An antisense transcript from within the ptsg promoter region in escherichia coli

Journal of Molecular Microbiology and Biotechnology

Volumn 18, Issue 4, 2010, Pages 230-240

  Pennetier, Carole ^a   Oberto, Jacques ^b   Plumbridge, Jacqueline ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

^b CNRS   (France)

Author keywords

Cryptic transcripts; CUT; Divergent promoters; Glucose; Mlc; sRNA

Indexed keywords

RNA POLYMERASE; TRANSFER RNA;

ARTICLE; BACTERIAL GENE; DNA FOOTPRINTING; ESCHERICHIA COLI; FUSION GENE; GENE EXPRESSION; GENE MAPPING; GENETIC TRANSCRIPTION; IN VITRO STUDY; LACZ GENE; NUCLEIC ACID PROBE; PROMOTER REGION; PTSG GENE; REPORTER GENE;

BIOTECHNOLOGY; DNA FOOTPRINTING; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; PROMOTER REGIONS, GENETIC; RNA, ANTISENSE; RNA, MESSENGER;

ESCHERICHIA COLI; PROKARYOTA;

EID: 77954940186     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000319598     Document Type: Article

References (44)

1. Aiba H: Mechanism of RNA silencing by Hfq-binding small RNAs. Curr Opin Microbiol 2007; 10: 134-139
2. 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
3. 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
4. Berretta J, Morillon A: Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep 2009; 10:973-982
5. 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
6. Deutscher J, Francke C, Postma P: How phos-photransferase system-related protein phos-phorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2006; 70: 939-1031
7. El Qaidi S, Plumbridge J: Switching control of expression of ptsG from the Mlc regulon to the NagC regulon. J Bacteriol 2008; 19 0 : 4677-4686 (erratum published in J Bacteriol 2008; 19 0: 5733)
8. Erni B, Zanolari B: Glucose-permease of the bacterial phosphotransferase system. Gene cloning, overproduction and amino acid sequence of enzyme II Glc . J Biol Chem 1986; 261: 16396-16403
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. 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
16. 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)
17. 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
18. 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
19. Matos C, Di Cola A, Robinson C: TatD is a central component of a Tat translocon-initiated quality control system for exported FeS pro-teins in Escherichia coli. EMBO Rep 2009; 10: 474-479
20. 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 IICB Glc recruits the global repressor Mlc. EMBO J 2001; 20:491-498
21. Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz L, Jacquier A: Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009; 457:1038-1042
22. Opdyke J, Kang J-G, Storz G: GadY, a sRNA regulator of acid response genes in Escherichia coli. J Bacteriol 2004; 186 : 6698-6705
23. Pennetier C, Domínguez-Ramírez L, Plum-bridge 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
24. 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
25. Plumbridge J: Expression of ptsG , the gene for the major glucose PTS transporter in Esche-richia coli, is repressed by Mlc and induced by growth on glucose. Mol Microbiol 1998b;29: 1053-1063
26. 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
27. 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
28. Rungrassamee W, Liu X, Pomposiello P: Activation of glucose transport under oxidative stress in Escherichia coli. Arch Microbiol 2008; 190: 41-49
29. Selinger D, Cheung K, Mei R , Johansson E , Rich-mond C, Blattner F, Lockhart D, Church G: RNA expression analysis using a 30 base pair resolution Escherichia coli genomearray . Nat Biotechnol 2000; 18 : 1262-1268
30. Sharma C, Hoffman S, Darfeuille F, Reignier J, Findeis S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler P, Vo-gel J: The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010; 464:250-255
31. Shin D, Cho N, Heu S, Ryu S: Selective regulation of ptsG expression by Fis. J Biol Chem 2003; 278: 14776-14781
32. Shin D, Lim S, Seok Y-J, Ryu S: Heat shock RNA polymerase (Eo32 ) 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
33. Simons RW, Houman F, Kleckner N: Improved single and multicopy lac based cloning vectors for protein and operon fusions. Gene 1987; 53: 85-96
34. 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
35. 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
36. 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
37. 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
38. Vogel J, Sharma C: How to find small non-coding RNAs in bacteria. Biol Chem 2005; 386: 1219-1238
39. Wadler C, Vanderpool C: Characterization of homologs of the small RNA SgrS reveals diversity of function. Nucleic Acids Res 2009; 37: 5477-5485
40. Wassarman K, Repoila F, Rosenow C, Storz G, Gottesman S: Identification of novel small RNAs using comparative genomics and mi-croarrays. Genes Dev 2001; 15:1637-1651
41. 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
42. 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
43. 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
44. 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.