Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling.
BACKGROUND
The classic paradigm of heterotrimeric G-protein signaling describes a heptahelical, membrane-spanning G-protein coupled receptor that physically interacts with an intracellular G alpha subunit of the G-protein heterotrimer to transduce signals. G-protein coupled receptors comprise the largest protein superfamily in metazoa and are physiologically important as they sense highly diverse stimuli and play key roles in human disease. The heterotrimeric G-protein signaling mechanism is conserved across metazoa, and also readily identifiable in plants, but the low sequence conservation of G-protein coupled receptors hampers the identification of novel ones. Using diverse computational methods, we performed whole-proteome analyses of the three dominant model plant species, the herbaceous dicot Arabidopsis thaliana (mouse-eared cress), the monocot Oryza sativa (rice), and the woody dicot Populus trichocarpa (poplar), to identify plant protein sequences most likely to be GPCRs.


RESULTS
Our stringent bioinformatic pipeline allowed the high confidence identification of candidate G-protein coupled receptors within the Arabidopsis, Oryza, and Populus proteomes. We extended these computational results through actual wet-bench experiments where we tested over half of our highest ranking Arabidopsis candidate G-protein coupled receptors for the ability to physically couple with GPA1, the sole G alpha in Arabidopsis. We found that seven out of eight tested candidate G-protein coupled receptors do in fact interact with GPA1. We show through G-protein coupled receptor classification and molecular evolutionary analyses that both individual G-protein coupled receptor candidates and candidate G-protein coupled receptor families are conserved across plant species and that, in some cases, this conservation extends to metazoans.


CONCLUSIONS
Our computational and wet-bench results provide the first step toward understanding the diversity, conservation, and functional roles of plant candidate G-protein coupled receptors.
Gookin
Timothy E
TE
Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA. tegookin@psu.edu
Kim
Junhyong
J
Assmann
Sarah M
SM
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D044385:GTP-Binding Protein alpha Subunits / Q000378:metabolism; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D032107:Populus / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000737:chemistry; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000145:classification* / Q000378:metabolism*; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid
D029681:Arabidopsis Proteins; D044385:GTP-Binding Protein alpha Subunits; D010940:Plant Proteins; D020543:Proteome; D043562:Receptors, G-Protein-Coupled