title: Transcriptomic analysis of the stationary phase response regulator SpdR in Caulobacter crescentus.
abstract: BACKGROUND
  As bacterial cells enter stationary phase, they adjust their growth rate to comply with nutrient restriction and acquire increased resistance to several stresses. These events are regulated by controlling gene expression at this phase, changing the mode of exponential growth into that of growth arrest, and increasing the expression of proteins involved in stress resistance. The two-component system SpdR/SpdS is required for the activation of transcription of the Caulobacter crescentus cspD gene at the onset of stationary phase.
  
  
  RESULTS
  In this work, we showed that both SpdR and SpdS are also induced upon entry into stationary phase, and this induction is partly mediated by ppGpp and it is not auto-regulated. Global transcriptional analysis at early stationary phase of a spdR null mutant strain compared to the wild type strain was carried out by DNA microarray. Twenty-three genes showed at least twofold decreased expression in the spdR deletion mutant strain relative to its parental strain, including cspD, while five genes showed increased expression in the mutant. The expression of a set of nine genes was evaluated by quantitative real time PCR, validating the microarray data, and indicating an important role for SpdR at stationary phase. Several of the differentially expressed genes can be involved in modulating gene expression, including four transcriptional regulators, and the RNA regulatory protein Hfq. The ribosomal proteins NusE and NusG, which also have additional regulatory functions in transcription and translation, were also downregulated in the spdR mutant, as well as the ParE1 toxin. The purified SpdR protein was shown to bind to the regulatory region of CC0517 by Electrophoretic Mobility Shift Assay, and the SpdR-regulated gene CC0731 was shown to be expressed at a lower level in the null cspD mutant, suggesting that at least part of the effect of SpdR on the expression of this gene is indirect.
  
  
  CONCLUSIONS
  The results indicate that SpdR regulates several genes encoding proteins of regulatory function, which in turn may be required for the expression of other genes important for the transition to stationary phase.
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, 05508-000, São Paulo, SP, Brazil.
authors.forename: Carolina A P T
authors.initials: CA
authors.lastname: da Silva
authors.affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil.
authors.forename: Rogério F
authors.initials: RF
authors.lastname: Lourenço
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, 05508-000, São Paulo, SP, Brazil.|Present address: Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Caixa postal 476, 88040-900, Florianópolis, SC, Brazil.
authors.forename: Ricardo R
authors.initials: RR
authors.lastname: Mazzon
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, 05508-000, São Paulo, SP, Brazil.
authors.forename: Rodolfo A
authors.initials: RA
authors.lastname: Ribeiro
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, 05508-000, São Paulo, SP, Brazil. mvmarque@usp.br.
authors.forename: Marilis V
authors.initials: MV
authors.lastname: Marques
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D016935:Caulobacter crescentus / Q000235:genetics / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D008297:Male; D051379:Mice; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic; D018085:Regulon; D013312:Stress, Physiological
chemical_list: D001426:Bacterial Proteins
keywords: Caulobacter; Stationary phase; Transcriptional regulation; Two-component system