Genome-wide analysis of haloacid dehalogenase genes reveals their function in phosphate starvation responses in rice.

Zezhen Du,Suren Deng,Chuang Wang,Zixuan Wu,Israel Silman

doi:10.1371/journal.pone.0245600

Abstract

The HAD superfamily is named after the halogenated acid dehalogenase found in bacteria, which hydrolyses a diverse range of organic phosphate substrates. Although certain studies have shown the involvement of HAD genes in Pi starvation responses, systematic classification and bioinformatics analysis of the HAD superfamily in plants is lacking. In this study, 41 and 40 HAD genes were identified by genomic searching in rice and Arabidopsis, respectively. According to sequence similarity, these proteins are divided into three major groups and seven subgroups. Conserved motif analysis indicates that the majority of the identified HAD proteins contain phosphatase domains. A further structural analysis showed that HAD proteins have four conserved motifs and specified cap domains. Fewer HAD genes show collinearity relationships in both rice and Arabidopsis, which is consistent with the large variations in the HAD genes. Among the 41 HAD genes of rice, the promoters of 28 genes contain Pi-responsive cis-elements. Mining of transcriptome data and qRT-PCR results showed that at least the expression of 17 HAD genes was induced by Pi starvation in shoots or roots. These HAD proteins are predicted to be involved in intracellular or extracellular Po recycling under Pi stress conditions in plants.

Highlights

Phosphorus (P) is one of the essential macronutrients for plant growth and development
Hidden Markov models (HMMs) of the HAD family were obtained from the Pfam protein database and constructed from reported plant HAD proteins [31]
Genome-wide analysis of haloacid dehalogenase genes in plant were used to search against the Arabidopsis and rice protein sequence data by HMMER software using default parameters (E-value = 0.5) [32]

Summary

Introduction

Phosphorus (P) is one of the essential macronutrients for plant growth and development. There are two different forms of P in soil: inorganic P (Pi) and organic P (Po), of which plants can only absorb and utilize water-soluble Pi. P is abundant in the Earth’s crust, it is usually present in soil in the form of Po or fixed with other metals, making it unavailable to plants and insufficient to support the optimal growth of plants [1, 2]. To cope with Pi deficiency stress, plants have evolved a series of physiological and biochemical strategies to enhance the uptake and utilization of P [3]. Inducing the expression and synthesis of phosphatases is one of the important responses to Pi stress in plants [4]. It was reported that Pi starvation induced the synthesis of both

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Conclusion