title: The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum.
abstract: BACKGROUND
  Small non-coding RNAs (sRNA) are emerging as major components of the cell's regulatory network, several possessing their own regulons. A few sRNAs have been reported as being involved in general or toxic-metabolite stress, mostly in Gram- prokaryotes, but hardly any in Gram+ prokaryotes. Significantly, the role of sRNAs in the stress response remains poorly understood at the genome-scale level. It was previously shown that toxic-metabolite stress is one of the most comprehensive and encompassing stress responses in the cell, engaging both the general stress (or heat-shock protein, HSP) response as well as specialized metabolic programs.
  
  
  RESULTS
  Using RNA deep sequencing (RNA-seq) we examined the sRNome of C. acetobutylicum in response to the native but toxic metabolites, butanol and butyrate. 7.5% of the RNA-seq reads mapped to genome outside annotated ORFs, thus demonstrating the richness and importance of the small RNome. We used comparative expression analysis of 113 sRNAs we had previously computationally predicted, and of annotated mRNAs to set metrics for reliably identifying sRNAs from RNA-seq data, thus discovering 46 additional sRNAs. Under metabolite stress, these 159 sRNAs displayed distinct expression patterns, a select number of which was verified by Northern analysis. We identified stress-related expression of sRNAs affecting transcriptional (6S, S-box &solB) and translational (tmRNA & SRP-RNA) processes, and 65 likely targets of the RNA chaperone Hfq.
  
  
  CONCLUSIONS
  Our results support an important role for sRNAs for understanding the complexity of the regulatory network that underlies the stress response in Clostridium organisms, whether related to normophysiology, pathogenesis or biotechnological applications.
authors.forename: Keerthi P
authors.initials: KP
authors.lastname: Venkataramanan
authors.forename: Shawn W
authors.initials: SW
authors.lastname: Jones
authors.forename: Kevin P
authors.initials: KP
authors.lastname: McCormick
authors.forename: Sridhara G
authors.initials: SG
authors.lastname: Kunjeti
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Ralston
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA. epaps@udel.edu.
authors.forename: Eleftherios T
authors.initials: ET
authors.lastname: Papoutsakis
mesh_terms: D001665:Binding Sites; D000440:Butanols / Q000494:pharmacology; D020148:Butyric Acid / Q000494:pharmacology; D046969:Clostridium acetobutylicum / Q000235:genetics* / Q000378:metabolism*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D023281:Genomics / Q000379:methods; D006360:Heat-Shock Proteins / Q000378:metabolism; D035001:Host Factor 1 Protein / Q000378:metabolism; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011485:Protein Binding; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological
chemical_list: D000440:Butanols; D006360:Heat-Shock Proteins; D035001:Host Factor 1 Protein; D058727:RNA, Small Untranslated; D020148:Butyric Acid