Identification and Expression Profiling of Protein Phosphatases (PP2C) Gene Family in Gossypium hirsutum L.

Hamna Shazadee,Zhongyi Huang,Jianguo Zeng,Xinyu Wang,Jingjing Wang,Chencan Wang,Nadeem Khan

doi:10.3390/ijms20061395

Hamna Shazadee, Zhongyi Huang + Show 5 more

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https://doi.org/10.3390/ijms20061395

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Abstract

The protein phosphatase (PP2C) gene family, known to participate in cellular processes, is one of the momentous and conserved plant-specific gene families that regulate signal transduction in eukaryotic organisms. Recently, PP2Cs were identified in Arabidopsis and various other crop species, but analysis of PP2C in cotton is yet to be reported. In the current research, we found 87 (Gossypium arboreum), 147 (Gossypium barbadense), 181 (Gossypium hirsutum), and 99 (Gossypium raimondii) PP2C-encoding genes in total from the cotton genome. Herein, we provide a comprehensive analysis of the PP2C gene family in cotton, such as gene structure organization, gene duplications, expression profiling, chromosomal mapping, protein motif organization, and phylogenetic relationships of each species. Phylogenetic analysis further categorized PP2C genes into 12 subgroups based on conserved domain composition analysis. Moreover, we observed a strong signature of purifying selection among duplicated pairs (i.e., segmental and dispersed) of Gossypium hirsutum. We also observed the tissue-specific response of GhPP2C genes in organ and fiber development by comparing the RNA-sequence (RNA-seq) data reported on different organs. The qRT-PCR validation of 30 GhPP2C genes suggested their critical role in cotton by exposure to heat, cold, drought, and salt stress treatments. Hence, our findings provide an overview of the PP2C gene family in cotton based on various bioinformatic tools that demonstrated their critical role in organ and fiber development, and abiotic stress tolerance, thereby contributing to the genetic improvement of cotton for the resistant cultivar.

Highlights

The protein kinases (PKs) and protein phosphatases (PPs) are known to regulate the protein function, and are the fundamental molecular mechanism, by reversing protein phosphorylation during cellular signaling
The Arabidopsis 94 PP2C genes were obtained from TAIR with the help of Interpro scan domain (IPR001932) and used as queries against G. arboreum, G. barbadense, G. hirsutum, and G. raimondii databases
We have studied different gene features of the PP2C genes including the chromosomal location, coding sequence length (CDS), protein length, molecular weight (MW), isoelectric point (PI), grand average of hydropathicity (GRAVY), aliphatic index, and subcellular localization (Supplementary Tables S1–S4)

Summary

Introduction

The protein kinases (PKs) and protein phosphatases (PPs) are known to regulate the protein function, and are the fundamental molecular mechanism, by reversing protein phosphorylation during cellular signaling. It is involved in many biological processes, such as signal transduction, development, and environmental stimuli [1]. The PKs phosphorylate largely serine (Ser), threonine (Thr), and tyrosine (Tyr), whereas PPs can reverse this functioning by eliminating the phosphate group [2]. The PPs are subcategorized into three major groups based on their requirement for substrate specificity, namely Ser/Thr phosphatases (STPs), protein Tyr phosphatases (PTPs), and dual-specificity phosphatases (DSPTPs) [3,4]. In the PPP family, PP2A rigorously affects root hair growth during the elongation phase by denaturing the shape of the cells [6]

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