Papain-like and legumain-like proteases in rice: genome-wide identification, comprehensive gene feature characterization and expression analysis

Abstract

BackgroundPapain-like and legumain-like proteases are proteolytic enzymes which play key roles in plant development, senescence and defense. The activities of proteases in both families could be inhibited by a group of small proteins called cystatin. Cystatin family genes have been well characterized both in tobacco and rice, suggesting their potential roles in seed development. However, their potential targets, papain-like and legumain-like proteases, have not been well characterized in plants, especially in rice, a model plant for cereal biology.ResultsHere, 33 papain-like and 5 legumain-like proteases have been identified in rice genome, respectively. Gene structure, distribution in rice chromosome, and evolutionary relationship to their counterparts in other plants have been well characterized. Comprehensive expression profile analysis revealed that two family genes display divergent expression pattern, which are regulated temporally and spatially during the process of seed development and germination. Our experiments also revealed that the expression of most genes in these two families is sensitively responsive to plant hormones and different abiotic stresses.ConclusionsGenome-wide identification and comprehensive gene expression pattern analysis of papain-like and legumain-like proteases in rice suggests their multiple and cooperative roles in seed development and response to environmental variations, which provides several useful cues for further in-depth study.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1298-1) contains supplementary material, which is available to authorized users.

A VPE‐like protease NtTPE8 exclusively expresses in the integumentary tapetum and is involved in seed development

“…LLCPs, located in the peptidase C13 family, are a group of Asn‐specific proteinases, and have conserved enzymatic activities and catalytic residues (cysteine and histidine) (Hiraiwa et al ; Wang et al ). NtTPE8, one of seven legumains in tobacco, contains the conserved amino acid residues for asparaginyl endopeptidase, possesses AANase activity and also cleaves the VPE substrate.…”

Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L.

“…With A. thaliana , 31 proteases were reported [52], 33 in rice [17], 43 in rubber [53] and 33 in papaya [43]. Subfamilies of PLCPs (already described for A. thaliana [52] and rice [17]) were also identified. Moreover, given that no known homologs from other organisms were found, eight groups of PLCPs were defined as being unique to the species subfamilies (Figure 3, in red).…”

“…It is known that the human genome contains 588 genes for proteases, including about 150 proteases that are transcriptionally active, depending on the type of tissue [15]. The number of encoded proteases amounts to 723 in Arabidopsis thaliana L. [16], 997 for rice [17,18,19] and 901 for tomatoes [20].…”

Programmed Cell Death in the Developing Brachypodium distachyon Grain

“…The same approach was used to obtain A1 and C1 protein sequences of Arabidopsis , barley, rice and wheat. Protein sequences of C13 and C14 of Arabidopsis , barley and rice were gathered from published reports on these proteins for each species (Bostancioglu et al ., 2018; Julián et al ., 2013; Rocha et al ., 2013; Vercammen et al ., 2004; Wang et al ., 2018). Further information on sequences used in phylogenetic analysis is provided in the Table S2.…”