Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.).

Lu Lu,Quancan Hou,Jinping Li,Lina Zhao,Tianye Zhang,Xiangyuan Wan,Tingwei Yan,Wei Zhao,Linlin Wang

doi:10.3390/ijms221910722

Lu Lu, Quancan Hou + Show 7 more

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https://doi.org/10.3390/ijms221910722

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Abstract

Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.

Highlights

Introduction published maps and institutional affilPolygalacturonases (PGs, EC 3.2.1.15) belong to one of the largest hydrolase families, which are polysaccharide lyases, and catalyze α-1,4 linkages among D-galacturonic acid residues in homogalacturonan [1,2]
We identified 55 ZmPGs from the maize genome and performed comprehensive phylogenetic, gene structure, conserved motif and gene expression analysis
The 55 ZmPG genes are randomly distributed across 10 chromosomes, while only one gene is scattered on a constitutive chromosome (Table 1)

Summary

Introduction

Introduction published maps and institutional affilPolygalacturonases (PGs, EC 3.2.1.15) belong to one of the largest hydrolase families, which are polysaccharide lyases, and catalyze α-1,4 linkages among D-galacturonic acid residues in homogalacturonan [1,2]. There are four conserved domains in plant PG proteins, and the core amino acid sequences of domains I and II are SPNTDG and GDDC, respectively. The three aspartic acids (D) in domain I and domain II may be the components of the catalytic sites [4]. Domain III is composed of CGPGHG, of which the histidine residue (H) is supposed to be involved in catalytic reaction [5]. The amino acid sequence of domain IV is RIK, which may be related to ion interaction at the carboxyl end of substrates [5]. Proteins that have the above four conserved domains are identified as PGs, but domain III is relatively less iations

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