A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways

Lianyong Wang, Weronika Patena, Kelly A. Van Baalen, Yihua Xie, Emily R. Singer, Sophia Gavrilenko, Michelle Warren-Williams, Linqu Han, Henry R. Harrigan, Linnea D. Hartz, Vivian Chen, Vinh T.N.P. Ton, Saw Kyin, Henry H. Shwe, Matthew H. Cahn, Alexandra T. Wilson, Masayuki Onishi, Jianping Hu, Danny J. Schnell, Claire D. McWhiteMartin C. Jonikas

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.

Original languageEnglish (US)
Pages (from-to)3499-3518.e14
Issue number16
StatePublished - Aug 3 2023

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • Chlamydomonas reinhardtii
  • chloroplast
  • dual targeting
  • fluorescent tagging
  • nucleoid
  • plastoglobule
  • protein localization
  • protein localization prediction
  • protein-protein interaction
  • pyrenoid


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