Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis
Date
2008-11-20
Authors
Xue, Tongtong
Wang, Dong
Zhang, Shizhong
Ehlting, Juergen
Ni, Fei
Jakab, Stephen
Zheng, Chengchao
Zhong, Yuan
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: 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.
Results: 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 lineagespecific
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 ABAmediated
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.
Conclusion: 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.
Description
BioMed Central
Keywords
Citation
Xue et al.: Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis. BMC Genomics 2008, 9:550.