title: Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray.
abstract: Bacterial transcriptional networks are built on a hierarchy of regulators, on top of which lie the components of the RNA polymerase (in particular the sigma factors) and the global control elements, which play a pivotal role. We have designed a genome-wide oligonucleotide-based DNA microarray for Pseudomonas putida KT2440. In combination with real-time reverse transcription polymerase chain reaction (RT-PCR), we have used it to analyse the expression pattern of the genes encoding the RNA polymerase subunits (the core enzyme and the 24 sigma factors), and various proteins involved in global regulation (Crc, Lrp, Fur, Anr, Fis, CsrA, IHF, HupA, HupB, HupN, BipA and several MvaT-like proteins), during the shift from exponential growth in rich medium into starvation and stress brought about by the entry into stationary phase. Expression of the genes encoding the RNA polymerase core and the vegetative sigma factor decreased in stationary phase, while that of sigma(S) increased. Data obtained for sigma(N), sigma(H), FliA and for the 19 extracytoplasmic function (ECF)-like sigma factors suggested that their mRNA levels change little upon entry into stationary phase. Expression of Crc, BipA, Fis, HupB, HupN and the MvaT-like protein PP3693 decreased in stationary phase, while that of HupA and the MvaT-like protein PP3765 increased significantly. Expression of IHF was indicative of post-transcriptional control. These results provide the first global study of the expression of the transcriptional machinery through the exponential stationary-phase shift in P. putida.
authors.affiliation: Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 - Madrid, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Yuste
authors.forename: Ana B
authors.initials: AB
authors.lastname: Hervás
authors.forename: Inés
authors.initials: I
authors.lastname: Canosa
authors.forename: Raquel
authors.initials: R
authors.lastname: Tobes
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Jiménez
authors.forename: Juan
authors.initials: J
authors.lastname: Nogales
authors.forename: Manuel M
authors.initials: MM
authors.lastname: Pérez-Pérez
authors.forename: Eduardo
authors.initials: E
authors.lastname: Santero
authors.forename: Eduardo
authors.initials: E
authors.lastname: Díaz
authors.forename: Juan-Luis
authors.initials: JL
authors.lastname: Ramos
authors.forename: Víctor
authors.initials: V
authors.lastname: de Lorenzo
authors.forename: Fernando
authors.initials: F
authors.lastname: Rojo
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides; D016958:Pseudomonas putida / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D050436:Regulatory Elements, Transcriptional / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D009841:Oligonucleotides; D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases