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Global analysis of photosynthesis transcriptional regulatory networks.

Imam S, Noguera DR, Donohue TJ - PLoS Genet. (2014)

Bottom Line: PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis.Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant.We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA.

View Article: PubMed Central - PubMed

Affiliation: Program in Cellular and Molecular Biology, University of Wisconsin - Madison, Madison, Wisconsin, United States of America; Department of Bacteriology, University of Wisconsin - Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America; DOE Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, Wisconsin, United States of America.

ABSTRACT
Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

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Analysis of the PrrA regulon in R. sphaeroides.(A) PrrA binding sites across chromosome 1. Binding sites within the photosynthetic gene cluster are enlarged. (B) Heat map depicting the PrrA targets genes from a pair-wise comparison of transcript levels from WT and ΔprrA cells grown under anaerobic respiratory conditions. (C) Venn diagram showing the overlap between identified ChIP-seq binding sites for PrrA and differentially expressed operons from microarray analysis. It should be noted that some binding sites are located between two divergently transcribed operons, which were both differentially expressed. In such cases, both operons were considered as direct PrrA targets.
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pgen-1004837-g002: Analysis of the PrrA regulon in R. sphaeroides.(A) PrrA binding sites across chromosome 1. Binding sites within the photosynthetic gene cluster are enlarged. (B) Heat map depicting the PrrA targets genes from a pair-wise comparison of transcript levels from WT and ΔprrA cells grown under anaerobic respiratory conditions. (C) Venn diagram showing the overlap between identified ChIP-seq binding sites for PrrA and differentially expressed operons from microarray analysis. It should be noted that some binding sites are located between two divergently transcribed operons, which were both differentially expressed. In such cases, both operons were considered as direct PrrA targets.

Mentions: To determine which differentially expressed genes are directly regulated by PrrA, we conducted ChIP-seq analysis on exponentially growing cells using a 3X myc-tagged PrrA protein that complements the photosynthetic growth defect of PrrA3 (S2B Figure). We observed significant enrichment for PrrA at ∼140 sites across the R. sphaeroides genome (Fig. 2A). Analysis of the sequences under all of these peaks did not reveal any strong consensus sequence shared by a significant number of these sites. Thus, to help determine the transcriptionally regulated direct targets of PrrA, only operons with both a significant peak and which were differentially expressed in PrrA3, were considered as candidate direct targets of this TF. A total of 34 operons met these criteria, including 18 photosynthesis related operons (Table 2, Figs. 2B and 2C). In addition to photosynthesis-related genes to which PrrA had previously been linked, these analyses indicate that PrrA is also a direct regulator of electron transport (regulating operons encoding fbcFBC, fbcQ-soxDA and RSP_0820 (cytochrome B561)), tetrapyrrole synthesis (hemA, hemC and hemE) and terpenoid backbone biosynthesis (dxr). Our data predict that all but one of these operons are positively regulated by PrrA, since RNA levels from these genes were lower in PrrA3 (Fig. 2B, Table 2). Other enriched sites in the genome not included in this set of transcriptionally regulated direct PrrA targets are provided in S4 Table.


Global analysis of photosynthesis transcriptional regulatory networks.

Imam S, Noguera DR, Donohue TJ - PLoS Genet. (2014)

Analysis of the PrrA regulon in R. sphaeroides.(A) PrrA binding sites across chromosome 1. Binding sites within the photosynthetic gene cluster are enlarged. (B) Heat map depicting the PrrA targets genes from a pair-wise comparison of transcript levels from WT and ΔprrA cells grown under anaerobic respiratory conditions. (C) Venn diagram showing the overlap between identified ChIP-seq binding sites for PrrA and differentially expressed operons from microarray analysis. It should be noted that some binding sites are located between two divergently transcribed operons, which were both differentially expressed. In such cases, both operons were considered as direct PrrA targets.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263372&req=5

pgen-1004837-g002: Analysis of the PrrA regulon in R. sphaeroides.(A) PrrA binding sites across chromosome 1. Binding sites within the photosynthetic gene cluster are enlarged. (B) Heat map depicting the PrrA targets genes from a pair-wise comparison of transcript levels from WT and ΔprrA cells grown under anaerobic respiratory conditions. (C) Venn diagram showing the overlap between identified ChIP-seq binding sites for PrrA and differentially expressed operons from microarray analysis. It should be noted that some binding sites are located between two divergently transcribed operons, which were both differentially expressed. In such cases, both operons were considered as direct PrrA targets.
Mentions: To determine which differentially expressed genes are directly regulated by PrrA, we conducted ChIP-seq analysis on exponentially growing cells using a 3X myc-tagged PrrA protein that complements the photosynthetic growth defect of PrrA3 (S2B Figure). We observed significant enrichment for PrrA at ∼140 sites across the R. sphaeroides genome (Fig. 2A). Analysis of the sequences under all of these peaks did not reveal any strong consensus sequence shared by a significant number of these sites. Thus, to help determine the transcriptionally regulated direct targets of PrrA, only operons with both a significant peak and which were differentially expressed in PrrA3, were considered as candidate direct targets of this TF. A total of 34 operons met these criteria, including 18 photosynthesis related operons (Table 2, Figs. 2B and 2C). In addition to photosynthesis-related genes to which PrrA had previously been linked, these analyses indicate that PrrA is also a direct regulator of electron transport (regulating operons encoding fbcFBC, fbcQ-soxDA and RSP_0820 (cytochrome B561)), tetrapyrrole synthesis (hemA, hemC and hemE) and terpenoid backbone biosynthesis (dxr). Our data predict that all but one of these operons are positively regulated by PrrA, since RNA levels from these genes were lower in PrrA3 (Fig. 2B, Table 2). Other enriched sites in the genome not included in this set of transcriptionally regulated direct PrrA targets are provided in S4 Table.

Bottom Line: PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis.Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant.We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA.

View Article: PubMed Central - PubMed

Affiliation: Program in Cellular and Molecular Biology, University of Wisconsin - Madison, Madison, Wisconsin, United States of America; Department of Bacteriology, University of Wisconsin - Madison, Wisconsin Energy Institute, Madison, Wisconsin, United States of America; DOE Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, Wisconsin, United States of America.

ABSTRACT
Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

Show MeSH
Related in: MedlinePlus