The phytocyanin gene family in rice (Oryza sativa L.): genome-wide identification, classification and transcriptional analysis.

Zhi Liu,Haibing Yang,Heming Zhao,Haoli Ma,Jie Zhao

doi:10.1371/journal.pone.0025184

Abstract

BackgroundPhytocyanins (PCs) are plant-specific blue copper proteins involved in electron transport, and a large number of known PCs are considered to be chimeric arabinogalactan proteins (AGPs). To date there has not been a genome-wide overview of the OsPC gene family. Therefore, as the first step and a useful strategy to elucidate the functions of OsPCs, there is an urgent need for a thorough genome-wide analysis of this gene family.Methodology/Principal FindingsIn this study, a total of 62 OsPC genes were identified through a comprehensive bioinformatics analysis of the rice (Oryza sativa L.) genome. Based on phylogeny and motif constitution, the family of OsPCs was classified into three subclasses: uclacyanin-like proteins (OsUCLs), stellacyanin-like proteins (OsSCLs) and early nodulin-like proteins (OsENODLs). Structure and glycosylation prediction indicated that 46 OsPCs were glycosylphosphatigylinositol-anchored proteins and 38 OsPCs were chimeric AGPs. Gene duplication analysis revealed that chromosomal segment and tandem duplications contributed almost equally to the expansion of this gene family, and duplication events were mostly happened in the OsUCL subfamily. The expression profiles of OsPC genes were analyzed at different stages of vegetative and reproductive development and under abiotic stresses. It revealed that a large number of OsPC genes were abundantly expressed in the various stages of development. Moreover, 17 genes were regulated under the treatments of abiotic stresses.Conclusions/SignificanceThe genome-wide identification and expression analysis of OsPC genes should facilitate research in this gene family and give new insights toward elucidating their functions in higher plants.

Highlights

Phytocyanins (PCs) are ancient blue copper proteins which can bind with a single copper atom and function as electron transporter, and uclacyanins (UCs) and stellacyanins (SCs) are typical family members of PCs [1,2,3,4,5]
A total of 38 PCs were identified and classified into several groups based on their domain composition and phylogenetic relationship in Arabidopsis, including eight AtUCs, four AtSCs, one plantacyanin, 22 AtENODLs, and three unknown plastocyanin-like domain (PCLD)-containing proteins, 18 of which were regarded as chimeric arabinogalactan proteins (AGPs) [14]
Identification and classification of OsPCs BLASTP searches using PCLDs of 26 known PCs and name searches using multiple keywords were used to obtain the amino acid sequences of PCs against several rice protein databases, and to uncover the entire family of genes coding for PCs in the rice genome

Summary

Introduction

Phytocyanins (PCs) are ancient blue copper proteins which can bind with a single copper atom and function as electron transporter, and uclacyanins (UCs) and stellacyanins (SCs) are typical family members of PCs [1,2,3,4,5]. It was reported that 25 and 36 plastocyanin-like domain (PCLD)-containing proteins (UC-like, SC-like and ENOD-like) with a glycosylphosphatidylinisotol-anchor signal (GAS) were identified in Arabidopsis and rice, respectively, and 40% of them had putative arabinogalactan (AG) glycomodules [9,10]. Phytocyanins (PCs) are plant-specific blue copper proteins involved in electron transport, and a large number of known PCs are considered to be chimeric arabinogalactan proteins (AGPs). As the first step and a useful strategy to elucidate the functions of OsPCs, there is an urgent need for a thorough genome-wide analysis of this gene family

Methods

Results

Discussion

Conclusion