Open Access Highly Accessed Research article

Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis

Tongtong Xue1, Dong Wang134, Shizhong Zhang1, Juergen Ehlting5, Fei Ni1, Stephen Jakab2, Chengchao Zheng1 and Yuan Zhong12*

Author Affiliations

1 State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China

2 Biology Department, Millersville University of Pennsylvania, 288 Roddy Hall, 50 E Frederick St, PO Box 1002, Millersville PA, 17551-0302, USA

3 Department of Chemistry, Fudan University, 220 Handan Road, Shanghai 200433, PR China

4 Institutes of Biomedical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, PR China

5 Centre for Forest Biology & Department of Biology, University of Victoria, Victoria BC, V8W 3N5, Canada

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BMC Genomics 2008, 9:550  doi:10.1186/1471-2164-9-550

Published: 20 November 2008



The protein phosphatase 2Cs (PP2Cs) from various organisms have been implicated to act as negative modulators of protein kinase pathways involved in diverse environmental stress responses and developmental processes. A genome-wide overview of the PP2C gene family in plants is not yet available.


A comprehensive computational analysis identified 80 and 78 PP2C genes in Arabidopsis thaliana (AtPP2Cs) and Oryza sativa (OsPP2Cs), respectively, which denotes the PP2C gene family as one of the largest families identified in plants. Phylogenic analysis divided PP2Cs in Arabidopsis and rice into 13 and 11 subfamilies, respectively, which are supported by the analyses of gene structures and protein motifs. Comparative analysis between the PP2C genes in Arabidopsis and rice identified common and lineage-specific subfamilies and potential 'gene birth-and-death' events. Gene duplication analysis reveals that whole genome and chromosomal segment duplications mainly contributed to the expansion of both OsPP2Cs and AtPP2Cs, but tandem or local duplication occurred less frequently in Arabidopsis than rice. Some protein motifs are widespread among the PP2C proteins, whereas some other motifs are specific to only one or two subfamilies. Expression pattern analysis suggests that 1) most PP2C genes play functional roles in multiple tissues in both species, 2) the induced expression of most genes in subfamily A by diverse stimuli indicates their primary role in stress tolerance, especially ABA response, and 3) the expression pattern of subfamily D members suggests that they may constitute positive regulators in ABA-mediated signaling pathways. The analyses of putative upstream regulatory elements by two approaches further support the functions of subfamily A in ABA signaling, and provide insights into the shared and different transcriptional regulation machineries in dicots and monocots.


This comparative genome-wide overview of the PP2C family in Arabidopsis and rice provides insights into the functions and regulatory mechanisms, as well as the evolution and divergence of the PP2C genes in dicots and monocots. Bioinformatics analyses suggest that plant PP2C proteins from different subfamilies participate in distinct signaling pathways. Our results have established a solid foundation for future studies on the functional divergence in different PP2C subfamilies.