1
|
Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
Collapse
Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| |
Collapse
|
2
|
Ves-Urai P, Krobthong S, Thongsuk K, Roytrakul S, Yokthongwattana C. Comparative secretome analysis between salinity-tolerant and control Chlamydomonas reinhardtii strains. PLANTA 2021; 253:68. [PMID: 33594587 DOI: 10.1007/s00425-021-03583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
Secretome analysis of a salt-tolerant and control Chlamydomonas reinhardtii revealed 514 differentially expressed proteins. Membrane transport and trafficking, signal transduction and channel proteins were up-regulated in the ST secretome. Salinity is a major abiotic stress that limits crop production worldwide. Multiple adverse effects have been reported in many living organisms exposed to high-saline concentrations. Chlamydomonas reinhardtii is known for secreting proteins in response to many environmental stresses. A salinity-tolerant (ST) strain of Chlamydomonas has been developed, whose cells were able to grow at 300 mM NaCl. The current study analyzed the secretomes of ST grown in TAP medium supplemented with 300 mM NaCl and the laboratory strain CC-503 grown in TAP medium without NaCl supplement. In total, 514 secreted proteins were identified of which 203 were up-regulated and 110 were down-regulated. Bioinformatic analysis predicted 168 proteins to be secreted or in the conventional secretory pathway. Out of these, 70 were up-regulated, while 51 proteins were down-regulated. Proteins involved in membrane transport and trafficking, signal transduction and channel proteins were altered in their expression in the ST secretome, suggesting the response of saline stress acts toward not only the intracellular pool of proteins but also the extracellular proteins. This also suggested that the secreted proteins might have roles in the extracellular space. Signal peptide (SP) prediction revealed that almost 40% of the predicted secreted proteins contained a signal peptide; however, a high proportion of proteins lacked an SP, suggesting that these proteins might be secreted through an unconventional protein secretion pathway.
Collapse
Affiliation(s)
- Parthompong Ves-Urai
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Bangkok, Thailand
| | - Sucheewin Krobthong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Karnpitcha Thongsuk
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
| |
Collapse
|
3
|
Nakano RT, Ishihama N, Wang Y, Takagi J, Uemura T, Schulze-Lefert P, Nakagami H. Apoplastic Fluid Preparation from Arabidopsis thaliana Leaves Upon Interaction with a Nonadapted Powdery Mildew Pathogen. Methods Mol Biol 2020; 2139:79-88. [PMID: 32462579 DOI: 10.1007/978-1-0716-0528-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Proteins in the extracellular space (apoplast) play a crucial role at the interface between plant cells and their proximal environment. Consequently, it is not surprising that plants actively control the apoplastic proteomic profile in response to biotic and abiotic cues. Comparative quantitative proteomics of plant apoplastic fluids is therefore of general interest in plant physiology. We here describe an efficient method to isolate apoplastic fluids from Arabidopsis thaliana leaves inoculated with a nonadapted powdery mildew pathogen.
Collapse
Affiliation(s)
- Ryohei Thomas Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| | | | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Junpei Takagi
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Tomohiro Uemura
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
| |
Collapse
|
4
|
Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
Collapse
Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| |
Collapse
|
5
|
Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
Collapse
Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
| |
Collapse
|
6
|
Xie X, Wang Y. VqDUF642, a gene isolated from the Chinese grape Vitis quinquangularis, is involved in berry development and pathogen resistance. PLANTA 2016; 244:1075-1094. [PMID: 27424038 DOI: 10.1007/s00425-016-2569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
The DUF642 gene VqDUF642 , isolated from the Chinese grape species V. quinquangularis accession Danfeng-2, participates in berry development and defense responses against Erysiphe necator and Botrytis cinerea. The proteins with domains of unknown function 642 (DUF642) comprise a large protein family according to cell wall proteomic analyses in plants. However, the works about functional characterization of DUF642s in plant development and resistance to pathogens are scarce. In this study, a gene encoding a DUF642 protein was isolated from Chinese grape V. quinquangularis accession Danfeng-2, and designated as VqDUF642. Its full-length cDNA contains a 1107-bp open reading frame corresponding to a deduced 368-amino acid protein. Multiple sequence alignments and phylogenetic analysis showed that VqDUF642 is highly homologous to one of the DUF642 proteins (VvDUF642) in V. vinifera. The VqDUF642 was localized to the cell wall of tobacco epidermal cells. Accumulation of VqDUF642 protein and VqDUF642 transcript abundance increased at the later stage of grape berry development in Danfeng-2. Overexpression of VqDUF642 in transgenic tomato plants accelerated plant growth and reduced susceptibility to Botrytis cinerea. Transgenic Thompson Seedless grapevine plants overexpressing VqDUF642 exhibited enhanced resistance to Erysiphe necator and B. cinerea. Moreover, VqDUF642 overexpression affected the expression of a couple of pathogenesis-related (PR) genes in transgenic tomato and grapevine upon pathogen inoculation. Taken together, these results suggest that VqDUF642 is involved in plant development and defense against pathogenic infections.
Collapse
Affiliation(s)
- Xiaoqing Xie
- College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Yuejin Wang
- College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
7
|
Pérez-Bermúdez P, Blesa J, Soriano JM, Marcilla A. Extracellular vesicles in food: Experimental evidence of their secretion in grape fruits. Eur J Pharm Sci 2016; 98:40-50. [PMID: 27664331 DOI: 10.1016/j.ejps.2016.09.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 12/18/2022]
Abstract
In the last decade, the number of studies related with extracellular vesicles (EVs) has dramatically grown since their role as key part of intercellular communication has been confirmed. EVs, as transporter of distinct bioactive molecules, can take part in different physiological mechanisms and have been gaining attention as potential tools with a wide range of therapeutic effects. Whereas a high number of studies have been published related to mammalian derived EVs, including products as food source, the existence of EVs in plants still is controversial. Recent descriptions of vesicles derived from edible plants show that they might contain pharmacological active molecules. In this context, EVs from food are attracting increasing interest due to their relevance in modulating cellular processes (involved in health and disease), as well as therapeutic vehicles. The present work aims to summarize the current knowledge on exosomes in foods, actually limited to only four FAO groups (Milk, Starchy roots and tubers, Nuts and seeds, and Fruits). In addition, we have further characterized EVs isolated from grape berry juice by classical differential centrifugation, and described a preliminary dissection of their secretion in vivo.
Collapse
Affiliation(s)
- Pedro Pérez-Bermúdez
- Departament de Biologia Vegetal, Facultat de Farmàcia, Universitat de València, Burjassot, Valencia, Spain
| | - Jesús Blesa
- Grupo de Ciencias de la Alimentación Basada en la Evidencia y Experimentación (CiAlBEx), Instituto de Ciencias de los Materiales, Parque Científico, Universitat de València, Paterna, Spain; Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, Instituto de Investigación Sanitaria La Fe-Universitat de València, Valencia, Spain
| | - José Miguel Soriano
- Grupo de Ciencias de la Alimentación Basada en la Evidencia y Experimentación (CiAlBEx), Instituto de Ciencias de los Materiales, Parque Científico, Universitat de València, Paterna, Spain; Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, Instituto de Investigación Sanitaria La Fe-Universitat de València, Valencia, Spain
| | - Antonio Marcilla
- Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, Instituto de Investigación Sanitaria La Fe-Universitat de València, Valencia, Spain; Àrea de Parasitologia, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, Burjassot, Valencia, Spain.
| |
Collapse
|
8
|
Ivić JT, Dimitrijević A, Milosavić N, Bezbradica D, Drakulić BJ, Jankulović MG, Pavlović M, Rogniaux H, Veličković D. Assessment of the interacting mechanism between Candida rugosa lipases and hydroxyapatite and identification of the hydroxyapatite-binding sequence through proteomics and molecular modelling. RSC Adv 2016. [DOI: 10.1039/c6ra07521e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hydroxyapatite (HAP), a calcium-phosphate bioactive ceramic, is actively employed in medical and separation sciences.
Collapse
Affiliation(s)
| | - Aleksandra Dimitrijević
- Department of Molecular Biology and Biochemistry
- University of California Irvine
- 92697 Irvine
- USA
| | - Nenad Milosavić
- Division of Experimental Therapeutics
- Department of Medicine
- Columbia University
- 10032 New York
- USA
| | - Dejan Bezbradica
- Department of Biochemical Engineering and Biotechnology
- Faculty of Technology and Metallurgy
- 11000 Belgrade
- Serbia
| | - Branko J. Drakulić
- Department of Chemistry
- Institute of Chemistry
- Technology and Metallurgy
- University of Belgrade
- Belgrade
| | | | - Marija Pavlović
- INRA
- UR1268
- Biopolymers Interactions Assembles
- 44316 Nantes
- France
| | - Helene Rogniaux
- INRA
- UR1268
- Biopolymers Interactions Assembles
- 44316 Nantes
- France
| | - Dušan Veličković
- Department of Biochemistry
- Faculty of Chemistry
- 11000 Belgrade
- Serbia
| |
Collapse
|
9
|
Liu Y, Joly V, Dorion S, Rivoal J, Matton DP. The Plant Ovule Secretome: A Different View toward Pollen-Pistil Interactions. J Proteome Res 2015; 14:4763-75. [PMID: 26387803 DOI: 10.1021/acs.jproteome.5b00618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
During plant sexual reproduction, continuous exchange of signals between the pollen and the pistil (stigma, style, and ovary) plays important roles in pollen recognition and selection, establishing breeding barriers and, ultimately, leading to optimal seed set. After navigating through the stigma and the style, pollen tubes (PTs) reach their final destination, the ovule. This ultimate step is also regulated by numerous signals emanating from the embryo sac (ES) of the ovule. These signals encompass a wide variety of molecules, but species-specificity of the pollen-ovule interaction relies mainly on secreted proteins and their receptors. Isolation of candidate genes involved in pollen-pistil interactions has mainly relied on transcriptomic approaches, overlooking potential post-transcriptional regulation. To address this issue, ovule exudates were collected from the wild potato species Solanum chacoense using a tissue-free gravity-extraction method (tf-GEM). Combined RNA-seq and mass spectrometry-based proteomics led to the identification of 305 secreted proteins, of which 58% were ovule-specific. Comparative analyses using mature ovules (attracting PTs) and immature ovules (not attracting PTs) revealed that the last maturation step of ES development affected almost half of the ovule secretome. Of 128 upregulated proteins in anthesis stage, 106 were not regulated at the mRNA level, emphasizing the importance of post-transcriptional regulation in reproductive development.
Collapse
Affiliation(s)
- Yang Liu
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Valentin Joly
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Daniel P Matton
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| |
Collapse
|
10
|
Abstract
The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.
Collapse
|
11
|
Li X, Bi Y, Wang J, Dong B, Li H, Gong D, Zhao Y, Tang Y, Yu X, Shang Q. BTH treatment caused physiological, biochemical and proteomic changes of muskmelon (Cucumis melo L.) fruit during ripening. J Proteomics 2015; 120:179-93. [DOI: 10.1016/j.jprot.2015.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/24/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
|
12
|
Delaunois B, Jeandet P, Clément C, Baillieul F, Dorey S, Cordelier S. Uncovering plant-pathogen crosstalk through apoplastic proteomic studies. FRONTIERS IN PLANT SCIENCE 2014; 5:249. [PMID: 24917874 PMCID: PMC4042593 DOI: 10.3389/fpls.2014.00249] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/15/2014] [Indexed: 05/14/2023]
Abstract
Plant pathogens have evolved by developing different strategies to infect their host, which in turn have elaborated immune responses to counter the pathogen invasion. The apoplast, including the cell wall and extracellular space outside the plasma membrane, is one of the first compartments where pathogen-host interaction occurs. The plant cell wall is composed of a complex network of polysaccharides polymers and glycoproteins and serves as a natural physical barrier against pathogen invasion. The apoplastic fluid, circulating through the cell wall and intercellular spaces, provides a means for delivering molecules and facilitating intercellular communications. Some plant-pathogen interactions lead to plant cell wall degradation allowing pathogens to penetrate into the cells. In turn, the plant immune system recognizes microbial- or damage-associated molecular patterns (MAMPs or DAMPs) and initiates a set of basal immune responses, including the strengthening of the plant cell wall. The establishment of defense requires the regulation of a wide variety of proteins that are involved at different levels, from receptor perception of the pathogen via signaling mechanisms to the strengthening of the cell wall or degradation of the pathogen itself. A fine regulation of apoplastic proteins is therefore essential for rapid and effective pathogen perception and for maintaining cell wall integrity. This review aims to provide insight into analyses using proteomic approaches of the apoplast to highlight the modulation of the apoplastic protein patterns during pathogen infection and to unravel the key players involved in plant-pathogen interaction.
Collapse
Affiliation(s)
| | | | | | | | | | - Sylvain Cordelier
- *Correspondence: Sylvain Cordelier, Laboratoire Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne-EA 4707, Université de Reims Champagne-Ardenne, Moulin de la Housse – BP 1039, 51687 Reims cedex 2, France e-mail:
| |
Collapse
|
13
|
Tanveer T, Shaheen K, Parveen S, Kazi AG, Ahmad P. Plant secretomics: identification, isolation, and biological significance under environmental stress. PLANT SIGNALING & BEHAVIOR 2014; 9:e29426. [PMID: 25763623 PMCID: PMC4203502 DOI: 10.4161/psb.29426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 05/03/2023]
Abstract
Plant secretomes are the proteins secreted by the plant cells and are involved in the maintenance of cell wall structure, relationship between host and pathogen, communication between different cells in the plant, etc. Amalgamation of methodologies like bioinformatics, biochemical, and proteomics are used to separate, classify, and outline secretomes by means of harmonizing in planta systems and in vitro suspension cultured cell system (SSCs). We summed up and explained the meaning of secretome, methods used for the identification and isolation of secreted proteins from extracellular space and methods for the assessment of purity of secretome proteins in this review. Two D PAGE method and HPLC based methods for the analysis together with different bioinformatics tools used for the prediction of secretome proteins are also discussed. Biological significance of secretome proteins under different environmental stresses, i.e., salt stress, drought stress, oxidative stress, etc., defense responses and plant interactions with environment are also explained in detail.
Collapse
Affiliation(s)
- Tehreem Tanveer
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Kanwal Shaheen
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Sajida Parveen
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Alvina Gul Kazi
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Parvaiz Ahmad
- Department of Botany; S.P. College; Jammu and Kashmir, India
| |
Collapse
|