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Coppola M, Mach L, Gallois P. Plant cathepsin B, a versatile protease. FRONTIERS IN PLANT SCIENCE 2024; 15:1305855. [PMID: 38463572 PMCID: PMC10920296 DOI: 10.3389/fpls.2024.1305855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/19/2024] [Indexed: 03/12/2024]
Abstract
Plant proteases are essential enzymes that play key roles during crucial phases of plant life. Some proteases are mainly involved in general protein turnover and recycle amino acids for protein synthesis. Other proteases are involved in cell signalling, cleave specific substrates and are key players during important genetically controlled molecular processes. Cathepsin B is a cysteine protease that can do both because of its exopeptidase and endopeptidase activities. Animal cathepsin B has been investigated for many years, and much is known about its mode of action and substrate preferences, but much remains to be discovered about this potent protease in plants. Cathepsin B is involved in plant development, germination, senescence, microspore embryogenesis, pathogen defence and responses to abiotic stress, including programmed cell death. This review discusses the structural features, the activity of the enzyme and the differences between the plant and animal forms. We discuss its maturation and subcellular localisation and provide a detailed overview of the involvement of cathepsin B in important plant life processes. A greater understanding of the cell signalling processes involving cathepsin B is needed for applied discoveries in plant biotechnology.
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Affiliation(s)
- Marianna Coppola
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Patrick Gallois
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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Liu Y, Gong T, Kong X, Sun J, Liu L. XYLEM CYSTEINE PEPTIDASE 1 and its inhibitor CYSTATIN 6 regulate pattern-triggered immunity by modulating the stability of the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D. THE PLANT CELL 2024; 36:471-488. [PMID: 37820743 PMCID: PMC10827322 DOI: 10.1093/plcell/koad262] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
Plants produce a burst of reactive oxygen species (ROS) after pathogen infection to successfully activate immune responses. During pattern-triggered immunity (PTI), ROS are primarily generated by the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD). RBOHD is degraded in the resting state to avoid inappropriate ROS production; however, the enzyme mediating RBOHD degradation and how to prevent RBOHD degradation after pathogen infection is unclear. In this study, we identified an Arabidopsis (Arabidopsis thaliana) vacuole-localized papain-like cysteine protease, XYLEM CYSTEINE PEPTIDASE 1 (XCP1), and its inhibitor CYSTATIN 6 (CYS6). Pathogen-associated molecular pattern-induced ROS burst and resistance were enhanced in the xcp1 mutant but were compromised in the cys6 mutant, indicating that XCP1 and CYS6 oppositely regulate PTI responses. Genetic and biochemical analyses revealed that CYS6 interacts with XCP1 and depends on XCP1 to enhance PTI. Further experiments showed that XCP1 interacts with RBOHD and accelerates RBOHD degradation in a vacuole-mediated manner. CYS6 inhibited the protease activity of XCP1 toward RBOHD, which is critical for RBOHD accumulation upon pathogen infection. As CYS6, XCP1, and RBOHD are conserved in all plant species tested, our findings suggest the existence of a conserved strategy to precisely regulate ROS production under different conditions by modulating the stability of RBOHD.
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Affiliation(s)
- Yang Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Tingting Gong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xiangjiu Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jiaqi Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Lijing Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
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Santos N, Brandstetter H, Dall E. Arabidopsis thaliana Phytocystatin 6 Forms Functional Oligomer and Amyloid Fibril States. Biochemistry 2023; 62:3420-3429. [PMID: 37989209 PMCID: PMC10702442 DOI: 10.1021/acs.biochem.3c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
Cystatins encode a high functional variability not only because of their ability to inhibit different classes of proteases but also because of their propensity to form oligomers and amyloid fibrils. Phytocystatins, essential regulators of protease activity in plants, specifically inhibit papain-like cysteine proteases (PLCPs) and legumains through two distinct cystatin domains. Mammalian cystatins can form amyloid fibrils; however, the potential for amyloid fibril formation of phytocystatins remains unknown. In this study, we demonstrate that Arabidopsis thaliana phytocystatin 6 (AtCYT6) exists as a mixture of monomeric, dimeric, and oligomeric forms in solution. Noncovalent oligomerization was facilitated by the N-terminal cystatin domain, while covalent dimerization occurred through disulfide bond formation in the interdomain linker. The noncovalent dimeric form of AtCYT6 retained activity against its target proteases, papain and legumain, albeit with reduced inhibitory potency. Additionally, we observed the formation of amyloid fibrils by AtCYT6 under acidic pH conditions and upon heating. The amyloidogenic potential could be attributed to the AtCYT6's N-terminal domain (AtCYT6-NTD). Importantly, AtCYT6 amyloid fibrils harbored inhibitory activities against both papain and legumain. These findings shed light on the oligomerization and amyloidogenic behavior of AtCYT6, expanding our understanding of phytocystatin biology and its potential functional implications for plant protease regulation.
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Affiliation(s)
- Naiá
P. Santos
- Department of Biosciences and Medical
Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical
Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Elfriede Dall
- Department of Biosciences and Medical
Biology, University of Salzburg, 5020 Salzburg, Austria
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Santos NP, Soh WT, Demir F, Tenhaken R, Briza P, Huesgen PF, Brandstetter H, Dall E. Phytocystatin 6 is a context-dependent, tight-binding inhibitor of Arabidopsis thaliana legumain isoform β. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1681-1695. [PMID: 37688791 PMCID: PMC10952133 DOI: 10.1111/tpj.16458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/11/2023]
Abstract
Plant legumains are crucial for processing seed storage proteins and are critical regulators of plant programmed cell death. Although research on legumains boosted recently, little is known about their activity regulation. In our study, we used pull-down experiments to identify AtCYT6 as a natural inhibitor of legumain isoform β (AtLEGβ) in Arabidopsis thaliana. Biochemical analysis revealed that AtCYT6 inhibits both AtLEGβ and papain-like cysteine proteases through two separate cystatin domains. The N-terminal domain inhibits papain-like proteases, while the C-terminal domain inhibits AtLEGβ. Furthermore, we showed that AtCYT6 interacts with legumain in a substrate-like manner, facilitated by a conserved asparagine residue in its reactive center loop. Complex formation was additionally stabilized by charged exosite interactions, contributing to pH-dependent inhibition. Processing of AtCYT6 by AtLEGβ suggests a context-specific regulatory mechanism with implications for plant physiology, development, and programmed cell death. These findings enhance our understanding of AtLEGβ regulation and its broader physiological significance.
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Affiliation(s)
- Naiá P. Santos
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
| | - Wai Tuck Soh
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
- Present address:
Max Planck Institute for Multidisciplinary SciencesD‐37077GöttingenGermany
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics52428JülichZEA‐3, Forschungszentrum JülichGermany
- Present address:
Department of BiomedicineAarhus University8000Aarhus CDenmark
| | - Raimund Tenhaken
- Department of Environment and BiodiversityUniversity of Salzburg5020SalzburgAustria
| | - Peter Briza
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics52428JülichZEA‐3, Forschungszentrum JülichGermany
- CECADMedical Faculty and University Hospital, University of Cologne50931CologneGermany
- Institute for Biochemistry, Faculty of Mathematics and Natural SciencesUniversity of Cologne50674CologneGermany
| | - Hans Brandstetter
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
| | - Elfriede Dall
- Department of Biosciences and Medical BiologyUniversity of Salzburg5020SalzburgAustria
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Genome-Wide Identification and Characterization of the Cystatin Gene Family in Bread Wheat ( Triticum aestivum L.). Int J Mol Sci 2021; 22:ijms221910264. [PMID: 34638605 PMCID: PMC8508539 DOI: 10.3390/ijms221910264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 12/03/2022] Open
Abstract
Cystatins, as reversible inhibitors of papain-like and legumain proteases, have been identified in several plant species. Although the cystatin family plays crucial roles in plant development and defense responses to various stresses, this family in wheat (Triticum aestivum L.) is still poorly understood. In this study, 55 wheat cystatins (TaCystatins) were identified. All TaCystatins were divided into three groups and both the conserved gene structures and peptide motifs were relatively conserved within each group. Homoeolog analysis suggested that both homoeolog retention percentage and gene duplications contributed to the abundance of the TaCystatin family. Analysis of duplication events confirmed that segmental duplications played an important role in the duplication patterns. The results of codon usage pattern analysis showed that TaCystatins had evident codon usage bias, which was mainly affected by mutation pressure. TaCystatins may be regulated by cis-acting elements, especially abscisic acid and methyl jasmonate responsive elements. In addition, the expression of all selected TaCystatins was significantly changed following viral infection and cold stress, suggesting potential roles in response to biotic and abiotic challenges. Overall, our work provides new insights into TaCystatins during wheat evolution and will help further research to decipher the roles of TaCystatins under diverse stress conditions.
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Premachandran K, Srinivasan TS, Wilson Alphonse CR. In silico approach on sequential and structural variability in oryzacystatin and its interaction with cysteine protease enzymes of insect. PHYTOCHEMISTRY 2021; 186:112728. [PMID: 33721793 DOI: 10.1016/j.phytochem.2021.112728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
Phytoprotease inhibitors (PI) are important defence compounds produced by plants against microbes and insect herbivory. Oryzacystatins (OCs) are a group of protease inhibitors from Oryza sativa L. that are specific against cysteine protease enzymes. This study revealed the evolutionary relationship of eleven different oryzacystatins from rice and their interaction with cysteine protease enzymes from brown planthopper (BPH) and striped stem borer (SSB). Three-dimensional structure of eleven different oryzacystatins and six cysteine protease enzymes were homologically modelled, and their interaction was analysed to explore the sequence heterogeneity, structural variability and functional significance. OC XI and OC V showed higher docking score and hydrogen bond interaction with all the six tested cysteine protease enzymes. N terminal glycine residue, central conserved QVVXG, C terminal AVVXXXPW regions are involved in interacting with the active site residue of protease enzymes. Substitution of N terminal glycine by any other residue in OC VI significantly reduced the interaction efficiency with cysteine proteases. In OC XI, glutamine in the fourth position of QVVXG showed higher interaction efficiency with all cysteine proteases than serine at the fourth amino acid position. N terminal glycine plays a vital role in OC XI for interacting with active sites of cysteine protease enzymes whereas, in the OC V central conserved region QVVSG and C terminal PW region plays a major part in the interaction. However, either N terminal or C terminal region along with the central conserved region of oryzacystatin is involved in mediating an efficient interaction with the active site residues of cysteine proteases. Molecular dynamic (MD) simulation study revealed the stability of the OC X1 - cathepsin O2 like and OC V - cathepsin F like complexes during a simulation for 20 ns. Insilico results of the present study predict the potential of oryzacystatins interaction with cysteine protease enzymes of insects.
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Affiliation(s)
- Krishnamanikumar Premachandran
- Centre for Climate Change Studies, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - Thanga Suja Srinivasan
- Centre for Climate Change Studies, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India.
| | - Carlton Ranjith Wilson Alphonse
- Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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Shibao PYT, Santos-Júnior CD, Santiago AC, Mohan C, Miguel MC, Toyama D, Vieira MAS, Narayanan S, Figueira A, Carmona AK, Schiermeyer A, Soares-Costa A, Henrique-Silva F. Sugarcane cystatins: From discovery to biotechnological applications. Int J Biol Macromol 2020; 167:676-686. [PMID: 33285201 DOI: 10.1016/j.ijbiomac.2020.11.185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/01/2022]
Abstract
Phytocystatins are tight-binding cysteine protease inhibitors produced by plants. The first phytocystatin described was isolated from Oryza sativa and, since then, cystatins from several plant species were reported, including from sugarcane. Sugarcane cystatins were unraveled in Sugarcane EST project database, after sequencing of cDNA libraries from various sugarcane tissues at different developmental stages and six sugarcane cystatins were cloned, expressed and characterized (CaneCPI-1 to CaneCPI-6). These recombinant proteins were produced in different expression systems and inhibited several cysteine proteases, including human cathepsins B and L, which can be involved in pathologies, such as cancer. In this review, we summarize a comprehensive history of all sugarcane cystatins, presenting an updated phylogenetic analysis; chromosomal localization, and genomic organization. We also present protein docking of CaneCPI-5 in the active site of human cathepsin B, insights about canecystatins structures; recombinant expression in different systems, comparison of their inhibitory activities against human cysteine cathepsins B, K, L, S, V, falcipains from Plasmodium falciparum and a cathepsin L-like from the sugarcane weevil Sphenophorus levis; and enlighten their potential and current applications in agriculture and health.
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Affiliation(s)
- Priscila Yumi Tanaka Shibao
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Célio Dias Santos-Júnior
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | | | - Chakravarthi Mohan
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Mariana Cardoso Miguel
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Danyelle Toyama
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Subramonian Narayanan
- Genetic Transformation Laboratory, Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Antonio Figueira
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Adriana K Carmona
- Department of Biophysics, Federal University of São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Aachen, Germany
| | - Andrea Soares-Costa
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Flavio Henrique-Silva
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.
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Lima AM, Barros NLF, Freitas ACO, Tavares LSC, Pirovani CP, Siqueira AS, Gonçalves EC, de Souza CRB. A new Piper nigrum cysteine proteinase inhibitor, PnCPI, with antifungal activity: molecular cloning, recombinant expression, functional analyses and molecular modeling. PLANTA 2020; 252:16. [PMID: 32661769 DOI: 10.1007/s00425-020-03425-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
A new Piper nigrum cysteine proteinase inhibitor, PnCPI, belonging to group I of phytocystatins, with inhibitory activity against papain and growth of Fusarium solani f. sp. piperis, was isolated and characterized. Previous studies (de Souza et al. 2011) have identified a partial cDNA sequence of putative cysteine proteinase inhibitor differentially expressed in roots of black pepper (P. nigrum L.) infected by F. solani f. sp. piperis. Here, we aimed to isolate the full-length cDNA and genomic sequences of the P. nigrum cysteine proteinase inhibitor gene, named PnCPI. Sequence analyses showed that the PnCPI gene encodes a deduced protein of 108 amino acid residues with a predicted molecular mass of 12.3 kDa and isoelectric point of 6.51. Besides the LARFAV-like sequence, common to all phytocystatins, PnCPI contains three conserved motifs of the superfamily cystatin: a glycine residue at the N-terminal region, the QxVxG reactive site more centrally positioned, and one tryptophan in the C-terminal region. PnCPI, belonging to group I of phytocystatins, showed high identity with cystatins isolated from several plant species. Sequence analyses also revealed no putative signal peptide at the N-terminal of PnCPI, as well as no introns within the genomic sequence corresponding to the PnCPI coding region. Molecular modeling showed the ability of PnCPI to interact with papain, while its inhibitory activity against this protease was confirmed after heterologous expression in Escherichia coli. The effects of heat treatments on the inhibitory activity of recombinant PnCPI, rPnCPI, were evaluated. In addition, rPnCPI exhibited in vitro activity against F. solani f. sp. piperis, revealing a new cystatin with the potential antifungal application. The identification of PnCPI as a functional cystatin able to inhibit the in vitro growth of F. solani f. sp. piperis indicates other factors contributing to in vivo susceptibility of black pepper to root rot disease.
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Affiliation(s)
- Aline Medeiros Lima
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
- Universidade Federal Rural da Amazônia, Tomé-Açu, PA, 68680-000, Brazil
| | - Nicolle Louise Ferreira Barros
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Ana Camila Oliveira Freitas
- Laboratório de Proteômica, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, Km 16, Ilhéus, BA, 45662-900, Brazil
| | | | - Carlos Priminho Pirovani
- Laboratório de Proteômica, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, Km 16, Ilhéus, BA, 45662-900, Brazil
| | - Andrei Santos Siqueira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
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Buet A, Costa ML, Martínez DE, Guiamet JJ. Chloroplast Protein Degradation in Senescing Leaves: Proteases and Lytic Compartments. FRONTIERS IN PLANT SCIENCE 2019; 10:747. [PMID: 31275332 PMCID: PMC6593067 DOI: 10.3389/fpls.2019.00747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
Leaf senescence is characterized by massive degradation of chloroplast proteins, yet the protease(s) involved is(are) not completely known. Increased expression and/or activities of serine, cysteine, aspartic, and metalloproteases were detected in senescing leaves, but these studies have not provided information on the identities of the proteases responsible for chloroplast protein breakdown. Silencing some senescence-associated proteases has delayed progression of senescence symptoms, yet it is still unclear if these proteases are directly involved in chloroplast protein breakdown. At least four cellular pathways involved in the traffic of chloroplast proteins for degradation outside the chloroplast have been described (i.e., "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles"), which differ in their dependence on the autophagic machinery, and the identity of the proteins transported and/or degraded. Finding out the proteases involved in, for example, the degradation of Rubisco, may require piling up mutations in several senescence-associated proteases. Alternatively, targeting a proteinaceous protein inhibitor to chloroplasts may allow the inhibitor to reach "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles" in essentially the way as chloroplast-targeted fluorescent proteins re-localize to these vesicular structures. This might help to reduce proteolytic activity, thereby reducing or slowing down plastid protein degradation during senescence.
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Affiliation(s)
- Agustina Buet
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - M Lorenza Costa
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - Dana E Martínez
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - Juan J Guiamet
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
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Abstract
Dozens of studies have assessed the practical value of plant cystatins as ectopic inhibitors of Cys proteases in biological systems. The potential of these proteins in crop protection to control herbivorous pests and pathogens has been documented extensively over the past 25 years. Their usefulness to regulate endogenous Cys proteases in planta has also been considered recently, notably to implement novel traits of agronomic relevance in crops or to generate protease activity-depleted environments in plants or plant cells used as bioreactors for recombinant proteins. After a brief update on the basic structural characteristics of plant cystatins, we summarize recent advances on the use of these proteins in plant biotechnology. Attention is also paid to the molecular improvement of their structural properties for the improvement of their protease inhibitory effects or the fine-tuning of their biological target range.
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Melo IRS, Dias LP, Araújo NMS, Vasconcelos IM, Martins TF, de Morais GA, Gonçalves JFC, Nagano CS, Carneiro RF, Oliveira JTA. ClCPI, a cysteine protease inhibitor purified from Cassia leiandra seeds has antifungal activity against Candida tropicalis by inducing disruption of the cell surface. Int J Biol Macromol 2019; 133:1115-1124. [PMID: 31034905 DOI: 10.1016/j.ijbiomac.2019.04.174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 12/13/2022]
Abstract
Infections caused by Candida tropicalis have increased significantly worldwide in parallel with resistance to antifungal drugs. To overcome resistance novel drugs have to be discovered. The objective of this work was to purify and characterize a cysteine protease inhibitor from the seeds of the Amazon rainforest tree Cassia leiandra and test its inhibitory effect against C. tropicalis growth. The inhibitor, named ClCPI, was purified after ion exchange and affinity chromatography followed by ultrafiltration. ClCPI is composed of a single polypeptide chain and is not a glycoprotein. The molecular mass determined by SDS-PAGE in the absence or presence of β-mercaptoethanol and ESI-MS were 16.63 kDa and 18.362 kDa, respectively. ClCPI was stable in the pH range of 7.0-9.0 and thermostable up to 60 °C for 20 min. ClCPI inhibited cysteine proteases, but not trypsin, chymotrypsin neither alpha-amylase. Inhibition of papain was uncompetitive with a Ki of 4.1 × 10-7 M and IC50 of 8.5 × 10-7 M. ClCPI at 2.6 × 10-6 M reduced 50% C. tropicalis growth. ClCPI induced damages and morphological alterations in C. tropicalis cell surface, which led to death. These results suggest that ClCPI have great potential for the development of an antifungal drug against C. tropicalis.
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Affiliation(s)
- Ivna R S Melo
- Department of Biochemistry and Molecular Biology, Science Center, Federal University of Ceara (UFC), Fortaleza, CE 60020-181, Brazil
| | - Lucas P Dias
- Department of Biochemistry and Molecular Biology, Science Center, Federal University of Ceara (UFC), Fortaleza, CE 60020-181, Brazil.
| | - Nadine M S Araújo
- Department of Biochemistry and Molecular Biology, Science Center, Federal University of Ceara (UFC), Fortaleza, CE 60020-181, Brazil
| | - Ilka M Vasconcelos
- Department of Biochemistry and Molecular Biology, Science Center, Federal University of Ceara (UFC), Fortaleza, CE 60020-181, Brazil
| | - Thiago F Martins
- Department of Biochemistry and Molecular Biology, Science Center, Federal University of Ceara (UFC), Fortaleza, CE 60020-181, Brazil
| | | | | | - Celso S Nagano
- Department of Fisher Engineering, Center of Agricultural Sciences, UFC, Science Center, UFC, Fortaleza, CE 60020-181, Brazil
| | - Rômulo F Carneiro
- Department of Fisher Engineering, Center of Agricultural Sciences, UFC, Science Center, UFC, Fortaleza, CE 60020-181, Brazil
| | - Jose T A Oliveira
- Department of Biochemistry and Molecular Biology, Science Center, Federal University of Ceara (UFC), Fortaleza, CE 60020-181, Brazil.
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13
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Purification and characterization of a cystatin like thiol protease inhibitor from Brassica nigra. Int J Biol Macromol 2019; 125:1128-1139. [DOI: 10.1016/j.ijbiomac.2018.12.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 11/19/2022]
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14
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Siddiqui MF, Bano B. In-vitro assessment of the binding mechanism of oxyfluorfen (herbicide) with garlic phytocystatin: multi-spectroscopic and isothermal titration calorimetric study. J Biomol Struct Dyn 2019; 37:4120-4131. [DOI: 10.1080/07391102.2018.1544100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Bilqees Bano
- Department of Biochemistry, Aligarh Muslim University, Aligarh, UP, India
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15
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Guzmán-Ortiz FA, Castro-Rosas J, Gómez-Aldapa CA, Mora-Escobedo R, Rojas-León A, Rodríguez-Marín ML, Falfán-Cortés RN, Román-Gutiérrez AD. Enzyme activity during germination of different cereals: A review. FOOD REVIEWS INTERNATIONAL 2018. [DOI: 10.1080/87559129.2018.1514623] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - Javier Castro-Rosas
- Área Académica de Química (AAQ), Universidad Autónoma del Estado de Hidalgo, Hidalgo. CP, Mexico
| | | | - Rosalva Mora-Escobedo
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Zacatenco, Unidad Profesional “Adolfo López Mateos”, Calle Wilfrido Massieu esquina Cda, Mexico City, Mexico
| | - Adriana Rojas-León
- Área Académica de Química (AAQ), Universidad Autónoma del Estado de Hidalgo, Hidalgo. CP, Mexico
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Aceituno-Valenzuela U, Covarrubias MP, Aguayo MF, Valenzuela-Riffo F, Espinoza A, Gaete-Eastman C, Herrera R, Handford M, Norambuena L. Identification of a type II cystatin in Fragaria chiloensis: A proteinase inhibitor differentially regulated during achene development and in response to biotic stress-related stimuli. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:158-167. [PMID: 29883898 DOI: 10.1016/j.plaphy.2018.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/13/2018] [Accepted: 05/18/2018] [Indexed: 05/24/2023]
Abstract
The equilibrium between protein synthesis and degradation is key to maintaining efficiency in different physiological processes. The proteinase inhibitor cystatin regulates protease activities in different developmental and physiological contexts. Here we describe for the first time the identification and the biological function of the cysteine protease inhibitor cystatin of Fragaria chiloensis, FchCYS1. Based on primary sequence and 3D-structural homology modelling, FchCYS1 is a type II phytocystatin with high identity to other cystatins of the Fragaria genus. Both the papain-like and the legumain-like protease inhibitory domains are indeed functional, based on in vitro assays performed with Escherichia coli protein extracts containing recombinant FchCYS1. FchCYS1 is differentially-expressed in achenes of F. chiloensis fruits, with highest expression as the fruit reaches the ripened stage, suggesting a role in preventing degradation of storage proteins that will nourish the embryo during seed germination. Furthermore, FchCYS1 responds transcriptionally to the application of salicylic acid and to mechanical injury, strongly suggesting that FchCYS1 could be involved in the response against pathogen attack. Overall these results point to a role for FchCYS1 in diverse physiological processes in F. chiloensis.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - María Paz Covarrubias
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - María Francisca Aguayo
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | | | - Analía Espinoza
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | | | - Raúl Herrera
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Michael Handford
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Lorena Norambuena
- Plant Molecular Biology Centre, Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago, Chile.
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17
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Molecular Cloning, Recombinant Expression and Antifungal Activity of BnCPI, a Cystatin in Ramie (Boehmeria nivea L.). Genes (Basel) 2017; 8:genes8100265. [PMID: 29019965 PMCID: PMC5664115 DOI: 10.3390/genes8100265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 11/24/2022] Open
Abstract
Phytocystatins play multiple roles in plant growth, development and resistance to pests and other environmental stresses. A ramie (Boehmeria nivea L.) phytocystatin gene, designated as BnCPI, was isolated from a ramie cDNA library and its full-length cDNA was obtained by rapid amplification of cDNA ends (RACE). The full-length cDNA sequence (691 bp) consisted of a 303 bp open reading frame (ORF) encoding a protein of 100 amino acids with deduced molecular mass of 11.06 kDa and a theoretical isoelectric point (pI) of 6.0. The alignment of genome DNA (accession No. MF153097) and cDNA sequences of BnCPI showed that an intron (~104 bp) exists in the coding region. The BnCPI protein contains most of the highly conserved blocks including Gly5-Gly6 at the N-terminal, the reactive site motif QxVxG (Q49V50V51S52G53), the L79-W80 block and the [LVI]-[AGT]-[RKE]-[FY]-[AS]-[VI]-x-[EDQV]-[HYFQ]-N (L22G23R24 F25A26V27 D28D29H30 N31) block that is common among plant cystatins. BLAST analysis indicated that BnCPI is similar to cystatins from Glycine max (77%), Glycine soja (76%), Hevea brasiliensis (75%) and Ricinus communis (75%). The BnCPI was subcloned into expression vector pSmart-I and then overexpressed in Escherichia coli BL21 (DE3) as a His-tagged recombinant protein. The purified reBnCPI has a molecular mass of 11.4 kDa determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE). Purified reBnCPI can efficiently inhibit the protease activity of papain and ficin toward BANA (Nα-benzoyl-L-arginine-2-naphthyamide), as well as the mycelium growth of some important plant pathogenic fungi. The data further contribute to our understanding of the molecular functions of BnCPI.
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Monteiro Júnior JE, Valadares NF, Pereira HD, Dyszy FH, da Costa Filho AJ, Uchôa AF, de Oliveira AS, da Silveira Carvalho CP, Grangeiro TB. Expression in Escherichia coli of cysteine protease inhibitors from cowpea (Vigna unguiculata): The crystal structure of a single-domain cystatin gives insights on its thermal and pH stability. Int J Biol Macromol 2017; 102:29-41. [DOI: 10.1016/j.ijbiomac.2017.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/26/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
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Shamsi A, Ahmed A, Bano B. Structural transition of kidney cystatin induced by silicon dioxide nanoparticles: An implication for renal diseases. Int J Biol Macromol 2017; 94:754-761. [DOI: 10.1016/j.ijbiomac.2016.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/04/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023]
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Szewińska J, Simińska J, Bielawski W. The roles of cysteine proteases and phytocystatins in development and germination of cereal seeds. JOURNAL OF PLANT PHYSIOLOGY 2016; 207:10-21. [PMID: 27771502 DOI: 10.1016/j.jplph.2016.09.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteolysis is an important process for development and germination of cereal seeds. Among the many types of proteases identified in plants are the cysteine proteases (CPs) of the papain and legumain families, which play a crucial role in hydrolysing storage proteins during seed germination as well as in processing the precursors of these proteins and the inactive forms of other proteases. Moreover, all of the tissues of cereal seeds undergo progressive degradation via programed cell death, which is integral to their growth. In view of the important roles played by proteases, their uncontrolled activity could be harmful to the development of seeds and young seedlings. Thus, the activities of these enzymes are regulated by intracellular inhibitors called phytocystatins (PhyCys). The phytocystatins inhibit the activity of proteases of the papain family, and the presence of an additional motif in their C-termini allows them to also regulate the activity of members of the legumain family. A balance between the levels of cysteine proteases and phytocystatins is necessary for proper cereal seed development, and this is maintained through the antagonistic activities of gibberellins (GAs) and abscisic acid (ABA), which regulate the expression of the corresponding genes. Transcriptional regulation of cysteine proteases and phytocystatins is determined by cis-acting elements located in the promoters of these genes and by the expression of their corresponding transcription factors (TFs) and the interactions between different TFs.
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Affiliation(s)
- Joanna Szewińska
- Warsaw University of Life Sciences-SGGW, Faculty of Agriculture and Biology, Department of Biochemistry, Nowoursynowska 159 street, Warsaw 02-776, Poland.
| | - Joanna Simińska
- Warsaw University of Life Sciences-SGGW, Faculty of Agriculture and Biology, Department of Biochemistry, Nowoursynowska 159 street, Warsaw 02-776, Poland
| | - Wiesław Bielawski
- Warsaw University of Life Sciences-SGGW, Faculty of Agriculture and Biology, Department of Biochemistry, Nowoursynowska 159 street, Warsaw 02-776, Poland
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21
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Labudda M, Różańska E, Szewińska J, Sobczak M, Dzik JM. Protease activity and phytocystatin expression in Arabidopsis thaliana upon Heterodera schachtii infection. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 109:416-429. [PMID: 27816823 DOI: 10.1016/j.plaphy.2016.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 05/11/2023]
Abstract
The activity of plant proteases is important for amino acids recycling, removal of damaged proteins as well as defence responses. The second-stage juvenile of the beet cyst nematode Heterodera schachtii penetrates host roots and induces the feeding site called a syncytium. To determine whether infection by H. schachtii affects proteolysis, the protease activity was studied in Arabidopsis roots and shoots at the day of inoculation and 3, 7 and 15 days post inoculation (dpi). Nematode infection caused a decrease of protease activities in infected roots over the entire examination period at all studied pH values. In contrast, the activities of the low molecular mass as well as Ca2+-dependent cysteine proteases were found to be stimulated. In shoots of infected plants, the protease activity was diminished only at 15 dpi at all tested pH values. It was accompanied by changes in total soluble protein content, a higher protein carbonylation and a total polyphenol content. To go deeper into proteolysis regulation, the expression of phytocystatin genes, endogenous inhibitors of cysteine proteases, was examined in syncytia, roots and shoots. Expression of AtCYS1, AtCYS5 and AtCYS6 genes was enhanced upon cyst nematode infection. Our results suggest that changes in protease activities in roots and shoots and altered cystatin expression patterns in syncytia, roots and shoots are important for protein metabolism during cyst nematode infection.
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Affiliation(s)
- Mateusz Labudda
- Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Elżbieta Różańska
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Szewińska
- Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Mirosław Sobczak
- Department of Botany, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Jolanta Maria Dzik
- Department of Biochemistry, Faculty of Agriculture and Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
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Siddiqui AA, Khaki PSS, Bano B. Interaction of almond cystatin with pesticides: Structural and functional analysis. J Mol Recognit 2016; 30. [DOI: 10.1002/jmr.2586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Azad Alam Siddiqui
- Department of Biochemistry, Faculty of life Sciences; Aligarh Muslim University; Aligarh India
| | | | - Bilqees Bano
- Department of Biochemistry, Faculty of life Sciences; Aligarh Muslim University; Aligarh India
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Christoff AP, Passaia G, Salvati C, Alves-Ferreira M, Margis-Pinheiro M, Margis R. Rice bifunctional phytocystatin is a dual modulator of legumain and papain-like proteases. PLANT MOLECULAR BIOLOGY 2016; 92:193-207. [PMID: 27325119 DOI: 10.1007/s11103-016-0504-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/07/2016] [Indexed: 06/06/2023]
Abstract
Phytocystatins are well-known inhibitors of C1A cysteine proteinases. However, previous research has revealed legumain (C13) protease inhibition via a carboxy-extended phytocystatin. Among the 12 phytocystatins genes in rice, OcXII is the only gene possessing this carboxy-terminal extension. The specific legumain inhibition activity was confirmed, in our work, using a recombinant OcXII harboring only the carboxy-terminal domain and this part did not exhibit any effect on papain-like activities. Meanwhile, rice plants silenced at the whole OcXII gene presented higher legumain and papain-like proteolytic activities, resulting in a faster initial seedling growth. However, when germinated under stressful alkaline conditions, OcXII-silenced plants exhibited impaired root formation and delayed shoot growth. Interestingly, the activity of OcXII promoter gene was detected in the rice seed scutellum region, and decreases with seedling growth. Seeds from these plants also exhibited slower growth at germination under ABA or alkaline conditions, while maintaining very high levels of OcXII transcriptional activation. This likely reinforces the proteolytic control necessary for seed germination and growth. In addition, increased legumain activity was detected in OcXII RNAi plants subjected to a fungal elicitor. Overall, the results of this study highlight the association of OcXII with not only plant development processes, but also with stress response pathways. The results of this study reinforce the bifunctional ability of carboxy-extended phytocystatins in regulating legumain proteases via its carboxy-extended domain and papain-like proteases by its amino-terminal domain.
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Affiliation(s)
- Ana Paula Christoff
- PPGBM, Departamento de Genetica, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rs, Brazil
| | - Gisele Passaia
- PPGBM, Departamento de Genetica, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rs, Brazil
| | - Caroline Salvati
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul-UFRGS, Sala 213, Prédio 43431, PO Box 15005, Porto Alegre, Rs, CEP 91501-970, Brazil
| | - Márcio Alves-Ferreira
- Departamento de Genética, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, Rj, Brazil
| | - Marcia Margis-Pinheiro
- PPGBM, Departamento de Genetica, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rs, Brazil
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul-UFRGS, Sala 213, Prédio 43431, PO Box 15005, Porto Alegre, Rs, CEP 91501-970, Brazil
| | - Rogerio Margis
- PPGBM, Departamento de Genetica, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rs, Brazil.
- PPGBCM, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul-UFRGS, Sala 213, Prédio 43431, PO Box 15005, Porto Alegre, Rs, CEP 91501-970, Brazil.
- Departamento de Biofísica, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rs, Brazil.
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Rasoolizadeh A, Goulet MC, Sainsbury F, Cloutier C, Michaud D. Single substitutions to closely related amino acids contribute to the functional diversification of an insect-inducible, positively selected plant cystatin. FEBS J 2016; 283:1323-35. [DOI: 10.1111/febs.13671] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/12/2016] [Accepted: 01/25/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Frank Sainsbury
- Département de Phytologie; Université Laval; Québec City Canada
| | - Conrad Cloutier
- Département de Biologie; Université Laval; Québec City Canada
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25
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Ahmed A, Shamsi A, Bano B. Purification and biochemical characterization of phytocystatin from Brassica alba. J Mol Recognit 2016; 29:223-31. [PMID: 26748819 DOI: 10.1002/jmr.2522] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 10/24/2015] [Accepted: 10/26/2015] [Indexed: 11/10/2022]
Abstract
Phytocystatins belong to the family of cysteine proteinases inhibitors. They are ubiquitously found in plants and carry out various significant physiological functions. These plant derived inhibitors are gaining wide consideration as potential candidate in engineering transgenic crops and in drug designing. Hence it is crucial to identify these inhibitors from various plant sources. In the present study a phytocystatin has been isolated and purified by a simple two-step procedure using ammonium sulfate saturation and gel filtration chromatography on Sephacryl S-100HR from Brassica alba seeds (yellow mustard seeds).The protein was purified to homogeneity with 60.3% yield and 180-fold of purification. The molecular mass of the mustard seed cystatin was estimated to be nearly 26,000 Da by sodium dodecyl sulfate polyacrylamide gel electrophoresis as well as by gel filtration chromatography. The stokes radius and diffusion coefficient of the mustard cystatin were found to be 23A° and 9.4 × 10(-7) cm(2) s(-1) respectively. The isolated phytocystatin was found to be stable in the pH range of 6-8 and is thermostable up to 60 °C. Kinetic analysis revealed that the phytocystatin exhibited non-competitive type of inhibition and inhibited papain more efficiently (K(i) = 3 × 10(-7) M) than ficin (K(i) = 6.6 × 10(-7) M) and bromelain (K(i) = 7.7 × 10(-7) M respectively). CD spectral analysis shows that it possesses 17.11% alpha helical content.
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Affiliation(s)
- Azaj Ahmed
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Anas Shamsi
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
| | - Bilqees Bano
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India
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26
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Hébrard C, Peterson DG, Willems G, Delaunay A, Jesson B, Lefèbvre M, Barnes S, Maury S. Epigenomics and bolting tolerance in sugar beet genotypes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:207-25. [PMID: 26463996 PMCID: PMC4682430 DOI: 10.1093/jxb/erv449] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement.
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Affiliation(s)
- Claire Hébrard
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, 45067 Orléans, France INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans, France SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, 2 Research Blvd., Box 9627, Mississippi State, MS 39762, USA
| | - Glenda Willems
- SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium
| | - Alain Delaunay
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, 45067 Orléans, France INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans, France
| | - Béline Jesson
- IMAXIO/HELIXIO, Biopôle Clermont-Limagne, Saint-Beauzire, F-63360, France
| | - Marc Lefèbvre
- SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium
| | - Steve Barnes
- SESVanderHave N.V./S.A., Soldatenplein Z2 nr15, Industriepark, B-3300 Tienen, Belgium
| | - Stéphane Maury
- Université d'Orléans, Faculté des Sciences, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), UPRES EA 1207, 45067 Orléans, France INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), 45067 Orléans, France
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Simińska J, Orzechowski S, Bielawski W. Analysis of expression and inhibitory activity of a TrcC-6 phytocystatin present in developing and germinating seeds of triticale (×Triticosecale Wittm.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 96:209-216. [PMID: 26298807 DOI: 10.1016/j.plaphy.2015.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/09/2015] [Accepted: 08/10/2015] [Indexed: 06/04/2023]
Abstract
Storage proteins of cereal seeds are processed during accumulation and degraded during germination primarily by cysteine proteinases. One of the mechanisms controlling the activity of these enzymes is the synthesis of specific inhibitors named phytocystatins. Here we present the complete gene sequence of a triticale ( × Triticosecale Wittm.) phytocystatin, TrcC-6, which encodes a 152-amino acid protein with a putative 25-amino acid signal peptide. This protein has a calculated molecular mass of 16.2 kDa, and was assigned to phylogenetic group B of phytocystatins. Because TrcC-6 transcripts are present in triticale seeds, we hypothesized that this phytocystatin regulates storage protein accumulation and degradation. Therefore, changes in gene expression during the entire period of seed development and germination were examined. TrcC-6 transcripts and TrcC-6 protein levels increased during the maturation of seeds and remained high during the first hours of germination. This enabled us to conclude that TrcC-6 likely regulates seed germination by the regulation of storage protein hydrolysis. For the analysis of TrcC-6 inhibitory activity, recombinant protein was expressed in Escherichia coli BL21 (DE3) and purified. Recombinant TrcC-6 proved to be a potent inhibitor of cysteine proteinases. It inhibited the in vitro activity of papain (EC 3.4.22.2) and ficin (EC 3.4.22.3). Furthermore, native PAGE analysis revealed that recombinant TrcC-6 inhibits the activity of endogenous cysteine proteinases present in germinating seeds of triticale. Based on these results, TrcC-6 is likely one of the important factors that regulate cysteine proteinase activity during the accumulation and mobilization of storage proteins.
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Affiliation(s)
- Joanna Simińska
- Department of Biochemistry, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Sławomir Orzechowski
- Department of Biochemistry, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Wiesław Bielawski
- Department of Biochemistry, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
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Liang J, Wang Y, Ding G, Li W, Yang G, He N. Biotic stress-induced expression of mulberry cystatins and identification of cystatin exhibiting stability to silkworm gut proteinases. PLANTA 2015; 242:1139-1151. [PMID: 26070440 DOI: 10.1007/s00425-015-2345-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/01/2015] [Indexed: 06/04/2023]
Abstract
Biotic stresses induce the expression of mulberry cystatins. MaCPI-4 protein is stable in silkworm digestive fluid and accumulates in gut food debris and frass. Plant cystatins are considered to be involved in defense responses to insect herbivores though little is known about how cystatins from the natural host respond to a specialist herbivory and the following postingestive interaction is also poorly understood. Here, we studied the biotic stress-mediated inductions of cystatins from mulberry tree, and examined the stability of mulberry cystatin proteins in the gut of silkworm, Bombyx mori, a specialist insect feeding on mulberry leaf. First, we cloned and characterized six cystatin genes from a mulberry cultivar, Morus atropurpurea Roxb., named as MaCPI-1 to MaCPI-6. The recombinant MaCPI-1, MaCPI-3 and MaCPI-4 proteins, which showed inhibitory effects against papain in vitro, were produced. Silkworm herbivory as well as methyl jasmonate (MeJA) treatment induced the expression of five mulberry cystatin genes, and the highest inductions were observed from MaCPI-1 and MaCPI-6. Mechanical wounding led to the inductions of four cystatin genes. The differential induction occurred in MaCPI-2. The induced protein changes were detected from three mulberry cystatins comprising MaCPI-1, MaCPI-3 and MaCPI-4. In vivo and in vitro assays showed that MaCPI-1 and MaCPI-3 proteins were susceptible to silkworm digestive fluid and MaCPI-4 had an antidigestive stability, and was detected in silkworm gut and frass. Collectively, our data indicated that biotic stresses resulted in the transcriptional inductions and protein changes of mulberry cystatins (MaCPIs), and identified MaCPI-4 with stability in the gut of its specialist herbivore.
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Affiliation(s)
- Jiubo Liang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Yupeng Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Guangyu Ding
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Wensheng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Guangwei Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
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Vorster J, Rasoolizadeh A, Goulet MC, Cloutier C, Sainsbury F, Michaud D. Positive selection of digestive Cys proteases in herbivorous Coleoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 65:10-19. [PMID: 26264818 DOI: 10.1016/j.ibmb.2015.07.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 07/22/2015] [Accepted: 07/31/2015] [Indexed: 06/04/2023]
Abstract
Positive selection is thought to contribute to the functional diversification of insect-inducible protease inhibitors in plants in response to selective pressures exerted by the digestive proteases of their herbivorous enemies. Here we assessed whether a reciprocal evolutionary process takes place on the insect side, and whether ingestion of a positively selected plant inhibitor may translate into a measurable rebalancing of midgut proteases in vivo. Midgut Cys proteases of herbivorous Coleoptera, including the major pest Colorado potato beetle (Leptinotarsa decemlineata), were first compared using a codon-based evolutionary model to look for the occurrence of hypervariable, positively selected amino acid sites among the tested sequences. Hypervariable sites were found, distributed within -or close to- amino acid regions interacting with Cys-type inhibitors of the plant cystatin protein family. A close examination of L. decemlineata sequences indicated a link between their assignment to protease functional families and amino acid identity at positively selected sites. A function-diversifying role for positive selection was further suggested empirically by in vitro protease assays and a shotgun proteomic analysis of L. decemlineata Cys proteases showing a differential rebalancing of protease functional family complements in larvae fed single variants of a model cystatin mutated at positively selected amino acid sites. These data confirm overall the occurrence of hypervariable, positively selected amino acid sites in herbivorous Coleoptera digestive Cys proteases. They also support the idea of an adaptive role for positive selection, useful to generate functionally diverse proteases in insect herbivores ingesting functionally diverse, rapidly evolving dietary cystatins.
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Affiliation(s)
- Juan Vorster
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada; Department of Plant and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Asieh Rasoolizadeh
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Marie-Claire Goulet
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Conrad Cloutier
- Département de biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Frank Sainsbury
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada; The University of Queensland, Australian Institute for Bioengineering and Nanotechnology, Centre for Biomolecular Engineering, St. Lucia, Queensland 4072, Australia
| | - Dominique Michaud
- Département de phytologie, CRIV-Biotechnologie, Université Laval, Québec, QC G1V 0A6, Canada.
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Wang W, Zhao P, Zhou XM, Xiong HX, Sun MX. Genome-wide identification and characterization of cystatin family genes in rice (Oryza sativa L.). PLANT CELL REPORTS 2015; 34:1579-92. [PMID: 26007238 DOI: 10.1007/s00299-015-1810-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 05/26/2023]
Abstract
11 Cystatin genes in rice were identified, and their expression patterns were comprehensively analyzed, which reveals multiple roles in both seed development and plant response to environmental variations. Cystatin is a group of small proteins and known to inhibit the activities of cysteine proteases in the papain C1A and legumain C13 peptidase families in plants. Cystatin family genes have only been well characterized recently in a few plant species such as Hordeum vulgare and Nicotiana tabacum, which show their critical roles in programmed cell death and responses to biotic stresses. Up to now, little is known about cystatin family genes and their roles in Oryza sativa, a model plant for cereal biology study. Here, we identified 11 cystatin genes in rice genome. Comprehensive expression profile analysis reveals that cystatin family genes in rice display diverse expression pattern. They are temporally regulated at different developmental stages during the process of seed production and germination. Our experiments also reveal that the majority of cystatin genes are responsive to plant hormones and different environmental cues including cold, drought and other abiotic stresses, while some others are very stable under different stresses, indicating their fundamental roles in normal plant development. In addition, their distribution in rice chromosomes and their evolutionary relation to the members of Cystatin family in A. thaliana and N. tabacum have also been analyzed. These works suggest multiple roles of cystatin family genes in both seed development and plant response to environmental variations.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Hybrid Rice, Department of Cell and Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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31
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Zhao P, Zhou XM, Zou J, Wang W, Wang L, Peng XB, Sun MX. Comprehensive analysis of cystatin family genes suggests their putative functions in sexual reproduction, embryogenesis, and seed formation. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5093-107. [PMID: 24996653 PMCID: PMC4144781 DOI: 10.1093/jxb/eru274] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Cystatins are tightly bound and reversible inhibitors of cysteine proteases in C1A and C13 peptidase families, which have been identified in several species and shown to function in vegetative development and response to biotic/abiotic stresses in plants. Recent work revealed their critical role in regulating programmed cell death during embryogenesis in tobacco and suggested their more comprehensive roles in the process of sexual plant reproduction, although little is known about cystatin family genes in the processes. Here, 10 cystatin family genes in Nicotiana tabacum were identified using an expressed sequence tag (EST)-based gene clone strategy. Analysis of their biochemical properties showed that nine of them have the potency to inhibit the activities of both commercial cathepsin L-like proteases and extracted cysteine proteases from seeds, but with different K i values depending on the types of proteases and the developmental stages of the seed tested. This suggests that cystatin-dependent cathepsin L-like proteolytic pathways are probably important for early seed development. Comprehensive expression profile analysis revealed that cystatin family genes showed manifold variations in their transcription levels in different plant cell types, including the sperm, egg, and zygote, especially in the embryo and seed at different developmental stages. More interestingly, intracellular localization analysis of each cystatin revealed that most members of cystatin families are recognized as secretory proteins with signal peptides that direct them to the endoplasmic reticulum. These results suggest their widespread roles in cell fate determination and cell-cell communication in the process of sexual reproduction, especially in gamete and embryo development, as well as in seed formation.
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Affiliation(s)
- Peng Zhao
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Xue-mei Zhou
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Jie Zou
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Wei Wang
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
| | - Xiong-bo Peng
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
| | - Meng-xiang Sun
- Department of Cell and Developmental Biology, College of Life Sciences, State Key Laboratory of Plant Hybrid rice, Wuhan University, Wuhan 430072, China
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32
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The diversity of rice phytocystatins. Mol Genet Genomics 2014; 289:1321-30. [DOI: 10.1007/s00438-014-0892-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/24/2014] [Indexed: 11/29/2022]
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Tan Y, Wang S, Liang D, Li M, Ma F. Genome-wide identification and expression profiling of the cystatin gene family in apple (Malus × domestica Borkh.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 79:88-97. [PMID: 24704986 DOI: 10.1016/j.plaphy.2014.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 03/11/2014] [Indexed: 05/01/2023]
Abstract
Cystatins or phytocystatins (PhyCys) comprise a family of plant-specific inhibitors of cysteine proteinases. Such inhibitors are thought to be involved in the regulation of several endogenous processes as well as defense against biotic or abiotic stresses. However, information about this family is limited in apple. We identified 26 PhyCys genes within the entire apple genome. They were clustered into three distinct groups distributed across several chromosomes. All of their putative proteins contained one or two typical cystatin domains, which shared the characteristic motifs of PhyCys. Eight selected genes displayed differential expression patterns in various tissues. Moreover, their transcript levels were also up-regulated significantly in leaves during maturation, senescence or in response to treatment with one or more abiotic stresses. Our results indicated that members of this family may function in tissue development, leaf senescence, and adaptation to adverse environments in apple.
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Affiliation(s)
- Yanxiao Tan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Suncai Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Life Science and Chemistry, Tianshui Normal University, Tianshui, Gansu 748100, PR China
| | - Dong Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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34
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Sun X, Yang S, Sun M, Wang S, Ding X, Zhu D, Ji W, Cai H, Zhao C, Wang X, Zhu Y. A novel Glycine soja cysteine proteinase inhibitor GsCPI14, interacting with the calcium/calmodulin-binding receptor-like kinase GsCBRLK, regulated plant tolerance to alkali stress. PLANT MOLECULAR BIOLOGY 2014; 85:33-48. [PMID: 24407891 DOI: 10.1007/s11103-013-0167-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 12/13/2013] [Indexed: 05/08/2023]
Abstract
It has been well demonstrated that cystatins regulated plant stress tolerance through inhibiting the cysteine proteinase activity under environmental stress. However, there was limited information about the role of cystatins in plant alkali stress response, especially in wild soybean. Here, in this study, we focused on the biological characterization of a novel Glycine soja cystatin protein GsCPI14, which interacted with the calcium/calmodulin-binding receptor-like kinase GsCBRLK and positively regulated plant alkali stress tolerance. The protein-protein interaction between GsCBRLK and GsCPI14 was confirmed by using split-ubiquitin based membrane yeast two-hybrid analysis and bimolecular fluorescence complementation assay. Expression of GsCPI14 was greatly induced by salt, ABA and alkali stress in G. soja, and GsCBRLK overexpression (OX) in Glycine max promoted the stress induction of GmCPI14 expression under stress conditions. Furthermore, we found that GsCPI14-eGFP fusion protein localized in the entire Arabidopsis protoplast and onion epidermal cell, and GsCPI14 showed ubiquitous expression in different tissues of G. soja. In addition, we gave evidence that the GST-GsCPI14 fusion protein inhibited the proteolytic activity of papain in vitro. At last, we demonstrated that OX of GsCPI14 in Arabidopsis promoted the seed germination under alkali stress, as evidenced by higher germination rates. GsCPI14 transgenic Arabidopsis seedlings also displayed better growth performance and physiological index under alkali stress. Taken together, results presented in this study demonstrated that the G. soja cysteine proteinase inhibitor GsCPI14 interacted with the calcium/calmodulin-binding receptor-like kinase GsCBRLK and regulated plant tolerance to alkali stress.
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Affiliation(s)
- Xiaoli Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, People's Republic of China
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35
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Guo K, Bu Y, Takano T, Liu S, Zhang X. Arabidopsis cysteine proteinase inhibitor AtCYSb interacts with a Ca(2+)-dependent nuclease, AtCaN2. FEBS Lett 2013; 587:3417-21. [PMID: 24076026 DOI: 10.1016/j.febslet.2013.09.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/31/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
Plant cysteine proteinase inhibitors (cystatins) play important roles in plant defense mechanisms. Some proteins that interact with cystatins may defend against abiotic stresses. Here, we showed that AtCaN2, a Ca(2+)-dependent nuclease in Arabidopsis, is transcribed in senescent leaves and stems and interacts with an Arabidopsis cystatin (AtCYSb) in a yeast two-hybrid screen. The interaction between AtCYSb and AtCaN2 was confirmed by in vitro pull-down assay and bimolecular fluorescence complementation. Agarose gel electrophoresis showed that the nuclease activity of AtCaN2 against λDNA was inhibited by AtCYSb, which suggests that AtCYSb regulates nucleic acid degradation in cells.
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Affiliation(s)
- Kunyuan Guo
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin 150040, China
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36
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Gholizadeh A. Differential fusion expression and purification of a cystatin in two different bacterial strains. APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683813040054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Rawal HC, Singh NK, Sharma TR. Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants. Int J Genomics 2013; 2013:678969. [PMID: 23671845 PMCID: PMC3647544 DOI: 10.1155/2013/678969] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/04/2013] [Accepted: 01/11/2013] [Indexed: 01/03/2023] Open
Abstract
Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.
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Affiliation(s)
| | | | - T. R. Sharma
- Genoinformatics Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, Pusa Campus, New Delhi 110 012, India
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38
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Gao Y, Xu H, Shen Y, Wang J. Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique. PLANT MOLECULAR BIOLOGY 2013; 81:363-78. [PMID: 23322175 DOI: 10.1007/s11103-013-0009-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/31/2012] [Indexed: 05/11/2023]
Abstract
The endosperm plays an important role in seed formation and germination, especially in rice (Oryza sativa). We used a high-throughput sequencing technique (RNA-Seq) to reveal the molecular mechanisms involved in rice endosperm development. Three cDNA libraries were taken from rice endosperm at 3, 6 and 10 days after pollination (DAP), which resulted in the detection of 21,596, 20,910 and 19,459 expressed gens, respectively. By ERANGE, we identified 10,371 differentially expressed genes (log(2)Ratio ≥1, FDR ≤0.001). The results were compared against three public databases (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes and MapMan) in order to annotate the gene descriptions, associate them with gene ontology terms and to assign each to pathways. A large number of genes related to ribosomes, the spliceosome and oxidative phosphorylation were found to be expressed in the early and middle stages. Plant hormone, galactose metabolism and carbon fixation related genes showed a significant increase in expression at the middle stage, whereas genes for defense against disease or response to stress as well as genes for starch/sucrose metabolism were strongly expressed during the later stages of endosperm development. Interestingly, most metabolic pathways were down-regulated between 3 and 10 DAP except for those involved in the accumulation of material, such as starch/sucrose and protein metabolism. We also identified the expression of 1,118 putative transcription factor genes in endosperm development. The RNA-Seq results provide further systematic understanding of rice endosperm development at a fine scale and a foundation for future studies.
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Affiliation(s)
- Yi Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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39
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Wang Y, Zhan Y, Wu C, Gong S, Zhu N, Chen S, Li H. Cloning of a cystatin gene from sugar beet M14 that can enhance plant salt tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 191-192:93-9. [PMID: 22682568 DOI: 10.1016/j.plantsci.2012.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/27/2012] [Accepted: 05/01/2012] [Indexed: 05/08/2023]
Abstract
An open reading frame encoding a cysteine protease inhibitor, cystatin was isolated from the buds of sugar beet monosomic addition line M14 (BvM14) using 5'-/3'-RACE method. It encoded a polypeptide of 104 amino acids with conserved G and PW motifs, the consensus phytocystatin sequence LARFAV and the active site QVVAG. The protein showed significant homology to other plant cystatins. BvM14-cystatin was expressed ubiquitously in roots, stems, leaves and flower tissues with relatively high abundance in developing stems and roots. It was found to be localized in the nucleus, cytoplasm and plasma membrane. Recombinant BvM14-cystatin expressed in Escherichia coli was purified and it exhibited cysteine protease inhibitor activity. Salt-stress treatment induced BvM14-cystatin transcript levels in the M14 seedlings. Homozygous Arabidopsis plants over-expressing BvM14-cystatin showed enhanced salt tolerance. Taken together, these data improved understanding of the functions of BvM14-cystatin and highlighted the possibility of employing the cystatin in engineering plants for enhanced salt tolerance.
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MESH Headings
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Amino Acid Sequence
- Arabidopsis/drug effects
- Arabidopsis/genetics
- Arabidopsis/physiology
- Base Sequence
- Beta vulgaris/drug effects
- Beta vulgaris/genetics
- Beta vulgaris/physiology
- Cloning, Molecular
- Cystatins/chemistry
- Cystatins/genetics
- Cystatins/metabolism
- Cysteine Proteinase Inhibitors/pharmacology
- DNA, Complementary/genetics
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant/genetics
- Molecular Sequence Data
- Organ Specificity/drug effects
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified
- Recombinant Proteins/metabolism
- Salt Tolerance/drug effects
- Salt Tolerance/genetics
- Sequence Analysis, DNA
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Subcellular Fractions/drug effects
- Subcellular Fractions/metabolism
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Affiliation(s)
- Yuguang Wang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin 150080, China
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40
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Gholizadeh A. Molecular analysis of maize cystatin expression as fusion product in Escherichia coli. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2012; 18:237-44. [PMID: 23814438 PMCID: PMC3550510 DOI: 10.1007/s12298-012-0119-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nowadays, plant cysteine proteinase inhibitors "namely phytocystatins" have attracted researchers towards the identification of their molecular structures and novel physiological functions. Their important roles in plant developmental processes and different stress responses have been well known. In spite of advances in the understanding of phytocystatins, we lack enough data concerning their heterologous expression especially in the forms of fusion products that are most important whether for biochemical, pharmacological or clinical studies. The present work describes an easy method of expression, purification and functional characterization in Escherichia coli of maize cystatin as a part of maltose-binding fusion protein. Assessments revealed that upon expression of fused product the total antioxidation status of the induced recombinant cells is increased. This result leads to question 'Is there any parallel functional correlation between anti-proteolytic and anti-oxidative systems?' However, the present research will open a gate for the new studies regarding the putative communicative roles of these systems that may be existing in the biological world.
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Affiliation(s)
- Ashraf Gholizadeh
- Department of Molecular Biology, Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
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Szewińska J, Zdunek-Zastocka E, Pojmaj M, Bielawski W. Molecular Cloning and Expression Analysis of Triticale Phytocystatins During Development and Germination of Seeds. PLANT MOLECULAR BIOLOGY REPORTER 2012; 30:867-877. [PMID: 24415837 PMCID: PMC3881564 DOI: 10.1007/s11105-011-0384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Three triticale cDNAs encoding inhibitors of cysteine endopeptidases, belonging to phytocystatins, have been identified and designated as TrcC-1, TrcC-4 and TrcC-5. Full-length cDNAs of TrcC-1 (617 bp) and TrcC-4 (940 bp), as well as a fragment of TrcC-5 cDNA (369 bp), were obtained. A high-level identity of the deduced amino acid sequence of TrcCs with other known phytocystatins, especially with wheat and barley, has been observed. Moreover, the presence of conserved domain, containing the G and W residues, the sequence of QxVxG and the sequence of LARFAV, characteristic for plant cysteine endopeptidase inhibitors, has been noted. The profiles of TrcC-1 and TrcC-5 mRNA levels in the developing seeds of two triticale cultivars that differ in their resistance to preharvest sprouting (Zorro and Disco) were similar. However, the expression of TrcC-4 was, higher in the developing seeds, and in the scutellum of germinating seeds of a cultivar more resistant to preharvest sprouting (Zorro) than in the less resistant (Disco). Additionally, the expression of TrcC-4 remained longer in developing seeds of Zorro as compared to Disco. The performed studies suggest that TrcC-4 might have an influence on the higher resistance of Zorro cultivar to preharvest sprouting.
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Affiliation(s)
- Joanna Szewińska
- Department of Biochemistry, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Edyta Zdunek-Zastocka
- Department of Biochemistry, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | | | - Wiesław Bielawski
- Department of Biochemistry, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
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Carrillo L, Herrero I, Cambra I, Sánchez-Monge R, Diaz I, Martinez M. Differential in vitro and in vivo effect of barley cysteine and serine protease inhibitors on phytopathogenic microorganisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:1191-200. [PMID: 21482127 DOI: 10.1016/j.plaphy.2011.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 03/16/2011] [Indexed: 05/03/2023]
Abstract
Protease inhibitors from plants have been involved in defence mechanisms against pests and pathogens. Phytocystatins and trypsin/α-amylase inhibitors are two of the best characterized protease inhibitor families in plants. In barley, thirteen cystatins (HvCPI-1 to 13) and the BTI-CMe trypsin inhibitor have been previously studied. Their capacity to inhibit pest digestive proteases, and the negative in vivo effect caused by plants expressing these inhibitors on pests support the defence function of these proteins. Barley cystatins are also able to inhibit in vitro fungal growth. However, the antifungal effect of these inhibitors in vivo had not been previously tested. Moreover, their in vitro and in vivo effect on plant pathogenous bacteria is still unknown. In order to obtain new insights on this feature, in vitro assays were made against different bacterial and fungal pathogens of plants using the trypsin inhibitor BTI-CMe and the thirteen barley cystatins. Most barley cystatins and the BTI-CMe inhibitor were able to inhibit mycelial growth but no bacterial growth. Transgenic Arabidopsis plants independently expressing the BTI-CMe inhibitor and the cystatin HvCPI-6 were tested against the same bacterial and fungal pathogens. Neither the HvCPI-6 expressing transgenic plants nor the BTI-CMe ones were more resistant to plant pathogen fungi and bacteria than control Arabidopsis plants. The differences observed between the in vitro and in planta assays against phytopathogenic fungi are discussed.
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Affiliation(s)
- Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas, Campus Montegancedo, Universidad Politécnica de Madrid, Autovía M40 (Km 38), 28223-Pozuelo de Alarcón, Madrid, Spain
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43
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Martinez M. Plant protein-coding gene families: emerging bioinformatics approaches. TRENDS IN PLANT SCIENCE 2011; 16:558-567. [PMID: 21757395 DOI: 10.1016/j.tplants.2011.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 06/09/2011] [Accepted: 06/10/2011] [Indexed: 05/31/2023]
Abstract
Protein-coding gene families are sets of similar genes with a shared evolutionary origin and, generally, with similar biological functions. In plants, the size and role of gene families has been only partially addressed. However, suitable bioinformatics tools are being developed to cluster the enormous number of sequences currently available in databases. Specifically, comparative genomic databases promise to become powerful tools for gene family annotation in plant clades. In this review, I evaluate the data retrieved from various gene family databases, the ease with which they can be extracted and how useful the extracted information is.
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Affiliation(s)
- Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus Montegancedo, Universidad Politécnica de Madrid. Autovía M40 (Km 38), 28223-Pozuelo de Alarcón, Madrid, Spain.
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44
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Bangrak P, Chotigeat W. Molecular cloning and biochemical characterization of a novel cystatin from Hevea rubber latex. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:244-50. [PMID: 21247772 DOI: 10.1016/j.plaphy.2010.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 12/14/2010] [Accepted: 12/17/2010] [Indexed: 05/16/2023]
Abstract
A novel cDNA encoding a cysteine proteinase inhibitor or phytocystatin was isolated from Hevea brasiliensis RRIM600 rubber latex cDNA library. The full-length HbCPI obtained from rapid amplification of cDNA ends contains 588 bp. An open reading frame of 306 bp encodes for a protein of 101 amino acids with the typical inhibitory motifs of phytocystatin superfamily, namely the central signature motif QXVXG, a GG doublet and LARFAV-like motifs in the N-terminal part, and conserved A/PW residues in the C-terminal region. Sequence comparison showed that the deduced amino acid sequence was similar to that of cysteine protease inhibitor from Manihot esculenta (84% identity). The HbCPI was subcloned into expression vector pQE-40 and then overexpressed in Escherichia coli M15 strain (pREP4) as a His-tagged recombinant protein with molecular mass approximately 13 kDa. The purified HbCPI showed thermal stable property and efficiently inhibited the protease activity of papain by non-competitive inhibition with K(i) value of 15.4 nM. Beside latex, HbCPI also transcripted in leaf and young seed. The HbCPI message accumulation was induced by phytopathogenic fungi Phytophthora palmivora infection. These data suggest that HbCPI might play crucial roles in defense mechanism against biotic stimuli.
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Affiliation(s)
- Phuwadol Bangrak
- School of Science, Walailak University, 222 Thasala, Nakhon Si Thammarat, Thailand.
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45
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Han F, Zhu B. Evolutionary analysis of three gibberellin oxidase genes in rice, Arabidopsis, and soybean. Gene 2011; 473:23-35. [PMID: 21056641 DOI: 10.1016/j.gene.2010.10.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/19/2010] [Accepted: 10/25/2010] [Indexed: 02/06/2023]
Abstract
GAs are plant hormones that play fundamental roles in plant growth and development. GA2ox, GA3ox, and GA20ox are three key enzymes in GA biosynthesis. These enzymes belong to the 2OG-Fe (II) oxygenase superfamily and are independently encoded by different gene families. To date, genome-wide comparative analyses of GA oxidases in plant species have not been thoroughly carried out. In the present work, 61 GA oxidase family genes from rice (Oryza sativa), Arabidopsis, and soybean (Glycine max) were identified and a full study of these genes including phylogenetic tree construction, gene structure, gene family expansion and analysis of functional motifs was performed. Based on phylogeny, most of the GA oxidases were divided into four subgroups that reflected functional classifications. Intron/intron average length of GA oxidase genes in rice analysis revealed that GA oxidase genes in rice experienced substantial evolutionary divergence. Segmental duplication events were mainly found in soybean genome. However, in rice and Arabidopsis, no single expansion pattern exhibited dominance, indicating that GA oxidase genes from these species might have been subjected to a more complex evolutionary mechanism. In addition, special functional motifs were discovered in GA20ox, GA3ox, and GA2ox, which suggested that different functional motifs are associated with differences in protein function. Taken together our results suggest that GA oxidase family genes have undergone divergent evolutionary routes, especially at the monocot-dicot split, with dynamic evolution occurring in Arabidopsis thaliana and soybean.
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Affiliation(s)
- Fengming Han
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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46
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van der Hoorn RAL, Colby T, Nickel S, Richau KH, Schmidt J, Kaiser M. Mining the Active Proteome of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2011; 2:89. [PMID: 22639616 PMCID: PMC3355598 DOI: 10.3389/fpls.2011.00089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/08/2011] [Indexed: 05/20/2023]
Abstract
Assigning functions to the >30,000 proteins encoded by the Arabidopsis genome is a challenging task of the Arabidopsis Functional Genomics Network. Although genome-wide technologies like proteomics and transcriptomics have generated a wealth of information that significantly accelerated gene annotation, protein activities are poorly predicted by transcript or protein levels as protein activities are post-translationally regulated. To directly display protein activities in Arabidopsis proteomes, we developed and applied activity-based protein profiling (ABPP). ABPP is based on the use of small molecule probes that react with the catalytic residues of distinct protein classes in an activity-dependent manner. Labeled proteins are separated and detected from proteins gels and purified and identified by mass spectrometry. Using probes of six different chemotypes we have displayed activities of 76 Arabidopsis proteins. These proteins represent over 10 different protein classes that contain over 250 Arabidopsis proteins, including cysteine, serine, and metalloproteases, lipases, acyltransferases, and the proteasome. We have developed methods for identification of in vivo labeled proteins using click chemistry and for in vivo imaging with fluorescent probes. In vivo labeling has revealed additional protein activities and unexpected subcellular activities of the proteasome. Labeling of extracts displayed several differential activities, e.g., of the proteasome during immune response and methylesterases during infection. These studies illustrate the power of ABPP to display the functional proteome and testify to a successful interdisciplinary collaboration involving chemical biology, organic chemistry, and proteomics.
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Affiliation(s)
- Renier A. L. van der Hoorn
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Renier A. L. van der Hoorn, Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany. e-mail:
| | - Tom Colby
- Proteomics Service Unit, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Sabrina Nickel
- Fakultät für Biologie, Chemische Biologie, Zentrum für Medizinische Biotechnologie, University of Duisburg-EssenEssen, Germany
| | - Kerstin H. Richau
- Plant Chemetics Lab, Chemical Genomics Centre of the Max Planck Society, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Jürgen Schmidt
- Proteomics Service Unit, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Markus Kaiser
- Fakultät für Biologie, Chemische Biologie, Zentrum für Medizinische Biotechnologie, University of Duisburg-EssenEssen, Germany
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47
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Dutt S, Singh V, Marla SS, Kumar A. In silico analysis of sequential, structural and functional diversity of wheat cystatins and its implication in plant defense. GENOMICS PROTEOMICS & BIOINFORMATICS 2010; 8:42-56. [PMID: 20451161 PMCID: PMC5054136 DOI: 10.1016/s1672-0229(10)60005-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Phytocystatins constitute a multigene family that regulates the activity of endogenous and/or exogenous cysteine proteinases. Cereal crops like wheat are continuously threatened by a multitude of pathogens, therefore cystatins offer to play a pivotal role in deciding the plant response. In order to study the need of having diverse specificities and activities of various cystatins, we conducted comparative analysis of six wheat cystatins (WCs) with twelve rice, seven barley, one sorghum and ten corn cystatin sequences employing different bioinformatics tools. The obtained results identified highly conserved signature sequences in all the cystatins considered. Several other motifs were also identified, based on which the sequences could be categorized into groups in congruence with the phylogenetic clustering. Homology modeling of WCs revealed 3D structural topology so well shared by other cystatins. Protein-protein interaction of WCs with papain supported the notion that functional diversity is a consequence of existing differences in amino acid residues in highly conserved as well as relatively less conserved motifs. Thus there is a significant conservation at the sequential and structural levels; however, concomitant variations maintain the functional diversity in this protein family, which constantly modulates itself to reciprocate the diversity while counteracting the cysteine proteinases.
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48
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Hwang JE, Hong JK, Lim CJ, Chen H, Je J, Yang KA, Kim DY, Choi YJ, Lee SY, Lim CO. Distinct expression patterns of two Arabidopsis phytocystatin genes, AtCYS1 and AtCYS2, during development and abiotic stresses. PLANT CELL REPORTS 2010; 29:905-15. [PMID: 20526604 PMCID: PMC2903682 DOI: 10.1007/s00299-010-0876-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 05/09/2010] [Accepted: 05/19/2010] [Indexed: 05/21/2023]
Abstract
The phytocystatins of plants are members of the cystatin superfamily of proteins, which are potent inhibitors of cysteine proteases. The Arabidopsis genome encodes seven phytocystatin isoforms (AtCYSs) in two distantly related AtCYS gene clusters. We selected AtCYS1 and AtCYS2 as representatives for each cluster and then generated transgenic plants expressing the GUS reporter gene under the control of each gene promoter. These plants were used to examine AtCYS expression at various stages of plant development and in response to abiotic stresses. Histochemical analysis of AtCYS1 promoter- and AtCYS2 promoter-GUS transgenic plants revealed that these genes have similar but distinct spatial and temporal expression patterns during normal development. In particular, AtCYS1 was preferentially expressed in the vascular tissue of all organs, whereas AtCYS2 was expressed in trichomes and guard cells in young leaves, caps of roots, and in connecting regions of the immature anthers and filaments and the style and stigma in flowers. In addition, each AtCYS gene has a unique expression profile during abiotic stresses. High temperature and wounding stress enhanced the expression of both AtCYS1 and AtCYS2, but the temporal and spatial patterns of induction differed. From these data, we propose that these two AtCYS genes play important, but distinct, roles in plant development and stress responses.
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Affiliation(s)
- Jung Eun Hwang
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Joon Ki Hong
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Chan Ju Lim
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Huan Chen
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Jihyun Je
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Kyung Ae Yang
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Dool Yi Kim
- National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707 Korea
| | - Young Ju Choi
- Department of Food and Nutrition, Silla University, Pusan, 617-736 Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
| | - Chae Oh Lim
- Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center and PMBBRC, Graduate School of Gyeongsang National University, Jinju, 660-701 Korea
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49
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Benchabane M, Schlüter U, Vorster J, Goulet MC, Michaud D. Plant cystatins. Biochimie 2010; 92:1657-66. [PMID: 20558232 DOI: 10.1016/j.biochi.2010.06.006] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 06/08/2010] [Indexed: 01/07/2023]
Abstract
Plant cystatins have been the object of intense research since the publication of a first paper reporting their existence more than 20 years ago. These ubiquitous inhibitors of Cys proteases play several important roles in plants, from the control of various physiological and cellular processes in planta to the inhibition of exogenous Cys proteases secreted by herbivorous arthropods and pathogens to digest or colonize plant tissues. After an overview of current knowledge about the evolution, structure and inhibitory mechanism of plant cystatins, we review the different roles attributed to these proteins in plants. The potential of recombinant plant cystatins as effective pesticidal proteins in crop protection is also considered, as well as protein engineering approaches adopted over the years to improve their inhibitory potency and specificity towards Cys proteases of biotechnological interest.
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Affiliation(s)
- Meriem Benchabane
- Département de phytologie, CRH/INAF, Université Laval, Québec (QC), Canada G1V 0A6
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50
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Martinez M, Cambra I, Carrillo L, Diaz-Mendoza M, Diaz I. Characterization of the entire cystatin gene family in barley and their target cathepsin L-like cysteine-proteases, partners in the hordein mobilization during seed germination. PLANT PHYSIOLOGY 2009; 151:1531-45. [PMID: 19759340 PMCID: PMC2773090 DOI: 10.1104/pp.109.146019] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 09/07/2009] [Indexed: 05/18/2023]
Abstract
Plant cystatins are inhibitors of cysteine-proteases of the papain C1A and legumain C13 families. Cystatin data from multiple plant species have suggested that these inhibitors act as defense proteins against pests and pathogens and as regulators of protein turnover. In this study, we characterize the entire cystatin gene family from barley (Hordeum vulgare), which contain 13 nonredundant genes, and identify and characterize their target enzymes, the barley cathepsin L-like proteases. Cystatins and proteases were expressed and purified from Escherichia coli cultures. Each cystatin was found to have different inhibitory capability against barley cysteine-proteases in in vitro inhibitory assays using specific substrates. Real-time reverse transcription-polymerase chain reaction revealed that inhibitors and enzymes present a wide variation in their messenger RNA expression patterns. Their transcripts were mainly detected in developing and germinating seeds, and some of them were also expressed in leaves and roots. Subcellular localization of cystatins and cathepsin L-like proteases fused to green fluorescent protein demonstrated the presence of both protein families throughout the endoplasmic reticulum and the Golgi complex. Proteases and cystatins not only colocalized but also interacted in vivo in the plant cell, as revealed by bimolecular fluorescence complementation. The functional relationship between cystatins and cathepsin L-like proteases was inferred from their common implication as counterparts of mobilization of storage proteins upon barley seed germination. The opposite pattern of transcription expression in gibberellin-treated aleurones presented by inhibitors and enzymes allowed proteases to specifically degrade B, C, and D hordeins stored in the endosperm of barley seeds.
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