To upgrade the MySQL version one need to do the login into WHM interface and follow the below mentioned steps:
1) Go to Server Configuration/Tweak Settings.
2) Choose in the MySQL section the 5.0 radio button and click Save.
It will actually run the script: /scripts/mysqlup which will download and install the latest MySQL5 rpms available at the time. After completion one should rebuild the perl mysql libraries and rebuild apache to php build against the newly installed mysql library. One can use below mentioned command to rebuild the MySQL Libraries and Apache:
For MySQL Libraries:
/scripts/perlinstaller --force Bundle::BD::mysql
NOTE: The MySQL version upgrade is not reversible