Abstract
BackgroundFNR 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.ResultsOur 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2162-4) contains supplementary material, which is available to authorized users.
Highlights
FNR homologues constitute an important class of transcription factors that control a wide range of anaerobic physiological functions in a number of bacterial species
Much is known about its photosynthetic growth metabolism along with transcription factors that control anaerobic photosystem gene expression such as RegA, CrtJ, and AerR [1,2,3,4,5]
The redox responding transcription factor FnrL, which is a homologue of FNR from E. coli, has not been well characterized in Rba. capsulatus [5,6,7]
Summary
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. FnrL from Rba. capsulatus is reported to have a role in production of respiratory cytochromes but not in the production of the photosystem machinery [2, 5, 7, 8] Beyond these observations, the involvement of FnrL in controlling anaerobic gene expression is unknown. Under aerobic conditions, this cluster becomes oxidized leading to its
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