My guess this is a connection error due to the maximum time MySQL will allow an idle connection to exist. Check the 'wait_timeout' value of the 'show variables' command; this will be the number of seconds an open connection can exist before being implicitly closed by MySQL. You can increase this value to stop MySQL closing old connections.
If you are using a connection pooling architecture look at your pooling documentation for a similar value to recycle pooling connections. Juggling the timout values for both these should do the trick.
ServerMetrics DB Monitoring (www.servermetrics.com)