I think it's unlikely that MySQL is the problem, assuming you have a reasonable dedicated machine. There are a couple things to look for, though:
Connections usage - If connections are maintained for too long, or if a single query connects multiple times, depending on traffic, you could be exceeding the maximum connections, which will cause further queries to time out. The best place to start with this is to review how connections are used.
SQL - The actual SQL used can have a huge impact on query response times. Try to tune the queries the best you can.
Indexing - Could be the tables aren't indexed properly. In combination with the SQL, this is the biggest bang-for-your-buck and the most likely to improve performance. If you've already worked out indexes appropriate for the tables (maybe carried over from previous DB implementations), it could be something as simple as forgetting to create the indices. I don't know if it will help at all, but MySQL allows you to index only a prefix of a column value, which is useful for wide columns, such as text.
If you are certain that the database performance is the problem, you may want to try partitioning the tables. The latest version of MySQL provides a number of partitioning options, which can greatly enhance query performance.
I apologize if some of this seems elementary and redundant. I'm coming late to the party, so I'm not sure what's been discussed before.
Connections usage - If connections are maintained for too long, or if a single query connects multiple times, depending on traffic, you could be exceeding the maximum connections, which will cause further queries to time out. The best place to start with this is to review how connections are used.
SQL - The actual SQL used can have a huge impact on query response times. Try to tune the queries the best you can.
Indexing - Could be the tables aren't indexed properly. In combination with the SQL, this is the biggest bang-for-your-buck and the most likely to improve performance. If you've already worked out indexes appropriate for the tables (maybe carried over from previous DB implementations), it could be something as simple as forgetting to create the indices. I don't know if it will help at all, but MySQL allows you to index only a prefix of a column value, which is useful for wide columns, such as text.
If you are certain that the database performance is the problem, you may want to try partitioning the tables. The latest version of MySQL provides a number of partitioning options, which can greatly enhance query performance.
I apologize if some of this seems elementary and redundant. I'm coming late to the party, so I'm not sure what's been discussed before.