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LC-MS/MS identification and structural characterization of isolated cyclotides from precursor sequences of Viola odorata L. petiole tissue using computational approach

Abstract

Viola odorata L., known for its pharmacological properties, produces a plethora of structurally stable peptides called cyclotides. Cyclotides are macrocyclic peptides with a unique topology containing a cyclic cystine knot motif. The objective of the present study was to identify the precursor sequences and respective cyclotide domains from the petiole tissue of V. odorata. The study is based on the isolation, identification, and characterization of the cyclic peptides using LC-MS/MS followed by database searching and processing. Our study detected 47 precursor sequences encoded for 15 reported cyclotides, 4 putative novel cyclotides, and 3 acyclotides from the petiole tissue. The novel sequences identified were based on the hydrophobic nature, disulfide bonds, conserved cysteine residues, and presence of cyclic peptide backbone. Four putative novel and three acyclotides were also characterized for their sequence and subfamilies. A protein diversity wheel was used to reveal the variation in the amino acid sequence and cysteine residue conservation in the isolated cyclotides. The results provide information about the number of cyclotides and acyclotides from the petiole tissue and their sequence diversity, which may constitute novel tools for future research on this plant species.

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Acknowledgements

The authors are thankful to the School of Biotechnology, University of Jammu, Jammu, for providing the basic facilities, and to INSPIRE Fellowship, Department of Science and Technology, New Delhi. In addition, the authors acknowledge various funding agencies (of the Government of India) such as DST, JK-DST, UGC, NMPB for major research projects, RUSA, UGC-SAP, PURSE, the Central facility of their department, and the DBT-funded bioinformatics facility at the School of Biotechnology, University of Jammu.

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LA: methodology, software, original draft preparation; RK, SH: validation, software; NK: supervision; RM: conceptualization, resources, reviewing and editing.

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Correspondence to Ritu Mahajan.

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Corresponding editor: Sreenivas Chavali

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Aslam, L., Kaur, R., Hussain, S. et al. LC-MS/MS identification and structural characterization of isolated cyclotides from precursor sequences of Viola odorata L. petiole tissue using computational approach. J Biosci 47, 50 (2022). https://doi.org/10.1007/s12038-022-00283-6

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Keywords

  • Acyclotides
  • cyclotides
  • in silico analysis
  • LC-MS/MS
  • Viola odorata