Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley.

Shazia Rehman,Søren K Rasmussen,Samar Naseer,Bodil Jørgensen,Ejaz Aziz,Riffat Batool

doi:10.3390/plants9111439

Abstract

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

Highlights

The serpin superfamily is a member of the most ubiquitous and successful class of inhibitors and is found in all organisms, including animals, plants, bacteria, viruses and Archaea [1,2,3]
Plant serpins were named by using a five-letter abbreviation for species name (Brmdi for Brachypodium distachyon; Horvu for Hordeum vulgare) followed by the Z-numbering system ([1]; Table S2)
Brachypodium and barley are unusual in that they have twice the number of serpin genes compared to other species; i.e., 27 and 25 serpin encoding genes were identified in Brachypodium and barley, respectively

Summary

Introduction

The serpin superfamily is a member of the most ubiquitous and successful class of inhibitors and is found in all organisms, including animals, plants, bacteria, viruses and Archaea [1,2,3]. Some other serpins have bifunctional activity or no inhibitory activity [7]. Serpins are large proteins (340–440 aa) with a molecular weight of 40–45 KDa, and they contain a flexible bait loop that can form covalent and irreversible complexes with proteases [1]. A typical inhibitory serpin consists of several α-helices and β-strands, together with an external reactive center loop (RCL). The RCL region is usually composed of 20–24 amino acid residues and is of critical importance in determining the inhibitory capacity of serpins [8]. Structural studies revealed that the P1–P10 sessile bond in the RCL acts as bait for attacking proteases and the inhibitory specificity of serpins is mainly dependent on the identity of the active site residues (P4–P40 ), in

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Conclusion