51
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Haywood J, Schmidberger JW, James AM, Nonis SG, Sukhoverkov KV, Elias M, Bond CS, Mylne JS. Structural basis of ribosomal peptide macrocyclization in plants. eLife 2018; 7:32955. [PMID: 29384475 PMCID: PMC5834244 DOI: 10.7554/elife.32955] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions use the substrates amino terminus instead of water to deacylate, so a peptide bond is formed. How solvent-exposed plant AEPs macrocyclize is poorly understood. Here we present the crystal structure of an active plant AEP from the common sunflower, Helianthus annuus. The active site contained electron density for a tetrahedral intermediate with partial occupancy that predicted a binding mode for peptide macrocyclization. By substituting catalytic residues we could alter the ratio of cyclic to acyclic products. Moreover, we showed AEPs from other species lacking cyclic peptides can perform macrocyclization under favorable pH conditions. This structural characterization of AEP presents a logical framework for engineering superior enzymes that generate macrocyclic peptide drug leads. Most proteins are long, chain-like molecules that have two ends respectively called the N-terminus and C-terminus. However, certain proteins can close on themselves to become circular. This requires a chemical reaction between the N- and C-termini, which creates a strong bond between the two extremities. To go through this ‘cyclization’ process, a straight protein attaches to a certain type of protease, a class of enzyme that usually cuts proteins into smaller pieces. In plants that are distantly related, the same group of enzymes – called AEPs – has been selected to perform cyclization. Here, Haywood et al. study an AEP enzyme from sunflowers: they identify what about this enzyme’s structure is important to drive the complex chemical reaction that results in the protein being cyclized rather than simply cut. Using a technique called X-ray crystallography to see the positions of individual atoms in the enzyme, Haywood et al. caught a snapshot of the enzyme. Its structure explained how the enzyme’s shape can guide cyclization. In particular, the part of the enzyme that binds to the proteins, the active site, was relatively flat and open, but also flexible: this helped the N and C-termini react with each other and close the protein. Further experiments artificially mutated specific areas of the enzyme, which helped determine exactly which elements guide this succession of chemical reactions. The activity of AEPs is influenced by their local environment, such as acidity. In fact, Haywood et al. showed that certain AEPs, which do not normally carry out cyclization, can start performing this role when exposed to a different level of acidity. The pharmaceutical industry is increasingly interested in circular proteins, as these are stable, easily used by the body, and can be genetically customized to act only on specific targets. If the cyclization process is better understood, and then harnessed, new drug compounds could be produced.
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Affiliation(s)
- Joel Haywood
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Jason W Schmidberger
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Amy M James
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Samuel G Nonis
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Kirill V Sukhoverkov
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Charles S Bond
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.,The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia
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52
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Poon S, Harris KS, Jackson MA, McCorkelle OC, Gilding EK, Durek T, van der Weerden NL, Craik DJ, Anderson MA. Co-expression of a cyclizing asparaginyl endopeptidase enables efficient production of cyclic peptides in planta. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:633-641. [PMID: 29309615 PMCID: PMC5853369 DOI: 10.1093/jxb/erx422] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/04/2017] [Indexed: 05/18/2023]
Abstract
Cyclotides are ultra-stable, backbone-cyclized plant defence peptides that have attracted considerable interest in the pharmaceutical industry. This is due to their range of native bioactivities as well as their ability to stabilize other bioactive peptides within their framework. However, a hindrance to their widespread application is the lack of scalable, cost-effective production strategies. Plant-based production is an attractive, benign option since all biosynthetic steps are performed in planta. Nonetheless, cyclization in non-cyclotide-producing plants is poor. Here, we show that cyclic peptides can be produced efficiently in Nicotiana benthamiana, one of the leading plant-based protein production platforms, by co-expressing cyclotide precursors with asparaginyl endopeptidases that catalyse peptide backbone cyclization. This approach was successful in a range of other plants (tobacco, bush bean, lettuce, and canola), either transiently or stably expressed, and was applicable to both native and engineered cyclic peptides. We also describe the use of the transgenic system to rapidly identify new asparaginyl endopeptidase cyclases and interrogate their substrate sequence requirements. Our results pave the way for exploiting cyclotides for pest protection in transgenic crops as well as large-scale production of cyclic peptide pharmaceuticals in plants.
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Affiliation(s)
- Simon Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Karen S Harris
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Mark A Jackson
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Owen C McCorkelle
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Edward K Gilding
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole L van der Weerden
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - David J Craik
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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53
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Selvaraj A, Chen HT, Ya-Ting Huang A, Kao CL. Expedient on-resin modification of a peptide C-terminus through a benzotriazole linker. Chem Sci 2017; 9:345-349. [PMID: 29629103 PMCID: PMC5868309 DOI: 10.1039/c7sc03229c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/29/2017] [Indexed: 12/28/2022] Open
Abstract
Peptides with various C-terminal functionalization, including peptides and dendrimers, were prepared via SPPS and an efficient on-resin modification.
A convenient and efficient chemical toolbox was developed for the on-resin C-terminal functionalization of various peptides. By transforming resin-bound 3,4-diaminobenzoic acid species with isoamyl nitrite, the resulting resin-bound benzotriazole entity can be efficiently displaced by nucleophiles during cleavage of the peptide–resin connection in a short reaction time. The resin cleavage step allowed for the use of various nucleophiles including water, EtOH, amines, thiol, and G5 poly(amidoamino) dendrimers with yields ranging from 66% to 82% within 5 h. This method was successfully applied to prepare the elastin sequence (VPGVG)4 through on-resin ligation in 77% yield in one day and a head-to-tail cyclic peptide, sunflower trypsin inhibitor-1, in 42% yield.
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Affiliation(s)
- Anand Selvaraj
- Department of Medicinal and Applied Chemistry , Kaohsiung Medical University , Kaohsiung 807 , Taiwan .
| | - Hui-Ting Chen
- Department of Fragrance and Cosmetic Science , Kaohsiung Medical University , Kaohsiung 807 , Taiwan.,Department of Medical Research , Kaohsiung Medical University Hospital , Kaohsiung 807 , Taiwan
| | - Adela Ya-Ting Huang
- Department of Medicinal and Applied Chemistry , Kaohsiung Medical University , Kaohsiung 807 , Taiwan .
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry , Kaohsiung Medical University , Kaohsiung 807 , Taiwan . .,Department of Medical Research , Kaohsiung Medical University Hospital , Kaohsiung 807 , Taiwan.,Department of Chemistry , National Sun Yat-sen University , Kaohsiung 80424 , Taiwan
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54
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Jayasena AS, Fisher MF, Panero JL, Secco D, Bernath-Levin K, Berkowitz O, Taylor NL, Schilling EE, Whelan J, Mylne JS. Stepwise Evolution of a Buried Inhibitor Peptide over 45 My. Mol Biol Evol 2017; 34:1505-1516. [PMID: 28333296 DOI: 10.1093/molbev/msx104] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The de novo evolution of genes and the novel proteins they encode has stimulated much interest in the contribution such innovations make to the diversity of life. Most research on this de novo evolution focuses on transcripts, so studies on the biochemical steps that can enable completely new proteins to evolve and the time required to do so have been lacking. Sunflower Preproalbumin with SFTI-1 (PawS1) is an unusual albumin precursor because in addition to producing albumin it also yields a potent, bicyclic protease-inhibitor called SunFlower Trypsin Inhibitor-1 (SFTI-1). Here, we show how this inhibitor peptide evolved stepwise over tens of millions of years. To trace the origin of the inhibitor peptide SFTI-1, we assembled seed transcriptomes for 110 sunflower relatives whose evolution could be resolved by a chronogram, which allowed dates to be estimated for the various stages of molecular evolution. A genetic insertion event in an albumin precursor gene ∼45 Ma introduced two additional cleavage sites for protein maturation and conferred duality upon PawS1-Like genes such that they also encode a small buried macrocycle. Expansion of this region, including two Cys residues, enlarged the peptide ∼34 Ma and made the buried peptides bicyclic. Functional specialization into a protease inhibitor occurred ∼23 Ma. These findings document the evolution of a novel peptide inside a benign region of a pre-existing protein. We illustrate how a novel peptide can evolve without de novo gene evolution and, critically, without affecting the function of what becomes the protein host.
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Affiliation(s)
- Achala S Jayasena
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Mark F Fisher
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Jose L Panero
- Department of Integrative Biology, University of Texas, Austin, TX
| | - David Secco
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Kalia Bernath-Levin
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Nicolas L Taylor
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
| | - Edward E Schilling
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia
| | - Joshua S Mylne
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Australia
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55
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Craik DJ, Lee MH, Rehm FBH, Tombling B, Doffek B, Peacock H. Ribosomally-synthesised cyclic peptides from plants as drug leads and pharmaceutical scaffolds. Bioorg Med Chem 2017; 26:2727-2737. [PMID: 28818463 DOI: 10.1016/j.bmc.2017.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/12/2017] [Accepted: 08/06/2017] [Indexed: 12/28/2022]
Abstract
Owing to their exceptional stability and favourable pharmacokinetic properties, plant-derived cyclic peptides have recently attracted significant attention in the field of peptide-based drug design. This article describes the three major classes of ribosomally-synthesised plant peptides - the cyclotides, the PawS-derived peptides and the orbitides - and reviews their applications as leads or scaffolds in drug design. These ribosomally-produced peptides have a range of biological activities, including anti-HIV, cytotoxic and immunomodulatory activity. In addition, recent interest has focused on their use as scaffolds to stabilise bioactive peptide sequences, thereby enhancing their biopharmaceutical properties. There are now more than 30 published papers on such 'grafting' applications, most of which have been reported only in the last few years, and several such studies have reported in vivo activity of orally delivered cyclic peptides. In this article, we describe approaches to the synthesis of cyclic peptides and their pharmaceutically-grafted derivatives as well as outlining their biosynthetic routes. Finally, we describe possible bioproduction routes for pharmaceutically active cyclic peptides, involving plants and plant suspension cultures.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Meng-Han Lee
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fabian B H Rehm
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin Tombling
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin Doffek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hayden Peacock
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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56
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Franke B, James AM, Mobli M, Colgrave ML, Mylne JS, Rosengren KJ. Two proteins for the price of one: Structural studies of the dual-destiny protein preproalbumin with sunflower trypsin inhibitor-1. J Biol Chem 2017; 292:12398-12411. [PMID: 28536266 PMCID: PMC5535016 DOI: 10.1074/jbc.m117.776955] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/22/2017] [Indexed: 11/06/2022] Open
Abstract
Seed storage proteins are both an important source of nutrition for humans and essential for seedling establishment. Interestingly, unusual napin-type 2S seed storage albumin precursors in sunflowers contain a sequence that is released as a macrocyclic peptide during post-translational processing. The mechanism by which such peptides emerge from linear precursor proteins has received increased attention; however, the structural characterization of intact precursor proteins has been limited. Here, we report the 3D NMR structure of the Helianthus annuus PawS1 (preproalbumin with sunflower trypsin inhibitor-1) and provide new insights into the processing of this remarkable dual-destiny protein. In seeds, PawS1 is matured by asparaginyl endopeptidases (AEPs) into the cyclic peptide SFTI-1 (sunflower trypsin inhibitor-1) and a heterodimeric 2S albumin. The structure of PawS1 revealed that SFTI-1 and the albumin are independently folded into well-defined domains separated by a flexible linker. PawS1 was cleaved in vitro with recombinant sunflower HaAEP1 and in situ using a sunflower seed extract in a way that resembled the expected in vivo cleavages. Recombinant HaAEP1 cleaved PawS1 at multiple positions, and in situ, its flexible linker was removed, yielding fully mature heterodimeric albumin. Liberation and cyclization of SFTI-1, however, was inefficient, suggesting that specific seed conditions or components may be required for in vivo biosynthesis of SFTI-1. In summary, this study has revealed the 3D structure of a macrocyclic precursor protein and provided important mechanistic insights into the maturation of sunflower proalbumins into an albumin and a macrocyclic peptide.
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Affiliation(s)
- Bastian Franke
- School of Biomedical Sciences, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Amy M James
- School of Molecular Sciences and ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | | | - Joshua S Mylne
- School of Molecular Sciences and ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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57
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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58
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Li Y, Aboye T, Breindel L, Shekhtman A, Camarero JA. Efficient recombinant expression of SFTI-1 in bacterial cells using intein-mediated protein trans-splicing. Biopolymers 2017; 106:818-824. [PMID: 27178003 DOI: 10.1002/bip.22875] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/07/2016] [Accepted: 05/04/2016] [Indexed: 01/22/2023]
Abstract
We report for the first time the recombinant expression of bioactive wild-type sunflower trypsin inhibitor 1 (SFTI-1) inside E. coli cells by making use of intracellular protein trans-splicing in combination with a high efficient split-intein. SFTI-1 is a small backbone-cyclized polypeptide with a single disulfide bridge and potent trypsin inhibitory activity. Recombinantly produced SFTI-1 was fully characterized by NMR and was observed to actively inhibit trypsin. The in-cell expression of SFTI-1 was very efficient reaching intracellular concentration ≈ 40 µM. This study clearly demonstrates the possibility of generating genetically encoded SFTI-based peptide libraries in live E. coli cells, and is a critical first step for developing in-cell screening and directed evolution technologies using the cyclic peptide SFTI-1 as a molecular scaffold. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 818-824, 2016.
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Affiliation(s)
- Yilong Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121
| | - Teshome Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121
| | - Leonard Breindel
- Department of Chemistry, State University of New York, Albany, NY, 12222
| | | | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089-9121.,Department of Chemistry, University of Southern California, Los Angeles, CA, 90089-9121
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59
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Franke B, Jayasena AS, Fisher MF, Swedberg JE, Taylor NL, Mylne JS, Rosengren KJ. Diverse cyclic seed peptides in the Mexican zinnia (Zinnia haageana). Biopolymers 2017; 106:806-817. [PMID: 27352920 DOI: 10.1002/bip.22901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/19/2016] [Accepted: 06/25/2016] [Indexed: 12/18/2022]
Abstract
A new family of small plant peptides was recently described and found to be widespread throughout the Millereae and Heliantheae tribes of the sunflower family Asteraceae. These peptides originate from the post-translational processing of unusual seed-storage albumin genes, and have been termed PawS-derived peptides (PDPs). The prototypic family member is a 14-residue cyclic peptide with potent trypsin inhibitory activity named SunFlower Trypsin Inhibitor (SFTI-1). In this study we present the features of three new PDPs discovered in the seeds of the sunflower species Zinnia haageana by a combination of de novo transcriptomics and liquid chromatography-mass spectrometry. Two-dimensional solution NMR spectroscopy was used to elucidate their structural characteristics. All three Z. haageana peptides have well-defined folds with a head-to-tail cyclized peptide backbone and a single disulfide bond. Although two possess an anti-parallel β-sheet structure, like SFTI-1, the Z. haageana peptide PDP-21 has a more irregular backbone structure. Despite structural similarities with SFTI-1, PDP-20 was not able to inhibit trypsin, thus the functional roles of these peptides is yet to be discovered. Defining the structural features of the small cyclic peptides found in the sunflower family will be useful for guiding the exploitation of these peptides as scaffolds for grafting and protein engineering applications.
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Affiliation(s)
- Bastian Franke
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Achala S Jayasena
- School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Mark F Fisher
- School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Joakim E Swedberg
- The University of Queensland, Institute for Molecular Bioscience, St, Lucia, QLD, 4072, Australia
| | - Nicolas L Taylor
- School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Joshua S Mylne
- School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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60
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Qu H, Smithies BJ, Durek T, Craik DJ. Synthesis and Protein Engineering Applications of Cyclotides. Aust J Chem 2017. [DOI: 10.1071/ch16589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclotides are a group of plant-derived peptides with a head-to-tail cyclized backbone that is stabilized by three knotted disulfide bonds. Their exceptional stability and tolerance for residue substitutions have led to interest in their application as drug design scaffolds. To date, chemical synthesis has been the dominant methodology for producing cyclotides and their analogues. Native chemical ligation is the most common strategy to generate the cyclic backbone and has been highly successful at producing a wide range of cyclotides for studies of structure–activity relationships. Both this and other chemical approaches require a specific linker at the C-terminus and typically involve a non-directed folding (disulfide oxidation) regimen, which can sometimes be a limiting factor in final yields. Following the recent discovery of enzymes involved in peptide cyclization in planta, site-specific and highly efficient enzymatic ligations have been used for synthetic cyclotide backbone cyclization. In this review, chemical synthesis strategies and approaches involving cyclization via enzymes for the production of cyclotides are described.
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61
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Mahatmanto T. Review seed biopharmaceutical cyclic peptides: From discovery to applications. Biopolymers 2016; 104:804-14. [PMID: 26385189 DOI: 10.1002/bip.22741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/17/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Mini-proteins (or peptides) with disulfide bond/s and a cyclic backbone offer exciting opportunities for applications in medicine, as these ribosomally synthesized and posttranslationally modified peptides are exceptionally stable and amenable to grafting epitopes with desirable activities. Here I discuss important aspects of the discovery and applications of disulfide-bonded cyclic peptides from seeds, i.e., the trypsin inhibitor cyclotides and the preproalbumin with sunflower trypsin inhibitor-derived peptides, focusing on bioanalytical methods for and insights generated from their discovery as well as their potential use as engineering scaffolds for peptide-based drug design. The recent discovery of their precursors and processing enzymes could potentially enable in planta production of designer disulfide-bonded cyclic peptides, preferably in edible seeds, and address the demand for new biopharmaceutical peptides in a cost-effective manner.
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Affiliation(s)
- Tunjung Mahatmanto
- Department of Agricultural Product Technology, Faculty of Agricultural Technology, Brawijaya University, Malang, East Java, 65145, Indonesia
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62
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Natural structural diversity within a conserved cyclic peptide scaffold. Amino Acids 2016; 49:103-116. [PMID: 27695949 DOI: 10.1007/s00726-016-2333-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 09/09/2016] [Indexed: 10/20/2022]
Abstract
We recently isolated and described the evolutionary origin of a diverse class of small single-disulfide bonded peptides derived from Preproalbumin with SFTI-1 (PawS1) proteins in the seeds of flowering plants (Asteraceae). The founding member of the PawS derived peptide (PDP) family is the potent trypsin inhibitor SFTI-1 (sunflower trypsin inhibitor-1) from Helianthus annuus, the common sunflower. Here we provide additional structures and describe the structural diversity of this new class of small peptides, derived from solution NMR studies, in detail. We show that although most have a similar backbone framework with a single disulfide bond and in many cases a head-to-tail cyclized backbone, they all have their own characteristics in terms of projections of side-chains, flexibility and physiochemical properties, attributed to the variety of their sequences. Small cyclic and constrained peptides are popular as drug scaffolds in the pharmaceutical industry and our data highlight how amino acid side-chains can fine-tune conformations in these promising peptides.
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63
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Franke B, Colgrave ML, Mylne JS, Rosengren KJ. Mature forms of the major seed storage albumins in sunflower: A mass spectrometric approach. J Proteomics 2016; 147:177-186. [DOI: 10.1016/j.jprot.2016.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/15/2016] [Accepted: 05/06/2016] [Indexed: 11/27/2022]
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64
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Kuznetsova SS, Kolesanova EF, Talanova AV, Veselovsky AV. [Prospects for the design of new therapeutically significant protease inhibitors based on knottins and sunflower seed trypsin inhibitor (SFTI 1)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:353-68. [PMID: 27562989 DOI: 10.18097/pbmc20166204353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant seed knottins, mainly from the Cucurbitacea family, and sunflower seed trypsin inhibitor (SFTI 1) are the most low-molecular canonical peptide inhibitors of serine proteases. High efficiency of inhibition of various serine proteases, structure rigidity together with the possibility of limited variations of amino acid sequences, high chemical stability, lack of toxic properties, opportunity of production by either chemical synthesis or use of heterologous expression systems make these inhibitors attractive templates for design of new compounds for regulation of therapeutically significant serine protease activities. Hence the design of such compounds represents a prospective research field. The review considers structural characteristics of these inhibitors, their properties, methods of preparation and design of new analogs. Examples of successful employment of natural serine protease inhibitors belonging to knottin family and SFTI 1 as templates for the design of highly specific inhibitors of certain proteases are given.
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Affiliation(s)
| | | | - A V Talanova
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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65
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Truman AW. Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides. Beilstein J Org Chem 2016; 12:1250-68. [PMID: 27559376 PMCID: PMC4979651 DOI: 10.3762/bjoc.12.120] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/02/2016] [Indexed: 12/15/2022] Open
Abstract
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a large class of natural products that are remarkably chemically diverse given an intrinsic requirement to be assembled from proteinogenic amino acids. The vast chemical space occupied by RiPPs means that they possess a wide variety of biological activities, and the class includes antibiotics, co-factors, signalling molecules, anticancer and anti-HIV compounds, and toxins. A considerable amount of RiPP chemical diversity is generated from cyclisation reactions, and the current mechanistic understanding of these reactions will be discussed here. These cyclisations involve a diverse array of chemical reactions, including 1,4-nucleophilic additions, [4 + 2] cycloadditions, ATP-dependent heterocyclisation to form thiazolines or oxazolines, and radical-mediated reactions between unactivated carbons. Future prospects for RiPP pathway discovery and characterisation will also be highlighted.
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Affiliation(s)
- Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
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66
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Borra R, Camarero JA. Recombinant expression of backbone-cyclized polypeptides. Biopolymers 2016; 100:502-9. [PMID: 23893781 DOI: 10.1002/bip.22306] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/13/2013] [Accepted: 05/28/2013] [Indexed: 01/08/2023]
Abstract
Here we review the different biochemical approaches available for the expression of backbone-cyclized polypeptides, including peptides and proteins. These methods allow for the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Polypeptide circularization provides a valuable tool to study the effects of topology on protein stability and folding kinetics. Furthermore, having biosynthetic access to backbone-cyclized polypeptides makes the production of genetically encoded libraries of cyclic polypeptides possible. The production of such libraries, which was previously restricted to the domain of synthetic chemistry, now offers biologists access to highly diverse and stable molecular libraries that can be screened using high-throughput methods for the rapid selection of novel cyclic polypeptide sequences with new biological activities.
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Affiliation(s)
- Radhika Borra
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90033
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67
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Jayasena AS, Franke B, Rosengren J, Mylne JS. A tripartite approach identifies the major sunflower seed albumins. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:613-629. [PMID: 26767835 DOI: 10.1007/s00122-015-2653-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/11/2015] [Indexed: 06/05/2023]
Abstract
We have used a combination of genomic, transcriptomic, and proteomic approaches to identify the napin-type albumin genes in sunflower and define their contributions to the seed albumin pool. Seed protein content is determined by the expression of what are typically large gene families. A major class of seed storage proteins is the napin-type, water soluble albumins. In this work we provide a comprehensive analysis of the napin-type albumin content of the common sunflower (Helianthus annuus) by analyzing a draft genome, a transcriptome and performing a proteomic analysis of the seed albumin fraction. We show that although sunflower contains at least 26 genes for napin-type albumins, only 15 of these are present at the mRNA level. We found protein evidence for 11 of these but the albumin content of mature seeds is dominated by the encoded products of just three genes. So despite high genetic redundancy for albumins, only a small sub-set of this gene family contributes to total seed albumin content. The three genes identified as producing the majority of sunflower seed albumin are potential future candidates for manipulation through genetics and breeding.
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Affiliation(s)
- Achala S Jayasena
- School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Bastian Franke
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Joshua S Mylne
- School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.
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68
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Efficient backbone cyclization of linear peptides by a recombinant asparaginyl endopeptidase. Nat Commun 2015; 6:10199. [PMID: 26680698 PMCID: PMC4703859 DOI: 10.1038/ncomms10199] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/16/2015] [Indexed: 01/05/2023] Open
Abstract
Cyclotides are diverse plant backbone cyclized peptides that have attracted interest as pharmaceutical scaffolds, but fundamentals of their biosynthetic origin remain elusive. Backbone cyclization is a key enzyme-mediated step of cyclotide biosynthesis and confers a measure of stability on the resultant cyclotide. Furthermore, cyclization would be desirable for engineered peptides. Here we report the identification of four asparaginyl endopeptidases (AEPs), proteases implicated in cyclization, from the cyclotide-producing plant Oldenlandia affinis. We recombinantly express OaAEP1b and find it functions preferably as a cyclase by coupling C-terminal cleavage of propeptide substrates with backbone cyclization. Interestingly, OaAEP1b cannot cleave at the N-terminal site of O. affinis cyclotide precursors, implicating additional proteases in cyclotide biosynthesis. Finally, we demonstrate the broad utility of this enzyme by cyclization of peptides unrelated to cyclotides. We propose that recombinant OaAEP1b is a powerful tool for use in peptide engineering applications where increased stability of peptide products is desired. Cyclotides are plant backbone-cyclised peptides with potential as pharmaceutical scaffolds. Here the authors report on the efficient backbone cyclization of cyclotides and unrelated peptides by a newly identified asparaginyl endopeptidase from Oldenlandia affinis.
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69
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Structure and function of legumain in health and disease. Biochimie 2015; 122:126-50. [PMID: 26403494 DOI: 10.1016/j.biochi.2015.09.022] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022]
Abstract
The last years have seen a steady increase in our understanding of legumain biology that is driven from two largely uncoupled research arenas, the mammalian and the plant legumain field. Research on legumain, which is also referred to as asparaginyl endopeptidase (AEP) or vacuolar processing enzyme (VPE), is slivered, however. Here we summarise recent important findings and put them into a common perspective. Legumain is usually associated with its cysteine endopeptidase activity in lysosomes where it contributes to antigen processing for class II MHC presentation. However, newly recognized functions disperse previously assumed boundaries with respect to their cellular compartmentalisation and enzymatic activities. Legumain is also found extracellularly and even translocates to the cytosol and the nucleus, with seemingly incompatible pH and redox potential. These different milieus translate into changes of legumain's molecular properties, including its (auto-)activation, conformational stability and enzymatic functions. Contrasting its endopeptidase activity, legumain can develop a carboxypeptidase activity which remains stable at neutral pH. Moreover, legumain features a peptide ligase activity, with intriguing mechanistic peculiarities in plant and human isoforms. In pathological settings, such as cancer or Alzheimer's disease, the proper association of legumain activities with the corresponding cellular compartments is breached. Legumain's increasingly recognized physiological and pathological roles also indicate future research opportunities in this vibrant field.
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70
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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] [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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71
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Bernath-Levin K, Nelson C, Elliott AG, Jayasena AS, Millar AH, Craik DJ, Mylne JS. Peptide macrocyclization by a bifunctional endoprotease. ACTA ACUST UNITED AC 2015; 22:571-82. [PMID: 25960260 DOI: 10.1016/j.chembiol.2015.04.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/16/2015] [Accepted: 04/03/2015] [Indexed: 11/16/2022]
Abstract
Proteases usually cleave peptides, but under some conditions, they can ligate them. Seeds of the common sunflower contain the 14-residue, backbone-macrocyclic peptide sunflower trypsin inhibitor 1 (SFTI-1) whose maturation from its precursor has a genetic requirement for asparaginyl endopeptidase (AEP). To provide more direct evidence, we developed an in situ assay and used (18)O-water to demonstrate that SFTI-1 is excised and simultaneously macrocyclized from its linear precursor. The reaction is inefficient in situ, but a newfound breakdown pathway can mask this inefficiency by reducing the internal disulfide bridge of any acyclic-SFTI to thiols before degrading it. To confirm AEP can directly perform the excision/ligation, we produced several recombinant plant AEPs in E. coli, and one from jack bean could catalyze both a typical cleavage reaction and cleavage-dependent, intramolecular transpeptidation to create SFTI-1. We propose that the evolution of ligating endoproteases enables plants like sunflower and jack bean to stabilize bioactive peptides.
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Affiliation(s)
- Kalia Bernath-Levin
- The University of Western Australia, School of Chemistry and Biochemistry, 35 Stirling Highway, Crawley, Perth 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Clark Nelson
- ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Alysha G Elliott
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Achala S Jayasena
- The University of Western Australia, School of Chemistry and Biochemistry, 35 Stirling Highway, Crawley, Perth 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - David J Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Chemistry and Biochemistry, 35 Stirling Highway, Crawley, Perth 6009, Australia; ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth 6009, Australia.
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72
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Li Y, Bi T, Camarero JA. Chemical and biological production of cyclotides. ADVANCES IN BOTANICAL RESEARCH 2015; 76:271-303. [PMID: 27064329 PMCID: PMC4822716 DOI: 10.1016/bs.abr.2015.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cyclotides are fascinating naturally occurring micro-proteins (≈30 residues long) present in several plant families, and display various biological properties such as protease inhibitory, anti-microbial, insecticidal, cytotoxic, anti-HIV and hormone-like activities. Cyclotides share a unique head-to-tail circular knotted topology of three disulfide bridges, with one disulfide penetrating through a macrocycle formed by the two other disulfides and interconnecting peptide backbones, forming what is called a cystine knot topology. This cyclic cystine knot (CCK) framework gives the cyclotides exceptional rigidity, resistance to thermal and chemical denaturation, and enzymatic stability against degradation. Interestingly, cyclotides have been shown to be orally bioavailable, and other cyclotides have been shown to cross the cell membranes. Moreover, recent reports have also shown that engineered cyclotides can be efficiently used to target extracellular and intracellular protein-protein interactions, therefore making cyclotides ideal tools for drug development to selectively target protein-protein interactions. In this work we will review all the available methods for production of these interesting proteins using chemical or biological methods.
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Affiliation(s)
- Yilong Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Bi
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033, USA
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73
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Mahatmanto T, Mylne JS, Poth AG, Swedberg JE, Kaas Q, Schaefer H, Craik DJ. The evolution of Momordica cyclic peptides. Mol Biol Evol 2014; 32:392-405. [PMID: 25376175 DOI: 10.1093/molbev/msu307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cyclic proteins have evolved for millions of years across all kingdoms of life to confer structural stability over their acyclic counterparts while maintaining intrinsic functional properties. Here, we show that cyclic miniproteins (or peptides) from Momordica (Cucurbitaceae) seeds evolved in species that diverged from an African ancestor around 19 Ma. The ability to achieve head-to-tail cyclization of Momordica cyclic peptides appears to have been acquired through a series of mutations in their acyclic precursor coding sequences following recent and independent gene expansion event(s). Evolutionary analysis of Momordica cyclic peptides reveals sites that are under selection, highlighting residues that are presumably constrained for maintaining their function as potent trypsin inhibitors. Molecular dynamics of Momordica cyclic peptides in complex with trypsin reveals site-specific residues involved in target binding. In a broader context, this study provides a basis for selecting Momordica species to further investigate the biosynthesis of the cyclic peptides and for constructing libraries that may be screened against evolutionarily related serine proteases implicated in human diseases.
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Affiliation(s)
- Tunjung Mahatmanto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Chemistry and Biochemistry & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth, WA, Australia
| | - Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
| | - Hanno Schaefer
- Plant Biodiversity Research, Technische Universität München, Freising, Germany
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, Australia
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74
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Shariff L, Zhu Y, Cowper B, Di WL, Macmillan D. Sunflower trypsin inhibitor (SFTI-1) analogues of synthetic and biological origin via N→S acyl transfer: potential inhibitors of human Kallikrein-5 (KLK5). Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.06.059] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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75
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Abstract
Cyclic peptides are found in a diverse range of organisms and are characterized by their stability and role in defense. Why is only one class of cyclic peptides found in mammals? Possibly we have not looked hard enough for them, or the technologies needed to identify them are not fully developed. We also do not yet understand their intriguing biosynthesis from two separate gene products. Addressing these challenges will require the application of chemical tools and insights from other classes of cyclic peptides. Herein, we highlight recent developments in the characterization of theta defensins and describe the important role that chemistry has played in delineating their modes of action. Furthermore, we emphasize the potential of theta defensins as antimicrobial agents and scaffolds for peptide drug design.
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Affiliation(s)
- Anne C. Conibear
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD (Australia) http://www.imb.uq.edu.au/index.html?page=11695
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072 QLD (Australia) http://www.imb.uq.edu.au/index.html?page=11695
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76
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77
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Mylne JS, Hara-Nishimura I, Rosengren KJ. Seed storage albumins: biosynthesis, trafficking and structures. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:671-677. [PMID: 32481022 DOI: 10.1071/fp14035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/24/2014] [Indexed: 06/11/2023]
Abstract
Seed storage albumins are water-soluble and highly abundant proteins that are broken-down during seed germination to provide nitrogen and sulfur for the developing seedling. During seed maturation these proteins are subject to post-translational modifications and trafficking before they are deposited in great quantity and with great stability in dedicated vacuoles. This review will cover the subcellular movement, biochemical processing and mature structures of seed storage napins.
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Affiliation(s)
- Joshua S Mylne
- The University of Western Australia, School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
| | - Ikuko Hara-Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake cho Sakyo-ku, Kyoto, 606-8502, Japan
| | - K Johan Rosengren
- The University of Queensland, School of Biomedical Sciences, Brisbane, Qld 4072, Australia
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78
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Burman R, Gunasekera S, Strömstedt AA, Göransson U. Chemistry and biology of cyclotides: circular plant peptides outside the box. JOURNAL OF NATURAL PRODUCTS 2014; 77:724-36. [PMID: 24527877 DOI: 10.1021/np401055j] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cyclotides stand out as the largest family of circular proteins of plant origin hitherto known, with more than 280 sequences isolated at peptide level and many more predicted from gene sequences. Their unusual stability resulting from the signature cyclic cystine knot (CCK) motif has triggered a broad interest in these molecules for potential therapeutic and agricultural applications. Since the time of the first cyclotide discovery, our laboratory in Uppsala has been engaged in cyclotide discovery as well as the development of protocols to isolate and characterize these seamless peptides. We have also developed methods to chemically synthesize cyclotides by Fmoc-SPPS, which are useful in protein grafting applications. In this review, experience in cyclotide research over two decades and the recent literature related to their structures, synthesis, and folding as well the recent proof-of-concept findings on their use as "epitope" stabilizing scaffolds are summarized.
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Affiliation(s)
- Robert Burman
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University , Biomedical Centre, Box 574, SE-751 23 Uppsala, Sweden
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79
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Brust A, Schroeder CI, Alewood PF. High-Throughput Synthesis of Peptide α-Thioesters: A Safety Catch Linker Approach Enabling Parallel Hydrogen Fluoride Cleavage. ChemMedChem 2014; 9:1038-46. [DOI: 10.1002/cmdc.201300524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 11/06/2022]
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80
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Elliott AG, Delay C, Liu H, Phua Z, Rosengren KJ, Benfield AH, Panero JL, Colgrave ML, Jayasena AS, Dunse KM, Anderson MA, Schilling EE, Ortiz-Barrientos D, Craik DJ, Mylne JS. Evolutionary origins of a bioactive peptide buried within Preproalbumin. THE PLANT CELL 2014; 26:981-95. [PMID: 24681618 PMCID: PMC4001405 DOI: 10.1105/tpc.114.123620] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 01/27/2014] [Accepted: 03/04/2014] [Indexed: 05/25/2023]
Abstract
The de novo evolution of proteins is now considered a frequented route for biological innovation, but the genetic and biochemical processes that lead to each newly created protein are often poorly documented. The common sunflower (Helianthus annuus) contains the unusual gene PawS1 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage albumin; however, in a region usually discarded during albumin maturation, its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide with a motif homologous to unrelated inhibitors from legumes, cereals, and frogs. To understand how PawS1 acquired this additional peptide with novel biochemical functionality, we cloned PawS1 genes and showed that this dual destiny is over 18 million years old. This new family of mostly backbone-cyclic peptides is structurally diverse, but the protease-inhibitory motif was restricted to peptides from sunflower and close relatives from its subtribe. We describe a widely distributed, potential evolutionary intermediate PawS-Like1 (PawL1), which is matured into storage albumin, but makes no stable peptide despite possessing residues essential for processing and cyclization from within PawS1. Using sequences we cloned, we retrodict the likely stepwise creation of PawS1's additional destiny within a simple albumin precursor. We propose that relaxed selection enabled SFTI-1 to evolve its inhibitor function by converging upon a successful sequence and structure.
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Affiliation(s)
- Alysha G. Elliott
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Christina Delay
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Huanle Liu
- School of Biological Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Zaiyang Phua
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - K. Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane 4072, Australia
| | - Aurélie H. Benfield
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Jose L. Panero
- Section of Integrative Biology, University of Texas, Austin, Texas 78712
| | | | - Achala S. Jayasena
- The University of Western Australia, School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth 6009, Australia
| | - Kerry M. Dunse
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Marilyn A. Anderson
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Edward E. Schilling
- University of Tennessee, Department of Ecology and Evolutionary Biology, Knoxville, Tennessee 37996
| | | | - David J. Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
| | - Joshua S. Mylne
- The University of Queensland, Institute for Molecular Bioscience, Brisbane 4072, Australia
- The University of Western Australia, School of Chemistry and Biochemistry and ARC Centre of Excellence in Plant Energy Biology, Crawley, Perth 6009, Australia
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81
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Jayasena AS, Secco D, Bernath-Levin K, Berkowitz O, Whelan J, Mylne JS. Next generation sequencing and de novo transcriptomics to study gene evolution. PLANT METHODS 2014; 10:34. [PMID: 25364374 PMCID: PMC4216380 DOI: 10.1186/1746-4811-10-34] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/08/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Studying gene evolution in non-model species by PCR-based approaches is limited to highly conserved genes. The plummeting cost of next generation sequencing enables the application of de novo transcriptomics to any species. RESULTS Here we describe how to apply de novo transcriptomics to pursue the evolution of a single gene of interest. We follow a rapidly evolving seed protein that encodes small, stable peptides. We use software that needs limited bioinformatics background and assemble four de novo seed transcriptomes. To demonstrate the quality of the assemblies, we confirm the predicted genes at the peptide level on one species which has over ten copies of our gene of interest. We explain strategies that favour assembly of low abundance genes, what assembly parameters help capture the maximum number of transcripts, how to develop a suite of control genes to test assembly quality and we compare several sequence depths to optimise cost and data volume. CONCLUSIONS De novo transcriptomics is an effective approach for studying gene evolution in species for which genome support is lacking.
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Affiliation(s)
- Achala S Jayasena
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - David Secco
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - Kalia Bernath-Levin
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - Oliver Berkowitz
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
- />The University of Western Australia, School of Plant Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
| | - James Whelan
- />La Trobe University, Department of Botany, School of Life Sciences & ARC Centre of Excellence in Plant Energy Biology, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Melbourne, Bundoora Victoria 3086 Australia
| | - Joshua S Mylne
- />The University of Western Australia, School of Chemistry and Biochemistry & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley Perth, 6009 Australia
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82
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Craik DJ, Malik U. Cyclotide biosynthesis. Curr Opin Chem Biol 2013; 17:546-54. [PMID: 23809361 DOI: 10.1016/j.cbpa.2013.05.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/28/2013] [Indexed: 10/26/2022]
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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83
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Craik DJ. Joseph Rudinger memorial lecture: discovery and applications of cyclotides. J Pept Sci 2013; 19:393-407. [PMID: 23737440 DOI: 10.1002/psc.2523] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 05/02/2013] [Indexed: 12/31/2022]
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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84
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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85
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Quimbar P, Malik U, Sommerhoff CP, Kaas Q, Chan LY, Huang YH, Grundhuber M, Dunse K, Craik DJ, Anderson MA, Daly NL. High-affinity cyclic peptide matriptase inhibitors. J Biol Chem 2013; 288:13885-96. [PMID: 23548907 DOI: 10.1074/jbc.m113.460030] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sunflower trypsin inhibitor-1 (SFTI-1) and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II) are potent protease inhibitors comprising a cyclic backbone. RESULTS Elucidation of structure-activity relationships for SFTI-1 and MCoTI-II was used to design inhibitors with enhanced inhibitory activity. CONCLUSION An analog of MCoTI-II is one of the most potent inhibitors of matriptase. SIGNIFICANCE These results provide a solid basis for the design of selective peptide inhibitors of matriptase with therapeutic potential. The type II transmembrane serine protease matriptase is a key activator of multiple signaling pathways associated with cell proliferation and modification of the extracellular matrix. Deregulated matriptase activity correlates with a number of diseases, including cancer and hence highly selective matriptase inhibitors may have therapeutic potential. The plant-derived cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), is a promising drug scaffold with potent matriptase inhibitory activity. In the current study we have analyzed the structure-activity relationships of SFTI-1 and Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a structurally divergent trypsin inhibitor from Momordica cochinchinensis that also contains a cyclic backbone. We show that MCoTI-II is a significantly more potent matriptase inhibitor than SFTI-1 and that all alanine mutants of both peptides, generated using positional scanning mutagenesis, have decreased trypsin affinity, whereas several mutations either maintain or result in enhanced matriptase inhibitory activity. These intriguing results were used to design one of the most potent matriptase inhibitors known to date with a 290 pm equilibrium dissociation constant, and provide the first indication on how to modulate affinity for matriptase over trypsin in cyclic peptides. This information might be useful for the design of more selective and therapeutically relevant inhibitors of matriptase.
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Affiliation(s)
- Pedro Quimbar
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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86
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Barber CJS, Pujara PT, Reed DW, Chiwocha S, Zhang H, Covello PS. The two-step biosynthesis of cyclic peptides from linear precursors in a member of the plant family Caryophyllaceae involves cyclization by a serine protease-like enzyme. J Biol Chem 2013; 288:12500-10. [PMID: 23486480 DOI: 10.1074/jbc.m112.437947] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Caryophyllaceae-type cyclic peptides (CPs) of 5-12 proteinogenic amino acids occur in 10 plant families. In Saponaria vaccaria (Caryophyllaceae), they have been shown to be formed from linear peptide precursors derived from ribosomal translation. There is also evidence for such precursors in other members of the Caryophyllaceae, Rutaceae, and Linaceae families. The biosynthesis of CP in the developing seeds of S. vaccaria was investigated with respect to the enzymes involved in precursor processing. Through biochemical assays with seed extracts and synthetic peptides, an enzyme named oligopeptidase 1 (OLP1) was found that catalyzes the cleavage of intermediates at the N terminus of the incipient CP. A second enzyme, peptide cyclase 1 (PCY1), which was separated chromatographically from OLP1, was found to act on the product of OLP1, giving rise to a cyclic peptide and concomitant removal of a C-terminal flanking sequence. PCY1 was partially purified, and using the methods of proteomics, a full-length cDNA clone encoding an enzyme matching the properties of PCY1 was obtained. The substrate specificity of purified recombinant PCY1, believed to be the first cloned plant enzyme whose function is peptide cyclization, was tested with synthetic peptides. The results are discussed in the light of CP biosynthetic systems of other organisms.
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Affiliation(s)
- Carla J S Barber
- National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
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87
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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] [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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88
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Poth AG, Mylne JS, Grassl J, Lyons RE, Millar AH, Colgrave ML, Craik DJ. Cyclotides associate with leaf vasculature and are the products of a novel precursor in petunia (Solanaceae). J Biol Chem 2012; 287:27033-46. [PMID: 22700981 DOI: 10.1074/jbc.m112.370841] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclotides are a large family of plant peptides that are structurally defined by their cyclic backbone and a trifecta of disulfide bonds, collectively known as the cyclic cystine knot (CCK) motif. Structurally similar cyclotides have been isolated from plants within the Rubiaceae, Violaceae, and Fabaceae families and share the CCK motif with trypsin-inhibitory knottins from a plant in the Cucurbitaceae family. Cyclotides have previously been reported to be encoded by dedicated genes or as a domain within a knottin-encoding PA1-albumin-like gene. Here we report the discovery of cyclotides and related non-cyclic peptides we called "acyclotides" from petunia of the agronomically important Solanaceae plant family. Transcripts for petunia cyclotides and acyclotides encode the shortest known cyclotide precursors. Despite having a different precursor structure, their sequences suggest that petunia cyclotides mature via the same biosynthetic route as other cyclotides. We assessed the spatial distribution of cyclotides within a petunia leaf section by MALDI imaging and observed that the major cyclotide component Phyb A was non-uniformly distributed. Dissected leaf midvein extracts contained significantly higher concentrations of this cyclotide compared with the lamina and outer margins of leaves. This is the third distinct type of cyclotide precursor, and Solanaceae is the fourth phylogenetically disparate plant family to produce these structurally conserved cyclopeptides, suggesting either convergent evolution upon the CCK structure or movement of cyclotide-encoding sequences within the plant kingdom.
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Affiliation(s)
- Aaron G Poth
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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89
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Abstract
Circular proteins have now been discovered in all kingdoms of life and are characterized by their exceptional stability and the diversity of their biological activities, primarily in the realm of host defense functions. This thematic minireview series provides an overview of the distribution, evolution, activities, and biological synthesis of circular proteins. It also reviews approaches that biological chemists are taking to develop synthetic methods for making circular proteins in the laboratory. These approaches include solid-phase peptide synthesis based on an adaption of native chemical ligation technology and recombinant DNA approaches that are amenable to the in-cell production of cyclic peptide libraries. The thioester-mediated native chemical ligation approach mimics, to some extent, elements of the natural biosynthetic reaction, which, for disulfide-rich cyclic peptides, appears to involve asparaginyl endopeptidase-mediated processing from larger precursor proteins.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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90
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Göransson U, Burman R, Gunasekera S, Strömstedt AA, Rosengren KJ. Circular proteins from plants and fungi. J Biol Chem 2012; 287:27001-6. [PMID: 22700984 DOI: 10.1074/jbc.r111.300129] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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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91
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Abstract
Here, we review the use of different biochemical approaches for biological synthesis of circular or backbone-cyclized proteins and peptides. These methods allow the production of circular polypeptides either in vitro or in vivo using standard recombinant DNA expression techniques. Protein circularization can significantly impact protein engineering and research in protein folding. Basic polymer theory predicts that circularization should lead to a net thermodynamic stabilization of a folded protein by reducing the entropy associated with the unfolded state. Protein cyclization also provides a valuable tool for exploring the effects of topology on protein folding kinetics. Furthermore, the biological production of cyclic polypeptides makes possible the production of cyclic polypeptide libraries. The generation of such libraries, which was previously restricted to the domain of synthetic chemists, now offers biologists access to highly diverse and stable molecular libraries for probing protein structure and function.
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Affiliation(s)
- Teshome L Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90033, USA
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92
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Choi SJ, Jeong WJ, Kang SK, Lee M, Kim E, Ryu DY, Lim YB. Differential Self-Assembly Behaviors of Cyclic and Linear Peptides. Biomacromolecules 2012; 13:1991-5. [DOI: 10.1021/bm3005947] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sung-ju Choi
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering and§Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 120-749, Korea
| | - Woo-jin Jeong
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering and§Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 120-749, Korea
| | - Seong-Kyun Kang
- Center for Bio-Responsive Assembly
and Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | - Myongsoo Lee
- Center for Bio-Responsive Assembly
and Department of Chemistry, Seoul National University, Seoul 151-747, Korea
| | | | | | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering and§Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 120-749, Korea
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93
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Gould A, Ji Y, Aboye TL, Camarero JA. Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. Curr Pharm Des 2012; 17:4294-307. [PMID: 22204428 DOI: 10.2174/138161211798999438] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 09/15/2011] [Indexed: 11/22/2022]
Abstract
Cyclotides are a unique and growing family of backbone cyclized peptides that also contain a cystine knot motif built from six conserved cysteine residues. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Aside from the conserved residues forming the cystine knot, cyclotides have been shown to have high variability in their sequences. Consisting of over 160 known members, cyclotides have many biological activities, ranging from anti-HIV, antimicrobial, hemolytic, and uterotonic capabilities; additionally, some cyclotides have been shown to have cell penetrating properties. Originally discovered and isolated from plants, cyclotides can also be produced synthetically and recombinantly. The high sequence variability, stability, and cell penetrating properties of cyclotides make them potential scaffolds to be used to graft known active peptides or engineer peptide-based drug design. The present review reports recent findings in the biological diversity and therapeutic potential of natural and engineered cyclotides.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
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94
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Gründemann C, Koehbach J, Huber R, Gruber CW. Do plant cyclotides have potential as immunosuppressant peptides? JOURNAL OF NATURAL PRODUCTS 2012; 75:167-74. [PMID: 22272797 PMCID: PMC3399773 DOI: 10.1021/np200722w] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cyclotides are an abundant and diverse group of ribosomally synthesized plant peptides containing a cyclic cystine-knotted structure that confers them with remarkable stability. They are explored for their distribution in plants, although little is known about the individual peptide content of a single species. Therefore, we chemically analyzed the crude extract of the coffee-family plant Oldenlandia affinis using a rapid peptidomics workflow utilizing nano-LC-MS, peptide reconstruct with database identification, and MS/MS automated sequence analysis to determine its cyclotide content. Biologically, cyclotides are mainly explored for applications in agriculture and drug design; here we report their growth-inhibiting effects on primary cells of the human immune system using biological and immunological end points in cell-based test systems. LC-MS quantification of the active O. affinis plant extract triggered the characterization of the antiproliferative activity of kalata B1, one of the most abundant cyclotides in this extract, on primary activated human lymphocytes. The effect has a defined concentration range and was not due to cytotoxicity, thus opening a new avenue to utilize native and synthetically optimized plant cyclotides for applications in immune-related disorders and as immunosuppressant peptides.
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Affiliation(s)
- Carsten Gründemann
- Center for Complementary Medicine, Department of Environmental Health Sciences, University Medical Center Freiburg, Breisacher Straße 115B, D-79111 Freiburg, Germany
| | - Johannes Koehbach
- Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, A-1090 Vienna, Austria
| | - Roman Huber
- Center for Complementary Medicine, Department of Environmental Health Sciences, University Medical Center Freiburg, Breisacher Straße 115B, D-79111 Freiburg, Germany
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstraße 17, A-1090 Vienna, Austria
- Corresponding Author: Tel: +43-(0)1-4277-62511. Fax: +43-(0)1-4277-9623.
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95
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Craik DJ, Swedberg JE, Mylne JS, Cemazar M. Cyclotides as a basis for drug design. Expert Opin Drug Discov 2012; 7:179-94. [PMID: 22468950 DOI: 10.1517/17460441.2012.661554] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cyclotides are plant-made defence proteins with a head-to-tail cyclic backbone combined with a conserved, six cystine knot. They have a range of biological activities, including uterotonic and anti-HIV activity, which have attracted attention to their potential pharmaceutical applications. Furthermore, their unique structures and high stability make them appealing as peptide-based templates for drug design applications. Methods have been developed for their production, including solid phase peptide synthesis as well as recombinant methods. AREAS COVERED This article reviews the recent literature associated with therapeutic applications of naturally occurring and synthetically modified cyclotides. It includes applications of cyclotides and cyclotide-like molecules as peptide-based drug leads and diagnostic agents. EXPERT OPINION The ultra-stable cyclotides are promising templates for drug development applications and are currently being assessed for the potential breadth of their applications. For synthetic versions of cyclotides to enter human clinical trials further studies to examine their biopharmaceutical properties and toxicities are required. However, several promising proof-of-concept studies have established that pharmaceutically relevant bioactive peptide sequences can be grafted into cyclotide frameworks and thereby stabilised, while maintaining biological activity. These studies include examples directed at cancer, cardiovascular disease and infectious diseases. Solid phase peptide synthesis has been the preferred approach for making pharmaceutically modified cyclotides so far, but promising progress is being made in biological approaches to cyclotide production.
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Affiliation(s)
- David J Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Australia.
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96
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Abstract
Peptide-based toxins have attracted much attention in recent years for their exciting potential applications in drug design and development. This interest has arisen because toxins are highly potent and selectively target a range of physiologically important receptors. However, peptides suffer from a number of disadvantages, including poor in vivo stability and poor bioavailability. A number of naturally occurring cyclic peptides have been discovered in plants, animals, and bacteria that have exceptional stability and potentially ameliorate these disadvantages. The lessons learned from studies of the structures, stabilities, and biological activities of these cyclic peptides can be applied to the reengineering of toxins that are not naturally cyclic but are amenable to cyclization. In this chapter, we describe solid-phase chemical synthetic methods for the reengineering of peptide toxins to improve their suitability as therapeutic, diagnostic, or imaging agents. The focus is on small disulfide-rich peptides from the venoms of cone snails and scorpions, but the technology is potentially widely applicable to a number of other peptide-based toxins.
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Affiliation(s)
- Richard J Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
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97
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Thorstholm L, Craik D. Discovery and applications of naturally occurring cyclic peptides. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e1-e70. [PMID: 24064240 DOI: 10.1016/j.ddtec.2011.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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98
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99
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Lee J, Bogyo M. Synthesis and evaluation of aza-peptidyl inhibitors of the lysosomal asparaginyl endopeptidase, legumain. Bioorg Med Chem Lett 2011; 22:1340-3. [PMID: 22243962 DOI: 10.1016/j.bmcl.2011.12.079] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/13/2011] [Accepted: 12/14/2011] [Indexed: 11/16/2022]
Abstract
Legumain or asparaginly endopeptidase (AEP) is a lysosomal cysteine protease with a high level of specificity for cleavage of protein substrates after an asparagine residue. It is also capable of cleaving after aspartic acids sites when in the acidic environment of the lysosome. Legumain expression and activity is linked to a number of pathological conditions including cancer, atherosclerosis and inflammation, yet its biological role in these pathologies is not well-understood. Highly potent and selective inhibitors of legumain would not only be valuable for studying the functional roles of legumain in these conditions, but may have therapeutic potential as well. We describe here the design, synthesis and in vitro evaluation of selective legumain inhibitors based on the aza-asparaginyl scaffold. We synthesized a library of aza-peptidyl inhibitors with various non-natural amino acids and different electrophilic warheads, and characterized the kinetic properties of inactivation of legumain. We also synthesized fluorescently labeled inhibitors to investigate cell permeability and selectivity of the compounds. The inhibitors have second order rate constants of up to 5 × 10(4)M(-1)s(-1) and IC(50) values as low as 4 nM against recombinant mouse legumain. In addition, the inhibitors are highly selective toward legumain and have little or no cross-reactivity with cathepsins. Overall, we have identified several valuable new inhibitors of legumain that can be used to study legumain function in multiple disease models.
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Affiliation(s)
- Jiyoun Lee
- Department of Pathology and Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Dr. Stanford, CA 94305-5324, USA.
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100
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