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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Iron activated and repressed genes by functional category.Individual genes that were found to be differentially expressed between iron limiting and iron replete conditions were sorted by COG category and plotted based on their degree of differential expression (Panel A). Genes that were differentially expressed were grouped by COG category and the overall COG category was plotted base on its degree of differential expression (Panel B). The size of the ribbon reflects the degree of activation/repression seen for each gene/COG category. Figure made using Circos v0.54 [52].
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pone-0079475-g002: Iron activated and repressed genes by functional category.Individual genes that were found to be differentially expressed between iron limiting and iron replete conditions were sorted by COG category and plotted based on their degree of differential expression (Panel A). Genes that were differentially expressed were grouped by COG category and the overall COG category was plotted base on its degree of differential expression (Panel B). The size of the ribbon reflects the degree of activation/repression seen for each gene/COG category. Figure made using Circos v0.54 [52].

Mentions: In order to identify iron regulated genes, the number of reads aligning to each protein coding gene and the corresponding RPKM value was determined using SAMMate [22]. The different sequencing runs were found to be highly reproducible, with R2 values ranging from 0.88-0.95 (Figure S1). The presence of significantly differentially expressed genes was determined using the edgeR statistical package [23]. This analysis determined that 127 genes were differentially expressed under iron replete/limited conditions with 77 iron activated genes and 50 iron repressed genes (Figure 1A, Figure 2 and Tables S2, S3).


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

Butcher J, Stintzi A - PLoS ONE (2013)

Iron activated and repressed genes by functional category.Individual genes that were found to be differentially expressed between iron limiting and iron replete conditions were sorted by COG category and plotted based on their degree of differential expression (Panel A). Genes that were differentially expressed were grouped by COG category and the overall COG category was plotted base on its degree of differential expression (Panel B). The size of the ribbon reflects the degree of activation/repression seen for each gene/COG category. Figure made using Circos v0.54 [52].
© Copyright Policy
Related In: Results  -  Collection

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

pone-0079475-g002: Iron activated and repressed genes by functional category.Individual genes that were found to be differentially expressed between iron limiting and iron replete conditions were sorted by COG category and plotted based on their degree of differential expression (Panel A). Genes that were differentially expressed were grouped by COG category and the overall COG category was plotted base on its degree of differential expression (Panel B). The size of the ribbon reflects the degree of activation/repression seen for each gene/COG category. Figure made using Circos v0.54 [52].
Mentions: In order to identify iron regulated genes, the number of reads aligning to each protein coding gene and the corresponding RPKM value was determined using SAMMate [22]. The different sequencing runs were found to be highly reproducible, with R2 values ranging from 0.88-0.95 (Figure S1). The presence of significantly differentially expressed genes was determined using the edgeR statistical package [23]. This analysis determined that 127 genes were differentially expressed under iron replete/limited conditions with 77 iron activated genes and 50 iron repressed genes (Figure 1A, Figure 2 and Tables S2, S3).

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