The best spots to see and be seen in the chloroplast

Written by
Caitlin Sedwick for the Department of Molecular Biology, Princeton University
July 11, 2023

Princeton team publishes a comprehensive atlas of the chloroplast.

Chloroplasts are a specialized structure found inside the cells of land plants and red and green algae. Through the process of photosynthesis, chloroplasts convert sunlight and atmospheric carbon dioxide into the starches we eat and the oxygen we breathe. Despite their importance, we have only a fuzzy idea of how chloroplasts work. Now, a study by Princeton researchers Lianyong Wang, Weronika Patena, Claire McWhite, Martin Jonikas and colleagues, published online in the journal Cell on July 11, 2023 and in print on August 3rd, 2023, provides the sharpest picture yet of what’s going on in chloroplasts.

See caption for details.

(l-r) Weronika Patena, Senior Bioinformatics Analyst; Lianyong Wang, Associate Research Scholar; and Martin Jonikas, Associate Professor of Molecular Biology at the imaging system they and their collaborators used to find novel punctate structures in the chloroplast.

Photo by C. Todd Reichart

Perhaps we might be forgiven our ignorance. After all, the chloroplast is a fantastically complex construction that carries out many essential biochemical processes in plants; besides photosynthesis, chloroplasts are also involved the generation of fatty acids that form cellular membranes and the amino acids that make up proteins. The chloroplast contains a host of proteins—currently estimated at aro­und 3,000 different types—that could be involved in any of these activities. Only a few hundred of these have been studied and had their role identified, so Wang and colleagues set out to fill in the blanks.

The Princeton researchers reasoned that cells tend to compartmentalize different biochemical activities in distinct locations, so one can learn a lot about a protein simply by looking at where it is located. The chloroplast contains special sub-structures that operate like the different stations in a factory to perform specific steps of biosynthetic processes. For example, the chlorophyll pigments that convert light energy to the cellular energy store, ATP, are found on stacked, disc-shaped, fluid-filled compartments wrapped in membranes. The space between the discs is home to proteins that use ATP to power the incorporation of carbon into starches. Meanwhile, the chloroplast is bounded by a membrane envelope that controls what comes in and goes out of it.

To get a good look at chloroplast proteins, the team of researchers conducted their studies in the green alga Chlamydomonas reinhardtii, a single-celled organism with a rapid life cycle that makes it amenable to laboratory study. They created more than a thousand unique strains of the alga, each one expressing a different protein thought to be involved with chloroplast function. Each candidate protein was given a fluorescent tag that could be seen and located with a microscope. Using this approach, the team was able to map the location of 1,034 proteins and make several surprising observations.

Illustration. Details explained in caption.

Existing and newly-identified punctate structures in the chloroplast of Chlamydomonas reinhardtii (represented by the colored dots in the drawing at left) operate in different biochemical pathways. On the right are photographs, taken by microscope, of two types of punctate structures identified by the presence of different proteins; each image shows chlorophyll in fuchsia, and a chloroplast protein in green.

Illustration and photographs by Lianyong Wang

One surprise was that many of the proteins were found within punctate (that is, point-like) structures in the chloroplast. Prior research had already identified three punctate structures within chloroplasts, but the team discovered 11 other types of punctate structures that had never been observed before, each of which contained a unique subset of proteins. While many of the constituent proteins had not been studied before, it often proved possible to infer their function—and suggest an appropriate name—either by looking at their similarity to proteins of known function or whether other, more familiar proteins were present within the punctate structures. The researchers concluded that each type of puncta works as a hub for a different metabolic activity within the chloroplast.

The team also observed many new details about the location and potential partners of known and unknown proteins, several of which were quite surprising. Combining these new data with machine learning, the Princeton researchers created a computational model that can predict where other, as yet uncharacterized proteins might be found. With their work, Wang and colleagues have taken a big stride toward a comprehensive atlas of the chloroplast.


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. McWhite, and Martin C. Jonikas. A Chloroplast Protein Atlas Reveals Punctate Structures and Spatial Organization of Biosynthetic Pathways. Cell. 2023. doi:


Support for this work was provided by the following: the U.S. Department of Energy, Office of Science; Office of Biological and Environmental Research under Award Number; HHMI/Simons Foundation grant; the Lewis-Sigler Scholars Fund; and the Howard Hughes Medical Institute.

Funders: U.S. Department of Energy, Office of Science; Office of Biological and Environmental Research; HHMI/Simons Foundation; Lewis-Sigler Scholars Fund; Howard Hughes Medical Institute

Grant numbers: DE-SC0020195, 55108535