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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 iron transcriptomes determined in this work and previous studies. The results of the iron transcriptomes as determined in in this study and previous microarray (a) and RNA-seq (b) results were plotted according to Log2(fold change). Only genes found to be significantly expressed in each study are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple with down regulated genes in green. Genes not found to be differentially expressed in the current study are in orange and genes showing inverse regulation are in red. See Additional file 10: Table S7 for details for all differentially expressed genes
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Fig7: Comparison between iron transcriptomes determined in this work and previous studies. The results of the iron transcriptomes as determined in in this study and previous microarray (a) and RNA-seq (b) results were plotted according to Log2(fold change). Only genes found to be significantly expressed in each study are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple with down regulated genes in green. Genes not found to be differentially expressed in the current study are in orange and genes showing inverse regulation are in red. See Additional file 10: Table S7 for details for all differentially expressed genes

Mentions: Two previous studies from our laboratory have used similar growth conditions to determine iron-responsive genes in C. jejuni using both microarray profiling and RNA-seq [2, 7]. Iron-responsive genes were determined by comparing the wild-type transcriptomes in the presence and absence of iron. This analysis found 686 genes differentially expressed in response to iron as compared to 270 genes identified using microarray profiling and 127 genes identified in an earlier RNA-seq study (Fig. 7, Additional file 16: Table S10, Additional file 10: Table S7).Fig. 7


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 iron transcriptomes determined in this work and previous studies. The results of the iron transcriptomes as determined in in this study and previous microarray (a) and RNA-seq (b) results were plotted according to Log2(fold change). Only genes found to be significantly expressed in each study are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple with down regulated genes in green. Genes not found to be differentially expressed in the current study are in orange and genes showing inverse regulation are in red. See Additional file 10: Table S7 for details for all differentially expressed genes
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Comparison between iron transcriptomes determined in this work and previous studies. The results of the iron transcriptomes as determined in in this study and previous microarray (a) and RNA-seq (b) results were plotted according to Log2(fold change). Only genes found to be significantly expressed in each study are shown with the dashed lines representing the Log2(FC) cut-offs. Up-regulated genes are in purple with down regulated genes in green. Genes not found to be differentially expressed in the current study are in orange and genes showing inverse regulation are in red. See Additional file 10: Table S7 for details for all differentially expressed genes
Mentions: Two previous studies from our laboratory have used similar growth conditions to determine iron-responsive genes in C. jejuni using both microarray profiling and RNA-seq [2, 7]. Iron-responsive genes were determined by comparing the wild-type transcriptomes in the presence and absence of iron. This analysis found 686 genes differentially expressed in response to iron as compared to 270 genes identified using microarray profiling and 127 genes identified in an earlier RNA-seq study (Fig. 7, Additional file 16: Table S10, Additional file 10: Table S7).Fig. 7

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