The protease is targeted to be isolated only from plant sources not from microbes.
When the plant (fruit/vegetable) is already rotten, there would certainly microorganisms presence in such plant. If you analyses the protease activity, then the enzyme might be excreted from the microorganism, beside those excreted from your plant. However, in general, majority of plant protease belong to sulfhidryl type, such as papain and bromelain. Proteases originated from microorganism, can be alkaline, serine, acidic or metalo enzyme. Using specific inhibitors of the protease might help
Maggy hit the nail on the head. If the fruits and vegetables are rotting, as opposed to just being overripe, it is because of the action of fungi and bacteria, so the plant enzymes and fungi/bacterial enzymes will be mixed together. It's a very messy system to work with.
No. Not always but some fruits like rotted papaya may be possibly you can isolate some proteases
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