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  • Abril , M.A. , Michan , C. , Timmis , K.N. , and Ramos , J.L. ( 1989 ) Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway . J Bacteriol 171 : 67826790 .
  • Assinder , S.J. , and Williams , P.A. ( 1990 ) The TOL plasmids: determinants of the catabolism of toluene and the xylenes . Adv Microb Physiol 31 : 169 .
  • Bertoni , G. , Marques , S. , and de Lorenzo , V. ( 1998 ) Activation of the toluene-responsive regulator XylR causes a transcriptional switch between sigma 54 and sigma 70 promoters at the divergent Pr/Ps region of the TOL plasmid . Mol Microbiol 27 : 651659 .
  • Brinkmann , U. , and Reineke , W. ( 1992 ) Degradation of chlorotoluenes by in vivo constructed hybrid strains: problems of enzyme specificity, induction and prevention of meta-pathway . FEMS Microbiol Lett 75 : 8187 .
  • Buhler , B. , Schmid , A. , Hauer , B. , and Witholt , B. ( 2000 ) Xylene monooxygenase catalyzes the multistep oxygenation of toluene and pseudocumene to corresponding alcohols, aldehydes, and acids in Escherichia coli JM101 . J Biol Chem 275 : 1008510092 .
  • Carmona , M. , Fernandez , S. , Rodriguez , M.J. , and de Lorenzo , V. ( 2004 ) m-xylene responsive Pu/PnifH hybrid sigma 54 promoters that overcome physiological control in Pseudomonas putida Kt2442 . J Bacteriol 187 : 125134 .
  • Cases , I. , and de Lorenzo , V. ( 2005 ) Promoters in the environment: transcriptional regulation in its natural context . Nat Rev Microbiol 3 : 105118 .
  • Cases , I. , Perez-Martin , J. , and de Lorenzo , V. ( 1999 ) The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid . J Biol Chem 274 : 1556215568 .
  • Cases , I. , Ussery , D. , and de Lorenzo , V. ( 2003 ) The sigma 54 regulon (sigmulon) of Pseudomonas putida . Environ Microbiol 5 : 12811293 .
  • Denef , V.J. , Park , J. , Tsoi , T.V. , Rouillard , J.M. , Zhang , H. , Wibbenmeyer , J.A. , et al. ( 2004 ) Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400 . Appl Environ Microbiol 70 : 49614970 .
  • Duetz , W.A. , Marques , S. , de Jong , C. , Ramos , J.L. , and van Andel , J.G. ( 1994 ) Inducibility of the TOL catabolic pathway in Pseudomonas putida (pWW0) growing on succinate in continuous culture: evidence of carbon catabolite repression control . J Bacteriol 176 : 23542361 .
  • Duetz , W.A. , Marques , S. , Wind , B. , Ramos , J.L. , and van Andel , J.G. ( 1996 ) Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture . Appl Environ Microbiol 62 : 601606 .
  • Gallegos , M.T. , Marques , S. , and Ramos , J.L. ( 1996a ) Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a sigma 70-dependent promoter or from sigma 70- and sigma 54-dependent tandem promoters according to the compound used for growth . J Bacteriol 178 : 23562361 .
  • Gallegos , M.T. , Marques , S. , and Ramos , J.L. ( 1996b ) The TACAN4TGCA motif upstream from the −35 region in the sigma 70- sigma S-dependent Pm promoter of the TOL plasmid is the minimum DNA segment required for transcription stimulation by XylS regulators . J Bacteriol 178 : 64276434 .
  • Garmendia , J. , and de Lorenzo , V. ( 2000 ) The role of the interdomain B linker in the activation of the XylR protein of Pseudomonas putida . Mol Microbiol 38 : 401410 .
  • Greated , A. , Lambertsen , L. , Williams , P.A. , and Thomas , C.M. ( 2002 ) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida . Environ Microbiol 4 : 856871 .
  • Haro , M.A. , and de Lorenzo , V. ( 2001 ) Metabolic engineering of bacteria for environmental applications: construction of Pseudomonas strains for biodegradation of 2-chlorotoluene . J Biotechnol 85 : 103113 .
  • Hirsch , M. , and Elliott , T. ( 2002 ) Role of ppGpp in rpoS stationary-phase regulation in Escherichia coli . J Bacteriol 184 : 50775087 .
  • Holtel , A. , Marques , S. , Mohler , I. , Jakubzik , U. , and Timmis , K.N. ( 1994 ) Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid . J Bacteriol 176 : 17731776 .
  • Inouye , S. , Nakazawa , A. , and Nakazawa , T. ( 1987 ) Overproduction of the xylS gene product and activation of the xylDLEGF operon on the TOL plasmid . J Bacteriol 169 : 35873592 .
  • Jishage , M. , Kvint , K. , Shingler , V. , and Nystrom , T. ( 2002 ) Regulation of sigma factor competition by the alarmone ppGpp . Genes Dev 16 : 12601270 .
  • Kessler , B. , Herrero , M. , Timmis , K.N. , and de Lorenzo , V. ( 1994 ) Genetic evidence that the XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA–protein interactions . J Bacteriol 176 : 31713176 .
  • Kohler , T. , Harayama , S. , Ramos , J.L. , and Timmis , K.N. ( 1989 ) Involvement of Pseudomonas putida RpoN sigma factor in regulation of various metabolic functions . J Bacteriol 171 : 43264333 .
  • Lai , E.C. ( 2003 ) RNA sensors and riboswitches: self-regulating messages . Curr Biol 13 : R285R291 .
  • Laurie , A.D. , Bernardo , L.M. , Sze , C.C. , Skarfstad , E. , Szalewska-Palasz , A. , Nystrom , T. , and Shingler , V. ( 2003 ) The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase . J Biol Chem 278 : 14941503 .
  • de Lorenzo , V. , Eltis , L. , Kessler , B. , and Timmis , K.N. ( 1993 ) Analysis of Pseudomonas gene products using lacIq/Ptrp-lac plasmids and transposons that confer conditional phenotypes . Gene 123 : 1724 .
  • McPhee , J.B. , Lewenza , S. , and Hancock , R.E. ( 2003 ) Cationic antimicrobial peptides activate a two-component regulatory system, PmrA-PmrB, that regulates resistance to polymyxin B and cationic antimicrobial peptides in Pseudomonas aeruginosa . Mol Microbiol 50 : 205217 .
  • Marques , S. , Ramos , J.L. , and Timmis , K.N. ( 1993 ) Analysis of the mRNA structure of the Pseudomonas putida TOL meta fission pathway operon around the transcription initiation point, the xylTE and the xylFJ regions . Biochim Biophys Acta 1216 : 227236 .
  • Marques , S. , Gallegos , M.T. , Manzanera , M. , Holtel , A. , Timmis , K.N. , and Ramos , J.L. ( 1998 ) Activation and repression of transcription at the double tandem divergent promoters for the xylR and xylS genes of the TOL plasmid of Pseudomonas putida . J Bacteriol 180 : 28892894 .
  • Marques , S. , Manzanera , M. , Gonzalez-Perez , M.M. , Ruiz , R. , and Ramos , J.L. ( 1999a ) Biodegradation, plasmid-encoded catabolic pathways, host factors and cell metabolism . Environ Microbiol 1 : 103104 .
  • Marques , S. , Manzanera , M. , Gonzalez-Perez , M.M. , Gallegos , M.T. , and Ramos , J.L. ( 1999b ) The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma 32 or sigma 38 depending on the growth phase . Mol Microbiol 31 : 11051113 .
  • Martinez-Bueno , M.A. , Tobes , R. , Rey , M. , and Ramos , J.L. ( 2002 ) Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01 . Environ Microbiol 4 : 842855 .
  • Miller , J.H. ( 1972 ) Experiments in Molecular Genetics. Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press .
  • Nahvi , A. , Sudarsan , N. , Ebert , M.S. , Zou , X. , Brown , K.L. , and Breaker , R.R. ( 2002 ) Genetic control by a metabolite binding mRNA . Chem Biol 9 : 1043 .
  • Paul , B.J. , Barker , M.M. , Ross , W. , Schneider , D.A. , Webb , C. , Foster , J.W. , and Gourse , R.L. ( 2004 ) DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP . Cell 118 : 311322 .
  • Perez-Martin , J. , and de Lorenzo , V. ( 1995 ) The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR . J Bacteriol 177 : 37583763 .
  • Perron , K. , Comte , R. , and van Delden , C. ( 2005 ) DksA represses ribosomal gene transcription in Pseudomonas aeruginosa by interacting with RNA polymerase on ribosomal promoters . Mol Microbiol 56 : 10871102 .
  • Ramos , J.L. , Duque , E. , and Ramos-Gonzalez , M.I. ( 1991 ) Survival in soils of an herbicide-resistant Pseudomonas putida strain bearing a recombinant TOL plasmid . Appl Environ Microbiol 57 : 260266 .
  • Ramos , J.L. , Marques , S. , and Timmis , K.N. ( 1997 ) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators . Annu Rev Microbiol 51 : 341373 .
  • Ramos , J.L. , Gallegos , M.T. , Marques , S. , Ramos-Gonzalez , M.I. , Espinosa-Urgel , M. , and Segura , A. ( 2001 ) Responses of Gram-negative bacteria to certain environmental stressors . Curr Opin Microbiol 4 : 166171 .
  • Ramos , J.L. , Duque , E. , Gallegos , M.T. , Godoy , P. , Ramos-Gonzalez , M.I. , Rojas , A. , et al. ( 2002 ) Mechanisms of solvent tolerance in gram-negative bacteria . Annu Rev Microbiol 56 : 743768 .
  • Regenhardt , D. , Heuer , H. , Heim , S. , Fernandez , D.U. , Strompl , C. , Moore , E.R. , and Timmis , K.N. ( 2002 ) Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440 . Environ Microbiol 4 : 912915 .
  • Rojo , F. , and Dinamarca , A. ( 2004 ) Catabolic Repression and Physiological Control . New York : Kluwer Academic/Plenum Publishers .
  • Ruiz , R. , Aranda-Olmedo , M.I. , Dominguez-Cuevas , P. , Ramos-Gonzalez , M.I. , and Marques , S. ( 2004 ) Transcriptional Regulation of the Toluene Catabolic Pathways . New York : Kluwer Academic/Plenum Publishers .
  • Sarand , I.I. , Haario , H. , Jorgensen , K.S. , and Romantschuk , M. ( 2000 ) Effect of inoculation of a TOL plasmid containing mycorrhizosphere bacterium on development of Scots pine seedlings, their mycorrhizosphere and the microbial flora in m-toluate-amended soil . FEMS Microbiol Ecol 31 : 127141 .
  • Stein , D.C. ( 1992 ) Plasmids with easily excisable xylE cassettes . Gene 117 : 157158 .
  • Valls , M. , Buckle , M. , and de Lorenzo , V. ( 2002 ) In vivo UV laser footprinting of the Pseudomonas putida sigma 54 Pu promoter reveals that integration host factor couples transcriptional activity to growth phase . J Biol Chem 277 : 21692175 .
  • Velazquez , F. , di Bartolo , I. , and de Lorenzo , V. ( 2004 ) Genetic evidence that catabolites of the Entner–Doudoroff pathway signal C-source repression of the sigma 54 Pu promoter of Pseudomonas putida . J Bacteriol 186 : 82678275 .
  • Winkler , W.C. , Nahvi , A. , Roth , A. , Collins , J.A. , and Breaker , R.R. ( 2004 ) Control of gene expression by a natural metabolite-responsive ribozyme . Nature 428 : 281286 .
  • Xiang , C.C. , Kozhich , O.A. , Chen , M. , Inman , J.M. , Phan , Q.N. , Chen , Y. , and Brownstein , M.J. ( 2002 ) Amine-modified random primers to label probes for DNA microarrays . Nat Biotechnol 20 : 738742 .
  • Yuste , L. , Hervas , A.B. , Canosa , I. , Tobes , R. , Jimenez , J.J. , Nogales , J. , et al. ( 2005 ) Growth-phase dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analyzed with a genome-wide DNA microarray . Env Microbiol ( in press ).