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Expression of ZAT12 transcripts in transgenic tomato under various abiotic stresses and modeling of ZAT12 protein in silico

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Abstract

ZAT12 a C2H2-zinc-finger protein is an abiotic stress-responsive transcription factor in plants having less information about their structure. Transcription analysis proved that ZAT12 transcripts over-expressed during drought, heat and salt stress conditions which led to an interest in 3-D structural studies of ZAT12in Brassica carinata. Over-expression of BcZAT12 in transformed tomato plants under abiotic stresses, suggest role of ZAT12 in conferring stress-tolerance in tomato. Sequence analysis of ZAT12 protein (Accession No. ABB55254.1) from B. carinata revealed it as a 161 amino acid long protein with short conserved motif 140LDLXL144 in C-terminal, a leucine rich L-Box with—14EXXAXCLXXL23 motif in N-terminal region and presence of two conserved Zinc-Finger motifs “CXXCXXXXXXXQALGGHXXXH” between positions 42–62 and 85–105. The two zinc finger motifs have presence of two conserved glutamic acid (Glu) and phenylalanine (Phe) residues. Two methionine (Met) residues at position 94 and 102 present in ZF-motif-2 were absent in ZF-motif-1. The 94Met and 97Ala in ZF-motif-2 were found to be replaced by serine (Ser) in ZF-motif-1. Homology and ab initio structural modeling of ZAT12 encoded BcZAT12 protein of B. carinata resulted in robust 3-D models and were evaluated for structural motifs, associated GO terms and protein-DNA interactions. The BcZAT12 protein model, was of good quality, reliable, stable and is deposited in PMDB database (PMDB ID: PM0078213). BcZAT12 is annotated as an intracellular protein having molecular function in Zn-binding which in turn regulates signal transduction/translation processes in response to abiotic stresses in plants. Results suggest BcZAT12 protein to interact directly with one strand of dsDNA via electrostatic and H-bonds.

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Acknowledgments

The work is a part of Network Project on Transgenic Crops, funded by ICAR, New Delhi. The authors are grateful to the Bioinformatics Division, MMV, BHU for computational facilities and to www.molegro.com/mvd-products.php server for access to Molegro Virtual docker for conducting the research work. All computations were performed on linux high performance clusters. Authors are grateful to Mr. Gerard Charmasson for copyediting of manuscript for language usage, spelling and grammar.

Conflict of interest

The authors declare that there are no competing interests.

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Authors and Affiliations

  1. Department of Biochemistry, Faculty of Science, Banaras Hindu University, Varanasi, 221005, UP, India

    Avinash Chandra Rai

  2. Division of Vegetable Improvement, Indian Institute of Vegetable Research, Shahanshahpur, Jhakhini, Varanasi, 221305, UP, India

    Avinash Chandra Rai & Major Singh

  3. Bioinformatics Division, Banaras Hindu University, Varanasi, 221005, UP, India

    Indra Singh

  4. Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, UP, India

    Kavita Shah

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  1. Avinash Chandra Rai
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  2. Indra Singh
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Correspondence to Kavita Shah.

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Rai, A.C., Singh, I., Singh, M. et al. Expression of ZAT12 transcripts in transgenic tomato under various abiotic stresses and modeling of ZAT12 protein in silico. Biometals 27, 1231–1247 (2014). https://doi.org/10.1007/s10534-014-9785-9

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  • DOI: https://doi.org/10.1007/s10534-014-9785-9

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