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Faysal Ahmed F, Dola FS, Zohra FT, Rahman SM, Konak JN, Sarkar MAR. Genome-wide identification, classification, and characterization of lectin gene superfamily in sweet orange (Citrus sinensis L.). PLoS One 2023; 18:e0294233. [PMID: 37956187 PMCID: PMC10642848 DOI: 10.1371/journal.pone.0294233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Lectins are sugar-binding proteins found abundantly in plants. Lectin superfamily members have diverse roles, including plant growth, development, cellular processes, stress responses, and defense against microbes. However, the genome-wide identification and functional analysis of lectin genes in sweet orange (Citrus sinensis L.) remain unexplored. Therefore, we used integrated bioinformatics approaches (IBA) for in-depth genome-wide identification, characterization, and regulatory factor analysis of sweet orange lectin genes. Through genome-wide comparative analysis, we identified a total of 141 lectin genes distributed across 10 distinct gene families such as 68 CsB-Lectin, 13 CsLysin Motif (LysM), 4 CsChitin-Bind1, 1 CsLec-C, 3 CsGal-B, 1 CsCalreticulin, 3 CsJacalin, 13 CsPhloem, 11 CsGal-Lec, and 24 CsLectinlegB.This classification relied on characteristic domain and phylogenetic analysis, showing significant homology with Arabidopsis thaliana's lectin gene families. A thorough analysis unveiled common similarities within specific groups and notable variations across different protein groups. Gene Ontology (GO) enrichment analysis highlighted the predicted genes' roles in diverse cellular components, metabolic processes, and stress-related regulation. Additionally, network analysis of lectin genes with transcription factors (TFs) identified pivotal regulators like ERF, MYB, NAC, WRKY, bHLH, bZIP, and TCP. The cis-acting regulatory elements (CAREs) found in sweet orange lectin genes showed their roles in crucial pathways, including light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and more. These findings will aid in the in-depth molecular examination of these potential genes and their regulatory elements, contributing to targeted enhancements of sweet orange species in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Department of Biochemistry and Molecular Biology, Faculty of LifeScience, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Veremeichik GN, Bulgakov DV, Konnova YA, Brodovskaya EV, Grigorchuk VP, Bulgakov VP. Proteome-Level Investigation of Vitis amurensis Calli Transformed with a Constitutively Active, Ca 2+-Independent Form of the Arabidopsis AtCPK1 Gene. Int J Mol Sci 2023; 24:13184. [PMID: 37685990 PMCID: PMC10487732 DOI: 10.3390/ijms241713184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are one of the main Ca2+ decoders in plants. Among them, Arabidopsis thaliana AtCPK1 is one of the most studied CDPK genes as a positive regulator of plant responses to biotic and abiotic stress. The mutated form of AtCPK1, in which the autoinhibitory domain is inactivated (AtCPK1-Ca), provides constitutive kinase activity by mimicking a stress-induced increase in the Ca2+ flux. In the present study, we performed a proteomic analysis of Vitis amurensis calli overexpressing the AtCPK1-Ca form using untransformed calli as a control. In our previous studies, we have shown that the overexpression of this mutant form leads to the activation of secondary metabolism in plant cell cultures, including an increase in resveratrol biosynthesis in V. amurensis cell cultures. We analyzed upregulated and downregulated proteins in control and transgenic callus cultures using two-dimensional gel electrophoresis, and Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF). In calli transformed with AtCPK1-Ca, an increased amounts of pathogenesis-related proteins were found. A quantitative real-time PCR analysis confirmed this result.
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Affiliation(s)
- Galina N. Veremeichik
- Federal Scientific Centre of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia; (D.V.B.); (V.P.G.); (V.P.B.)
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Maasch JRMA, Torres MDT, Melo MCR, de la Fuente-Nunez C. Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning. Cell Host Microbe 2023; 31:1260-1274.e6. [PMID: 37516110 DOI: 10.1016/j.chom.2023.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 07/31/2023]
Abstract
Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted within extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides showed resistance to proteolysis and exhibited variable membrane permeabilization. Additionally, representative modern and archaic protein fragments showed anti-infective efficacy against A. baumannii in both a skin abscess infection model and a preclinical murine thigh infection model. These results suggest that machine-learning-based encrypted peptide prospection can identify stable, nontoxic peptide antibiotics. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.
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Affiliation(s)
- Jacqueline R M A Maasch
- Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcelo C R Melo
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Bhar A, Chakraborty A, Roy A. The captivating role of calcium in plant-microbe interaction. FRONTIERS IN PLANT SCIENCE 2023; 14:1138252. [PMID: 36938033 PMCID: PMC10020633 DOI: 10.3389/fpls.2023.1138252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Plant immune response is fascinating due to the complete absence of a humoral system. The adaptive immune response in plants relies on the intracellular orchestration of signalling molecules or intermediates associated with transcriptional reprogramming. Plant disease response phenomena largely depend on pathogen recognition, signal perception, and intracellular signal transduction. The pathogens possess specific pathogen-associated molecular patterns (PAMP) or microbe-associated molecular patterns (MAMP), which are first identified by pattern recognition receptors (PRRs) of host plants for successful infection. After successful pathogen recognition, the defence response is initiated within plants. The first line of non-specific defence response is called PAMP-triggered immunity (PTI), followed by the specific robust signalling is called effector-triggered immunity (ETI). Calcium plays a crucial role in both PTI and ETI. The biphasic induction of reactive oxygen species (ROS) is inevitable in any plant-microbe interaction. Calcium ions play crucial roles in the initial oxidative burst and ROS induction. Different pathogens can induce calcium accumulation in the cytosol ([Ca2+]Cyt), called calcium signatures. These calcium signatures further control the diverse defence-responsive proteins in the intracellular milieu. These calcium signatures then activate calcium-dependent protein kinases (CDPKs), calcium calmodulins (CaMs), calcineurin B-like proteins (CBLs), etc., to impart intricate defence signalling within the cell. Decoding this calcium ionic map is imperative to unveil any plant microbe interplay and modulate defence-responsive pathways. Hence, the present review is unique in developing concepts of calcium signature in plants and their subsequent decoding mechanism. This review also intends to articulate early sensing of calcium oscillation, signalling events, and comprehensive mechanistic roles of calcium within plants during pathogenic ingression. This will accumulate and summarize the exciting roles of calcium ions in plant immunity and provide the foundation for future research.
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Affiliation(s)
- Anirban Bhar
- Post Graduate Department of Botany, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
| | - Amrita Chakraborty
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
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Fondevilla S, Krezdorn N, Rubiales D, Rotter B, Winter P. Bulked segregant transcriptome analysis in pea identifies key expression markers for resistance to Peyronellaea pinodes. Sci Rep 2022; 12:18159. [PMID: 36307494 PMCID: PMC9616913 DOI: 10.1038/s41598-022-22621-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/17/2022] [Indexed: 12/31/2022] Open
Abstract
Peyronellaea pinodes is a devastating pathogen of pea crop. Quantitative trait loci (QTL) associated with resistance have been identified, as well as genes differentially expressed between resistant and susceptible pea lines. The key question is which of these many genes located into these QTLs, or differentially expressed, are the key genes that distinguish resistant from susceptible plants and could be used as markers. To identify these key genes, in the present study we applied MACE (Massive Analysis of cDNA Ends) -Seq to a whole Recombinant Inbred Line population segregating for resistance to this disease and their parental lines and identified those genes which expression was more correlated with the level of resistance. We also compared gene expression profiles between the most resistant and the most susceptible families of the RIL population. A total of 6780 transcripts were differentially expressed between the parental lines after inoculation. Of them, 803 showed the same expression pattern in the bulks formed by the most resistant and most susceptible RIL families. These genes, showing a consistent expression pattern, could be used as expression markers to distinguish resistant from susceptible plants. The analysis of these genes also discovered the crucial mechanisms acting against P. pinodes.
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Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain.
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
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Guo Q, Zheng J, Ba H, Sun H, Zhai J, Wang W, Li C. Calreticulin Identified as One of the Androgen Response Genes That Trigger Full Regeneration of the Only Capable Mammalian Organ, the Deer Antler. Front Cell Dev Biol 2022; 10:862841. [PMID: 35769266 PMCID: PMC9235033 DOI: 10.3389/fcell.2022.862841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Deer antlers are male secondary sexual characters that develop to become bone; they are unique appendages that, once lost, can fully regenerate from the permanent bony protuberances or pedicles. Pedicle periosteum (PP) is the tissue that gives rise to the regenerating antlers with three differentiation stages, namely, dormant (DoPP), potentiated (PoPP), and activated (AcPP). Thus far, the transition from the PoPP to the AcPP has not been studied. Our results showed that the AcPP cells maintained their original stem cell features by expressing mesenchymal stem cell (MSC) markers CD73, CD90, and CD105, although they had entered the proliferation mode. The differentially expressed genes (DEGs) in the AcPP compared with those of the PoPP were mainly involved in protein processing, cell cycle, and calcium signaling pathways. Calreticulin (CALR), an androgen response gene, was significantly differentially upregulated in the AcPP cells, and its expression level was negatively regulated by androgens, in contrast to the currently known model systems where all regulation is positive. The downregulation of CALR expression in the AcPP cells in vitro inhibited cell proliferation, induced apoptosis, and inhibited cell cycle progression at G1-S transition. Therefore, CALR is likely a downstream mediator of androgen hormones for triggering initiation of antler regeneration. We believe that the identification of CALR has not only discovered “one critical piece” of the “jigsaw puzzle” in the initiation of antler regeneration but also helps in revealing the mechanism underlying this unique mammalian epimorphic regeneration and has also opened a new avenue for the study of the nature of CALR regulation by androgen (putative binding partners), thus facilitating the identification of potential molecule(s) for investigation as targets for clinical evaluation.
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Affiliation(s)
- Qianqian Guo
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | - Junjun Zheng
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | - Hengxing Ba
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
| | - Hongmei Sun
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | - Jingjie Zhai
- Department of Oral Implantology, Jilin Provincial Key Laboratory of Sciences and Technology for Stomatology Nanoengineering, Hospital of Stomatology, Jilin University, Jilin, China
| | - Wenying Wang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
- *Correspondence: Chunyi Li,
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7
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Velásquez-Zapata V, Elmore JM, Fuerst G, Wise RP. An interolog-based barley interactome as an integration framework for immune signaling. Genetics 2022; 221:iyac056. [PMID: 35435213 PMCID: PMC9157089 DOI: 10.1093/genetics/iyac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem-, and stripe rust. We used interolog inference to construct a barley protein interactome (Hordeum vulgare predicted interactome, HvInt) comprising 66,133 edges and 7,181 nodes, as a foundation to explore signaling networks associated with MLA. HvInt was compared with the experimentally validated Arabidopsis interactome of 11,253 proteins and 73,960 interactions, verifying that the 2 networks share scale-free properties, including a power-law distribution and small-world network. Then, by successive layering of defense-specific "omics" datasets, HvInt was customized to model cellular response to powdery mildew infection. Integration of HvInt with expression quantitative trait loci (eQTL) enabled us to infer disease modules and responses associated with fungal penetration and haustorial development. Next, using HvInt and infection-time-course RNA sequencing of immune signaling mutants, we assembled resistant and susceptible subnetworks. The resulting differentially coexpressed (resistant - susceptible) interactome is essential to barley immunity, facilitates the flow of signaling pathways and is linked to mildew resistance locus a (Mla) through trans eQTL associations. Lastly, we anchored HvInt with new and previously identified interactors of the MLA coiled coli + nucleotide-binding domains and extended these to additional MLA alleles, orthologs, and NLR outgroups to predict receptor localization and conservation of signaling response. These results link genomic, transcriptomic, and physical interactions during MLA-specified immunity.
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Affiliation(s)
- Valeria Velásquez-Zapata
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
| | - James Mitch Elmore
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Gregory Fuerst
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
| | - Roger P Wise
- Program in Bioinformatics & Computational Biology, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, USA
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Ames, IA 50011, USA
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8
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Teplova AD, Serebryakova MV, Galiullina RA, Chichkova NV, Vartapetian AB. Identification of Phytaspase Interactors via the Proximity-Dependent Biotin-Based Identification Approach. Int J Mol Sci 2021; 22:13123. [PMID: 34884925 PMCID: PMC8658550 DOI: 10.3390/ijms222313123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 01/22/2023] Open
Abstract
Proteolytic enzymes are instrumental in various aspects of plant development, including senescence. This may be due not only to their digestive activity, which enables protein utilization, but also to fulfilling regulatory functions. Indeed, for the largest family of plant serine proteases, subtilisin-like proteases (subtilases), several members of which have been implicated in leaf and plant senescence, both non-specific proteolysis and regulatory protein processing have been documented. Here, we strived to identify the protein partners of phytaspase, a plant subtilase involved in stress-induced programmed cell death that possesses a characteristic aspartate-specific hydrolytic activity and unusual localization dynamics. A proximity-dependent biotin identification approach in Nicotiana benthamiana leaves producing phytaspase fused to a non-specific biotin ligase TurboID was employed. Although the TurboID moiety appeared to be unstable in the apoplast environment, several intracellular candidate protein interactors of phytaspase were identified. These were mainly, though not exclusively, represented by soluble residents of the endoplasmic reticulum, namely endoplasmin, BiP, and calreticulin-3. For calreticultin-3, whose gene is characterized by an enhanced expression in senescing leaves, direct interaction with phytaspase was confirmed in an in vitro binding assay using purified proteins. In addition, an apparent alteration of post-translational modification of calreticultin-3 in phytaspase-overproducing plant cells was observed.
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Affiliation(s)
- Anastasia D. Teplova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
| | - Raisa A. Galiullina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
| | - Nina V. Chichkova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
| | - Andrey B. Vartapetian
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (M.V.S.); (R.A.G.); (N.V.C.)
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Bhosle SM, Makandar R. Comparative proteomic analysis reveals molecular differences between incompatible and compatible interaction of Erysiphe pisi in garden pea. Microbiol Res 2021; 248:126736. [PMID: 33740672 DOI: 10.1016/j.micres.2021.126736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/15/2021] [Accepted: 02/28/2021] [Indexed: 10/22/2022]
Abstract
Comparative proteome analysis of Erysiphe pisi-infected pea genotypes; JI-2480 carrying er2 resistant gene and Arkel, the susceptible genotype by liquid chromatography- mass spectrometry (LCMS/MS QTOF) at 72 h post inoculation (hpi) revealed several differentially abundant proteins (DAPs) of both the host and the pathogen. The functional annotation of proteins through gene enrichment and KEGG pathway analyses revealed strong up-regulation of pathogenesis related protein NPR1, proteins related to defense, transportation and signal transduction, hypersensitive response, cell wall modifications, phenylpropanoid and metabolic pathways in J-72. Significant abundance of membrane-related polypeptides, kinase domains and small GTPase signal transduction-related proteins suggested their major role in plant defense. The abundance of cellular antioxidant protein, catalase and its isozyme along with calreticulin-1 and 2 in J-72 confirmed their intervention in maintaining a redox balance in powdery mildew defense. High abundance levels of Glycolysis-related proteins indicated it as a major pathway for energy source during fungal growth. The majority of pathogenicity and virulence genes were downregulated in J-72 compared to A-72, while four EKA (Effectors homologues to Avk1 and Avra10) like avirulence proteins were significantly upregulated in incompatible interaction suggesting their role in eliciting hypersensitive response in pea against E. pisi.
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Affiliation(s)
- Sheetal M Bhosle
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad, 500046, India
| | - Ragiba Makandar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad, 500046, India.
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10
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Shin YJ, König-Beihammer J, Vavra U, Schwestka J, Kienzl NF, Klausberger M, Laurent E, Grünwald-Gruber C, Vierlinger K, Hofner M, Margolin E, Weinhäusel A, Stöger E, Mach L, Strasser R. N-Glycosylation of the SARS-CoV-2 Receptor Binding Domain Is Important for Functional Expression in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:689104. [PMID: 34211491 PMCID: PMC8239413 DOI: 10.3389/fpls.2021.689104] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/20/2021] [Indexed: 05/17/2023]
Abstract
Nicotiana benthamiana is used worldwide as production host for recombinant proteins. Many recombinant proteins such as monoclonal antibodies, growth factors or viral antigens require posttranslational modifications like glycosylation for their function. Here, we transiently expressed different variants of the glycosylated receptor binding domain (RBD) from the SARS-CoV-2 spike protein in N. benthamiana. We characterized the impact of variations in RBD-length and posttranslational modifications on protein expression, yield and functionality. We found that a truncated RBD variant (RBD-215) consisting of amino acids Arg319-Leu533 can be efficiently expressed as a secreted soluble protein. Purified RBD-215 was mainly present as a monomer and showed binding to the conformation-dependent antibody CR3022, the cellular receptor angiotensin converting enzyme 2 (ACE2) and to antibodies present in convalescent sera. Expression of RBD-215 in glycoengineered ΔXT/FT plants resulted in the generation of complex N-glycans on both N-glycosylation sites. While site-directed mutagenesis showed that the N-glycans are important for proper RBD folding, differences in N-glycan processing had no effect on protein expression and function.
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Affiliation(s)
- Yun-Ji Shin
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Julia König-Beihammer
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Jennifer Schwestka
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Nikolaus F. Kienzl
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Miriam Klausberger
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, Core Facility Biomolecular and Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Department of Chemistry, Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Klemens Vierlinger
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Manuela Hofner
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Andreas Weinhäusel
- Competence Unit Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Eva Stöger
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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Liu GT, Wang BB, Lecourieux D, Li MJ, Liu MB, Liu RQ, Shang BX, Yin X, Wang LJ, Lecourieux F, Xu Y. Proteomic analysis of early-stage incompatible and compatible interactions between grapevine and P. viticola. HORTICULTURE RESEARCH 2021; 8:100. [PMID: 33931609 PMCID: PMC8087781 DOI: 10.1038/s41438-021-00533-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/16/2021] [Accepted: 02/24/2021] [Indexed: 05/04/2023]
Abstract
Wild grapevines can show strong resistance to the downy mildew pathogen P. viticola, but the associated mechanisms are poorly described, especially at early stages of infection. Here, we performed comparative proteomic analyses of grapevine leaves from the resistant genotype V. davidii "LiuBa-8" (LB) and susceptible V. vinifera "Pinot Noir" (PN) 12 h after inoculation with P. viticola. By employing the iTRAQ technique, a total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN, respectively. The majority of these DEPs were related to photosynthesis, respiration, cell wall modification, protein metabolism, stress, and redox homeostasis. Compared with PN, LB showed fewer downregulated proteins associated with photosynthesis and more upregulated proteins associated with metabolism. At least a subset of PR proteins (PR10.2 and PR10.3) was upregulated upon inoculation in both genotypes, whereas HSP (HSP70.2 and HSP90.6) and cell wall-related XTH and BXL1 proteins were specifically upregulated in LB and PN, respectively. In the incompatible interaction, ROS signaling was evident by the accumulation of H2O2, and multiple APX and GST proteins were upregulated. These DEPs may play crucial roles in the grapevine response to downy mildew. Our results provide new insights into molecular events associated with downy mildew resistance in grapevine, which may be exploited to develop novel protection strategies against this disease.
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Affiliation(s)
- Guo-Tian Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
- UMR1287 EGFV, CNRS, Université de Bordeaux, INRAE, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, France
| | - Bian-Bian Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - David Lecourieux
- UMR1287 EGFV, CNRS, Université de Bordeaux, INRAE, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, France
| | - Mei-Jie Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ming-Bo Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Rui-Qi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Bo-Xing Shang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Xiao Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Li-Jun Wang
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Fatma Lecourieux
- UMR1287 EGFV, CNRS, Université de Bordeaux, INRAE, Bordeaux Sciences Agro, ISVV, Villenave d'Ornon, France.
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China.
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12
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Katsuyama Y, Doi M, Shioya S, Hane S, Yoshioka M, Date S, Miyahara C, Ogawa T, Takada R, Okumura H, Ikusawa R, Kitajima S, Oda K, Sato K, Tanaka Y, Tezuka T, Mino M. The role of chaperone complex HSP90-SGT1-RAR1 as the associated machinery for hybrid inviability between Nicotiana gossei Domin and N. tabacum L. Gene 2021; 776:145443. [PMID: 33484759 DOI: 10.1016/j.gene.2021.145443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/01/2021] [Accepted: 01/13/2021] [Indexed: 12/18/2022]
Abstract
Two cultured cell lines (GTH4 and GTH4S) of a Nicotiana interspecific F1 hybrid (N. gossei × N. tabacum) were comparatively analyzed to find genetic factors related to hybrid inviability. Both cell lines proliferated at 37 °C, but after shifting to 26 °C, GTH4 started to die similar to the F1 hybrid seedlings, whereas GTH4S survived. As cell death requires de novo expression of genes and proteins, we compared expressed protein profiles between the two cell lines, and found that NgSGT1, a cochaperone of the chaperone complex (HSP90-SGT1-RAR1), was expressed in GTH4 but not in GTH4S. Agrobacterium-mediated transient expression of NgSGT1, but not NtSGT1, induced cell death in leaves of N. tabacum, suggesting its possible role in hybrid inviability. Cell death in N. tabacum was also induced by transient expression of NgRAR1, but not NtRAR1. In contrast, transient expression of any parental combinations of three components revealed that NgRAR1 promoted cell death, whereas NtRAR1 suppressed it in N. tabacum. A specific inhibitor of HSP90, geldanamycin, inhibited the progression of hypersensitive response-like cell death in GTH4 and leaf tissue after agroinfiltration. The present study suggested that components of the chaperone complex are involved in the inviability of Nicotiana interspecific hybrid.
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Affiliation(s)
- Yushi Katsuyama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Mizuho Doi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Sachi Shioya
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Sanae Hane
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Momoko Yoshioka
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Shuichi Date
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Chika Miyahara
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Tomomichi Ogawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Ryo Takada
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hanako Okumura
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Rie Ikusawa
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Sakihito Kitajima
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kenji Oda
- Research Institute for Biological Sciences, Okayama, 7549-1 Yoshikawa, Kibi Chuou-chou, Kaga-gun, Okayama 716-1241, Japan
| | - Kenji Sato
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshikazu Tanaka
- Biotechnology Division Research & Development Department, The Wakasa Wan Energy Research Center, 64-52-1 Ngatani, Tsuruga, Fukui 914-0135, Japan
| | - Takahiro Tezuka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Masanobu Mino
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.
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Mani SD, Pandey S, Govindan M, Muthamilarasan M, Nagarathnam R. Transcriptome dynamics underlying elicitor-induced defense responses against Septoria leaf spot disease of tomato ( Solanum lycopersicum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:873-888. [PMID: 33967469 PMCID: PMC8055812 DOI: 10.1007/s12298-021-00970-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Elicitor-induced defense response against potential plant pathogens has been widely reported in several crop plants; however, transcriptome dynamics underlying such defense response remains elusive. Our previous study identified and characterized a novel elicitor, κ-carrageenan, from Kappaphycus alvarezii, a marine red seaweed. Our preliminary studies have shown that the elicitor-treatment enhances the tolerance of a susceptible tomato cultivar to Septoria lycopersici (causative agent of leaf spot disease). To gain further insights into the genes regulated during elicitor treatment followed by pathogen infection, we have performed RNA-Seq experiments under different treatments, namely, control (untreated and uninfected), elicitor treatment, pathogen infection alone, and elicitor treatment followed by pathogen infection. To validate the results, forty-three genes belonging to five different classes, namely, ROS activating and detoxifying enzyme encoding genes, DEAD-box RNA helicase genes, autophagy-related genes, cysteine proteases, and pathogenesis-related genes, were chosen. Expression profiling of each gene was performed using qRT-PCR, and the data was correlated with the RNA-seq data. Altogether, the study has pinpointed a repertoire of genes that could be potential candidates for further functional characterization to provide insights into novel elicitor-induced fungal defense and develop transgenic lines resistant to foliar diseases. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00970-y.
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Affiliation(s)
- Sumithra Devi Mani
- Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India
| | - Saurabh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110 067 India
| | - Muthukumar Govindan
- Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500 046 Telangana India
| | - Radhakrishnan Nagarathnam
- Unit of Plant Pathology, Center for Advanced Studies in Botany, University of Madras, Tamil Nadu, Guindy Campus, Chennai, 600 025 India
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14
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Bhosle SM, Makandar R. Comparative transcriptome of compatible and incompatible interaction of Erysiphe pisi and garden pea reveals putative defense and pathogenicity factors. FEMS Microbiol Ecol 2021; 97:fiab006. [PMID: 33476382 DOI: 10.1093/femsec/fiab006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Comparative transcriptome analysis of Erysiphe pisi-infected pea (Pisum sativum) genotypes JI-2480 (resistant) and Arkel (susceptible) at 72 hours post-inoculation (hpi) was carried to detect molecular components involved in compatible and incompatible interactions. Differential gene expression was observed in Arkel and JI-2480 genotype at 72 hpi with E. pisi isolate (Ep01) using EdgeR software. Out of 32 217 transcripts, 2755 transcripts showed significantly altered gene expression in case of plants while 530 were related to E. pisi (P < 0.05). The higher transcript number of differentially expressed genes demonstrated peak activity of pathogenicity genes in plants at 72 hpi. Glycolysis was observed to be the major pathway for energy source during fungal growth. Differential gene expression of plant transcripts revealed significant expression of putative receptor and regulatory sequences involved in defense in the resistant, JI-2480 compared to susceptible, Arkel genotype. Expression of genes involved in defense and hormonal signaling, genes related to hypersensitive response, reactive oxygen species and phenylpropanoid pathway in JI-2480 indicated their crucial role in disease resistance against E. pisi. Down-regulation of transcription factors like-WRKY-28 and up-regulation of several putative pattern recognition receptors in JI-2480 compared to Arkel also suggested activation of host-mediated defense responses against E. pisi in pea.
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Affiliation(s)
- Sheetal M Bhosle
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
| | - Ragiba Makandar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500046, India
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15
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Liu J, Peng H, Su W, Liu M, Huang W, Dai L, Peng D. HaCRT1 of Heterodera avenae Is Required for the Pathogenicity of the Cereal Cyst Nematode. FRONTIERS IN PLANT SCIENCE 2020; 11:583584. [PMID: 33329646 PMCID: PMC7717957 DOI: 10.3389/fpls.2020.583584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Cereal cyst nematodes are sedentary biotrophic endoparasites that secrete effector proteins into plant tissues to transit normal cells into specialized feeding sites and suppress plant defenses. To understand the function of nematode effectors in Heterodera avenae, here, we identified a calreticulin protein HaCRT1, which could suppress the cell death induced by Bax when expressed in Nicotiana benthamiana. HaCRT1 is synthetized in the subventral gland cells of pre-parasitic second-stage nematodes. Real-time PCR assays indicated that the expression of HaCRT1 was highest in parasitic second-stage juveniles. The expression of an HaCRT1-RFP fusion in N. benthamiana revealed that it was localized in the endoplasmic reticulum of the plant cell. The ability of H. avenae infecting plants was significantly reduced when HaCRT1 was knocked down by RNA interference in vitro. Arabidopsis thaliana plants expressing HaCRT1 were more susceptible than wild-type plants to Pseudomonas syringae. The induction of defense-related genes, PAD4, WRKY33, FRK1, and WRKY29, after treatment with flg22 was suppressed in HaCRT1-transgenic plants. Also, the ROS accumulation induced by flg22 was reduced in the HaCRT1-transgenic plants compared to wild-type plants. HaCRT1 overexpression increased the cytosolic Ca2+ concentration in A. thaliana. These data suggested that HaCRT1 may contribute to the pathogenicity of H. avenae by suppressing host basal defense.
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Affiliation(s)
- Jing Liu
- Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wen Su
- Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Maoyan Liu
- Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liangying Dai
- Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Joshi R, Paul M, Kumar A, Pandey D. Role of calreticulin in biotic and abiotic stress signalling and tolerance mechanisms in plants. Gene 2019; 714:144004. [PMID: 31351124 DOI: 10.1016/j.gene.2019.144004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
Abstract
Calreticulin (CRT) is calcium binding protein of endoplasmic reticulum (ER) which performs plethora of functions besides it's role as molecular chaperone. Among the three different isoforms of this protein, CRT3 is most closely related to primitive CRT gene of higher plants. Based on their distinct structural and functional organisation, the plant CRTs have been known to contain three different domains: N, P and the C domain. The domain organisation and various biochemical characterstics of plant and animal CRTs are common with the exception of some differences. In plant calreticulin, the important N-glycosylation site(s) are replaced by the glycan chain(s) and several consensus sequences for in vitro phosphorylation by protein kinase CK2 (casein kinase-2), are also present unlike the animal calreticulin. Biotic and abiotic stresses play a significant role in bringing down the crop production. The role of various phytohormones in defense against fungal pathogens is well documented. CRT3 has been reported to play important role in protecting the plants against fungal and bacterial pathogens and in maintaining plant innate immunity. There is remarkable crosstalk between CRT mediated signalling and biotic, abiotic stress, and phytohormone mediated signalling pathways The role of CRT mediated pathway in mitigating biotic and abiotic stress can be further explored in plants so as to strategically modify it for development of stress tolerant plants.
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Affiliation(s)
- Rini Joshi
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Ag.& Tech., Pantnagar 263145, Uttarakhand, India
| | - Meenu Paul
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Ag.& Tech., Pantnagar 263145, Uttarakhand, India
| | - Anil Kumar
- Rani Laxmi Bai Central Agriculture University, Jhansi, Uttar Pradesh 284003, India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Ag.& Tech., Pantnagar 263145, Uttarakhand, India.
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17
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Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Castaño E, Rodríguez-Zapata LC. Global Dynamics in Protein Disorder during Maize Seed Development. Genes (Basel) 2019; 10:genes10070502. [PMID: 31262071 PMCID: PMC6678312 DOI: 10.3390/genes10070502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco. División de Biotecnología Industrial. Camino Arenero 1227, El Bajío, Zapopan, Jalisco. C.P. 45019
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México.
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18
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Wu X, Yan J, Wu Y, Zhang H, Mo S, Xu X, Zhou F, Ding H. Proteomic analysis by iTRAQ-PRM provides integrated insight into mechanisms of resistance in pepper to Bemisia tabaci (Gennadius). BMC PLANT BIOLOGY 2019; 19:270. [PMID: 31226939 PMCID: PMC6588876 DOI: 10.1186/s12870-019-1849-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/24/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND The Bemisia tabaci is a major leaf feeding insect pest to pepper (Capsicum annuum), causing serious damage to pepper growth and yield. It is particularly important to study the mechanism of pepper resistance to B. tabaci, and to breed and promote the varieties of pepper resistant to B. tabaci. However, very limited molecular mechanism is available about how plants perceive and defend themselves from the destructive pest. Proteome technologies have provided an idea method for studying plant physiological processes in response to B. tabaci. RESULTS Here, a highly resistant genotype and a highly susceptible genotype were exposed to B. tabaci feeding for 48 h to explore the defense mechanisms of pepper resistance to B. tabaci. The proteomic differences between both genotypes were compared using isobaric tag for relative and absolute quantification (iTRAQ). The quantitative data were validated by parallel reaction monitoring (PRM). The results showed that 37 differential abundance proteins (DAPs) were identified in the RG (resistant genotype), while 17 DAPs were identified in the SG (susceptible genotype) at 48 h after B. tabaci feeding. 77 DAPs were identified when comparing RG with SG without feeding. The DAP functions were determined for the classification of the pathways, mainly involved in redox regulation, stress response, protein metabolism, lipid metabolism and carbon metabolism. Some candidate DAPs are closely related to B. tabaci resistance such as annexin D4-like (ANN4), calreticulin-3 (CRT3), heme-binding protein 2-like (HBP1), acidic endochitinase pcht28-like (PR3) and lipoxygenase 2 (LOX2). CONCLUSIONS Taken together, this study indicates complex resistance-related events in B. tabaci interaction, provides novel insights into the molecular mechanism underlying the response of plant to B. tabaci, and identifies some candidate proteins against B. tabaci attack.
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Affiliation(s)
- Xiaoxia Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Jiaxing Yan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Yahong Wu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Haibo Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Shuangrong Mo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Xiaoying Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
| | - Fucai Zhou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Haidong Ding
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009 China
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19
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Quantitative proteomics analysis reveals resistance differences of banana cultivar 'Brazilian' to Fusarium oxysporum f. sp. cubense races 1 and 4. J Proteomics 2019; 203:103376. [PMID: 31078632 DOI: 10.1016/j.jprot.2019.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 05/02/2019] [Indexed: 12/29/2022]
Abstract
Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases in banana production. Foc is classified into three physiological races. However, the resistance mechanisms of banana against different Foc races are poorly understood. In this study, we performed a comparative proteomics analysis to investigate the resistance mechanisms of 'Brazilian' against Foc1 and Foc4. The proteomes of 'Brazilian' roots inoculated with Foc1 and Foc4 and mock inoculated control at 48 h were analyzed using TMT based quantitative analysis technique. A total of 7325 unique protein species were identified, of which 689, 744, and 1222 protein species were differentially accumulated in Foc1 vs. CK, Foc4 vs. CK, and Foc1 vs. Foc4, respectively. The differential accumulations of candidate protein species were further confirmed by RT-qPCR, PRM, and physiological and biochemical assays. Bioinformatics analysis revealed that the differentially abundance protein species (DAPS) related to pattern recognition receptors, plant cell wall modification, redox homeostasis, and defense responses were differentially accumulated after Foc1 and Foc4 infection, suggesting that 'Brazilian' differed in resistance to the two Foc races. Our study lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level. SIGNIFICANCE: The banana fusarium wilt disease is one of the most destructive disease of banana and is caused by Fusarium oxysporum f. sp. cubense (Foc). Foc is classified into three physiological races, namely, Foc1, Foc2, and Foc4. Among these races, Foc1 and Foc4 are widely distributed in south China and significantly lose yield. Although both physiological races (Foc1 and Foc4) can invade the Cavendish banana cultivar 'Brazilian', they have significant pathogenicity differences. Unfortunately, how the resistance differences are produced between two races is still largely unclear to date. In this study, we addressed this issue by performing TMT-based comparative quantitative proteomics analysis of 'Brazilian' roots after inoculation with Foc1 and Foc4 as well as sterile water as the control. We revealed that the series of protein species associated with pattern recognition receptors, plant cell wall modification, redox homeostasis, pathogenesis, phytohormones and signal transduction, plant secondary metabolites and programmed cell death etc. were involved in the response to Foc infection. Notably, the potential role of lipid signaling in banana defense against Foc are not reported previously but rather unveiled for the first time in this study. The current study represents the most extensive analysis of the protein profile of 'Brazilian' in response to Foc inoculation and includes for the first time the results from comparison quantitative proteomics analysis between plants inoculated with a pathogenic strain Foc4 and a nonpathogenic strain Foc1 of 'Brazilian', which will lay the foundation for an in-depth understanding of the interaction between bananas and Foc at the proteome level.
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The membrane tethered transcription factor EcbZIP17 from finger millet promotes plant growth and enhances tolerance to abiotic stresses. Sci Rep 2018; 8:2148. [PMID: 29391403 PMCID: PMC5794737 DOI: 10.1038/s41598-018-19766-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/22/2017] [Indexed: 11/08/2022] Open
Abstract
The occurrence of various stresses, as the outcome of global climate change, results in the yield losses of crop plants. Prospecting of genes in stress tolerant plant species may help to protect and improve their agronomic performance. Finger millet (Eleusine coracana L.) is a valuable source of superior genes and alleles for stress tolerance. In this study, we isolated a novel endoplasmic reticulum (ER) membrane tethered bZIP transcription factor from finger millet, EcbZIP17. Transgenic tobacco plants overexpressing this gene showed better vegetative growth and seed yield compared with wild type (WT) plants under optimal growth conditions and confirmed upregulation of brassinosteroid signalling genes. Under various abiotic stresses, such as 250 mM NaCl, 10% PEG6000, 400 mM mannitol, water withdrawal, and heat stress, the transgenic plants showed higher germination rate, biomass, primary and secondary root formation, and recovery rate, compared with WT plants. The transgenic plants exposed to an ER stress inducer resulted in greater leaf diameter and plant height as well as higher expression of the ER stress-responsive genes BiP, PDIL, and CRT1. Overall, our results indicated that EcbZIP17 improves plant growth at optimal conditions through brassinosteroid signalling and provide tolerance to various environmental stresses via ER signalling pathways.
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21
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Xiong YM, Yan ZH, Zhang JE, Li HY. Analysis of albumen gland proteins suggests survival strategies of developing embryos of Pomacea canaliculata. MOLLUSCAN RESEARCH 2017. [DOI: 10.1080/13235818.2017.1385896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ya-Ming Xiong
- Department of Aquiculture, College of Animal Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zhi-Hui Yan
- Department of Aquiculture, College of Animal Science, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Jia-En Zhang
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, People’s Republic of China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture, Guangzhou, People’s Republic of China
- Guangdong Provincial Engineering Technology Research Center of Modern Eco-agriculture and Circular Agriculture, Guangzhou, People’s Republic of China
| | - Hai-Yun Li
- Department of Aquiculture, College of Animal Science, South China Agricultural University, Guangzhou, People’s Republic of China
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22
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Yin X, Komatsu S. Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial-flooding stress. J Proteomics 2017; 169:225-232. [PMID: 28137666 DOI: 10.1016/j.jprot.2017.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, which markedly reduces its growth and yield. Morphological and biochemical changes such as an increase of fresh weight and a decrease of ATP content happen in early-stage soybean at initial-flooding stress, indicating that soybean responses to flooding stress are keys for its survival and seedling growth. Phosphoproteomics and nuclear proteomics are useful tools to detect protein-phosphorylation status and to identify transcriptional factors. In the review, the effect of flooding on soybean response to initial flooding stress is discussed based on recent results of proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies. In addition, soybean survival under flooding stress, which is defined as tolerance mechanism, is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. BIOLOGICAL SIGNIFICANCE Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, especially soybean responses to initial flooding stress is key for its survival and seedling growth. Recently, proteomic techniques are applied to investigate the response and tolerant mechanisms of soybean at initial flooding condition. In this review, the progress in proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies about the initial-flooding response mechanism in early-stage soybean is presented. In addition, the tolerant mechanism in soybean is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. Through this review, the key proteins and genes involved in initial flooding response and tolerance at early stage soybean are summarized and they contribute greatly to uncover response and tolerance mechanism at early stage under stressful environmental conditions in soybean.
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Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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23
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Ferreira RA, Roma-Rodrigues C, Davies LC, Sá-Correia I, Martins-Dias S. A quantitative proteomic approach to highlight Phragmites sp. adaptation mechanisms to chemical stress induced by a textile dyeing pollutant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 573:788-798. [PMID: 27592466 DOI: 10.1016/j.scitotenv.2016.08.169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/23/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
Phragmites sp. is present worldwide in treatment wetlands though the mechanisms involved in the phytoremediation remain unclear. In this study a quantitative proteomic approach was used to study the prompt response and adaptation of Phragmites to the textile dyeing pollutant, Acid Orange 7 (AO7). Previously, it was demonstrated that AO7 could be successfully removed from wastewater and mineralized in a constructed wetland planted with Phragmites sp. This azo dye is readily taken up by roots and transported to the plant aerial part by the xylem. Phragmites leaf samples were collected from a pilot scale vertical flow constructed wetland after 0.25, 3.25 and 24.25h exposure to AO7 (400mgL-1) immediately after a watering cycle used as control. Leaf soluble protein extraction yielded an average of 1560 proteins in a broad pI range (pH3-10) by two-dimensional gel electrophoresis. A time course comparative analysis of leaf proteome revealed that 40 proteins had a differential abundance compared to control (p<0.05) within a 3.25h period. After 24.25h in contact with AO7, leaf proteome was similar to control. Adaptation to AO7 involved proteins related with cellular signalling (calreticulin, Ras-related protein Rab11D and 20S proteasome), energy production and conversion (adenosine triphosphate synthase beta subunit) carbohydrate transport and metabolism (phosphoglucose isomerase, fructose-bisphosphate aldolase, monodehydroascorbate reductase, frutockinase-1 and Hypothetical protein POPTR_0003s12000g and the Uncharacterized protein LOC100272772) and photosynthesis (sedoheptulose-1,7-bisphosphatase and ferredoxin-NADP+ reductase). Therefore, the quantitative proteomic approach used in this work indicates that mechanisms associated with stress cell signalling, energy production, carbohydrate transport and metabolism as well as proteins related with photosynthesis are key players in the initial chemical stress response in the phytoremediation process of AO7.
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Affiliation(s)
- R A Ferreira
- Centre for Natural Resources and the Environment (CERENA), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - C Roma-Rodrigues
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - L C Davies
- Centre for Natural Resources and the Environment (CERENA), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - I Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - S Martins-Dias
- Centre for Natural Resources and the Environment (CERENA), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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Moreau C, Cioci G, Iannello M, Laffly E, Chouquet A, Ferreira A, Thielens NM, Gaboriaud C. Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties. IUCRJ 2016; 3:408-419. [PMID: 27840680 PMCID: PMC5094443 DOI: 10.1107/s2052252516012847] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
Calreticulin (CRT) is a multifaceted protein, initially discovered as an endoplasmic reticulum (ER) chaperone protein, that is essential in calcium metabolism. Various implications in cancer, early development and immunology have been discovered more recently for CRT, as well as its role as a dominant 'eat-me' prophagocytic signal. Intriguingly, cell-surface exposure/secretion of CRT is among the infective strategies used by parasites such as Trypanosoma cruzi, Entamoeba histolytica, Taenia solium, Leishmania donovani and Schistosoma mansoni. Because of the inherent flexibility of CRTs, their analysis by X-ray crystallography requires the design of recombinant constructs suitable for crystallization, and thus only the structures of two very similar mammalian CRT lectin domains are known. With the X-ray structures of two distant parasite CRTs, insights into species structural determinants that might be harnessed to fight against the parasites without affecting the functions of the host CRT are now provided. Moreover, although the hypothesis that CRT can exhibit both open and closed conformations has been proposed in relation to its chaperone function, only the open conformation has so far been observed in crystal structures. The first evidence is now provided of a complex conformational transition with the junction reoriented towards P-domain closure. SAXS experiments also provided additional information about the flexibility of T. cruzi CRT in solution, thus complementing crystallographic data on the open conformation. Finally, regarding the conserved lectin-domain structure and chaperone function, evidence is provided of its dual carbohydrate/protein specificity and a new scheme is proposed to interpret such unusual substrate-binding properties. These fascinating features are fully consistent with previous experimental observations, as discussed considering the broad spectrum of CRT sequence conservations and differences.
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Affiliation(s)
- Christophe Moreau
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Gianluca Cioci
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Marina Iannello
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Emmanuelle Laffly
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Anne Chouquet
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Arturo Ferreira
- Program of Immunology, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nicole M. Thielens
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Christine Gaboriaud
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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25
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Kim TK, Ibelli AMG, Mulenga A. Amblyomma americanum tick calreticulin binds C1q but does not inhibit activation of the classical complement cascade. Ticks Tick Borne Dis 2016; 6:91-101. [PMID: 25454607 DOI: 10.1016/j.ttbdis.2014.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/08/2014] [Accepted: 10/13/2014] [Indexed: 01/02/2023]
Abstract
In this study we characterized Amblyomma americanum (Aam) tick calreticulin (CRT) homolog in tick feeding physiology. In nature, different tick species can be found feeding on the same animal host. This suggests that different tick species found feeding on the same host can modulate the same host anti-tick defense pathways to successfully feed. From this perspective it's plausible that different tick species can utilize universally conserved proteins such as CRT to regulate and facilitate feeding. CRT is a multi-functional protein found in most taxa that is injected into the vertebrate host during tick feeding. Apart from it's current use as a biomarker for human tick bites, role(s) of this protein in tick feeding physiology have not been elucidated. Here we show that annotated functional CRT amino acid motifs are well conserved in tick CRT. However our data show that despite high amino acid identity levels to functionally characterized CRT homologs in other organisms, AamCRT is apparently functionally different. Pichia pastoris expressed recombinant (r) AamCRT bound C1q, the first component of the classical complement system, but it did not inhibit activation of this pathway. This contrast with reports of other parasite CRT that inhibited activation of the classical complement pathway through sequestration of C1q. Furthermore rAamCRT did not bind factor Xa in contrast to reports of parasite CRT binding factor Xa, an important protease in the blood clotting system. Consistent with this observation, rAamCRT did not affect plasma clotting or platelet aggregation. We discuss our findings in the context of tick feeding physiology.
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Affiliation(s)
- Tae Kwon Kim
- Texas A & M University AgriLife Research, Department of Entomology, 2475 TAMU, College Station, TX 77843, United States
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Cao JY, Xu YP, Cai XZ. TMT-based quantitative proteomics analyses reveal novel defense mechanisms of Brassica napus against the devastating necrotrophic pathogen Sclerotinia sclerotiorum. J Proteomics 2016; 143:265-277. [PMID: 26947552 DOI: 10.1016/j.jprot.2016.03.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/24/2016] [Accepted: 03/02/2016] [Indexed: 12/31/2022]
Abstract
UNLABELLED The white mould disease, caused by Sclerotinia sclerotiorum, is one of the most important diseases in the vital oil crop Brassica napus. Nevertheless, the defense mechanisms of B. napus against S. sclerotiorum are poorly understood. In this study, we performed comparative quantitative proteomics analyses to reveal B. napus defense mechanisms against S. sclerotiorum. The proteomes of B. napus leaves inoculated with S. sclerotiorum wild-type strain 1980 and nonpathogenic mutant strain Ep-1PB as well as empty agar plug as the control were analyzed using TMT label-based quantitative analysis technique. A total of 79, 299 and 173 proteins consistently differentially expressed between Ep-1PB- and mock-inoculated leaves, 1980- and mock-inoculated leaves, as well as 1980- and Ep-1PB-inoculated leaves, respectively, were identified. The differential expression of 12 selected proteins was confirmed by qRT-PCR analyses. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction prediction analyses revealed that redox homeostasis, lipid signaling, calcium signaling, histone and DNA methylation-mediated transcription regulation and defense-related proteins such as defensin and defensin-like proteins and cyanate lyase, contribute to defense against S. sclerotiorum. Our results provide new insights into molecular mechanisms that may be involved in defense responses of B. napus to S. sclerotiorum. SIGNIFICANCE The Sclerotinia white mould disease is one of the most important diseases in the significant oil crop Brassica napus. Nevertheless, the defense mechanisms of B. napus against S. sclerotiorum are still largely unknown to date. In this study, we addressed this issue by performing TMT label-based comparative quantitative analyses of the proteomes of B. napus leaves inoculated with S. sclerotiorum wild-type strain 1980 and nonpathogenic mutant strain Ep-1PB as well as empty agar plug as the control. Through comparative analyses on 79, 299, and 173 proteins that are consistently differentially expressed in between Ep-1PB-inoculated and the control leaves, 1980-inoculated and the control leaves, as well as 1980-inoculated and Ep-1PB-inoculated leaves, respectively, we revealed that redox homeostasis, lipid signaling, calcium signaling, histone and DNA methylation-mediated transcription regulation and defense-related proteins such as defensin and defensin-like proteins as well as cyanate lyase, contribute to B. napus defenses against S. sclerotiorum. Notably, the potential role of lipid signaling, calcium signaling, histone and DNA methylation-mediated transcription regulation and cyanate lyase in B. napus defense against S. sclerotiorum are not reported previously but rather unveiled for the first time in this study. The current study represents the most extensive analysis of the protein profile of B. napus in response to S. sclerotiorum inoculation and includes for the first time the results from comparison between plants inoculated with the wild-type strain and a nonpathogenic mutant strain of S. sclerotiorum. Collectively, our results provide new insights into the molecular mechanisms of interactions between B. napus and S. sclerotiorum.
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Affiliation(s)
- Jia-Yi Cao
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - You-Ping Xu
- Centre of Analysis and Measurement, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China
| | - Xin-Zhong Cai
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou 310058, China.
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27
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Niedojadło K, Lenartowski R, Lenartowska M, Bednarska-Kozakiewicz E. Late progamic phase and fertilization affect calreticulin expression in the Hyacinthus orientalis female gametophyte. PLANT CELL REPORTS 2015; 34:2201-15. [PMID: 26354004 PMCID: PMC4636998 DOI: 10.1007/s00299-015-1863-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 05/11/2023]
Abstract
Calreticulin expression is upregulated during sexual reproduction of Hyacinthus orientalis, and the protein is localized both in the cytoplasm and a highly specialized cell wall within the female gametophyte. Several evidences indicate calreticulin (CRT) as an important calcium (Ca(2+))-binding protein that is involved in the generative reproduction of higher plants, including both pre-fertilization and post-fertilization events. Because CRT is able to bind and sequester exchangeable Ca(2+), it can serve as a mobile intracellular store of easily releasable Ca(2+) and control its local cytosolic concentrations in the embryo sac. This phenomenon seems to be essential during the late progamic phase, gamete fusion, and early embryogenesis. In this report, we demonstrate the differential expression of CRT within Hyacinthus female gametophyte cells before and during anthesis, during the late progamic phase when the pollen tube enters the embryo sac, and at the moment of fertilization and zygote/early endosperm activation. CRT mRNA and the protein localize mainly to the endoplasmic reticulum (ER) and Golgi compartments of the cells, which are involved in sexual reproduction events, such as those in sister synergids, the egg cell, the central cell, zygote and the developing endosperm. Additionally, immunogold research demonstrates selective CRT distribution in the filiform apparatus (FA), a highly specific component of the synergid cell wall. In the light of our previous data showing the total transcriptional activity of the Hyacinthus female gametophyte and the results presented here, we discuss the possible functions of CRT with respect to the critical role of Ca(2+) homeostasis during key events of sexual plant reproduction. Moreover, we propose that the elevated expression of CRT within the female gametophyte is a universal phenomenon in the cells involved in double fertilization in higher plants.
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Affiliation(s)
- Katarzyna Niedojadło
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland.
| | - Robert Lenartowski
- Laboratory of Isotope and Instrumental Analysis, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Marta Lenartowska
- Laboratory of Developmental Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Elżbieta Bednarska-Kozakiewicz
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
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28
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Zhu W, Hu J, Wang X, Tian J, Komatsu S. Organ-Specific Analysis of Mahonia Using Gel-Free/Label-Free Proteomic Technique. J Proteome Res 2015; 14:2669-85. [DOI: 10.1021/acs.jproteome.5b00208] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wei Zhu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Jin Hu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Xin Wang
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Setsuko Komatsu
- National
Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
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29
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Lenartowski R, Suwińska A, Lenartowska M. Calreticulin expression in relation to exchangeable Ca(2+) level that changes dynamically during anthesis, progamic phase, and double fertilization in Petunia. PLANTA 2015; 241:209-27. [PMID: 25262422 PMCID: PMC4282720 DOI: 10.1007/s00425-014-2178-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/15/2014] [Indexed: 05/25/2023]
Abstract
Calcium (Ca(2+)) plays essential roles in plant sexual reproduction, but the sites and the mechanism of Ca(2+) mobile storage during pollen-pistil interactions have not been fully defined. Because the Ca(2+)-buffering protein calreticulin (CRT) is able to bind and sequester Ca(2+), it can serve as a mobile intracellular store of easily releasable Ca(2+) and control its local concentration within the cytoplasm. Our previous studies showed an enhanced expression of Petunia hybrida CRT gene (PhCRT) during pistil transmitting tract maturation, pollen germination and tube outgrowth on the stigma, gamete fusion, and early embryogenesis. Here, we demonstrate that elevated expression of CRT results in the accumulation of this protein in response to anthesis, pollination, sperm cells deposition within the receptive synergid and fertilization, when the level of exchangeable Ca(2+) changes dynamically. CRT localizes mainly to the endoplasmic reticulum and Golgi compartments in the pistil transmitting tract cells, germinated pollen/tubes, and sporophytic/gametophytic cells of the ovule and corresponds with loosely bound Ca(2+). Additionally, the immunogold research shows, for the first time, highly selective CRT distribution in specific nuclear sub-domains. On the basis of our results, we discuss the possible functions of CRT with respect to the critical role of Ca(2+) homeostasis during key events of the multi-step process of generative reproduction in angiosperms.
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Affiliation(s)
- Robert Lenartowski
- Laboratory of Isotope and Instrumental Analysis, Faculty of Biology and Environment Protection, Nicolaus Copernicus University, Toruń, Poland,
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30
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Zhang Q, Wang XQ, Jiang HS, Jia WM, Zhao XF, Wang JX. Calnexin functions in antibacterial immunity of Marsupenaeus japonicus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 46:356-363. [PMID: 24858031 DOI: 10.1016/j.dci.2014.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/04/2014] [Accepted: 05/04/2014] [Indexed: 06/03/2023]
Abstract
Calnexin (Cnx) is an endoplasmic reticulum membrane-bound lectin chaperone that comprises a dedicated maturation system with another lectin chaperone calreticulin (Crt). This maturation system is known as the Cnx/Crt cycle. The main functions of Cnx are Ca(2+) storage, glycoprotein folding, and quality control of synthesis. Recent studies have shown that Cnx is important in phagocytosis and in optimizing dendritic cell immunity. However, the functions of Cnx in invertebrate innate immunity remain unclear. In this research, we characterized Cnx in the kuruma shrimp Marsupenaeus japonicus (designated as MjCnx) and detected its function in shrimp immunity. The expression of MjCnx was upregulated in several tissues challenged with Vibrio anguillarum. Recombinant MjCnx could bind to bacteria by binding polysaccharides. MjCnx protein existed in the cytoplasm and on the membrane of hemocytes and was upregulated by bacterial challenge. The recombinant MjCnx enhanced the clearance of V. anguillarum in vivo, and the clearance effects were impaired after silencing MjCnx with RNA interference assay. Recombinant MjCnx promoted phagocytosis efficiency of hemocytes. These results suggest that MjCnx functions as one of the pattern recognition receptors and has crucial functions in shrimp antibacterial immunity.
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Affiliation(s)
- Qing Zhang
- MOE Key Laboratory of Plant Cell Engineering and Germplasm Innovation/Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Xiu-Qing Wang
- School of Clinical Laboratory of Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, China
| | - Hai-Shan Jiang
- MOE Key Laboratory of Plant Cell Engineering and Germplasm Innovation/Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Wen-Ming Jia
- MOE Key Laboratory of Plant Cell Engineering and Germplasm Innovation/Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Xiao-Fan Zhao
- MOE Key Laboratory of Plant Cell Engineering and Germplasm Innovation/Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Jin-Xing Wang
- MOE Key Laboratory of Plant Cell Engineering and Germplasm Innovation/Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, China.
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Kiirika LM, Schmitz U, Colditz F. The alternative Medicago truncatula defense proteome of ROS-defective transgenic roots during early microbial infection. FRONTIERS IN PLANT SCIENCE 2014; 5:341. [PMID: 25101099 PMCID: PMC4101433 DOI: 10.3389/fpls.2014.00341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 05/29/2023]
Abstract
ROP-type GTPases of plants function as molecular switches within elementary signal transduction pathways such as the regulation of ROS synthesis via activation of NADPH oxidases (RBOH-respiratory burst oxidase homolog in plants). Previously, we reported that silencing of the Medicago truncatula GTPase MtROP9 led to reduced ROS production and suppressed induction of ROS-related enzymes in transgenic roots (MtROP9i) infected with pathogenic (Aphanomyces euteiches) and symbiotic microorganisms (Glomus intraradices, Sinorhizobium meliloti). While fungal infections were enhanced, S. meliloti infection was drastically impaired. In this study, we investigate the temporal proteome response of M. truncatula MtROP9i transgenic roots during the same microbial interactions under conditions of deprived potential to synthesize ROS. In comparison with control roots (Mtvector), we present a comprehensive proteomic analysis using sensitive MS protein identification. For four early infection time-points (1, 3, 5, 24 hpi), 733 spots were found to be different in abundance: 213 spots comprising 984 proteins (607 unique) were identified after S. meliloti infection, 230 spots comprising 796 proteins (580 unique) after G. intraradices infection, and 290 spots comprising 1240 proteins (828 unique) after A. euteiches infection. Data evaluation by GelMap in combination with a heatmap tool allowed recognition of key proteome changes during microbial interactions under conditions of hampered ROS synthesis. Overall, the number of induced proteins in MtROP9i was low as compared with controls, indicating a dual function of ROS in defense signaling as well as alternative response patterns activated during microbial infection. Qualitative analysis of induced proteins showed that enzymes linked to ROS production and scavenging were highly induced in control roots, while in MtROP9i the majority of proteins were involved in alternative defense pathways such as cell wall and protein degradation.
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Affiliation(s)
| | | | - Frank Colditz
- Department of Plant Molecular Biology, Institute of Plant Genetics, Leibniz University HannoverHannover, Germany
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Abreu IA, Farinha AP, Negrão S, Gonçalves N, Fonseca C, Rodrigues M, Batista R, Saibo NJM, Oliveira MM. Coping with abiotic stress: proteome changes for crop improvement. J Proteomics 2013; 93:145-68. [PMID: 23886779 DOI: 10.1016/j.jprot.2013.07.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/20/2022]
Abstract
Plant breeders need new and more precise tools to accelerate breeding programs that address the increasing needs for food, feed, energy and raw materials, while facing a changing environment in which high salinity and drought have major impacts on crop losses worldwide. This review covers the achievements and bottlenecks in the identification and validation of proteins with relevance in abiotic stress tolerance, also mentioning the unexpected consequences of the stress in allergen expression. While addressing the key pathways regulating abiotic stress plant adaptation, comprehensive data is presented on the proteins confirmed as relevant to confer tolerance. Promising candidates still to be confirmed are also highlighted, as well as the specific protein families and protein modifications for which detection and characterization is still a challenge. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Isabel A Abreu
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Genomics of Plant Stress Laboratory (GPlantS Lab), Av. da República, 2780-157 Oeiras, Portugal; iBET, Apartado 12, 2781-901 Oeiras, Portugal
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