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.

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    $\begingroup$ This is a site for specific problems about biology that can be regarded as of general interest. It is not a site for discussing the research data of particular individuals. As for the function of the actual pad gene, you have found out more than anyone here is likely to know. I assume that you know what sigma factors are, or can read about them. $\endgroup$
    – David
    Aug 14, 2021 at 23:19

1 Answer 1


Clarification of the Question

It appears to me that the question posed in the title of this question, “What is sigma factor PvdS?” is answered by the poster — it is a sigma factor that is specific for, and allows transcription of, genes involved in pyoverdin synthesis in Pseudomonas aeruginosa. I assume that the poster knows that a sigma factor is a subunit of bacterial RNA polymerase that must associate with it before it is capable of initiating transcription. (The information is readily available on Wikipedia or in Berg et al.)

The bulk of the actual question is devoted to describing the results of computer analysis of the genome of an unspecified archaeon. Towards the end the poster poses a question:

…can I say that my genes could be upregulated or downregulated by this PvdS sigma factor…

[The sentence continues for several lines. The emphasis is mine.]

I therefore interpret the question as asking

What conclusions can be drawn from computer analysis of the type performed, with particular reference to the biological system described?


It is necessary to emphasize at the outset that the conclusions that can be derived from studies performed in silico are severely constrained.

Sequence similarity allows you to suggest that an experimentally uncharacterised gene might encode a protein with a similar function to a related gene. No more. Only experimental analysis of the protein allows you to state what its function actually is.

The usual type of annotation of such proteins (and by extension their genes) is one of:

Likewise, the occurrence of a motif that allows pyoverdin genes to be recognized by a transcription factor in P. aeruginosa can only suggest that a functionally uncharacterized gene from a different organism might be similarly recognized and its transcription regulated in a similar manner.

In the example in question the most it is possible to say is that a system of gene regulation similar to that in P. aeruginosa may exist in the archaeon. To go any further one would need to identify (the gene for) for the putative sigma factor, show that it allowed the RNA polymerase to bind to the genes, and either show this affected transcription directly or perform genetic experiments that would allow the same conclusion.

Furthermore, I would be wary of describing the putative sigma factor as ‘PvdS’ unless the proteins predicted to be encoded by genes on which this motif is found bear a similarity to the genes for synthesis of pyoverdin, from which its gene name, pvdS, is derived. (A BLAST search should, of course, be done on the genes to determine this — probably blastx.)

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    $\begingroup$ I think the OP is not a native English speaker and so some of the question phrasing is cumbersome as a result. I interpreted "could" as similar in meaning to your "suggest". $\endgroup$
    – Armand
    Aug 15, 2021 at 5:18
  • $\begingroup$ Since the objection about the fact that I was discussing my research data and the different votes to close the question for the same reason (I think), I removed the last part (I already imagined that it could be source of troubles). So just knowing what sigma factor PvdS means would be great ! @David $\endgroup$
    – Manuela
    Aug 15, 2021 at 6:32
  • $\begingroup$ Anyway, I was asking if my genes could be regulated by the same factor indicated by the software (sigma factor PvdS) . I did not ask if they might encode a certain protein... $\endgroup$
    – Manuela
    Aug 15, 2021 at 6:41
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    $\begingroup$ @Armand I am aware that the poster is not a native speaker as I have helped her previously. My impression is that she wants to go further than "suggest" — modal verbs in English and romance or germanic languages do tend to differ in usage, but they are one of the things that are emphasized and one learns early on in a language. Even if this were so she is asking a question that is impossible to answer without seeing all of her data, and is even then off-topic as it does not constitute a general biological problem. $\endgroup$
    – David
    Aug 15, 2021 at 13:56
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    $\begingroup$ @Manuela —My guess is that you are at some advanced level of education with a training in the numeric sciences but no real knowledge of molecular biology trying to use bioinformatics tools on a problem. It would helpt to know if it is one of your own devising, one given you in a Bioinformatics course or in a lab where you are doing a project is relevant in terms of advice. To answer your question, you should do a BLAST search on each of the genes (or probably better protein translations) that have the motif associated with PvdS to see what they are related to. Surely you know BLAST? $\endgroup$
    – David
    Aug 15, 2021 at 17:15

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