title: Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of Salmonella enterica serovar typhimurium.
abstract: Small RNAs (sRNAs) are short (∼50-200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. Salmonella enterica starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent Salmonella enterica subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from "gene-empty" regions, we identify 58 wholly undescribed Salmonella sRNA genes potentially regulating SSR averaging an ∼1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ∼70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel Salmonella enterica genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that Salmonella sRNAs may actually number in the thousands.
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Shivam V
authors: SV
authors: Amin
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Justin T
authors: JT
authors: Roberts
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Dillon G
authors: DG
authors: Patterson
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Alexander B
authors: AB
authors: Coley
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Jonathan A
authors: JA
authors: Allred
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Jason M
authors: JM
authors: Denner
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Justin P
authors: JP
authors: Johnson
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Genevieve E
authors: GE
authors: Mullen
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Trenton K
authors: TK
authors: O'Neal
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Jason T
authors: JT
authors: Smith
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Sara E
authors: SE
authors: Cardin
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Hank T
authors: HT
authors: Carr
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Stacie L
authors: SL
authors: Carr
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Holly E
authors: HE
authors: Cowart
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: David H
authors: DH
authors: DaCosta
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Brendon R
authors: BR
authors: Herring
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Valeria M
authors: VM
authors: King
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Caroline J
authors: CJ
authors: Polska
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Erin E
authors: EE
authors: Ward
authors: a Department of Biology , University of South Alabama , Mobile , AL.
authors: Alice A
authors: AA
authors: Wise
authors: b Department of Biomedical Sciences , University of South Alabama , Mobile , AL.
authors: Kathleen N
authors: KN
authors: McAllister
authors: c Department of Biology , East Georgia State College , Swainsboro , GA.
authors: David
authors: D
authors: Chevalier
authors: b Department of Biomedical Sciences , University of South Alabama , Mobile , AL.
authors: Michael P
authors: MP
authors: Spector
authors: a Department of Biology , University of South Alabama , Mobile , AL.|d Department of Pharmacology , USA College of Medicine , Mobile , AL.
authors: Glen M
authors: GM
authors: Borchert
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D012329:RNA, Bacterial / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D012486:Salmonella typhimurium / Q000235:genetics / Q000254:growth & development*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013312:Stress, Physiological
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated
keywords: Carbon-starvation; Salmonella; noncoding RNA; sRNA; starvation-stress; transcriptomics