Genome-Wide Identification of Wheat ZIP Gene Family and Functional Characterization of the TaZIP13-B in Plants

Abstract

The ZIP (Zn-regulated, iron-regulated transporter-like protein) transporter plays an important role in regulating the uptake, transport, and accumulation of microelements in plants. Although some studies have identified ZIP genes in wheat, the significance of this family is not well understood, particularly its involvement under Fe and Zn stresses. In this study, we comprehensively characterized the wheat ZIP family at the genomic level and performed functional verification of three TaZIP genes by yeast complementary analysis and of TaZIP13-B by transgenic Arabidopsis. Totally, 58 TaZIP genes were identified based on the genome-wide search against the latest wheat reference (IWGSC_V1.1). They were then classified into three groups, based on phylogenetic analysis, and the members within the same group shared the similar exon-intron structures and conserved motif compositions. Expression pattern analysis revealed that the most of TaZIP genes were highly expressed in the roots, and nine TaZIP genes displayed high expression at grain filling stage. When exposed to ZnSO4 and FeCl3 solutions, the TaZIP genes showed differential expression patterns. Additionally, six ZIP genes responded to zinc-iron deficiency. A total of 57 miRNA-TaZIP interactions were constructed based on the target relationship, and three miRNAs were downregulated when exposed to the ZnSO4 and FeCl3 stresses. Yeast complementation analysis proved that TaZIP14-B, TaZIP13-B, and TaIRT2-A could transport Zn and Fe. Finally, overexpression of TaZIP13-B in Arabidopsis showed that the transgenic plants displayed better tolerance to Fe/Zn stresses and could enrich more metallic elements in their seeds than wild-type Arabidopsis. This study systematically analyzed the genomic organization, gene structure, expression profiles, regulatory network, and the biological function of the ZIP family in wheat, providing better understanding of the regulatory roles of TaZIPs and contributing to improve nutrient quality in wheat crops.

Genome-Wide Identification of OsZIPs in Rice and Gene Expression Analysis under Manganese and Selenium Stress

“…With advancements in bioinformatics, an increasing number of ZIP members have gradually been discovered in various plant species, including Arabidopsis thaliana [17], cowpea (Vigna sinensis) [18], wheat (Triticum aestivum) [19], and potato (Solanum tuberosum) [20]. ZIP transporters are located primarily in the plasma membrane and on the membranes of various intracellular organelles [58].…”

“…With advancements in whole-genome sequencing and bioinformatics, diverse types of ZIP proteins have been discovered in different plant species. In all, 16 ZIP genes have been authenticated in A. thaliana [17], 14 ZIP genes in Vigna unguiculata [18], and 58 ZIP genes in wheat (Triticum aestivum), 44 of which are homologous to rice ZIP proteins [19]. In potato (Solanum tuberosum), 29 ZIP genes have been identified [20] Selenium (Se) is a nonmetallic element classified in Group 16 of the periodic table along with sulfur (S), due to its similar chemical properties [21].…”

Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat (Triticum asetivum)

“…Genome-wide analysis of a gene family is a way of rapidly and efficiently analyzing pathways to characterize gene functions and evolution [ 36 , 37 , 38 , 39 ]. In wheat, various genes are involved in drought, salt and metal stress responses by characterizing genes families [ 40 , 41 , 42 ]. In this study, 64 FKBPs were identified in the wheat genome by systematic in silico analysis ( Table 1 ).…”

Genome-wide identification of the ZIP gene family in lettuce (Lactuca sativa L.) and expression analysis under different element stress

“…We downloaded the complete genome sequence databases of lettuce from the NCBI database (Genome v7: ID:6720851) and downloaded the hidden Markov model (HMM) file of the ZIP domain (PF02535) from the Pfam protein family database (http://pfam.xfam.org/). The ZIP protein search was performed using the standard HMMER 3.0 software parameters from the Salad Gene database [30][31][32][33]. For the candidate genes obtained from the search, we used the SMART and PFAM programs to confirm that they contained specific domains, and manually removed ZIP genes that did not contain domains and duplicates [34,35].…”