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Open Access Research article

Serpins in rice: protein sequence analysis, phylogeny and gene expression during development

Sheila E Francis1, Renan A Ersoy1, Joon-Woo Ahn14, Brian J Atwell2 and Thomas H Roberts13*

Author Affiliations

1 Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, 2109, Australia

2 Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia

3 Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Sydney, NSW, 2006, Australia

4 Green Bio Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon, 305-806, Korea

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BMC Genomics 2012, 13:449  doi:10.1186/1471-2164-13-449

Published: 4 September 2012

Abstract

Background

Most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. Inhibitory serpins are distinguished from members of other families of proteinase inhibitors by their metastable structure and unique suicide-substrate mechanism. Animal serpins exert control over a remarkable diversity of physiological processes including blood coagulation, fibrinolysis, innate immunity and aspects of development. Relatively little is known about the complement of serpin genes in plant genomes and the biological functions of plant serpins.

Results

A structurally refined amino-acid sequence alignment of the 14 full-length serpins encoded in the genome of the japonica rice Oryza sativa cv. Nipponbare (a monocot) showed a diversity of reactive-centre sequences (which largely determine inhibitory specificity) and a low degree of identity with those of serpins in Arabidopsis (a eudicot). A new convenient and functionally informative nomenclature for plant serpins in which the reactive-centre sequence is incorporated into the serpin name was developed and applied to the rice serpins. A phylogenetic analysis of the rice serpins provided evidence for two main clades and a number of relatively recent gene duplications. Transcriptional analysis showed vastly different levels of basal expression among eight selected rice serpin genes in callus tissue, during seedling development, among vegetative tissues of mature plants and throughout seed development. The gene OsSRP-LRS (Os03g41419), encoding a putative orthologue of Arabidopsis AtSerpin1 (At1g47710), was expressed ubiquitously and at high levels. The second most highly expressed serpin gene was OsSRP-PLP (Os11g11500), encoding a non-inhibitory serpin with a surprisingly well-conserved reactive-centre loop (RCL) sequence among putative orthologues in other grass species.

Conclusions

The diversity of reactive-centre sequences among the putatively inhibitory serpins of rice point to a range of target proteases with different proteolytic specificities. Large differences in basal expression levels of the eight selected rice serpin genes during development further suggest a range of functions in regulation and in plant defence for the corresponding proteins.

Keywords:
Serpin; Protease inhibitor; Rice; Oryza sativa; Arabidopsis thaliana; Expression