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Feng H, Jander G. Serine proteinase inhibitors from Nicotiana benthamiana, a nonpreferred host plant, inhibit the growth of Myzus persicae (green peach aphid). PEST MANAGEMENT SCIENCE 2024. [PMID: 38666388 DOI: 10.1002/ps.8148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND The green peach aphid (Myzus persicae) is a severe agricultural crop pest that has developed resistance to most current control methods, requiring the urgent development of novel strategies. Plant proteinase inhibitors (PINs) are small proteins that protect plants against pathogens and/or herbivores, likely by preventing efficient protein digestion. RESULTS We identified 67 protease genes in the transcriptomes of three M. persicae lineages (USDA-Red, G002 and G006). Comparison of gene expression levels in aphid guts and whole aphids showed that several proteases, including a highly expressed serine protease, are significantly overexpressed in the guts. Furthermore, we identified three genes encoding serine protease inhibitors (SerPIN-II1, 2 and 3) in Nicotiana benthamiana, which is a nonpreferred host for M. persicae. Using virus-induced gene silencing (VIGS) with a tobacco rattle virus (TRV) vector and overexpression with a turnip mosaic virus (TuMV) vector, we demonstrated that N. benthamiana SerPIN-II1 and SerPIN-II2 cause reduced survival and growth, but do not affect aphid protein content. Likewise, SerPIN-II3 overexpression reduced survival and growth, and serpin-II3 knockout mutations, which we generated using CRISPR/Cas9, increased survival and growth. Protein content was significantly increased in aphids fed on SerPIN-II3 overexpressing plants, yet it was decreased in aphids fed on serpin-II3 mutants. CONCLUSION Our results show that three PIN-IIs from N. benthamiana, a nonpreferred host plant, effectively inhibit M. persicae survival and growth, thereby representing a new resource for the development of aphid-resistant crop plants. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Honglin Feng
- Boyce Thompson Institute, Ithaca, NY, USA
- Department of Entomology, Louisiana State University AgCenter, Baton Rouge, LA, USA
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Ferreira MM, Santos AS, Santos AS, Zugaib M, Pirovani CP. Plant Serpins: Potential Inhibitors of Serine and Cysteine Proteases with Multiple Functions. PLANTS (BASEL, SWITZERLAND) 2023; 12:3619. [PMID: 37896082 PMCID: PMC10609998 DOI: 10.3390/plants12203619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 10/29/2023]
Abstract
Plant serpins are a superfamily of protein inhibitors that have been continuously studied in different species and have great biotechnological potential. However, despite ongoing studies with these inhibitors, the biological role of this family in the plant kingdom has not yet been fully clarified. In order to obtain new insights into the potential of plant serpins, this study presents the first systematic review of the topic, whose main objective was to scrutinize the published literature to increase knowledge about this superfamily. Using keywords and the eligibility criteria defined in the protocol, we selected studies from the Scopus, PubMed, and Web of Science databases. According to the eligible studies, serpins inhibit different serine and non-serine proteases from plants, animals, and pathogens, and their expression is affected by biotic and abiotic stresses. Moreover, serpins like AtSerpin1, OSP-LRS, MtSer6, AtSRP4, AtSRP5, and MtPiI4, act in resistance and are involved in stress-induced cell death in the plant. Also, the system biology analysis demonstrates that serpins are related to proteolysis control, cell regulation, pollen development, catabolism, and protein dephosphorylation. The information systematized here contributes to the design of new studies of plant serpins, especially those aimed at exploring their biotechnological potential.
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Affiliation(s)
- Monaliza Macêdo Ferreira
- Center for Biotechnology and Genetics, Department of Biological Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil; (A.S.S.); (M.Z.); (C.P.P.)
| | - Ariana Silva Santos
- Center for Biotechnology and Genetics, Department of Biological Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil; (A.S.S.); (M.Z.); (C.P.P.)
| | | | - Maria Zugaib
- Center for Biotechnology and Genetics, Department of Biological Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil; (A.S.S.); (M.Z.); (C.P.P.)
| | - Carlos Priminho Pirovani
- Center for Biotechnology and Genetics, Department of Biological Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil; (A.S.S.); (M.Z.); (C.P.P.)
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3
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Liu Z, Wang C, Li X, Lu X, Liu M, Liu W, Wang T, Zhang X, Wang N, Gao L, Zhang W. The role of shoot-derived RNAs transported to plant root in response to abiotic stresses. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 328:111570. [PMID: 36563939 DOI: 10.1016/j.plantsci.2022.111570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
A large number of RNA molecules are transported over long-distance between shoots and roots via phloem in higher plants. Mobile RNA signals are important for plants to tackle abiotic stresses. Shoot-derived mobile RNAs can be involved in the response to different developmental or environmental signals in the root. Some environmental conditions such as climate change, water deficit, nutrient deficiency challenge modern agriculture with more expeditious abiotic stress conditions. Root architecture determines the ability of water and nutrient uptake and further abiotic stress tolerance, and shoot tissue also determines the balance between shoot-root relationship in plant growth and adaptations. Thus, it is necessary to understand the roles of shoot-derived RNA signals and their potential function in roots upon abiotic stresses in the model plants (Arabidopsis thaliana and Nicotiana benthamiana) and agricultural crops. In this review, we summarize the so-far discovered shoot-derived mobile RNA transportation to the root under abiotic stress conditions, e.g. drought, cold stress and nutrient deficiencies. Furthermore, we will focus on the biological relevance and the potential roles of these RNAs in root development and stress responses which will be an asset for the future breeding strategies.
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Affiliation(s)
- Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Cuicui Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Mengshuang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojing Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Naonao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China.
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4
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Dong C, Huang TC, Roberts TH. Genes Encoding Structurally Conserved Serpins in the Wheat Genome: Identification and Expression Profiles during Plant Development and Abiotic and Biotic Stress. Int J Mol Sci 2023; 24:ijms24032707. [PMID: 36769030 PMCID: PMC9917288 DOI: 10.3390/ijms24032707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
Serpins constitute a family of proteins with a very wide distribution in nature. Serpins have a well-conserved tertiary structure enabling irreversible protease inhibition or other specific biochemical functions. We examined the 189 putative wheat serpin genes previously identified by Benbow et al. (2019) via analysis of gene annotations (RefSeq v1.0) and combined our previous examinations of wheat ESTs and the 454 genome assembly. We found that 81 of the 189 putative serpin genes, plus two manually annotated genes, encode full-length, structurally conserved serpins. Expression of these serpin genes during wheat development and disease/abiotic stress responses was analysed using a publicly available RNAseq database. Results showed that the wheat LR serpins, homologous to Arabidopsis AtSerpin1 and barley BSZx, are ubiquitously expressed across all tissues throughout the wheat lifecycle, whereas the expression of other wheat serpin genes is tissue-specific, including expression only in the grain, only in the root, and only in the anther and microspore. Nine serpin genes were upregulated in both biotic and abiotic responses. Two genes in particular were highly expressed during disease and abiotic challenges. Our findings provide valuable information for further functional study of the wheat serpins, which in turn may lead to their application as molecular markers in wheat breeding.
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Affiliation(s)
- Chongmei Dong
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Plant Breeding Institute, University of Sydney, Cobbitty, NSW 2570, Australia
| | - Ting-Chun Huang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Thomas H. Roberts
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
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5
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Kalemba EM, Valot B, Job D, Bailly C, Meimoun P. Are Methionine Sulfoxide-Containing Proteins Related to Seed Longevity? A Case Study of Arabidopsisthaliana Dry Mature Seeds Using Cyanogen Bromide Attack and Two-Dimensional-Diagonal Electrophoresis. PLANTS (BASEL, SWITZERLAND) 2022; 11:569. [PMID: 35214905 PMCID: PMC8875303 DOI: 10.3390/plants11040569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
In recent years, several reports pointed out the role of protein oxidation in seed longevity, notably regarding the oxidation of methionine (Met) residues to methionine sulfoxide (MetO) in proteins. To further consider this question, we present a handy proteomic method based on the use of two-dimensional diagonal electrophoresis (2Dd) and cyanogen bromide (CNBr) cleavage, which we refer to as 2Dd-CNBr. CNBr treatment of proteins causes the non-enzymatic hydrolysis of peptide bonds on the carboxyl side of reduced Met residues. However, Met oxidation causes a lack of cleavage, thus modifying the electrophoretic mobility of CNBr-induced peptides. This approach was first validated using bovine serum albumin as a model protein, which confirmed the possibility of distinguishing between oxidized and non-oxidized forms of Met-containing peptides in gels. Then, the 2Dd-CNBr method was applied to the Arabidopsis thaliana seed protein extract in a control (non-oxidized) condition and in an oxidized one (as obtained following hypochlorous acid treatment). Twenty-four oxidized Met residues in 19 proteins identified by mass spectrometry were found to be surface exposed in these proteins. In the three-dimensional environment of the oxidized Met, we detected amino acid residues that could be converted by oxidation (carbonylation) or by phosphorylation, suggesting a possible interplay between Met oxidation and the other protein modifications. The identification of the proteins oxidatively modified in Met residues revealed the finding that MetO-containing proteins are related to seed longevity. Based on these results, we suggest that the method presently described also has the potential for wider applications.
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Affiliation(s)
- Ewa Marzena Kalemba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland;
- UMR 7622 Biologie du Développement, IBPS, Sorbonne Université, CNRS, F-75005 Paris, France;
| | - Benoît Valot
- PAPPSO, INRA, CNRS, AgroParisTech, Université Paris-Saclay, GQE-Le Moulon, 91190 Gif-sur-Yvette, France;
- UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Dominique Job
- UMR5240, CNRS, Université Claude Bernarnard Lyon 1, INSA, Bayer CropScience, 69622 Lyon, France;
| | - Christophe Bailly
- UMR 7622 Biologie du Développement, IBPS, Sorbonne Université, CNRS, F-75005 Paris, France;
| | - Patrice Meimoun
- UMR 7622 Biologie du Développement, IBPS, Sorbonne Université, CNRS, F-75005 Paris, France;
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6
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Luke CJ, Markovina S, Good M, Wight IE, Thomas BJ, Linneman JM, Lanik WE, Koroleva O, Coffman MR, Miedel MT, Gong Q, Andress A, Campos Guerrero M, Wang S, Chen L, Beatty WL, Hausmann KN, White FV, Fitzpatrick JAJ, Orvedahl A, Pak SC, Silverman GA. Lysoptosis is an evolutionarily conserved cell death pathway moderated by intracellular serpins. Commun Biol 2022; 5:47. [PMID: 35022507 PMCID: PMC8755814 DOI: 10.1038/s42003-021-02953-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/07/2021] [Indexed: 01/02/2023] Open
Abstract
Lysosomal membrane permeabilization (LMP) and cathepsin release typifies lysosome-dependent cell death (LDCD). However, LMP occurs in most regulated cell death programs suggesting LDCD is not an independent cell death pathway, but is conscripted to facilitate the final cellular demise by other cell death routines. Previously, we demonstrated that Caenorhabditis elegans (C. elegans) null for a cysteine protease inhibitor, srp-6, undergo a specific LDCD pathway characterized by LMP and cathepsin-dependent cytoplasmic proteolysis. We designated this cell death routine, lysoptosis, to distinguish it from other pathways employing LMP. In this study, mouse and human epithelial cells lacking srp-6 homologues, mSerpinb3a and SERPINB3, respectively, demonstrated a lysoptosis phenotype distinct from other cell death pathways. Like in C. elegans, this pathway depended on LMP and released cathepsins, predominantly cathepsin L. These studies suggested that lysoptosis is an evolutionarily-conserved eukaryotic LDCD that predominates in the absence of neutralizing endogenous inhibitors. Cliff Luke et al. report that lysoptosis is a eukaryotic stand-alone regulated cell death pathway. They identify that this new cell death modality predominates in the absence of neutralizing endogenous inhibitors.
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Affiliation(s)
- Cliff J Luke
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Siteman Cancer Center, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.
| | - Stephanie Markovina
- Siteman Cancer Center, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.,Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Misty Good
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Ira E Wight
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Brian J Thomas
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - John M Linneman
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Wyatt E Lanik
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Olga Koroleva
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Maggie R Coffman
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Mark T Miedel
- Department of Computational and Systems biology, Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qingqing Gong
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Arlise Andress
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Marlene Campos Guerrero
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Songyan Wang
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - LiYun Chen
- Radiation Oncology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Wandy L Beatty
- Molecular Microbiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Kelsey N Hausmann
- Molecular Microbiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Frances V White
- Department of Pathology and Immunology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - James A J Fitzpatrick
- Cell Biology and Physiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.,Neuroscience, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Anthony Orvedahl
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Stephen C Pak
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA
| | - Gary A Silverman
- Departments of Pediatrics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Siteman Cancer Center, and Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Cell Biology and Physiology, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA. .,Genetics, Washington University School of Medicine and the Children's Discovery Institute of St. Louis Children's Hospital, St. Louis, MO, USA.
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7
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Wu S, Li X, Wang G. tRNA-like structures and their functions. FEBS J 2021; 289:5089-5099. [PMID: 34117728 DOI: 10.1111/febs.16070] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 06/10/2021] [Indexed: 11/27/2022]
Abstract
tRNA-like structures (TLSs) were first identified in the RNA genomes of turnip yellow mosaic virus. Since then, TLSs have been found in many other species including mammals, and the RNAs harboring these structures range from viral genomic RNAs to mRNAs and noncoding RNAs. Some progress has also been made on understanding their functions that include regulation of RNA replication, translation enhancement, RNA-protein interaction, and more. In this review, we summarize the current knowledge about the regulations and functions of these TLSs. Possible future directions of the field are also briefly discussed.
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Affiliation(s)
- Sipeng Wu
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Xiang Li
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key Laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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8
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Chen G, Li R, Shen X. ApSerpin-ZX from Agapanthus praecox, is a potential cryoprotective agent to plant cryopreservation. Cryobiology 2020; 98:103-111. [PMID: 33316226 DOI: 10.1016/j.cryobiol.2020.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 10/22/2022]
Abstract
Cryopreservation-induced cell death is regarded as an important problem faced by cryobiologists. Oxidative stress and programmed cell death are detrimental to cell survival. Serine protease inhibitors (serpins) inhibit pro-cell-death proteases and play a pro-survival role in excessive cell death induced by abiotic stress. In this study, ApSerpin-ZX was isolated from Agapanthus praecox and characterized as a protective protein in plant cryopreservation. The mRNA level of ApSerpin-ZX was elevated under abiotic stress, such as salt, osmosis, oxidative, cold, and cryoinjury. The purified recombinant protein expressed in E. coli was added to the plant vitrification solution and used for A. praecox embryogenic callus cryopreservation. The concentration of 0.6-4.8 mg∙L-1 of ApSerpin-ZX protein was beneficial to the survival of cryopreserved embryogenic callus of A. praecox. The most effective concentration was 1.2 mg∙L-1, which elevated the survival by 37.15%. Subsequently, the cryopreservation procedure with 1.2 mg∙L-1 of ApSerpin-ZX protein was regarded as the treated group, compared to standard procedure, to determine the physiological mechanism of ApSerpin-ZX protein on cryopreserved cell. The MDA and H2O2 contents were significantly decreased in the treated group, along with reduced OH· generation activity in the recovery stage. After the addition of ApSerpin-ZX, the POD and CAT activities keep increased, while SOD activity increased only after dehydration. Besides, the caspase-1-like and caspase-3-like activities were lower than the standard procedure. This study indicated that ApSerpin-ZX was a potential cryoprotective agent that alleviated oxidative stress and cell death induced by cryopreservation.
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Affiliation(s)
- Guanqun Chen
- School of Design, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Ruilian Li
- School of Design, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaohui Shen
- School of Design, Shanghai Jiao Tong University, Shanghai, 200240, China.
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9
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Rehman S, Jørgensen B, Aziz E, Batool R, Naseer S, Rasmussen SK. Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley. PLANTS 2020; 9:plants9111439. [PMID: 33114466 PMCID: PMC7692276 DOI: 10.3390/plants9111439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/15/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2-P1') identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.
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Affiliation(s)
- Shazia Rehman
- Department of Botany, Rawalpindi Women University, 6th Road, Satellite Town, Rawalpindi 46200, Pakistan
- Department of Botany, Govt. Gordon College Rawalpindi, Rawalpindi 46000, Pakistan
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark;
- Correspondence: (S.R.); (S.K.R.)
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark;
| | - Ejaz Aziz
- Department of Botany, Government Degree College Khanpur, Haripur 22650, Pakistan;
| | - Riffat Batool
- University Institute of Biochemistry and Biotechnology, PMAS, Arid Agriculture University, Rawalpindi, Rawalpindi 46300, Pakistan;
| | - Samar Naseer
- Department of Biology and Environmental Science, Faculty of Sciences, Allama Iqbal Open University, Islamabad 44000, Pakistan;
| | - Søren K. Rasmussen
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark;
- Correspondence: (S.R.); (S.K.R.)
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10
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Valandro F, Menguer PK, Cabreira-Cagliari C, Margis-Pinheiro M, Cagliari A. Programmed cell death (PCD) control in plants: New insights from the Arabidopsis thaliana deathosome. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110603. [PMID: 32900441 DOI: 10.1016/j.plantsci.2020.110603] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/28/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Programmed cell death (PCD) is a genetically controlled process that leads to cell suicide in both eukaryotic and prokaryotic organisms. In plants PCD occurs during development, defence response and when exposed to adverse conditions. PCD acts controlling the number of cells by eliminating damaged, old, or unnecessary cells to maintain cellular homeostasis. Unlike in animals, the knowledge about PCD in plants is limited. The molecular network that controls plant PCD is poorly understood. Here we present a review of the current mechanisms involved with the genetic control of PCD in plants. We also present an updated version of the AtLSD1 deathosome, which was previously proposed as a network controlling HR-mediated cell death in Arabidopsis thaliana. Finally, we discuss the unclear points and open questions related to the AtLSD1 deathosome.
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Affiliation(s)
- Fernanda Valandro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | - Paloma Koprovski Menguer
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | | | - Márcia Margis-Pinheiro
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), RS, Brazil.
| | - Alexandro Cagliari
- Programa de Pós-Graduação em Ambiente e Sustentabilidade, Universidade Estadual do Rio Grande do Sul, RS, Brazil; Universidade Estadual do Rio Grande do Sul (UERGS), RS, Brazil.
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11
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Tolstyko EA, Lezzhov AA, Morozov SY, Solovyev AG. Phloem transport of structured RNAs: A widening repertoire of trafficking signals and protein factors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110602. [PMID: 32900440 DOI: 10.1016/j.plantsci.2020.110602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/20/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
The conducting sieve tubes of the phloem consist of sieve elements (SEs), which are enucleate cells incapable of transcription and translation. Nevertheless, SEs contain a large variety of RNAs, and long-distance RNA trafficking via the phloem has been documented. The phloem transport of certain RNAs, as well as the further unloading of these RNAs at target tissues, is essential for plant individual development and responses to environmental cues. The translocation of such RNAs via the phloem is believed to be directed by RNA structural elements serving as phloem transport signals (PTSs), which are recognized by proteins that direct the PTS-containing RNAs into the phloem translocation pathway. The ability of phloem transport has been reported for several classes of structured RNAs including viroids, genuine tRNAs, mRNAs with tRNA sequences embedded into mRNA untranslated regions, tRNA-like structures in the genomic RNAs of plant viruses, and micro-RNA (miRNA) precursors (pri-miRNA). Here, three distinct types of such RNAs are discussed, along with the proteins that may specifically interact with these structures in the phloem. Three-dimensional (3D) motifs, which are characteristic of imperfect RNA duplexes, are discussed as elements of phloem-mobile structured RNAs specifically recognized by proteins involved in phloem transport, thus serving as PTSs.
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Affiliation(s)
- Eugeny A Tolstyko
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119991, Russia
| | - Sergey Y Morozov
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.
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12
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Expression and function assessment of two serpin-type serine protease inhibitors from Haemaphysalis doenitzi. Res Vet Sci 2020; 132:1-9. [PMID: 32464311 DOI: 10.1016/j.rvsc.2020.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 04/17/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022]
Abstract
Serine protease inhibitors (serpins) in ticks are implicated in the modulation of the vertebrate host response to the tick bite. Experimentally, it has been demonstrated that serpins interfere with tick-borne pathogen transmission. However, knowledge on serpins in the tick Haemaphysalis doenitzi is lacking. In this study, the expression of two serpin genes, named HDS1 and HDS2, were assessed in H. doenitzi, and their roles in immune regulation were further investigated. The expression of HDS1 and HDS2 showed no tissue specificity, with maximum expression levels detected in the hemolymph and salivary gland, respectively. Among the developmental stages, the highest expression of HDS1 and HDS2 were detected in larvae and adults, respectively. The recombinant protein rHDS1 displayed obvious inhibitory effects on trypsin and thrombin, whereas rHDS2 clearly inhibited thrombin only. In addition, rHDS1 and rHDS2 showed certain inhibitory activities against bacteria and fungi. The female engorgement body weight, female engorgement rate, and egg hatchability were significantly decreased after injection of double-stranded RNA (dsRNA) of HDS1 gene, whereas no significant effects were observed concerning the feeding period or attachment rate at 24 h after introduction via rabbit ears. When injected with dsRNA of HDS2 gene, no significant effect was observed on the attachment rate at 24 h after introduction into the rabbit ears, but the engorgement body weight and engorgement rate of female ticks were significantly decreased, and no egg hatchment occurred. The above results contribute to better understanding the function of serpins in the development and innate immunity of H. doenitzi.
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13
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Detection and in vitro studies of Cucurbita maxima phloem serpin-1 RNA-binding properties. Biochimie 2020; 170:118-127. [PMID: 31935442 DOI: 10.1016/j.biochi.2020.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/09/2020] [Indexed: 11/22/2022]
Abstract
Apart from being a conduit for photoassimilate transport in plants, the phloem serves as a pathway for transport of proteins and RNAs from sites of their synthesis to distant plant parts. As demonstrated for mRNAs and small RNAs such as miRNA and siRNA, their phloem transport is largely involved in responses to environmental cues including stresses and pathogen attacks. RNA molecules are believed to be transported in the phloem in the form of complexes with RNA-binding proteins; however, proteins forming such complexes are generally poorly studied. Here, we demonstrate that the Cucurbita maxima phloem serpin-1 (CmPS1), which has been previously described as a functional protease inhibitor capable of long-distance transport via the phloem, is able to bind RNA in vitro. Among different RNAs tested, CmPS1 exhibits a preference for imperfect RNA duplexes and the highest affinity to tRNA. A characteristic complex formed by CmPS1 with tRNA is not observed upon CmPS1 binding to tRNA-like structures of plant viruses. Mutational analysis demonstrates that the CmPS1 N-terminal region is not involved in RNA binding. Since antithrombin-III, the human protease inhibitor of serpin family most closely sequence-related to CmPS1, is found to be unable to bind RNA, one can suggest that, in its evolution, CmPS1 has gained the RNA binding capability as an additional function likely relevant to its specific activities in the plant phloem.
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14
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Lai Y, Zhang D, Wang J, Wang J, Ren P, Yao L, Si E, Kong Y, Wang H. Integrative Transcriptomic and Proteomic Analyses of Molecular Mechanism Responding to Salt Stress during Seed Germination in Hulless Barley. Int J Mol Sci 2020; 21:ijms21010359. [PMID: 31935789 PMCID: PMC6981547 DOI: 10.3390/ijms21010359] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Hulless barley (Hordeum vulgare L. var. nudum) is one of the most important crops in the Qinghai-Tibet Plateau. Soil salinity seriously affects its cultivation. To investigate the mechanism of salt stress response during seed germination, two contrasting hulless barley genotypes were selected to first investigate the molecular mechanism of seed salinity response during the germination stage using RNA-sequencing and isobaric tags for relative and absolute quantitation technologies. Compared to the salt-sensitive landrace lk621, the salt-tolerant one lk573 germinated normally under salt stress. The changes in hormone contents also differed between lk621 and lk573. In lk573, 1597 differentially expressed genes (DEGs) and 171 differentially expressed proteins (DEPs) were specifically detected at 4 h after salt stress, and correspondingly, 2748 and 328 specifically detected at 16 h. Most specific DEGs in lk573 were involved in response to oxidative stress, biosynthetic process, protein localization, and vesicle-mediated transport, and most specific DEPs were assigned to an oxidation-reduction process, carbohydrate metabolic process, and protein phosphorylation. There were 96 genes specifically differentially expressed at both transcriptomic and proteomic levels in lk573. These results revealed the molecular mechanism of salt tolerance and provided candidate genes for further study and salt-tolerant improvement in hulless barley.
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Affiliation(s)
- Yong Lai
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (D.Z.)
| | - Dangquan Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (D.Z.)
| | - Jinmin Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China
| | - Panrong Ren
- Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- State Key Laboratory of Plant Genomics, National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lirong Yao
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China
| | - Erjing Si
- Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Yuhua Kong
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (D.Z.)
- Correspondence: (Y.K.); (H.W.)
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou 730070, China
- Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: (Y.K.); (H.W.)
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15
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Fan Y, Yang W, Yan Q, Chen C, Li J. Genome-Wide Identification and Expression Analysis of the Protease Inhibitor Gene Families in Tomato. Genes (Basel) 2019; 11:E1. [PMID: 31861342 PMCID: PMC7017114 DOI: 10.3390/genes11010001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 12/22/2022] Open
Abstract
The protease inhibitors (PIs) in plants are involved primarily in defense against pathogens and pests and in response to abiotic stresses. However, information about the PI gene families in tomato (Solanumlycopersicum), one of the most important model plant for crop species, is limited. In this study, in silico analysis identified 55 PI genes and their conserved domains, phylogenetic relationships, and chromosome locations were characterized. According to genetic structure and evolutionary relationships, the PI gene families were divided into seven families. Genome-wide microarray transcription analysis indicated that the expression of SlPI genes can be induced by abiotic (heat, drought, and salt) and biotic (Botrytiscinerea and tomato spotted wilt virus (TSWV)) stresses. In addition, expression analysis using RNA-seq in various tissues and developmental stages revealed that some SlPI genes were highly or preferentially expressed, showing tissue- and developmental stage-specific expression profiles. The expressions of four representative SlPI genes in response to abscisic acid (ABA), salicylic acid (SA), ethylene (Eth), gibberellic acid (GA). and methyl viologen (MV) were determined. Our findings indicated that PI genes may mediate the response of tomato plants to environmental stresses to balance hormone signals. The data obtained here will improve the understanding of the potential function of PI gene and lay a foundation for tomato breeding and transgenic resistance to stresses.
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Affiliation(s)
- Yuxuan Fan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Educatio, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.F.); (W.Y.); (Q.Y.); (C.C.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Yang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Educatio, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.F.); (W.Y.); (Q.Y.); (C.C.)
| | - Qingxia Yan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Educatio, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.F.); (W.Y.); (Q.Y.); (C.C.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Chunrui Chen
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Educatio, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.F.); (W.Y.); (Q.Y.); (C.C.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jinhua Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Educatio, College of Horticulture and Landscape Architecture, Southwest University, No.2 Tiansheng Road, Beibei, Chongqing 400715, China; (Y.F.); (W.Y.); (Q.Y.); (C.C.)
- State Cultivation Base of Crop Stress Biology for Southern Mountainous land of Southwest University, Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
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16
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Ferreira GC, Duran AFA, da Silva FRS, Bomediano LDM, Machado GC, Sasaki SD. Neutrophil elastase inhibitor purification strategy from cowpea seeds. PLoS One 2019; 14:e0223713. [PMID: 31600323 PMCID: PMC6786636 DOI: 10.1371/journal.pone.0223713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/27/2019] [Indexed: 01/09/2023] Open
Abstract
Serine proteases and its inhibitors are involved in physiological process and its deregulation lead to various diseases like Chronic Obstructive Pulmonary Disease (COPD), pulmonary emphysema, skin diseases, atherosclerosis, coagulation diseases, cancer, inflammatory diseases, neuronal disorders and other diseases. Serine protease inhibitors have been described in many species, as well as in plants, including cowpea beans (Vigna unguiculata (L.) Walp). Here, we purified and characterized a protease inhibitor, named VuEI (Vigna unguiculata elastase inhibitor), from Vigna unguiculata, with inhibitory activity against HNE (human neutrophil elastase) and chymotrypsin but has no inhibitory activity against trypsin and thrombin. VuEI was obtained by alkaline protein extraction followed by three different chromatographic steps in sequence. First, an ion exchange chromatography using Hitrap Q column was employed, followed by two reversed-phase chromatography using Source15RPC and ACE18 columns. The molecular mass of VuEI was estimated in 10.99 kDa by MALDI-TOF mass spectrometry. The dissociation constant (Ki) to HNE was 9 pM. These data indicate that VuEI is a potent inhibitor of human neutrophil elastase, besides to inhibit chymotrypsin.
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Affiliation(s)
- Graziele Cristina Ferreira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | | | | | - Livia de Moraes Bomediano
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Gabriel Capella Machado
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
| | - Sergio Daishi Sasaki
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, São Paulo, Brazil
- * E-mail:
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17
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Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in Triticum aestivum. G3-GENES GENOMES GENETICS 2019; 9:2709-2722. [PMID: 31227524 PMCID: PMC6686943 DOI: 10.1534/g3.119.400444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The serine protease inhibitor (serpin) gene family is the largest family of protease inhibitors. Serine protease inhibitors have an active, but under-characterized, role in grain development and defense against pathogen attack in cereal crops. By exploiting publicly available genomic, transcriptomic and proteomic data for wheat (Triticum aestivum), we have identified and annotated the entire ’serpinome’ of wheat and constructed a high-quality and robust phylogenetic tree of the gene family, identifying paralogous and homeologous clades from the hexaploid wheat genome, including the Serpin-Z group that have been well characterized in barley. Using publicly available RNAseq data (http://www.wheat-expression.com/), expression profiles of the wheat serpins were explored across a variety of tissues from the developing grain, spikelet and spike. We show that the SERPIN-Z clade, among others, are highly expressed during grain development, and that there is homeologous and paralogous functional redundancy in this gene family. Further to their role in grain development, serpins play an important but under-explored role in response to fungal pathogens. Using 13 RNAseq datasets of wheat tissues infected by fungal pathogens, we identified 37 serpins with a significant disease response. The majority of the disease-responsive serpins were upregulated by Fusarium graminearum, a destructive fungal pathogen that attacks the spike and developing grain of wheat. As serpins are ubiquitous in wheat grain, the genes encoding serpins may be linked to grain development, with their disease response a result of pleiotropy.
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18
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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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19
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Cohen M, Davydov O, Fluhr R. Plant serpin protease inhibitors: specificity and duality of function. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2077-2085. [PMID: 30721992 DOI: 10.1093/jxb/ery460] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/19/2018] [Indexed: 05/24/2023]
Abstract
The serpins are a family of structurally conserved protease inhibitors found in all animal and plant kingdoms. After interaction with their cognate substrate(s), their native energetically stressed state is relaxed by hydrolysis, resulting in a semi-stable covalent bond that disables the protease. The inherent flexible serpin structure supports additional non-inhibitory functions. This review will focus on several biological functions attributed to plant serpins, ranging from specific cell death protease inhibitors to a stabilizing role for β-amylase in seeds. Functional conservation of a particular serpin type, the LR serpins, is suggested by its compelling ubiquity throughout the plant kingdom. The multiple target specificity of plant serpins including the LR serpins enables them to perform dual functions that are not mutually exclusive both as a regulator of cell death and as a protective anti-pathogenic protein.
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Affiliation(s)
- Maja Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Olga Davydov
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Robert Fluhr
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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20
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Clemente M, Corigliano MG, Pariani SA, Sánchez-López EF, Sander VA, Ramos-Duarte VA. Plant Serine Protease Inhibitors: Biotechnology Application in Agriculture and Molecular Farming. Int J Mol Sci 2019; 20:E1345. [PMID: 30884891 PMCID: PMC6471620 DOI: 10.3390/ijms20061345] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 11/12/2022] Open
Abstract
The serine protease inhibitors (SPIs) are widely distributed in living organisms like bacteria, fungi, plants, and humans. The main function of SPIs as protease enzymes is to regulate the proteolytic activity. In plants, most of the studies of SPIs have been focused on their physiological role. The initial studies carried out in plants showed that SPIs participate in the regulation of endogenous proteolytic processes, as the regulation of proteases in seeds. Besides, it was observed that SPIs also participate in the regulation of cell death during plant development and senescence. On the other hand, plant SPIs have an important role in plant defense against pests and phytopathogenic microorganisms. In the last 20 years, several transgenic plants over-expressing SPIs have been produced and tested in order to achieve the increase of the resistance against pathogenic insects. Finally, in molecular farming, SPIs have been employed to minimize the proteolysis of recombinant proteins expressed in plants. The present review discusses the potential biotechnological applications of plant SPIs in the agriculture field.
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Affiliation(s)
- Marina Clemente
- Instituto Tecnológico Chascomús (INTECH), UNSAM-CONICET, Chascomús, Provincia de Buenos Aires B7130, Argentina.
| | - Mariana G Corigliano
- Instituto Tecnológico Chascomús (INTECH), UNSAM-CONICET, Chascomús, Provincia de Buenos Aires B7130, Argentina.
| | - Sebastián A Pariani
- Instituto Tecnológico Chascomús (INTECH), UNSAM-CONICET, Chascomús, Provincia de Buenos Aires B7130, Argentina.
| | - Edwin F Sánchez-López
- Instituto Tecnológico Chascomús (INTECH), UNSAM-CONICET, Chascomús, Provincia de Buenos Aires B7130, Argentina.
| | - Valeria A Sander
- Instituto Tecnológico Chascomús (INTECH), UNSAM-CONICET, Chascomús, Provincia de Buenos Aires B7130, Argentina.
| | - Víctor A Ramos-Duarte
- Instituto Tecnológico Chascomús (INTECH), UNSAM-CONICET, Chascomús, Provincia de Buenos Aires B7130, Argentina.
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21
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Hoernstein SNW, Fode B, Wiedemann G, Lang D, Niederkrüger H, Berg B, Schaaf A, Frischmuth T, Schlosser A, Decker EL, Reski R. Host Cell Proteome of Physcomitrella patens Harbors Proteases and Protease Inhibitors under Bioproduction Conditions. J Proteome Res 2018; 17:3749-3760. [PMID: 30226384 DOI: 10.1021/acs.jproteome.8b00423] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Host cell proteins are inevitable contaminants of biopharmaceuticals. Here, we performed detailed analyses of the host cell proteome of moss ( Physcomitrella patens) bioreactor supernatants using mass spectrometry and subsequent bioinformatics analysis. Distinguishing between the apparent secretome and intracellular contaminants, a complex extracellular proteolytic network including subtilisin-like proteases, metallo-proteases, and aspartic proteases was identified. Knockout of a subtilisin-like protease affected the overall extracellular proteolytic activity. Besides proteases, also secreted protease-inhibiting proteins such as serpins were identified. Further, we confirmed predicted cleavage sites of 40 endogenous signal peptides employing an N-terminomics approach. The present data provide novel aspects to optimize both product stability of recombinant biopharmaceuticals as well as their maturation along the secretory pathway. Data are available via ProteomeXchange with identifier PXD009517.
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Affiliation(s)
- Sebastian N W Hoernstein
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany
| | - Benjamin Fode
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany.,Plant Genome and System Biology , Helmholtz Center Munich , D-85764 Neuherberg , Germany
| | - Holger Niederkrüger
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Birgit Berg
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Andreas Schaaf
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Thomas Frischmuth
- Greenovation Biotech GmbH , Hans-Bunte-Strasse 19 , D-79108 Freiburg , Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Center for Experimental Biomedicine , University of Wuerzburg , D-97080 Wuerzburg , Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology , University of Freiburg , Schaenzlestrasse 1 , D-79104 Freiburg , Germany.,BIOSS - Centre for Biological Signalling Studies , University of Freiburg , D-79104 Freiburg , Germany
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22
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Dhanushkodi R, Matthew C, McManus MT, Dijkwel PP. Drought-induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels. THE NEW PHYTOLOGIST 2018; 220:196-208. [PMID: 29974467 DOI: 10.1111/nph.15298] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 05/20/2018] [Indexed: 05/09/2023]
Abstract
Drought is a major constraint for legume growth and yield. Senescence of nitrogen-fixing nodules is one of the early drought responses and may cause nutrient stress in addition to water stress in legumes. For nodule senescence to function as part of a drought-survival strategy, we propose that the intrinsically destructive senescence process must be tightly regulated. Medicago truncatula protease inhibitor and iron scavenger-encoding genes, possibly involved in controlling nodule senescence, were identified. RNA interference (RNAi) lines were constructed in which expression of a serpin or ferritins was knocked down. Both wild-type and RNAi lines were subjected to drought stress and nodule activity and plant physiological responses were measured. Drought caused M. truncatula to initiate nodule senescence before plant growth was affected and before an increase in papain-like proteolytic activity and free iron levels was apparent. Knock-down expression of serpin6 and ferritins caused increased protease activity, free iron levels, early nodule senescence and reduced plant growth. The results suggest that M. truncatula nodule-expressed serpin6 and ferritins mediate ordered drought-induced senescence by regulating papain-like cysteine protease activity and free iron levels. This strategy may allow the drought-stressed plants to benefit maximally from residual nitrogen fixation and nutrient recovery resulting from break down of macromolecules.
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Affiliation(s)
- Ramadoss Dhanushkodi
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Cory Matthew
- Institute of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Michael T McManus
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - Paul P Dijkwel
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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23
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Grosse‐Holz F, Madeira L, Zahid MA, Songer M, Kourelis J, Fesenko M, Ninck S, Kaschani F, Kaiser M, van der Hoorn RA. Three unrelated protease inhibitors enhance accumulation of pharmaceutical recombinant proteins in Nicotiana benthamiana. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1797-1810. [PMID: 29509983 PMCID: PMC6131417 DOI: 10.1111/pbi.12916] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 05/21/2023]
Abstract
Agroinfiltrated Nicotiana benthamiana is a flexible and scalable platform for recombinant protein (RP) production, but its great potential is hampered by plant proteases that degrade RPs. Here, we tested 29 candidate protease inhibitors (PIs) in agroinfiltrated N. benthamiana leaves for enhancing accumulation of three unrelated RPs: glycoenzyme α-Galactosidase; glycohormone erythropoietin (EPO); and IgG antibody VRC01. Of the previously described PIs enhancing RP accumulation, we found only cystatin SlCYS8 to be effective. We identified three additional new, unrelated PIs that enhance RP accumulation: N. benthamiana NbPR4, NbPot1 and human HsTIMP, which have been reported to inhibit cysteine, serine and metalloproteases, respectively. Remarkably, accumulation of all three RPs is enhanced by each PI similarly, suggesting that the mechanism of degradation of unrelated RPs follows a common pathway. Inhibitory functions HsTIMP and SlCYS8 are required to enhance RP accumulation, suggesting that their target proteases may degrade RPs. Different PIs additively enhance RP accumulation, but the effect of each PI is dose-dependent. Activity-based protein profiling (ABPP) revealed that the activities of papain-like Cys proteases (PLCPs), Ser hydrolases (SHs) or vacuolar processing enzymes (VPEs) in leaves are unaffected upon expression of the new PIs, whereas SlCYS8 expression specifically suppresses PLCP activity only. Quantitative proteomics indicates that the three new PIs affect agroinfiltrated tissues similarly and that they all increase immune responses. NbPR4, NbPot1 and HsTIMP can be used to study plant proteases and improve RP accumulation in molecular farming.
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Affiliation(s)
| | - Luisa Madeira
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Muhammad Awais Zahid
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Molly Songer
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Jiorgos Kourelis
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Mary Fesenko
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordOxfordUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstrEssenGermany
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24
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Lema Asqui S, Vercammen D, Serrano I, Valls M, Rivas S, Van Breusegem F, Conlon FL, Dangl JL, Coll NS. AtSERPIN1 is an inhibitor of the metacaspase AtMC1-mediated cell death and autocatalytic processing in planta. THE NEW PHYTOLOGIST 2018; 218:1156-1166. [PMID: 28157265 DOI: 10.1111/nph.14446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 12/16/2016] [Indexed: 05/10/2023]
Abstract
The hypersensitive response (HR) is a localized programmed cell death phenomenon that occurs in response to pathogen recognition at the site of attempted invasion. Despite more than a century of research on HR, little is known about how it is so tightly regulated and how it can be contained spatially to a few cells. AtMC1 is an Arabidopsis thaliana plant metacaspase that positively regulates the HR. Here, we used an unbiased approach to identify new AtMC1 regulators. Immunoaffinity purification of AtMC1-containing complexes led us to the identification of the protease inhibitor AtSerpin1. Our data clearly showed that coimmunoprecipitation between AtMC1 and AtSerpin1 and formation of a complex between them was lost upon mutation of the AtMC1 catalytic site, and that the AtMC1 prodomain was not required for the interaction. AtSerpin1 blocked AtMC1 self-processing and inhibited AtMC1-mediated cell death. Our results constitute an in vivo example of a Serpin acting as a suicide inhibitor in plants, reminiscent of the activity of animal or viral serpins on immune/cell death regulators, including caspase-1. These results indicate a conserved function of a protease inhibitor on cell death regulators from different kingdoms with unrelated modes of action (i.e. caspases vs metacaspases).
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Affiliation(s)
- Saul Lema Asqui
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Dominique Vercammen
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
| | - Irene Serrano
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Marc Valls
- Department of Genetics, Universitat de Barcelona and Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB) Edifici CRAG, Campus UAB, Bellaterra, Catalonia, 08193, Spain
| | - Susana Rivas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Ghent, 9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- Department of Medical Protein Research, VIB, Ghent, 9000, Belgium
- Department of Biochemistry, Ghent University, Ghent, 9000, Belgium
| | - Frank L Conlon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
| | - Núria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
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25
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Cohen M, Fluhr R. Noncanonical interactions between serpin and β-amylase in barley grain improve β-amylase activity in vitro. PLANT DIRECT 2018; 2:e00054. [PMID: 31245723 PMCID: PMC6508567 DOI: 10.1002/pld3.54] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 05/31/2023]
Abstract
Serpin protease inhibitors and β-amylase starch hydrolases are very abundant seed proteins in the endosperm of grasses. β-amylase is a crucial enzyme in the beer industry providing maltose for fermenting yeast. In animals and plants, inhibitory serpins form covalent linkages that inactivate their cognate proteases. Additionally, in animals, noninhibitory functions for serpins are observed such as metabolite carriers and chaperones. The function of serpins in seeds has yet to be unveiled. In developing endosperm, serpin Z4 and β-amylase showed similar in vivo spatio-temporal accumulation properties and colocalize in the cytosol of transformed tobacco leaves. A molecular interaction between recombinant proteins of serpin Z4 and β-amylase was revealed by surface plasmon resonance and microscale thermophoresis yielding a dissociation constant of 10-7 M. Importantly, the addition of serpin Z4 significantly changes β-amylase enzymatic properties by increasing its maximal catalytic velocity. The presence of serpin Z4 stabilizes β-amylase activity during heat treatment without affecting its critical denaturing temperature. Oxidative stress, simulated by the addition of CuCl2, leads to the formation of high molecular weight polymers of β-amylase similar to those detected in vivo. The polymers were cross-linked through disulfide bonds, the formation of which was repressed when serpin Z4 was present. The results suggest an unprecedented function for a plant seed serpin as a β-amylase-specific chaperone-like partner that could optimize β-amylase activity upon germination. This report is the first to describe a noninhibitory function for a serpin in plants.
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Affiliation(s)
- Maja Cohen
- Department of Plant SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Robert Fluhr
- Department of Plant SciencesWeizmann Institute of ScienceRehovotIsrael
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26
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Losvik A, Beste L, Stephens J, Jonsson L. Overexpression of the aphid-induced serine protease inhibitor CI2c gene in barley affects the generalist green peach aphid, not the specialist bird cherry-oat aphid. PLoS One 2018; 13:e0193816. [PMID: 29554141 PMCID: PMC5858787 DOI: 10.1371/journal.pone.0193816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/20/2018] [Indexed: 11/18/2022] Open
Abstract
Aphids are serious pests in crop plants. In an effort to identify plant genes controlling resistance against aphids, we have here studied a protease inhibitor, CI2c in barley (Hordeum vulgare L.). The CI2c gene was earlier shown to be upregulated by herbivory of the bird cherry-oat aphid (Rhopalosiphum padi L.) in barley genotypes with moderate resistance against this aphid, but not in susceptible lines. We hypothesized that CI2c contributes to the resistance. To test this idea, cDNA encoding CI2c was overexpressed in barley and bioassays were carried out with R. padi. For comparison, tests were carried out with the green peach aphid (Myzus persicae Sulzer), for which barley is a poor host. The performance of R. padi was not different on the CI2c-overexpressing lines in comparison to controls in test monitoring behavior and fecundity. M. persicae preference was affected as shown in the choice test, this species moved away from control plants, but remained on the CI2c-overexpressing lines. R. padi-induced responses related to defense were repressed in the overexpressing lines as compared to in control plants or the moderately resistant genotypes. A putative susceptibility gene, coding for a β-1,3-glucanase was more strongly induced by aphids in one of the CI2c-overexpressing lines. The results indicate that the CI2c inhibitor in overexpressing lines affects aphid-induced responses by suppressing defense. This is of little consequence to the specialist R.padi, but causes lower non-host resistance towards the generalist M. persicae in barley.
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Affiliation(s)
- Aleksandra Losvik
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Lisa Beste
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Jennifer Stephens
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Lisbeth Jonsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- * E-mail:
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27
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Rustgi S, Boex-Fontvieille E, Reinbothe C, von Wettstein D, Reinbothe S. The complex world of plant protease inhibitors: Insights into a Kunitz-type cysteine protease inhibitor of Arabidopsis thaliana. Commun Integr Biol 2017; 11:e1368599. [PMID: 29497469 PMCID: PMC5824933 DOI: 10.1080/19420889.2017.1368599] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/11/2017] [Accepted: 08/11/2017] [Indexed: 12/05/2022] Open
Abstract
Plants have evolved an intricate regulatory network of proteases and corresponding protease inhibitors (PI), which operate in various biological pathways and serve diverse spatiotemporal functions during the sedentary life of a plant. Intricacy of the regulatory network can be anticipated from the observation that, depending on the developmental stage and environmental cue(s), either a single PI or multiple PIs regulate the activity of a given protease. On the other hand, the same PI often interacts with different targets at different places, necessitating another level of fine control to be added in planta. Here, it is reported on how the activity of a papain-like cysteine protease dubbed RD21 (RESPONSIVE TO DESICCATION 21) is differentially regulated by serpin and Kunitz PIs over plant development and how this mechanism contributes to defenses against herbivorous arthropods and microbial pests.
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Affiliation(s)
- Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University, Pee Dee Research and Education Center, Florence, SC, USA.,Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Edouard Boex-Fontvieille
- Laboratoire de Génétique Moléculaire des Plantes and Biologie Environnementale et Systémique (BEeSy), Université Grenoble Alpes, Grenoble, France
| | - Christiane Reinbothe
- Laboratoire de Génétique Moléculaire des Plantes and Biologie Environnementale et Systémique (BEeSy), Université Grenoble Alpes, Grenoble, France
| | - Diter von Wettstein
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Steffen Reinbothe
- Laboratoire de Génétique Moléculaire des Plantes and Biologie Environnementale et Systémique (BEeSy), Université Grenoble Alpes, Grenoble, France
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28
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Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D. Improved maize reference genome with single-molecule technologies. Nature 2017; 546:524-527. [PMID: 28605751 DOI: 10.1101/079004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/14/2017] [Indexed: 05/21/2023]
Abstract
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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Affiliation(s)
- Yinping Jiao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Paul Peluso
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Jinghua Shi
- BioNano Genomics, San Diego, California 92121, USA
| | | | - Michelle C Stitzer
- Department of Plant Sciences and Center for Population Biology, University of California, Davis, Davis, California 95616, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Xuehong Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Katherine Guill
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Kevin L Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Thomas K Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Michael R May
- Department of Evolution and Ecology, University of California, Davis, California 95616, USA
| | - Nathan M Springer
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Eric Antoniou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Gernot G Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Michael McMullen
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri 65211, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology, and Genome Center, University of California, Davis, California 95616, USA
| | - R Kelly Dawe
- University of Georgia, Athens, Georgia 30602, USA
| | - Alex Hastie
- BioNano Genomics, San Diego, California 92121, USA
| | - David R Rank
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- USDA-ARS, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853, USA
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29
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Improved maize reference genome with single-molecule technologies. Nature 2017; 546:524-527. [PMID: 28605751 PMCID: PMC7052699 DOI: 10.1038/nature22971] [Citation(s) in RCA: 693] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 05/14/2017] [Indexed: 01/01/2023]
Abstract
An improved reference genome for maize, using single-molecule sequencing and high-resolution optical mapping, enables characterization of structural variation and repetitive regions, and identifies lineage expansions of transposable elements that are unique to maize. The maize genome was initially reported in 2009 but with some accuracy limitations. Doreen Ware and colleagues report a new reference genome for maize using single-molecule sequencing and high-resolution optical mapping. The technique shows improvements in the gene space including resolution of gaps and misassemblies and correction of order and orientation of genes. The authors characterize structural variation and repetitive regions, and identify transposable element lineage expansions unique to maize. Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation1. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions2. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome3, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing4. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
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30
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Bhattacharjee L, Singh D, Gautam JK, Nandi AK. Arabidopsis thaliana serpins AtSRP4 and AtSRP5 negatively regulate stress-induced cell death and effector-triggered immunity induced by bacterial effector AvrRpt2. PHYSIOLOGIA PLANTARUM 2017; 159:329-339. [PMID: 27709637 DOI: 10.1111/ppl.12516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Protease inhibitors and their cognate proteases regulate growth, development and defense. Serine protease inhibitors (serpins) constitute a large family of genes in most metazoans and plants. Drosophila NECROTIC (NEC) gene and its homologues in the mammalian system are well-characterized serpins, which play a role in regulating proteases that participate in cell death pathways. Although the Arabidopsis genome contains several serpin homologs, biological function is not known for most of them. Here we show that two Arabidopsis serpins, AtSRP4 and AtSRP5, are closest sequence homologue of Drosophila NEC protein, and are involved in stress-induced cell death and defense. Expression of both AtSRP4 and AtSRP5 genes induced upon ultra-violet (UV)-treatment and inoculation with avirulent pathogens. The knockout mutants and amiRNA lines of AtSRP4 and AtSRP5 exaggerated UV- and hypersensitive response (HR)-induced cell death. Over-expression of AtSRP4 reduced UV- and HR-induced cell death. Mutants of AtSRP4 and AtSRP5 suppressed whereas over-expression of AtSRP4 supported the growth of bacterial pathogen Pseudomonas syringae pv. tomato DC3000 carrying the AvrRpt2 effector, but not other avirulent or virulent pathogens. Results altogether identified AtSRP4 and AtSRP5 as negative regulators of stress-induced cell death and AvrRpt2-triggered immunity; however, the influence of AtSRP4 was more prominent than AtSRP5.
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Affiliation(s)
| | - Deepjyoti Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Janesh Kumar Gautam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ashis Kumar Nandi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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31
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Srikanth S, Chen Z. Plant Protease Inhibitors in Therapeutics-Focus on Cancer Therapy. Front Pharmacol 2016; 7:470. [PMID: 28008315 PMCID: PMC5143346 DOI: 10.3389/fphar.2016.00470] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/18/2016] [Indexed: 12/28/2022] Open
Abstract
Plants are known to have many secondary metabolites and phytochemical compounds which are highly explored at biochemical and molecular genetics level and exploited enormously in the human health care sector. However, there are other less explored small molecular weight proteins, which inhibit proteases/proteinases. Plants are good sources of protease inhibitors (PIs) which protect them against diseases, insects, pests, and herbivores. In the past, proteinaceous PIs were considered primarily as protein-degrading enzymes. Nevertheless, this view has significantly changed and PIs are now treated as very important signaling molecules in many biological activities such as inflammation, apoptosis, blood clotting and hormone processing. In recent years, PIs have been examined extensively as therapeutic agents, primarily to deal with various human cancers. Interestingly, many plant-based PIs are also found to be effective against cardiovascular diseases, osteoporosis, inflammatory diseases and neurological disorders. Several plant PIs are under further evaluation in in vitro clinical trials. Among all types of PIs, Bowman-Birk inhibitors (BBI) have been studied extensively in the treatment of many diseases, especially in the field of cancer prevention. So far, crops such as beans, potatoes, barley, squash, millet, wheat, buckwheat, groundnut, chickpea, pigeonpea, corn, and pineapple have been identified as good sources of PIs. The PI content of such foods has a significant influence on human health disorders, particularly in the regions where people mostly depend on these kind of foods. These natural PIs vary in concentration, protease specificity, heat stability, and sometimes several PIs may be present in the same species or tissue. However, it is important to carry out individual studies to identify the potential effects of each PI on human health. PIs in plants make them incredible sources to determine novel PIs with specific pharmacological and therapeutic effects due to their peculiarity and superabundance.
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Affiliation(s)
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological UniversitySingapore, Singapore
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32
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Three sorghum serpin recombinant proteins inhibit midgut trypsin activity and growth of corn earworm. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.aggene.2016.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Zamyatnin AA. Plant Proteases Involved in Regulated Cell Death. BIOCHEMISTRY (MOSCOW) 2016; 80:1701-15. [PMID: 26878575 DOI: 10.1134/s0006297915130064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Each plant genome encodes hundreds of proteolytic enzymes. These enzymes can be divided into five distinct classes: cysteine-, serine-, aspartic-, threonine-, and metalloproteinases. Despite the differences in their structural properties and activities, members of all of these classes in plants are involved in the processes of regulated cell death - a basic feature of eukaryotic organisms. Regulated cell death in plants is an indispensable mechanism supporting plant development, survival, stress responses, and defense against pathogens. This review summarizes recent advances in studies of plant proteolytic enzymes functioning in the initiation and execution of distinct types of regulated cell death.
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Affiliation(s)
- A A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia
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34
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Ghorbani S, Hoogewijs K, Pečenková T, Fernandez A, Inzé A, Eeckhout D, Kawa D, De Jaeger G, Beeckman T, Madder A, Van Breusegem F, Hilson P. The SBT6.1 subtilase processes the GOLVEN1 peptide controlling cell elongation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4877-87. [PMID: 27315833 PMCID: PMC4983112 DOI: 10.1093/jxb/erw241] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The GOLVEN (GLV) gene family encode small secreted peptides involved in important plant developmental programs. Little is known about the factors required for the production of the mature bioactive GLV peptides. Through a genetic suppressor screen in Arabidopsis thaliana, two related subtilase genes, AtSBT6.1 and AtSBT6.2, were identified that are necessary for GLV1 activity. Root and hypocotyl GLV1 overexpression phenotypes were suppressed by mutations in either of the subtilase genes. Synthetic GLV-derived peptides were cleaved in vitro by the affinity-purified SBT6.1 catalytic enzyme, confirming that the GLV1 precursor is a direct subtilase substrate, and the elimination of the in vitro subtilase recognition sites through alanine substitution suppressed the GLV1 gain-of-function phenotype in vivo Furthermore, the protease inhibitor Serpin1 bound to SBT6.1 and inhibited the cleavage of GLV1 precursors by the protease. GLV1 and its homolog GLV2 were expressed in the outer cell layers of the hypocotyl, preferentially in regions of rapid cell elongation. In agreement with the SBT6 role in GLV precursor processing, both null mutants for sbt6.1 and sbt6.2 and the Serpin1 overexpression plants had shorter hypocotyls. The biosynthesis of the GLV signaling peptides required subtilase activity and might be regulated by specific protease inhibitors. The data fit with a model in which the GLV1 signaling pathway participates in the regulation of hypocotyl cell elongation, is controlled by SBT6 subtilases, and is modulated locally by the Serpin1 protease inhibitor.
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Affiliation(s)
- Sarieh Ghorbani
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Kurt Hoogewijs
- Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium
| | - Tamara Pečenková
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Ana Fernandez
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Annelies Inzé
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dorota Kawa
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Annemieke Madder
- Department of Organic Chemistry, Ghent University, B-9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Saclay Plant Science, F-78026 Versailles, France
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Grosse-Holz FM, van der Hoorn RAL. Juggling jobs: roles and mechanisms of multifunctional protease inhibitors in plants. THE NEW PHYTOLOGIST 2016; 210:794-807. [PMID: 26800491 DOI: 10.1111/nph.13839] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/01/2015] [Indexed: 05/13/2023]
Abstract
Multifunctional protease inhibitors juggle jobs by targeting different enzymes and thereby often controlling more than one biological process. Here, we discuss the biological functions, mechanisms and evolution of three types of multifunctional protease inhibitors in plants. The first type is double-headed inhibitors, which feature two inhibitory sites targeting proteases with different specificities (e.g. Bowman-Birk inhibitors) or even different hydrolases (e.g. α-amylase/protease inhibitors preventing both early germination and seed predation). The second type consists of multidomain inhibitors which evolved by intragenic duplication and are released by processing (e.g. multicystatins and potato inhibitor II, implicated in tuber dormancy and defence, respectively). The third type consists of promiscuous inhibitory folds which resemble mouse traps that can inhibit different proteases cleaving the bait they offer (e.g. serpins, regulating cell death, and α-macroglobulins). Understanding how multifunctional inhibitors juggle biological jobs increases our knowledge of the connections between the networks they regulate. These examples show that multifunctionality evolved independently from a remarkable diversity of molecular mechanisms that can be exploited for crop improvement and provide concepts for protein design.
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Affiliation(s)
- Friederike M Grosse-Holz
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Renier A L van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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Leboffe L, Angelini R, Menegatti E, Polticelli F, Ascenzi P. Different disulfide bridge connectivity drives alternative folds in highly homologous Brassicaceae trypsin inhibitors. IUBMB Life 2015; 67:966-70. [PMID: 26545561 DOI: 10.1002/iub.1447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/08/2015] [Indexed: 11/11/2022]
Abstract
Low-molecular-mass trypsin inhibitors from Arabidopsis thaliana, Brassica napus var. oleifera, and Sinapis alba L. (ATTI, RTI, and MTI, respectively) display more than 69% amino acid sequence identity. Among others, the amino acid sequence Cys-Ala-Pro-Arg-Ile building up the inhibitor reactive site, and the eight Cys residues forming four disulfide bridges are conserved. However, the disulfide bridge connectivity of RTI and MTI (C1-C3, C2-C4, C5-C6, and C7-C8) is different from that of ATTI Cys (C1-C8, C2-C5, C3-C6, and C4-C7). Despite the different disulfide bridge connectivity, the reactive site loop of ATTI, RTI, and MTI is solvent exposed permitting trypsin recognition. Structural considerations here reported suggest that proteins showing high amino acid sequence identity and common functional properties could display different three-dimensional structures. This may reflect high inhibitor plasticity in relation to plant-pathogen interactions, plant tissue development as well as the different redox potential of cell compartments.
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Affiliation(s)
- Loris Leboffe
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Roma, Italy
| | | | - Enea Menegatti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Ferrara, Ferrara, Italy
| | - Fabio Polticelli
- Dipartimento di Scienze, Università Roma Tre, Roma, Italy.,Istituto Nazionale di Fisica Nucleare, Sezione Università Roma Tre, Roma, Italy
| | - Paolo Ascenzi
- Laboratorio Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Roma, Italy
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Ma C, Zhou J, Chen G, Bian Y, Lv D, Li X, Wang Z, Yan Y. iTRAQ-based quantitative proteome and phosphoprotein characterization reveals the central metabolism changes involved in wheat grain development. BMC Genomics 2014; 15:1029. [PMID: 25427527 PMCID: PMC4301063 DOI: 10.1186/1471-2164-15-1029] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/10/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is an economically important grain crop. Two-dimensional gel-based approaches are limited by the low identification rate of proteins and lack of accurate protein quantitation. The recently developed isobaric tag for relative and absolute quantitation (iTRAQ) method allows sensitive and accurate protein quantification. Here, we performed the first iTRAQ-based quantitative proteome and phosphorylated proteins analyses during wheat grain development. RESULTS The proteome profiles and phosphoprotein characterization of the metabolic proteins during grain development of the elite Chinese bread wheat cultivar Yanyou 361 were studied using the iTRAQ-based quantitative proteome approach, TiO2 microcolumns, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Among 1,146 non-redundant proteins identified, 421 showed at least 2-fold differences in abundance, and they were identified as differentially expressed proteins (DEPs), including 256 upregulated and 165 downregulated proteins. Of the 421 DEPs, six protein expression patterns were identified, most of which were up, down, and up-down expression patterns. The 421 DEPs were classified into nine functional categories mainly involved in different metabolic processes and located in the membrane and cytoplasm. Hierarchical clustering analysis indicated that the DEPs involved in starch biosynthesis, storage proteins, and defense/stress-related proteins significantly accumulated at the late grain development stages, while those related to protein synthesis/assembly/degradation and photosynthesis showed an opposite expression model during grain development. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 12 representative genes encoding different metabolic proteins showed certain transcriptional and translational expression differences during grain development. Phosphorylated proteins analyses demonstrated that 23 DEPs such as AGPase, sucrose synthase, Hsp90, and serpins were phosphorylated in the developing grains and were mainly involved in starch biosynthesis and stress/defense. CONCLUSIONS Our results revealed a complex quantitative proteome and phosphorylation profile during wheat grain development. Numerous DEPs are involved in grain starch and protein syntheses as well as adverse defense, which set an important basis for wheat yield and quality. Particularly, some key DEPs involved in starch biosynthesis and stress/defense were phosphorylated, suggesting their roles in wheat grain development.
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Affiliation(s)
- Chaoying Ma
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Jianwen Zhou
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Guanxing Chen
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Yanwei Bian
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Dongwen Lv
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Xiaohui Li
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
| | - Zhimin Wang
- />College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100094 China
| | - Yueming Yan
- />College of Life Sciences, Capital Normal University, Beijing, 100048 China
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Porter L, Radulović Ž, Kim T, Braz GRC, Da Silva Vaz I, Mulenga A. Bioinformatic analyses of male and female Amblyomma americanum tick expressed serine protease inhibitors (serpins). Ticks Tick Borne Dis 2014; 6:16-30. [PMID: 25238688 DOI: 10.1016/j.ttbdis.2014.08.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/20/2014] [Accepted: 08/28/2014] [Indexed: 12/31/2022]
Abstract
Serine protease inhibitors (serpins) are a diverse family of proteins that is conserved across taxa. The diversity of Amblyomma americanum serpins (AAS) is far more complex than previously thought as revealed by discovery of 57 and 33 AAS transcripts that are respectively expressed in male and female A. americanum ticks, with 30 found in both. While distinct reproductively, both male and female metastriate ticks, such as A. americanum, require a blood meal. Thus, 30 AAS sequences found in both male and female ticks could play important role(s) in regulating tick feeding and thus represent attractive candidates for anti-tick vaccine development. Of significant interest, 19 AAS sequences expressed in male and female ticks are also part of the 48 AAS sequences expressed in fed female tick salivary glands or midguts; two organs through which the tick interacts with host blood and immune response factors. Considered the most important domain for serpin function, the reactive center loop (RCL) is further characterized by a single 'P1' site amino acid residue, which is central to determining the protease regulated by the serpin. In this study, a diversity of 17 different P1 site amino acid residues were predicted, suggesting that A. americanum serpins potentially regulate a large number of proteolytic pathways. Our data also indicate that some serpins in this study could regulate target protease common to all tick species, in that more than 40% of AAS show 58-97% inter-species amino acid conservation. Of significance, 24% of AAS showed 62-100% inter-species conservation within the functional RCL domain, with 10 RCLs showing ≥90-100% conservation. In vertebrates, serpins with basic residues at the P1 site regulate key host defense pathways, which the tick must evade to feed successfully. Interestingly, we found that AAS sequences with basic or polar uncharged residues at the putative P1 site are more likely to be conserved across tick species. Another notable observation from our data is that AAS sequences found only in female ticks and those found in both males and females, but not those found only in male ticks, were highly conserved in other tick species. While descriptive, this study provides the basis for more in-depth studies exploring the roles of serpins in tick feeding physiology.
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Affiliation(s)
- Lindsay Porter
- Texas A & M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, United States
| | - Željko Radulović
- Texas A & M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, United States
| | - Tae Kim
- Texas A & M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, United States
| | - Gloria R C Braz
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Itabajara Da Silva Vaz
- Centro de Biotecnologia and Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Prédio 43421, Porto Alegre 91501-970, RS, Brazil
| | - Albert Mulenga
- Texas A & M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, United States.
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Li J, Zhu L, Lu G, Zhan XB, Lin CC, Zheng ZY. Curdlan β-1,3-glucooligosaccharides induce the defense responses against Phytophthora infestans infection of potato (Solanum tuberosum L. cv. McCain G1) leaf cells. PLoS One 2014; 9:e97197. [PMID: 24816730 PMCID: PMC4016274 DOI: 10.1371/journal.pone.0097197] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/15/2014] [Indexed: 01/06/2023] Open
Abstract
Activation of the innate immune system before the invasion of pathogens is a promising way to improve the resistance of plant against infection while reducing the use of agricultural chemicals. Although several elicitors were used to induce the resistance of potato plant to microbial pathogen infection, the role of curdlan oligosaccharide (CurdO) has not been established. In the current study, the defense responses were investigated at biochemical and proteomic levels to elucidate the elicitation effect of CurdOs in foliar tissues of potato (Solanum tuberosum L. cv. McCain G1). The results indicate that the CurdOs exhibit activation effect on the early- and late-defense responses in potato leaves. In addition, glucopentaose was proved to be the shortest active curdlan molecule based on the accumulation of H₂O₂ and salicylic acid and the activities of phenylalanine amino-lyase, β-1,3-glucanase and chitinase. The 2D-PAGE analysis reveals that CurdOs activate the integrated response reactions in potato cells, as a number of proteins with various functions are up-regulated including disease/defense, metabolism, transcription, and cell structure. The pathogenesis assay shows that the ratio of lesion area of potato leaf decreased from 15.82%±5.44% to 7.79%±3.03% when the plants were treated with CurdOs 1 day before the infection of Phytophthora infestans. Furthermore, the results on potato yield and induction reactions indicate that the defense responses induced by CurdOs lasted for short period of time but disappeared gradually.
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Affiliation(s)
- Jing Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Zhu
- Jiangsu Rayguang Biotech Company, Ltd., Wuxi, Jiangsu, China
| | - Guangxing Lu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao-Bei Zhan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Rayguang Biotech Company, Ltd., Wuxi, Jiangsu, China
| | - Chi-Chung Lin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhi-Yong Zheng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology of Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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Lampl N, Alkan N, Davydov O, Fluhr R. Set-point control of RD21 protease activity by AtSerpin1 controls cell death in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:498-510. [PMID: 23398119 DOI: 10.1111/tpj.12141] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/01/2013] [Indexed: 05/23/2023]
Abstract
Programmed cell death (PCD) in plants plays a key role in defense response and is promoted by the release of compartmentalized proteases to the cytoplasm. Yet the exact identity and control of these proteases is poorly understood. Serpins are an important group of proteins that uniquely curb the activity of proteases by irreversible inhibition; however, their role in plants remains obscure. Here we show that during cell death the Arabidopsis serpin protease inhibitor, AtSerpin1, exhibits a pro-survival function by inhibiting its target pro-death protease, RD21. AtSerpin1 accumulates in the cytoplasm and RD21 accumulates in the vacuole and in endoplasmic reticulum bodies. Elicitors of cell death, including the salicylic acid agonist benzothiadiazole and the fungal toxin oxalic acid, stimulated changes in vacuole permeability as measured by the changes in the distribution of marker dye. Concomitantly, a covalent AtSerpin1-RD21 complex was detected indicative of a change in protease compartmentalization. Furthermore, mutant plants lacking RD21 or plants with AtSerpin1 over-expression exhibited significantly less elicitor-stimulated PCD than plants lacking AtSerpin1. The necrotrophic fungi Botrytis cinerea and Sclerotina sclerotiorum secrete oxalic acid as a toxin that stimulates cell death. Consistent with a pro-death function for RD21 protease, the growth of these necrotrophs was compromised in plants lacking RD21 but accelerated in plants lacking AtSerpin1. The results indicate that AtSerpin1 controls the pro-death function of compartmentalized protease RD21 by determining a set-point for its activity and limiting the damage induced during cell death.
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Affiliation(s)
- Nardy Lampl
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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