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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 CRISPR region is defined and strand specific in the miRNA sequencing library.Representation of the total number of reads mapping to the CRISPR region in either miRNA (Panel A) or standard (Panel B) Illumina sequencing libraries. Negative values refer to reads aligning on the negative strand. CRISPR repeat elements are highlighted in grey while the CRISPR spacers are in light orange.
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pone-0079475-g004: The CRISPR region is defined and strand specific in the miRNA sequencing library.Representation of the total number of reads mapping to the CRISPR region in either miRNA (Panel A) or standard (Panel B) Illumina sequencing libraries. Negative values refer to reads aligning on the negative strand. CRISPR repeat elements are highlighted in grey while the CRISPR spacers are in light orange.

Mentions: The presence of novel transcripts and putative sRNAs was determined using the Illumina miRNA sequencing protocol to identify intergenic regions that displayed transcriptional activity. Analysis of the miRNA reads revealed the presence of widespread antisense RNA transcription throughout the C. jejuni genome with approximately 190 genes containing an antisense transcript (Table S7). The strand specificity and sensitivity of this approach was confirmed by analyzing the C. jejuni CRISPR region. Our analysis identified transcriptional activity from all five CRISPR elements present in the C. jejuni NCTC11168 genome in a strand specific manner (Figure 4). Moreover in most cases we could identify the individual processed CRISPR elements.


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

Butcher J, Stintzi A - PLoS ONE (2013)

The CRISPR region is defined and strand specific in the miRNA sequencing library.Representation of the total number of reads mapping to the CRISPR region in either miRNA (Panel A) or standard (Panel B) Illumina sequencing libraries. Negative values refer to reads aligning on the negative strand. CRISPR repeat elements are highlighted in grey while the CRISPR spacers are in light orange.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0079475-g004: The CRISPR region is defined and strand specific in the miRNA sequencing library.Representation of the total number of reads mapping to the CRISPR region in either miRNA (Panel A) or standard (Panel B) Illumina sequencing libraries. Negative values refer to reads aligning on the negative strand. CRISPR repeat elements are highlighted in grey while the CRISPR spacers are in light orange.
Mentions: The presence of novel transcripts and putative sRNAs was determined using the Illumina miRNA sequencing protocol to identify intergenic regions that displayed transcriptional activity. Analysis of the miRNA reads revealed the presence of widespread antisense RNA transcription throughout the C. jejuni genome with approximately 190 genes containing an antisense transcript (Table S7). The strand specificity and sensitivity of this approach was confirmed by analyzing the C. jejuni CRISPR region. Our analysis identified transcriptional activity from all five CRISPR elements present in the C. jejuni NCTC11168 genome in a strand specific manner (Figure 4). Moreover in most cases we could identify the individual processed CRISPR elements.

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