I am using MEME suite tool for de novo motif discovery and when I use TomTom to compare my motifs with known motif database, I find that my genes could potentially be upregulated or downregulated by sigma factor PvdS. I would like to understand what sigma factor PvdS exactly means.
I am not really able to interpret the UniProt page. It indicates the protein: sigma factor PvdS and gene: PvdS. Then it is difficult for me to put together the GO-Molecular Function and the GO-Biological Function in order to understand what sigma factor PvdS means.
From the paper by Miyazaki et al., I find:
In response to iron limitation Pseudomonas aeruginosa PAO induces production of pyoverdin, a low-molecular-weight siderophore able to capture ferric ion with a very high affinity. The pvd genes involved in the pyoverdin biosynthesis are organized in a chromosomal region termed the pvd region, and expression of some pvd genes is regulated at the transcriptional level. Two sets of promoter regions for the pvd genes were defined that were transcriptionally derepressed under iron-limiting conditions. Analysis of transcription from such promoters in Escherichia coli led to isolation and identification of a positive regulatory gene, pvdS, for expression of the pvd genes, and pvdS was localized in the pvd region.
From this extract, I can understand that PvdS is a positive regulatory gene that is, from Wikipedia:
A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. Regulatory sequences, which encode regulatory genes, are often at the five prime end (5') to the start site of transcription of the gene they regulate.
And so PvdS regulates the expression of the pvd gene involved in the pyoverdin biosynthesis.
Then in the paper by Tracey et al I find that:
PvdS is an alternative sigma factor regulated by the global iron regulator Fur
So putting all the pieces together, can I say that my genes could be upregulated or downregulated by this PvdS sigma factor, that is a sigma factor that means a protein needed for initiation of transcription in bacteria and this protein, in this particular case, is encoded by the regulatory gene PvdS that regulates the expression of the pvd gene involved in the pyoverdin biosynthesis? And thus the PvdS sigma factor is a protein for initiation of transcription of the pvd genes?
Thank you in advance.