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Chekan JR, Mydy LS, Pasquale MA, Kersten RD. Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides. Nat Prod Rep 2024; 41:1020-1059. [PMID: 38411572 PMCID: PMC11253845 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Indexed: 02/28/2024]
Abstract
Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.
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Affiliation(s)
- Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Michael A Pasquale
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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2
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Sidharthan VK, Reddy V, Kiran G, Rajeswari V, Baranwal VK, Kumar MK, Kumar KS. Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae. Arch Virol 2024; 169:150. [PMID: 38898334 DOI: 10.1007/s00705-024-06076-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India.
| | - Vijayprakash Reddy
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - G Kiran
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - V Rajeswari
- School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - M Kiran Kumar
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - K Sudheer Kumar
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
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3
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Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
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4
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Debat H, Bejerman N. Two novel flavi-like viruses shed light on the plant-infecting koshoviruses. Arch Virol 2023; 168:184. [PMID: 37338667 DOI: 10.1007/s00705-023-05813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/09/2023] [Indexed: 06/21/2023]
Abstract
The family Flaviviridae is composed of viruses with a positive-sense single-stranded RNA genome and includes viruses that are important veterinary and human pathogens. Most members of the family are arthropod- and vertebrate-infecting viruses, but more recently, divergent flavi-like viruses have been identified in marine invertebrate and vertebrate hosts. The striking discovery of gentian Kobu-sho-associated virus (GKaV), along with a recent report of a related virus from carrot, has expanded the known host range of flavi-like viruses to plants, suggesting they could be grouped in a proposed genus tentatively named "Koshovirus". Here, we report the identification and characterization of two novel RNA viruses that show a genetic and evolutionary relationship to the previously identified "koshoviruses". Their genome sequences were obtained from transcriptomic datasets of the flowering plants Coptis teeta and Sonchus asper. These two new viruses, which we have named "coptis flavi-like virus 1" (CopFLV1) and "sonchus flavi-like virus 1" (SonFLV1), are members of novel species characterized by the longest monopartite RNA genome observed so far among plant-associated RNA viruses, which is ca. 24 kb in size. Structural and functional annotations of the polyproteins of all koshoviruses resulted in the detection not only of the expected helicase and RNA-dependent RNA polymerase but also of several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains. Phylogenetic analysis showed that CopFLV1, SonFLV1, GKaV, and the carrot flavi-like virus were grouped together in a monophyletic clade, strongly supporting the recent proposal for creation of the genus "Koshovirus" for the group of related plant-infecting flavi-like viruses.
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Affiliation(s)
- Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina.
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina.
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Sidharthan VK, Rajeswari V, Baranwal VK. Broadening the host range and genetic diversity of waikaviruses. Virology 2023; 582:106-113. [PMID: 37043910 DOI: 10.1016/j.virol.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023]
Abstract
Waikaviruses are monopartite, positive sense, single-stranded RNA viruses that cause economically important plant diseases. Despite their importance, waikaviruses are poorly understood and only ten members are currently recognized. The present study on Sequence Read Archive (SRA)-based data-driven virus discovery (DDVD) identified 22 putative new waikaviruses, nearly doubling the number of known waikaviruses, in SRA libraries of diverse plant species, from ferns to trees. Besides, a highly divergent secoviral sequence with distinct genome features was identified in a wheat transcriptome. Other significant findings of the study include identification of a new waikavirus in a library derived from diseased water chestnut sample wherein a caulimovirus was reported, prediction of coiled-coils in hypothetical protein region of waikaviral polyprotein alignment and phylogenetic clustering of tree-infecting waikaviruses. The study not only reiterates the importance of DDVD in unveiling hitherto hidden viral sequences in plant SRA libraries but also deepens our understanding of waikaviral diversity.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India.
| | - V Rajeswari
- School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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6
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Debat H, Garcia ML, Bejerman N. Expanding the Repertoire of the Plant-Infecting Ophioviruses through Metatranscriptomics Data. Viruses 2023; 15:v15040840. [PMID: 37112821 PMCID: PMC10144540 DOI: 10.3390/v15040840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3–12.5 kb), encompassing three or four linear segments. In total, these segments encode four to seven proteins in the sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand the current diversity of ophioviruses ca. 4.5-fold. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, the viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches, suggesting that there is still plenty of unsampled hidden diversity within the genus. This study represents a significant expansion of the genomics of ophioviruses, opening the door to future works on the molecular and evolutionary peculiarity of this virus genus.
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Affiliation(s)
- Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Correspondence: (H.D.); (N.B.)
| | - Maria Laura Garcia
- Instituto de Biotecnología y Biología Molecular (IBBM-CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 50 y 115, La Plata 1900, Argentina
| | - Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Correspondence: (H.D.); (N.B.)
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7
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Bejerman N, Dietzgen RG, Debat H. Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses. Pathogens 2022; 11:1127. [PMID: 36297184 PMCID: PMC9608074 DOI: 10.3390/pathogens11101127] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 09/28/2023] Open
Abstract
The genus Varicosavirus is one of six genera of plant-infecting rhabdoviruses. Varicosaviruses have non-enveloped, flexuous, rod-shaped virions and a negative-sense, single-stranded RNA genome. A distinguishing feature of varicosaviruses, which is shared with dichorhaviruses, is a bi-segmented genome. Before 2017, a sole varicosavirus was known and characterized, and then two more varicosaviruses were identified through high-throughput sequencing in 2017 and 2018. More recently, the number of known varicosaviruses has substantially increased in concert with the extensive use of high-throughput sequencing platforms and data mining approaches. The novel varicosaviruses have revealed not only sequence diversity, but also plasticity in terms of genome architecture, including a virus with a tentatively unsegmented genome. Here, we report the discovery of 45 novel varicosavirus genomes which were identified in publicly available metatranscriptomic data. The identification, assembly, and curation of the raw Sequence Read Archive reads has resulted in 39 viral genome sequences with full-length coding regions and 6 with nearly complete coding regions. The highlights of the obtained sequences include eight varicosaviruses with unsegmented genomes, which are linked to a phylogenetic clade associated with gymnosperms. These findings have resulted in the most complete phylogeny of varicosaviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses. Thus, the extensive use of sequence data mining for virus discovery has allowed us to unlock of the hidden genetic diversity of varicosaviruses, the largely neglected plant rhabdoviruses.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina
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8
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Payne CD, Vadlamani G, Hajiaghaalipour F, Muhammad T, Fisher MF, Andersson HS, Göransson U, Clark RJ, Bond CS, Mylne JS, Rosengren KJ. Solution NMR and racemic crystallography provide insights into a novel structural class of cyclic plant peptides. RSC Chem Biol 2021; 2:1682-1691. [PMID: 34977583 PMCID: PMC8637875 DOI: 10.1039/d1cb00155h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/13/2021] [Indexed: 11/21/2022] Open
Abstract
Head-to-tail cyclic and disulfide-rich peptides are natural products with applications in drug design. Among these are the PawS-Derived Peptides (PDPs) produced in seeds of the daisy plant family. PDP-23 is a unique member of this class in that it is twice the typical size and adopts two β-hairpins separated by a hinge region. The β-hairpins, both stabilised by a single disulfide bond, fold together into a V-shaped tertiary structure creating a hydrophobic core. In water two PDP-23 molecules merge their hydrophobic cores to form a square prism quaternary structure. Here, we synthesised PDP-23 and its enantiomer comprising d-amino acids and achiral glycine, which allowed us to confirm these solution NMR structural data by racemic crystallography. Furthermore, we discovered the related PDP-24. NMR analysis showed that PDP-24 does not form a dimeric structure and it has poor water solubility, but in less polar solvents adopts near identical secondary and tertiary structure to PDP-23. The natural role of these peptides in plants remains enigmatic, as we did not observe any antimicrobial or insecticidal activity. However, the plasticity of these larger PDPs and their ability to change structure under different conditions make them appealing peptide drug scaffolds. Larger members of the PawS-Derived family of cyclic plant peptides form complex structures. The graphical abstract shows the racemic crystal structure of the homodimeric PDP-23 as well as the solution NMR structure of PDP-24.![]()
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Affiliation(s)
- Colton D Payne
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Grishma Vadlamani
- Curtin University, Centre for Crop and Disease Management, School of Molecular and Life Sciences Bentley WA 6102 Australia.,The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia.,The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences Crawley WA 6009 Australia
| | | | - Taj Muhammad
- Uppsala University, Division of Pharmacognosy, Department of Pharmaceutical Biosciences 75124 Uppsala Sweden
| | - Mark F Fisher
- Curtin University, Centre for Crop and Disease Management, School of Molecular and Life Sciences Bentley WA 6102 Australia.,The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia.,The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences Crawley WA 6009 Australia
| | - Håkan S Andersson
- Uppsala University, Division of Pharmacognosy, Department of Pharmaceutical Biosciences 75124 Uppsala Sweden.,Karolinska Institute, Department of Medical Biochemistry and Biophysics 17177 Stockholm Sweden
| | - Ulf Göransson
- Uppsala University, Division of Pharmacognosy, Department of Pharmaceutical Biosciences 75124 Uppsala Sweden
| | - Richard J Clark
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Charles S Bond
- The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia
| | - Joshua S Mylne
- Curtin University, Centre for Crop and Disease Management, School of Molecular and Life Sciences Bentley WA 6102 Australia.,The University of Western Australia, School of Molecular Sciences Crawley WA 6009 Australia.,The University of Western Australia, ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences Crawley WA 6009 Australia
| | - K Johan Rosengren
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
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Payne CD, Fisher MF, Mylne JS, Rosengren KJ. Structural Characterization of the PawL-Derived Peptide Family, an Ancient Subfamily of Orbitides. JOURNAL OF NATURAL PRODUCTS 2021; 84:2914-2922. [PMID: 34672199 DOI: 10.1021/acs.jnatprod.1c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plants are an excellent source of bioactive peptides, often with disulfide bonds and/or a cyclic backbone. While focus has predominantly been directed at disulfide-rich peptides, a large family of small, cyclic plant peptides lacking disulfide bonds, known as orbitides, has been relatively ignored. A recently discovered subfamily of orbitides is the PawL-derived peptides (PLPs), produced during the maturation of precursors for seed storage albumins. Although their evolutionary origins have been dated, in-depth exploration of the family's structural characteristics and potential bioactivities remains to be conducted. Here we present an extensive and systematic characterization of the PLP family. Nine PLPs were chosen and prepared by solid phase peptide synthesis. Their structural features were studied using solution NMR spectroscopy, and seven were found to possess regions of backbone order. Ordered regions consist of β-turns, with some PLPs adopting two well-defined β-turns within sequences as short as seven residues, which are largely the result of side chain interactions. Our data highlight that the sequence diversity within this family results in equally diverse structures. None of these nine PLPs showed antibacterial or antifungal activity.
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Affiliation(s)
- Colton D Payne
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark F Fisher
- School of Molecular Sciences and The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Joshua S Mylne
- School of Molecular Sciences and The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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10
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Plant derived cyclic peptides. Biochem Soc Trans 2021; 49:1279-1285. [PMID: 34156400 PMCID: PMC8286818 DOI: 10.1042/bst20200881] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/19/2022]
Abstract
Cyclic peptides are widespread throughout the plant kingdom, and display diverse sequences, structures and bioactivities. The potential applications attributed to these peptides and their unusual biosynthesis has captivated the attention of researchers for many years. Several gene sequences for plant cyclic peptides have been discovered over the last two decades but it is only recently that we are beginning to understand the intricacies associated with their biosynthesis. Recent studies have focussed on three main classes of plant derived cyclic peptides, namely orbitides, SFTI related peptides and cyclotides. In this mini-review, we discuss the expansion of the known sequence and structural diversity in these families, insights into the enzymes involved in the biosynthesis, the exciting applications which includes a cyclotide currently in clinical trials for the treatment of multiple sclerosis, and new production methods that are being developed to realise the potential of plant cyclic peptides as pharmaceutical or agricultural agents.
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11
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Nonis SG, Haywood J, Mylne JS. Plant asparaginyl endopeptidases and their structural determinants of function. Biochem Soc Trans 2021; 49:965-976. [PMID: 33666219 PMCID: PMC8106488 DOI: 10.1042/bst20200908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are versatile enzymes that in biological systems are involved in producing three different catalytic outcomes for proteins, namely (i) routine cleavage by bond hydrolysis, (ii) peptide maturation, including macrocyclisation by a cleavage-coupled intramolecular transpeptidation and (iii) circular permutation involving separate cleavage and transpeptidation reactions resulting in a major reshuffling of protein sequence. AEPs differ in their preference for cleavage or transpeptidation reactions, catalytic efficiency, and preference for asparagine or aspartate target residues. We look at structural analyses of various AEPs that have laid the groundwork for identifying important determinants of AEP function in recent years, with much of the research impetus arising from the potential biotechnological and pharmaceutical applications.
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Affiliation(s)
- Samuel G. Nonis
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joel Haywood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
- The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth 6009, Australia
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Payne CD, Franke B, Fisher MF, Hajiaghaalipour F, McAleese CE, Song A, Eliasson C, Zhang J, Jayasena AS, Vadlamani G, Clark RJ, Minchin RF, Mylne JS, Rosengren KJ. A chameleonic macrocyclic peptide with drug delivery applications. Chem Sci 2021; 12:6670-6683. [PMID: 34040741 PMCID: PMC8132947 DOI: 10.1039/d1sc00692d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/06/2021] [Indexed: 11/21/2022] Open
Abstract
Head-to-tail cyclized peptides are intriguing natural products with unusual properties. The PawS-Derived Peptides (PDPs) are ribosomally synthesized as part of precursors for seed storage albumins in species of the daisy family, and are post-translationally excised and cyclized during proteolytic processing. Here we report a PDP twice the typical size and with two disulfide bonds, identified from seeds of Zinnia elegans. In water, synthetic PDP-23 forms a unique dimeric structure in which two monomers containing two β-hairpins cross-clasp and enclose a hydrophobic core, creating a square prism. This dimer can be split by addition of micelles or organic solvent and in monomeric form PDP-23 adopts open or closed V-shapes, exposing different levels of hydrophobicity dependent on conditions. This chameleonic character is unusual for disulfide-rich peptides and engenders PDP-23 with potential for cell delivery and accessing novel targets. We demonstrate this by conjugating a rhodamine dye to PDP-23, creating a stable, cell-penetrating inhibitor of the P-glycoprotein drug efflux pump.
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Affiliation(s)
- Colton D Payne
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Bastian Franke
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Mark F Fisher
- The University of Western Australia, School of Molecular Sciences, The ARC Centre of Excellence in Plant Energy Biology Crawley WA 6009 Australia
| | | | - Courtney E McAleese
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Angela Song
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Carl Eliasson
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Jingjing Zhang
- The University of Western Australia, School of Molecular Sciences, The ARC Centre of Excellence in Plant Energy Biology Crawley WA 6009 Australia
| | - Achala S Jayasena
- The University of Western Australia, School of Molecular Sciences, The ARC Centre of Excellence in Plant Energy Biology Crawley WA 6009 Australia
| | - Grishma Vadlamani
- The University of Western Australia, School of Molecular Sciences, The ARC Centre of Excellence in Plant Energy Biology Crawley WA 6009 Australia
| | - Richard J Clark
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Rodney F Minchin
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Molecular Sciences, The ARC Centre of Excellence in Plant Energy Biology Crawley WA 6009 Australia
| | - K Johan Rosengren
- The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia
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13
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Zhang J, Yuan J, Li Z, Fu C, Xu M, Yang J, Jiang X, Zhou B, Ye X, Xu C. Exploring and exploiting plant cyclic peptides for drug discovery and development. Med Res Rev 2021; 41:3096-3117. [PMID: 33599316 DOI: 10.1002/med.21792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/10/2021] [Accepted: 01/31/2021] [Indexed: 01/07/2023]
Abstract
Ever since the discovery of insulin, natural peptides have become an important resource for therapeutic development. Decades of research has led to the discovery of a long list of peptide drugs with broad applications in clinics, from antibiotics to hypertension treatment to pain management. Many of these US FDA-approved peptide drugs are derived from microorganisms and animals. By contrast, the great potential of plant cyclic peptides as therapeutics remains largely unexplored. These macrocyclic peptides typically have rigid structures, good bioavailability and membrane permeability, making them appealing candidates for drug development and engineering. In this review, we introduce the three major classes of plant cyclic peptides and summarize their potential medical applications. We discuss how we can leverage the genome information of many different plants to quickly search for new cyclic peptides and how we can take advantage of the insights gained from their biosynthetic pathways to transform the process of production and drug development. These recent developments have provided a new angle for exploring and exploiting plant cyclic peptides, and we believe that many more peptide drugs derived from plants are about to come.
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Affiliation(s)
- Jingjing Zhang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Jimin Yuan
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Zhijie Li
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chunjin Fu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Menglong Xu
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Jing Yang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xin Jiang
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Boping Zhou
- Department of Infectious Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Xiufeng Ye
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Chengchao Xu
- Department of Geriatric Medicine, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
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14
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de Veer SJ, White AM, Craik DJ. Sunflower Trypsin Inhibitor-1 (SFTI-1): Sowing Seeds in the Fields of Chemistry and Biology. Angew Chem Int Ed Engl 2020; 60:8050-8071. [PMID: 32621554 DOI: 10.1002/anie.202006919] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 12/24/2022]
Abstract
Nature-derived cyclic peptides have proven to be a vast source of inspiration for advancing modern pharmaceutical design and synthetic chemistry. The focus of this Review is sunflower trypsin inhibitor-1 (SFTI-1), one of the smallest disulfide-bridged cyclic peptides found in nature. SFTI-1 has an unusual biosynthetic pathway that begins with a dual-purpose albumin precursor and ends with the production of a high-affinity serine protease inhibitor that rivals other inhibitors much larger in size. Investigations on the molecular basis for SFTI-1's rigid structure and adaptable function have planted seeds for thought that have now blossomed in several different fields. Here we survey these applications to highlight the growing potential of SFTI-1 as a versatile template for engineering inhibitors, a prototypic peptide for studying inhibitory mechanisms, a stable scaffold for grafting bioactive peptides, and a model peptide for evaluating peptidomimetic motifs and platform technologies.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew M White
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
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15
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Veer SJ, White AM, Craik DJ. Der Sonnenblumen‐Trypsin‐Inhibitor 1 (SFTI‐1) in der Chemie und Biologie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Simon J. Veer
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
| | - Andrew M. White
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
| | - David J. Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
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16
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Gitlin-Domagalska A, Maciejewska A, Dębowski D. Bowman-Birk Inhibitors: Insights into Family of Multifunctional Proteins and Peptides with Potential Therapeutical Applications. Pharmaceuticals (Basel) 2020; 13:E421. [PMID: 33255583 PMCID: PMC7760496 DOI: 10.3390/ph13120421] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Bowman-Birk inhibitors (BBIs) are found primarily in seeds of legumes and in cereal grains. These canonical inhibitors share a highly conserved nine-amino acids binding loop motif CTP1SXPPXC (where P1 is the inhibitory active site, while X stands for various amino acids). They are natural controllers of plants' endogenous proteases, but they are also inhibitors of exogenous proteases present in microbials and insects. They are considered as plants' protective agents, as their elevated levels are observed during injury, presence of pathogens, or abiotic stress, i.a. Similar properties are observed for peptides isolated from amphibians' skin containing 11-amino acids disulfide-bridged loop CWTP1SXPPXPC. They are classified as Bowman-Birk like trypsin inhibitors (BBLTIs). These inhibitors are resistant to proteolysis and not toxic, and they are reported to be beneficial in the treatment of various pathological states. In this review, we summarize up-to-date research results regarding BBIs' and BBLTIs' inhibitory activity, immunomodulatory and anti-inflammatory activity, antimicrobial and insecticidal strength, as well as chemopreventive properties.
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Affiliation(s)
| | | | - Dawid Dębowski
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (A.G.-D.); (A.M.)
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17
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Payne CD, Vadlamani G, Fisher MF, Zhang J, Clark RJ, Mylne JS, Rosengren KJ. Defining the Familial Fold of the Vicilin-Buried Peptide Family. JOURNAL OF NATURAL PRODUCTS 2020; 83:3030-3040. [PMID: 32997497 DOI: 10.1021/acs.jnatprod.0c00594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Plants and their seeds have been shown to be a rich source of cystine-stabilized peptides. Recently a new family of plant seed peptides whose sequences are buried within precursors for seed storage vicilins was identified. Members of this Vicilin-Buried Peptide (VBP) family are found in distantly related plant species including the monocot date palm, as well as dicotyledonous species like pumpkin and sesame. Genetic evidence for their widespread occurrence indicates that they are of ancient origin. Limited structural studies have been conducted on VBP family members, but two members have been shown to adopt a helical hairpin fold. We present an extensive characterization of VBPs using solution NMR spectroscopy, to better understand their structural features. Four peptides were produced by solid phase peptide synthesis and shown to favor a helix-loop-helix hairpin fold, as a result of the I-IV/II-III ladderlike connectivity of their disulfide bonds. Interhelical interactions, including hydrophobic contacts and salt bridges, are critical for the fold stability and control the angle at which the antiparallel α-helices interface. Activities reported for VBPs include trypsin inhibitory activity and inhibition of ribosomal function; however, their diverse structural features despite a common fold suggest that additional bioactivities yet to be revealed are likely.
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Affiliation(s)
- Colton D Payne
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | | | - Richard J Clark
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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18
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Fisher MF, Payne CD, Chetty T, Crayn D, Berkowitz O, Whelan J, Rosengren KJ, Mylne JS. The genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides. J Biol Chem 2020; 295:14510-14521. [PMID: 32817170 PMCID: PMC7573267 DOI: 10.1074/jbc.ra120.014781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/11/2020] [Indexed: 01/03/2023] Open
Abstract
Cyclic peptides are reported to have antibacterial, antifungal, and other bioactivities. Orbitides are a class of cyclic peptides that are small, head-to-tail cyclized, composed of proteinogenic amino acids and lack disulfide bonds; they are also known in several genera of the plant family Rutaceae. Melicope xanthoxyloides is the Australian rain forest tree of the Rutaceae family in which evolidine, the first plant cyclic peptide, was discovered. Evolidine (cyclo-SFLPVNL) has subsequently been all but forgotten in the academic literature, so to redress this we used tandem MS and de novo transcriptomics to rediscover evolidine and decipher its biosynthetic origin from a short precursor just 48 residues in length. We also identified another six M. xanthoxyloides orbitides using the same techniques. These peptides have atypically diverse C termini consisting of residues not recognized by either of the known proteases plants use to macrocyclize peptides, suggesting new cyclizing enzymes await discovery. We examined the structure of two of the novel orbitides by NMR, finding one had a definable structure, whereas the other did not. Mining RNA-seq and whole genome sequencing data from other species of the Rutaceae family revealed that a large and diverse family of peptides is encoded by similar sequences across the family and demonstrates how powerful de novo transcriptomics can be at accelerating the discovery of new peptide families.
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Affiliation(s)
- Mark F Fisher
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
| | - Colton D Payne
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Thaveshini Chetty
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland, 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
| | - 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
| | - K Johan Rosengren
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, Queensland, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Molecular Sciences & The ARC Centre of Excellence in Plant Energy Biology, Crawley, Australia
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19
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Rubin GM, Ding Y. Recent advances in the biosynthesis of RiPPs from multicore-containing precursor peptides. J Ind Microbiol Biotechnol 2020; 47:659-674. [PMID: 32617877 PMCID: PMC7666021 DOI: 10.1007/s10295-020-02289-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) compose a large structurally and functionally diverse family of natural products. The biosynthesis system of RiPPs typically involves a precursor peptide comprising of a leader and core motif and nearby processing enzymes that recognize the leader and act on the core for producing modified peptides. Interest in RiPPs has increased substantially in recent years as improvements in genome mining techniques have dramatically improved access to these peptides and biochemical and engineering studies have supported their applications. A less understood, intriguing feature in the RiPPs biosynthesis is the precursor peptides of multiple RiPPs families produced by bacteria, fungi and plants carrying multiple core motifs, which we term "multicore". Herein, we present the prevalence of the multicore systems, their biosynthesis and engineering for applications.
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Affiliation(s)
- Garret M Rubin
- Department of Medicinal Chemistry, and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, and Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA.
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20
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Fisher MF, Zhang J, Berkowitz O, Whelan J, Mylne JS. Cyclic Peptides in Seed of Annona muricata Are Ribosomally Synthesized. JOURNAL OF NATURAL PRODUCTS 2020; 83:1167-1173. [PMID: 32239926 DOI: 10.1021/acs.jnatprod.9b01209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Small, cyclic peptides are reported to have many bioactivities. In bacteria and fungi, they can be made by nonribosomal peptide synthetases, but in plants they are exclusively ribosomal. Cyclic peptides from the Annona genus possess cytotoxic and anti-inflammatory activities, but their biosynthesis is unknown. The medicinal soursop plant, Annona muricata, contains annomuricatins A (cyclo-PGFVSA) and B (cyclo-PNAWLGT). Here, using de novo transcriptomics and tandem mass spectrometry, we identify a suite of short transcripts for precursor proteins for 10 validated annomuricatins, 9 of which are novel. In their precursors, annomuricatins are preceded by an absolutely conserved Glu and each peptide sequence has a conserved proto-C-terminal Pro, revealing parallels with the segetalin orbitides from the seed of Vaccaria hispanica, which are processed through ligation by a prolyl oligopeptidase in a transpeptidation reaction.
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Affiliation(s)
- Mark F Fisher
- The University of Western Australia, School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Jingjing Zhang
- The University of Western Australia, School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Industrial Transformation Research Hub in Medicinal Agriculture, AgriBio building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences & ARC Industrial Transformation Research Hub in Medicinal Agriculture, AgriBio building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Joshua S Mylne
- The University of Western Australia, School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
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21
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De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. Cell Syst 2019; 10:99-108.e5. [PMID: 31864964 DOI: 10.1016/j.cels.2019.11.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/18/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
Abstract
Cyclic and branch cyclic peptides (cyclopeptides) represent a class of bioactive natural products that include many antibiotics and anti-tumor compounds. Despite the recent advances in metabolomics analysis, still little is known about the cyclopeptides in the human gut and their possible interactions due to a lack of computational analysis pipelines that are applicable to such compounds. Here, we introduce CycloNovo, an algorithm for automated de novo cyclopeptide analysis and sequencing that employs de Bruijn graphs, the workhorse of DNA sequencing algorithms, to identify cyclopeptides in spectral datasets. CycloNovo reconstructed 32 previously unreported cyclopeptides (to the best of our knowledge) in the human gut and reported over a hundred cyclopeptides in other environments represented by various spectra on Global Natural Products Social Molecular Network (GNPS). https://github.com/bbehsaz/cyclonovo.
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22
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Fisher MF, Mylne JS. Sequencing Orbitides by Acid-Mediated Ring Cleavage Followed by Tandem Mass Spectrometry. J Proteome Res 2019; 18:4065-4071. [DOI: 10.1021/acs.jproteome.9b00516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark F. Fisher
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology (M310), The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Joshua S. Mylne
- School of Molecular Sciences & ARC Centre of Excellence in Plant Energy Biology (M310), The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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23
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Fisher MF, Payne CD, Rosengren KJ, Mylne JS. An Orbitide from Ratibida columnifera Seed Containing 16 Amino Acid Residues. JOURNAL OF NATURAL PRODUCTS 2019; 82:2152-2158. [PMID: 31392883 DOI: 10.1021/acs.jnatprod.9b00111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cyclic peptides are abundant in plants and have attracted interest due to their bioactivity and potential as drug scaffolds. Orbitides are head-to-tail cyclic peptides that are ribosomally synthesized, post-translationally modified, and lack disulfide bonds. All known orbitides contain 5-12 amino acid residues. Here we describe PLP-53, a novel orbitide from the seed of Ratibida columnifera. PLP-53 consists of 16 amino acids, four residues larger than any known orbitide. NMR structural studies showed that, compared to previously characterized orbitides, PLP-53 is more flexible and, under the studied conditions, did not adopt a single ordered conformation based on analysis of NOEs and chemical shifts.
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Affiliation(s)
- Mark F Fisher
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
| | - Colton D Payne
- Faculty of Medicine, School of Biomedical Sciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - K Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Joshua S Mylne
- School of Molecular Sciences , The University of Western Australia , 35 Stirling Highway , Crawley , WA 6009 , Australia
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24
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Franke B, Mylne JS, Rosengren KJ. Buried treasure: biosynthesis, structures and applications of cyclic peptides hidden in seed storage albumins. Nat Prod Rep 2019; 35:137-146. [PMID: 29379937 DOI: 10.1039/c7np00066a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Covering: 1999 up to the end of 2017The small cyclic peptide SunFlower Trypsin Inhibitor-1 (SFTI-1) from sunflower seeds is the prototypic member of a novel family of natural products. The biosynthesis of these peptides is intriguing as their gene-encoded peptide backbone emerges from a precursor protein that also contains a seed storage albumin. The peptide sequence is cleaved out from the precursor and cyclised by the albumin-maturing enzymatic machinery. Three-dimensional solution NMR structures of a number of these peptides, and of the intact precursor protein preproalbumin with SFTI-1, have now been elucidated. Furthermore, the evolution of the family has been described and a detailed understanding of the biosynthetic steps, which are necessary to produce cyclic SFTI-1, is emerging. Macrocyclisation provides peptide stability and thus represents a key strategy in peptide drug development. Consequently the constrained structure of SFTI-1 has been explored as a template for protein engineering, for tuning selectivity towards clinically relevant proteases and for grafting in sequences with completely novel functions. Here we review the discovery of the SFTI-1 peptide family, their evolution, biosynthetic origin, and structural features, as well as highlight the potential applications of this unique class of natural products.
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Affiliation(s)
- B Franke
- The University of Queensland, Faculty of Medicine, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
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25
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Pouvreau B, Fenske R, Ivanova A, Murcha MW, Mylne JS. An interstitial peptide is readily processed from within seed proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:175-183. [PMID: 31203882 DOI: 10.1016/j.plantsci.2019.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/25/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
The importance of de novo protein evolution is apparent, but most examples are de novo coding transcripts evolving from silent or non-coding DNA. The peptide macrocycle SunFlower Trypsin Inhibitor 1 (SFTI-1) evolved over 45 million years from genetic expansion within the N-terminal 'discarded' region of an ancestral seed albumin precursor. SFTI-1 and its adjacent albumin are both processed into separate, mature forms by asparaginyl endopeptidase (AEP). Here to determine whether the evolution of SFTI-1 in a latent region of its precursor was critical, we used a transgene approach in A. thaliana analysed by peptide mass spectrometry and RT-qPCR. SFTI could emerge from alternative locations within preproalbumin as well as emerge with precision from unrelated seed proteins via AEP-processing. SFTI production was possible with the adjacent albumin, but peptide levels dropped greatly without the albumin. The ability for SFTI to be processed from multiple sequence contexts and different proteins suggests that to make peptide, it was not crucial for the genetic expansion that gave rise to SFTI and its family to be within a latent protein region. Interstitial peptides, evolving like SFTI within existing proteins, might be more widespread and as a mechanism, SFTI exemplifies a stable, new, functional peptide that did not need a new gene to evolve de novo.
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Affiliation(s)
- Benjamin Pouvreau
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Ricarda Fenske
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.
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Zhang J, Payne CD, Pouvreau B, Schaefer H, Fisher MF, Taylor NL, Berkowitz O, Whelan J, Rosengren KJ, Mylne JS. An Ancient Peptide Family Buried within Vicilin Precursors. ACS Chem Biol 2019; 14:979-993. [PMID: 30973714 DOI: 10.1021/acschembio.9b00167] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
New proteins can evolve by duplication and divergence or de novo, from previously noncoding DNA. A recently observed mechanism is for peptides to evolve within a "host" protein and emerge by proteolytic processing. The first examples of such interstitial peptides were ones hosted by precursors for seed storage albumin. Interstitial peptides have also been observed in precursors for seed vicilins, but current evidence for vicilin-buried peptides (VBPs) is limited to seeds of the broadleaf plants pumpkin and macadamia. Here, an extensive sequence analysis of vicilin precursors suggested that peptides buried within the N-terminal region of preprovicilins are widespread and truly ancient. Gene sequences indicative of interstitial peptides were found in species from Amborellales to eudicots and include important grass and legume crop species. We show the first protein evidence for a monocot VBP in date palm seeds as well as protein evidence from other crops including the common tomato, sesame and pumpkin relatives, cucumber, and the sponge loofah ( Luffa aegyptiaca). Their excision was consistent with asparaginyl endopeptidase-mediated maturation, and sequences were confirmed by tandem mass spectrometry. Our findings suggest that the family is large and ancient and that based on the NMR solution structures for loofah Luffin P1 and tomato VBP-8, VBPs adopt a helical hairpin fold stapled by two internal disulfide bonds. The first VBPs characterized were a protease inhibitor, antimicrobials, and a ribosome inactivator. The age and evolutionary retention of this peptide family suggest its members play important roles in plant biology.
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Affiliation(s)
| | - Colton D. Payne
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Hanno Schaefer
- Department of Ecology and Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, 85354, Freising, Germany
| | | | | | - Oliver Berkowitz
- Department of Animal, Plant, and Soil Sciences, School of Life Sciences and ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086 Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Sciences, School of Life Sciences and ARC Centre of Excellence in Plant Energy Biology, AgriBio, The Centre for AgriBioscience, La Trobe University, Bundoora, Victoria 3086 Australia
| | - K. Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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Guo L, Qiu J, Li LF, Lu B, Olsen K, Fan L. Genomic Clues for Crop-Weed Interactions and Evolution. TRENDS IN PLANT SCIENCE 2018; 23:1102-1115. [PMID: 30293809 DOI: 10.1016/j.tplants.2018.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 09/11/2018] [Indexed: 05/11/2023]
Abstract
Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop-weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop-weed interactions, and further the development of practical applications in agricultural weed control and crop breeding.
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Affiliation(s)
- Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; These authors contributed equally to this work
| | - Jie Qiu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; These authors contributed equally to this work
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Baorong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kenneth Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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28
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Ravet K, Patterson EL, Krähmer H, Hamouzová K, Fan L, Jasieniuk M, Lawton-Rauh A, Malone JM, McElroy JS, Merotto A, Westra P, Preston C, Vila-Aiub MM, Busi R, Tranel PJ, Reinhardt C, Saski C, Beffa R, Neve P, Gaines TA. The power and potential of genomics in weed biology and management. PEST MANAGEMENT SCIENCE 2018; 74:2216-2225. [PMID: 29687580 DOI: 10.1002/ps.5048] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 05/11/2023]
Abstract
There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the 'state of the art' in genomics and weed genomics, including technologies, applications, and on-going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Karl Ravet
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Eric L Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | | | - Kateřina Hamouzová
- Department of Agroecology and Biometeorology, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Marie Jasieniuk
- Department of Plant Sciences, University of California-Davis, Davis, CA, USA
| | - Amy Lawton-Rauh
- Department of Genetics and Biochemistry, 316 Biosystems Research Complex, Clemson University, Clemson, SC, USA
| | - Jenna M Malone
- School of Agriculture, Food & Wine, University of Adelaide, Glen Osmond, Australia
| | - J Scott McElroy
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Philip Westra
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Christopher Preston
- School of Agriculture, Food & Wine, University of Adelaide, Glen Osmond, Australia
| | - Martin M Vila-Aiub
- Facultad de Agronomía, Departamento de Ecología, IFEVA-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roberto Busi
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Crawley, Australia
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Carl Reinhardt
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Christopher Saski
- Clemson University Genomics and Computational Biology Laboratory, Clemson University, Clemson, SC, USA
| | - Roland Beffa
- Bayer AG, Industriepark Hoechst, Frankfurt am Main, Germany
| | - Paul Neve
- Biointeractions & Crop Protection Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, UK
| | - Todd A Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
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29
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Ongpipattanakul C, Nair SK. Biosynthetic Proteases That Catalyze the Macrocyclization of Ribosomally Synthesized Linear Peptides. Biochemistry 2018; 57:3201-3209. [PMID: 29553721 DOI: 10.1021/acs.biochem.8b00114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Circular peptides have long been sought after as scaffolds for drug design as they demonstrate protein-like properties in the context of small, constrained peptides. Traditional routes toward the production of cyclic peptides rely on synthesis or semisynthetic methods, which restrict their use as platforms for the production of large, structurally diverse chemical libraries. Here, we discuss the biosynthetic routes toward the N-C macrocyclization of linear peptide precursors, specifically, those transformations that are catalyzed by peptidases. While canonical peptidases catalyze the proteolysis of linear peptides, the biosynthetic macrocyclases couple proteolytic cleavage with cyclization to produce macrocyclic compounds. In this Perspective, we explore the different structural features that impart on each of these biosynthetic proteases the distinct ability to perform macrocyclization and focus on their potential use in biotechnology.
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30
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Lu TC, Leu JY, Lin WC. A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts. Mol Biol Evol 2018; 34:2823-2838. [PMID: 28981695 PMCID: PMC5850716 DOI: 10.1093/molbev/msx210] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Novel genes arising from random DNA sequences (de novo genes) have been suggested to be widespread in the genomes of different organisms. However, our knowledge about the origin and evolution of de novo genes is still limited. To systematically understand the general features of de novo genes, we established a robust pipeline to analyze >20,000 transcript-supported coding sequences (CDSs) from the budding yeast Saccharomyces cerevisiae. Our analysis pipeline combined phylogeny, synteny, and sequence alignment information to identify possible orthologs across 20 Saccharomycetaceae yeasts and discovered 4,340 S. cerevisiae-specific de novo genes and 8,871 S. sensu stricto-specific de novo genes. We further combine information on CDS positions and transcript structures to show that >65% of de novo genes arose from transcript isoforms of ancient genes, especially in the upstream and internal regions of ancient genes. Fourteen identified de novo genes with high transcript levels were chosen to verify their protein expressions. Ten of them, including eight transcript isoform-associated CDSs, showed translation signals and five proteins exhibited specific cytosolic localizations. Our results suggest that de novo genes frequently arise in the S. sensu stricto complex and have the potential to be quickly integrated into ancient cellular network.
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Affiliation(s)
- Tzu-Chiao Lu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Chang Lin
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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31
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Fisher MF, Zhang J, Taylor NL, Howard MJ, Berkowitz O, Debowski AW, Behsaz B, Whelan J, Pevzner PA, Mylne JS. A family of small, cyclic peptides buried in preproalbumin since the Eocene epoch. PLANT DIRECT 2018; 2:e00042. [PMID: 30417166 PMCID: PMC6223261 DOI: 10.1002/pld3.42] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Orbitides are cyclic ribosomally-synthesized and post-translationally modified peptides (RiPPs) from plants; they consist of standard amino acids arranged in an unbroken chain of peptide bonds. These cyclic peptides are stable and range in size and topologies making them potential scaffolds for peptide drugs; some display valuable biological activities. Recently two orbitides whose sequences were buried in those of seed storage albumin precursors were said to represent the first observable step in the evolution of larger and hydrophilic bicyclic peptides. Here, guided by transcriptome data, we investigated peptide extracts of 40 species specifically for the more hydrophobic orbitides and confirmed 44 peptides by tandem mass spectrometry, as well as obtaining solution structures for four of them by NMR. Acquiring transcriptomes from the phylogenetically important Corymboideae family confirmed the precursor genes for the peptides (called PawS1-Like or PawL1) are confined to the Asteroideae, a subfamily of the huge plant family Asteraceae. To be confined to the Asteroideae indicates these peptides arose during the Eocene epoch around 45 Mya. Unlike other orbitides, all PawL-derived Peptides contain an Asp residue, needed for processing by asparaginyl endopeptidase. This study has revealed what is likely to be a very large new family of orbitides, uniquely buried alongside albumin and processed by asparaginyl endopeptidase.
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Affiliation(s)
- Mark F. Fisher
- School of Molecular SciencesThe University of Western Australia, CrawleyPerthWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyPerthWAAustralia
| | - Jingjing Zhang
- School of Molecular SciencesThe University of Western Australia, CrawleyPerthWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyPerthWAAustralia
| | - Nicolas L. Taylor
- School of Molecular SciencesThe University of Western Australia, CrawleyPerthWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyPerthWAAustralia
| | - Mark J. Howard
- School of Molecular SciencesThe University of Western Australia, CrawleyPerthWAAustralia
- Centre for Microscopy, Characterisation and AnalysisThe University of Western AustraliaCrawleyPerthWAAustralia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil SciencesSchool of Life Sciences & ARC Centre of Excellence in Plant Energy BiologyAgriBioThe Centre for AgriBioscienceLa Trobe UniversityBundooraVic.Australia
| | - Aleksandra W. Debowski
- School of Molecular SciencesThe University of Western Australia, CrawleyPerthWAAustralia
- Marshall Centre for Infectious Disease Research and TrainingSchool of Biomedical SciencesThe University of Western AustraliaCrawleyPerthWAAustralia
| | - Bahar Behsaz
- Department of Computer Science & EngineeringUniversity of CaliforniaLa JollaSan DiegoCAUSA
| | - James Whelan
- Department of Animal, Plant and Soil SciencesSchool of Life Sciences & ARC Centre of Excellence in Plant Energy BiologyAgriBioThe Centre for AgriBioscienceLa Trobe UniversityBundooraVic.Australia
| | - Pavel A. Pevzner
- Department of Computer Science & EngineeringUniversity of CaliforniaLa JollaSan DiegoCAUSA
| | - Joshua S. Mylne
- School of Molecular SciencesThe University of Western Australia, CrawleyPerthWAAustralia
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaCrawleyPerthWAAustralia
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