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Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter

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Abstract

Intergenic regions of divergent gene pairs show bidirectional promoter activity but whether regulatory sequences for gene expression in opposite directions are shared is not established. In this study, promoters of divergently arranged gene pair At4g35640–At4g35650 (SERAT3;2-IDH-III) of Arabidopsis thaliana were analyzed to identify overlapping regulatory regions. Both genes showed the highest expression in flower buds and flowers. 5′ RACE experiments extended the intergenic region from 161 bp shown in TAIR annotation to 512 bp. GUS analysis of transgenic A. thaliana plants carrying the 691 bp fragment (512 bp intergenic region plus 5′ UTR of both the genes) linked to uidA gene revealed that SERAT3;2 promoter drives gene expression in the tapetum, whereas IDH-III promoter functions specifically in microspores/pollen. Serial 5′ deletion of the 691 bp fragment showed SERAT3;2 promoter extends up to −355 position, whereas IDH-III promoter encompasses the 512 bp intergenic region. In transgenics, uidA transcript levels were lower than native SERAT3;2 and IDH-III transcripts indicating presence of additional cis regulatory elements beyond the 691 bp fragment. The present study demonstrated for the first time occurrence of a nested promoter in plants and identified a novel bidirectional promoter capable of driving gene expression in tapetum and microspores/pollen.

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Acknowledgements

The financial support for this work was obtained from the Indian Council of Agricultural Research grant under the National Agricultural Science Fund. We thank the National Phytotron Facility, Indian Agricultural Research Institute, New Delhi for providing space for growing Arabidopsis under contained conditions.

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Authors and Affiliations

  1. ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India

    Ritesh Kumar Raipuria, Vajinder Kumar & Shripad Ramachandra Bhat

  2. School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, Madhya Pradesh, 452001, India

    Ritesh Kumar Raipuria & Kadur Narayan Guruprasad

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  1. Ritesh Kumar Raipuria
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  2. Vajinder Kumar
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  3. Kadur Narayan Guruprasad
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Correspondence to Shripad Ramachandra Bhat.

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Supplementary Fig. 1

Expression profile of IDH-III gene at eFP bowser (DOC 270 kb)

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Raipuria, R.K., Kumar, V., Guruprasad, K.N. et al. Analysis of Promoters of Arabidopsis thaliana Divergent Gene Pair SERAT3;2 and IDH-III Shows SERAT3;2 Promoter is Nested Within the IDH-III Promoter. Mol Biotechnol 59, 294–304 (2017). https://doi.org/10.1007/s12033-017-0016-9

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  • DOI: https://doi.org/10.1007/s12033-017-0016-9

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