Genome prediction of PhoB regulated promoters in Sinorhizobium meliloti and twelve proteobacteria.
In proteobacteria, genes whose expression is modulated in response to the external concentration of inorganic phosphate are often regulated by the PhoB protein which binds to a conserved motif (Pho box) within their promoter regions. Using a position weight matrix algorithm derived from known Pho box sequences, we identified 96 putative Pho regulon members whose promoter regions contained one or more Pho boxs in the Sinorhizobium meliloti genome. Expression of these genes was examined through assays of reporter gene fusions and through comparison with published microarray data. Of 96 genes, 31 were induced and 3 were repressed by Pi starvation in a PhoB dependent manner. Novel Pho regulon members included several genes of unknown function. Comparative analysis across 12 proteobacterial genomes revealed highly conserved Pho regulon members including genes involved in Pi metabolism (pstS, phnC and ppdK). Genes with no obvious association with Pi metabolism were predicted to be Pho regulon members in S.meliloti and multiple organisms. These included smc01605 and smc04317 which are annotated as substrate binding proteins of iron transporters and katA encoding catalase. This data suggests that the Pho regulon overlaps and interacts with several other control circuits, such as the oxidative stress response and iron homeostasis.
Yuan
Ze-Chun
ZC
Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4K1.
Zaheer
Rahat
R
Morton
Richard
R
Finan
Turlough M
TM
D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D011122:Polyphosphates / Q000378:metabolism; D011401:Promoter Regions, Genetic; D020560:Proteobacteria / Q000235:genetics* / Q000378:metabolism; D018085:Regulon; D016962:Sinorhizobium meliloti / Q000235:genetics* / Q000378:metabolism
D001426:Bacterial Proteins; D011122:Polyphosphates; C061278:PhoB protein, Bacteria