Skip to main page content
U.S. flag

An official website of the United States government

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Mar;187(6):2148-56.
doi: 10.1128/JB.187.6.2148-2156.2005.

Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development

Oleg V Moskvin  1 , Larissa Gomelsky, Mark Gomelsky
Affiliations

Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development

Oleg V Moskvin et al. J Bacteriol. 2005 Mar.

Abstract

PpsR from the anoxygenic phototrophic bacterium Rhodobacter sphaeroides has been known as an oxygen- and light-dependent repressor of bacteriochlorophyll and carotenoid biosynthesis genes and puc operons involved in photosystem development. However, the putative PpsR-binding sites, TGTN12ACA, are also located upstream of numerous nonphotosystem genes, thus raising the possibility that the role of PpsR is broader. To characterize the PpsR regulon, transcriptome profiling was performed on the wild-type strain grown at high and low oxygen tensions, on the strain overproducing PpsR, and on the ppsR mutant. Transcriptome analysis showed that PpsR primarily regulates photosystem genes; the consensus PpsR binding sequence is TGTcN10gACA (lowercase letters indicate lesser conservation); the presence of two binding sites is required for repression in vivo. These findings explain why numerous single TGTN12ACA sequences are nonfunctional. In addition to photosystem genes, the hemC and hemE genes involved in the early steps of tetrapyrrole biosynthesis were identified as new direct targets of PpsR repression. Unexpectedly, PpsR was found to indirectly repress the puf and puhA operons encoding photosystem core proteins. The upstream regions of these operons contain no PpsR binding sites. Involvement in regulation of these operons suggests that PpsR functions as a master regulator of photosystem development. Upregulation of the puf and puhA operons that resulted from ppsR inactivation was sufficient to restore the ability to grow phototrophically to the prrA mutant. PrrA, the global redox-dependent activator, was previously considered indispensable for phototrophic growth. It is revealed that the PrrBA and AppA-PpsR systems, believed to work independently, in fact interact and coordinately regulate photosystem development.

PubMed Disclaimer

Figures

FIG. 1.
FIG. 1.
Photosynthetic complexes of the R. sphaeroides strains grown at high (20%) and low (0.5%) oxygen.
FIG. 2.
FIG. 2.
(Upper panel) R. sphaeroides PpsR regulon. Each gene is represented by a box colored according to its function. Green, bch genes; red, crt genes; blue, genes encoding structural polypeptides of photocomplexes; grey, genes encoding assembly factors or proteins of unknown function; orange, genes encoding regulatory factors; pink, genes encoding enzymes common to Bchl and ubiquinone biosynthesis; magenta, protoporphyrin IX biosynthesis genes. PpsR-binding sites are shown as red vertical arrows. Putative transcripts are shown as black horizontal arrows. Genes that are either known or predicted to be directly repressed by PpsR are circles. (Lower panels) Relative expression of PpsR-dependent genes measured by genechips (compared to that in the wild-type strain grown at high [20%] oxygen). Expression levels are according to the presented color scheme. The expression of every gene in 2.4.1 grown at high (20%) oxygen is assigned a value of 1 (data not shown).
FIG. 3.
FIG. 3.
Expression changes (plotted as relative changes with a logarithmic scale) of selected PpsR-dependent genes as measured by qPCR. The expression of every gene in 2.4.1 grown at high (20%) oxygen (data not shown) is assigned a value of 1. White, 2.4.1 grown at low (0.5%) oxygen; vertical stripes, PPS2-4; horizontal stripes, 2.4.1(pPNs); black, APP11. Expression values are derived from RNA from two to four independent experiments, with each done in three replicates. Error bars represent standard deviations.
FIG. 4.
FIG. 4.
Sequence logo of the consensus sequence for PpsR binding created by using WebLogo (http://weblogo.berkeley.edu) (8).
FIG. 5.
FIG. 5.
(A) Scheme of genetic organization of the hemC-hemE region. Putative PpsR binding sites are shown. (B) Expression of the hemC::lacZ and hemE::lacZ transcriptional fusions in P. denitrificans containing in trans either vector pRK415 (white bars) or plasmid pPNs (pRK415::ppsR) (grey bars). One unit of β-galactosidase is equal to 1 nmol of o-nitrophenyl-β-d-galactopyranoside ΔA600−1 ml of culture−1 min−1. Average data from three independent experiments are shown, with standard deviations not exceeding 13% of the averages.
FIG. 6.
FIG. 6.
Photosynthetic complexes of the R. sphaeroides strains grown under anaerobic phototrophic conditions at 10 W of white light m−2 (2.4.1 and RPS1) or under anaerobic-dark-DMSO conditions (PRRA1). Cultures were started from the inoculum grown under anaerobic-dark-DMSO conditions. Strain PRRA1 is unable to grow phototrophically.
FIG. 7.
FIG. 7.
Expression changes (plotted as relative changes with a logarithmic scale) of selected regulatory genes controlling PS gene expression as measured by genechips. The expression of every gene in 2.4.1 grown at high (20%) oxygen (data not shown) was assigned a value of 1. White, 2.4.1 grown at low (0.5%) oxygen; vertical stripes, PPS2-4; horizontal stripes, 2.4.1(pPNs); black, APP11.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Bauer, C., S. Elsen, L. R. Swem, D. L. Swem, and S. Masuda. 2003. Redox and light regulation of gene expression in photosynthetic prokaryotes. Philos. Trans. R. Soc. Lond. B 358:147-153. - PMC - PubMed
    1. Bauer, C. E., J. J. Buggy, Z. M. Yang, and B. L. Marrs. 1991. The superoperonal organization of genes for pigment biosynthesis and reaction center proteins is a conserved feature in Rhodobacter capsulatus: analysis of overlapping bchB and puhA transcripts. Mol. Gen. Genet. 228:443-454. - PubMed
    1. Braatsch, S., M. Gomelsky, S. Kuphal, and G. Klug. 2002. The single flavoprotein, AppA, from Rhodobacter sphaeroides integrates both redox and light signals. Mol. Microbiol. 45:827-836. - PubMed
    1. Braatsch, S., O. V. Moskvin, G. Klug, and M. Gomelsky. 2004. Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions. J. Bacteriol. 186:7726-7735. - PMC - PubMed
    1. Cho, S. H., S. H. Youn, S. R. Lee, H. S. Yim, and S. O. Kang. 2004. Redox property and regulation of PpsR, a transcriptional repressor of photosystem gene expression in Rhodobacter sphaeroides. Microbiology 150:697-706. - PubMed

Publication types

MeSH terms