Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon.

José F Da Silva Neto,Tie Koide,Suely L Gomes,Marilis V Marques

doi:10.1186/1471-2180-10-231

José F Da Silva Neto, Tie Koide + Show 2 more

Open Access

https://doi.org/10.1186/1471-2180-10-231

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Abstract

BackgroundXylella 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.ResultsIn 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.ConclusionsTogether, 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.

Highlights

Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis
Transcriptome of Xylella cells grown under nitrogen starvation In this work, DNA microarray experiments were used to reveal the global transcriptional profile of X. fastidiosa under nitrogen starvation conditions
The experiments compared changes in the expression profile of cells growing in the absence of nitrogen (XDM0 medium) for 2, 8 and 12 hours compared to cells maintained in defined medium containing amino acids serine, methionine, asparagine and glutamine as nitrogen source (XDM2 medium, zero-time)

Summary

Introduction

A Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. Xylella fastidiosa colonizes the xylem elements of many plants, causing diseases in economically important crops, such as citrus variegated chlorosis in citrus species and Pierce’s disease in grapevines [1] This Gramnegative fastidious bacterium, transmitted by sap-feeding insect vectors, utilizes a plethora of virulence determinants such as adhesins, type IV pili, gum and extracellular cell wall-degrading enzymes to efficiently colonize the plant xylem [2]. In E. coli and other enterobacteria, nitrogen limitation causes changes in expression of about 100 genes, whose products are involved in ammonium assimilation and scavenging for nitrogen-containing compounds [12]. Most of these genes are transcribed by the RNA polymerase containing the sigma factor RpoN (s54) and activated by the nitrogen regulatory protein C (NtrC). In the oligotrophic alphaproteobacterium Caulobacter crescentus s54 does not regulate the majority of genes induced under nitrogen limitation [14]

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