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Huerta-Ocampo JÁ, Batista-Roche LG, Morales-Amparano MB, Robles-Burgueño MDR, Ramos-Clamont Montfort G, Vázquez-Moreno L, Ramírez-Jiménez F, Terán LM. Identification of Allergenic Proteins in Velvet Mesquite ( Prosopis velutina) Pollen: An Immunoproteomics Approach. Life (Basel) 2022; 12:1421. [PMID: 36143457 PMCID: PMC9502229 DOI: 10.3390/life12091421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Velvet mesquite (Prosopis velutina) is a native legume of the southwestern United States and northwestern Mexico, contributing significantly to the desert ecosystem and playing key ecological roles. It is also an important cause of allergic respiratory disease widely distributed in the Sonoran, Chihuahuan, and Mojave Deserts. However, no allergens from velvet mesquite pollen have been identified to date. Pollen proteins were extracted and analyzed by one- and two-dimensional electrophoresis and immunoblotting using a pool of 11 sera from mesquite-sensitive patients as the primary antibody. IgE-recognized protein spots were identified by mass spectrometry and bioinformatics analysis. Twenty-four unique proteins, including proteins well known as pollen, food, airway, or contact allergens and four proteins not previously reported as pollen allergens, were identified. This is the first report on allergenic proteins in velvet mesquite pollen. These findings will contribute to the development of specific diagnosis and treatment of mesquite pollen allergy.
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Affiliation(s)
- José Ángel Huerta-Ocampo
- Consejo Nacional de Ciencia y Tecnología, Mexico City 03940, Mexico
- Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Hermosillo 83304, Mexico
| | | | | | | | | | - Luz Vázquez-Moreno
- Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Hermosillo 83304, Mexico
| | - Fernando Ramírez-Jiménez
- Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Mexico City 14080, Mexico
| | - Luis M. Terán
- Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Mexico City 14080, Mexico
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2
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Bianco M, Ventura G, Calvano CD, Losito I, Cataldi TRI. A new paradigm to search for allergenic proteins in novel foods by integrating proteomics analysis and in silico sequence homology prediction: Focus on spirulina and chlorella microalgae. Talanta 2022; 240:123188. [PMID: 34990986 DOI: 10.1016/j.talanta.2021.123188] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
Since novel nutrient sources with high protein content, such as yeast, fungi, bacteria, algae, and insects, are increasingly introduced in the consumer market, safety evaluation studies on their potentially allergenic proteins are required. A pipeline for in silico establishing the sequence-based homology between proteins of spirulina (Arthrospira platensis) and chlorella (Chlorella vulgaris) micro-algae and those included in the AllergenOnline (AO) database (AllergenOnline.org) is described. The extracted proteins were first identified through tryptic peptides analysis by reversed-phase liquid chromatography and high resolution/accuracy Fourier-transform tandem mass spectrometry (RPLC-ESI-FTMS/MS), followed by a quest on the UniProt database. The AO database was subsequently interrogated to assess sequence similarity between identified microalgal proteins and known allergens, based on criteria established by the World Health Organization (WHO) and Food and Agriculture Organization (FAO). A direct search for microalgal proteins already included in allergen databases was also performed using the Allergome database. Six proteins exhibiting a significant homology with food allergens were identified in spirulina extracts. Five of them, i.e., two thioredoxins (D4ZSU6, K1VP15), a superoxide dismutase (C3V3P3), a glyceraldehyde-3-phosphate dehydrogenase (K1W168), and a triosephosphate isomerase (D5A635), resulted from the search on AO. The sixth protein, C-phycocyanin beta subunit (P72508), was directly obtained after examining the Allergome database. Two proteins exhibiting significant sequence homology with food allergens were retrieved in chlorella extracts, viz. calmodulin (A0A2P6TFR8), which is related to troponin c (D7F1Q2), and fructose-bisphosphate aldolase (A0A2P6TDD0). Specific serum screenings based on immunochemical tests should be undertaken to confirm or rule out the allergenicity of the identified proteins.
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Affiliation(s)
- Mariachiara Bianco
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
| | - Cosima Damiana Calvano
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Tommaso R I Cataldi
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
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3
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Xu ZQ, Zhu LX, Lu C, Jiao YX, Zhu DX, Guo M, Yang YS, Cao MD, Zhang LS, Tian M, Sun JL, Wei JF. Identification of Per a 13 as a novel allergen in American cockroach. Mol Immunol 2022; 143:41-49. [PMID: 35033813 DOI: 10.1016/j.molimm.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cockroaches are an important source of indoor allergens. Environmental exposure to cockroach allergens is closely associated with the development of immunoglobulin E (IgE)-mediated allergic diseases. However, the allergenic components in the American cockroaches are not fully studied yet. In order to develop novel diagnostic and therapeutic strategies for cockroach allergy, it is necessary to comprehensively investigate this undescribed allergen in the American cockroach. METHODS The full-length cDNA of the potential allergen was isolated from the cDNA library of the American cockroach by PCR cloning. Both the recombinant and natural protein molecules were purified and characterized. The allergenicity was further analyzed by enzyme linked immunosorbent assay, immunoblot, and basophil activation test using sera from cockroach allergic patients. RESULTS A novel allergen belonging to glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was firstly identified in the American cockroach and named as Per a 13. The cDNA of this allergen is 1255 base pairs in length and contains an open reading frame of 999 base pairs, encoding 332 amino acids. The purified Per a 13 was fully characterized and assessed to react with IgEs from 49.3 % of cockroach allergic patients, and patients with allergic rhinitis were more sensitized to it. Moreover, the allergenicity was further confirmed by immunoblot and basophil activation test. CONCLUSIONS We firstly identified GAPDH (Per a 13) in the American cockroach, which is a novel type of inhalant allergen derived from animal species. These findings could be useful in developing novel diagnostic and therapeutic strategies for cockroach allergy.
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Affiliation(s)
- Zhi-Qiang Xu
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li-Xiang Zhu
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chen Lu
- Precision Medicine Center, the First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Yong-Xin Jiao
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dan-Xuan Zhu
- Clinical Allergy Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Miao Guo
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong-Shi Yang
- Department of Allergy, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Meng-Da Cao
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li-Shan Zhang
- Department of Allergy, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Man Tian
- Department of Respiratory Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China.
| | - Jin-Lyu Sun
- Department of Allergy, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Pharmacy, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Institute of Cancer Research, Nanjing, China; Clinical Allergy Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Department of Clinical Pharmacy, School of Pharmacy, Nanjing Medical University, Nanjing, China.
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4
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Gracz-Bernaciak J, Mazur O, Nawrot R. Functional Studies of Plant Latex as a Rich Source of Bioactive Compounds: Focus on Proteins and Alkaloids. Int J Mol Sci 2021; 22:12427. [PMID: 34830309 PMCID: PMC8620047 DOI: 10.3390/ijms222212427] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 01/03/2023] Open
Abstract
Latex, a sticky emulsion produced by specialized cells called laticifers, is a crucial part of a plant's defense system against herbivory and pathogens. It consists of a broad spectrum of active compounds, which are beneficial not only for plants, but for human health as well, enough to mention the use of morphine or codeine from poppy latex. Here, we reviewed latex's general role in plant physiology and the significance of particular compounds (alkaloids and proteins) to its defense system with the example of Chelidonium majus L. from the poppy family. We further attempt to present latex chemicals used so far in medicine and then focus on functional studies of proteins and other compounds with potential pharmacological activities using modern techniques such as CRISPR/Cas9 gene editing. Despite the centuries-old tradition of using latex-bearing plants in therapies, there are still a lot of promising molecules waiting to be explored.
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Affiliation(s)
| | | | - Robert Nawrot
- Molecular Virology Research Unit, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (J.G.-B.); (O.M.)
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5
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Identification and Characterization of Glycoproteins and Their Responsive Patterns upon Ethylene Stimulation in the Rubber Latex. Int J Mol Sci 2020; 21:ijms21155282. [PMID: 32722428 PMCID: PMC7432319 DOI: 10.3390/ijms21155282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Natural rubber is an important industrial material, which is obtained from the only commercially cultivated rubber tree, Hevea brasiliensis. In rubber latex production, ethylene has been extensively used as a stimulant. Recent research showed that post-translational modifications (PTMs) of latex proteins, such as phosphorylation, glycosylation and ubiquitination, are crucial in natural rubber biosynthesis. In this study, comparative proteomics was performed to identify the glycosylated proteins in rubber latex treated with ethylene for different days. Combined with Pro-Q Glycoprotein gel staining and mass spectrometry techniques, we provided the first visual profiling of glycoproteomics of rubber latex and finally identified 144 glycosylated protein species, including 65 differentially accumulated proteins (DAPs) after treating with ethylene for three and/or five days. Gene Ontology (GO) functional annotation showed that these ethylene-responsive glycoproteins are mainly involved in cell parts, membrane components and metabolism. Pathway analysis demonstrated that these glycosylated rubber latex proteins are mainly involved in carbohydrate metabolism, energy metabolism, degradation function and cellular processes in rubber latex metabolism. Protein-protein interaction analysis revealed that these DAPs are mainly centered on acetyl-CoA acetyltransferase and hydroxymethylglutaryl-CoA synthase (HMGS) in the mevalonate pathway for natural rubber biosynthesis. In our glycoproteomics, three protein isoforms of HMGS2 were identified from rubber latex, and only one HMGS2 isoform was sharply increased in rubber latex by ethylene treatment for five days. Furthermore, the HbHMGS2 gene was over-expressed in a model rubber-producing grass Taraxacum Kok-saghyz and rubber content in the roots of transgenic rubber grass was significantly increased over that in the wild type plant, indicating HMGS2 is the key component for natural rubber production.
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6
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [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] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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7
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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8
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Proteomic Landscape Has Revealed Small Rubber Particles Are Crucial Rubber Biosynthetic Machines for Ethylene-Stimulation in Natural Rubber Production. Int J Mol Sci 2019; 20:ijms20205082. [PMID: 31614967 PMCID: PMC6829444 DOI: 10.3390/ijms20205082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Rubber particles are a specific organelle for natural rubber biosynthesis (NRB) and storage. Ethylene can significantly improve rubber latex production by increasing the generation of small rubber particles (SRPs), regulating protein accumulation, and activating many enzyme activities. We conducted a quantitative proteomics study of different SRPs upon ethylene stimulation by differential in-gel electrophoresis (DIGE) and using isobaric tags for relative and absolute quantification (iTRAQ) methods. In DIGE, 79 differentially accumulated proteins (DAPs) were determined as ethylene responsive proteins. Our results show that the abundance of many NRB-related proteins has been sharply induced upon ethylene stimulation. Among them, 23 proteins were identified as rubber elongation factor (REF) and small rubber particle protein (SRPP) family members, including 16 REF and 7 SRPP isoforms. Then, 138 unique phosphorylated peptides, containing 129 phosphorylated amino acids from the 64 REF/SRPP family members, were identified, and most serine and threonine were phosphorylated. Furthermore, we identified 226 DAPs from more than 2000 SRP proteins by iTRAQ. Integrative analysis revealed that almost all NRB-related proteins can be detected in SRPs, and many proteins are positively responsive to ethylene stimulation. These results indicate that ethylene may stimulate latex production by regulating the accumulation of some key proteins. The phosphorylation modification of REF and SRPP isoforms might be crucial for NRB, and SRP may act as a complex natural rubber biosynthetic machine.
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9
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Shahali Y, Sénéchal H, Poncet P. The Use of Combinatorial Hexapeptide Ligand Library (CPLL) in Allergomics. Methods Mol Biol 2019; 1871:393-403. [PMID: 30276749 DOI: 10.1007/978-1-4939-8814-3_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
The recent progress of proteomic protocols led to more efficient protein extraction and concentration procedures to remove nonprotein interfering compounds present in the starting material and to increase the concentration of underrepresented proteins. Combinatorial hexapeptide ligand libraries (CPLL) were recently applied to both plant- and animal-derived tissues for capturing the low- and very low-abundance allergens. Several IgE-binding proteins which were previously absent or poorly represented by using conventional proteomics tools have been detected and characterized through a CPLL-based approach. In the present chapter, a protocol based on improved protein extraction and enrichment by CPLL, allowing the immunochemical characterization of several "hidden allergens" in cypress pollen, is described in detail.
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Affiliation(s)
- Youcef Shahali
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension organization (AREEO), Karaj, Iran.
| | - Hélène Sénéchal
- Armand Trousseau Children Hospital, AP-HP, Biochemistry Department, Allergy and Environment Team, Paris, France
| | - Pascal Poncet
- Armand Trousseau Children Hospital, AP-HP, Biochemistry Department, Allergy and Environment Team, Paris, France
- Institut Pasteur, Center for Innovation and Technological Research, Paris, France
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10
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Xie Q, Ding G, Zhu L, Yu L, Yuan B, Gao X, Wang D, Sun Y, Liu Y, Li H, Wang X. Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass Taraxacum Kok-saghyz. Int J Mol Sci 2019; 20:ijms20102596. [PMID: 31137823 PMCID: PMC6566844 DOI: 10.3390/ijms20102596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
The rubber grass Taraxacum kok-saghyz (TKS) contains large amounts of natural rubber (cis-1,4-polyisoprene) in its enlarged roots and it is an alternative crop source of natural rubber. Natural rubber biosynthesis (NRB) and storage in the mature roots of TKS is a cascade process involving many genes, proteins and their cofactors. The TKS genome has just been annotated and many NRB-related genes have been determined. However, there is limited knowledge about the protein regulation mechanism for NRB in TKS roots. We identified 371 protein species from the mature roots of TKS by combining two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Meanwhile, a large-scale shotgun analysis of proteins in TKS roots at the enlargement stage was performed, and 3545 individual proteins were determined. Subsequently, all identified proteins from 2-DE gel and shotgun MS in TKS roots were subject to gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses and most proteins were involved in carbon metabolic process with catalytic activity in membrane-bounded organelles, followed by proteins with binding ability, transportation and phenylpropanoid biosynthesis activities. Fifty-eight NRB-related proteins, including eight small rubber particle protein (SRPP) and two rubber elongation factor(REF) members, were identified from the TKS roots, and these proteins were involved in both mevalonate acid (MVA) and methylerythritol phosphate (MEP) pathways. To our best knowledge, it is the first high-resolution draft proteome map of the mature TKS roots. Our proteomics of TKS roots revealed both MVA and MEP pathways are important for NRB, and SRPP might be more important than REF for NRB in TKS roots. These findings would not only deepen our understanding of the TKS root proteome, but also provide new evidence on the roles of these NRB-related proteins in the mature TKS roots.
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Affiliation(s)
- Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Guohua Ding
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Liping Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Li Yu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Boxuan Yuan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Xuan Gao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China.
| | - Yong Sun
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China.
| | - Yang Liu
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
| | - Xuchu Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.
- Key Laboratory for Ecology of Tropical Islands, Ministry of Education, College of Life Sciences, Hainan Normal University, Haikou 571158, Hainan, China.
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11
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Men X, Wang F, Chen GQ, Zhang HB, Xian M. Biosynthesis of Natural Rubber: Current State and Perspectives. Int J Mol Sci 2018; 20:E50. [PMID: 30583567 PMCID: PMC6337083 DOI: 10.3390/ijms20010050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Natural rubber is a kind of indispensable biopolymers with great use and strategic importance in human society. However, its production relies almost exclusively on rubber-producing plants Hevea brasiliensis, which have high requirements for growth conditions, and the mechanism of natural rubber biosynthesis remains largely unknown. In the past two decades, details of the rubber chain polymerization and proteins involved in natural rubber biosynthesis have been investigated intensively. Meanwhile, omics and other advanced biotechnologies bring new insight into rubber production and development of new rubber-producing plants. This review summarizes the achievements of the past two decades in understanding the biosynthesis of natural rubber, especially the massive information obtained from the omics analyses. Possibilities of natural rubber biosynthesis in vitro or in genetically engineered microorganisms are also discussed.
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Affiliation(s)
- Xiao Men
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Fan Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guo-Qiang Chen
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Hai-Bo Zhang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No.189 Songling Road, Laoshan District, Qingdao 266101, China.
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12
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Double One-Dimensional Electrophoresis (D1-DE) Adapted for Immunoproteomics. Methods Mol Biol 2018. [PMID: 30276737 DOI: 10.1007/978-1-4939-8814-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The classical proteomics approach for the identification of allergen candidates consists on the separation of proteins by high-resolution two-dimensional electrophoresis (2-DE) with subsequent IgE immunoblotting and further analysis of IgE-reactive protein spots with mass spectrometry. In this approach at least two gels most be run. One gel is used for staining and the other is for immunoblotting by antibodies labeled with specific immunostains. Additional functional characterizations require either protein purification or 2-DE replicates and appear to be time- and reagent-consuming. Here we described a modified double one-dimensional electrophoresis (D1-DE) allowing the conversion of a protein spot previously visualized by 2-DE into an extended protein band. In D1-DE, the purity of the protein of interest is similar to 2-DE spots, but its abundance is many times higher than what can be found in a 2-DE single spot allowing many other functional analyses from a single D1-DE separation.
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13
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Novel low-abundance allergens from mango via combinatorial peptide libraries treatment: A proteomics study. Food Chem 2018; 269:652-660. [PMID: 30100485 DOI: 10.1016/j.foodchem.2018.06.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/22/2018] [Accepted: 06/21/2018] [Indexed: 11/24/2022]
Abstract
Mango allergy is a rare condition, which may cause severe hypersensitivity reactions, such as anaphylaxis, angioedema, asthma and contact dermatitis. By exploiting the combinatorial peptide ligand library (CPLL) technology, mango proteomes have been extracted and the presence of traces of allergens assessed via Western blot analysis two-dimensional maps. Upon reactive spot elution and mass spectrometry analyses, four major mango allergens could be identified for the first time and shown to be in common with three of the five known banana species. These allergens include: Mus a 1, Mus a 2 and Mus a 5. Additional mango allergens detected do not seem to be in common with the banana species. In particular, a pectinesterase and a superoxide dismutase, both widely described as allergens, could be identified in mango extracts. Conversely, plain mango extracts not treated with CPLLs did not exhibit any reactive spots in Western blot analysis.
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Gao L, Sun Y, Wu M, Wang D, Wei J, Wu B, Wang G, Wu W, Jin X, Wang X, He P. Physiological and Proteomic Analyses of Molybdenum- and Ethylene-Responsive Mechanisms in Rubber Latex. FRONTIERS IN PLANT SCIENCE 2018; 9:621. [PMID: 29868077 PMCID: PMC5962772 DOI: 10.3389/fpls.2018.00621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Molybdenum (Mo) is an essential micronutrient in many plants. In the rubber tree Hevea brasiliensis, Mo application can reduce the shrinkage of the tapping line, decrease tapping panel dryness, and finally increase rubber latex yield. After combined Mo with ethylene (Eth), these effects become more obvious. However, the molecular mechanism remains unclear. Here, we compared the changed patterns of physiological parameters and protein accumulation in rubber latex after treated with Mo and/or Eth. Our results demonstrated that both Eth and Mo can improve the contents of thiol, sucrose, and dry yield in rubber latex. However, lutoid bursting is significantly inhibited by Mo. Comparative proteomics identified 169 differentially expressed proteins, including 114 unique proteins, which are mainly involved in posttranslational modification, carbohydrate metabolism, and energy production. The abundances of several proteins involved in rubber particle aggregation are decreased upon Mo stimulation, while many enzymes related to natural rubber biosynthesis are increased. Comparison of the accumulation patterns of 25 proteins revealed that a large portion of proteins have different changed patterns with their gene expression levels. Activity assays of six enzymes revealed that Mo stimulation can increase latex yield by improving the activity of some Mo-responsive enzymes. These results not only deepen our understanding of the rubber latex proteome but also provide new insights into the molecular mechanism of Mo-stimulated rubber latex yield.
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Affiliation(s)
- Le Gao
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
| | - Yong Sun
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
| | - Min Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashao Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Bingsun Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Guihua Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenguan Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiang Jin
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xuchu Wang
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Peng He
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- College of Life Sciences, Key Laboratory for Ecology of Tropical Islands, Ministry of Education, Hainan Normal University, Haikou, China
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Wang D, Sun Y, Chang L, Tong Z, Xie Q, Jin X, Zhu L, He P, Li H, Wang X. Subcellular proteome profiles of different latex fractions revealed washed solutions from rubber particles contain crucial enzymes for natural rubber biosynthesis. J Proteomics 2018; 182:53-64. [PMID: 29729991 DOI: 10.1016/j.jprot.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 01/20/2023]
Abstract
Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species. We further performed shotgun analysis of CS, WS and RP and identified 1837, 1799 and 1020 unique proteins, respectively. Together with 2-DE, we finally identified 1825 proteins from WS, 246 were WS-specific. These WS-specific proteins were annotated in Gene Ontology, indicating most abundant pathways are organic substance metabolic process, protein degradation, primary metabolic process, and energy metabolism. Protein-protein interaction analysis revealed these WS-specific proteins are mainly involved in ribosomal metabolism, proteasome system, vacuolar protein sorting and endocytosis. Label free and Western blotting revealed many WS-specific proteins and protein complexes are crucial for NRB initiation. These findings not only deepen our understanding of WS proteome, but also provide new evidences on the roles of RP membrane proteins in NRB. SIGNIFICANCE Natural rubber is stored in rubber particle from the rubber tree. Rubber particles were traditionally purified by repeated washing, but many proteins were identified from the washing solutions (WS). We obtained the first visualization proteome profiles with 1825 proteins from WS, including 246 WS-specific ones. These WS proteins contain almost all enzymes for polyisoprene initiation and may play important roles in rubber biosynthesis.
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Affiliation(s)
- Dan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan 571158, China
| | - Yong Sun
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China
| | - Lili Chang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Zheng Tong
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Quanliang Xie
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Xiang Jin
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan 571158, China
| | - Liping Zhu
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Peng He
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Xuchu Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; College of Life Sciences, Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Normal University, Haikou, Hainan 571158, China; College of Life Sciences, Key Laboratory of Agrobiotechnology, Shihezi University, Shihezi, Xinjiang 832003, China.
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Limonier F, Van Steendam K, Waeterloos G, Brusselmans K, Sneyers M, Deforce D. An application of mass spectrometry for quality control of biologicals: Highly sensitive profiling of plasma residuals in human plasma-derived immunoglobulin. J Proteomics 2017; 152:312-320. [DOI: 10.1016/j.jprot.2016.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 01/02/2023]
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17
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Mousavi F, Majd A, Shahali Y, Ghahremaninejad F, Shokouhi Shoormasti R, Pourpak Z. Immunoproteomics of tree of heaven (Ailanthus atltissima) pollen allergens. J Proteomics 2016; 154:94-101. [PMID: 28041857 DOI: 10.1016/j.jprot.2016.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022]
Abstract
Ailanthus altissima pollen (AAP) is considered as an emerging cause of respiratory allergy in United States, Italy and Iran. However, the allergenic composition of AAP is still unknown and has yet to be characterized. The present study aimed to identify AAP allergens using a proteomics-based approach. For this purpose, optimized AAP protein extracts were analyzed using 1D- and 2D- gel electrophoresis and confronted to twenty sera from individuals with respiratory allergy during the AAP season. Candidate allergens were detected using the serum from an allergic patient with clinical history of AAP pollinosis. IgE-binding spots were identified using MALDI-TOF/TOF mass spectrometry and database searching. According to our results, AAP extracts were rich in proteins (up to 16.25mg/ml) with a molecular-weight distribution ranging from 10 to 175kDa. Two-D electrophoresis of AAP extracts revealed 125 protein spots from which 13 were IgE reactive. These IgE-binding proteins were identified as enolase, calreticulin, probable pectate lyase 6, conserved hypothetical protein and ras-related protein RHN1-like. By our knowledge, this study is the first report identifying AAP allergens. These findings will open up further avenues for the diagnosis and immunotherapy of the AAP allergy as well as for the cloning and molecular characterization of relevant allergens. BIOLOGICAL SIGNIFICANCE Ailanthus altissima colonizes new areas every year in Iran and is spreading aggressively worldwide. According to USDA, the tree of heaven is now present as an invasive plant in 30 states in US (www.invasivespeciesinfo.gov/plants/treeheaven.shtml) and come to dominate large areas in many regions. Up to now, several cases of allergy to A. altissima pollen have been reported in United States, Italy and Iran [1-4]. However, there is still no information on the sensitizing allergens and the molecular origin of these clinical symptoms, which constitutes a serious threat to patients suffering from respiratory allergies in these regions. To our knowledge, the current study describes, therefore, the first panel of proteins responsible for IgE-mediated A. altissima pollinosis by using a gel-based proteomic approach. This work represents the pioneer proteomic investigation on Simaroubaceae spp. and provides useful insights for further studies on the allergens of this widely distributed plant family.
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Affiliation(s)
- Fateme Mousavi
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Ahmad Majd
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran; Department of Biology, Faculty of Biological Sciences, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Youcef Shahali
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Farrokh Ghahremaninejad
- Department of Plant Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | | | - Zahra Pourpak
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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Tiotiu A, Brazdova A, Longé C, Gallet P, Morisset M, Leduc V, Hilger C, Broussard C, Couderc R, Sutra JP, Sénéchal H, Poncet P. Urtica dioica pollen allergy: Clinical, biological, and allergomics analysis. Ann Allergy Asthma Immunol 2016; 117:527-534. [PMID: 27788883 DOI: 10.1016/j.anai.2016.09.426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/01/2016] [Accepted: 09/08/2016] [Indexed: 01/06/2023]
Abstract
BACKGROUND The most emblematic members of Urticaceae at allergic risk level are wall pellitories (Parietaria), whereas nettle (Urtica) pollen is considered as poorly allergenic. No allergen from nettle pollen has yet been characterized, whereas 4 are listed for Parietaria pollen by the International Union of Immunological Societies. Clinical and biological profiles of 2 adult men who developed symptoms against nettle pollen and/or leaves were studied. OBJECTIVE To characterize the allergic reaction and identify the potential nettle pollen sensitizing allergens. METHODS IgE-mediated reaction to nettle pollen extract was evaluated by skin prick test, immunoassay, nasal provocation, and basophil activation test. To characterize specific nettle pollen allergens, an allergomic (IgE immunoproteomic) analysis was performed combining 1- and 2-dimensional electrophoresis, IgE immunoblots of nettle pollen extract, identification of allergens by mass spectrometry, and database queries. RESULTS The results of biological and immunochemical analyses revealed that the allergic rhinitis was due to Urtica dioica pollen in both patients. The allergomic analysis of nettle pollen extract allowed the characterization of 4 basic protein allergens: a thaumatin-like protein (osmotin) with a relative molecular mass of 27 to 29 kDa, a pectinesterase (relative molecular mass, 40 kDa), and 2 other basic proteins with relative molecular masses of 14 to 16 kDa and 43 kDa. There is no or only very weak allergen associations between pellitory and nettle pollen. CONCLUSION Exposure to nettle pollen can be responsible of allergic symptoms, and several allergens were characterized. Unravelling the allergens of this underestimated allergy might help to improve diagnosis and care for patients, to predict cross-reactivities and design adapted specific immunotherapy.
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Affiliation(s)
- Angelica Tiotiu
- Pneumology-Allergology Department, University Hospital, Nancy, France
| | - Andrea Brazdova
- Biochemistry Laboratory, Allergy & Environment Team, Armand Trousseau Children Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Immunopathology and Immunoregulation Section, INSERM U1098, University of Burgundy, Dijon, France
| | - Cyril Longé
- Biochemistry Laboratory, Allergy & Environment Team, Armand Trousseau Children Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Patrice Gallet
- Pneumology-Allergology Department, University Hospital, Nancy, France
| | - Martine Morisset
- Immunology-Allergology Department, Luxembourg Hospital, Luxembourg-Ville, Luxembourg
| | | | - Christiane Hilger
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Cédric Broussard
- Cochin Institute, INSERM U1016, Centre National de la Recherche Scientifique, UMR8104, Paris-Descartes University, Paris, France; Proteomics Plateform 3P5, Paris-Descartes University, Sorbonne Paris Cité, Paris, France
| | - Rémy Couderc
- Biochemistry Laboratory, Allergy & Environment Team, Armand Trousseau Children Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Jean-Pierre Sutra
- Biochemistry Laboratory, Allergy & Environment Team, Armand Trousseau Children Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Hélène Sénéchal
- Biochemistry Laboratory, Allergy & Environment Team, Armand Trousseau Children Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Pascal Poncet
- Biochemistry Laboratory, Allergy & Environment Team, Armand Trousseau Children Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France; Center for Innovation and Technological Research, Pasteur Institute, Paris, France.
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19
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Highlights on Hevea brasiliensis (pro)hevein proteins. Biochimie 2016; 127:258-70. [DOI: 10.1016/j.biochi.2016.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022]
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20
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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21
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Bioanalytical methods for food allergy diagnosis, allergen detection and new allergen discovery. Bioanalysis 2016; 7:1175-90. [PMID: 26039813 DOI: 10.4155/bio.15.49] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
For effective monitoring and prevention of the food allergy, one of the emerging health problems nowadays, existing diagnostic procedures and allergen detection techniques are constantly improved. Meanwhile, new methods are also developed, and more and more putative allergens are discovered. This review describes traditional methods and summarizes recent advances in the fast evolving field of the in vitro food allergy diagnosis, allergen detection in food products and discovery of the new allergenic molecules. A special attention is paid to the new diagnostic methods under laboratory development like various immuno- and aptamer-based assays, including immunoaffinity capillary electrophoresis. The latter technique shows the importance of MS application not only for the allergen detection but also for the allergy diagnosis.
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22
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Nguyen-Kim H, San Clemente H, Balliau T, Zivy M, Dunand C, Albenne C, Jamet E. Arabidopsis thaliana
root cell wall proteomics: Increasing the proteome coverage using a combinatorial peptide ligand library and description of unexpected Hyp in peroxidase amino acid sequences. Proteomics 2016; 16:491-503. [DOI: 10.1002/pmic.201500129] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/07/2015] [Accepted: 11/10/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Huan Nguyen-Kim
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Thierry Balliau
- CNRS; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
- INRA; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
| | - Michel Zivy
- CNRS; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
- INRA; PAPPSO; UMR 0320/UMR 8120 Génétique Végétale Quantitative et Evolution; Le Moulon Gif sur Yvette France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Cécile Albenne
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, UMR 5546, UPS, Université de Toulouse; BP 42617 Castanet-Tolosan France
- UMR 5546; CNRS; BP 42617 Castanet-Tolosan France
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Comparative proteomic analysis of latex from Hevea brasiliensis treated with Ethrel and methyl jasmonate using iTRAQ-coupled two-dimensional LC-MS/MS. J Proteomics 2015; 132:167-75. [PMID: 26581641 DOI: 10.1016/j.jprot.2015.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/24/2015] [Accepted: 11/09/2015] [Indexed: 11/23/2022]
Abstract
UNLABELLED Ethrel (ET) is an effective and widely used latex yield stimulant of Hevea brasiliensis (Pará rubber tree), and jasmonate (JA) is a key inducer of laticifer differentiation in this plant. To examine variations in the latex proteome caused by these phytohormones, ET and methyl jasmonate (MeJA) were applied to Reyan 7-33-97 rubber tree clones, and comparative proteomic analyses were conducted. On the basis of a transcriptome shotgun assembly (TSA) sequence database and an iTRAQ-coupled two-dimensional LC-MS/MS approach, 1499 latex proteins belonging to 1078 clusters were identified. With a 1.5-fold cut-off value to determine up- and down-regulated proteins, a total of 101 latex proteins were determined to be regulated by ET and/or MeJA via pairwise comparisons among the three exposure durations (0 h, 6 h, and 48 h). Proteins associated with latex regeneration, including phosphoenolpyruvate carboxylase and acetyl-CoA C-acetyltransferase, and those associated with latex flow, such as chitinase and a sieve element occlusion protein, were affected by the application of ET. Chitinase and polyphenol oxidase were also found to be regulated by MeJA. The findings of this study may provide new insight into the roles of phytohormones in latex yield and the causative mechanisms of laticifer differentiation in rubber trees. SIGNIFICANCE On the basis of a transcriptome shotgun assembly (TSA) sequence database and an iTRAQ-coupled two-dimensional LC-MS/MS approach, the most comprehensive proteome of the latex was profiled, and the ethylene-/jasmonate-responsive proteins were identified in the latex of H. brasiliensis. The findings of this study may provide new insight into the role of phytohormones in latex yield and the causative mechanisms of laticifer differentiation in rubber trees.
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Wang X, Wang D, Sun Y, Yang Q, Chang L, Wang L, Meng X, Huang Q, Jin X, Tong Z. Comprehensive Proteomics Analysis of Laticifer Latex Reveals New Insights into Ethylene Stimulation of Natural Rubber Production. Sci Rep 2015; 5:13778. [PMID: 26348427 PMCID: PMC4562231 DOI: 10.1038/srep13778] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 08/05/2015] [Indexed: 12/02/2022] Open
Abstract
Ethylene is a stimulant to increase natural rubber latex. After ethylene application, both fresh yield and dry matter of latex are substantially improved. Moreover, we found that ethylene improves the generation of small rubber particles. However, most genes involved in rubber biosynthesis are inhibited by exogenous ethylene. Therefore, we conducted a proteomics analysis of ethylene-stimulated rubber latex, and identified 287 abundant proteins as well as 143 ethylene responsive latex proteins (ERLPs) with mass spectrometry from the 2-DE and DIGE gels, respectively. In addition, more than 1,600 proteins, including 404 ERLPs, were identified by iTRAQ. Functional classification of ERLPs revealed that enzymes involved in post-translational modification, carbohydrate metabolism, hydrolase activity, and kinase activity were overrepresented. Some enzymes for rubber particle aggregation were inhibited to prolong latex flow, and thus finally improved latex production. Phosphoproteomics analysis identified 59 differential phosphoproteins; notably, specific isoforms of rubber elongation factor and small rubber particle protein that were phosphorylated mainly at serine residues. This post-translational modification and isoform-specific phosphorylation might be important for ethylene-stimulated latex production. These results not only deepen our understanding of the rubber latex proteome but also provide new insights into the use of ethylene to stimulate rubber latex production.
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Affiliation(s)
- Xuchu Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Dan Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Yong Sun
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Qian Yang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Lili Chang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Limin Wang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Xueru Meng
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Qixing Huang
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Xiang Jin
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
| | - Zheng Tong
- Key Laboratory of Biology and Genetic Resources for Tropical Crops, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou Hainan 571101, China
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Abstract
One of the main challenges in proteomics investigation, protein biomarker research, and protein purity and contamination analysis is how to efficiently enrich and detect low-abundance proteins in biological samples. One approach that makes the detection of rare species possible is the treatment of biological samples with solid-phase combinatorial peptide ligand libraries, ProteoMiner. This method utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but remove most of the high-abundance proteins, therefore compresses the protein abundance range in the samples. This work describes optimized protocols and highlights on the successful application of ProteoMiner to protein identification and analysis.
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Affiliation(s)
- Lei Li
- Protein Technologies R&D, Life Science Group, Bio-Rad Laboratories, 1000 Alfred Nobel Drive, Hercules, CA, 94547, USA,
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26
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Aoki Y, Takahashi S, Takayama D, Ogata Y, Sakurai N, Suzuki H, Asawatreratanakul K, Wititsuwannakul D, Wititsuwannakul R, Shibata D, Koyama T, Nakayama T. Identification of laticifer-specific genes and their promoter regions from a natural rubber producing plant Hevea brasiliensis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:1-8. [PMID: 25017153 DOI: 10.1016/j.plantsci.2014.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 06/03/2023]
Abstract
Latex, the milky cytoplasm of highly differentiated cells called laticifers, from Hevea brasiliensis is a key source of commercial natural rubber production. One way to enhance natural rubber production would be to express genes involved in natural rubber biosynthesis by a laticifer-specific overexpression system. As a first step to identify promoters which could regulate the laticifer-specific expression, we identified random clones from a cDNA library of H. brasiliensis latex, resulting in 4325 expressed sequence tags (ESTs) assembled into 1308 unigenes (692 contigs and 617 singletons). Quantitative analyses of the transcription levels of high redundancy clones in the ESTs revealed genes highly and predominantly expressed in laticifers, such as Rubber Elongation Factor (REF), Small Rubber Particle Protein and putative protease inhibitor proteins. HRT1 and HRT2, cis-prenyltransferases involved in rubber biosynthesis, was also expressed predominantly in laticifers, although these transcript levels were 80-fold lower than that of REF. The 5'-upstream regions of these laticifer-specific genes were cloned and analyzed in silico, revealing seven common motifs consisting of eight bases. Furthermore, transcription factors specifically expressed in laticifers were also identified. The common motifs in the laticifer-specific genes and the laticifer-specific transcription factors are potentially involved in the regulation of gene expression in laticifers.
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Affiliation(s)
- Yuichi Aoki
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan.
| | - Daisuke Takayama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Yoshiyuki Ogata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Nozomu Sakurai
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hideyuki Suzuki
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kasem Asawatreratanakul
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan; Research and Development Institute, Thaksin University, Songkhla, Thailand
| | | | | | - Daisuke Shibata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tanetoshi Koyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Toru Nakayama
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
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Slade WO, Werth EG, Chao A, Hicks LM. Phosphoproteomics in photosynthetic organisms. Electrophoresis 2014; 35:3441-51. [PMID: 24825726 DOI: 10.1002/elps.201400154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/18/2014] [Accepted: 04/29/2014] [Indexed: 02/04/2023]
Abstract
As primarily sessile organisms, photosynthetic species survive in dynamic environments by using elegant signaling pathways to manifest molecular responses to extracellular cues. These pathways exploit phosphorylation of specific amino acids (e.g. serine, threonine, tyrosine), which impact protein structure, function, and localization. Despite substantial progress in implementation of phosphoproteomics to understand photosynthetic organisms, researchers still struggle to translate a biological question into an experimental strategy and vice versa. This review evaluates the current status of phosphoproteomics in photosynthetic organisms and concludes with recommendations based on current knowledge.
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Affiliation(s)
- William O Slade
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Volpicella M, Leoni C, Fanizza I, Placido A, Pastorello EA, Ceci LR. Overview of plant chitinases identified as food allergens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5734-5742. [PMID: 24841122 DOI: 10.1021/jf5007962] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Food allergies are induced by proteins belonging to a limited number of families. Unfortunately, relationships between protein structure and capacity to induce the immune response have not been completely clarified yet, which precludes possible improvements in the diagnosis, prevention, and therapy of allergies. Plant chitinases constitute a good example of food allergenic proteins for which structural analysis of allergenicity has only been carried out partially. In plants, there are at least five structural classes of chitinases plus a number of chitinase-related polypeptides. Their allergenicity has been mostly investigated for chitinases of class I, due to both their higher prevalence among plant chitinases and by the high structural similarity between their substrate-binding domain and hevein, a well-known allergen present in the latex of rubber trees. Even if allergenic molecules have been identified for at least three other classes of plant chitinases, the involvement of the different structural motifs in the allergenicity of molecules has been disregarded so far. In this review, we provide a structurally based catalog of plant chitinases investigated for allergenicity, which could be a useful base for further studies aimed at better clarifying the structure-allergenicity relationships for this protein family.
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Affiliation(s)
- Mariateresa Volpicella
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari , Via Amendola 165/A, 70126 Bari, Italy
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Fonseca C, Planchon S, Pinheiro C, Renaut J, Ricardo CP, Oliveira MM, Batista R. Maize IgE binding proteins: each plant a different profile? Proteome Sci 2014; 12:17. [PMID: 24650160 PMCID: PMC3999935 DOI: 10.1186/1477-5956-12-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 03/11/2014] [Indexed: 01/06/2023] Open
Abstract
Background Allergies are nearly always triggered by protein molecules and the majority of individuals with documented immunologic reactions to foods exhibit IgE hypersensitivity reactions. In this study we aimed to understand if natural differences, at proteomic level, between maize populations, may induce different IgE binding proteins profiles among maize-allergic individuals. We also intended to deepen our knowledge on maize IgE binding proteins. Results In order to accomplish this goal we have used proteomic tools (SDS-PAGE and 2-D gel electrophoresis followed by western blot) and tested plasma IgE reactivity from four maize-allergic individuals against four different protein fractions (albumins, globulins, glutelins and prolamins) of three different maize cultivars. We have observed that maize cultivars have different proteomes that result in different IgE binding proteins profiles when tested against plasma from maize-allergic individuals. We could identify 19 different maize IgE binding proteins, 11 of which were unknown to date. Moreover, we found that most (89.5%) of the 19 identified potential maize allergens could be related to plant stress. Conclusions These results lead us to conclude that, within each species, plant allergenic potential varies with genotype. Moreover, considering the stress-related IgE binding proteins identified, we hypothesise that the environment, particularly stress conditions, may alter IgE binding protein profiles of plant components.
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Affiliation(s)
| | | | | | | | | | | | - Rita Batista
- National Health Institute Dr, Ricardo Jorge, Av, Padre Cruz, 1649-016 Lisboa, Portugal.
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Integration of latex protein sequence data provides comprehensive functional overview of latex proteins. Mol Biol Rep 2014; 41:1469-81. [PMID: 24395295 DOI: 10.1007/s11033-013-2992-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 12/24/2013] [Indexed: 01/03/2023]
Abstract
The laticiferous system is one of the most important conduit systems in higher plants, which produces a milky-like sap known as latex. Latex contains diverse secondary metabolites with various ecological functions. To obtain a comprehensive overview of the latex proteome, we integrated available latex proteins sequences and constructed a comprehensive dataset composed of 1,208 non-redundant latex proteins from 20 various latex-bearing plants. The results of functional analyses revealed that latex proteins are involved in various biological processes, including transcription, translation, protein degradation and the plant response to environmental stimuli. The results of the comparative analysis showed that the functions of the latex proteins are similar to those of phloem, suggesting the functional conservation of plant vascular proteins. The presence of latex proteins in mitochondria and plastids suggests the production of diverse secondary metabolites. Furthermore, using a BLAST search, we identified 854 homologous latex proteins in eight plant species, including three latex-bearing plants, such as papaya, caster bean and cassava, suggesting that latex proteins were newly evolved in vascular plants. Taken together, this study is the largest and most comprehensive in silico analysis of the latex proteome. The results obtained here provide useful resources and information for characterizing the evolution of the latex proteome.
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Abstract
The question of low-abundance proteins from biological tissues is still a major issue. Technologies have been devised to improve the situation and in the last few years a method based on solid-phase combinatorial peptide ligand libraries has been extensively applied to animal extracts. This method has also been extended to plant extracts taking advantage of findings from previous experience. Detailed methods are described and their pertinence highlighted according to various situations of plant sample origin, size of the sample, and analytical methods intended to be used for protein identifications.
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Making Progress in Plant Proteomics for Improved Food Safety. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-62650-9.00006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Fasoli E, Righetti PG. The peel and pulp of mango fruit: A proteomic samba. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2539-45. [DOI: 10.1016/j.bbapap.2013.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 09/10/2013] [Indexed: 12/31/2022]
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Wang X, Shi M, Wang D, Chen Y, Cai F, Zhang S, Wang L, Tong Z, Tian WM. Comparative proteomics of primary and secondary lutoids reveals that chitinase and glucanase play a crucial combined role in rubber particle aggregation in Hevea brasiliensis. J Proteome Res 2013; 12:5146-59. [PMID: 23991906 DOI: 10.1021/pr400378c] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lutoids are specific vacuole-based organelles within the latex-producing laticifers in rubber tree Hevea brasiliensis. Primary and secondary lutoids are found in the primary and secondary laticifers, respectively. Although both lutoid types perform similar roles in rubber particle aggregation (RPA) and latex coagulation, they vary greatly at the morphological and proteomic levels. To compare the differential proteins and determine the shared proteins of the two lutoid types, a proteomic analysis of lutoid membranes and inclusions was performed, revealing 169 proteins that were functionally classified into 14 families. Biological function analysis revealed that most of the proteins are involved in pathogen defense, chitin catabolism, and proton transport. Comparison of the gene and protein changed patterns and determination of the specific roles of several main lutoid proteins, such as glucanase, hevamine, and hevein, demonstrated that Chitinase and glucanase appeared to play crucial synergistic roles in RPA. Integrative analysis revealed a protein-based metabolic network mediating pH and ion homeostasis, defense response, and RPA in lutoids. From these findings, we developed a modified regulation model for lutoid-mediated RPA that will deepen our understanding of potential mechanisms involved in lutoid-mediated RPA and consequent latex coagulation.
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Affiliation(s)
- Xuchu Wang
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resources of Rubber Tree, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences , Danzhou Hainan 571737, P. R. China
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Combinatorial peptide libraries to overcome the classical affinity-enrichment methods in proteomics. Amino Acids 2013; 45:219-29. [DOI: 10.1007/s00726-013-1505-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/20/2013] [Indexed: 12/11/2022]
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Proteomics-based allergen analysis in plants. J Proteomics 2013; 93:40-9. [PMID: 23568023 DOI: 10.1016/j.jprot.2013.03.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 03/16/2013] [Accepted: 03/19/2013] [Indexed: 01/12/2023]
Abstract
UNLABELLED Plants may trigger hypersensitivity reactions when individuals with allergies consume foods derived from plant materials or inhale plant pollen. As each plant food or pollen contains multiple allergens, proteomics is a powerful tool to detect the allergens present. Allergen-targeted proteomics, termed allergenomics, has been used for comprehensive identification and/or quantification of plant allergens, because it is a simple and inexpensive tool for rapid detection of proteins that bind to IgE. There are increasing numbers of reports on the applications of allergenomics. In this review, we outline some of the applications of proteomics, including: (i) identification of novel allergens, (ii) allergic diagnoses, (iii) quantification of allergens, and (iv) natural diversity of allergens, and finally discuss (v) the use of allergenomics for safety assessment of genetically modified (GM) plants. BIOLOGICAL SIGNIFICANCE Recently, the number of allergic patients is increasing. Therefore, a comprehensive analysis of allergens (allergenomics) in plants is highly important for not only risk assessment of food plants but also diagnosis of allergic symptoms. In this manuscript, we reviewed the recent progress of allergenomics for identification, quantification and profiling of allergens. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Gaupels F, Ghirardo A. The extrafascicular phloem is made for fighting. FRONTIERS IN PLANT SCIENCE 2013; 4:187. [PMID: 23781225 PMCID: PMC3678090 DOI: 10.3389/fpls.2013.00187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/23/2013] [Indexed: 05/05/2023]
Affiliation(s)
- Frank Gaupels
- Helmholtz Zentrum München, German Research Center for Environmental Health, Department of Environmental Sciences, Institute of Biochemical Plant PathologyNeuherberg, Germany
- *Correspondence:
| | - Andrea Ghirardo
- Helmholtz Zentrum München, German Research Center for Environmental Health, Department of Environmental Sciences, Institute of Biochemical Plant Pathology, Research Unit Environmental SimulationNeuherberg, Germany
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Allergomic study of cypress pollen via combinatorial peptide ligand libraries. J Proteomics 2012; 77:101-10. [DOI: 10.1016/j.jprot.2012.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 01/29/2023]
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Boschetti E, Righetti PG. Breakfast at Tiffany's? Only with a low-abundance proteomic signature! Electrophoresis 2012; 33:2228-39. [DOI: 10.1002/elps.201200003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Fröhlich A, Gaupels F, Sarioglu H, Holzmeister C, Spannagl M, Durner J, Lindermayr C. Looking deep inside: detection of low-abundance proteins in leaf extracts of Arabidopsis and phloem exudates of pumpkin. PLANT PHYSIOLOGY 2012; 159:902-14. [PMID: 22555880 PMCID: PMC3387715 DOI: 10.1104/pp.112.198077] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 04/24/2012] [Indexed: 05/20/2023]
Abstract
The field of proteomics suffers from the immense complexity of even small proteomes and the enormous dynamic range of protein concentrations within a given sample. Most protein samples contain a few major proteins, which hamper in-depth proteomic analysis. In the human field, combinatorial hexapeptide ligand libraries (CPLL; such as ProteoMiner) have been used for reduction of the dynamic range of protein concentrations; however, this technique is not established in plant research. In this work, we present the application of CPLL to Arabidopsis (Arabidopsis thaliana) leaf proteins. One- and two-dimensional gel electrophoresis showed a decrease in high-abundance proteins and an enrichment of less abundant proteins in CPLL-treated samples. After optimization of the CPLL protocol, mass spectrometric analyses of leaf extracts led to the identification of 1,192 proteins in control samples and an additional 512 proteins after the application of CPLL. Upon leaf infection with virulent Pseudomonas syringae DC3000, CPLL beads were also used for investigating the bacterial infectome. In total, 312 bacterial proteins could be identified in infected Arabidopsis leaves. Furthermore, phloem exudates of pumpkin (Cucurbita maxima) were analyzed. CPLL prefractionation caused depletion of the major phloem proteins 1 and 2 and improved phloem proteomics, because 67 of 320 identified proteins were detectable only after CPLL treatment. In sum, our results demonstrate that CPLL beads are a time- and cost-effective tool for reducing major proteins, which often interfere with downstream analyses. The concomitant enrichment of less abundant proteins may facilitate a deeper insight into the plant proteome.
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Affiliation(s)
| | | | - Hakan Sarioglu
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Christian Holzmeister
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Manuel Spannagl
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology (A.F., F.G., C.H., J.D., C.L.), Department of Protein Science (H.S.), and Institute of Bioinformatics and Systems Biology (M.S.), Helmholtz Zentrum München, German Research Center for Environmental Health, D–85764 Neuherberg, Germany
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41
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Assessment of the floral origin of honey via proteomic tools. J Proteomics 2012; 75:3688-93. [DOI: 10.1016/j.jprot.2012.04.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/20/2012] [Accepted: 04/21/2012] [Indexed: 11/19/2022]
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Wahler D, Colby T, Kowalski NA, Harzen A, Wotzka SY, Hillebrand A, Fischer R, Helsper J, Schmidt J, Schulze Gronover C, Prüfer D. Proteomic analysis of latex from the rubber-producing plant Taraxacum brevicorniculatum. Proteomics 2012; 12:901-5. [DOI: 10.1002/pmic.201000778] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Thomas Colby
- Proteomics Group, Max Planck Institute for Plant Breeding Research; Cologne Germany
| | - Natalie A. Kowalski
- Institute for Biology and Biotechnology of Plants, Westphalian Wilhelms-University Münster; Münster Germany
| | - Anne Harzen
- Proteomics Group, Max Planck Institute for Plant Breeding Research; Cologne Germany
| | - Sandra Y. Wotzka
- Institute for Biology and Biotechnology of Plants, Westphalian Wilhelms-University Münster; Münster Germany
| | - Andrea Hillebrand
- Institute for Biology and Biotechnology of Plants, Westphalian Wilhelms-University Münster; Münster Germany
| | - Rainer Fischer
- Molecular Biotechnology, RWTH Aachen; Aachen Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology; Aachen Germany
| | | | - Jürgen Schmidt
- Proteomics Group, Max Planck Institute for Plant Breeding Research; Cologne Germany
| | | | - Dirk Prüfer
- Institute for Biology and Biotechnology of Plants, Westphalian Wilhelms-University Münster; Münster Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology; Aachen Germany
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Boschetti E, Righetti P. Mixed Beds. ADVANCES IN CHROMATOGRAPHY 2012. [DOI: 10.1201/b11636-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Aleksic I, Popovic M, Dimitrijevic R, Andjelkovic U, Vassilopoulou E, Sinaniotis A, Atanaskovic-Markovic M, Lindner B, Petersen A, Papadopoulos NG, Gavrovic-Jankulovic M. Molecular and immunological characterization of Mus a 5 allergen from banana fruit. Mol Nutr Food Res 2011; 56:446-53. [PMID: 22162266 DOI: 10.1002/mnfr.201100541] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 11/07/2022]
Abstract
SCOPE Banana fruit has become an important cause of fruit allergy in the recent years. Among the five registered IUIS allergens, Mus a 1 and Mus a 2 have been characterized in detail. In this study, molecular characterization and evaluation of the allergenic properties of β-1,3-glucanase from banana (Musa acuminata), denoted as Mus a 5, were performed. METHODS AND RESULTS The gene of Mus a 5 was cloned and sequenced. The obtained cDNA revealed a novel Mus a 5 isoform with an open reading frame encoding a protein of 340 amino acids comprising a putative signal peptide of 28 amino acid residues. By MALDI-TOF analysis Mus a 5 isolated from banana fruit revealed a molecular mass of 33451±67 Da. Two Mus a 5 isoforms (pI 7.7 and 8.0) were detected by 2D immunoblot with an identical N-terminal sequence. By mass fingerprint, 76 and 83% of the primary structure was confirmed for the two mature Mus a 5 isoforms, respectively. IgE reactivity to Mus a 5 was found in 74% of patients sensitized to banana fruit. Upregulation of basophil activation markers CD63 and CD203c was achieved with Mus a 5 in a concentration-dependent manner. CONCLUSION Mus a 5 is a functional allergen and a candidate for the component-resolved allergy diagnosis of banana allergy.
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Affiliation(s)
- Ivana Aleksic
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
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Santos KS, Galvao CE, Gadermaier G, Resende VMF, de Oliveira Martins C, Misumi DS, Yang AC, Ferreira F, Palma MS, Kalil J, Castro FFM. Allergic reactions to manioc (Manihot esculenta Crantz): Identification of novel allergens with potential involvement in latex-fruit syndrome. J Allergy Clin Immunol 2011; 128:1367-9. [DOI: 10.1016/j.jaci.2011.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 07/08/2011] [Accepted: 07/12/2011] [Indexed: 11/27/2022]
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Cox J, M.A.Heeren R, James P, Jorrin-Novo JV, Kolker E, Levander F, Morrice N, Picotti P, Righetti PG, Sánchez JC, Turck CW, Zubarev R, Alexandre BM, Corrales FJ, Marko-Varga G, O'Donovan S, O'Neil S, Prechl J, Simões T, Weckwerth W, Penque D. Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010. J Proteomics 2011; 75:4-17. [DOI: 10.1016/j.jprot.2011.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 04/22/2011] [Indexed: 12/17/2022]
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47
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Abril N, Gion JM, Kerner R, Müller-Starck G, Cerrillo RMN, Plomion C, Renaut J, Valledor L, Jorrin-Novo JV. Proteomics research on forest trees, the most recalcitrant and orphan plant species. PHYTOCHEMISTRY 2011; 72:1219-42. [PMID: 21353265 DOI: 10.1016/j.phytochem.2011.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 12/27/2010] [Accepted: 01/06/2011] [Indexed: 05/06/2023]
Abstract
The contribution of proteomics to the knowledge of forest tree (the most recalcitrant and almost forgotten plant species) biology is being reviewed and discussed, based on the author's own research work and papers published up to November 2010. This review is organized in four introductory sections starting with the definition of forest trees (1), the description of the environmental and economic importance (2) and its derived current priorities and research lines for breeding and conservation (3) including forest tree genomics (4). These precede the main body of this review: a general overview to proteomics (5) for introducing the forest tree proteomics section (6). Proteomics, defined as scientific discipline or experimental approach, it will be discussed both from a conceptual and methodological point of view, commenting on realities, challenges and limitations. Proteomics research in woody plants is limited to a reduced number of genera, including Pinus, Picea, Populus, Eucalyptus, and Fagus, mainly using first-generation approaches, e.g., those based on two-dimensional electrophoresis coupled to mass spectrometry. This area joins the own limitations of the technique and the difficulty and recalcitrance of the plant species as an experimental system. Furthermore, it contributes to a deeper knowledge of some biological processes, namely growth, development, organogenesis, and responses to stresses, as it is also used in the characterization and cataloguing of natural populations and biodiversity (proteotyping) and in assisting breeding programmes.
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Affiliation(s)
- Nieves Abril
- Dpt. of Biochemistry and Molecular Biology, ETSIAM, University of Cordoba, Campus de Rabanales, Ed. Severo Ochoa, Cordoba, Spain
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Boschetti E, Righetti PG. Mixed-bed chromatography as a way to resolve peculiar protein fractionation situations. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:827-35. [DOI: 10.1016/j.jchromb.2011.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 02/28/2011] [Accepted: 03/03/2011] [Indexed: 11/26/2022]
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Deep insights into the plant proteome by pretreatment with combinatorial hexapeptide ligand libraries. J Proteomics 2011; 74:1182-9. [PMID: 21354349 DOI: 10.1016/j.jprot.2011.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/11/2011] [Accepted: 02/16/2011] [Indexed: 01/21/2023]
Abstract
Proteome analyses suffer from the large complexity of even small proteomes. Additionally, in many protein samples a few highly abundant proteins are hindering detailed proteomic studies, since they mask low abundant proteins. Recently, a new technology has emerged, which reduces dynamic range of protein concentrations within a given sample using combinatorial hexapeptide ligand libraries (CPLLs). This technique has been widely used in the microbial, animal and human fields and is now going to enter plant research. It can be a useful tool for fractionation of protein samples and might help to get a deeper insight into specific plant proteomes. In this review we describe the CPLL protein fractionation, summarize its possible applications in the plant field and discuss the limitations of this method.
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Balbuena TS, Dias LLC, Martins MLB, Chiquieri TB, Santa-Catarina C, Floh EIS, Silveira V. Challenges in proteome analyses of tropical plants. ACTA ACUST UNITED AC 2011. [DOI: 10.1590/s1677-04202011000200001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genome sequencing of various organisms allow global analysis of gene expression, providing numerous clues on the biological function and involvement in the biological processes studied. Proteomics is a branch of molecular biology and biotechnology that has undergone considerable development in the post-genomic era. Despite the recent significant advancements in proteomics techniques, still there is much to be improved. Due to peculiarities to the plant kingdom, proteomics approaches require adaptations, so as to improve efficiency and accuracy of results in plants. Data generated by proteomics can substantially contribute to the understanding and monitoring of plant physiological events and development of biotechnological strategies. Especially for tropical species, challenges are even greater, in the light of the abundance of secondary metabolites, as well as of the lack of complete genome sequences. This review discusses current topics in proteomics concerning challenges and perspectives, with emphasis on the proteomics of tropical plant species.
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