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GreenCut2: Algorithm to ID Plant Protein Functions

Soybean, one of the plants studied using GreenCut (Scott Bauer, USDA)

Soybean, one of the plants studied using GreenCut (Scott Bauer, USDA)

Researchers use genome sequencing to inform various cellular processes in land plants and algae, including the details of photosynthesis.  Despite the access to an increasing number of plant genomes (most of which have been generated by the DOE JGI), it remains difficult to correlate protein information with function, until now.  For example, identifying the role proteins play in the evolution of chloroplasts and how the photosynthetic apparatus responds under different conditions.

DOE JGI bioinformaticist Simon Prochnik and collaborators at UCLA and the Carnegie Institution at Stanford have developed and deployed a computer algorithm that can distinguish proteins involved in photosynthesis present in plant and green algal genomes, but not in non-photosynthetic organisms.

This tool is called the GreenCut2.  In the June 17, 2011 issue of The Journal of Biological Chemistry, researchers used GreenCut2 to derive an inventory of proteins specific to the plant lineage and to identify the function of 286 out of 597 proteins from 20 plant genomes.   

The remaining proteins have not been associated with a specific biological process and are called “unknowns.” Evidence suggests that these may be involved with such processes as regulation of metabolism and control of DNA transcription.
Comparison of GreenCut2 proteins is opening windows for discoveries about the roles that these proteins play in photosynthetic cells, the evolution of chloroplasts, and how photosynthetic cells might be tailored for survival under different environmental conditions.