since mRNA level does not change, it is unlikely the stability of mRNA is
the cause. it is more likely to be translation efficiency or protein
stability changed. I suggest you to check the association of ribosome with
this mRNA first, then check if protein level is higher in a protease
deficient strain, another thing you can check is the de novo synthesis of
mRNA by ChIP. maybe only newly synthesized mRNA can be translated. Good
luck!