Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis

Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides

The legume albumin-1 gene family, arising after nodulation, encodes linear a- and b-chain peptides for nutrient storage and defense. Intriguingly, in one prominent legume, Clitoria ternatea, the b-chains are replaced by domains producing ultra-stable cyclic peptides called cyclotides. The mechanism of this gene hijacking is until now unknown. Cyclotides require recruitment of ligase-type asparaginyl endopeptidases (AEPs) for maturation (cyclization), necessitating co-evolution of two gene families. Here we compare a chromosome-level C. ternatea genome with grain legumes to reveal an 8 to 40-fold expansion of the albumin-1 gene family, enabling the additional loci to undergo diversification. Iterative rounds of albumin-1 duplication and diversification create four albumin-1 enriched genomic islands encoding cyclotides, where they are physically grouped by similar pI and net charge values. We identify an ancestral hydrolytic AEP that exhibits neofunctionalization and multiple duplication events to yield two ligase-type AEPs. We propose cyclotides arise by convergence in C. ternatea where their presence enhances defense from biotic attack, thus increasing fitness compared to lineages with linear b-chains and ultimately driving the replacement of b-chains with cyclotides.

Comparative analysis of cyclotide-producing plant cell suspensions presents opportunities for cyclotide plant molecular farming

Cyclotides are a class of ribosomally-synthesized plant peptides that function in plants as a defense against insects and fungal pathogens. Their unique structure comprises a cyclized peptide backbone threaded by three disulfide bonds, that imparts structural stability, a desirable quality for peptide-based therapeutics or insecticides. Producing these peptides synthetically is challenging due to the amount of chemical waste produced and inefficiency of folding certain cyclotides. Thus, it is desirable to develop a means to access cyclotide biosynthesis in their native hosts, cultured in defined conditions, at both laboratory and commercial scale. Here we developed suspension cell cultures from two species previously unexplored for cyclotide production in suspension cells, Clitoria ternatea L., Hybanthus enneaspermus F. Muell., as well as with Oldenlandia affinis (Roem. & Schult.) DC., a species reported previously to accumulate cyclotides in cell suspensions. We assessed the growth rate, cyclotide production and gene expression for the various species. We found that while many cyclotides had reduced expression in Oldenlandia affinis suspension cells when compared to plant organs, those in Clitoria ternatea and Hybanthus enneaspermus maintained or increased expression levels. The cyclotides that continued to be expressed in suspension cultures shared similar sequence and biophysical properties as a group, regardless of phylogenetic origin of the host. Of particular interest was the discovery of inducibility by NaCl of cyclotide expression in O. affinis, cycloviolacin O2 expression in O. affinis, and the scale up of cycloviolacin O2 production in H. enneaspermus. Together the results presented here highlight the utility of plant cell suspensions as modalities to produce macrocyclic peptides.

Cationic Clitoria ternatea Seed Peptide as a Potential Novel Bioactive Molecule

BACKGROUND

While several biologics have been reported from different parts of Clitoria ternatea, a herbaceous climber of the family Fabaceae, specific production of cationic peptides other than cyclotides (<3.7 kDa) has barely been investigated or their bioactive potential looked into.

OBJECTIVE

To uncover potential bioactivities and characteristics of novel cationic peptides from C. ternatea seeds.

METHODS

C. ternatea seed cationic peptide purified by simple and cost-effective procedures was analyzed by electrophoresis and mass spectrometry. Antimicrobial efficacy was evaluated against bacterial and fungal pathogens. Antioxidant potential was quantified by in vitro antioxidant assays. Physicochemical characterization and Tandem mass spectrometry were performed.

RESULTS

An 8.5 kDa cationic peptide purified from C. ternatea seeds was active against Candida albicans, Staphylococcus aureus, Aeromonas hydrophila and Escherichia coli at a minimum inhibitory concentration in the range of 8-32 μg/ml. This activity was totally uncompromised at pH 5-8 or after 1 h of heat treatment at 70-80 ºC, but was sensitive to protease treatment. Concentration-dependent free-radical scavenging activity and ferric-reducing capacity demonstrated the antioxidant potential of the peptide. Tandem MS analysis of trypsin-digested peptide based on shotgun proteomics detected matching peptide sequences with one or two cysteine residues but had low sequence coverage (≤17%) to known sequences in the C. ternatea protein database. Taken together, the distinct characteristics of this novel 8.5 kDa peptide clearly distinguishes it from known cyclotides of C. ternatea.

CONCLUSIONS

Insights have been obtained into the functional characteristics of what appears to be a novel cationic peptide from C. ternatea seeds, exhibiting significant antimicrobial and antioxidant activities.

Mass Spectrometric Analysis of Cyclotides from Clitoria ternatea: Xxx-Pro Bond Fragmentation as Convenient Diagnostic of Pro Residue Positioning

Cyclotides, a class of macrocyclic plant peptides, characterized by a cyclic backbone and three inter-locking disulfide bonds, may be divided into two major structural subfamilies, Möbius and Bracelet, based on the presence or absence of a specific proline residue. The present study describes the suite of cyclotides obtained from Clitoria ternatea, characterized by LC-MS and MS/MS techniques. Notable variations in product ion distributions were observed in cyclotides belonging to different structural subfamilies based on the number and positions of proline residues. For instance, Cter M which is an abundant Möbius cyclotide in this plant containing three proline residues, displayed distinct b- and y- ion characteristics in the MS/MS spectra compared to Cliotide T1, another commonly identified cyclotide but belonging to the Bracelet subfamily having two proline residues. The distinct fragmentation pattern of prototypical cyclotides of each structural subfamily, determined by Xxx-Pro bond fragmentation, was used to rapidly identify and sequence a novel cyclotide ctr pep 30 from this plant.

Disulfide-Rich Cyclic Peptides from Clitoria ternatea Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic Caenorhabditis elegans

Neurotoxic aggregation of β-amyloid (Aβ) peptides is a hallmark of Alzheimer's disease and increased reactive oxygen species (ROS) is an associated process. In the present study, we report the neuroprotective effects of disulfide-rich, circular peptides from Clitoria ternatea (C. ternatea) (butterfly pea) on Aβ-induced toxicity in transgenic Caenorhabditis elegans. Cyclotides (∼30 amino acids long) are a special class of cyclic cysteine knot peptides. We show that cyclotide-rich fractions from different plant tissues delay Aβ-induced paralysis in the transgenic CL4176 strain expressing the human muscle-specific Aβ_1-42 gene. They also improved Aβ-induced chemotaxis defects in CL2355 strain expressing Aβ_1-42 in the neuronal cells. ROS assay suggests that this protection is likely mediated by the inhibition of Aβ oligomerization. Furthermore, Aβ deposits were reduced in the CL2006 strain treated with the fractions. The study shows that cyclotides from C. ternatea could be a source of a novel pharmacophore scaffold against neurodegenerative diseases.