Limits...
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

DNA binding motifs of FnrL/FNR orthologues. DNA consensus binding site was determined using MEME server from ChIP enriched sequences.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: DNA binding motifs of FnrL/FNR orthologues. DNA consensus binding site was determined using MEME server from ChIP enriched sequences.

Mentions: A consensus FnrL recognition sequence was obtained using the MEME server from called ChIP-seq sites (Fig. 2). The derived sequence (T/C/A)TGA-N6-TCAA has second and third positions that were invariably TG while the 12th and 13th positions were invariably CA. The first position was somewhat variable with T, C, or A accounting for 37, 34 and 24 %, respectively, whereas the 14th position was an A at a frequency of 90 %. As shown in Fig. 2, the derived FnrL consensus sequence is highly similar to consensus sequences derived from similar studies from Rba. sphaeroides and E. coli. Variants of the Rba. capsulatus FnrL recognition sequence were identified by MEME in 69 out of 82 called ChIP-seq sites (Additional file 1: Table S1) with potential FnrL binding recognition sequences also manually found in ChIP peaks where no consensus sequence was identified by MEME. These manually identified potential recognition sequences are not listed in Additional file 1: Table S1 since flanking TTG/CAA sequences are common throughout the genome.Fig. 2


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)

DNA binding motifs of FnrL/FNR orthologues. DNA consensus binding site was determined using MEME server from ChIP enriched sequences.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: DNA binding motifs of FnrL/FNR orthologues. DNA consensus binding site was determined using MEME server from ChIP enriched sequences.
Mentions: A consensus FnrL recognition sequence was obtained using the MEME server from called ChIP-seq sites (Fig. 2). The derived sequence (T/C/A)TGA-N6-TCAA has second and third positions that were invariably TG while the 12th and 13th positions were invariably CA. The first position was somewhat variable with T, C, or A accounting for 37, 34 and 24 %, respectively, whereas the 14th position was an A at a frequency of 90 %. As shown in Fig. 2, the derived FnrL consensus sequence is highly similar to consensus sequences derived from similar studies from Rba. sphaeroides and E. coli. Variants of the Rba. capsulatus FnrL recognition sequence were identified by MEME in 69 out of 82 called ChIP-seq sites (Additional file 1: Table S1) with potential FnrL binding recognition sequences also manually found in ChIP peaks where no consensus sequence was identified by MEME. These manually identified potential recognition sequences are not listed in Additional file 1: Table S1 since flanking TTG/CAA sequences are common throughout the genome.Fig. 2

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