Auxin analysis of the maize ARF gene family

Auxin
response factors (ARF) are key players in plant development. We performed a extensively bioinformatics analysis of the
maize ARF gene family including analysis of the protein-protein
interaction, conserved motifs, chromosomal locations, and phylogenetic relationships.  In this study, a set of publicly available 38
ARF maize (Zea mays) nucleotide sequences were downloaded.  The 38 
maize ARF genes were categorized into three groups (Class I, II,
and III).  ARF genes have been
studied by molecular methods in several different plant species however to
better understand the mechanisms of these genes more studies are needed. Gene
cluster analysis showed that the numbers of genes on chromosomes were
positively correlated with the number of clusters. Analysis  of the amino acid composition revealed that
Serin, Alanine and Proline were the most frequent residues present in the genes
while tryptophan had the lowest frequency. The main aims of the present study
were to obtain genomic information for the ZmARF gene family and to
study phylogenic relationships among genes.

 

 

Keywords : Zea
mays, Gene
family, Auxin, ARF, Promoter

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Introduction

Auxin has an important role in the various stages of plants growth
and development. The plant
hormone auxin regulates  a variety of physiological processes including lateral root
initiation and shoot elongation (De
Smet and Ju¨rgens 2007).  During recent  decades, many studies  have been conducted on rapid effects of auxin
on gene expression and regulation.  Auxin
is involved in regulation of  a large
number of genes  having roles in growth
and developmental processes in Arabidopsis and other plant species (Di etal.,2015; Guilfoyle, 2015).

 According to many reports, these processes are controlled by genes
responsive to auxin at the molecular level. 
Auxin activates early responsive genes such as Aux / IAA, GH3, and the
smallest auxin uptake (SAUR) gene family, activating or inhibiting these genes
by binding ARF to auxin-responsive elements (AuxRs).  AuxRs elements may include the following   sequences 
of TGTCTC, (, TGTCAC elements or 
TGTCCC in their promoter region (Hagen and Guilfoyle, 2002).  Auxin
transcription factors are important gene family in response to auxin. ARFs are
important  gene families in the
auxin-related response involved in the specific binding to the auxin-responsive
elements (AuxREs) (Wang and Estelle, 2014). The first step in identifying and
studying the function of different genes is the use of data from databases
using bioinformatic tools. 
Bioinformatics is the science of categorizing, organizing, analyzing,
interpreting molecular information and biological sequences. The main aim of
bioinformatics is to increase the understanding of biological processes
(Hogeweg, 2011).

ARFs
are important in diverse biological and physiological processes and are
essential for their potential applications for the development of improved
stress-tolerant transgenic crop plants. 
Recently, this gene family has extensively been investigated using
molecular and bioinformatic analysis (Di et al., 2015).   Bioinformatics and molecular analyses of
several crops such as citrus, Medicago truncatula and Gossypium raimondii
have been performed (Li et al., 2015; Shen et al., 2015; Sun et al., 2015).

Most
ARF proteins consist of an amino-terminal DNA-binding domain (DBD), a middle
region that functions as an activation domain (AD) or repression domain (RD),
and a carboxy-terminal dimerization domain(CTD) which are involved in protein–
protein interactions by dimerizing with auxin/indole-3-acetic acid(Aux/IAA)
gene family (Kim et al., 1997; Piya et al., 2014).  In some studies it has been  indicated that glutamine (Q)-rich middle
regions function as activation regions but that serine (S)-rich, serine and
proline (SP)-rich, and serine and glycine (SG)-rich middle regions function as
repression regions in ARFs from A. thaliana (Tiwari et al., 2003; Ulmasov et
al., 1999).

 In this study, insilico analysis revealed at least 38 putative members of maize ARF
genes (ZmARFs). We investigated the maize ARF gene number, chromosomal
map, and promoter analysis.  The
phylogenetic analysis of ARF genes would be useful for studying and
understanding of their roles in plants. The study of this gene family would be
helpful in order to adopt strategies for increasing tolerance of crop plants
against stresses.