An Antisense Transcript from within the ptsG Promoter Region in Escherichia coliPennetier C.a · Oberto J.b · Plumbridge J.a
aUPR9073-CNRS Institut de Biologie Physico-Chimique, Paris, bUMR8621-CNRS Institut de Génétique et Microbiologie, Université Paris X1, Orsay, France
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The ptsG gene, encoding the major glucose uptake system in Escherichia coli, is expressed from 2 promoters, a minor promoter p2 and a major downstream promoter p1. Transcription from both promoters is repressed by Mlc, and expression of p1 is activated by the cAMP/catabolite activator protein complex. Expression from p1 is also regulated post-transcriptionally in response to sugar stress via an sRNA, SgrS, which results in translational inhibition and mRNA degradation. Here, we demonstrate an additional level of complexity to the transcriptional pattern surrounding ptsG. A third promoter, p3, located between p1 and p2, was found to express a transcript antisense to ptsG. This promoter was detected by in vitro transcription and by RNA polymerase footprinting techniques and in vivo by S1 analysis and fusions with a lacZ reporter gene. Although the intrinsic strength of the p3 promoter was comparable to that of ptsG, it proved difficult to identify a full-length transcript. A faint transcript of greater than 400 nt could be detected. The transcript thus has more of the characteristics of a divergently expressed cryptic unstable transcript (CUT) than a prokaryotic sRNA.
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- Aiba H: Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 2007;10:134–139.
- Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner E, Margalit H, Altuvia S: Novel small RNA-encoding genes in the intergenic regions of Escherchia coli. Curr Biol 2001;11:1–20.
- Becker A-K, Zeppenfeld T, Staab A, Seitz S, Boos W, Morita T, Aiba H, Mahr K, Titgemeyer F, Jahreis K: YeeI, a novel protein involved in modulation of the activity of the glucose-phosphotransferase system in Escherichia col K-12. J Bacteriol 2006;188:5439–5449.
- Berretta J, Morillon A: Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep 2009;10:973–982.
- Berretta J, Pinskaya M, Morillon A: A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 2008;22:615–626.
- Deutscher J, Francke C, Postma P: How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2006;70:939–1031.
- El Qaidi S, Plumbridge J: Switching control of expression of ptsG from the Mlc regulon to the NagC regulon. J Bacteriol 2008;190:4677–4686 (erratum published in J Bacteriol 2008;190:5733).
Erni B, Zanolari B: Glucose-permease of the bacterial phosphotransferase system. Gene cloning, overproduction and amino acid sequence of enzyme IIGlc. J Biol Chem 1986;261:16396–16403.
- Görke B, Stülke J: Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 2008;6:613–624.
- Horler R, Vanderpool C: Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have changed in size and sequence. Nucleic Acids Res 2009;37:5465–5476.
- Jeong J-Y, Kim Y-J, Cho N, Shin D, Nam T-W, Ryu S, Seok Y-J: Expression of ptsG encoding the major glucose transporter is regulated by ArcA in Escherichia coli. J Biol Chem 2004;279:38513–38518.
- Kawano M, Reynolds AA, Miranda-Rios J, Storz G: Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 2005;33:1040–1050.
- Kimata K, Inada T, Tagami H, Aiba H: A global repressor (Mlc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli. Mol Microbiol 1998;29:1509–1519.
- Kimata K, Takahashi H, Inada T, Postma P, Aiba H: cAMP receptor protein-cAMP plays a crucial role in glucose-lactose diauxie by activating the major glucose transporter gene in Escherichia coli. Proc Natl Acad Sci USA 1997;94:12914–12919.
- Lee S-J, Boos W, Bouché J-P, Plumbridge J: Signal transduction between a membrane bound transporter and a soluble transcription factor, Mlc, of Escherichia coli. EMBO J 2000;19:5353–5361.
Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R: Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominately in antisense transcripts. Nucleic Acids Res 2010, in press (doi: 10.1093/nar/gkq032).
- Maki K, Morita T, Otaka H, Aiba H: A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA. Mol Microbiol 2010;76:782–792.
- Massé E, Gottesman S: A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli. Proc Natl Acad Sci USA 2002;99:4620–4625.
- Matos C, Di Cola A, Robinson C: TatD is a central component of a Tat translocon-initiated quality control system for exported FeS proteins in Escherichia coli. EMBO Rep 2009;10:474–479.
- Nam T-W, Cho S-H, Shin D, Kim J-H, Jeong J-Y, Lee J-H, Roe J-H, Peterkofsky A, Kang S-O, Ryu S, Seok Y-J: The Escherichia coli glucose transporter enzyme IICBGlc recruits the global repressor Mlc. EMBO J 2001;20:491–498.
- Neil H, Malabat C, d’Aubenton-Carafa Y, Xu Z, Steinmetz L, Jacquier A: Widespread bi-directional promoters are the major source of cryptic transcripts in yeast. Nature 2009;457:1038–1042.
- Opdyke J, Kang J-G, Storz G: GadY, a sRNA regulator of acid response genes in Escherichia coli. J Bacteriol 2004;186:6698–6705.
- Pennetier C, Domínguez-Ramírez L, Plumbridge J: Different regions of Mlc and NagC, homologous transcriptional repressors controlling expression of the glucose and N-acetylglucosamine phosphotransferase systems in Escherichia coli, are required for inducer signal recognition. Mol Microbiol 2008;67:364–377.
- Plumbridge J: Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS. Mol Microbiol 1998a;27:369–381.
- Plumbridge J: Expression of ptsG, the gene for the major glucose PTS transporter in Escherichia coli, is repressed by Mlc and induced by growth on glucose. Mol Microbiol 1998b;29:1053–1063.
- Plumbridge J, Pellegrini O: Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP. Mol Microbiol 2004;52:437–449.
- Rivas E, Klein R, Jones T, Eddy S: Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol 2001;11:1369–1373.
- Rungrassamee W, Liu X, Pomposiello P: Activation of glucose transport under oxidative stress in Escherichia coli. Arch Microbiol 2008;190:41–49.
- Selinger D, Cheung K, Mei R, Johansson E, Richmond C, Blattner F, Lockhart D, Church G: RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 2000;18:1262–1268.
- Sharma C, Hoffman S, Darfeuille F, Reignier J, Findeis S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler P, Vogel J: The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010;464:250–255.
- Shin D, Cho N, Heu S, Ryu S: Selective regulation of ptsG expression by Fis. J Biol Chem 2003;278:14776–14781.
- Shin D, Lim S, Seok Y-J, Ryu S: Heat shock RNA polymerase (Eσ32) is involved in the transcription of mlc and crucial for induction of the Mlc Regulon by glucose in Escherichia coli. J Biol Chem 2001;276:25871–25875.
- Simons RW, Houman F, Kleckner N: Improved single and multicopy lac based cloning vectors for protein and operon fusions. Gene 1987;53:85–96.
- Tanaka Y, Kimata K, Aiba H: A novel regulatory role of glucose transporter of Escherichia coli: membrane sequestration of a global repressor Mlc. EMBO J 2000;19:5344–5352.
- Tjaden B, Saxena R, Stolyar S, Haynor D, Kolker E, Rosenow C: Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res 2002;30:3732–3738.
- Vanderpool C, Gottesman S: Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system. Mol Microbiol 2004;54:1076–1089.
- Vogel J, Bartels V, Tang T, Churakov G, Slagter-Jager J, Hüttenhofer A, Wagner E: RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 2003;31:6435–6443.
- Vogel J, Sharma C: How to find small non-coding RNAs in bacteria. Biol Chem 2005;386:1219–1238.
- Wadler C, Vanderpool C: Characterization of homologs of the small RNA SgrS reveals diversity of function. Nucleic Acids Res 2009;37:5477–5485.
- Wassarman K, Repoila F, Rosenow C, Storz G, Gottesman S: Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev 2001;15:1637–1651.
- Wexler M, Sargent F, Jack R, Stanley N, Bogsch E, Robinson C, Berks B, Palmer T: TatD is a cytoplasmic protein with DNase activity. J Biol Chem 2000;275:16717–16722.
- Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Münster S, Camblong J, Guffanti E, Stutz F, Huber W, Steinmetz L: Bidirectrional promoters generate pervasive transcription in yeast. Nature 2009;457:1033–1037.
- Yachie N, Numata K, Saito R, Kanai A, Tomita M: Prediction of non-coding and antisense RNA genes in Escherichia coli with gapped Markov Model. Gene 2006;372:171–181.
- Zhang A, Wassarman K, Rosenow C, Tjaden B, Storz G, Gottesman S: Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 2003;50:1111–1124.
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