Global transcriptional response of Caulobacter crescentus to iron availability

Abstract

BackgroundIn the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown.ResultsIn this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identified 42 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB-dependent receptor gene clusters, and feoAB), riboflavin biosynthesis and genes encoding hypothetical proteins. Most of these genes are associated with predicted Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 27 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, included in this group are also TonB-dependent receptors genes and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of 113 more genes, including induction of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as repression of genes implicated in amino acid metabolism, chemotaxis and motility.ConclusionsUsing a global transcriptional approach, we determined the C. crescentus iron stimulon. Many but not all of iron responsive genes were directly or indirectly controlled by Fur. The iron limitation stimulon overlaps with other regulatory systems, such as the RpoH and FixK regulons. Altogether, our results showed that adaptation of C. crescentus to iron limitation not only involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins, but also includes novel genes and regulatory mechanisms.

Discrete Responses to Limitation for Iron and Manganese in Agrobacterium tumefaciens: Influence on Attachment and Biofilm Formation

“…Alternatively, the observed decline and ultimate cessation in growth may be due to reduced activity of iron-dependent metabolic enzymes and a shift in the metabolic balance of the cell. Similar strategies to maintain iron homeostasis, including transcriptional control of iron acquisition, an iron-sparing response, or both have been observed for E. coli as well as in the alphaproteobacteria Sinorhizobium meliloti, B. japonicum, and Caulobacter crescentus, and our current data highlight the conservation of these responses (55)(56)(57)(58)(59).…”

Global Transcriptional Response to Organic Hydroperoxide and the Role of OhrR in the Control of Virulence Traits in Chromobacterium violaceum

“…An interesting finding of our work was the altered expression levels of several genes that belong to the Fur regulon (42)(43)(44). The CHP-mediated upregulation of Furrepressed genes and downregulation of Fur-activated genes suggest that CHP may affect the Fur protein.…”

“…CHPupregulated iron acquisition systems included outer membrane TonB-dependent receptors (CV_0077, CV_1491, CV_1982, CV_3896, fepA, and fhuA), energy-transducing TonB-ExbB-ExbD protein complexes (CV_0400-CV_0399-CV_0398, CV_1971-CV_1972- CV_1973-CV_1974, CV_1983, CV_1986, and CV_4254), ABC transporters (CV_3895-CV_3896-CV_3897-CV_3898-CV_3899, CV_1491-CV_1490-CV_1489-CV_1488-CV_1487, and CV_2236-CV_2235-CV_2234), and enzymes for the synthesis of iron-chelating molecules such as riboflavin (CV_2387-CV_2388-CV_2389) and the siderophore enterobactin (entFCEBA and CV_2231-CV_2232-CV_2233). As the above-mentioned genes are members of the Fur regulon in many bacteria (42)(43)(44) and the C. violaceum genome encodes the Fur protein (21), we hypothesize that CHP is derepressing the Fur regulon. CHP could be causing either direct iron starvation due to a reaction with Fe(II) (45) or the oxidation of the holo-Fur protein, disrupting its DNA binding activity (46).…”

Iron Deficiency Generates Oxidative Stress and Activation of the SOS Response in Caulobacter crescentus

“…Global transcriptional analyses using DNA microarrays allowed to define the Fur regulon, identifying 42 genes repressed and 27 genes activated by Fe-Fur (da Silva Neto et al, 2013). …”