Abstract
P-type ATPases are transmembrane pumps of cations and phospholipids. They are energized by hydrolysis of ATP and play important roles in a wide range of fundamental cellular and physiological processes during plant growth and development. However, the P-type ATPase superfamily genes have not been characterized in soybean. Here, we performed genome-wide bioinformatic and expression analyses of the P-type ATPase superfamily genes in order to explore the potential functions of P-type ATPases in soybean. A total of 105 putative P-type ATPase genes were identified in the soybean genome. Phylogenetic relationship analysis of the P-type ATPase genes indicated that they can be divided into five subfamilies including P1B, P2A/B, P3A, P4 and P5. Proteins belonging to the same subfamily shared conserved domains. Forty-seven gene pairs were related to segmental duplication, which contributed to the expansion of the P-type ATPase genes during the evolution of soybean. Most of the P-type ATPase genes contained hormonal- and/or stress-related cis-elements in their promoter regions. Expression analysis by retrieving RNA-sequencing datasets suggested that almost all of the P-type ATPase genes could be detected in soybean tissues, and some genes showed tissue-specific expression patterns. Nearly half of the P-type ATPase genes were found to be significantly induced or repressed under stresses like salt, drought, cold, flooding, and/or phosphate starvation. Four genes were significantly affected by rhizobia inoculation in root hairs. The induction of two P2B-ATPase genes, GmACA1 and GmACA2, by phosphate starvation was confirmed by quantitative RT-PCR. This study provides information for understanding the evolution and biological functions of the P-type ATPase superfamily genes in soybean.
Highlights
The P-type ATPases are cation and lipid pumps energized by hydrolysis of ATP
To investigate the P-type ATPase gene superfamily in the soybean genome, the BLAST algorithm was used to search the soybean genome database in the SoyBase website using Arabidopsis and rice P-type ATPase protein sequences as the query
These genes can be classified into five subfamilies, e.g., P1B, P2A/B, P3A, P4, and P5, based on their homologues in Arabidopsis and rice (Figure 1 and Table S1)
Summary
The P-type ATPases are cation and lipid pumps energized by hydrolysis of ATP. They were named P-type ATPases because they form a phosphorylated ( P-type) reaction cycle intermediate during catalysis [1]. The ATP hydrolyzing machinery of P-type ATPases consists of three interconnected cytoplasmic domains: the phosphorylation (P), nucleotide binding (N), and actuator (A) domain. A conserved sequence motif, DKTGT, is contained in the P domain of P-type ATPases, where the Asp (D) residue is phosphorylated during catalysis [1]. The P-type ATPases form a large superfamily that can be divided into five distinct evolutionarily related subfamilies, P1–P5. Each of the subfamilies can be further divided into subgroups [2,3]. The major subgroups of P-type ATPases include P1A-ATPases (part of bacterial K+ transport system), P1B-ATPases (heavy metal pumps), P2A-ATPases (Ca2+ pumps), P2B-ATPases (Ca2+ pumps), P2C-ATPases (Na+ /K+ and H+ /K+ pumps of animals), P2D-ATPases (Na+ pumps of fungi), P3A-ATPases (H+ pumps), P4-ATPases (phospholipid pumps), and P5-ATPases (the substrate of P5-ATPases is still unclear) [1,4,5]
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