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Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli.

Kumka JE, Bauer CE - BMC Genomics (2015)

Bottom Line: ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL.Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation.Furthermore, we also show that the E. coli FNR regulon has limited transcriptional overlap with the FnrL regulons from either Rhodobacter species.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Simon Hall MSB, 212 S. Hawthorne Dr, Bloomington, IN, 47405-7003, USA.

ABSTRACT

Background: FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most pervasive transcription factors, an understanding of their involvement in regulating anaerobic gene expression in different species sheds light on evolutionary similarity and differences. To address this question, we used a combination of high throughput RNA-Seq and ChIP-Seq analysis to define the extent of the FnrL regulon in Rhodobacter capsulatus and related our results to that of FnrL in Rhodobacter sphaeroides and FNR in Escherichia coli.

Results: Our RNA-seq results show that FnrL affects the expression of 807 genes, which accounts for over 20 % of the Rba. capsulatus genome. ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL. Importantly, this includes genes involved in the synthesis of the anoxygenic photosystem. Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation.

Conclusions: We show that FnrL in Rba. capsulatus activates photosynthesis while in Rba. sphaeroides FnrL regulation reported to involve repression of the photosystem. This analysis highlights important differences in transcriptional control of photosynthetic events and other metabolic processes controlled by FnrL orthologues in closely related Rhodobacter species. Furthermore, we also show that the E. coli FNR regulon has limited transcriptional overlap with the FnrL regulons from either Rhodobacter species.

No MeSH data available.


Related in: MedlinePlus

fnrL mutant in Rba. capsulatus show a reduction in photopigments. Photopigments from whole cell extracts of Rba. capsulatus shown in solid black, fnrL mutant in dotted red and fnrL mutant complemented with 3xFLAG tag shown in dashed purple
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Fig5: fnrL mutant in Rba. capsulatus show a reduction in photopigments. Photopigments from whole cell extracts of Rba. capsulatus shown in solid black, fnrL mutant in dotted red and fnrL mutant complemented with 3xFLAG tag shown in dashed purple

Mentions: Even though the ΔfnrL strain is capable of photosynthetic growth, it appears that FnrL is directly involved in regulating photosynthesis in this species. This conclusion is supported by spectral analysis of anaerobically grown ΔfnrL mutant strain of Rba. capsulatus which exhibits a clear reduction in photosystem spectral components relative to that observed with wild type cells (Fig. 5). A mechanism for this reduction in pigment synthesis is revealed by the presence of an FnrL ChIP-seq peak containing a FnrL recognition sequence in the intergenic region between the divergently transcribed bacteriochlorophyll biosynthesis gene bchF and the bacteriochlorophyll regulator aerR (Fig. 4d). Two potential FnrL binding sites were identified within the bchF-aerR intergenic region with both sites exhibiting good similarity to the consensus sequence. AerR is a cobalamin binding anti-repressor of the bacteriochlorophyll/carotenoid/light harvesting repressor CrtJ and thus the 2-fold activation of AerR expression by FnrL would relieve repression by CrtJ (Fig. 6) [1]. Furthermore this RNA–seq data is validated by a previous in vivo expression study using lacZ reporter plasmids which showed that AerR expression increases 2-fold under anaerobic conditions [7, 23].Fig. 5


Analysis of the FnrL regulon in Rhodobacter capsulatus reveals limited regulon overlap with orthologues from Rhodobacter sphaeroides and Escherichia coli.

Kumka JE, Bauer CE - BMC Genomics (2015)

fnrL mutant in Rba. capsulatus show a reduction in photopigments. Photopigments from whole cell extracts of Rba. capsulatus shown in solid black, fnrL mutant in dotted red and fnrL mutant complemented with 3xFLAG tag shown in dashed purple
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4634722&req=5

Fig5: fnrL mutant in Rba. capsulatus show a reduction in photopigments. Photopigments from whole cell extracts of Rba. capsulatus shown in solid black, fnrL mutant in dotted red and fnrL mutant complemented with 3xFLAG tag shown in dashed purple
Mentions: Even though the ΔfnrL strain is capable of photosynthetic growth, it appears that FnrL is directly involved in regulating photosynthesis in this species. This conclusion is supported by spectral analysis of anaerobically grown ΔfnrL mutant strain of Rba. capsulatus which exhibits a clear reduction in photosystem spectral components relative to that observed with wild type cells (Fig. 5). A mechanism for this reduction in pigment synthesis is revealed by the presence of an FnrL ChIP-seq peak containing a FnrL recognition sequence in the intergenic region between the divergently transcribed bacteriochlorophyll biosynthesis gene bchF and the bacteriochlorophyll regulator aerR (Fig. 4d). Two potential FnrL binding sites were identified within the bchF-aerR intergenic region with both sites exhibiting good similarity to the consensus sequence. AerR is a cobalamin binding anti-repressor of the bacteriochlorophyll/carotenoid/light harvesting repressor CrtJ and thus the 2-fold activation of AerR expression by FnrL would relieve repression by CrtJ (Fig. 6) [1]. Furthermore this RNA–seq data is validated by a previous in vivo expression study using lacZ reporter plasmids which showed that AerR expression increases 2-fold under anaerobic conditions [7, 23].Fig. 5

Bottom Line: ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL.Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation.Furthermore, we also show that the E. coli FNR regulon has limited transcriptional overlap with the FnrL regulons from either Rhodobacter species.

View Article: PubMed Central - PubMed

Affiliation: Molecular and Cellular Biochemistry Department, Indiana University, Simon Hall MSB, 212 S. Hawthorne Dr, Bloomington, IN, 47405-7003, USA.

ABSTRACT

Background: FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species. Since FNR homologues are some of the most pervasive transcription factors, an understanding of their involvement in regulating anaerobic gene expression in different species sheds light on evolutionary similarity and differences. To address this question, we used a combination of high throughput RNA-Seq and ChIP-Seq analysis to define the extent of the FnrL regulon in Rhodobacter capsulatus and related our results to that of FnrL in Rhodobacter sphaeroides and FNR in Escherichia coli.

Results: Our RNA-seq results show that FnrL affects the expression of 807 genes, which accounts for over 20 % of the Rba. capsulatus genome. ChIP-seq results indicate that 42 of these genes are directly regulated by FnrL. Importantly, this includes genes involved in the synthesis of the anoxygenic photosystem. Similarly, FnrL in Rba. sphaeroides affects 24 % of its genome, however, only 171 genes are differentially expressed in common between two Rhodobacter species, suggesting significant divergence in regulation.

Conclusions: We show that FnrL in Rba. capsulatus activates photosynthesis while in Rba. sphaeroides FnrL regulation reported to involve repression of the photosystem. This analysis highlights important differences in transcriptional control of photosynthetic events and other metabolic processes controlled by FnrL orthologues in closely related Rhodobacter species. Furthermore, we also show that the E. coli FNR regulon has limited transcriptional overlap with the FnrL regulons from either Rhodobacter species.

No MeSH data available.


Related in: MedlinePlus