Limits...
The transcriptional landscape of Campylobacter jejuni under iron replete and iron limited growth conditions.

Butcher J, Stintzi A - PLoS ONE (2013)

Bottom Line: Interestingly, these experiments have revealed that iron is an important modulator of flagellar biogenesis with almost all the components of the flagella found to be iron activated.The expression of selected ncRNAs was confirmed and quantified with qRT-PCR.The qRT-PCR results indicate that several of these novel transcripts are either Fur and/or iron responsive.

View Article: PubMed Central - PubMed

Affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.

ABSTRACT
The genome-wide Campylobacter jejuni transcriptional response under iron replete and iron limited conditions was characterized using RNA-seq. We have identified 111 novel C. jejuni 5'UTRs and mapped 377 co-transcribed genes into 230 transcriptional operons. In contrast to previous microarray results, the C. jejuni iron stimulon is less extensive than previously believed and consists of 77 iron activated genes and 50 iron repressed genes. As anticipated, the iron repressed genes are primarily those involved in iron acquisition or oxidative stress defense. Interestingly, these experiments have revealed that iron is an important modulator of flagellar biogenesis with almost all the components of the flagella found to be iron activated. Given that motility is a well-known C. jejuni colonization factor, this suggests that there is an important regulatory coupling of flagellar biogenesis and iron level in C. jejuni. In addition we have identified several consensus mutations in the C. jejuni NCTC11168 strain that are widespread in the Campylobacter research community and which may explain conflicting phenotypic reports for this strain. Comparative analysis of iron responsive genes with the known Fur regulon indicates that many iron responsive genes are not Fur responsive; suggesting that additional iron regulatory factors remain to be characterized in C. jejuni. Further analysis of the RNA-seq data identified multiple novel transcripts including 19 potential ncRNAs. The expression of selected ncRNAs was confirmed and quantified with qRT-PCR. The qRT-PCR results indicate that several of these novel transcripts are either Fur and/or iron responsive. The fact that several of these ncRNAs are iron responsive or Fur regulated suggests that they may perform regulatory roles in iron homeostasis.

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The overall transcriptome of C. jejuni is relatively unchanged under iron limitation.The absolute abundance of each gene in the C. jejuni genome was calculated and used to determine its contribution to the total transcriptome. These contributions were summed and grouped by COG category to determine the overall contribution of each COG category to the C. jejuni transcriptome under each condition (Panel A). The only statistically significant differences are enrichment for the COG category for inorganic ion transport and metabolism under iron limited conditions and enrichment for DNA replication and repair under iron replete conditions (Panel B) (* p<0.05). Figure made using Circos v0.54.
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pone-0079475-g003: The overall transcriptome of C. jejuni is relatively unchanged under iron limitation.The absolute abundance of each gene in the C. jejuni genome was calculated and used to determine its contribution to the total transcriptome. These contributions were summed and grouped by COG category to determine the overall contribution of each COG category to the C. jejuni transcriptome under each condition (Panel A). The only statistically significant differences are enrichment for the COG category for inorganic ion transport and metabolism under iron limited conditions and enrichment for DNA replication and repair under iron replete conditions (Panel B) (* p<0.05). Figure made using Circos v0.54.

Mentions: To estimate the absolute transcript abundance, the RPKM value for each gene was calculated and used to determine the percent contribution of each gene to the total transcriptional profile of the cell (Table S4) and to compute the 90th percentile of expressed genes in either condition (Figure 1B). The most abundant transcripts in either iron state are very similar with Cj0170, porA, cheV, cj1325, cj1360c, cj0168c and hupB representing the most highly expressed genes in either condition (Figure 1B). As expected, the iron limited state is also characterized by relatively high expression of many iron acquisition genes including p19, cfbpA, chuZ and cfrA, while the iron replete state is characterized by the higher expression of flagellar (flaA, flaB) and energy metabolism (cj0073c, oorD) genes. The contribution of each COG category to the overall transcriptome was determined by grouping genes by COG function and summing their relative contributions (Table S5). As shown Figure 3 the overall COG transcriptional profile is quite similar between iron replete and limited conditions, with the exception of the COG categories for inorganic ion transport and metabolism, and DNA replication and repair, which were enriched in iron limited and iron replete conditions respectively (p<0.05).


The transcriptional landscape of Campylobacter jejuni under iron replete and iron limited growth conditions.

Butcher J, Stintzi A - PLoS ONE (2013)

The overall transcriptome of C. jejuni is relatively unchanged under iron limitation.The absolute abundance of each gene in the C. jejuni genome was calculated and used to determine its contribution to the total transcriptome. These contributions were summed and grouped by COG category to determine the overall contribution of each COG category to the C. jejuni transcriptome under each condition (Panel A). The only statistically significant differences are enrichment for the COG category for inorganic ion transport and metabolism under iron limited conditions and enrichment for DNA replication and repair under iron replete conditions (Panel B) (* p<0.05). Figure made using Circos v0.54.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815106&req=5

pone-0079475-g003: The overall transcriptome of C. jejuni is relatively unchanged under iron limitation.The absolute abundance of each gene in the C. jejuni genome was calculated and used to determine its contribution to the total transcriptome. These contributions were summed and grouped by COG category to determine the overall contribution of each COG category to the C. jejuni transcriptome under each condition (Panel A). The only statistically significant differences are enrichment for the COG category for inorganic ion transport and metabolism under iron limited conditions and enrichment for DNA replication and repair under iron replete conditions (Panel B) (* p<0.05). Figure made using Circos v0.54.
Mentions: To estimate the absolute transcript abundance, the RPKM value for each gene was calculated and used to determine the percent contribution of each gene to the total transcriptional profile of the cell (Table S4) and to compute the 90th percentile of expressed genes in either condition (Figure 1B). The most abundant transcripts in either iron state are very similar with Cj0170, porA, cheV, cj1325, cj1360c, cj0168c and hupB representing the most highly expressed genes in either condition (Figure 1B). As expected, the iron limited state is also characterized by relatively high expression of many iron acquisition genes including p19, cfbpA, chuZ and cfrA, while the iron replete state is characterized by the higher expression of flagellar (flaA, flaB) and energy metabolism (cj0073c, oorD) genes. The contribution of each COG category to the overall transcriptome was determined by grouping genes by COG function and summing their relative contributions (Table S5). As shown Figure 3 the overall COG transcriptional profile is quite similar between iron replete and limited conditions, with the exception of the COG categories for inorganic ion transport and metabolism, and DNA replication and repair, which were enriched in iron limited and iron replete conditions respectively (p<0.05).

Bottom Line: Interestingly, these experiments have revealed that iron is an important modulator of flagellar biogenesis with almost all the components of the flagella found to be iron activated.The expression of selected ncRNAs was confirmed and quantified with qRT-PCR.The qRT-PCR results indicate that several of these novel transcripts are either Fur and/or iron responsive.

View Article: PubMed Central - PubMed

Affiliation: Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.

ABSTRACT
The genome-wide Campylobacter jejuni transcriptional response under iron replete and iron limited conditions was characterized using RNA-seq. We have identified 111 novel C. jejuni 5'UTRs and mapped 377 co-transcribed genes into 230 transcriptional operons. In contrast to previous microarray results, the C. jejuni iron stimulon is less extensive than previously believed and consists of 77 iron activated genes and 50 iron repressed genes. As anticipated, the iron repressed genes are primarily those involved in iron acquisition or oxidative stress defense. Interestingly, these experiments have revealed that iron is an important modulator of flagellar biogenesis with almost all the components of the flagella found to be iron activated. Given that motility is a well-known C. jejuni colonization factor, this suggests that there is an important regulatory coupling of flagellar biogenesis and iron level in C. jejuni. In addition we have identified several consensus mutations in the C. jejuni NCTC11168 strain that are widespread in the Campylobacter research community and which may explain conflicting phenotypic reports for this strain. Comparative analysis of iron responsive genes with the known Fur regulon indicates that many iron responsive genes are not Fur responsive; suggesting that additional iron regulatory factors remain to be characterized in C. jejuni. Further analysis of the RNA-seq data identified multiple novel transcripts including 19 potential ncRNAs. The expression of selected ncRNAs was confirmed and quantified with qRT-PCR. The qRT-PCR results indicate that several of these novel transcripts are either Fur and/or iron responsive. The fact that several of these ncRNAs are iron responsive or Fur regulated suggests that they may perform regulatory roles in iron homeostasis.

Show MeSH
Related in: MedlinePlus