What vector are you using? If you need to express in both species then a shuttle vector would be good. If you only need to express in pseudomonas then use a vector for pseudomonas expression.

I am using pUCP24 and pBBR1-MCS2 which are broad-host vectors to express 2 subunits of my transcription factor. I am sure they are active because I did reporter assays in pseudomonas. But i want enough protein to perform a Chip-seq. By the way, should the protein be expressed in huge amounts to perform Chip-Seq?

Actually, I would not suggest getting over-expression for ChIP-seq. This could just increase background of non-specific binding.

I don't know how prevalent are the DNA binding sites for your protein but the sentence above is even more true if you expect only a few binding sites.

If you see expression by Western, I would just suggest scaling up the ChIP assay - e.g. take 5-10-50 times more cells. If you know at least one DNA site for sure, I would try several ChIPs with different cell amounts, and choose the best one to go to seq with, by PCR/qPCR.

(Scaling up can also increase background, but I think its easier to optimize it than re-designing plasmids and trying to figure out how to increase expression, which could be by various reasons - different promoter yields, different translation yields, different protein or RNA stability or localization etc...)

I agree with Gal, you will simply enhance non-specific interactions.

yes gal i am expecting only few sites and i know one binding site for sure. I will do as you suggested. Thanks everyone for the help.

As Gal mentioned, this might be problematic. What you could do to get around this problem is to correlate the binding sites of your TF in question with RNA Polymerase II and/or Histone methylation status, like it has been done in this paper: http://www.ncbi.nlm.nih.gov/pubmed/21258399.

Then you will look only at sites, which are actively transcribed.