Identification and characterization of important mineral transporters in rice (Oryza spp.)
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Date
2020
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DRPCAU, Pusa
Abstract
A study involving genome wide analysis of genomic and peptide sequences of eleven species and sub-species of rice (Oryza spp.) was undertaken for identification and characterization of Calcium and Cadmium mineral transporters. Retrieval and analysis of genomic and peptide sequences was carried out with the help of different methodologies and tools including SMART, MeV, FASTA, Clustal, Ortho-Venn, MEME suite, HAMMER and Cygwin64. Only 577 genes were identified as true transporters through annotation program among 797 calcium transporter gene sequences isolated from the database. Among these transporter genes, 452 proteins were orthologues, whereas, 25 genes were species specific. The maximum (63) and minimum (44) number of calcium transporters were identified in Oryza sativa indica and Oryza sativa japonica, respectively. Computational analysis of cadmium transporters revealed 885 genes for true transporters among 893 gene ids. Across all the species and sub-species, 585 proteins were orthologues, whereas 32 genes were species specific. The maximum (95) and minimum (67) number of cadmium transporters were identified in Oryza sativa indica and Oryza longistaminata, respectively.
Phylogenetic analysis grouped the identified 452 calcium transporters in to five major super families, namely, PM_ATPase, CT_ATPase, CZT/CuT, PLT_ATPase, CACC/CPCC with majority of the mineral transporters belonging CT_ATPase family and a smaller number of transporters belonged to CZT/CuT_HMA family. Similarly, cadmium transporters were grouped into six major super families, namely, ABC type transporter; ATPase_type transporter; Sulphate transporter; Protein NRT1/ PTR family; Metal
transporter NRAMP5 and MACPF domain-containing protein CAD1. Most of these mineral transporters belonged to ATPase_Type family and lowest number was found in NRAMP5 and CAD1 family. For calcium transporters, orthologous determination study revealed the maximum number of orthologous protein count in Oryza sativa indica (45), while its minimum number in Oryza sativa japonica (35) for calcium transporters. Similarly, for cadmium transporters, maximum number of orthologous protein count was found in three species (58), namely, Oryza barthii, Oryza sativa indica and Oryza punctata, whereas its minimum was recorded in Oryza sativa japonica (44).
Motif analysis revealed the presence of some conserved domain ids in all the species and sub-species of rice under investigation in this study. Family distribution pattern of highest clustered protein indicated highest predominance of CT-ATPase (Calcium Transporter ATPase Transporter) sub-family of transporter proteins in the case of calcium. Similarly, ATPase-type transporter (ATPase dependent Transporter) sub-family was abundant with highest number of transporter sequences in the case of cadmium.
Computational results provided the basis to infer gene expression in shoot tissues in the case of calcium, while gene expression seemed to occur only in seed without any expression in shoot/root/leaves in the case of cadmium. Furthermore, high level of expression of predicted calcium transporter genes into seeds and its parts rather than the shoot portion suggested that these proteins might be involved in calcium accumulation in seeds, embryo and endosperm parts. Nine gene ids (Os02t0176700-00, Os02t0196600-01, Os03t0203700-01, Os03t0281600-01, Os03t0689300-01, Os04t0605500-01, Os04t0656100-01, Os07t0191200-01, Os12t0638700-01) had sequence similarity in the case of both the minerals, reflecting that these genes are responsible for the transportation of both calcium and cadmium in Oryza sativa japonica. So, these may be considered as calcium-cadmium co-transporters.
Experimental results showed that many of the sequences are distributed in the genome of different species and sub-species of rice. Significant evidences were generated for exploring the expression and function of these calcium and cadmium transporters under different environmental conditions at different tissues in plant to understand the molecular basis of mineral accumulation in developing grains.