Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray

Authors

  • Luis Yuste,

    1. Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 – Madrid, Spain.
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  • Ana B. Hervás,

    1. Centro Andaluz de Biología del Desarrollo, Facultad de Ciencias Experimentales, Universidad Pablo de Olavide. Ctra. Utrera, Km. 1. 41013 – Sevilla, Spain.
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  • Inés Canosa,

    1. Centro Andaluz de Biología del Desarrollo, Facultad de Ciencias Experimentales, Universidad Pablo de Olavide. Ctra. Utrera, Km. 1. 41013 – Sevilla, Spain.
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  • Raquel Tobes,

    1. Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 – Granada, Spain.
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  • José Ignacio Jiménez,

    1. Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 – Madrid, Spain.
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  • Juan Nogales,

    1. Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 – Madrid, Spain.
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  • Manuel M. Pérez-Pérez,

    1. Servicio de Genómica, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 – Madrid, Spain.
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  • Eduardo Santero,

    1. Centro Andaluz de Biología del Desarrollo, Facultad de Ciencias Experimentales, Universidad Pablo de Olavide. Ctra. Utrera, Km. 1. 41013 – Sevilla, Spain.
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  • Eduardo Díaz,

    1. Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 – Madrid, Spain.
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  • Juan-Luis Ramos,

    1. Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 – Granada, Spain.
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  • Víctor De Lorenzo,

    1. Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 – Madrid, Spain.
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  • Fernando Rojo

    Corresponding author
    1. Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 – Madrid, Spain.
      *E-mail frojo@cnb.uam.es; Tel. (+34) 91 585 45 39; Fax (+34) 91 585 45 06.
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*E-mail frojo@cnb.uam.es; Tel. (+34) 91 585 45 39; Fax (+34) 91 585 45 06.

Summary

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 σS increased. Data obtained for σN, σH, 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.

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