After you upgraded mysql from your package manager did you run the mysql_upgrade command from the cli? The mysql_upgrade command does this according to the man page:
"mysql_upgrade - check and upgrade MySQL tables"
Upgrading the db is not enough you need to run that command too.
If you need to dump your data or restore it you can use a service called www.freemysql.org
to host your database, its running the latest version of mysql. Hope this helps. Let me know if it works.