Combining microarray and genomic data to predict DNA binding motifs

Mao, Linyong; MacKenzie, Cameron A.; Roh, Jung Hyeob; Eraso, Jesus M.; Kaplan, Samuel; Resat, Haluk

doi:10.1099/mic.0.28167-0

Cited by 48 publications

(60 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Attempts to describe a consensus DNA binding sequence for PrrA have been hampered in part by the apparent variable lengths of the sequences. However, reports by several investigators agree that the most conserved DNA sequence motif is a GCG inverted repeat with variable spacing that is between 0 and 12 nt (23,26). This same sequence motif had been described previously as the recognition sequence for RegA (33), the R. capsulatus PrrA homologue that is 100% identical at the amino acid sequence level in the DNA binding domain.…”

Section: Discussionmentioning

confidence: 99%

“…mutated the hemA sequences by using mutagenic oligonucleotides that introduced changes encompassing 6 residues at a time, scanning across the DNase I-protected region. While studies have demonstrated that the sequences associated with PrrA binding are highly variable (8,9,22,23,26), the one consistent feature is a preponderance of G/C nucleotides. Therefore, we deliberately chose alterations that are AT rich.…”

mentioning

confidence: 99%

See 1 more Smart Citation

In Vitro and In Vivo Analysis of the Role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA Gene Expression

et al. 2006

View full text Add to dashboard Cite

The hemA gene codes for one of two synthases in Rhodobacter sphaeroides 2.4.1 which catalyze the formation of 5-aminolevulinic acid. We have examined the role of PrrA, a DNA binding protein that is associated with the metabolic switch between aerobic growth and anoxygenic photosynthetic growth, in hemA expression and found that hemA transcription is directly activated by PrrA. Using electrophoretic mobility shift assays and DNase I protection assays, we have mapped two binding sites for PrrA within the hemA upstream sequences, each of which contains an identical 9-bp motif. Using lacZ transcription reporter plasmids in wild-type strain 2.4.1 and PrrA ؊ mutant strain PRRA2, we showed that PrrA was required for maximal expression. We also found that the relative impacts of altering DNA sequences within the two binding sites are different depending on whether cells are growing aerobically or anaerobically. This reveals a greater level of complexity associated with PrrA-mediated regulation of transcription than has been heretofore described. Our findings are of particular importance with respect to those genes regulated by PrrA having more than one upstream binding site. In the case of the hemA gene, we discuss possibilities as to how these new insights can be accommodated within the context of what has already been established for hemA transcription regulation in R. sphaeroides.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

In Vitro and In Vivo Analysis of the Role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA Gene Expression

et al. 2006

View full text Add to dashboard Cite

show abstract

“…Recombinant PrrA isolated from Escherichia coli resulted in retardation of a DNA fragment spanning this upstream region (Fig. S1) and also bound to the puc promoter (RSP_0314 upstream region) with a known PrrA binding site (20) in the presence of unspecific competitor DNA.…”

Section: Resultsmentioning

confidence: 99%

“…More recently CryB, a member of a newly described cryptochrome family (15), was shown to affect expression of photosynthesis genes in R. sphaeroides and to interact with AppA (16,17). Remarkably, the different signaling pathways for control of photosynthesis genes are also interconnected, e.g., the appA gene is controlled by PrrA (18,19) and a PpsR binding site is located in the ppaA promoter region (20). Thus, a complex network comprising several regulatory proteins controls the formation of the photosynthetic apparatus.…”

mentioning

confidence: 99%

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

Mank

Berghoff

Hermanns

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/ PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.α-proteobacteria | protochlorophyllide reductase

show abstract

“…An optimized procedure for isolation of intact mRNA for DNA microarrays has been described previously (29,44).…”

Section: Methodsmentioning

confidence: 99%

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

et al. 2008

Self Cite

View full text Add to dashboard Cite

The expression of genes involved in photosystem development in Rhodobacter sphaeroides is dependent upon three major regulatory networks: FnrL, the PrrBA (RegBA) two-component system, and the transcriptional repressor/antirepressor PpsR/AppA. Of the three regulators, PpsR appears to have the narrowest range of physiological effects, which are limited to effects on the structural and pigment biosynthetic activities involved in photosynthetic membrane function. Although a PrrA ؊ mutant is unable to grow under photosynthetic conditions, when a ppsR mutation was present, photosynthetic growth occurred. An examination of the double mutant under anaerobic-dark-dimethyl sulfoxide conditions using microarray analysis revealed the existence of an "extended" PpsR regulon and new physiological roles. To characterize the PpsR regulon and to better ascertain the significance of degeneracy within the PpsR binding sequence in vivo, we adapted the chromatin immunoprecipitation technique to R. sphaeroides. We demonstrated that in vivo there was direct and significant binding by PpsR to newly identified genes involved in microaerobic respiration and periplasmic stress resistance, as well as to photosynthesis genes. The new members of the PpsR regulon are located outside the photosynthesis gene cluster and have degenerate PpsR binding sequences. The possible interaction under physiologic conditions with degenerate binding sequences in the presence of other biologically relevant molecules is discussed with respect to its importance in physiological processes and to the existence of complex phenotypes associated with regulatory mutants. This study further defines the DNA structure necessary for PpsR binding in situ.

show abstract

Combining microarray and genomic data to predict DNA binding motifs

Cited by 48 publications

References 46 publications

In Vitro and In Vivo Analysis of the Role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA Gene Expression

In Vitro and In Vivo Analysis of the Role of PrrA in Rhodobacter sphaeroides 2.4.1 hemA Gene Expression

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

Contact Info

Product

Resources

About