SEARCH

SEARCH BY CITATION

References

  • Aiba , H. , Adhya , S. , and de Crombrugghe , B. ( 1981 ) Evidence for two functional gal promoters in intact Escherichia coli cells . J Biol Chem 256 : 1190511910 .
  • Alefounder , P.R. , and Perham , R.N. ( 1989 ) Identification, molecular cloning and sequence analysis of a gene cluster encoding the class II fructose 1,6-bisphosphate aldolase, 3-phosphoglycerate kinase and a putative second glyceraldehyde 3-phosphate dehydrogenase of Escherichia coli . Mol Microbiol 3 : 723732 .
  • Arraiano , C.M. , Yancey , S.D. , and Kushner , S.R. ( 1988 ) Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12 . J Bacteriol 170 : 46254633 .
  • Bachellier , S. , Clement , J.M. , and Hofnung , M. ( 1999 ) Short palindromic repetitive DNA elements in enterobacteria: a survey . Res Microbiol 150 : 627639 .
  • Baker , K.E. , and Mackie , G.A. ( 2003 ) Ectopic RNase E sites promote bypass of 5′-end-dependent mRNA decay in Escherichia coli . Mol Microbiol 47 : 7588 .
  • Bardey , V. ( 2000 ) Organisation et régulation de l’expression des gènes de la Glycéraldéhyde-3-phosphate déshydrogénase, la Phosphoglycérate kinase et l’Erythrose-4-phosphate déshydrogénase chez les protéobactéries de la subdivision gamma . Thesis , UHP-Nancy I.
  • Berry , A. , and Marshall , K.E. ( 1993 ) Identification of zinc-binding ligands in the class II fructose-1,6-bisphosphate aldolase of Escherichia coli . FEBS Lett 318 : 1116 .
  • Blattner , F.R. , Plunkett , G. , 3rd, Bloch , C.A. , Perna , N.T. , Burland , V. , Riley , M. , et al. ( 1997 ) The complete genome sequence of Escherichia coli K-12 . Science 277 : 14531474 .
  • Boschi-Muller , S. , Azza , S. , Pollastro , D. , Corbier , C. , and Branlant , G. ( 1997 ) Comparative enzymatic properties of GapB-encoded erythrose-4-phosphate dehydrogenase of Escherichia coli and phosphorylating glyceraldehyde-3-phosphate dehydrogenase . J Biol Chem 272 : 1510615112 .
  • Bown , J.A. , Barne , K.A. , Minchin , S.D. , and Busby , S.J.W. ( 1997 ) Extended -10 promoters . In Nucleic Acids and Molecular Biology . Eckstein , F. , and Lilley , D.M.J. (eds) . Berlin : Springer , 11: 4152 .
  • Branlant , G. , and Branlant , C. ( 1985 ) Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of d-glyceraldehyde-3-phosphate dehydrogenase . Eur J Biochem 150 : 6166 .
  • Branlant , C. , Krol , A. , Machatt , M.A. , Pouyet , J. , Ebel , J.P. , Edwards , K. , and Kossel , H. ( 1981 ) Primary and secondary structures of Escherichia coli MRE 600, 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs . Nucleic Acids Res 9 : 43034324 .
  • Branlant , C. , Oster , T. , and Branlant , G. ( 1989 ) Nucleotide sequence determination of the DNA region coding for Bacillus stearothermophilus glyceraldehyde-3-phosphate dehydrogenase and of the flanking DNA regions required for its expression in Escherichia coli . Gene 75 : 145155 .
  • Branny , P. , de la Torre , F. , and Garel , J.R. ( 1998 ) An operon encoding three glycolytic enzymes in Lactobacillus delbrueckii subsp. bulgaricus: glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and triosephosphate isomerase . Microbiology 144 : 905914 .
  • Braun , F. , Hajnsdorf , E. , and Regnier , P. ( 1996 ) Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3′ hairpin . Mol Microbiol 19 : 9971005 .
  • Burchhardt , G. , Keshav , K.F. , Yomano , L. , and Ingram , L.O. ( 1993 ) Mutational analysis of segmental stabilization of transcripts from the Zymomonas mobilis gap-pgk operon . J Bacteriol 175 : 23272333 .
  • Carpousis , A.J. , Van Houwe , G. , Ehretsmann , C. , and Krisch , H.M. ( 1994 ) Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation . Cell 76 : 889900 .
  • Charpentier , B. ( 1994 ) Etude de promoteurs transcriptionnels des gènes gapA et gapB codant la Glycéraldéhyde-3-phosphate déshydrogénase d’Escherichia coli. Relation structure/fonction . Thesis , UHP-Nancy I.
  • Charpentier , B. , Bardey , V. , Robas , N. , and Branlant , C. ( 1998 ) The EIIGlc protein is involved in glucose-mediated activation of Escherichia coli gapA and gapB-pgk transcription . J Bacteriol 180 : 64766483 .
  • Christian , W. ( 1955 ) Aldolase from yeast . Methods Enzymol 1 : 315320 .
  • Condon , C. , Squires , C. , and Squires , C.L. ( 1995 ) Control of rRNA transcription in Escherichia coli . Microbiol Rev 59 : 623645 .
  • Conway , T. , and Ingram , L.O. ( 1988 ) Phosphoglycerate kinase gene from Zymomonas mobilis: cloning, sequencing, and localization within the gap operon . J Bacteriol 170 : 19261933 .
  • Della Seta , F. , Boschi-Muller , S. , Vignais , M.L. , and Branlant , G. ( 1997 ) Characterization of Escherichia coli strains with gapA and gapB genes deleted . J Bacteriol 179 : 52185221 .
  • Doan , T. , and Aymerich , S. ( 2003 ) Regulation of glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate . Mol Microbiol 47 : 17091721 .
  • Ehretsmann , C.P. , Carpousis , A.J. , and Krisch , H.M. ( 1992 ) Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site . Genes Dev 6 : 149159 .
  • Eikmanns , B.J. ( 1992 ) Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase . J Bacteriol 174 : 60766086 .
  • Espeli , O. , Moulin , L. , and Boccard , F. ( 2001 ) Transcription attenuation associated with bacterial repetitive extragenic BIME elements . J Mol Biol 314 : 375386 .
  • Fillinger , S. , Boschi-Muller , S. , Azza , S. , Dervyn , E. , Branlant , G. , and Aymerich , S. ( 2000 ) Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium . J Biol Chem 275 : 1403114037 .
  • Fraenkel , D.G. ( 1996 ) Glycolysis . In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology , 2nd edn . Vol. 1 . Neidhardt , F.C. (ed.). Washington, DC : American Society for Microbiology Press , pp. 189198 .
  • Gebbia , J.A. , Backenson , P.B. , Coleman , J.L. , Anda , P. , and Benach , J.L. ( 1997 ) Glycolytic enzyme operon of Borrelia burgdorferi: characterization and evolutionary implications . Gene 188 : 221228 .
  • Grunberg-Manago , M. ( 1999 ) Messenger RNA stability and its role in control of gene expression in bacteria and phages . Annu Rev Genet 33 : 193227 .
  • Hajnsdorf , E. , Steier , O. , Coscoy , L. , Teysset , L. , and Regnier , P. ( 1994 ) Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant . EMBO J 13 : 33683377 .
  • Harley , C.B. , and Reynolds , R.P. ( 1987 ) Analysis of E. coli promoter sequences . Nucleic Acids Res 15 : 23432361 .
  • Hillman , J.D. , and Fraenkel , D.G. ( 1975 ) Glyceraldehyde 3-phosphate dehydrogenase mutants of Escherichia coli . J Bacteriol 122 : 11751179 .
  • Jacquenet , S. , Ropers , D. , Bilodeau , P.S. , Damier , L. , Mougin , A. , Stoltzfus , C.M. , and Branlant , C. ( 2001 ) Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3′ splice site and its cis-regulatory element: possible involvement in RNA splicing . Nucleic Acids Res 29 : 464478 .
  • Jiang , X. , and Belasco , J.G. ( 2004 ) Catalytic activation of multimeric RNase E and RNase G by 5′-monophosphorylated RNA . Proc Natl Acad Sci USA 101 : 92119216 .
  • Kaberdin , V.R. ( 2003 ) Probing the substrate specificity of Escherichia coli RNase E using a novel oligonucleotide-based assay . Nucleic Acids Res 31 : 47104716 .
  • Kaberdin , V.R. , Walsh , A.P. , Jakobsen , T. , McDowall , K.J. , and von Gabain , A. ( 2000 ) Enhanced cleavage of RNA mediated by an interaction between substrates and the arginine-rich domain of E. coli ribonuclease E . J Mol Biol 301 : 257264 .
  • Karlin , S. , Mrazek , J. , Campbell , A. , and Kaiser , D. ( 2001 ) Characterizations of highly expressed genes of four fast-growing bacteria . J Bacteriol 183 : 50255040 .
  • Keilty , S. , and Rosenberg , M. ( 1987 ) Constitutive function of a positively regulated promoter reveals new sequences essential for activity . J Biol Chem 262 : 63896395 .
  • Kramer , W. , Drutsa , V. , Jansen , H.W. , Kramer , B. , Pflugfelder , M. , and Fritz , H.J. ( 1984 ) The gapped duplex DNA approach to oligonucleotide-directed mutation construction . Nucleic Acids Res 12 : 94419456 .
  • Lee , K. , Bernstein , J.A. , and Cohen , S.N. ( 2002 ) RNase G complementation of rne null mutation identifies functional interrelationships with RNase E in Escherichia coli . Mol Microbiol 43 : 14451456 .
  • Lesnik , E.A. , Sampath , R. , Levene , H.B. , Henderson , T.J. , McNeil , J.A. , and Ecker , D.J. ( 2001 ) Prediction of rho-independent transcriptional terminators in Escherichia coli . Nucleic Acids Res 29 : 35833594 .
  • Li , Y. , and Altman , S. ( 2003 ) A specific endoribonuclease, RNase P, affects gene expression of polycistronic operon mRNAs . Proc Natl Acad Sci USA 100 : 1321313218 .
  • Lisser , S. , and Margalit , H. ( 1993 ) Compilation of E. coli mRNA promoter sequences . Nucleic Acids Res 21 : 15071516 .
  • Ludwig , H. , Homuth , G. , Schmalisch , M. , Dyka , F.M. , Hecker , M. , and Stulke , J. ( 2001 ) Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon . Mol Microbiol 41 : 409422 .
  • Ma , J. , Campbell , A. , and Karlin , S. ( 2002 ) Correlations between Shine–Dalgarno sequences and gene features such as predicted expression levels and operon structures . J Bacteriol 184 : 57335745 .
  • Mackie , G.A. ( 1998 ) Ribonuclease E is a 5′-end-dependent endonuclease . Nature 395 : 720723 .
  • Marchand , I. , Nicholson , A.W. , and Dreyfus , M. ( 2001 ) Bacteriophage T7 protein kinase phosphorylates RNase E and stabilizes mRNAs synthesized by T7 RNA polymerase . Mol Microbiol 42 : 767776 .
  • Marmier-Gourrier , N. , Clery , A. , Senty-Segault , V. , Charpentier , B. , Schlotter , F. , Leclerc , F. , et al. ( 2003 ) A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA . RNA 9 : 821838 .
  • Martin , W. , Brinkmann , H. , Savonna , C. , and Cerff , R. ( 1993 ) Evidence for a chimeric nature of nuclear genomes: eubacterial origin of eukaryotic glyceraldehyde-3-phosphate dehydrogenase genes . Proc Natl Acad Sci USA 90 : 86928696 .
  • Meijer , W.G. , van den Bergh , E.R. , and Smith , L.M. ( 1996 ) Induction of the gap-pgk operon encoding glyceraldehyde-3-phosphate dehydrogenase and 3-phosphoglycerate kinase of Xanthobacter flavus requires the LysR-type transcriptional activator CbbR . J Bacteriol 178 : 881887 .
  • Miller , J.H. ( 1972 ) Experiments in Molecular Genetics. Cold Spring Harbor, New York : Cold Spring Harbor Laboratory Press.
  • Mitchell , J.E. , Zheng , D. , Busby , S.J. , and Minchin , S.D. ( 2003 ) Identification and analysis of ‘extended -10’ promoters in Escherichia coli . Nucleic Acids Res 31 : 46894695 .
  • Mougin , A. , Gregoire , A. , Banroques , J. , Segault , V. , Fournier , R. , Brule , F. , et al. ( 1996 ) Secondary structure of the yeast Saccharomyces cerevisiae pre-U3A snoRNA and its implication for splicing efficiency . RNA 2 : 10791093 .
  • Negre , D. , Oudot , C. , Prost , J.F. , Murakami , K. , Ishihama , A. , Cozzone , A.J. , and Cortay , J.C. ( 1998 ) FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli . J Mol Biol 276 : 355365 .
  • Nellemann , L.J. , Holm , F. , Atlung , T. , and Hansen , F.G. ( 1989 ) Cloning and characterization of the Escherichia coli phosphoglycerate kinase (pgk) gene . Gene 77 : 185191 .
  • Peng , L. , and Shimizu , K. ( 2003 ) Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement . Appl Microbiol Biotechnol 61 : 163178 .
  • Plumbridge , J. , and Soll , D. ( 1989 ) Characterization of cis-acting mutations which increase expression of a glnS–lacZ fusion in Escherichia coli . Mol Gen Genet 216 : 113119 .
  • Powell , B.S. , Rivas , M.P. , Court , D.L. , Nakamura , Y. , and Turnbough , C.L. , Jr ( 1994 ) Rapid confirmation of single copy lambda prophage integration by PCR . Nucleic Acids Res 22 : 57655766 .
  • Prost , J.F. , and Cozzone , A.J. ( 1999 ) Detection of an extended-10 element in the promoter region of the pckA gene encoding phosphoenolpyruvate carboxykinase in Escherichia coli . Biochimie 81 : 197200 .
  • Ramseier , T.M. , Bledig , S. , Michotey , V. , Feghali , R. , and Saier , M.H. , Jr ( 1995 ) The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli . Mol Microbiol 16 : 11571169 .
  • Redko , Y. , Tock , M.R. , Adams , C.J. , Kaberdin , V.R. , Grasby , J.A. , and McDowall , K.J. ( 2003 ) Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates . J Biol Chem 278 : 4400144008 .
  • Romby , P. , and Springer , M. ( 2003 ) Bacterial translational control at atomic resolution . Trends Genet 19 : 155161 .
  • Saier , M.H. , Jr, and Ramseier , , T.M. ( 1996 ) The catabolite repressor/activator (Cra) protein of enteric bacteria . J Bacteriol 178 : 34113417 .
  • Salgado , H. , Gama-Castro , S. , Martinez-Antonio , A. , Diaz-Peredo , E. , Sanchez-Solano , F. , Peralta-Gil , M. , et al. ( 2004 ) Regulondb (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 . Nucleic Acids Res 32 Database issue : D303306 .
  • Sambrook , J. , Fritsch , F.F. , and Maniatis , T. ( 1989 ) Molecular Cloning: a Laboratory Manual , 2nd edn . Cold Spring Harbor, New York : Cold Spring Harbor Laboratory.
  • Schlapfer , B.S. , and Zuber , H. ( 1992 ) Cloning and sequencing of the genes encoding glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and triosephosphate isomerase (gap operon) from mesophilic Bacillus megaterium: comparison with corresponding sequences from thermophilic Bacillus stearothermophilus . Gene 122 : 5362 .
  • Selinger , D.W. , Saxena , R.M. , Cheung , K.J. , Church , G.M. , and Rosenow , C. ( 2003 ) Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation . Genome Res 13 : 216223 .
  • Simons , R.W. , Houman , F. , and Kleckner , N. ( 1987 ) Improved single and multicopy lac-based cloning vectors for protein and operon fusions . Gene 53 : 8596 .
  • Stokes , N.R. , Murray , H.D. , Subramaniam , C. , Gourse , R.L. , Louis , P. , Bartlett , W. , et al. ( 2003 ) A role for mechanosensitive channels in survival of stationary phase: regulation of channel expression by RpoS . Proc Natl Acad Sci USA 100 : 1595915964 .
  • Sunohara , T. , Jojima , K. , Yamamoto , Y. , Inada , T. , and Aiba , H. ( 2004 ) Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA . RNA 10 : 378386 .
  • Thouvenot , B. , Charpentier , B. , and Branlant , C. ( 2004 ) The strong efficiency of the Escherichia coli gapA P1 promoter depends upon a complex combination of functional determinants . Biochem J 383 : 371382 .
  • Wachi , M. , and Nagai , K. ( 2001 ) Escherichia coli ribonuclease G . Methods Enzymol 342 : 5563 .
  • Zhao , G. , Pease , A.J. , Bharani , N. , and Winkler , M.E. ( 1995 ) Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5′-phosphate biosynthesis . J Bacteriol 177 : 28042812 .
  • Zuker , M. ( 2003 ) Mfold web server for nucleic acid folding and hybridization prediction . Nucleic Acids Res 31 : 34063415 .