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Artículos de revistas sobre el tema "Plant proteomics"

Autor: Grafiati

Publicado: 4 de junio de 2021

Última modificación: 5 de septiembre de 2024

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1

Mahajan, R. y P. Gupta. "Proteomics: taking over where genomics leaves off". Czech Journal of Genetics and Plant Breeding 46, No. 2 (29 de junio de 2010): 47–53. http://dx.doi.org/10.17221/34/2009-cjgpb.

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The proteomic studies are simultaneously developed in several directions and significantly influence our notions on the capabilities of biological sciences. The need for proteomics research is necessary as there are certain genes in a cell that encode proteins with specific functions. Using a variety of techniques, proteomics can be used to study how proteins interact within a system or how the protein expression changes in different parts of the body, in different stages of its life cycle and in different environmental conditions as every individual has one genome and many proteomes. Besides the qualitative and quantitative description of the expressed proteins, proteomics also deals with the analysis of mutual interactions of proteins. Thereby, candidate proteins can be identified which may be used as starting-points for diagnostic or even therapeutic approaches.

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2

González-Fernández, Raquel, Elena Prats y Jesús V. Jorrín-Novo. "Proteomics of Plant Pathogenic Fungi". Journal of Biomedicine and Biotechnology 2010 (2010): 1–36. http://dx.doi.org/10.1155/2010/932527.

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Plant pathogenic fungi cause important yield losses in crops. In order to develop efficient and environmental friendly crop protection strategies, molecular studies of the fungal biological cycle, virulence factors, and interaction with its host are necessary. For that reason, several approaches have been performed using both classical genetic, cell biology, and biochemistry and the modern, holistic, and high-throughput, omic techniques. This work briefly overviews the tools available for studying Plant Pathogenic Fungi and is amply focused on MS-based Proteomics analysis, based on original papers published up to December 2009. At a methodological level, different steps in a proteomic workflow experiment are discussed. Separate sections are devoted to fungal descriptive (intracellular, subcellular, extracellular) and differential expression proteomics and interactomics. From the work published we can conclude that Proteomics, in combination with other techniques, constitutes a powerful tool for providing important information about pathogenicity and virulence factors, thus opening up new possibilities for crop disease diagnosis and crop protection.

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3

Jorrín–Novo, Jesus V. "Plant Proteomics". Journal of Proteomics 72, n.º 3 (abril de 2009): 283–84. http://dx.doi.org/10.1016/j.jprot.2009.03.002.

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4

Vítámvás, P., K. Kosová y I. T. Prášil. "Proteome analysis in plant stress research: a review". Czech Journal of Genetics and Plant Breeding 43, No. 1 (7 de enero de 2008): 1–6. http://dx.doi.org/10.17221/1903-cjgpb.

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Proteomic techniques that allow the identification and quantification of stress-related proteins, mapping of dynamics of their expression and posttranslational modifications represent an important approach in the research of plant stresses. In this review, we show an outline of proteomics methods and their applications in the research of plant resistance to various types of stresses.

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5

Ephritikhine, Geneviève, Myriam Ferro y Norbert Rolland. "Plant membrane proteomics". Plant Physiology and Biochemistry 42, n.º 12 (diciembre de 2004): 943–62. http://dx.doi.org/10.1016/j.plaphy.2004.11.004.

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6

Navrot, Nicolas, Christine Finnie, Birte Svensson y Per Hägglund. "Plant redox proteomics". Journal of Proteomics 74, n.º 8 (agosto de 2011): 1450–62. http://dx.doi.org/10.1016/j.jprot.2011.03.008.

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7

Lilley, Kathryn S. y Paul Dupree. "Plant organelle proteomics". Current Opinion in Plant Biology 10, n.º 6 (diciembre de 2007): 594–99. http://dx.doi.org/10.1016/j.pbi.2007.08.006.

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8

Bindschedler, Laurence V. y Rainer Cramer. "Quantitative plant proteomics". PROTEOMICS 11, n.º 4 (18 de enero de 2011): 756–75. http://dx.doi.org/10.1002/pmic.201000426.

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9

., Ch Muhammad Ishtiaq, Q. He ., J. P. Huang ., Yi Wang ., P. G. Xiao . y Yi Yu Cheng . "Biosystematics and Plant Proteomics: Role of Proteomics in Plant Phylogenetic Analysis". Pakistan Journal of Biological Sciences 10, n.º 20 (1 de octubre de 2007): 3487–96. http://dx.doi.org/10.3923/pjbs.2007.3487.3496.

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10

Yu, LIANG, JING Yu-Xiang y SHEN Shi-Hua. "Advances in Plant Proteomics". Chinese Journal of Plant Ecology 28, n.º 1 (2004): 114–25. http://dx.doi.org/10.17521/cjpe.2004.0017.

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11

Barbier-Brygoo, Hélène y Jacques Joyard. "Focus on plant proteomics". Plant Physiology and Biochemistry 42, n.º 12 (diciembre de 2004): 913–17. http://dx.doi.org/10.1016/j.plaphy.2004.10.012.

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12

Handakumbura, Pubudu P., Kim K. Hixson, Samuel O. Purvine, Christer Jansson y Ljiljana Paša-Tolić. "Plant iTRAQ-Based Proteomics". Current Protocols in Plant Biology 2, n.º 2 (junio de 2017): 158–72. http://dx.doi.org/10.1002/cppb.20052.

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13

Chen, Sixue y Alice C. Harmon. "Advances in plant proteomics". PROTEOMICS 6, n.º 20 (octubre de 2006): 5504–16. http://dx.doi.org/10.1002/pmic.200600143.

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14

Balotf, Sadegh, Richard Wilson, Robert S. Tegg, David S. Nichols y Calum R. Wilson. "Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant–Pathogen Interactions". Proteomes 10, n.º 1 (19 de enero de 2022): 5. http://dx.doi.org/10.3390/proteomes10010005.

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The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant–pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant–pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant–pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant–pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.

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15

Jenkins, Conor y Benjamin Orsburn. "The Cannabis Proteome Draft Map Project". International Journal of Molecular Sciences 21, n.º 3 (31 de enero de 2020): 965. http://dx.doi.org/10.3390/ijms21030965.

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Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources.

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16

Smythers, Amanda L. y Leslie M. Hicks. "Mapping the plant proteome: tools for surveying coordinating pathways". Emerging Topics in Life Sciences 5, n.º 2 (23 de febrero de 2021): 203–20. http://dx.doi.org/10.1042/etls20200270.

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Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein–protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.

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17

Komatsu, Setsuko, Myeong W. Oh, Hee Y. Jang, Soo J. Kwon, Hye R. Kim, Jung H. Ko, Sun H. Woo y Yohei Nanjo. "Proteomic Analyses of Soybean Root Tips During Germination". Protein & Peptide Letters 21, n.º 12 (5 de noviembre de 2014): 1308–19. http://dx.doi.org/10.2174/0929866521666140526152426.

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Plant root systems form complex networks with the surrounding soil environment and are controlled by both internal and external factors. To better understand the function of root tips of soybean during germination, three proteomic techniques were used to analyze the protein profiles of root tip cells. Proteins were extracted from the root tips of 4-dayold soybean seedlings and analyzed using two-dimensional (2D) gel electrophoresis-based proteomics, SDS-gel based proteomics, and gel-free proteomics techniques. A total of 121, 862, and 341 proteins were identified in root tips using the 2D gel-based, SDS gel-based, and gel-free proteomic techniques, respectively. The proteins identified by 2D gel-based proteomic analysis were predominantly localized in the cytoplasm, whereas nuclear-localized proteins were most commonly identified by the SDS gel-based and gel-free proteomics techniques. Of the 862 proteins identified in the SDS gelbased proteomic analysis, 190 were protein synthesis-related proteins. Furthermore, 24 proteins identified using the 2Dgel based proteomic technique shifted between acidic and basic isoelectric points, and 2 proteins, heat shock protein 70.2 and AAA-type ATPase, displayed two different molecular weights at the same isoelectric point. Taken together, these results suggest that a number of proteins related to protein synthesis and modification are activated in the root tips of soybean seedlings during germination.

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18

Dunkley, T. P. J., P. Dupree, R. B. Watson y K. S. Lilley. "The use of isotope-coded affinity tags (ICAT) to study organelle proteomes in Arabidopsis thaliana". Biochemical Society Transactions 32, n.º 3 (1 de junio de 2004): 520–23. http://dx.doi.org/10.1042/bst0320520.

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Organelle proteomics is the analysis of the protein contents of a subcellular compartment. Proteins identified in subcellular proteomic studies can only be assigned to an organelle if there are no contaminants present in the sample preparation. As a result, the majority of plant organelle proteomic studies have focused on the chloroplast and mitochondria, which can be isolated relatively easily. However, the isolation of components of the endomembrane system is far more difficult due to their similar sizes and densities. For this reason, quantitative proteomics methods are being developed to enable the assignment of proteins to a specific component of the endomembrane system without the need to obtain pure organelles.

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19

Sergeant, Kjell y Jenny Renaut. "Plant Biotic Stress and Proteomics". Current Proteomics 7, n.º 4 (1 de diciembre de 2010): 275–97. http://dx.doi.org/10.2174/157016410793611765.

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20

Komatsu, Setsuko y Klaas J. van Wijk. "Plant Proteomics Coming of Age". Journal of Proteome Research 11, n.º 1 (13 de diciembre de 2011): 2. http://dx.doi.org/10.1021/pr2011999.

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21

Whitelegge, Julian P., Setsuko Komatsu y Jesus Jorrin-Novo. "Diverse facets of plant proteomics". Phytochemistry 72, n.º 10 (julio de 2011): 961–62. http://dx.doi.org/10.1016/j.phytochem.2011.04.004.

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22

Takáč, Tomáš, Tibor Pechan y Jozef Šamaj. "Differential proteomics of plant development". Journal of Proteomics 74, n.º 5 (mayo de 2011): 577–88. http://dx.doi.org/10.1016/j.jprot.2011.02.002.

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23

Agrawal, Ganesh Kumar, Romina Pedreschi, Bronwyn J. Barkla, Laurence Veronique Bindschedler, Rainer Cramer, Abhijit Sarkar, Jenny Renaut, Dominique Job y Randeep Rakwal. "Translational plant proteomics: A perspective". Journal of Proteomics 75, n.º 15 (agosto de 2012): 4588–601. http://dx.doi.org/10.1016/j.jprot.2012.03.055.

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24

Champagne, Antoine y Marc Boutry. "Proteomics of nonmodel plant species". PROTEOMICS 13, n.º 3-4 (7 de enero de 2013): 663–73. http://dx.doi.org/10.1002/pmic.201200312.

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25

Cramer, Rainer, Laurence Bindschedler y Ganesh Agrawal. "Plant Proteomics in Crop Improvement". PROTEOMICS 13, n.º 12-13 (junio de 2013): 1771. http://dx.doi.org/10.1002/pmic.201370104.

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26

Lee, Young-Woo, Suh-Yeon Bea, Sang-Gyu Seo, Ie-Sung Shim, Sun-Hyung Kim, Sang-Gon Kim, Kyu-Young Kang y Sun-Tae Kim. "Korean plant proteomics: pioneers in plant stress physiology". Journal of Plant Biotechnology 38, n.º 2 (30 de junio de 2011): 151–61. http://dx.doi.org/10.5010/jpb.2011.38.2.151.

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27

Mittapelly, Priyanka y Swapna Priya Rajarapu. "Applications of Proteomic Tools to Study Insect Vector–Plant Virus Interactions". Life 10, n.º 8 (7 de agosto de 2020): 143. http://dx.doi.org/10.3390/life10080143.

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Proteins are crucial players of biological interactions within and between the organisms and thus it is important to understand the role of proteins in successful partnerships, such as insect vectors and their plant viruses. Proteomic approaches have identified several proteins at the interface of virus acquisition and transmission by their insect vectors which could be potential molecular targets for sustainable pest and viral disease management strategies. Here we review the proteomic techniques used to study the interactions of insect vector and plant virus. Our review will focus on the techniques available to identify the infection, global changes at the proteome level in insect vectors, and protein-protein interactions of insect vectors and plant viruses. Furthermore, we also review the integration of other techniques with proteomics and the available bioinformatic tools to analyze the proteomic data.

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28

Jorrin-Novo, Jesus V. "Mike Dunn: Proteomics in Spain, and the field of plant proteomics". PROTEOMICS 16, n.º 22 (noviembre de 2016): 2842–44. http://dx.doi.org/10.1002/pmic.201600031.

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29

Khatoon, Amana, Setsuko Komatsu y Shafiq Rehman. "Proteomics Analysis of Flooding-stressed Plant". Current Proteomics 9, n.º 4 (1 de diciembre de 2012): 217–31. http://dx.doi.org/10.2174/157016412805219198.

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30

Zabrouskov, Vlad, Lisa Giacomelli, Klaas J. van Wijk y Fred W. McLafferty. "A New Approach for Plant Proteomics". Molecular & Cellular Proteomics 2, n.º 12 (22 de septiembre de 2003): 1253–60. http://dx.doi.org/10.1074/mcp.m300069-mcp200.

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31

Morel, Johanne, Stéphane Claverol, Sébastien Mongrand, Fabienne Furt, Jérôme Fromentin, Jean-Jacques Bessoule, Jean-Pierre Blein y Françoise Simon-Plas. "Proteomics of Plant Detergent-resistant Membranes". Molecular & Cellular Proteomics 5, n.º 8 (28 de abril de 2006): 1396–411. http://dx.doi.org/10.1074/mcp.m600044-mcp200.

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32

van Wijk, Klaas J. "Challenges and Prospects of Plant Proteomics". Plant Physiology 126, n.º 2 (1 de junio de 2001): 501–8. http://dx.doi.org/10.1104/pp.126.2.501.

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33

Komatsu, S., H. Konishi y M. Hashimoto. "The proteomics of plant cell membranes". Journal of Experimental Botany 58, n.º 1 (27 de junio de 2006): 103–12. http://dx.doi.org/10.1093/jxb/erj209.

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34

Ytterberg, A. Jimmy y Ole N. Jensen. "Modification-specific proteomics in plant biology". Journal of Proteomics 73, n.º 11 (octubre de 2010): 2249–66. http://dx.doi.org/10.1016/j.jprot.2010.06.002.

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35

Wang, Xuchu. "Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era". International Journal of Molecular Sciences 20, n.º 20 (21 de octubre de 2019): 5222. http://dx.doi.org/10.3390/ijms20205222.

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In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.

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36

Olanrewaju, Gbolaga O., Colin P. S. Kruse y Sarah E. Wyatt. "Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments". International Journal of Molecular Sciences 24, n.º 19 (22 de septiembre de 2023): 14425. http://dx.doi.org/10.3390/ijms241914425.

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The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life’s adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant’s responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis’ spaceflight adaptation mechanisms and informing strategies for successful space farming.

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37

Zhou, Ming, Shengnan Zhu, Xiaohui Mo, Qi Guo, Yaxue Li, Jiang Tian y Cuiyue Liang. "Proteomic Analysis Dissects Molecular Mechanisms Underlying Plant Responses to Phosphorus Deficiency". Cells 11, n.º 4 (14 de febrero de 2022): 651. http://dx.doi.org/10.3390/cells11040651.

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Phosphorus (P) is an essential nutrient for plant growth. In recent decades, the application of phosphate (Pi) fertilizers has contributed to significant increases in crop yields all over the world. However, low efficiency of P utilization in crops leads to intensive application of Pi fertilizers, which consequently stimulates environmental pollution and exhaustion of P mineral resources. Therefore, in order to strengthen the sustainable development of agriculture, understandings of molecular mechanisms underlying P efficiency in plants are required to develop cultivars with high P utilization efficiency. Recently, a plant Pi-signaling network was established through forward and reverse genetic analysis, with the aid of the application of genomics, transcriptomics, proteomics, metabolomics, and ionomics. Among these, proteomics provides a powerful tool to investigate mechanisms underlying plant responses to Pi availability at the protein level. In this review, we summarize the recent progress of proteomic analysis in the identification of differential proteins that play roles in Pi acquisition, translocation, assimilation, and reutilization in plants. These findings could provide insights into molecular mechanisms underlying Pi acquisition and utilization efficiency, and offer new strategies in genetically engineering cultivars with high P utilization efficiency.

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38

Balbuena, Tiago S., Leonardo L. C. Dias, Mariana L. B. Martins, Tatiana B. Chiquieri, Claudete Santa-Catarina, Eny I. S. Floh y Vanildo Silveira. "Challenges in proteome analyses of tropical plants". Brazilian Journal of Plant Physiology 23, n.º 2 (2011): 91–104. http://dx.doi.org/10.1590/s1677-04202011000200001.

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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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39

Sidiq, Yasir, Daisuke Tamaoki y Takumi Nishiuchi. "Proteomic Profiling of Plant and Pathogen Interaction on the Leaf Epidermis". International Journal of Molecular Sciences 23, n.º 20 (12 de octubre de 2022): 12171. http://dx.doi.org/10.3390/ijms232012171.

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The plant epidermis is the first line of plant defense against pathogen invasion, and likely contains important regulatory proteins related to the plant–pathogen interaction. This study aims to identify the candidates of these regulatory proteins expressed in the plant epidermis. We performed comparative proteomic studies to identify rapidly and locally expressed proteins in the leaf epidermis inoculated with fungal phytopathogen. The conidia solutions were dropped onto the Arabidopsis leaf surface, and then, we collected the epidermal tissues from inoculated and mock-treated leaves at 4 and 24 hpi. The label-free quantification methods showed that expressions of Arabidopsis proteins, which are related to defense signals, such as BAK1, MKK5, receptor-like protein kinases, transcription factors, and stomatal functions, were rapidly induced in the epidermal tissues of inoculated leaves. In contrast, most of them were not differentially regulated by fugal inoculation in the whole leaves. These findings clearly indicate that epidermal proteomics can monitor locally expressed proteins in inoculated areas of plant tissues. We also identified the 61 fungal proteins, including effector-like proteins specifically expressed on the Arabidopsis epidermis. Our new findings suggested that epidermal proteomics is useful for understanding the local expressions of plant and fungal proteins related to their interactions.

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40

Rampitsch, Christof y Murali Srinivasan. "The application of proteomics to plant biology: a review". Canadian Journal of Botany 84, n.º 6 (junio de 2006): 883–92. http://dx.doi.org/10.1139/b06-061.

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The term proteomics, although still less than a decade old, is becoming commonplace in the vocabulary of biologists. Advances made in yeast and humans have been remarkable, sustained by equally remarkable progress in mass spectrometry, bioinformatics, and separation techniques. Progress in plants has been more recent, much of it in the model organisms Arabidopsis thaliana (L.) Heynh. and rice ( Oryza sativa L.), reflecting the tremendous advantage of a complete genomic sequence for proteomics endeavours. Other plants have also been the subject of investigation and this review deals with recent progress in proteomics under three main subheadings: total proteome studies, stress and post-translational modifications, and symbiotic plant–microbe interactions. Examples from the current literature are used to illustrate how proteomics can be used by itself or as part of a larger strategy to gain insight into the functioning of plants at the molecular level.

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41

Abdallah, Cosette, Eliane Dumas-Gaudot, Jenny Renaut y Kjell Sergeant. "Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance". International Journal of Plant Genomics 2012 (20 de noviembre de 2012): 1–17. http://dx.doi.org/10.1155/2012/494572.

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Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.

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42

Brajkovic, Sarah, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer y Bernhard Kuster. "Getting Ready for Large-Scale Proteomics in Crop Plants". Nutrients 15, n.º 3 (3 de febrero de 2023): 783. http://dx.doi.org/10.3390/nu15030783.

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Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.

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van Wijk, Klaas J. "Plastid proteomics". Plant Physiology and Biochemistry 42, n.º 12 (diciembre de 2004): 963–77. http://dx.doi.org/10.1016/j.plaphy.2004.10.015.

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Rey, María-Dolores, María Castillejo, Rosa Sánchez-Lucas, Victor Guerrero-Sanchez, Cristina López-Hidalgo, Cristina Romero-Rodríguez, José Valero-Galván et al. "Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?" International Journal of Molecular Sciences 20, n.º 3 (6 de febrero de 2019): 692. http://dx.doi.org/10.3390/ijms20030692.

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Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.

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Millar, A. Harvey. "Location, location, location: surveying the intracellular real estate through proteomics in plants". Functional Plant Biology 31, n.º 6 (2004): 563. http://dx.doi.org/10.1071/fp04034.

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Knowledge of cellular compartmentation is critical to an understanding of many aspects of biological function in plant cells but it remains an under-emphasised concept in the use of and investment in plant functional genomic tools. The emerging effort in plant subcellular proteomics is discussed, and the current datasets that are available for a series of organelles and cellular membranes isolated from a range of plant species are noted. The benefit of knowing subcellular location in determining the role of proteins of unknown function is considered alongside the challenges faced in this endeavour. These include clear problems in dealing with contamination during the isolation of subcellular compartments, the meaningful integration of these datasets once completed to assemble a jigsaw of the cellular proteome as a whole, and the use of the wider literature in supplementing this proteomic discovery effort.

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Cherry, Ashley, Brian Fisher, William Branch, Christopher Peralta, Lissa Gilliam, Olga Pahom, Chris Liebold y Julie Marshall. "Proteomic Analysis of Arachis hypogaea Seeds from Different Maturity Classes". Plants 13, n.º 8 (16 de abril de 2024): 1111. http://dx.doi.org/10.3390/plants13081111.

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Physiological maturity impacts seed quality through various mechanisms including vigor, desiccation tolerance, dormancy induction, synthesis of raw materials (including seed storage proteins), and the reorganization of metabolisms. Peanut seed development can be classified into seven classes with four incremental stages per class. Based on the mesocarp color, the final three stages are commonly referred to as “orange”, “brown”, and “black”. In 2017, freshly harvested pods from one genotype of runner market-type peanuts grown under conventional practices were obtained from the University of Georgia research facility. The pods were removed from the plant material and ‘pod blasted’ to reveal the mesocarp. After separation, the remainder of the pod outer layer was removed, and the seeds were segregated for proteomic analysis. The raw peanuts were analyzed by bottom-up LC-MS/MS proteomics, which was conducted by the Proteomics Resource Center at the Rockefeller University, to identify the significant protein composition differences in each maturity class. The proteomic data revealed differentially expressed proteins as a function of maturity class with multiple functions including plant defense, metabolism, cell signaling, nutrient accumulation, and packaging. Understanding the processes needed for seed maturation will enable peanut scientists to evaluate the traits needed for robust germination, hardiness of the seed in response to disease, and nutrient quality.

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Xu, Kai y Peter D. Nagy. "Dissecting Virus-Plant Interactions Through Proteomics Approaches". Current Proteomics 7, n.º 4 (1 de diciembre de 2010): 316–27. http://dx.doi.org/10.2174/157016410793611792.

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48

Komatsu, Setsuko. "Plant Proteomics Databases: Their Status in 2005". Current Bioinformatics 1, n.º 1 (1 de enero de 2006): 33–36. http://dx.doi.org/10.2174/157489306775330651.

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Jamet, Elisabeth y Véronique Santoni. "Editorial for Special Issue: 2017 Plant Proteomics". Proteomes 6, n.º 3 (21 de junio de 2018): 28. http://dx.doi.org/10.3390/proteomes6030028.

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50

Whitelegge, J. P. "Plant proteomics: BLASTing out of a MudPIT". Proceedings of the National Academy of Sciences 99, n.º 18 (23 de agosto de 2002): 11564–66. http://dx.doi.org/10.1073/pnas.192449199.

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