Genome-wide identification, evolution and expression analysis of the aspartic protease gene family during rapid growth of moso bamboo (Phyllostachys edulis) shoots

Xiaqin Wang,Lianfeng Gu,Shubin Li,Shuangquan Zou,Jin Zhang,Xinyang Yan,Bobin Liu,Yun Jing

doi:10.1186/s12864-020-07290-7

Xiaqin Wang, Lianfeng Gu + Show 6 more

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https://doi.org/10.1186/s12864-020-07290-7

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Abstract

BackgroundAspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. However, there are few reports about APs in fast-growing moso bamboo.ResultIn this study, we identified a total of 129 AP proteins (PhAPs) encoded by the moso bamboo genome. Phylogenetic and gene structure analyses showed that these 129 PhAPs could be divided into three categories (categories A, B and C). The PhAP gene family in moso bamboo may have undergone gene expansion, especially the members of categories A and B, although homologs of some members in category C have been lost. The chromosomal location of PhAPs suggested that segmental and tandem duplication events were critical for PhAP gene expansion. Promoter analysis revealed that PhAPs in moso bamboo may be involved in plant development and responses to environmental stress. Furthermore, PhAPs showed tissue-specific expression patterns and may play important roles in rapid growth, including programmed cell death, cell division and elongation, by integrating environmental signals such as light and gibberellin signals.ConclusionComprehensive analysis of the AP gene family in moso bamboo suggests that PhAPs have experienced gene expansion that is distinct from that in rice and may play an important role in moso bamboo organ development and rapid growth. Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth.

Highlights

Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms
Our results provide a direction and lay a foundation for further analysis of plant AP genes to clarify their function during rapid growth
Plant APs are considered to be responsible for protein processing and degradation, such as plant senescence, programmed cell death (PCD), reproduction, and stress responses [2, 15,16,17,18,19,20], which are critical for plant development

Summary

Introduction

Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant development and environmental adaptation. Aspartic proteinases (APs; Enzyme Commission 3.4.23) are proteolytic enzymes and play important roles in protein maturation and degradation [1, 2]. Most plant APs are grouped into the A1 family and exhibit the two basic features of A1 family members: one features is that they are active under acidic conditions, and the other is that their catalytic activity can be inhibited by pepstatin A [1, 9]. Typical APs contain a plant-specific insert (PSI) similar to that of saposin-like proteins, but it is removed during protein maturation [1, 2]. Pepstatin A activity has been detected in immature, mature, and germinated seeds in wheat, and the expression pattern showed a role of APs in regulating protein degradation [13, 14]. With the development of DNA sequencing technology, members of plant AP gene families have been identified in Arabidopsis [9], rice [12], grape [21], and poplar [22], revealing gene expansion and functional diversity [12, 22]

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