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Refined analysis of the Campylobacter jejuni iron-dependent/independent Fur- and PerR-transcriptomes.

Butcher J, Handley RA, van Vliet AH, Stintzi A - BMC Genomics (2015)

Bottom Line: It was found that 202 genes were differentially expressed in at least one mutant under iron-replete conditions and 331 genes were differentially expressed in at least one mutant under iron-limited conditions.The CjFur and CjPerR transcriptomes characterized in this study were compared to those previously identified using microarray profiling and found to be more extensive than previously understood.Moreover, subsets of genes were found which are only differentially expressed when both CjFur and CjPerR are deleted and includes genes that appear to be simultaneously activated by CjFur and repressed by CjPerR.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada. jbutc076@uottawa.ca.

ABSTRACT

Background: The genome of Campylobacter jejuni contains two iron activated Fur-family transcriptional regulators, CjFur and CjPerR, which are primarily responsible for regulating iron homeostasis and oxidative stress respectively. Both transcriptional regulators have been previously implicated in regulating diverse functions beyond their primary roles in C. jejuni. To further characterize their regulatory networks, RNA-seq was used to define the transcriptional profiles of C. jejuni NCTC11168 wild type, Δfur, ΔperR and ΔfurΔperR isogenic deletion mutants under both iron-replete and iron-limited conditions.

Results: It was found that 202 genes were differentially expressed in at least one mutant under iron-replete conditions and 331 genes were differentially expressed in at least one mutant under iron-limited conditions. The CjFur and CjPerR transcriptomes characterized in this study were compared to those previously identified using microarray profiling and found to be more extensive than previously understood. Interestingly, our results indicate that CjFur/CjPerR appear to co-regulate the expression of flagellar biogenesis genes in an opposing and iron-independent fashion. Moreover the ΔfurΔperR isogenic deletion mutant revealed that CjFur and CjPerR can compensate for each other in certain cases, suggesting that both regulators may compete for binding to specific promoters.

Conclusions: The CjFur and CjPerR transcriptomes are larger than previously reported. In particular, deletion of perR results in the differential expression of a large group of genes in the absence of iron, suggesting that CjPerR may also regulate genes in an iron-independent manner, similar to what has already been demonstrated with CjFur. Moreover, subsets of genes were found which are only differentially expressed when both CjFur and CjPerR are deleted and includes genes that appear to be simultaneously activated by CjFur and repressed by CjPerR. In particular the iron-independent co-regulation of flagellar biogenesis by CjFur/CjPerR represents a potentially novel regulatory function for these proteins. These findings represent additional modes of co-regulation by these two transcriptional regulators in C. jejuni.

No MeSH data available.


Related in: MedlinePlus

Genes enriched in KEGG’s “Flagellar Assembly” category under iron limitation. Genes that belong to the KEGG’s “Flagellar Assembly” category under iron-limited conditions in the Δfur mutant (a) and ΔperR mutant (b) are shown. Genes absent from C. jejuni are denoted in white, unchanged genes in grey, up-regulated genes in blue and down-regulated genes in yellow. To note, the scale of differential expression is normalized from the highest to lowest expressed gene. Most of the genes down-regulated in the Δfur mutant are conversely up-regulated in the ΔperR mutant
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Fig5: Genes enriched in KEGG’s “Flagellar Assembly” category under iron limitation. Genes that belong to the KEGG’s “Flagellar Assembly” category under iron-limited conditions in the Δfur mutant (a) and ΔperR mutant (b) are shown. Genes absent from C. jejuni are denoted in white, unchanged genes in grey, up-regulated genes in blue and down-regulated genes in yellow. To note, the scale of differential expression is normalized from the highest to lowest expressed gene. Most of the genes down-regulated in the Δfur mutant are conversely up-regulated in the ΔperR mutant

Mentions: Gene-set enrichment analysis was used to determine if there were significantly enriched KEGG pathways present in the differentially expressed genes found in each strain under each growth condition. This analysis identified five KEGG categories that were enriched under at least one condition (Additional file 14: Table S8 and Additional file 15: Table S9). Interestingly, the KEGG category for “Flagellar Assembly” was enriched under both the Δfur and ΔperR iron-limited conditions but not in the ΔfurΔperR deletion mutant (Fig. 5).Fig. 5


Refined analysis of the Campylobacter jejuni iron-dependent/independent Fur- and PerR-transcriptomes.

Butcher J, Handley RA, van Vliet AH, Stintzi A - BMC Genomics (2015)

Genes enriched in KEGG’s “Flagellar Assembly” category under iron limitation. Genes that belong to the KEGG’s “Flagellar Assembly” category under iron-limited conditions in the Δfur mutant (a) and ΔperR mutant (b) are shown. Genes absent from C. jejuni are denoted in white, unchanged genes in grey, up-regulated genes in blue and down-regulated genes in yellow. To note, the scale of differential expression is normalized from the highest to lowest expressed gene. Most of the genes down-regulated in the Δfur mutant are conversely up-regulated in the ΔperR mutant
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4491227&req=5

Fig5: Genes enriched in KEGG’s “Flagellar Assembly” category under iron limitation. Genes that belong to the KEGG’s “Flagellar Assembly” category under iron-limited conditions in the Δfur mutant (a) and ΔperR mutant (b) are shown. Genes absent from C. jejuni are denoted in white, unchanged genes in grey, up-regulated genes in blue and down-regulated genes in yellow. To note, the scale of differential expression is normalized from the highest to lowest expressed gene. Most of the genes down-regulated in the Δfur mutant are conversely up-regulated in the ΔperR mutant
Mentions: Gene-set enrichment analysis was used to determine if there were significantly enriched KEGG pathways present in the differentially expressed genes found in each strain under each growth condition. This analysis identified five KEGG categories that were enriched under at least one condition (Additional file 14: Table S8 and Additional file 15: Table S9). Interestingly, the KEGG category for “Flagellar Assembly” was enriched under both the Δfur and ΔperR iron-limited conditions but not in the ΔfurΔperR deletion mutant (Fig. 5).Fig. 5

Bottom Line: It was found that 202 genes were differentially expressed in at least one mutant under iron-replete conditions and 331 genes were differentially expressed in at least one mutant under iron-limited conditions.The CjFur and CjPerR transcriptomes characterized in this study were compared to those previously identified using microarray profiling and found to be more extensive than previously understood.Moreover, subsets of genes were found which are only differentially expressed when both CjFur and CjPerR are deleted and includes genes that appear to be simultaneously activated by CjFur and repressed by CjPerR.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada. jbutc076@uottawa.ca.

ABSTRACT

Background: The genome of Campylobacter jejuni contains two iron activated Fur-family transcriptional regulators, CjFur and CjPerR, which are primarily responsible for regulating iron homeostasis and oxidative stress respectively. Both transcriptional regulators have been previously implicated in regulating diverse functions beyond their primary roles in C. jejuni. To further characterize their regulatory networks, RNA-seq was used to define the transcriptional profiles of C. jejuni NCTC11168 wild type, Δfur, ΔperR and ΔfurΔperR isogenic deletion mutants under both iron-replete and iron-limited conditions.

Results: It was found that 202 genes were differentially expressed in at least one mutant under iron-replete conditions and 331 genes were differentially expressed in at least one mutant under iron-limited conditions. The CjFur and CjPerR transcriptomes characterized in this study were compared to those previously identified using microarray profiling and found to be more extensive than previously understood. Interestingly, our results indicate that CjFur/CjPerR appear to co-regulate the expression of flagellar biogenesis genes in an opposing and iron-independent fashion. Moreover the ΔfurΔperR isogenic deletion mutant revealed that CjFur and CjPerR can compensate for each other in certain cases, suggesting that both regulators may compete for binding to specific promoters.

Conclusions: The CjFur and CjPerR transcriptomes are larger than previously reported. In particular, deletion of perR results in the differential expression of a large group of genes in the absence of iron, suggesting that CjPerR may also regulate genes in an iron-independent manner, similar to what has already been demonstrated with CjFur. Moreover, subsets of genes were found which are only differentially expressed when both CjFur and CjPerR are deleted and includes genes that appear to be simultaneously activated by CjFur and repressed by CjPerR. In particular the iron-independent co-regulation of flagellar biogenesis by CjFur/CjPerR represents a potentially novel regulatory function for these proteins. These findings represent additional modes of co-regulation by these two transcriptional regulators in C. jejuni.

No MeSH data available.


Related in: MedlinePlus