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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

Comparison between CjFur and CjPerR transcriptomes as determined by RNA-seq and microarray profiling. The results of the RNA-seq in this study and previous CjFur (a, c) or CjPerR (b, d) microarray profiling results were plotted according to Log2(fold change). Only genes found to be differentially expressed in either the RNA-seq or microarrays are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple and down-regulated genes in green. Genes not found to be differentially expressed in the present study are in orange and genes showing opposite regulation are in red. Genes mentioned in the text are highlighted. See Additional file 14: Table S8 for details for all differentially expressed genes
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Fig6: Comparison between CjFur and CjPerR transcriptomes as determined by RNA-seq and microarray profiling. The results of the RNA-seq in this study and previous CjFur (a, c) or CjPerR (b, d) microarray profiling results were plotted according to Log2(fold change). Only genes found to be differentially expressed in either the RNA-seq or microarrays are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple and down-regulated genes in green. Genes not found to be differentially expressed in the present study are in orange and genes showing opposite regulation are in red. Genes mentioned in the text are highlighted. See Additional file 14: Table S8 for details for all differentially expressed genes

Mentions: To validate the results from the RNA-seq analysis we compared the obtained CjFur and CjPerR transcriptomes to the transcriptomes previously defined using a microarray platform under similar growth conditions [2, 4]. The correlation between the two platforms was assessed by plotting the log-transformed values of the fold change obtained by RNA-seq against the log-transformed values of the fold change obtained by microarrays (only the differentially expressed genes identified by either platform were included). These two independent measures of differential gene expression showed poor correlation with correlation coefficients of 0.57/0.43 for Δfur (iron-replete/limited) and 0.08/0.13 for ΔperR (iron-replete/limited). However, for both the Δfur and ΔperR mutants there was a greater agreement between the genes identified as up-regulated as compared to down-regulated in each condition (Fig. 6, Additional file 14: Table S8). In addition, the RNA-seq analysis identified more genes as being differentially expressed as compared to the microarrays: 86/31 vs 49/30 for Δfur (RNA-seq vs microarray, iron-replete/limited) and 111/272 vs 23/49 for ΔperR (RNA-seq vs microarray, iron-replete/limited). For the Δfur mutant under iron-replete conditions, genes commonly identified as up-regulated include most of the known iron acquisition pathways (ceuBCE, chuABCDZ, cfrA, cfbpABC, chaN/ctuA, cj1658/p19, cj1660-1665, exbB1/D1, exbB2/D2, feoB, tonB3), as well as the highly iron responsive cj1383c-cj1384c genes located upstream from katA. The only genes found to be downregulated in the Δfur mutant by both platforms were rrc-cj0011c. Genes identified in the RNA-seq but not the microarray profiling include the iron acquisition proteins ctuA/cj0178 (transferrin/lactoferrin) and ceuBC (enterobactin). The commonly identified up-regulated genes for the Δfur mutant under iron-limited conditions include rrc, fdxA, cj1386 and cj0948c-0949c.Fig. 6


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)

Comparison between CjFur and CjPerR transcriptomes as determined by RNA-seq and microarray profiling. The results of the RNA-seq in this study and previous CjFur (a, c) or CjPerR (b, d) microarray profiling results were plotted according to Log2(fold change). Only genes found to be differentially expressed in either the RNA-seq or microarrays are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple and down-regulated genes in green. Genes not found to be differentially expressed in the present study are in orange and genes showing opposite regulation are in red. Genes mentioned in the text are highlighted. See Additional file 14: Table S8 for details for all differentially expressed genes
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4491227&req=5

Fig6: Comparison between CjFur and CjPerR transcriptomes as determined by RNA-seq and microarray profiling. The results of the RNA-seq in this study and previous CjFur (a, c) or CjPerR (b, d) microarray profiling results were plotted according to Log2(fold change). Only genes found to be differentially expressed in either the RNA-seq or microarrays are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple and down-regulated genes in green. Genes not found to be differentially expressed in the present study are in orange and genes showing opposite regulation are in red. Genes mentioned in the text are highlighted. See Additional file 14: Table S8 for details for all differentially expressed genes
Mentions: To validate the results from the RNA-seq analysis we compared the obtained CjFur and CjPerR transcriptomes to the transcriptomes previously defined using a microarray platform under similar growth conditions [2, 4]. The correlation between the two platforms was assessed by plotting the log-transformed values of the fold change obtained by RNA-seq against the log-transformed values of the fold change obtained by microarrays (only the differentially expressed genes identified by either platform were included). These two independent measures of differential gene expression showed poor correlation with correlation coefficients of 0.57/0.43 for Δfur (iron-replete/limited) and 0.08/0.13 for ΔperR (iron-replete/limited). However, for both the Δfur and ΔperR mutants there was a greater agreement between the genes identified as up-regulated as compared to down-regulated in each condition (Fig. 6, Additional file 14: Table S8). In addition, the RNA-seq analysis identified more genes as being differentially expressed as compared to the microarrays: 86/31 vs 49/30 for Δfur (RNA-seq vs microarray, iron-replete/limited) and 111/272 vs 23/49 for ΔperR (RNA-seq vs microarray, iron-replete/limited). For the Δfur mutant under iron-replete conditions, genes commonly identified as up-regulated include most of the known iron acquisition pathways (ceuBCE, chuABCDZ, cfrA, cfbpABC, chaN/ctuA, cj1658/p19, cj1660-1665, exbB1/D1, exbB2/D2, feoB, tonB3), as well as the highly iron responsive cj1383c-cj1384c genes located upstream from katA. The only genes found to be downregulated in the Δfur mutant by both platforms were rrc-cj0011c. Genes identified in the RNA-seq but not the microarray profiling include the iron acquisition proteins ctuA/cj0178 (transferrin/lactoferrin) and ceuBC (enterobactin). The commonly identified up-regulated genes for the Δfur mutant under iron-limited conditions include rrc, fdxA, cj1386 and cj0948c-0949c.Fig. 6

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