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Gomes GDS, Espósito PC, Baracat-Pereira MC. Carboxypeptidase inhibitors from Solanaceae as a new subclass of pathogenesis related peptide aiming biotechnological targets for plant defense. Front Mol Biosci 2023; 10:1259026. [PMID: 38033385 PMCID: PMC10687636 DOI: 10.3389/fmolb.2023.1259026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Background: Plant protease inhibitors play a crucial role in inhibiting proteases produced by phytopathogens and exhibiting inhibitory effects on nematodes, fungi, and insects, making them promising candidates for crop protection. Specifically, carboxypeptidase inhibitors, a subset of proteinase inhibitors, have been extensively studied in potato and tomato of Solanaceae plant family. However, further research is needed to fully understand the functions and biotechnological potential of those inhibitors in plants. This work aimed to in silico characterize carboxypeptidase inhibitors from Solanaceae as potential antimicrobial and defense agents focused on biotechnological targets. Methods: The methodology employed involved search in UniProt, PDB, KNOTTIN, NCBI, and MEROPS databases for solanaceous carboxypeptidase inhibitors, phylogenetic relationships and conservation patterns analyzes using MEGA-X software and Clustal Omega/MView tools, physicochemical properties and antimicrobial potential prediction using ProtParam, ToxinPred, iAMPred, and APD3 tools, and structural features prediction using PSIPRED. Results and discussion: A systematic literature search was conducted to identify relevant studies on Solanaceae carboxypeptidase inhibitors and their activities against pathogens. The selected studies were reviewed and the main findings compiled. The characterization of Solanaceae carboxypeptidase inhibitors proposed for the first time the global sequence consensus motif CXXXCXXXXDCXXXXXCXXC, shedding light on carboxypeptidase inhibitors distribution, sequence variability, and conservation patterns. Phylogenetic analysis showed evolutionary relationships within the Solanaceae family, particularly in Capsicum, Nicotiana, and Solanum genera. Physicochemical characteristics of those peptides indicated their similarity to antimicrobial peptides. Predicted secondary structures exhibited variations, suggesting a broad spectrum of action, and studies had been demonstrated their activities against various pathogens. Conclusion: Carboxypeptidase inhibitors are being proposed here as a new subclass of PR-6 pathogenesis-related proteins, which will aid in a focused understanding of their functional roles in plant defense mechanisms. These findings confirm the Solanaceae carboxypeptidase inhibitors potential as defense agents and highlight opportunities for their biotechnological applications in pathogen control.
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Affiliation(s)
| | | | - Maria Cristina Baracat-Pereira
- Laboratory of Proteomics and Protein Biochemistry, Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Brazil
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Identification and characterization of a wolfberry carboxypeptidase inhibitor from Lycium barbarum. Food Chem 2021; 351:129338. [PMID: 33647700 DOI: 10.1016/j.foodchem.2021.129338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/22/2021] [Accepted: 02/06/2021] [Indexed: 01/13/2023]
Abstract
Hyperstable cysteine-rich peptides (CRPs) represent an underexplored superfamily of bioactives in functional foods. An example is wolfberry of the Lycium barbarum family. Previously, we discovered a CRP, designated α-lybatide, from L. barbarum bark. Herein, we report the discovery of β-lybatide, a novel carboxypeptidase inhibitor belonging to a different CRP family from the wolfberry plant. Proteomic and transcriptomic analyses showed that β-lybatide contains 36 amino acids with six cysteine residues. NMR spectroscopy revealed that β-lybatide displays a knottin-like structure that renders it highly resistant to thermal, chemical and enzymatic degradation, conditions important for keeping its structural integrity in gastrointestinal tract. Biochemical assays showed that β-lybatide is a potent carboxypeptidase inhibitor which could contribute to the wolfberry biological activities. Bioinformatics analysis revealed an additional 49 β-lybatide-like plant carboxypeptidase inhibitors. Together, our results show that β-lybatide is the first and the smallest plant-derived hyperstable carboxypeptidase inhibitor discovered from a functional food.
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Cotabarren J, Lufrano D, Parisi MG, Obregón WD. Biotechnological, biomedical, and agronomical applications of plant protease inhibitors with high stability: A systematic review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110398. [PMID: 32005400 DOI: 10.1016/j.plantsci.2019.110398] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/29/2019] [Accepted: 12/30/2019] [Indexed: 06/10/2023]
Abstract
Protease inhibitors (PIs) are regulatory proteins found in numerous animal tissues and fluids, plants, and microorganisms that reduce and inhibit the exacerbated and uncontrolled activity of the target proteases. Specific PIs are also effective tools for inactivating proteases involved in human diseases like arthritis, pancreatitis, hepatitis, cancer, AIDS, thrombosis, emphysema, hypertension, and muscular dystrophy among others. Plant PIs-small peptides with a high content of cystine residues in disulfide bridges-possess a remarkable resistance to heat treatment and a high stability against shifts in pH, denaturing agents, ionic strength, and proteolysis. In recent years, novel biologic activities have been reported for plant PIs, including antimicrobial, anticoagulant, antioxidant action plus inhibition of tumor-cell growth; thus pointing to possible applications in medicine, agriculture, and biotechnology. In this review, we provide a comparative overview of plant-PIs classifying them in four groups according of their thermal and pH stability (high stability and hyperstable -to temperature and to pHs-, respectively), then emphasizing the relevance of the physicochemical characteristics of these proteins for potential biotechnological and industrial applications. Finally, we analyze the biologic activities of the stable protease inhibitors previously characterized that are the most relevant to potential applications in biomedicine, the food industry, and agriculture.
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Affiliation(s)
- Juliana Cotabarren
- Centro de Investigación de Proteínas Vegetales (CIProVe-CICPBA-UNLP), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 y 115 S/N, B1900AVW, La Plata, Argentina.
| | - Daniela Lufrano
- Centro de Investigación de Proteínas Vegetales (CIProVe-CICPBA-UNLP), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 y 115 S/N, B1900AVW, La Plata, Argentina.
| | - Mónica Graciela Parisi
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Ruta 5 y Avenida Constitución, Luján, 6700, Buenos Aires, Argentina.
| | - Walter David Obregón
- Centro de Investigación de Proteínas Vegetales (CIProVe-CICPBA-UNLP), Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 y 115 S/N, B1900AVW, La Plata, Argentina.
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Crystal structure and mechanism of human carboxypeptidase O: Insights into its specific activity for acidic residues. Proc Natl Acad Sci U S A 2018; 115:E3932-E3939. [PMID: 29636417 DOI: 10.1073/pnas.1803685115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human metallocarboxypeptidase O (hCPO) is a recently discovered digestive enzyme localized to the apical membrane of intestinal epithelial cells. Unlike pancreatic metallocarboxypeptidases, hCPO is glycosylated and produced as an active enzyme with distinctive substrate specificity toward C-terminal (C-t) acidic residues. Here we present the crystal structure of hCPO at 1.85-Å resolution, both alone and in complex with a carboxypeptidase inhibitor (NvCI) from the marine snail Nerita versicolor The structure provides detailed information regarding determinants of enzyme specificity, in particular Arg275, placed at the bottom of the substrate-binding pocket. This residue, located at "canonical" position 255, where it is Ile in human pancreatic carboxypeptidases A1 (hCPA1) and A2 (hCPA2) and Asp in B (hCPB), plays a dominant role in determining the preference of hCPO for acidic C-t residues. Site-directed mutagenesis to Asp and Ala changes the specificity to C-t basic and hydrophobic residues, respectively. The single-site mutants thus faithfully mimic the enzymatic properties of CPB and CPA, respectively. hCPO also shows a preference for Glu over Asp, probably as a consequence of a tighter fitting of the Glu side chain in its S1' substrate-binding pocket. This unique preference of hCPO, together with hCPA1, hCPA2, and hCPB, completes the array of C-t cleavages enabling the digestion of the dietary proteins within the intestine. Finally, in addition to activity toward small synthetic substrates and peptides, hCPO can also trim C-t extensions of proteins, such as epidermal growth factor, suggesting a role in the maturation and degradation of growth factors and bioactive peptides.
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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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Cotabarren J, Tellechea ME, Tanco SM, Lorenzo J, Garcia-Pardo J, Avilés FX, Obregón WD. Biochemical and MALDI-TOF Mass Spectrometric Characterization of a Novel Native and Recombinant Cystine Knot Miniprotein from Solanum tuberosum subsp. andigenum cv. Churqueña. Int J Mol Sci 2018; 19:ijms19030678. [PMID: 29495576 PMCID: PMC5877539 DOI: 10.3390/ijms19030678] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 02/03/2023] Open
Abstract
Cystine-knot miniproteins (CKMPs) are an intriguing group of cysteine-rich molecules that combine the characteristics of proteins and peptides. Typically, CKMPs are fewer than 50 residues in length and share a characteristic knotted scaffold characterized by the presence of three intramolecular disulfide bonds that form the singular knotted structure. The knot scaffold confers on these proteins remarkable chemical, thermal, and proteolytic stability. Recently, CKMPs have emerged as a novel class of natural molecules with interesting pharmacological properties. In the present work, a novel cystine-knot metallocarboxypeptidase inhibitor (chuPCI) was isolated from tubers of Solanum tuberosum, subsp. andigenum cv. Churqueña. Our results demonstrated that chuPCI is a member of the A/B-type family of metallocarboxypeptidases inhibitors. chuPCI was expressed and characterized by a combination of biochemical and mass spectrometric techniques. Direct comparison of the MALDI-TOF mass spectra for the native and recombinant molecules allowed us to confirm the presence of four different forms of chuPCI in the tubers. The majority of such forms have a molecular weight of 4309 Da and contain a cyclized Gln in the N-terminus. The other three forms are derived from N-terminal and/or C-terminal proteolytic cleavages. Taken together, our results contribute to increase the current repertoire of natural CKMPs.
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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, Argentina.
| | - Mariana Edith Tellechea
- 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, Argentina.
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Campus Universitari, Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Sebastián Martín Tanco
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Campus Universitari, Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Julia Lorenzo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Campus Universitari, Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Javier Garcia-Pardo
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193 Barcelona, Spain.
| | - Francesc Xavier Avilés
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Campus Universitari, Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - 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, Argentina.
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Tellechea M, Garcia-Pardo J, Cotabarren J, Lufrano D, Bakas L, Avilés F, Obregon W, Lorenzo J, Tanco S. Microplate Assay to Study Carboxypeptidase A Inhibition in Andean Potatoes. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.2032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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