Dichotomy in the NRT Gene Families of Dicots and Grass Species

Abstract

A large proportion of the nitrate (NO3 −) acquired by plants from soil is actively transported via members of the NRT families of NO3 − transporters. In Arabidopsis, the NRT1 family has eight functionally characterised members and predominantly comprises low-affinity transporters; the NRT2 family contains seven members which appear to be high-affinity transporters; and there are two NRT3 (NAR2) family members which are known to participate in high-affinity transport. A modified reciprocal best hit (RBH) approach was used to identify putative orthologues of the Arabidopsis NRT genes in the four fully sequenced grass genomes (maize, rice, sorghum, Brachypodium). We also included the poplar genome in our analysis to establish whether differences between Arabidopsis and the grasses may be generally applicable to monocots and dicots. Our analysis reveals fundamental differences between Arabidopsis and the grass species in the gene number and family structure of all three families of NRT transporters. All grass species possessed additional NRT1.1 orthologues and appear to lack NRT1.6/NRT1.7 orthologues. There is significant separation in the NRT2 phylogenetic tree between NRT2 genes from dicots and grass species. This indicates that determination of function of NRT2 genes in grass species will not be possible in cereals based simply on sequence homology to functionally characterised Arabidopsis NRT2 genes and that proper functional analysis will be required. Arabidopsis has a unique NRT3.2 gene which may be a fusion of the NRT3.1 and NRT3.2 genes present in all other species examined here. This work provides a framework for future analysis of NO3 − transporters and NO3 − transport in grass crop species.

Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice

“…Given the central role of AtNRT1.1 in nitrate utilization, it was very attractive to further explore the function and application of the NRT1.1 homologs in NUE improvement, especially in crops. However, the function of NRT1.1s is still largely unknown in crops, even though it has been noted that the major grain crops like rice, wheat (Triticum aestivum), and maize possess additional members of the NRT1.1 family (Plett et al, 2010). Our previous work demonstrated that OsNRT1.1B is the functional homolog of AtNRT1.1 in rice (Hu et al, 2015).…”

“….1A Displays Ammonium-Inducible Expression and OsNRT1.1A Predominantly Localizes to the Tonoplast Rice has three putative homologs of AtNRT1.1: OsNRT1.1A, OsNRT1.1B, and OsNRT1.1C (OsNPF6.4) (Plett et al, 2010). Among these, OsNRT1.1A clusters closest to and shares the highest protein sequence identity with AtNRT1.1 ( Figure 1A; Supplemental Figure 1 and Supplemental File 1).…”

“…Monocots and eudicots differ in the number of their NRT1.1 genes, with grass species typically having three to four NRT1.1 members and most eudicot species having only one NRT1.1 gene (Plett et al, 2010). Recently, Wen et al (2017) reported that two putative homologs of AtNRT1.1 (AtNPF6.3) in maize (Zea mays ssp mays), ZmNPF6.4 and ZmNPF6.6, display distinct substrates affinity for nitrate and chloride, indicating a possible functional divergence among different members of the NRT1.1 family in grasses.…”

The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber

“…Multiplication among NRT1s has already been reported. For AtNRT1.1, there is one homolog in cucumber and poplar, whereas in the grasses, multiplied closely related NRT1.1-like genes have been identified: three in rice (OsNRT1.1A/B/C) and sorghum (SbNRT1.1A/B/ C) and four in maize (ZmNRT1.1A/B/C/D) and Brachypodium (BdNRT1.1A/B/C/D) (Plett et al 2010) (Fig. 1).…”

“…1). For AtNRT1.3 and AtNRT1.4, there is at least one member from grass species with an extra representatives for NRT1.3 and NRT1.4 in rice, maize (Plett et al 2010) and V. vinifera (GenBank) (Fig. 1).…”