Genome-Wide Identification and Analysis of Apple NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER Family (NPF) Genes Reveals MdNPF6.5 Confers High Capacity for Nitrogen Uptake under Low-Nitrogen Conditions

Abstract

The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) proteins play important roles in moving substrates such as nitrate, peptides, amino acids, dicarboxylates, malate, glucosinolates, indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid. Although a unified nomenclature of NPF members in plants has been reported, this gene family has not been studied as thoroughly in apple (Malus × domestica Borkh.) as it has in other species. Our objective was to provide general information about apple MdNPFs and analyze the transcriptional responses of some members to different levels of nitrate supplies. We identified 73 of these genes from the apple genome and used phylogenetic analysis to organize them into eight major groups. These apple NPFs are structurally conserved, based on alignment of amino acid sequences and analyses of phylogenetics and conserved domains. Examination of their genomic structures indicated that these genes are highly conserved among other species. We monitored 14 cloned MdNPFs that showed varied expression patterns under different nitrate concentrations and in different tissues. Among them, NPF6.5 was significantly induced by both low and high levels of nitrate. When compared with the wild type, 35S:MdNPF6.5 transgenic apple calli were more tolerant to low-N stress, which demonstrated that this gene confers greater capacity for nitrogen uptake under those conditions. We also analyzed the expression patterns of those 73 genes in various tissues. Our findings benefit future research on this family of genes.

Genome-Wide Systematic Characterization of the NPF Family Genes and Their Transcriptional Responses to Multiple Nutrient Stresses in Allotetraploid Rapeseed

“…The NPF genes encode numerous proteins that comprise a large family of members broadly distributed in eukaryotes [ 32 , 35 , 43 ]. They facilitate transport of a wide variety of nitrogenous compounds [ 11 , 44 ].…”

“…They facilitate transport of a wide variety of nitrogenous compounds [ 11 , 44 ]. NPF genes have been identified within many species over the last decades, such as Arabidopsis [ 8 ], poplar [ 32 ], Medicago truncatula [ 34 ], rice [ 5 , 43 ], apple [ 35 ] and sugarcane [ 36 ]. However, the number of NPF family members varies largely among species.…”

“…However, the gene structure differed in different subfamilies ( Figures S1 and S2 , Table S2 ). In terms of protein motif, most of the BnaNPF genes possess six conserved motifs ( Figure S2 ), while NPF genes from rice and apple contain three conserved motifs [ 5 , 35 ]. This might suggest the functional diversity of BnaNPF members due to the variation in aa residues except the conserved domain.…”

“…N shortage in the soil may inhibit the growth of B. napus , and its yield production and quality [ 30 , 31 ]. NPF families have been identified in various plant species, such as poplar [ 32 ], wheat [ 33 ], legumes [ 34 ], apple [ 35 ] and sugarcane [ 36 ]. However, little is known about the NPF family genes in oil crops such as B. napus .…”

Identification of Phytochrome-Interacting Factor Family Members and Functional Analysis of MdPIF4 in Malus domestica

“…AtPIF protein sequences were obtained from the Arabidopsis database [ 71 , 77 ]. The PIF protein sequences of rice were obtained from the rice annotation project [ 78 ].…”