Some [NiFe]-containing proteins are known to sense H and thus regulate transcription.
Copper-containing proteins are known to sense ethylene, which is known to be a hormone relevant to the ripening of fruit.  This example illustrates the essential role of organometallic chemistry in nature, as few molecules outside of low-valent transition metal complexes reversibly bind alkenes.  Cyclopropenes inhibit ripening by binding to the copper(I) center.  Binding to copper is also implicated in the mammalian olfaction of olefins.
Carbon monoxide occurs naturally and is a transcription factor via its complex with a sensor protein based on ferrous porphyrins.