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bioRxiv · 10.1101/2020.10.03.324913

In silico characterization and expression profiles of zinc transporter-like (LOC100037509) gene of tomato

Kabir, A. H.
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Abstract

Zinc (Zn) is an essential microelement for plants. ZIP transporters play a critical role in Zn homeostasis in plants. This in silico study characterizes different characteristics of putative Zn transporter of tomato (Solyc07g065380) and its homologs. A total of 10 ZIP protein homologs were identified across nine plant species by protein BLAST. All these ZIP protein homologs located at chromosome 7 showed 305-350 amino acid residues, 7-8 transmembrane helices, and stable instability index. Further, these ZIP protein homologs are localized in the plasma membrane at the subcellular level corresponding to the ZIP zinc transporter (PF02535) domain. Gene organization analysis reveals the presence of 3 exon along with the position of the promoter, TATA-box, transcriptional start site, and splice sites in these ZIP transporter homologs, in which tomato ZIP transporter (NM_001247420.1) contains a promoter, TATA-box, transcriptional start site at 500, 911 and 946 bp, respectively along with several splice sites, which may be useful for targeting binding sites and transcription factor analysis. Further, the cutting sites and restriction enzymes of each ZIP gene homologs might be helpful for future transgenic studies underlying Zn homeostasis. MEMO displayed five conserved motifs associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site. Phylogenetic studies reveal a closet relationship of Solyc07g065380 with Solanum pennellii homolog, while ZIP transporter of Nicotiana sylvestris and Nicotiana tabacum predicted to be in close connection. The Solyc07g065380 transporter is predominantly linked to several uncharacterized zinc metal ion transporters and expressed in diverse anatomical part, developmental stage, and subjected to pathogen and heat stress. The secondary structural prediction reveals unique signal peptide in the ZIP protein homologs of S. lycopersicum and S. pennellii along with extended alpha-helix. These bioinformatics analyses might provide essential background to perform wet-lab experiments and to understand Zn homeostasis for the development of Zn-biofortified crops. Key message{diamondsuit} ZIP protein homologs are localized in the plasma membrane and are linked to ZIP zinc transporter (PF02535) domain at chromosome 7. {diamondsuit}ZIP protein motifs are associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site. {diamondsuit}Phylogenetic studies reveal a closet relationship of Solyc07g065380 with Solanum pennellii homolog. {diamondsuit}ZIP protein homologs of S. lycopersicum and S. pennellii show unique signal peptide along with extended alpha-helix.

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Kabir, A. H.. 2020-10-04. In silico characterization and expression profiles of zinc transporter-like (LOC100037509) gene of tomato. https://doi.org/10.1101/2020.10.03.324913

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