title: Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon.
abstract: BACKGROUND
  Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat.
  
  
  RESULTS
  In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter.
  
  
  CONCLUSIONS
  Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av Prof Lineu Prestes 1374, 05508-000 São Paulo, Brazil. jfsneto@usp.br
authors.forename: José F
authors.initials: JF
authors.lastname: da Silva Neto
authors.forename: Tie
authors.initials: T
authors.lastname: Koide
authors.forename: Suely L
authors.initials: SL
authors.lastname: Gomes
authors.forename: Marilis V
authors.initials: MV
authors.lastname: Marques
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D051877:RNA Polymerase Sigma 54 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D018085:Regulon; D044167:Xylella / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D051877:RNA Polymerase Sigma 54; D009584:Nitrogen
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