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Cotabarren J, Ozón B, Claver S, Geier F, Rossotti M, Garcia-Pardo J, Obregón WD. A Multifunctional Trypsin Protease Inhibitor from Yellow Bell Pepper Seeds: Uncovering Its Dual Antifungal and Hypoglycemic Properties. Pharmaceutics 2023; 15:pharmaceutics15030781. [PMID: 36986642 PMCID: PMC10054557 DOI: 10.3390/pharmaceutics15030781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Fungal infections are a growing public health concern worldwide and the emergence of antifungal resistance has limited the number of therapeutic options. Therefore, developing novel strategies for identifying and developing new antifungal compounds is an active area of research in the pharmaceutical industry. In this study, we purified and characterized a trypsin protease inhibitor obtained from Yellow Bell Pepper (Capsicum annuum L.) seeds. The inhibitor not only showed potent and specific activity against the pathogenic fungus Candida albicans, but was also found to be non-toxic against human cells. Furthermore, this inhibitor is unique in that it also inhibits α-1,4-glucosidase, positioning it as one of the first plant-derived protease inhibitors with dual biological activity. This exciting discovery opens new avenues for the development of this inhibitor as a promising antifungal agent and highlights the potential of plant-derived protease inhibitors as a rich source for the discovery of novel multifunctional bioactive molecules.
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Affiliation(s)
- Juliana Cotabarren
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, 47 y 115 s/N, La Plata B1900AVW, Buenos Aires, Argentina
- Correspondence: (J.C.); (J.G.-P.); (W.D.O.); Tel.: +54-221-423-5333 (ext. 57) (J.C. & W.D.O.); +34-93-586-8936 (J.G.-P.)
| | - Brenda Ozón
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, 47 y 115 s/N, La Plata B1900AVW, Buenos Aires, Argentina
| | - Santiago Claver
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, 47 y 115 s/N, La Plata B1900AVW, Buenos Aires, Argentina
| | - Florencia Geier
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, 47 y 115 s/N, La Plata B1900AVW, Buenos Aires, Argentina
| | - Martina Rossotti
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, 47 y 115 s/N, La Plata B1900AVW, Buenos Aires, Argentina
| | - Javier Garcia-Pardo
- Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Correspondence: (J.C.); (J.G.-P.); (W.D.O.); Tel.: +54-221-423-5333 (ext. 57) (J.C. & W.D.O.); +34-93-586-8936 (J.G.-P.)
| | - Walter David Obregón
- Centro de Investigación de Proteínas Vegetales (CIPROVE), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, 47 y 115 s/N, La Plata B1900AVW, Buenos Aires, Argentina
- Correspondence: (J.C.); (J.G.-P.); (W.D.O.); Tel.: +54-221-423-5333 (ext. 57) (J.C. & W.D.O.); +34-93-586-8936 (J.G.-P.)
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Finkina EI, Melnikova DN, Bogdanov IV, Ovchinnikova TV. Peptides of the Innate Immune System of Plants. Part II. Biosynthesis, Biological Functions, and Possible Practical Applications. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019020043] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gartia J, Anangi R, Joshi RS, Giri AP, King GF, Barnwal RP, Chary KVR. NMR structure and dynamics of inhibitory repeat domain variant 12, a plant protease inhibitor from Capsicum annuum, and its structural relationship to other plant protease inhibitors. J Biomol Struct Dyn 2019; 38:1388-1397. [PMID: 31038412 DOI: 10.1080/07391102.2019.1607559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Although several plant protease inhibitors have been structurally characterized using X-ray crystallography, very few have been studied using NMR techniques. Here, we report an NMR study of the solution structure and dynamics of an inhibitory repeat domain (IRD) variant 12 from the wound-inducible Pin-II type proteinase inhibitor from Capsicum annuum. IRD variant 12 (IRD12) showed strong anti-metabolic activity against the Lepidopteran insect pest, Helicoverpa armigera. The NMR-derived three-dimensional structure of IRD12 reveals a three-stranded anti-parallel β-sheet rigidly held together by four disulfide bridges and shows structural homology with known IRDs. It is interesting to note that the IRD12 structure containing ∼75% unstructured part still shows substantial amount of rigidity of N-H bond vectors with respect to its molecular motion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Janeka Gartia
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Gopanpally, Hyderabad, India
| | - Raveendra Anangi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Rakesh S Joshi
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Pune, India
| | - Ashok P Giri
- CSIR - National Chemical Laboratory, Pune, India
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | - Kandala V R Chary
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Gopanpally, Hyderabad, India.,Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.,Indian Institute of Science Education and Research, Berhampur, Odisha, India
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Cotabarren J, Tellechea ME, Avilés FX, Lorenzo Rivera J, Obregón WD. Biochemical characterization of the YBPCI miniprotein, the first carboxypeptidase inhibitor isolated from Yellow Bell Pepper ( Capsicum annuum L). A novel contribution to the knowledge of miniproteins stability. Protein Expr Purif 2018; 144:55-61. [DOI: 10.1016/j.pep.2017.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
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Widana Gamage SMK, McGrath DJ, Persley DM, Dietzgen RG. Transcriptome Analysis of Capsicum Chlorosis Virus-Induced Hypersensitive Resistance Response in Bell Capsicum. PLoS One 2016; 11:e0159085. [PMID: 27398596 PMCID: PMC4939944 DOI: 10.1371/journal.pone.0159085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Capsicum chlorosis virus (CaCV) is an emerging pathogen of capsicum, tomato and peanut crops in Australia and South-East Asia. Commercial capsicum cultivars with CaCV resistance are not yet available, but CaCV resistance identified in Capsicum chinense is being introgressed into commercial Bell capsicum. However, our knowledge of the molecular mechanisms leading to the resistance response to CaCV infection is limited. Therefore, transcriptome and expression profiling data provide an important resource to better understand CaCV resistance mechanisms. METHODOLOGY/PRINCIPAL FINDINGS We assembled capsicum transcriptomes and analysed gene expression using Illumina HiSeq platform combined with a tag-based digital gene expression system. Total RNA extracted from CaCV/mock inoculated CaCV resistant (R) and susceptible (S) capsicum at the time point when R line showed a strong hypersensitive response to CaCV infection was used in transcriptome assembly. Gene expression profiles of R and S capsicum in CaCV- and buffer-inoculated conditions were compared. None of the genes were differentially expressed (DE) between R and S cultivars when mock-inoculated, while 2484 genes were DE when inoculated with CaCV. Functional classification revealed that the most highly up-regulated DE genes in R capsicum included pathogenesis-related genes, cell death-associated genes, genes associated with hormone-mediated signalling pathways and genes encoding enzymes involved in synthesis of defense-related secondary metabolites. We selected 15 genes to confirm DE expression levels by real-time quantitative PCR. CONCLUSION/SIGNIFICANCE DE transcript profiling data provided comprehensive gene expression information to gain an understanding of the underlying CaCV resistance mechanisms. Further, we identified candidate CaCV resistance genes in the CaCV-resistant C. annuum x C. chinense breeding line. This knowledge will be useful in future for fine mapping of the CaCV resistance locus and potential genetic engineering of resistance into CaCV-susceptible crops.
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Affiliation(s)
- Shirani M. K. Widana Gamage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
| | - Desmond J. McGrath
- Queensland Department of Agriculture and Fisheries, AgriScience Queensland, Gatton, Queensland, Australia
| | - Denis M. Persley
- Queensland Department of Agriculture and Fisheries, AgriScience Queensland, EcoSciences Precinct, Dutton Park, Queensland, Australia
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland, Australia
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Vieira Bard GC, Nascimento VV, Ribeiro SFF, Rodrigues R, Perales J, Teixeira-Ferreira A, Carvalho AO, Fernandes KVS, Gomes VM. Characterization of Peptides from Capsicum annuum Hybrid Seeds with Inhibitory Activity Against α-Amylase, Serine Proteinases and Fungi. Protein J 2015; 34:122-9. [DOI: 10.1007/s10930-015-9604-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Cheraghi R, Hosseinkhani S, Davoodi J, Nazari M, Amini-Bayat Z, Karimi H, Shamseddin M, Gheidari F. Structural and functional effects of circular permutation on firefly luciferase: In vitro assay of caspase 3/7. Int J Biol Macromol 2013; 58:336-42. [DOI: 10.1016/j.ijbiomac.2013.04.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 02/08/2023]
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8
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F. Ribeiro SF, S. Fernandes KV, Santos IS, Taveira GB, Carvalho AO, Lopes JLS, Beltramini LM, Rodrigues R, Vasconcelos IM, Da Cunha M, Souza-Filho GA, Gomes VM. New small proteinase inhibitors fromCapsicum annuumseeds: Characterization, stability, spectroscopic analysis and a cDNA cloning. Biopolymers 2013; 100:132-40. [DOI: 10.1002/bip.22172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/01/2012] [Accepted: 10/08/2012] [Indexed: 11/12/2022]
Affiliation(s)
- Suzanna F. F. Ribeiro
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - Kátia V. S. Fernandes
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - Izabela S. Santos
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - Gabriel B. Taveira
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - André O. Carvalho
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - José Luiz S. Lopes
- Instituto de Física de São Carlos; Grupo de Biofísica Molecular; Universidade de São Paulo; 13560-970; São Paulo; Brazil
| | - Leila M. Beltramini
- Instituto de Física de São Carlos; Grupo de Biofísica Molecular; Universidade de São Paulo; 13560-970; São Paulo; Brazil
| | - Rosana Rodrigues
- Centro de Ciências e Tecnologias Agropecuárias; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - Ilka M. Vasconcelos
- Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Ceará; Fortaleza; Ceará; Brazil
| | - Maura Da Cunha
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - Gonçalo A. Souza-Filho
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
| | - Valdirene M. Gomes
- Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense; Campos dos Goytacazes; 28015-602; Rio de Janeiro; Brazil
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Joshi RS, Mishra M, Tamhane VA, Ghosh A, Sonavane U, Suresh CG, Joshi R, Gupta VS, Giri AP. The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen bond density in the reactive site loop. J Biomol Struct Dyn 2012; 32:13-26. [PMID: 23256852 DOI: 10.1080/07391102.2012.745378] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Capsicum annuum (L.) expresses diverse potato type II family proteinase inhibitors comprising of inhibitory repeat domain (IRD) as basic functional unit. Most IRDs contain eight conserved cysteines forming four disulfide bonds, which are indispensible for their stability and activity. We investigated the functional significance of evolutionary variations in IRDs and their role in mediating interaction between the inhibitor and cognate proteinase. Among the 18 IRDs encoded by C. annuum, IRD-7, -9, and -12 were selected for further characterization on the basis of variation in their reactive site loop, number of conserved cysteine residues, and higher theoretical ΔGbind for interaction with Helicoverpa armigera trypsin. Moreover, inhibition kinetics showed that IRD-9, despite loss of some of the disulfide bonds, was a more potent proteinase inhibitor among the three selected IRDs. Molecular dynamic simulations revealed that serine residues in the place of cysteines at seventh and eighth positions of IRD-9 resulted in an increase in the density of intramolecular hydrogen bonds and reactive site loop flexibility. Results of the serine residues chemical modification also supported this observation and provided a possible explanation for the remarkable inhibitory potential of IRD-9. Furthermore, this natural variant among IRDs showed special attributes like stability to proteolysis and synergistic inhibitory effect on other IRDs. It is likely that IRDs have coevolved selective specialization of their structure and function as a response towards specific insect proteases they encountered. Understanding the molecular mechanism of pest protease-plant proteinaceous inhibitor interaction will help in developing effective pest control strategies. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:39.
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Affiliation(s)
- Rakesh S Joshi
- a Plant Molecular Biology Unit, Biochemical Sciences Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune , 411 008 , MS , India
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Mishra M, Mahajan N, Tamhane VA, Kulkarni MJ, Baldwin IT, Gupta VS, Giri AP. Stress inducible proteinase inhibitor diversity in Capsicum annuum. BMC PLANT BIOLOGY 2012; 12:217. [PMID: 23153298 PMCID: PMC3511207 DOI: 10.1186/1471-2229-12-217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 11/07/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Wound-inducible Pin-II Proteinase inhibitors (PIs) are one of the important plant serine PIs which have been studied extensively for their structural and functional diversity and relevance in plant defense against insect pests. To explore the functional specialization of an array of Capsicum annuum (L.) proteinase inhibitor (CanPIs) genes, we studied their expression, processing and tissue-specific distribution under steady-state and induced conditions. Inductions were performed by subjecting C. annuum leaves to various treatments, namely aphid infestation or mechanical wounding followed by treatment with either oral secretion (OS) of Helicoverpa armigera or water. RESULTS The elicitation treatments regulated the accumulation of CanPIs corresponding to 4-, 3-, and 2-inhibitory repeat domains (IRDs). Fourty seven different CanPI genes composed of 28 unique IRDs were identified in total along with those reported earlier. The CanPI gene pool either from uninduced or induced leaves was dominated by 3-IRD PIs and trypsin inhibitory domains. Also a major contribution by 4-IRD CanPI genes possessing trypsin and chymotrypsin inhibitor domains was specifically revealed in wounded leaves treated with OS. Wounding displayed the highest number of unique CanPIs while wounding with OS treatment resulted in the high accumulation of specifically CanPI-4, -7 and -10. Characterization of the PI protein activity through two dimensional gel electrophoresis revealed tissue and induction specific patterns. Consistent with transcript abundance, wound plus OS or water treated C. annuum leaves exhibited significantly higher PI activity and isoform diversity contributed by 3- and 4-IRD CanPIs. CanPI accumulation and activity was weakly elicited by aphid infestation yet resulted in the higher expression of CanPI-26, -41 and -43. CONCLUSIONS Plants can differentially perceive various kinds of insect attacks and respond appropriately through activating plant defenses including regulation of PIs at transcriptional and post-translational levels. Based on the differentially elicited CanPI accumulation patterns, it is intriguing to speculate that generating sequence diversity in the form of multi-IRD PIs is a part of elaborative plant defense strategy to obtain a diverse pool of functional units to confine insect attack.
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Affiliation(s)
- Manasi Mishra
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Neha Mahajan
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Vaijayanti A Tamhane
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
- Present address: Institute of Bioinformatics and Biotechnology, University of Pune, Pune, MS, 411 007, India
| | - Mahesh J Kulkarni
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Vidya S Gupta
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
| | - Ashok P Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, MS, 411 008, India
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Mishra M, Tamhane VA, Khandelwal N, Kulkarni MJ, Gupta VS, Giri AP. Interaction of recombinant CanPIs with Helicoverpa armigera
gut proteases reveals their processing patterns, stability and efficiency. Proteomics 2010; 10:2845-57. [DOI: 10.1002/pmic.200900853] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Tamhane VA, Giri AP, Kumar P, Gupta VS. Spatial and temporal expression patterns of diverse Pin-II proteinase inhibitor genes in Capsicum annuum Linn. Gene 2009; 442:88-98. [PMID: 19393726 DOI: 10.1016/j.gene.2009.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 04/14/2009] [Accepted: 04/17/2009] [Indexed: 01/09/2023]
Abstract
Pin-II type proteinase inhibitor (PI) genes were cloned from fruit and stem tissues of Capsicum annuum L. var Phule Jyoti using primers designed from reported CanPI gene sequence (AF039398). In total, 21 novel CanPIs, members of the Pin-II PI family, were identified in the study, with three isoforms of 1-inhibitory repeat domain (IRD), eight isoforms of 2-IRD, three isoforms of 3-IRD, five isoforms of 4-IRD and two partial CanPI sequences. Most of the sequences showed variation (2 to 20%) in the deduced AA sequences which were pronounced close to the reactive site loop. Expression patterns of CanPIs in the fruit and stem tissues of mature C. annuum plants were shown to vary qualitatively and quantitatively using semi-quantitative RT-PCR expression analysis. In the fruit tissue, CanPIs with different IRDs (from 1 to 4) were expressed simultaneously. In stem tissue, 1- and 2-IRD CanPIs were strongly expressed along moderate expression of 3- and 4-IRD genes. Analysis of CanPI protein activity showed a range of active forms across the tissues. CanPI expression was differentially up-regulated upon wounding and insect attack. Although infestation by aphids (Myzus persicae) and lepidopteran pests (Spodoptera litura) specifically induced 4-IRD CanPIs, virus-infected leaves did not affect CanPI expression. Analysis of CanPI protein activity indicated that the up-regulation in CanPI expression was not always correlated with increase in PI activity. Our results demonstrated that CanPI expression is regulated spatially, temporally as well as qualitatively and quantitatively.
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Affiliation(s)
- Vaijayanti A Tamhane
- Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune, MS, India
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Kong L, Ranganathan S. Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. BMC Bioinformatics 2008; 9 Suppl 1:S22. [PMID: 18315854 PMCID: PMC2259423 DOI: 10.1186/1471-2105-9-s1-s22] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background The Potato type II (Pot II) family of proteinase inhibitors plays critical roles in the defense system of plants from Solanaceae family against pests. To better understand the evolution of this family, we investigated the correlation between sequence and structural repeats within this family and the evolution and molecular adaptation of Pot II genes through computational analysis, using the putative ancestral domain sequence as the basic repeat unit. Results Our analysis discovered the following interesting findings in Pot II family. (1) We classified the structural domains in Pot II family into three types (original repeat domain, circularly permuted domain, the two-chain domain) according to the existence of two linkers between the two domain components, which clearly show the circular permutation relationship between the original repeat domain and circularly permuted domain. (2) The permuted domains appear more stable than original repeat domain, from available structural information. Therefore, we proposed a multiple-repeat sequence is likely to adopt the permuted domain from contiguous sequence segments, with the N- and C-termini forming a single non-contiguous structural domain, linking the bracelet of tandem repeats. (3) The analysis of nonsynonymous/synonymous substitution rates ratio in Pot II domain revealed heterogeneous selective pressures among amino acid sites: the reactive site is under positive Darwinian selection (providing different specificity to target varieties of proteinases) while the cysteine scaffold is under purifying selection (essential for maintaining the fold). (4) For multi-repeat Pot II genes from Nicotiana genus, the proteolytic processing site is under positive Darwinian selection (which may improve the cleavage efficiency). Conclusion This paper provides comprehensive analysis and characterization of Pot II family, and enlightens our understanding on the strategies (Gene and domain duplication, structural circular permutation and molecular adaptation) of Solanaceae plants for defending pathogenic attacks through the evolution of Pot II genes.
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Affiliation(s)
- Lesheng Kong
- Computational Biology Group, Temasek Life Sciences Laboratory, 1 Reseach Link National University of Singapore, Singapore 117604.
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Lo WC, Lyu PC. CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol 2008; 9:R11. [PMID: 18201387 PMCID: PMC2395249 DOI: 10.1186/gb-2008-9-1-r11] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 11/19/2007] [Accepted: 01/18/2008] [Indexed: 12/04/2022] Open
Abstract
CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation) is an efficient database search tool that provides a new way for rapidly detecting novel relationships among proteins. Circular permutation of a protein can be visualized as if the original amino- and carboxyl termini were linked and new ones created elsewhere. It has been well-documented that circular permutants usually retain native structures and biological functions. Here we report CPSARST (Circular Permutation Search Aided by Ramachandran Sequential Transformation) to be an efficient database search tool. In this post-genomics era, when the amount of protein structural data is increasing exponentially, it provides a new way to rapidly detect novel relationships among proteins.
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Affiliation(s)
- Wei-Cheng Lo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
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Tamhane VA, Giri AP, Sainani MN, Gupta VS. Diverse forms of Pin-II family proteinase inhibitors from Capsicum annuum adversely affect the growth and development of Helicoverpa armigera. Gene 2007; 403:29-38. [PMID: 17870253 DOI: 10.1016/j.gene.2007.07.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2007] [Revised: 07/19/2007] [Accepted: 07/21/2007] [Indexed: 10/23/2022]
Abstract
Novel forms of Pin-II type proteinase inhibitor (PIs) cDNAs (CanPIs) having three or four inhibitory repeat domains (IRD) were isolated from the developing green fruits of Capsicum annuum. Deduced amino acid (aa) sequences of the CanPIs showed up to 15% sequence divergence among each other or reported inhibitors (CanPI-1AF039398, CanPI-2AF221097). Amino acid sequence analysis of these CanPIs revealed that three IRD PIs have trypsin inhibitory sites, while four IRD CanPIs have both trypsin and chymotrypsin inhibitory sites. Four CanPIs, two having three IRD (CanPI-3AY986465 and CanPI-5DQ005912) and two having four IRD (CanPI-7DQ005913 and CanPI-9DQ005915), were cloned in Pichia pastoris to express recombinant CanPIs. Recombinant CanPIs inhibited 90% of bovine trypsin (TI), while chymotrypsin inhibition (CI) varied with the number of chymotrypsin inhibitory sites in the CanPIs. Recombinant inhibitors inhibited over 70% of the gut proteinase activity of Helicoverpa armigera. H. armigera larvae fed on recombinant CanPIs individually incorporated into artificial diet, showed 35% mortality; in addition, weight gain in H. armigera larvae and pupae was severely reduced compared to controls. Of the four CanPIs, CanPI-7, which has two sites for TI and CI, was the only one to have a consistently antagonistic effect on H. armigera growth and development. We conclude that among the four recombinant PIs tested, CanPIs containing diverse IRDs are best suited for developing insect-resistant transgenic plants.
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Affiliation(s)
- Vaijayanti A Tamhane
- Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008 (MS), India
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16
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Damle MS, Giri AP, Sainani MN, Gupta VS. Higher accumulation of proteinase inhibitors in flowers than leaves and fruits as a possible basis for differential feeding preference of Helicoverpa armigera on tomato (Lycopersicon esculentum Mill, Cv. Dhanashree). PHYTOCHEMISTRY 2005; 66:2659-67. [PMID: 16256155 DOI: 10.1016/j.phytochem.2005.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Accepted: 09/12/2005] [Indexed: 05/05/2023]
Abstract
Tomato (Lycopersicon esculentum, Mill; cultivar- Dhanashree) proteinase inhibitors (PIs) were tested for their trypsin inhibitory (TI) and Helicoverpa armigera gut proteinases inhibitory (HGPI) activity in different organs of the tomato plants. Analysis of TI and HGPI distribution in various parts of the plant showed that flowers accumulated about 300 and 1000 times higher levels of TI while 700 and 400 times higher levels of HGPI as compared to those in leaves and fruits, respectively. Field observation that H. armigera larvae infest leaves and fruits but not the flowers could be at least partially attributed to the protective role-played by the higher levels of PIs in the flower tissue. Tomato PIs inhibited about 50-80% HGP activity of H. armigera larvae feeding on various host plants including tomato, of larvae exposed to non-host plant PIs and of various larval instars. Tomato PIs were found to be highly stable to insect proteinases wherein incubation of inhibitor with HGP even for 3h at optimum conditions did not affect inhibitory activity. Bioassay using H. armigera larvae fed on artificial diet containing tomato PIs revealed adverse effect on larval growth, pupae development, adult formation and fecundity.
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Affiliation(s)
- Mrunal S Damle
- Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411 008, India
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17
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Abstract
The interaction of proteinase inhibitors produced, in most cases, by host organisms and the invasive proteinases of pathogens or parasites or the dietary proteinases of predators, results in an evolutionary 'arms race' of rapid and ongoing change in both interacting proteins. The importance of these interactions in pathogenicity and predation is indicated by the high level and diversity of observable evolutionary activity that has been found. At the initial level of evolutionary change, recruitment of other functional protein-folding families has occurred, with the more recent evolution of one class of proteinase inhibitor from another, using the same mechanism and proteinase contact residues. The combination of different inhibitor domains into a single molecule is also observed. The basis from which variation is possible is shown by the high rate of retention of gene duplication events and by the associated process of inhibitory domain multiplication. At this level of reorganization, mutually exclusive splicing is also observed. Finally, the major mechanism by which variation is achieved rapidly is hypervariation of contact residues, an almost ubiquitous feature of proteinase inhibitors. The diversity of evolutionary mechanisms in a single class of proteins is unlikely to be common, because few systems are under similar pressure to create variation. Proteinase inhibitors are therefore a potential model system in which to study basic evolutionary process such as functional diversification.
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Affiliation(s)
- John T Christeller
- Horticulture and Food Research Institute of NZ, Palmerston North, New Zealand.
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18
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Tsoi AYK, Wong RCH, Ng TB, Fong WP. First report on a potato I family chymotrypsin inhibitor from the seeds of a Cucurbitaceous plant, Momordica cochinchinensis. Biol Chem 2004; 385:185-9. [PMID: 15101561 DOI: 10.1515/bc.2004.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A 7514-Da chymotrypsin inhibitor was isolated from the seed extract of Momordica cochinchinensis (Family Cucurbitaceae) by chromatography on chymotrypsin-Sepharose 4B and subsequently by C18 reversed-phase HPLC. This inhibitor, named MCoCl, possessed remarkable thermostability and was stable from pH 2 to 12. MCoCl also inhibited subtilisin, but had at least 50-fold lower inhibitory activity towards trypsin and elastase. Amino acid sequencing of a peptide fragment of MCoCl revealed a sequence of 23 amino acids. Comparison of this sequence and the molecular mass with those of other protease inhibitors suggests that MCoCl belongs to the potato I inhibitor family.
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Affiliation(s)
- Alex Y K Tsoi
- Department of Biochemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China
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19
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Zavala JA, Patankar AG, Gase K, Hui D, Baldwin IT. Manipulation of endogenous trypsin proteinase inhibitor production in Nicotiana attenuata demonstrates their function as antiherbivore defenses. PLANT PHYSIOLOGY 2004; 134:1181-90. [PMID: 14976235 PMCID: PMC389942 DOI: 10.1104/pp.103.035634] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2003] [Revised: 11/30/2003] [Accepted: 12/04/2003] [Indexed: 05/18/2023]
Abstract
Evidence for the in planta defensive function of trypsin protease inhibitors (TPIs) comes from observations of enhanced herbivore resistance after heterologous TPI expression or the manipulation of signal cascades that activate numerous defense responses, including TPI production; no studies have altered the expression of an endogenous pi gene to examine defensive function. We isolated two genes with seven- and six-repeat TPI domains from Nicotiana attenuata from the potato (Solanum tuberosum) PI-II family. To determine whether endogenous TPIs in N. attenuata function defensively against the native herbivores, hornworm (Manduca sexta) and mirids (Tupiocoris notatus), we expressed 175 bp of the seven-domain pi from N. attenuata in an antisense orientation in a TPI-producing genotype to reduce TPI expression and expressed the full-length seven-domain pi in a sense orientation under control of a constitutive promoter to restore TPI activity in a natural genotype from Arizona unable to produce TPIs. Constitutive and inducible TPI production in two antisense lines were diminished by 80% to 90% and 33% to 52%, respectively, and sense expression restored 67% of the activity found in the TPI-producing genotype after caterpillar attack in the TPI-deficient A genotype. Hornworm larvae fed on genotypes with low or no TPI activity grew faster, had higher survivorship, and produced heavier pupae than those that fed on genotypes with high TPI activity. T. notatus showed higher preference for genotypes with low or no TPI activity than for genotypes with high TPI levels. We conclude that endogenous TPIs are an effective defense against these native herbivores.
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Affiliation(s)
- Jorge A Zavala
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
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20
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Tsai LC, Shyur LF, Lee SH, Lin SS, Yuan HS. Crystal structure of a natural circularly permuted jellyroll protein: 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes. J Mol Biol 2003; 330:607-20. [PMID: 12842475 DOI: 10.1016/s0022-2836(03)00630-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes (Fsbeta-glucanase) is classified as one of the family 16 glycosyl hydrolases. It hydrolyzes the glycosidic bond in the mixed-linked glucans containing beta-1,3- and beta-1,4-glycosidic linkages. We constructed a truncated form of recombinant Fsbeta-glucanase containing the catalytic domain from amino acid residues 1-258, which exhibited a higher thermal stability and enzymatic activity than the full-length enzyme. The crystal structure of the truncated Fsbeta-glucanase was solved at a resolution of 1.7A by the multiple wavelength anomalous dispersion (MAD) method using the anomalous signals from the seleno-methionine-labeled protein. The overall topology of the truncated Fsbeta-glucanase consists mainly of two eight-stranded anti-parallel beta-sheets arranged in a jellyroll beta-sandwich, similar to the fold of many glycosyl hydrolases and carbohydrate-binding modules. Sequence comparison with other bacterial glucanases showed that Fsbeta-glucanase is the only naturally occurring circularly permuted beta-glucanase with reversed sequences. Structural comparison shows that the engineered circular-permuted Bacillus enzymes are more similar to their parent enzymes with which they share approximately 70% sequence identity, than to the naturally occurring Fsbeta-glucanase of similar topology with 30% identity. This result suggests that protein structure relies more on sequence identity than topology. The high-resolution structure of Fsbeta-glucanase provides a structural rationale for the different activities obtained from a series of mutant glucanases and a basis for the development of engineered enzymes with increased activity and structural stability.
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Affiliation(s)
- Li-Chu Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
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21
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Barta E, Pintar A, Pongor S. Repeats with variations: accelerated evolution of the Pin2 family of proteinase inhibitors. Trends Genet 2002; 18:600-3. [PMID: 12446136 DOI: 10.1016/s0168-9525(02)02771-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Pin2 genes encode potato type II proteinase inhibitors that act against pathogenic attack. The first examples were found only in the Solanaceae family, but, using new EST and genomic data, we have found 11 homologous genes dispersed through almost the whole range of mono- and di-cotyledonous plants. In contrast to the repetitive precursor sequences of the Solanaceae Pin2 genes, the new homologs have only a single repeat unit. The gene family appears to have evolved from a single-domain ancestral gene through a series of gene-duplication and domain-duplication steps. A number of unequal cross-over and gene conversion events could explain the current gene and domain pattern of the Solanaceae Pin2 subfamily.
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Affiliation(s)
- Endre Barta
- Agricultural Biotechnology Center, 2100, Gödöllo, Hungary
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