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Microproteins encoded by small open reading frames (smORFs) located on long non-coding RNAs (lncRNAs) constitute a significant but insufficiently studied part of the plant cell proteome. Previously, we confirmed translation of an sORF encoding a conserved 41 a.a. microprotein located on a transcript annotated as lncRNA in the moss Physcomitrium patens. Because of the characteristic phenotype of the mutant lines, the microprotein was named FAMOSS (FAst-growing MOSS). We showed that this microprotein is localized in the thylakoid membrane of chloroplasts. The analysis of the microprotein interactome suggested its interaction with the light harvesting-like proteins. Plants overexpressing the microprotein have increased sensitivity to high light due to reduced non-photochemical quenching (NPQ). In addition, we observed changes in vesicular trafficking in mutant lines, which may be associated with the regulation of photosynthesis. Thus, we consider that the FAMOSS microprotein has role in NPQ regulation and influences vesicular trafficking in apical protonema cells.