First question: Has the regulator that is deleted been shown to negatively regulate HcpB? Some regulators can have positive or negative effects on gene regulation depending on where and how they bind the promoter region.

Second question: How exclusive are these two systems? Often when there are two similar secretion systems there is overlap in what they secrete and their regulation. Thus, you may be seeing compensation due to loss of secretion of HcpA.

Just a couple of thoughts, with more info I might be able to give more ideas.

Thank you Jonathan Tabb Sullivan for your answer. Is it possible that the regulatory protein is  downregulating HcpB and and upregulating HcpA under nitrogen fixing conditions and therefore upon its deletion an opposite effect is seen? As far as I know, it is not show that it has a negative effect. 

To your second question, these two secretion system are homologous and also few core components are missing in the secretion system B so could it be speculated that the other copy of the secretion system is compensating for these componenents? 

Additionally, is it possible that the Hcp of one secretion system is secreted my the other type VI machinery?

*by the other type VI machinery?

Nilima,

Without knowing too much about your system I would say all of the cases you state are possible. However, until you or somebody else does the experiments to rule them out they remain hypotheses.

I would look to a better understood secretion system as a model of how homologous secretion systems can work together. Read more about Salmonella Type III secretion systems for an example. For these secretion systems some of the secreted proteins are secreted by one or the other secretion system and other proteins are secreted by both. And interestingly the flagellin subunit FliC is secreted by both pathogenicity Type III secretions systems and the homologous flagellin secretion system.

Thanks a lot. I tried looking for papers on type iii machinery  but I did not come across anything I was interested in. But now that you mentioned, I would search again. Thank you very much for your response once again.