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head1 Children: Item: Title: Introduction Destination: seckiag600-s1 Item: Title: Results Destination: seckiag600-s2 Children: Item: Title: Lincomycin impacts Chlamydomonas growth and physiology Destination: seckiag600-s2.1 Item: Title: Chloroplast structure and pigment profile of the yellow-in-the-dark chlL mutant under different light regimes Destination: seckiag600-s2.2 Item: Title: Dark-grown yellow chlL mutant rapidly builds a functional chloroplast when exposed to light, a process impaired in the presence of lincomycin Destination: seckiag600-s2.3 Item: Title: Light induces early accumulation of photosynthesis-related proteins during chloroplast biogenesis Destination: seckiag600-s2.4 Item: Title: Discussion Destination: seckiag600-s3 Item: Title: Materials and methods Destination: seckiag600-s4 Children: Item: Title: Strains, media, and growth conditions Destination: seckiag600-s4.1 Item: Title: Chlorophyll fluorescence-based measurements Destination: seckiag600-s4.2 Item: Title: Oxygen evolution and consumption measurements Destination: seckiag600-s4.3 Item: Title: Pigment extraction and quantification Destination: seckiag600-s4.4 Item: Title: Light microscopy Destination: seckiag600-s4.5 Item: Title: Electron microscopy Destination: seckiag600-s4.6 Item: Title: Starch extraction and quantification Destination: seckiag600-s4.7 Item: Title: Protein preparation and immunobloting Destination: seckiag600-s4.8 Item: Title: Gene expression Destination: seckiag600-s4.9 Item: Title: Statistical analysis Destination: seckiag600-s4.10 Item: Title: Acknowledgments Destination: acknow Item: Title: Author contributions Destination: seckiag600-s5 Item: Title: Supplementary material Destination: seckiag600-s6 Item: Title: Funding Destination: seckiag600-s7 Item: Title: Conflicts of interest Destination: seckiag600-s8 Item: Title: References Destination: reflist Info: Creator: Servigistics Arbortext Advanced Print Publisher 11.1.4546/W-x64 Producer: PDFlib+PDI 9.0.7p3 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Registry: Adobe Registry: Identity Supplement: 0 FontDescriptor: FontName: XEKZXZ+NotoSans-SemiBold Flags: Nonsymbolic, ForceBold FontBBox: -628, -510, 2801, 1067 FontFile2: true XMP: uuid:F5813395-E3C4-0B58-7A14-5AE3A657043E uuid:26B3CEC5-A120-A594-9FE1-4D3E22AFC035 True application/pdf 10.1093/plphys/kiag600 en Oxford University Press The yellow-in-the-dark chIL Chlamydomonas mutant as a model for time-resolved chloroplast biogenesis and retrograde signaling M. Águila Ruiz-Sola Mariano A. De Silvio Mario Becerra-Tinoco Andrea M. Quintero-Moreno Beatrice Pacenza José L. Crespo Elena Monte DOI: 10.1093/plphys/kiag600; Plant Physiology, 201, 4, 2026-08-17.; Abstract: Understanding chloroplast biogenesis is key given the importance of photosynthesis and chloroplast metabolism. Chloroplast assembly has been extensively studied in angiosperms, where the main hallmarks have been established, including the need for nuclear and plastid genome coordination through anterograde and retrograde signals. However, recent works in other photosynthetic lineages have revealed both divergent and conserved regulators. These differences likely represent adaptive strategies that emerged during the evolution of the green lineage and highlight the need for evolutionary studies to fully elucidate the mechanisms controlling chloroplast biogenesis, a light-promoted process. Here, we characterize the yellow-in-the-dark chIL mutant of Chlamydomonas reinhardtii, which carries a mutation in the CHLL subunit of the dark-operative POR enzyme. Dark-adapted chIL cells cannot synthesize chlorophylls and display a de-differentiated chloroplast, and our results show that upon exposure to light, chloroplast biogenesis is initiated very rapidly based on starch reserves. We demonstrate that accumulation of pigments, photosynthesis-related proteins, and functional chloroplast activity is detected within 1 to 3 h of illumination. Additionally, we show that lincomycin, an inhibitor of plastid translation, specifically affects chloroplast physiology, blocks light-induced chloroplast biogenesis and cell growth, and triggers retrograde signaling, establishing lincomycin as a valuable tool for investigating chloroplast physiology and plastid-to-nucleus communication in Chlamydomonas. Together, this study introduces the chIL mutant as a powerful model system to dissect light-induced, time-resolved chloroplast biogenesis, as well as the responses and signaling triggered by lincomycin. By promoting broader adoption of this model, we aim to help inform strategies to enhance photosynthesis and stress tolerance and optimize bioproduct production. © The Author(s) 2026. Published by Oxford University Press on behalf of American Society of Plant Biologists. PDFlib+PDI 9.0.7p3 (C++/Win64); modified using iTextSharp.LGPLv2.Core 3.7.4.0 Journal Plant Physiology © The Author(s) 2026. 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