1
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Lian Y, Tang X, Hu G, Miao C, Cui Y, Zhangsun D, Wu Y, Luo S. Characterization and evaluation of cytotoxic and antimicrobial activities of cyclotides from Viola japonica. Sci Rep 2024; 14:9733. [PMID: 38679643 PMCID: PMC11056381 DOI: 10.1038/s41598-024-60246-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024] Open
Abstract
Cyclotides are a type of defense peptide most commonly found in the Violaceae family of plants, exhibiting various biological activities. In this study, we focused on the Viola japonica as our research subject and conducted transcriptome sequencing and analysis using high-throughput transcriptomics techniques. During this process, we identified 61 cyclotides, among which 25 were previously documented, while the remaining 36 were designated as vija 1 to vija 36. Mass spectrometry detection showed that 21 putative cyclotides were found in the extract of V. japonica. Through isolation, purification and tandem mass spectrometry, we characterized and investigated the activities of five cyclotides. Our results demonstrated inhibitory effects of these cyclotides on the growth of Acinetobacter baumannii and Bacillus subtilis, with minimum inhibitory concentrations (MICs) of 4.2 μM and 2.1 μM, respectively. Furthermore, time killing kinetic assays revealed that cyclotides at concentration of 4 MICs achieved completely bactericidal effects within 2 h. Additionally, fluorescence staining experiments confirmed that cyclotides disrupt microbial membranes. Moreover, cytotoxicity studies showed that cyclotides possess cytotoxic effects, with IC50 values ranging from 0.1 to 3.5 μM. In summary, the discovery of new cyclotide sequences enhances our understanding of peptide diversity and the exploration of their activity lays the foundation for a deeper investigation into the mechanisms of action of cyclotides.
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Affiliation(s)
- Yuanyuan Lian
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China
| | - Xue Tang
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China
| | - Gehui Hu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China
| | - Chenfang Miao
- Department of Pharmacy, The 900Th Hospital of Joint Logistics Team of the PLA, Fuzhou General Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Yunfei Cui
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China
| | - Dongting Zhangsun
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China
| | - Yong Wu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China.
| | - Sulan Luo
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, China.
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, China.
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2
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Barashkova AS, Smirnov AN, Zorina ES, Rogozhin EA. Diversity of Cationic Antimicrobial Peptides in Black Cumin ( Nigella sativa L.) Seeds. Int J Mol Sci 2023; 24:ijms24098066. [PMID: 37175769 PMCID: PMC10179141 DOI: 10.3390/ijms24098066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Black cumin (Nigella sativa L.) is known to possess a wide variety of antimicrobial peptides belonging to different structural families. Three novel antimicrobial peptides have been isolated from black cumin seeds. Two of them were attributed as members of the non-specific lipid transfer proteins family, and one as a defensin. We have made an attempt of using the proteomic approach for novel antimicrobial peptides search in N. sativa seeds as well. The use of a well-established approach that includes extraction and fractionation stages remains relevant even in the case of novel peptides search because of the lacking N. sativa genome data. Novel peptides demonstrate a spectrum of antimicrobial activity against plant pathogenic organisms that may cause economically important crop diseases. These results obtained allow considering these molecules as candidates to be applied in "next-generation" biopesticides development for agricultural use.
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Affiliation(s)
- Anna S Barashkova
- Laboratory of Neuroreceptors and Neuroregulators, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117437 Moscow, Russia
- Laboratory of Biochemistry and Ecology of Microorganisms, All-Russian Institute for Plant Protection, 196608 Pushkin, Russia
| | - Alexey N Smirnov
- Department of Plant Protection, Timiryazev Russian State Agrarian University, 127434 Moscow, Russia
| | - Elena S Zorina
- Orekhovich Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Eugene A Rogozhin
- Laboratory of Neuroreceptors and Neuroregulators, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, 117437 Moscow, Russia
- Laboratory of Biochemistry and Ecology of Microorganisms, All-Russian Institute for Plant Protection, 196608 Pushkin, Russia
- Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, 152742 Borok, Russia
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3
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Tyler TJ, Durek T, Craik DJ. Native and Engineered Cyclic Disulfide-Rich Peptides as Drug Leads. Molecules 2023; 28:molecules28073189. [PMID: 37049950 PMCID: PMC10096437 DOI: 10.3390/molecules28073189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Bioactive peptides are a highly abundant and diverse group of molecules that exhibit a wide range of structural and functional variation. Despite their immense therapeutic potential, bioactive peptides have been traditionally perceived as poor drug candidates, largely due to intrinsic shortcomings that reflect their endogenous heritage, i.e., short biological half-lives and poor cell permeability. In this review, we examine the utility of molecular engineering to insert bioactive sequences into constrained scaffolds with desired pharmaceutical properties. Applying lessons learnt from nature, we focus on molecular grafting of cyclic disulfide-rich scaffolds (naturally derived or engineered), shown to be intrinsically stable and amenable to sequence modifications, and their utility as privileged frameworks in drug design.
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Affiliation(s)
- Tristan J. Tyler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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4
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Rajendran S, Slazak B, Mohotti S, Strömstedt AA, Göransson U, Hettiarachchi CM, Gunasekera S. Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis. Phytochemistry 2021; 187:112749. [PMID: 33932786 DOI: 10.1016/j.phytochem.2021.112749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Cyclotides are an extremely stable class of peptides, ubiquitously distributed in Violaceae. The aim of the present study was to investigate the presence of cyclotides in Sri Lankan Violaceae plants, using combined tools of transcriptomics and mass spectrometry. New cyclotides were discovered for the first time in the wild flora of Sri Lanka, within Viola betonicifolia, a plant used in traditional medicine as an antimicrobial. Plant extracts prepared in small scale from Viola betonicifolia were first subjected to LC-MS analysis. Subsequent transcriptome de novo sequencing of Viola betonicifolia uncovered 25 new (vibe 1-25) and three known (varv A/kalata S, viba 17, viba 11) peptide sequences from Möbius and bracelet cyclotide subfamilies as well as hybrid cyclotides. Among the transcripts, putative linear acyclotide sequences (vibe 4, vibe 10, vibe 11 and vibe 22) that lack a conserved asparagine or aspartic acid vital for cyclisation were also present. Four asparagine endopeptidases (AEPs), VbAEP1-4 were found within the Viola betonicifolia transcriptome, including a peptide asparaginyl ligase (PAL), potentially involved in cyclotide backbone cyclisation, showing >93% sequence homology to Viola yedoensis peptide asparaginyl ligases, VyPALs. In addition, we identified two protein disulfide isomerases (PDIs), VbPDI1-2, likely involved in cyclotide oxidative folding, having high sequence homology (>74%) with previously reported Rubiaceae and Violaceae PDIs. The current study highlights the ubiquity of cyclotides in Violaceae as well as the utility of transcriptomic analysis for cyclotides and their putative processing enzyme discovery. The high variability of cyclotide sequences in terms of loop sizes and residues in V. betonicifolia showcase the cyclotide structure as an adaptable scaffold as well as their importance as a combinatorial library, implicated in plant defense.
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Affiliation(s)
- Sanjeevan Rajendran
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden; Department of Chemistry, Faculty of Science, University of Colombo, Thurston Rd, Colombo 03, Sri Lanka
| | - Blazej Slazak
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden; W. Szafer Institute of Botany, Polish Academy of Science, 46 Lubicz St., 31-512, Cracow, Poland
| | - Supun Mohotti
- Department of Chemistry, Faculty of Science, University of Colombo, Thurston Rd, Colombo 03, Sri Lanka
| | - Adam A Strömstedt
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden
| | - Ulf Göransson
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden
| | - Chamari M Hettiarachchi
- Department of Chemistry, Faculty of Science, University of Colombo, Thurston Rd, Colombo 03, Sri Lanka
| | - Sunithi Gunasekera
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden.
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Slazak B, Kaltenböck K, Steffen K, Rogala M, Rodríguez-Rodríguez P, Nilsson A, Shariatgorji R, Andrén PE, Göransson U. Cyclotide host-defense tailored for species and environments in violets from the Canary Islands. Sci Rep 2021; 11:12452. [PMID: 34127703 DOI: 10.1038/s41598-021-91555-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/19/2021] [Indexed: 11/08/2022] Open
Abstract
Cyclotides are cyclic peptides produced by plants. Due to their insecticidal properties, they are thought to be involved in host defense. Violets produce complex mixtures of cyclotides, that are characteristic for each species and variable in different environments. Herein, we utilized mass spectrometry (LC–MS, MALDI-MS), transcriptomics and biological assays to investigate the diversity, differences in cyclotide expression based on species and different environment, and antimicrobial activity of cyclotides found in violets from the Canary Islands. A wide range of different habitats can be found on these islands, from subtropical forests to dry volcano peaks at high altitudes. The islands are inhabited by the endemic Viola palmensis, V. cheiranthifolia, V. anagae and the common V. odorata. The number of cyclotides produced by a given species varied in plants from different environments. The highest diversity was noted in V. anagae which resides in subtropical forest and the lowest in V. cheiranthifolia from the Teide volcano. Transcriptome sequencing and LC–MS were used to identify 23 cyclotide sequences from V. anagae. Cyclotide extracts exhibited antifungal activities with the lowest minimal inhibitory concentrations noted for V. anagae (15.62 μg/ml against Fusarium culmorum). The analysis of the relative abundance of 30 selected cyclotides revealed patterns characteristic to both species and populations, which can be the result of genetic variability or environmental conditions in different habitats. The current study exemplifies how plants tailor their host defense peptides for various habitats, and the usefulness of cyclotides as markers for chemosystematics.
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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7
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Zheng W, Zhou T, Li J, Jiang W, Zhang J, Xiao C, Wei D, Yang C, Xu R, Gong A, Zhang C, Bi Y. The Biosynthesis of Heterophyllin B in Pseudostellaria heterophylla From prePhHB-Encoded Precursor. Front Plant Sci 2019; 10:1259. [PMID: 31749814 PMCID: PMC6842982 DOI: 10.3389/fpls.2019.01259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Plant cyclic peptides (CPs) are a large group of small molecule metabolites found in a wide variety of plants, including traditional Chinese medicinal plants. However, the majority of plant CPs have not been studied for their biosynthetic mechanisms, including heterophyllin B (HB), which is one of the characteristic chemical components of Pseudostellaria heterophylla. Here, we screened the precursor gene (prePhHB) of HB in P. heterophylla and functionally identified its correctness in vivo and in vitro. First, we developed a new method to screen the precursors of HB from 16 candidate linear peptides. According to transcriptome sequencing data, we cloned the genes that encoded the HB precursor peptides and confirmed that the prePhHB-encoded precursor peptide could enzymatically synthesize HB. Next, we generated the transgenic tobacco that expressed prePhHB, and the results showed that HB was detected in transgenic tobacco. Moreover, we revealed that prePhHB gene expression is positively correlated with HB accumulation in P. heterophylla. Mutations in the prePhHB gene may influence the accumulation of HB in P. heterophylla. These results suggest that HB is ribosomally synthesized and posttranslationally modified peptide (RiPP) derived from the precursor gene prePhHB-encoded precursor peptide, and the core peptide sequence of HB is IFGGLPPP in P. heterophylla. This study developed a new idea for the rapid identification of Caryophyllaceae-type CP precursor peptides via RNA-sequencing data mining.
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Affiliation(s)
- Wei Zheng
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Tao Zhou
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jun Li
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weike Jiang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jinqiang Zhang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chenghong Xiao
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Dequn Wei
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Changgui Yang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Rong Xu
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Anhui Gong
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Chen Zhang
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yan Bi
- Experiment Center, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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8
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Huang YH, Du Q, Craik DJ. Cyclotides: Disulfide-rich peptide toxins in plants. Toxicon 2019; 172:33-44. [DOI: 10.1016/j.toxicon.2019.10.244] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
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9
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Abstract
Cyclotides are globular microproteins with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to chemical, thermal, and biological degradation compared to other peptides of similar size. In addition, cyclotides have been shown to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides can also cross cellular membranes and are able to modulate intracellular protein-protein interactions, both in vitro and in vivo. All of these features make cyclotides highly promising as leads or frameworks for the design of peptide-based diagnostic and therapeutic tools. This article provides an overview on cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA
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10
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Ravipati AS, Poth AG, Troeira Henriques S, Bhandari M, Huang YH, Nino J, Colgrave ML, Craik DJ. Understanding the Diversity and Distribution of Cyclotides from Plants of Varied Genetic Origin. J Nat Prod 2017; 80:1522-1530. [PMID: 28471681 DOI: 10.1021/acs.jnatprod.7b00061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cyclotides are a large family of naturally occurring plant-derived macrocyclic cystine-knot peptides, with more than 400 having been identified in species from the Violaceae, Rubiaceae, Cucurbitaceae, Fabaceae, and Solanaceae families. Nevertheless, their specialized distribution within the plant kingdom remains poorly understood. In this study, the diversity of cyclotides was explored through the screening of 197 plants belonging to 43 different families. In total, 28 cyclotides were sequenced from 15 plant species, one of which belonged to the Rubiaceae and 14 to the Violaceae. Every Violaceae species screened contained cyclotides, but they were only sparsely represented in Rubiaceae and nonexistent in other families. The study thus supports the hypothesis that cyclotides are ubiquitous in the Violaceae, and it adds to the list of plants found to express kalata S and cycloviolacin O12. Finally, previous studies suggested the existence of cyclotide isoforms with either an Asn or an Asp at the C-terminal processing site of the cyclotide domain within the precursor proteins. Here we found that despite the discovery of a few cyclotides genuinely containing an Asp in loop 6 as evidenced by gene sequencing, deamidation of Asn during enzymatic digestion resulted in the artifactual presence of Asp isoforms. This result is consistent with studies suggesting that peptides can undergo deamidation after being subjected to external factors, including pH, temperature, and enzymatic digestion.
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Affiliation(s)
- Anjaneya S Ravipati
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Murari Bhandari
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
| | - Jaime Nino
- Universidad Tecnológica de Pereira , Cra 27 No 10-02-Los Álamos, Pereira, Risaralda, Colombia
| | - Michelle L Colgrave
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, St Lucia 4067, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane 4072, Queensland Australia
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Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD, Australia
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12
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Park S, Yoo KO, Marcussen T, Backlund A, Jacobsson E, Rosengren KJ, Doo I, Göransson U. Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets ( Viola). Front Plant Sci 2017; 8:2058. [PMID: 29326730 PMCID: PMC5741643 DOI: 10.3389/fpls.2017.02058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/17/2017] [Indexed: 05/20/2023]
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.
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Affiliation(s)
- Sungkyu Park
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ki-Oug Yoo
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea
| | - Thomas Marcussen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Anders Backlund
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Erik Jacobsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - K. Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Inseok Doo
- Biotech Research Team, Biotech Research Center of Dong-A Pharm Co Ltd., Seoul, South Korea
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
- *Correspondence: Ulf Göransson
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13
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Koehbach J, Clark RJ. Unveiling the diversity of cyclotides by combining peptidome and transcriptome analysis. Biopolymers 2016; 106:774-783. [DOI: 10.1002/bip.22858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Affiliation(s)
- Johannes Koehbach
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
| | - Richard J. Clark
- School of Biomedical Sciences; The University of Queensland; 4072 St. Lucia QLD Australia
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14
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Abstract
Cyclotides are plant-derived cyclic peptides that have a head-to-tail cyclic backbone and three conserved disulphide bonds that form a cyclic cystine knot motif. They occur in plants from the Violaceae, Rubiaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, typically with 10-100 cyclotides in a given plant species, in a wide range of tissues, including flowers, leaves, stems, and roots. Some cyclotides are expressed in large amounts (up to 1g kg(-1) wet plant weight) and their natural function appears to be to protect plants from pests or pathogens. This article provides a brief overview of their discovery, distribution in plants, and applications. In particular, their exceptional stability has led to their use as peptide-based scaffolds in drug design applications. They also have potential as natural 'ecofriendly' insecticides, and as protein engineering frameworks.
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Affiliation(s)
- Joachim Weidmann
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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15
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Ravipati AS, Henriques ST, Poth AG, Kaas Q, Wang CK, Colgrave ML, Craik DJ. Lysine-rich Cyclotides: A New Subclass of Circular Knotted Proteins from Violaceae. ACS Chem Biol 2015; 10:2491-500. [PMID: 26322745 DOI: 10.1021/acschembio.5b00454] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclotides are macrocyclic proteins produced by plants for host defense. Although they occur sparsely in other plant families, cyclotides have been detected in every Violaceae plant species so far screened. Many of the Violaceae species examined until now have been from closely related geographical regions or habitats. To test the hypothesis that cyclotides are ubiquitous in this family, two geographically isolated (and critically endangered) species of Australasian Violaceae, namely Melicytus chathamicus and M. latifolius, were examined. Surprisingly, we discovered a suite of cyclotides possessing novel sequence features, including a lysine-rich nature, distinguishing them from "conventional" cyclotides and suggesting that they might have different physiological activities in plants to those reported to date. The newly discovered cyclotides were found to bind to lipid membranes and were cytotoxic against cancer cell lines but had low toxicity against red blood cells, which is advantageous for potential therapeutic applications. This suite of novel Lys-rich cyclotides emphasizes the broad diversity of cyclotides in Violaceae species.
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Affiliation(s)
- Anjaneya S. Ravipati
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Aaron G. Poth
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K. Wang
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Michelle L. Colgrave
- Commonwealth Scientific and Industrial Research Organization, Agriculture Flagship, St. Lucia, Queensland 4067, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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Hellinger R, Koehbach J, Soltis DE, Carpenter EJ, Wong GKS, Gruber CW. Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining. J Proteome Res 2015; 14:4851-62. [PMID: 26399495 PMCID: PMC4642221 DOI: 10.1021/acs.jproteome.5b00681] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Cyclotides are plant-derived mini proteins. They are genetically
encoded as precursor proteins that become post-translationally modified
to yield circular cystine-knotted molecules. Because of this structural
topology cyclotides resist enzymatic degradation in biological fluids,
and hence they are considered as promising lead molecules for pharmaceutical
applications. Despite ongoing efforts to discover novel cyclotides
and analyze their biodiversity, it is not clear how many individual
peptides a single plant specimen can express. Therefore, we investigated
the transcriptome and cyclotide peptidome of Viola tricolor. Transcriptome mining enabled the characterization of cyclotide
precursor architecture and processing sites important for biosynthesis
of mature peptides. The cyclotide peptidome was explored by mass spectrometry
and bottom-up proteomics using the extracted peptide sequences as
queries for database searching. In total 164 cyclotides were discovered
by nucleic acid and peptide analysis in V. tricolor. Therefore, violaceous plants at a global scale may be the source
to as many as 150 000 individual cyclotides. Encompassing the
diversity of V. tricolor as a combinatorial library
of bioactive peptides, this commercially available medicinal herb
may be a suitable starting point for future bioactivity-guided screening
studies.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Koehbach
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida , Gainesville, Florida 32611, United States
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada.,Department of Medicine, University of Alberta , Edmonton, Alberta T6G 2E1, Canada.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
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Slazak B, Jacobsson E, Kuta E, Göransson U. Exogenous plant hormones and cyclotide expression in Viola uliginosa (Violaceae). Phytochemistry 2015; 117:527-536. [PMID: 26246035 DOI: 10.1016/j.phytochem.2015.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/30/2015] [Accepted: 07/20/2015] [Indexed: 05/18/2023]
Abstract
Plants from Violaceae produce cyclotides, peptides characterized by a circular peptide backbone and a cystine knot. This signature motif gives stability that can harness a wide spectrum of biological activities, with implications in plant defense and with applications in medicine and biotechnology. In the current work, cyclotide expressing in vitro cultures were established from Viola uliginosa. These cultures are useful models for studying biosynthesis of cyclotides and can also be used in their production. The cyclotide expression pattern is shown to be dependent on exogenous plant growth regulators, both on peptide and gene expression levels. The highest yields of cyclotides were obtained on media containing only a cytokinin and were correlated with storage material accumulation. Exposure to auxins decreased cyclotide production and caused shifting of the biosynthesis pattern to root specific cyclotides. The response to stimuli in terms of cyclotide expression pattern appears to be developmental, and related to polar auxin transportation and the auxin/cytokinin ratio regulating tissue differentiation. By the use of whole transcriptome shotgun sequencing (WTSS) and peptidomics, 20 cyclotide sequences from V. uliginosa (including 12 new) and 12 complete precursor proteins could be identified. The most abundant cyclotides were cycloviolacin O3 (CyO3), CyO8 and CyO13. A suspension culture was obtained that grew exponentially with a doubling time of approximately 3 days. After ten days of growth, the culture provided a yield of more than 4 mg CyO13 per gram dry mass.
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Affiliation(s)
- Blazej Slazak
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, 9 Gronostajowa Str., 30-387 Cracow, Poland; Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, 751 23 Uppsala, Sweden; W. Szafer Istitute of Botany, Polish Academy of Sciences, 46 Lubicz St., 31-512 Cracow, Poland.
| | - Erik Jacobsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, 751 23 Uppsala, Sweden
| | - Elżbieta Kuta
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, 9 Gronostajowa Str., 30-387 Cracow, Poland
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, 751 23 Uppsala, Sweden
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18
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Zhang J, Hua Z, Huang Z, Chen Q, Long Q, Craik DJ, Baker AJM, Shu W, Liao B. Two Blast-independent tools, CyPerl and CyExcel, for harvesting hundreds of novel cyclotides and analogues from plant genomes and protein databases. Planta 2015; 241:929-940. [PMID: 25528148 DOI: 10.1007/s00425-014-2229-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Two high-throughput tools harvest hundreds of novel cyclotides and analogues in plants. Cyclotides are gene-encoded backbone-cyclized polypeptides displaying a diverse range of bioactivities associated with plant defense. However, genome-scale or database-scale evaluations of cyclotides have been rare so far. Here, a novel time-efficient Perl program, CyPerl, was developed for searching cyclotides from predicted ORFs of 34 available plant genomes and existing plant protein sequences from Genbank databases. CyPerl-isolated sequences were further analyzed by removing repeats, evaluating their cysteine-distributed regions (CDRs) and comparing with CyBase-collected cyclotides in a user-friendly Excel (Microsoft Office) template, CyExcel. After genome-screening, 186 ORFs containing 145 unique cyclotide analogues were identified by CyPerl and CyExcel from 30 plant genomes tested from 10 plant families. Phaseolus vulgaris and Zea mays were the richest two species containing cyclotide analogues in the plants tested. After screening protein databases, 266 unique cyclotides and analogues were identified from seven plant families. By merging with 288 unique CyBase-listed cyclotides, 510 unique cyclotides and analogues were obtained from 13 plant families. In total, seven novel plant families containing cyclotide analogues and 202 novel cyclotide analogues were identified in this study. This study has established two Blast-independent tools for screening cyclotides from plant genomes and protein databases, and has also significantly widened the plant distribution and sequence diversity of cyclotides and their analogues.
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Affiliation(s)
- Jun Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, 510006, China,
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19
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Burman R, Yeshak MY, Larsson S, Craik DJ, Rosengren KJ, Göransson U. Distribution of circular proteins in plants: large-scale mapping of cyclotides in the Violaceae. Front Plant Sci 2015; 6:855. [PMID: 26579135 PMCID: PMC4621522 DOI: 10.3389/fpls.2015.00855] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/28/2015] [Indexed: 05/02/2023]
Abstract
During the last decade there has been increasing interest in small circular proteins found in plants of the violet family (Violaceae). These so-called cyclotides consist of a circular chain of approximately 30 amino acids, including six cysteines forming three disulfide bonds, arranged in a cyclic cystine knot (CCK) motif. In this study we map the occurrence and distribution of cyclotides throughout the Violaceae. Plant material was obtained from herbarium sheets containing samples up to 200 years of age. Even the oldest specimens contained cyclotides in the preserved leaves, with no degradation products observable, confirming their place as one of the most stable proteins in nature. Over 200 samples covering 17 of the 23-31 genera in Violaceae were analyzed, and cyclotides were positively identified in 150 species. Each species contained a unique set of between one and 25 cyclotides, with many exclusive to individual plant species. We estimate the number of different cyclotides in the Violaceae to be 5000-25,000, and propose that cyclotides are ubiquitous among all Violaceae species. Twelve new cyclotides from six phylogenetically dispersed genera were sequenced. Furthermore, the first glycosylated derivatives of cyclotides were identified and characterized, further increasing the diversity and complexity of this unique protein family.
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Affiliation(s)
- Robert Burman
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
| | - Mariamawit Y. Yeshak
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
- Department of Pharmacognosy, School of Pharmacy, Addis Ababa UniversityAddis Ababa, Ethiopia
| | - Sonny Larsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
| | - David J. Craik
- Craik Lab, Chemistry and Structural Biology Division, Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - K. Johan Rosengren
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
- Laboratory for Peptide Structural Biology, School of Biomedical Sciences, The University of QueenslandBrisbane, QLD, Australia
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala UniversityUppsala, Sweden
- *Correspondence: Ulf Göransson
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20
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Ryazantsev DY, Rogozhin EA, Dimitrieva TV, Drobyazina PE, Khadeeva NV, Egorov TA, Grishin EV, Zavriev SK. A novel hairpin-like antimicrobial peptide from barnyard grass (Echinochloa crusgalli L.) seeds: Structure-functional and molecular-genetics characterization. Biochimie 2013; 99:63-70. [PMID: 24275143 DOI: 10.1016/j.biochi.2013.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/08/2013] [Indexed: 11/26/2022]
Abstract
A novel plant hairpin-like defense polypeptide named EcAMP3 was isolated from latent barnyard grass (Echinochloa crusgalli L.) seeds. The native peptide and its recombinant analogue were characterized. EcAMP3 displays antifungal and antibacterial activity in vitro. The gene family encoding EcAMPs precursor protein was also characterized; the genes and pseudogenes of this family show 97-100% homology. Every member of EcAMPs precursor family contains seven identical cysteine motifs: C1XXXC2(11-13)C3XXXC4. One of those motifs corresponds to the isolated peptide. EcAMP3 is the first member of the plant hairpin-like peptide family that inhibits the growth of phytopathogenic bacteria. Obtained results can explain the nature of the complex resistance of barnyard grass to a variety of pathogenic microorganisms.
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Affiliation(s)
- Dmitry Yu Ryazantsev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation.
| | - Eugene A Rogozhin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation.
| | - Tatiana V Dimitrieva
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation.
| | - Polina E Drobyazina
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; All-Russian Research Institute of Biotechnology, Russian Academy of Agricultural Sciences, ul. Timiryazevskaya 42, 127550 Moscow, Russian Federation.
| | - Natalia V Khadeeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, ul. Gubkina 3, 117809 Moscow, Russian Federation.
| | - Tsezi A Egorov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Eugene V Grishin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation.
| | - Sergey K Zavriev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation.
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21
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Deane CD, Mitchell DA. Lessons learned from the transformation of natural product discovery to a genome-driven endeavor. J Ind Microbiol Biotechnol 2013; 41:315-31. [PMID: 24142337 DOI: 10.1007/s10295-013-1361-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 09/30/2013] [Indexed: 12/24/2022]
Abstract
Natural product discovery is currently undergoing a transformation from a phenotype-driven field to a genotype-driven one. The increasing availability of genome sequences, coupled with improved techniques for identifying biosynthetic gene clusters, has revealed that secondary metabolomes are strikingly vaster than previously thought. New approaches to correlate biosynthetic gene clusters with the compounds they produce have facilitated the production and isolation of a rapidly growing collection of what we refer to as "reverse-discovered" natural products, in analogy to reverse genetics. In this review, we present an extensive list of reverse-discovered natural products and discuss seven important lessons for natural product discovery by genome-guided methods: structure prediction, accurate annotation, continued study of model organisms, avoiding genome-size bias, genetic manipulation, heterologous expression, and potential engineering of natural product analogs.
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Affiliation(s)
- Caitlin D Deane
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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22
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Abstract
Cyclotides are bioactive macrocyclic peptides from plants that are characterized by their exceptional stability and potential applications as protein engineering or drug design frameworks. Their stability arises from their unique cyclic cystine knot structure, which combines a head-to-tail cyclic peptide backbone with three conserved disulfide bonds having a knotted topology. Cyclotides are ribosomally synthesized by plants and expressed in a wide range of tissues, including leaves, flowers, stems and roots. Here we describe recent studies that have examined the biosynthesis of cyclotides and in particular the mechanism associated with post-translational backbone cyclization.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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23
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Abstract
Cyclotides are plant-derived peptides of approximately 30 amino acids that have the characteristic structural features of a head-to-tail cyclized backbone and a cystine knot arrangement of their three conserved disulfide bonds. This article gives a personal account of the discovery of cyclotides, their characterization and their applications, based on work carried out in my laboratory over the last 20 years. It describes some of the background to their discovery and focuses on how their unique structural features lead to exceptional stability. This stability and their amenability to chemical synthesis have made it possible to use cyclotides as templates in protein engineering and drug design applications. These applications complement the interest in cyclotides deriving from their unique structures and natural function as host defense molecules.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia.
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24
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Conlan BF, Colgrave ML, Gillon AD, Guarino R, Craik DJ, Anderson MA. Insights into processing and cyclization events associated with biosynthesis of the cyclic Peptide kalata B1. J Biol Chem 2012; 287:28037-46. [PMID: 22700963 PMCID: PMC3431668 DOI: 10.1074/jbc.m112.347823] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 05/31/2012] [Indexed: 11/06/2022] Open
Abstract
Plant cyclotides are the largest family of gene-encoded cyclic proteins. They act as host defense molecules to protect plants and are promising candidates as insecticidal and nematocidal agents in agriculture. For this promise to be realized a greater understanding of the post-translational processing of these proteins is needed. Cyclotides are cleaved from precursor proteins with subsequent ligation of the N and C termini to form a continuous peptide backbone. This cyclization step is inefficient in transgenic plants and our work aims to shed light on the specificity requirements at the excision sites for cyclic peptide production. Using the prototypic cyclotide kalata B1 (kB1) expressed from the Oak1 gene, MALDI-TOF mass spectrometry was used to examine the cyclization efficiency when mutants of the Oak1 gene were expressed in transgenic Nicotiana benthamiana. Cleavage at the N terminus of the cyclotide domain occurs rapidly with no strict specificity requirements for amino acids at the cleavage site. In contrast, the C-terminal region of the cyclotide domain in the P2, P1, P1', and P2' positions is highly conserved and only specific amino acids can occupy these positions. The cyclization reaction requires an Asn at position P1 followed by a small amino acid (Ala, Gly, Ser) at the P1' position. The P2' position must be filled by Leu or Ile; in their absence an unusual post-translational modification occurs. Substitution of the P2' Leu with Ala leads to hydroxylation of the neighboring proline. Through mutational analysis this novel proline hydroxylation motif was determined to be Gly-Ala-Pro-Ser.
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Affiliation(s)
- Brendon F. Conlan
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
| | | | - Amanda D. Gillon
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
| | - Rosemary Guarino
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
| | - David J. Craik
- the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marilyn A. Anderson
- From the Department of Biochemistry, La Trobe University, Melbourne Victoria 3086
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Abstract
Circular proteins, defined as head-to-tail cyclized polypeptides originating from ribosomal synthesis, represent a novel class of natural products attracting increasing interest. From a scientific point of view, these compounds raise questions of where and why they occur in nature and how they are formed. From a rational point of view, these proteins and their structural concept may be exploited for crop protection and novel pharmaceuticals. Here, we review the current knowledge of three protein families: cyclotides and circular sunflower trypsin inhibitors from the kingdom of plants and the Amanita toxins from fungi. A particular emphasis is placed on their biological origin, structure, and activity. In addition, the opportunity for discovery of novel circular proteins and recent insights into their mechanism of action are discussed.
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Affiliation(s)
- Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, SE-75123 Uppsala, Sweden.
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27
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Velásquez JE, van der Donk WA. Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol 2011; 15:11-21. [PMID: 21095156 DOI: 10.1016/j.cbpa.2010.10.027] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/20/2010] [Accepted: 10/25/2010] [Indexed: 11/20/2022]
Abstract
In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides. In this review, we describe the strategies used for the identification of these ribosomally synthesized and posttranslationally modified peptides (RiPPs) and the structures of newly identified compounds. The increasing number of chemical entities and their remarkable structural and functional diversity may lead to novel pharmaceutical applications.
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28
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Abstract
Circular peptides and proteins of great number and diversity have been discovered in bacteria, plants, and animals. Cyclotides--disulfide-knotted and head-to-tail cyclized plant peptides that exhibit various bioactivities--are by far the largest group of circular proteins. Since their first discovery over three decades ago, there has been a lot of progress in the elucidation of structural characteristics and applications of cyclotides as novel peptide drug grafting frameworks, but there is a lack of information about their native occurrence in various plant families. The "global cyclotide adventure" was initiated as a plant collection and analysis project to advance our understanding of the origin and distribution of cyclotides in flowering plants. Here, I will provide a chronological overview of the preparation of this project, including background information on plant taxonomy and morphology, summarize, and comment on the recent progress about the discovery of cyclotide-producing plants and will give an outlook on the future of cyclotide analysis and further discoveries to be made.
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Affiliation(s)
- Christian W Gruber
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria.
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