title: RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated in biofilm versus planktonic growth conditions.
abstract: Biofilm development, specifically the fundamentally adaptive switch from acute to chronic infection phenotypes, requires global regulators and small non-coding regulatory RNAs (sRNAs). This work utilized RNA-sequencing (RNA-seq) to detect sRNAs differentially expressed in Pseudomonas aeruginosa biofilm versus planktonic state.
  
  
  
  A computational algorithm was devised to detect and categorize sRNAs into 5 types: intergenic, intragenic, 5'-UTR, 3'-UTR, and antisense. Here we report a novel RsmY/RsmZ-type sRNA, termed RsmW, in P. aeruginosa up-transcribed in biofilm versus planktonic growth. RNA-Seq, 5'-RACE and Mfold predictions suggest RsmW has a secondary structure with 3 of 7 GGA motifs located on outer stem loops. Northern blot revealed two RsmW binding bands of 400 and 120 bases, suggesting RsmW is derived from the 3'-UTR of the upstream hypothetical gene, PA4570. RsmW expression is elevated in late stationary versus logarithmic growth phase in PB minimal media, at higher temperatures (37 °C versus 28 °C), and in both gacA and rhlR transposon mutants versus wild-type. RsmW specifically binds to RsmA protein in vitro and restores biofilm production and reduces swarming in an rsmY/rsmZ double mutant. PA4570 weakly resembles an RsmA/RsmN homolog having 49 % and 51 % similarity, and 16 % and 17 % identity to RsmA and RsmN amino acid sequences, respectively. PA4570 was unable to restore biofilm and swarming phenotypes in ΔrsmA deficient strains.
  
  
  
  Collectively, our study reveals an interesting theme regarding another sRNA regulator of the Rsm system and further unravels the complexities regulating adaptive responses for Pseudomonas species.
authors.affiliation: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA.
authors.forename: Christine L
authors.initials: CL
authors.lastname: Miller
authors.affiliation: School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
authors.forename: Manuel
authors.initials: M
authors.lastname: Romero
authors.affiliation: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA.
authors.forename: S L Rajasekhar
authors.initials: SL
authors.lastname: Karna
authors.affiliation: The Forsyth Institute, Cambridge, Massachusetts, USA.
authors.forename: Tsute
authors.initials: T
authors.lastname: Chen
authors.affiliation: School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
authors.forename: Stephan
authors.initials: S
authors.lastname: Heeb
authors.affiliation: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, Institute of Surgical Research, JBSA Fort Sam Houston, TX, USA. kai.p.leung.civ@mail.mil.
authors.forename: Kai P
authors.initials: KP
authors.lastname: Leung
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D018441:Biofilms; D002876:Chromosomes, Bacterial; D015964:Gene Expression Regulation, Bacterial; D009154:Mutation; D011550:Pseudomonas aeruginosa / Q000235:genetics / Q000254:growth & development / Q000378:metabolism / Q000502:physiology*; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000096:biosynthesis / Q000235:genetics* / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000096:biosynthesis / Q000235:genetics* / Q000378:metabolism*; D015533:Transcriptional Activation; D015854:Up-Regulation; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; C091100:GacA protein, Bacteria; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D016601:RNA-Binding Proteins; C086515:RhlR protein, Pseudomonas aeruginosa; D001618:beta-Lactamases; C000611877:beta-lactamase PoxB, Pseudomonas aeruginosa