michael
authors.initials: M
authors.lastname: Givskov
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D018441:Biofilms / Q000187:drug effects / Q000254:growth & development; D002688:Chitinases / Q000096:biosynthesis; D049452:Green Fluorescent Proteins / Q000235:genetics; D017879:Isothiocyanates / Q000494:pharmacology*; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000096:biosynthesis*; D010447:Peptide Hydrolases / Q000096:biosynthesis; D010936:Plant Extracts / Q000494:pharmacology; D040901:Proteomics / Q000379:methods; D011552:Pseudomonas Infections / Q000188:drug therapy / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000187:drug effects*; D053038:Quorum Sensing / Q000187:drug effects*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000187:drug effects* / Q000235:genetics; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D017879:Isothiocyanates; D009842:Oligopeptides; D010936:Plant Extracts; D038621:Regulatory Sequences, Ribonucleic Acid; D014157:Transcription Factors; D049452:Green Fluorescent Proteins; C082585:iberin; C042453:pyoverdin; C074165:lemA protein, bacterial; D002688:Chitinases; D010447:Peptide Hydrolases; C030732:protease IV