updating single row in MYSQL
Consider using the MEMORY storage engine, so the changes will happen in memory. In case of a crash, you can rely on the binlog to recover the latest value. And if you have a slave, you can use InnoDB on the slave.

If you want to stay on InnoDB, consider the HandlerSocket plugin. It provides an SQL-less interface to InnoDB, and it should be much faster in your scenario.