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United States Department of Agriculture

Agricultural Research Service

Research Project: Modification of Soybeans for Food, Feed, and Industrial Applications

Location: Plant Genetics Research

Title: A functional genomic analysis of Arabidopsis thaliana PP2C clade D

Authors
item Tovar-Mendez, Alejandro -
item Miernyk, Jan
item Hoyos, Mary -
item Randall, Douglas -

Submitted to: Protoplasma
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 24, 2013
Publication Date: July 7, 2013
Repository URL: http://handle.nal.usda.gov/10113/58416
Citation: Tovar-Mendez, A., Miernyk, J.A., Hoyos, M.E., Randall, D.D. 2013. A functional genomic analysis of Arabidopsis thaliana PP2C clade D. Protoplasma. 251:265-271.

Interpretive Summary: A method was developed to visualize the cellular location of a family of important regulatory proteins. Results obtained using this method indicate that the different members of the family are each located in a different part of the cell. Levels of the RNA for each family member were determined and compared. Low levels of RNA were found in all plant parts, while very high levels for three of the nine family members were found in pollen. Our results indicate that while these proteins have been previously assigned to the same family, the have distinct, specialized functions in the plant. Results from this study will be useful to both breeders and molecular biologists in their efforts to develop a line of soybeans that have a modified biochemical composition. They will additionally be useful to scientists who study the effects of organ and tissue specialization in plant biology.

Technical Abstract: In the reference dicot plant Arabidopsis thaliana, the PP2C family of P-protein phosphatases includes the products of 80 genes that have been separated into 10 multi-protein clades plus six singletons. Clade D includes the products of nine genes distributed among 3 chromosomes (PPD1, At3g12620; PPD2, At3g17090; PPD3, At3g51370; PPD4, At3g55050; PPD5, At4g33920; PPD6, At4g38520; PPD7, At5g02760; PPD8, At5g06750; and PPD9, At5g66080).As part of a functional genomics analysis of protein phosphorylation, we retrieved expression data from public databases and determined subcellular protein localization of the members of Clade D. While the nine proteins have been grouped together based upon primary sequence alignments, we observed no obvious common patterns in expression or localization. We found chimera with the GFP associated with the nucleus, plasma membrane, the endomembrane system, and mitochondria in transgenic plants.

Last Modified: 12/22/2014
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