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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

Comparison of FNR/FnrL homologues. Similarities of FnrL from Rba. capsulatus and Rba. sphaeroides and their differences to FNR from E. coli. Fe/S motif was taken from the N-terminus (solid) and HTH domain was taken from the C-terminus (dashed). Red colored amino acids denote critical residues, green denote similarities between Rhodobacter species, blue denote similarities between E. coli and Rhodobacter species, grey are unique to each organism and redundantly represented by ‘.’, ‘*’ and ‘!’
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Fig8: Comparison of FNR/FnrL homologues. Similarities of FnrL from Rba. capsulatus and Rba. sphaeroides and their differences to FNR from E. coli. Fe/S motif was taken from the N-terminus (solid) and HTH domain was taken from the C-terminus (dashed). Red colored amino acids denote critical residues, green denote similarities between Rhodobacter species, blue denote similarities between E. coli and Rhodobacter species, grey are unique to each organism and redundantly represented by ‘.’, ‘*’ and ‘!’

Mentions: This study shows that genes constituting the FnrL regulon from Rba. capsulatus are remarkably dissimilar from the published FnrL regulon from Rba. sphaeroides. Indeed only 9 genes in these two photosynthetic species have FnrL binding sites upstream from common targets. This dissimilarity is striking given that these organisms share similar anoxygenic photosynthetic physiologies and therefore presumably face similar challenges in controlling energy balance (redox poise) in response to light, oxygen, and nutrient availability. The fact that these FnrL orthologues exhibit high sequence identity (Fig. 8) and utilize similar target sequences (Fig. 2), and yet control many different target genes, indicates that there is significant evolutionary drift in the location of transcription factor recognition sequences even among related species that occupy similar environmental niches (Fig. 9).Fig. 8


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)

Comparison of FNR/FnrL homologues. Similarities of FnrL from Rba. capsulatus and Rba. sphaeroides and their differences to FNR from E. coli. Fe/S motif was taken from the N-terminus (solid) and HTH domain was taken from the C-terminus (dashed). Red colored amino acids denote critical residues, green denote similarities between Rhodobacter species, blue denote similarities between E. coli and Rhodobacter species, grey are unique to each organism and redundantly represented by ‘.’, ‘*’ and ‘!’
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig8: Comparison of FNR/FnrL homologues. Similarities of FnrL from Rba. capsulatus and Rba. sphaeroides and their differences to FNR from E. coli. Fe/S motif was taken from the N-terminus (solid) and HTH domain was taken from the C-terminus (dashed). Red colored amino acids denote critical residues, green denote similarities between Rhodobacter species, blue denote similarities between E. coli and Rhodobacter species, grey are unique to each organism and redundantly represented by ‘.’, ‘*’ and ‘!’
Mentions: This study shows that genes constituting the FnrL regulon from Rba. capsulatus are remarkably dissimilar from the published FnrL regulon from Rba. sphaeroides. Indeed only 9 genes in these two photosynthetic species have FnrL binding sites upstream from common targets. This dissimilarity is striking given that these organisms share similar anoxygenic photosynthetic physiologies and therefore presumably face similar challenges in controlling energy balance (redox poise) in response to light, oxygen, and nutrient availability. The fact that these FnrL orthologues exhibit high sequence identity (Fig. 8) and utilize similar target sequences (Fig. 2), and yet control many different target genes, indicates that there is significant evolutionary drift in the location of transcription factor recognition sequences even among related species that occupy similar environmental niches (Fig. 9).Fig. 8

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