I know in Arabidopsis people will often use something like tubulin, which is constitutively expressed, as something to normalize the amount of gene expression.
I've seen people use 16s rRNA for this, but I was wondering if there was a common gene that is used?
In fact, you have already answered your question :) Indeed, in many cases, including Synechocystis 6803, 16s RNA is used as a control. However, whether you will chose this marker as control depends on particular experimental conditions applied to the cultures. Just check, if 16s RNA level is affected by your growth (stress or any environmental) conditions. If not - green light with that marker :) Cloning of the house-keeping gene(s) on a plasmid.. hm.. To me, not the best idea as number of plasmids may be altered by growth conditions. Alternative approach is to insert marker gene into a silent part of genome. The best marker is a gene determining resistance to some antibiotics (e,g, Km-resistance gene from the pUC4K plasmid). There are such examples. These genes are expressed constitutively and their mRNA level is constant.
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