Light capture and photosynthetic energy conversion depend on photosynthetic complexes that are embedded within lipid membranes. Components of these complexes are vulnerable to damage by reactive oxygen species, byproducts of photosynthesis that accumulate under environmental stress. Here we explore the basis for a lipid-based sensing mechanism allowing plants or algae to assess and respond to damage to the photosynthetic membranes. In Chlamydomonas reinhardtii, Low Carbon Inducible2 (LCI2) and Fatty Acid Desaturase4 (FAD4) are two proteins derived from the same locus by a differential splicing event, sharing an N-terminus encoded by the first two exons. FAD4 produces a 16-carbon, trans double bond-containing fatty acid found exclusively in phosphatidylglycerol of chloroplast membranes, while LCI2 recruits peroxidase activity to the membrane. The unique organization and transcriptional regulation of the LCI2/FAD4 locus represents a regulatory interface that allows cells to initiate the biosynthesis of a fatty acid unique to the photosynthetic membranes while also linking it to the production of an enzyme involved in the mitigation of reactive oxygen species.