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Isolation and characterization of cyclotides from the leaves of Viola odorata L. using peptidomic and bioinformatic approach

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Abstract

Cyclotides are true gene products characterized by the presence of six conserved cysteine residues and knotted arrangement of three disulfide bonds. These macrocyclic peptides show exceptional resistance to thermal, chemical and enzymatic degradation which is defined due to their three-dimensional folding. The current study describes an efficient strategy involving reduction, enzymatic digestion and mass spectroscopy sequencing for the identification of the precursor sequences and the cyclotide domains present in the leaf tissue of Viola odorata. We observed 122 partial peptide sequences containing 31 cyclotide domains along with 19 unique sequences consisting of putative novel cyclotides and acyclotides. Four precursor sequences consisting of putative new and already reported domains were further characterized for cyclotide domains, their structure and subfamilies. The sequences revealed the presence of classic knotted cyclotide folds with similar six characteristic loops but different amino acid residues. Molecular modeling indicated that the secondary structures present in the cyclotides are mainly α-helix and random coils. Variation in the sequences and conservation in cysteine residues in the cyclotides was revealed by protein diversity wheel. The significant information observed in the current study expands our knowledge about the structure and type of cyclic peptides in V. odorata leaves.

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Acknowledgements

INSPIRE Fellowship, Department of Science and Technology, New Delhi is highly acknowledged. Authors are thankful to the School of Biotechnology, University of Jammu, Jammu for providing basic facilities. We are also thankful to Dr Manoj Khushwaha, IIIM Jammu and Dr. Sunny Sharma, School of Biotechnology for providing the necessary guidance throughout the work.

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This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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  1. School of Biotechnology, University of Jammu, Jammu and Kashmir, India

    Lubna Aslam, Ramanjeet Kaur, Venu Sharma, Nisha Kapoor & Ritu Mahajan

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  1. Lubna Aslam
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  2. Ramanjeet Kaur
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  3. Venu Sharma
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  4. Nisha Kapoor
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  5. Ritu Mahajan
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LA: methodology, software, original draft preparation; RK: validation, software; VS: methodology; NK: supervision; RM: conceptualization, resources, reviewing and editing.

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Correspondence to Ritu Mahajan.

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Aslam, L., Kaur, R., Sharma, V. et al. Isolation and characterization of cyclotides from the leaves of Viola odorata L. using peptidomic and bioinformatic approach. 3 Biotech 11, 211 (2021). https://doi.org/10.1007/s13205-021-02763-2

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