What Makes a Plant a Plant?

Functions localized to the present day plastid depend on both plastid- and nucleus-encoded proteins.

The Science

The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, researchers performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants.

Researchers demonstrated that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific.


DNA sequencing has generated vast collections of genes for all types of organisms; however, determining the roles of the proteins coded within those genes is a difficult task and the functions of many of those proteins are still unknown. Researchers at the UCLA-DOE Institute for Genomics and Proteomics and at the DOE Joint Genome Institute in Walnut Creek, California, have now provided new information on the function of genes that are uniquely found in plants and green algae. Comparing the genes present in the genomes of 20 photosynthetic organisms with those of non-photosynthetic organisms, the investigators compiled GreenCut2, an inventory of nearly 600 plant-specific genes. As the function of more than half of those 600 genes is not known, this work sheds new light on genes needed for plant-specific processes, including those related to the chloroplast (the photosynthetic organelle of plant cells). Further analysis of those proteins of unknown function showed that many of them are likely involved in protein modification, gene regulation, and transport of molecules to the chloroplast. This new knowledge provides insights on plant evolution and will help researchers better understand how plants work, enabling them to harness their potential to provide alternative energy sources.

BER Program Manager

Pablo Rabinowicz

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


Karpowicz, S., S. E. Prochnik, A. R. Grossman, and S. S. Merchant. 2011. “The GreenCut2 Resource: A Phylogenomically-Derived Inventory of Proteins Specific to the Plant Lineage,” Journal of Biological Chemistry 286, 21427–439. DOI:10.1074/jbc.M111.233734.