If they're on the same server just use shell() or exec().
If they're on separate servers you can do the same using rsh calls if they're available to you. Not aware of any direct way to do it through the PHP->MySQL connection.
There is also all different kind of admin commands that can just be sent as a SQL string. Therefore, you might not want to connect to the server as root unless it is from the local system. A certain risk is taken when the superuser can connect from anywhere.
Alternatively create a reload user who has only reload privileges, but no shutdown, delete privs. That would curtail any excessive rights and possible abuse.
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