Scientists Build a Spatial Atlas of the Chloroplast Proteome, the Home of Photosynthesis

By collecting the locations of 1,000-plus chloroplast-associated proteins, the atlas offers insights into protein functions and chloroplast organization.

The Science

Plants and algae convert solar energy into chemical energy through photosynthesis. This process is vital for life on Earth and provides us with oxygen, food, fuels, and other valuable products. Photosynthesis occurs inside the cells, in structures called chloroplasts. To better understand the inner workings of these structures, researchers mapped the locations of 1,034 proteins inside the chloroplast of the unicellular green alga Chlamydomonas. This map is a spatial atlas of the chloroplast proteome—all of the proteins that the organism can produce. This atlas offers scientists insights into the function of proteins and the organization of the chloroplast in the organism. Using this atlas and artificial intelligence algorithms, the investigators were also able to predict the locations for all proteins in Chlamydomonas.

The Impact

Engineering crop plants will help address food, fuel, and product production challenges that arise from climate change. Scientists need a basic biological understanding of photosynthesis to engineer crops with improved productivity. This research lays the groundwork to decipher the inner workings of the chloroplast, the cell structure at the heart of photosynthesis. The spatial atlas of chloroplast proteins discovered previously unknown organizational features of these organelles. The research generated location mapping, insights into protein function, and research tools. These results will help scientists advance their understanding of the chloroplast function. This will enable them to design bioenergy crops with improved photosynthetic capacity.


This research develops a comprehensive spatial atlas of proteins in the chloroplast, the cellular structure key to photosynthesis. This systematic characterization of the location of 1,034 chloroplast-associated proteins from the unicellular green alga Chlamydomonas provides fresh insight into the spatial organization of chloroplasts and how they function to support photosynthesis. The localization patterns of distinct proteins uncovered new chloroplast structures and revealed novel spatial organization inside the chloroplast. The researchers also identified new components of known chloroplast structures such as the chloroplast envelope, its DNA-protein complexes, fat storage microcompartments, and protein bodies involved in capturing carbon dioxide from the atmosphere. The team identified these new components by investigating their interaction with known proteins. They found many proteins that resided in both the chloroplast and other cellular structures, suggesting new function and communication between those structures.

Next, the scientists applied machine learning methods on the protein atlas to generate predictions for the location of all of the proteins in Chlamydomonas. This enabled them to assign putative functions to many uncharacterized proteins based on their cellular location. Altogether, this research establishes a valuable resource that opens new avenues of investigation and guides future work in deciphering and manipulating photosynthesis function.

Principal Investigator

Martin C. Jonikas
Princeton University
[email protected]

Related Links

BER Program Manager

Shing Kwok

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


This research was supported by the Department of Energy Office of Science, Office of Biological and Environmental Research, the HHMI/Simons Foundation, and the Lewis-Sigler Scholars Fund.


Wang, L., et al., A Chloroplast Protein Atlas Reveals Novel Structures and Spatial Organization of Biosynthetic PathwaysCell 186, 16 (2023). [DOI: 10.1016/j.cell.2023.06.008]