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Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution

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Abstract

Zingiberaceae or ‘ginger family’ is the largest family in the order ‘Zingiberales’ with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS ‘a representative from Zingiberaceae’ suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance.

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Acknowledgments

We thank the anonymous reviewers for the useful comments, which helped us to improve the manuscript. The authors are thankful to Council of Scientific and Industrial Research (CSIR) for Senior Research Fellowship (09/716/(0146)/2012/EMR-I) and Department of Science and Technology (DST) for financial support. Authors are also acknowledging Department of Biotechnology (DBT) for the facilities provided.

Author contributions

Conceived and designed the experiments: VM, PTG, AR and EVS. Performed the experiments: VM, PTG and AR. Analysed the data: VM and GA. Wrote the paper: VM, GA and EVS

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  1. Plant Molecular Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India

    Vijayanathan Mallika, Girija Aiswarya, Paily Thottathil Gincy, Appukuttan Remakanthan & Eppurathu Vasudevan Soniya

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  1. Vijayanathan Mallika
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  2. Girija Aiswarya
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  3. Paily Thottathil Gincy
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  4. Appukuttan Remakanthan
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Correspondence to Eppurathu Vasudevan Soniya.

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Communicated by Sureshkumar Balasubramanian

P. T. Gincy and A. Remakanthan have contributed equally to this work.

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Mallika, V., Aiswarya, G., Gincy, P.T. et al. Type III polyketide synthase repertoire in Zingiberaceae: computational insights into the sequence, structure and evolution. Dev Genes Evol 226, 269–285 (2016). https://doi.org/10.1007/s00427-016-0548-1

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