title: Discovery of ethanol-responsive small RNAs in Zymomonas mobilis.
abstract: Zymomonas mobilis is a bacterium that can produce ethanol by fermentation. Due to its unique metabolism and efficient ethanol production, Z. mobilis has attracted special interest for biofuel energy applications; an important area of study is the regulation of those specific metabolic pathways. Small RNAs (sRNAs) have been studied as molecules that function as transcriptional regulators in response to cellular stresses. While sRNAs have been discovered in various organisms by computational prediction and experimental approaches, their discovery in Z. mobilis has not yet been reported. In this study, we have applied transcriptome analysis and computational predictions to facilitate identification and validation of 15 novel sRNAs in Z. mobilis. We furthermore characterized their expression in the context of high and low levels of intracellular ethanol. Here, we report that 3 of the sRNAs (Zms2, Zms4, and Zms6) are differentially expressed under aerobic and anaerobic conditions, when low and high ethanol productions are observed, respectively. Importantly, when we tested the effect of ethanol stress on the expression of sRNAs in Z. mobilis, Zms2, Zms6, and Zms18 showed differential expression under 5% ethanol stress conditions. These data suggest that in this organism regulatory RNAs can be associated with metabolic functions involved in ethanol stress responses.
authors.affiliation: Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.
authors.forename: Seung Hee
authors.initials: SH
authors.lastname: Cho
authors.affiliation: Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, Texas, USA.
authors.forename: Roy
authors.initials: R
authors.lastname: Lei
authors.affiliation: Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, Texas, USA.
authors.forename: Trey D
authors.initials: TD
authors.lastname: Henninger
authors.affiliation: Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, Texas, USA lcontrer@che.utexas.edu.
authors.forename: Lydia M
authors.initials: LM
authors.lastname: Contreras
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology; D003470:Culture Media; D000431:Ethanol / Q000378:metabolism*; D005285:Fermentation; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D012329:RNA, Bacterial / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D017355:Zymomonas / Q000235:genetics* / Q000378:metabolism
chemical_list: D003470:Culture Media; D012329:RNA, Bacterial; D000431:Ethanol; D005947:Glucose