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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. [PMID: 38411572 DOI: 10.1039/d3np00042g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [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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de Oliveira Silva L, da Silva Pereira L, Pereira JL, Gomes VM, Grativol C. Divergence and conservation of defensins and lipid transfer proteins (LTPs) from sugarcane wild species and modern cultivar genomes. Funct Integr Genomics 2022; 22:235-250. [PMID: 35195843 DOI: 10.1007/s10142-022-00832-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/24/2021] [Accepted: 02/15/2022] [Indexed: 11/04/2022]
Abstract
Plant defensins and lipid transfer proteins (LTPs) constitute a large and evolutionarily diverse family of antimicrobial peptides. Defensins and LTPs are two pathogenesis-related proteins (PR proteins) whose characterization may help to uncover aspects about the sugarcane response to pathogens attack. LTPs have also been investigated for their participation in the response to different types of stress. Despite the important roles of defensins and LTPs in biotic and abiotic stresses, scarce knowledge is found about these proteins in sugarcane. By using bioinformatics approaches, we characterized defensins and LTPs in the sugarcane wild species and modern cultivar genomes. The identification of defensins and LTPs showed that all five defensins groups and eight of the nine LTPs have their respective genes loci, although some was only identified in the cultivar genome. Phylogenetic analysis showed that defensins appear to be more conserved among groups of plants than LTPs. Some defensins and LTPs showed opposite expression during pathogenic and benefic bacterial interactions. Interestingly, the expression of defensins and LTPs in shoots and roots was completely different in plants submitted to benefic bacteria or water depletion. Finally, the modeling and comparison of isoforms of LTPs and defensins in wild species and cultivars revealed a high conservation of tertiary structures, with variation of amino acids in different regions of proteins, which could impact their antimicrobial activity. Our data contributed to the characterization of defensins and LTPs in sugarcane and provided new elements for understanding the involvement of these proteins in sugarcane response to different types of stress.
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Affiliation(s)
- Leandro de Oliveira Silva
- Laboratório de Química, Função de Proteínas E Peptídeos, Centro de Biociências E Biotecnologia, Universidade Estadual Do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Lídia da Silva Pereira
- Laboratório de Fisiologia E Bioquímica de Microrganismos, Centro de Biociências E Biotecnologia, Universidade Estadual Do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Jacymara Lopes Pereira
- Laboratório de Química, Função de Proteínas E Peptídeos, Centro de Biociências E Biotecnologia, Universidade Estadual Do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Valdirene Moreira Gomes
- Laboratório de Fisiologia E Bioquímica de Microrganismos, Centro de Biociências E Biotecnologia, Universidade Estadual Do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Clícia Grativol
- Laboratório de Química, Função de Proteínas E Peptídeos, Centro de Biociências E Biotecnologia, Universidade Estadual Do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
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3
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Jabeen R, Iqbal A, Deeba F, Zulfiqar F, Mustafa G, Nawaz H, Habiba U, Nafees M, Zaid A, Siddique KHM. Isolation and characterization of peroxidase P7-like gene and Rab-GDI like gene from potential medicinal plants: A step toward understanding cell defense signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:975852. [PMID: 36119597 PMCID: PMC9478186 DOI: 10.3389/fpls.2022.975852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
Defensin genes form part of a plant's defense system and are activated when exposed to biotic or abiotic stress. They play a vital role in controlling many signaling pathways involved in various plant defense mechanisms. This research aimed to isolate and characterize novel defensin genes from selected medicinally important plants to explore their signaling mechanisms and defense associated roles for breeding. The DNA of Albizia lebbeck and Moringa oleifera was subjected to PCR amplification using gene-specific primers of defensin genes. Two novel defensin genes were isolated in each species, with sequence lengths of 300 bp in A. lebbeck and 150 bp in M. oleifera. In-silico analysis undertaken to retrieve and align their orthologous sequences revealed 100% similarity of the A. lebbeck gene with the Musa acuminate peroxidase P7-like gene and 85% similarity of the M. oleifera gene with the Manihot esculenta GDP dissociation inhibitor gene. The reliability, stability and physiochemical properties of homology models of these sequences was confirmed through online computational studies. This preliminary study confirmed the presence of novel genes with peroxidase P7 and Rab GDP dissociation inhibitor gene-like activity in A. lebbeck and M. oleifera, respectively, and their potential defense role in plants. Thus, the defensin genes of both species could be used in the synthesis of transgenic self-defensive plants with increased disease resistance and as potential candidates for improved crop production and thraputic formulation in the future.
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Affiliation(s)
- Raheela Jabeen
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
- *Correspondence: Raheela Jabeen,
| | - Atia Iqbal
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Punjab, Pakistan
| | - Farah Deeba
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Faisal Zulfiqar,
| | - Ghulam Mustafa
- Department of Biochemsitry, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Haq Nawaz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Ume Habiba
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Punjab, Pakistan
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Abbu Zaid
- Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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4
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Struyfs C, Cammue BPA, Thevissen K. Membrane-Interacting Antifungal Peptides. Front Cell Dev Biol 2021; 9:649875. [PMID: 33912564 PMCID: PMC8074791 DOI: 10.3389/fcell.2021.649875] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
The incidence of invasive fungal infections is increasing worldwide, resulting in more than 1.6 million deaths every year. Due to growing antifungal drug resistance and the limited number of currently used antimycotics, there is a clear need for novel antifungal strategies. In this context, great potential is attributed to antimicrobial peptides (AMPs) that are part of the innate immune system of organisms. These peptides are known for their broad-spectrum activity that can be directed toward bacteria, fungi, viruses, and/or even cancer cells. Some AMPs act via rapid physical disruption of microbial cell membranes at high concentrations causing cell leakage and cell death. However, more complex mechanisms are also observed, such as interaction with specific lipids, production of reactive oxygen species, programmed cell death, and autophagy. This review summarizes the structure and mode of action of antifungal AMPs, thereby focusing on their interaction with fungal membranes.
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Affiliation(s)
- Caroline Struyfs
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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Habiba U, Nisar J, Choohan MA, Shah SMA, Nisar Z, Mustafa I. Antibacterial Activity of Tris NaCl and PBS Buffer Protein Extract of Cassia fistula, Saccharum officinarum, Albizia lebbeck and Cymbopogon citrates Against Bacterial Strains. Dose Response 2021; 19:1559325821992239. [PMID: 33628155 PMCID: PMC7883167 DOI: 10.1177/1559325821992239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/03/2021] [Accepted: 01/08/2021] [Indexed: 11/21/2022] Open
Abstract
Medicinal plants are gaining popularity over synthetic medicines because antibiotic resistance demands the alternative source of medication. In the present research, the crude protein extraction of 4 medicinal plants Cassia fistula, Saccharum officinarum, Albizia lebbeck and Cymbopogon citrates was carried out. Crude protein extraction was done by 2 different buffers i.e. Tris NaCl buffer and PBS buffer. Protein confirmation was done by Bradford assay in the spectrophotometer. Antibacterial potential was checked and compared against Escherichia coli, Bacillus subtilis, Neisseria gonorrhoea, Bacillus cereus and Proteus mirabilis. Antibacterial assay was performed by disc diffusion method, agar well method and zones of inhibition were calculated. The study results indicated that Tris NaCl extracts' antimicrobial potential is higher than that of the PBS buffer. On disc diffusion method the Tris NaCl buffer extracts of Cymbopogon citrates showed maximum zone of inhibition 11 mm and 9 mm against Bacillus subtilis and Bacillus cereus respectively and control chloramphenicol showed maximum zone of inhibition 26 mm against Bacillus subtilis. Cassia fistula showed maximum zone of inhibition of 7 mm against Bacillus cereus while Saccharum officinarum and Albizia lebbeck didn't show the any antibacterial activity. On the other hand, Protein extracts from PBS buffer didn't show zone of inhibition against any bacteria. Only Albizia lebbeck showed minute zone of inhibition against Neisseria gonorrhea. On well diffusion method, Cassia fistula Tris NaCl protein extract showed the maximum zone of inhibition 20 mm and 18 mm against Proteus mirabilis and Bacillus subtilis respectively. While Albizia lebbeck PBS protein extract showed the maximum zone of inhibition 19 mm and 17 mm against Bacillus subtilis and Bacillus cereus. The results revealed that the protein extract of Albizia lebbeck, Cymbopogon citrates and Cassia fistula can be used tosynthesize antimicrobial drugs to treat the bacterial infections.
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Affiliation(s)
- Ume Habiba
- Department of Microbiology and Molecular genetics, The Women University Multan, Multan, Punjab, Pakistan
- University College of Conventional Medicine, Islamia University of Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Jaweria Nisar
- Department of Eastern Medicine, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Muhammad Akram Choohan
- University College of Conventional Medicine, Islamia University of Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Syed Muhammad Ali Shah
- Department of Eastern Medicine, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Zonaira Nisar
- Department of Eastern Medicine, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Imtiaz Mustafa
- Department of Physiology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
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6
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Costa LSM, Pires ÁS, Damaceno NB, Rigueiras PO, Maximiano MR, Franco OL, Porto WF. In silico characterization of class II plant defensins from Arabidopsis thaliana. PHYTOCHEMISTRY 2020; 179:112511. [PMID: 32931963 DOI: 10.1016/j.phytochem.2020.112511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Defensins comprise a polyphyletic group of multifunctional defense peptides. Cis-defensins, also known as cysteine stabilized αβ (CSαβ) defensins, are one of the most ancient defense peptide families. In plants, these peptides have been divided into two classes, according to their precursor organization. Class I defensins are composed of the signal peptide and the mature sequence, while class II defensins have an additional C-terminal prodomain, which is proteolytically cleaved. Class II defensins have been described in Solanaceae and Poaceae species, indicating this class could be spread among all flowering plants. Here, a search by regular expression (RegEx) was applied to the Arabidopsis thaliana proteome, a model plant with more than 300 predicted defensin genes. Two sequences were identified, A7REG2 and A7REG4, which have a typical plant defensin structure and an additional C-terminal prodomain. TraVA database indicated they are expressed in flower, ovules and seeds, and being duplicated genes, this indicates they could be a result of a subfunctionalization process. The presence of class II defensin sequences in Brassicaceae and Solanaceae and evolutionary distance between them suggest class II defensins may be present in other eudicots. Discovery of class II defensins in other plants could shed some light on flower, ovules and seed physiology, as this class is expressed in these locations.
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Affiliation(s)
- Laura S M Costa
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Departamento de Biologia, Programa de Pós-Graduação em Genética e Biotecnologia, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, MG, Brazil
| | - Állan S Pires
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Neila B Damaceno
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Pietra O Rigueiras
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Mariana R Maximiano
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas. Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Departamento de Biologia, Programa de Pós-Graduação em Genética e Biotecnologia, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, MG, Brazil; S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - William F Porto
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Porto Reports, Brasília, DF, Brazil.
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Odintsova TI, Slezina MP, Istomina EA. Defensins of Grasses: A Systematic Review. Biomolecules 2020; 10:biom10071029. [PMID: 32664422 PMCID: PMC7407236 DOI: 10.3390/biom10071029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022] Open
Abstract
The grass family (Poaceae) is one of the largest families of flowering plants, growing in all climatic zones of all continents, which includes species of exceptional economic importance. The high adaptability of grasses to adverse environmental factors implies the existence of efficient resistance mechanisms that involve the production of antimicrobial peptides (AMPs). Of plant AMPs, defensins represent one of the largest and best-studied families. Although wheat and barley seed γ-thionins were the first defensins isolated from plants, the functional characterization of grass defensins is still in its infancy. In this review, we summarize the current knowledge of the characterized defensins from cultivated and selected wild-growing grasses. For each species, isolation of defensins or production by heterologous expression, peptide structure, biological activity, and structure–function relationship are described, along with the gene expression data. We also provide our results on in silico mining of defensin-like sequences in the genomes of all described grass species and discuss their potential functions. The data presented will form the basis for elucidation of the mode of action of grass defensins and high adaptability of grasses to environmental stress and will provide novel potent molecules for practical use in medicine and agriculture.
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Pinheiro-Aguiar R, do Amaral VSG, Pereira IB, Kurtenbach E, Almeida FCL. Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters. Proteins 2020; 88:242-246. [PMID: 31294889 DOI: 10.1002/prot.25783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/26/2019] [Accepted: 07/06/2019] [Indexed: 11/12/2022]
Abstract
Pisum sativum defensin 2 (Psd2) is a small (4.7 kDa) antifungal peptide whose structure is held together by four conserved disulfide bridges. Psd2 shares the cysteine-stabilized alpha-beta (CSαβ) fold, which lacks a regular hydrophobic core. All hydrophobic residues are exposed to the surface, except for leucine 6. They are clustered in the surface formed by two loops, between β1 and α-helix and β2 and β3 sheets. The observation of surface hydrophobic clusters reveals a remarkable evolution of the CSαβ fold to expose and reorganize hydrophobic residues, which facilitates creating versatile binding sites.
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Affiliation(s)
- Ramon Pinheiro-Aguiar
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Virginia S G do Amaral
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Iuri B Pereira
- Campus Macaé Professor Aloísio Teixeira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Eleonora Kurtenbach
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Fabio C L Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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Boonpa K, Tantong S, Weerawanich K, Panpetch P, Pringsulaka O, Roytrakul S, Sirikantaramas S. In Silico Analyses of Rice Thionin Genes and the Antimicrobial Activity of OsTHION15 Against Phytopathogens. PHYTOPATHOLOGY 2019; 109:27-35. [PMID: 30028233 DOI: 10.1094/phyto-06-17-0217-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Thionins are a family of antimicrobial peptides. We performed in silico expression analyses of the 44 rice (Oryza sativa) thionins (OsTHIONs). Modulated expression levels of OsTHIONs under different treatments suggest their involvement in many processes, including biotic, abiotic, and nutritional stress responses, and in hormone signaling. OsTHION15 (LOC_Os06g32600) was selected for further characterization based on several in silico analyses. OsTHION15 in O. sativa subsp. indica 'KDML 105' was expressed in all of the tissues and organs examined, including germinating seed, leaves, and roots of seedlings and mature plants, and inflorescences. To investigate the antimicrobial activity of OsTHION15, we produced a recombinant peptide in Escherichia coli Rosetta-gami (DE3). The recombinant OsTHION15 exhibited inhibitory activities toward rice-pathogenic bacteria such as Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum pv. atroseptica, with minimum inhibitory concentrations of 112.6 and 14.1 µg ml-1, respectively. A significant hyphal growth inhibition was also observed toward Fusarium oxysporum f. sp. cubense and Helminthosporium oryzae. In addition, we demonstrated the in planta antibacterial activity of this peptide in Nicotiana benthamiana against X. campestris pv. glycines. These activities suggest the possible application of OsTHION15 in plant disease control.
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Affiliation(s)
- Krissana Boonpa
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Suparuk Tantong
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Kamonwan Weerawanich
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Pawinee Panpetch
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Onanong Pringsulaka
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Sittiruk Roytrakul
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Supaart Sirikantaramas
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
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Machado LESF, De Paula VS, Pustovalova Y, Bezsonova I, Valente AP, Korzhnev DM, Almeida FCL. Conformational Dynamics of a Cysteine-Stabilized Plant Defensin Reveals an Evolutionary Mechanism to Expose Hydrophobic Residues. Biochemistry 2018; 57:5797-5806. [PMID: 30207151 DOI: 10.1021/acs.biochem.8b00753] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sugar cane defensin 5 (Sd5) is a small antifungal protein, whose structure is held together by four conserved disulfide bridges. Sd5 and other proteins sharing a cysteine-stabilized α-β (CSαβ) fold lack a regular hydrophobic core. Instead, they are stabilized by tertiary contacts formed by surface-exposed hydrophilic and hydrophobic residues. Despite excessive cross-links, Sd5 exhibits complex millisecond conformational dynamics involving all secondary structure elements. We used Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) measurements performed at different temperatures and denaturant concentrations to probe brief excursions of Sd5 to a sparsely populated "excited" state. Temperature-dependent CPMG RD experiments reveal that the excited state is enthalpically unfavorable, suggesting a rearrangement of stabilizing contacts formed by surface-exposed side chains and/or secondary structure, while the experiments performed at different denaturant concentrations suggest a decrease in accessible surface area of Sd5 in the excited state. The measured backbone 15N chemical shift changes point to a global conformational rearrangement such as a potential α- to β-transition of the Sd5 α-helix or other major secondary structure reorganization and concomitant conformational changes in other parts of the protein. Overall, the emerging picture of Sd5 dynamics suggests this protein can populate two alternative well-ordered conformational states, with the excited conformer being more compact than the native state and having a distinct secondary structure and side-chain arrangements. The observation of an energetically unfavorable yet more compact excited state reveals a remarkable evolution of the CSαβ fold to expose and reorganize hydrophobic residues, which enables the creation of versatile binding sites.
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Affiliation(s)
- Luciana E S F Machado
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica e Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO) , Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
- Department of Molecular Biology and Biophysics , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Viviane S De Paula
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica e Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO) , Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Ana Paula Valente
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica e Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO) , Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics , University of Connecticut Health Center , Farmington , Connecticut 06030 , United States
| | - Fabio C L Almeida
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica e Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO) , Universidade Federal do Rio de Janeiro , Rio de Janeiro 21941-902 , Brazil
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11
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Souza TP, Dias RO, Silva-Filho MC. Defense-related proteins involved in sugarcane responses to biotic stress. Genet Mol Biol 2017; 40:360-372. [PMID: 28222203 PMCID: PMC5452140 DOI: 10.1590/1678-4685-gmb-2016-0057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/27/2016] [Indexed: 11/22/2022] Open
Abstract
Sugarcane is one of the most important agricultural crops in the world. However, pathogen infection and herbivore attack cause constant losses in yield. Plants respond to pathogen infection by inducing the expression of several protein types, such as glucanases, chitinases, thaumatins, peptidase inhibitors, defensins, catalases and glycoproteins. Proteins induced by pathogenesis are directly or indirectly involved in plant defense, leading to pathogen death or inducing other plant defense responses. Several of these proteins are induced in sugarcane by different pathogens or insects and have antifungal or insecticidal activity. In this review, defense-related proteins in sugarcane are described, with their putative mechanisms of action, pathogen targets and biotechnological perspectives.
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Affiliation(s)
- Thais P Souza
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Renata O Dias
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Marcio C Silva-Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
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12
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Polar characterization of antifungal peptides from APD2 Database. Cell Biochem Biophys 2014; 70:1479-88. [PMID: 24980861 DOI: 10.1007/s12013-014-0085-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The increase in the number of pathogens due to fungi that are tolerant to therapies does not grow at the same speed than the advance on new antifungal drugs. In this sense, it is imperative to find anti-fungi peptides that are not detrimental to mammalian cells and have an effective toxicity to fungi. In this work, we use a method called polarity index, to identify anti-fungi peptides with an efficiency of 70 %. This method already published, initially identified selective antibacterial peptides from APD2 Database, and was characterized by developing a comprehensive analysis of the polar dynamics of a peptide from its linear sequence. Discriminating tests showed that in addition to being efficient in this identification, it was also good at rejecting other classifications of peptides found in that same database.
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13
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Revealing the properties of plant defensins through dynamics. Molecules 2013; 18:11311-26. [PMID: 24064452 PMCID: PMC6270066 DOI: 10.3390/molecules180911311] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/07/2013] [Accepted: 09/10/2013] [Indexed: 12/11/2022] Open
Abstract
Defensins are potent, ancient natural antibiotics that are present in organisms ranging from lower organisms to humans. Although the structures of several defensins have been well characterized, the dynamics of only a few have been studied. This review discusses the diverse dynamics of two plant defensins for which the structure and dynamics have been characterized, both in the free state and in the presence of target membranes. Multiple motions are observed in loops and in secondary structure elements and may be related to twisting or breathing of the α-helix and β-sheet. This complex behavior is altered in the presence of an interface and is responsive to the presence of the putative target. The stages of membrane recognition and disruption can be mapped over a large time scale range, demonstrating that defensins in solution exist as an ensemble of different conformations, a subset of which is selected upon membrane binding. Therefore, studies on the dynamics have revealed that defensins interact with membranes through a mechanism of conformational selection.
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14
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De Coninck B, Cammue BP, Thevissen K. Modes of antifungal action and in planta functions of plant defensins and defensin-like peptides. FUNGAL BIOL REV 2013. [DOI: 10.1016/j.fbr.2012.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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15
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Lay FT, Mills GD, Poon IKH, Cowieson NP, Kirby N, Baxter AA, van der Weerden NL, Dogovski C, Perugini MA, Anderson MA, Kvansakul M, Hulett MD. Dimerization of plant defensin NaD1 enhances its antifungal activity. J Biol Chem 2012; 287:19961-72. [PMID: 22511788 PMCID: PMC3370180 DOI: 10.1074/jbc.m111.331009] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 04/16/2012] [Indexed: 11/06/2022] Open
Abstract
The plant defensin, NaD1, from the flowers of Nicotiana alata, is a member of a family of cationic peptides that displays growth inhibitory activity against several filamentous fungi, including Fusarium oxysporum. The antifungal activity of NaD1 has been attributed to its ability to permeabilize membranes; however, the molecular basis of this function remains poorly defined. In this study, we have solved the structure of NaD1 from two crystal forms to high resolution (1.4 and 1.58 Å, respectively), both of which contain NaD1 in a dimeric configuration. Using protein cross-linking experiments as well as small angle x-ray scattering analysis and analytical ultracentrifugation, we show that NaD1 forms dimers in solution. The structural studies identified Lys(4) as critical in formation of the NaD1 dimer. This was confirmed by site-directed mutagenesis of Lys(4) that resulted in substantially reduced dimer formation. Significantly, the reduced ability of the Lys(4) mutant to dimerize correlated with diminished antifungal activity. These data demonstrate the importance of dimerization in NaD1 function and have implications for the use of defensins in agribiotechnology applications such as enhancing plant crop protection against fungal pathogens.
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Affiliation(s)
- Fung T. Lay
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
- Hexima Limited, Melbourne, Victoria 3000, and
| | - Grant D. Mills
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
- Hexima Limited, Melbourne, Victoria 3000, and
| | - Ivan K. H. Poon
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Nathan P. Cowieson
- the Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Nigel Kirby
- the Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Amy A. Baxter
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
- Hexima Limited, Melbourne, Victoria 3000, and
| | - Nicole L. van der Weerden
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
- Hexima Limited, Melbourne, Victoria 3000, and
| | - Con Dogovski
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Matthew A. Perugini
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Marilyn A. Anderson
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
- Hexima Limited, Melbourne, Victoria 3000, and
| | - Marc Kvansakul
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
| | - Mark D. Hulett
- From the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086
- Hexima Limited, Melbourne, Victoria 3000, and
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16
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Lay FT, Mills GD, Hulett MD, Kvansakul M. Crystallization and preliminary X-ray crystallographic analysis of the plant defensin NaD1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:85-8. [PMID: 22232180 PMCID: PMC3253843 DOI: 10.1107/s1744309111049530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 11/19/2011] [Indexed: 11/10/2022]
Abstract
Plant defensins are small (~5 kDa) basic cysteine-rich proteins that are being explored in important agricultural crops for their ability to confer enhanced disease resistance against fungal pathogens. NaD1, isolated from the flowers of the ornamental tobacco (Nicotiana alata), is a particularly well characterized antifungal defensin. Here, the crystallization and preliminary X-ray crystallographic analysis of NaD1 is reported. Crystals of NaD1 were crystallized using the sitting-drop vapour-diffusion method at 291 K. Data were collected from two crystal forms to 1.4 and 1.6 Å resolution, respectively. The crystals of form A belonged to the monoclinic space group P2(1), with unit-cell parameters a = 32.697, b = 32.685, c = 41.977 Å, α = 90, β = 100.828, γ = 90°, whereas crystals of form B belonged to the trigonal space group P3(2)21, with unit-cell parameters a = b = 33.091, c = 128.77 Å, α = β = 90, γ = 120°.
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Affiliation(s)
- Fung T. Lay
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Hexima Limited, Melbourne, VIC 3000, Australia
| | - Grant D. Mills
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mark D. Hulett
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Hexima Limited, Melbourne, VIC 3000, Australia
| | - Marc Kvansakul
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
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17
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Wilmes M, Cammue BPA, Sahl HG, Thevissen K. Antibiotic activities of host defense peptides: more to it than lipid bilayer perturbation. Nat Prod Rep 2011; 28:1350-8. [PMID: 21617811 DOI: 10.1039/c1np00022e] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Defensins are small basic amphiphilic peptides (up to 5 kDa) that have been shown to be important effector molecules of the innate immune system of animals, plants and fungi. In addition to immune modulatory functions, they have potent direct antimicrobial activity against a broad spectrum of bacteria, fungi and/or viruses, which makes them promising lead compounds for the development of next-generation antiinfectives. The mode of antibiotic action of defensins was long thought to result from electrostatic interaction between the positively charged defensins and negatively charged microbial membranes, followed by unspecific membrane permeabilization or pore-formation. Microbial membranes are more negatively charged than human membranes, which may explain to some extent the specificity of defensin action against microbes and associated low toxicity for the host. However, research during the past decade has demonstrated that defensin activities can be much more targeted and that microbe-specific lipid receptors are involved in the killing activity of various defensins. In this respect, human, fungal and invertebrate defensins have been shown to bind to and sequester the bacterial cell wall building block lipid II, thereby specifically inhibiting cell wall biosynthesis. Moreover, plant and insect defensins were found to interact with fungal sphingolipid receptors, resulting in fungal cell death. This review summarizes the current knowledge on the mode of action and structure of defensins from different kingdoms, with specific emphasis on their interaction with microbial lipid receptors.
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Affiliation(s)
- Miriam Wilmes
- Institute of Medical Microbiology, Immunology and Parasitology - Pharmaceutical Microbiology Section, University of Bonn, Meckenheimer Allee 168. 53115, Bonn. Germany
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de Paula VS, Razzera G, Barreto-Bergter E, Almeida FCL, Valente AP. Portrayal of complex dynamic properties of sugarcane defensin 5 by NMR: multiple motions associated with membrane interaction. Structure 2011; 19:26-36. [PMID: 21220113 DOI: 10.1016/j.str.2010.11.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/16/2010] [Accepted: 11/17/2010] [Indexed: 10/18/2022]
Abstract
Defensins are essentially ancient natural antibiotics with potent activity extending from lower organisms to humans. Sd5 is a recently described antifungal defensin that appears to be the result of a recent gain of function. We reported here the solution NMR structure of Sd5 and characterized the backbone dynamics in the free state and in the presence of membrane models. (15)N relaxation dispersion measurements indicate intrinsic conformational exchange processes, showing two clear distinct k(ex), 490 and 1800 s(-1). These multiple motions may be related to transient twisting or breathing of the α helix and β sheet. The stages of membrane recognition and disruption by Sd5 over a large timescale range were mapped and demonstrated that Sd5 in solution sampled an ensemble of different conformations, of which a subset is selected upon membrane binding. Defensins share similar structures, but we demonstrated here that their dynamics can be extremely diverse.
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Affiliation(s)
- Viviane Silva de Paula
- Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Instituto de Bioquímica Médica, Rio de Janeiro, RJ 21941-902, Brazil
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19
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Portieles R, Ayra C, Gonzalez E, Gallo A, Rodriguez R, Chacón O, López Y, Rodriguez M, Castillo J, Pujol M, Enriquez G, Borroto C, Trujillo L, Thomma BPHJ, Borrás-Hidalgo O. NmDef02, a novel antimicrobial gene isolated from Nicotiana megalosiphon confers high-level pathogen resistance under greenhouse and field conditions. PLANT BIOTECHNOLOGY JOURNAL 2010; 8:678-90. [PMID: 20626828 DOI: 10.1111/j.1467-7652.2010.00501.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant defensins are small cysteine-rich peptides that inhibit the growth of a broad range of microbes. In this article, we describe NmDef02, a novel cDNA encoding a putative defensin isolated from Nicotiana megalosiphon upon inoculation with the tobacco blue mould pathogen Peronospora hyoscyami f.sp. tabacina. NmDef02 was heterologously expressed in the yeast Pichia pastoris, and the purified recombinant protein was found to display antimicrobial activity in vitro against important plant pathogens. Constitutive expression of NmDef02 gene in transgenic tobacco and potato plants enhanced resistance against various plant microbial pathogens, including the oomycete Phytophthora infestans, causal agent of the economically important potato late blight disease, under greenhouse and field conditions.
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