Combined Transcriptome and Proteome Analysis of Maize (Zea mays L.) Reveals A Complementary Profile in Response to Phosphate Deficiency.

Zhi Nie,Xuan He,Bowen Luo,Jialei Guo,Duojiang Gao,Xiao Zhang,Shibin Gao,Dan Liu,Ling Wu,Shiqiang Gao

doi:10.3390/cimb43020081

Abstract

A deficiency in the macronutrient phosphate (Pi) brings about various changes in plants at the morphological, physiological and molecular levels. However, the molecular mechanism for regulating Pi homeostasis in response to low-Pi remains poorly understood, particularly in maize (Zea mays L.), which is a staple crop and requires massive amounts of Pi. Therefore, in this study, we performed expression profiling of the shoots and roots of maize seedlings with Pi-tolerant genotype at both the transcriptomic and proteomic levels using RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ). We identified 1944 differentially expressed transcripts and 340 differentially expressed proteins under low-Pi conditions. Most of the differentially expressed genes were clustered as regulators, such as transcription factors involved in the Pi signaling pathway at the transcript level. However, the more functional and metabolism-related genes showed expression changes at the protein level. Moreover, under low-Pi conditions, Pi transporters and phosphatases were specifically induced in the roots at both the transcript and protein levels, and increased amounts of mRNA and protein of two purple acid phosphatases (PAPs) and one UDP-sulfoquinovose synthase (SQD) were specifically detected in the roots. The new insights provided by this study will help to improve the P-utilization efficiency of maize.

Highlights

Phosphate (Pi) is a basic component of biomacromolecules, such as nucleic acids, proteins and phospholipids [1], is involved in cellular metabolism, signal transduction and photosynthesis [2], and plays a critical role in plant development, making it an essential macronutrient for plants
To recognize the Pi-starvation-responsive genes in maize, seedlings of inbred line 178, which has a high tolerance for Pi deficiency, were exposed to two Pi concentrations: control (CK, 1 mmol/L KH2PO4) and low-Pi treatment (T, 1 μmol/L KH2PO4) (Figure 1A)
The key goal was to identify the candidate genes involved in the Pi deficiency responding mechanism in maize

Summary

Introduction

Phosphate (Pi) is a basic component of biomacromolecules, such as nucleic acids, proteins and phospholipids [1], is involved in cellular metabolism, signal transduction and photosynthesis [2], and plays a critical role in plant development, making it an essential macronutrient for plants. Plants have evolved complex regulatory signaling to cope with Pi limitation, an understanding of which will help us to address a Pi deficiency in agriculture. Under Pideprived conditions, Pi acquisition is enhanced through the joint action of Pi transporters, the secretion of organic acids and phosphatases, and a change in root system architecture (RSA) [3]. Modification of the RSA is a critical trait in agriculture, with variation in the primary and lateral roots depending on the plant species [3]. During Pi homeostasis, a central regulator, PHR1, controls a large subset of Pi-responsive genes [13] and the PHR1–miR399–PHO2 signaling pathway plays a key role in the homeostasis process [14]. Much progress has been made in understanding Pi-responsive signaling in Arabidopsis and rice, we still have a poor understanding of this mechanism in maize (Zea mays L.), despite the economic importance of this crop

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