Defining the Plant Peroxisomal Proteome: From Arabidopsis to Rice

Abstract

Peroxisomes are small subcellular organelles mediating a multitude of processes in plants. Proteomics studies over the last several years have yielded much needed information on the composition of plant peroxisomes. In this review, the status of peroxisome proteomics studies in Arabidopsis and other plant species and the cumulative advances made through these studies are summarized. A reference Arabidopsis peroxisome proteome is generated, and some unique aspects of Arabidopsis peroxisomes that were uncovered through proteomics studies and hint at unanticipated peroxisomal functions are also highlighted. Knowledge gained from Arabidopsis was utilized to compile a tentative list of peroxisome proteins for the model monocot plant, rice. Differences in the peroxisomal proteome between these two model plants were drawn, and novel facets in rice were expounded upon. Finally, we discuss about the current limitations of experimental proteomics in decoding the complete and dynamic makeup of peroxisomes, and complementary and integrated approaches that would be beneficial to defining the peroxisomal metabolic and regulatory roadmaps. The synteny of genomes in the grass family makes rice an ideal model to study peroxisomes in cereal crops, in which these organelles have received much less attention, with the ultimate goal to improve crop yield.

Proteome Analysis of Peroxisomes from Etiolated Arabidopsis Seedlings Identifies a Peroxisomal Protease Involved in β-Oxidation and Development

“…To this end, proteomics should be combined with other largescale approaches such as transcriptomics and metabolomics. Finally, technologies employed in the reference plant Arabidopsis may also be applied to the study of crop species, such as rice, which was predicted to contain a conserved peroxisomal proteome with Arabidopsis (Kaur and Hu, 2011), and other economically important plants.…”

“…We also compared the identified proteins with a list of known peroxisomal proteins (Kaur and Hu, 2011) to assign proteins unambiguously to the peroxisome. Proteins newly validated to be peroxisomal in this study were later included in this list.…”

Plant acyl-CoA-binding proteins: An emerging family involved in plant development and stress responses

“…The unique peroxisomal localization of OsACBP6 implies that diversity in Class IV evolved could have split between monocots and eudicots. Obvious differences between the proteomes of Arabidopsis and rice peroxisomes have been reported [139]. Substrate transport for β-oxidation in rice may possibly differ from Arabidopsis.…”

Plant Peroxisomes: Biogenesis and Function

“…In addition to efforts aimed at engineering plants for improved biomass production by manipulating photorespiration and lipid metabolism, it is also time to translate peroxisomal research from reference plants to agronomically important crops. The extensive conservation of the peroxisomal proteome of Arabidopsis and the predicted rice peroxisomal proteome (Kaur and Hu, 2011) suggests that knowledge gained from model plants can aid in the study of peroxisomes in other prominent cereal crops.…”

“…Because plant peroxisomes are difficult to separate from mitochondria and plastids, validation of peroxisome targeting using methods such as transient expression of the candidate proteins tagged by a GFP variant generally is required. Many new Arabidopsis proteins have been established in the past few years by the peroxisome community, with major contributions from the Arabidopsis Peroxisome 2010 project (www.peroxisome.msu.edu; reviewed in Kaur and Hu, 2011;Reumann, 2011).…”