Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola).

Sungkyu Park,Anders Backlund,K Johan Rosengren,Inseok Doo,Erik Jacobsson,Ki-Oug Yoo,Thomas Marcussen,Ulf Göransson

doi:10.3389/fpls.2017.02058

Abstract

Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species). Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.

Highlights

Cyclotides are proteins of ∼30 amino acid residues that are characterized by the cyclic cystine knot (CCK) motif (Craik et al, 1999; Burman et al, 2014)
The cyclotides have been classified into two main subfamilies, the Möbius and the bracelets, based on a single structural trait: the presence or absence of a conceptual 180◦ twist in the cyclic backbone caused by a conserved cis-Pro residue in loop 5 (Craik et al, 1999; Figure 1B)
The discovery of other cyclotides has created a need for a more versatile classification system (Ireland et al, 2006; Nguyen et al, 2013; Ravipati et al, 2015). These varieties include socalled hybrid cyclotides that exhibit sequence characteristics of both the Möbius and bracelet subfamilies (Daly et al, 2006), as well as minor subfamily known as the trypsin inhibitors originating from gourd plants (Hernandez et al, 2000)

Summary

INTRODUCTION

Cyclotides are proteins of ∼30 amino acid residues that are characterized by the cyclic cystine knot (CCK) motif (Craik et al, 1999; Burman et al, 2014). The discovery of other cyclotides has created a need for a more versatile classification system (Ireland et al, 2006; Nguyen et al, 2013; Ravipati et al, 2015) These varieties include socalled hybrid cyclotides that exhibit sequence characteristics of both the Möbius and bracelet subfamilies (Daly et al, 2006), as well as minor subfamily known as the trypsin inhibitors originating from gourd plants (Hernandez et al, 2000). They contain the CCK motif but do not otherwise exhibit any sequence similarity with the other subfamilies. Full precursor sequences are used to obtain insights into the evolutionary history of the cyclotides, and we connect the evolution of new mature cyclotides with the emergence of new functions

MATERIALS AND METHODS

Findings

AND DISCUSSION