1. If you want to emphasize the responsibility, 由______负责。

由 has the meaning of 原由（reason）.

Some bad things may caused by 公司, or it is none business of the person, but 公司 hope to take responsibility. choose 由.

2. If you want to emphasize the source or origin, 由 他 开始 count off. scandal 由 华尔街日报 report

In other situations, you can choose 被

这件事 被 公司解决。