Genome-Wide Identification, Cloning and Functional Analysis of the Zinc/Iron-Regulated Transporter-Like Protein (ZIP) Gene Family in Trifoliate Orange (Poncirus trifoliata L. Raf.)

Abstract

Zinc (Zn) and iron (Fe) deficiency are widespread among citrus plants, but the molecular mechanisms regarding uptake and transport of these two essential metal ions in citrus are still unclear. In the present study, 12 members of the Zn/Fe-regulated transporter (ZRT/IRT)-related protein (ZIP) gene family were identified and isolated from a widely used citrus rootstock, trifoliate orange (Poncirus trifoliata L. Raf.), and the genes were correspondingly named as PtZIPs according to the sequence and functional similarity to Arabidopsis thaliana ZIPs. The 12 PtZIP genes were predicted to encode proteins of 334–419 amino acids, harboring 6–9 putative transmembrane (TM) domains. All of the PtZIP proteins contained the highly conserved ZIP signature sequences in TM-IV, and nine of them showed a variable region rich in histidine residues between TM-III and TM-IV. Phylogenetic analysis subdivided the PtZIPs into four groups, similar as found for the ZIP family of A. thaliana, with clustered PtZIPs sharing a similar gene structure. Expression analysis showed that the PtZIP genes were very differently induced in roots and leaves under conditions of Zn, Fe and Mn deficiency. Yeast complementation tests indicated that PtIRT1, PtZIP1, PtZIP2, PtZIP3, and PtZIP12 were able to complement the zrt1zrt2 mutant, which was deficient in Zn uptake; PtIRT1 and PtZIP7 were able to complement the fet3fet4 mutant, which was deficient in Fe uptake, and PtIRT1 was able to complement the smf1 mutant, which was deficient in Mn uptake, suggesting their respective functions in Zn, Fe, and Mn transport. The present study broadens our understanding of metal ion uptake and transport and functional divergence of the various PtZIP genes in citrus plants.

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

“…The genomes of several citrus varieties have been released, including the sweet orange (Citrus sinensis) genome published by Xu et al (2011) [40], the clementine mandarin genome published by Wu et al (2014) [41], and the pummelo, papeda (Citrus ichangensis) and citron (Citrus medica) genomes published by [38]. After the completion of these genomes, systematic identification and analysis of important gene families have been widely reported for citrus [1,[42][43][44]. These studies have provided us a comprehensive understanding of potential gene functions and have promoted related research progress.…”

“…fao.org/default.aspx). However, citrus production is also continuously influenced by many environmental factors, such as diseases, cold, drought, heat, and nutrient disorders, among which iron (Fe) deficiency is a common problem that can cause severe chlorosis of leaves, impaired tree vigor, and reduction of fruit yield and quality in citrus production [1]. In particular, in calcareous soils, citrus plants are highly sensitive to low Fe availability because bioavailable forms of ferrous Fe (II) are oxidized into insoluble ferric Fe (III) in a high-pH and oxygen-rich environment [2,3].…”

Zn/Cd status-dependent accumulation of Zn and Cd in root parts in tobacco is accompanied by specific expression of ZIP genes

“…Bioinformatics analysis to determine the subcellular localization of NtZIP5B was performed with the use of the ProtComp programme [38,39]. As shown in Additional file 5, the NtZIP5B protein was predicted to be localized at the plasma membrane.…”

Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

“…CgbHLH16, CgbHLH29.4, CgbHLH30, CgbHLH39, CgbHLH48, CgbHLH63, CgbHLH68, CgbHLH73.1, CgbHLH79, CgbHLH80, CgbHLH102.1, CgbHLH104, CgbHLH105.1, CgbHLH107.2, CgbHLH122, CgbHLH123 and CgbHLH128, was up-regulated from an early period (0.5 d), which indicated an early response of these genes to Fe deficiency. The second type, such as CgbHLH14 1,. CgbHLH33.1, CgbHLH49, CgbHLH69.1, CgbHLH91, CgbHLH93.1, CgbHLH96.1, CgbHLH105.2 and CgbHLH153, was up-regulated at medium periods but was down-regulated during early and late periods.…”

“…Discussion The genomes of several citrus varieties have been released, including the sweet orange (Citrus sinensis) genome published by Xu et al (2011) [39], the clementine mandarin genome published by Wu et al (2014) [40], and the pummelo, papeda (Citrus ichangensis) and citron (Citrus medica) genomes published by Wang et al (2017)[37]. After the completion of these genomes, systematic identification and analysis of important gene families have been widely reported for citrus[1,[41][42][43].…”