Proteomics and plant biology: contributions to date and a look towards the next decade

Novo, Jesús V. Jorrín

doi:10.1080/14789450.2021.1910028

Cited by 25 publications

(10 citation statements)

References 133 publications

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“…Over time, an increasing number of proteomics branches have emerged, attempting to identify, catalog, and characterize a specific structural or functional group of proteins (proteases, phosphoproteins, membrane proteins, etc.) [ 106 ]. The field of plant proteomics was extensively reviewed from a conceptual, historical, methodological, and biological point of view by the authors’ group from 2003 [ 107 ] to 2021 [ 106 ].…”

Section: The “Omics” and Their Integration With Other Approaches (How)mentioning

confidence: 99%

“…The field of plant proteomics was extensively reviewed from a conceptual, historical, methodological, and biological point of view by the authors’ group from 2003 [ 107 ] to 2021 [ 106 ]. Several of these studies discuss, in depth, the contribution of proteomics to plant biology [ 8 , 106 , 108 , 109 , 110 , 111 ], forest trees [ 6 ] or Quercus [ 7 , 8 , 112 ] knowledge. The field of proteomics, in relation to its application to the study of Mediterranean forest trees, was also reviewed by Pinheiro et al [ 113 ].…”

Section: The “Omics” and Their Integration With Other Approaches (How)mentioning

confidence: 99%

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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Maldonado‐Alconada

Castillejo

Rey

et al. 2022

IJMS

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The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

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Section: The “Omics” and Their Integration With Other Approaches (How)mentioning

confidence: 99%

Section: The “Omics” and Their Integration With Other Approaches (How)mentioning

confidence: 99%

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Maldonado‐Alconada

Castillejo

Rey

et al. 2022

IJMS

Self Cite

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“…It is critical to select appropriate proteomic techniques for protein identification and modification that may contribute to crop development. Recent advancements in quantitative proteomics research utilizing high-resolution and mass accuracy instruments have contributed to the identification of proteins and their expression profiles, post-translational modifications (PTMs), and protein–protein interactions under stressed and normal conditions [ 4 , 224 , 225 ]. Plant proteomic analysis is achieved through systematic high-throughput methodologies, including 2D-PAGE (2-Dimensional-Poly Acrylamide Gel-Electrophoresis), MALDI-TOF/MS/MS, and LC-MS/MS.…”

Section: Proteomics Approaches To Identify the Functional And Structu...mentioning

confidence: 99%

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

Rakkammal

Priya

Subramanian

et al. 2022

Plants

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Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.

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confidence: 99%

“…Numerous advances in protein mass spectrometry have been applied to plant systems over the past few decades ( Jorrin-Novo, 2021 ). The intention of this Research Topic was to highlight some of these approaches in plants at a suitable level of detail to enable easy adoption by researchers.…”

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confidence: 99%

Editorial: Advances in plant proteomics

Heazlewood

Wallace²,

Xu³

2022

Front. Plant Sci.

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Numerous advances in protein mass spectrometry have been applied to plant systems over the past few decades (Jorrin-Novo, 2021). The intention of this Research Topic was to highlight some of these approaches in plants at a suitable level of detail to enable easy adoption by researchers.The unifying feature of submissions to the Research Topic were associated with the application of protein quantitation or quantitative proteomics. Whole sample quantification of mRNA (expression profiling) has been possible since the 1990s with the development of techniques such as DNA microarray technologies (Bumgarner, 2013), and these approaches have rapidly expanded with the advent of massively parallel sequencing technologies. By contrast, quantification of whole-proteome dynamics (e.g., cell, organ or tissue) is still not possible, even with the considerable technical advances in mass spectrometry that have occurred in the past 20 years (Timp and Timp, 2020). Nonetheless, quantitative proteomic approaches are a major driver for many plant biologists engaging with protein mass spectrometry to gain functional proteome or subproteome insights into the dynamics of protein abundance in plant systems (Mergner and Kuster, 2022).The resolving power of mass spectrometers for proteomics enabled quantitative approaches that incorporate isotopic labelling with stable heavy isotopes such as 15 N (Schulze and Usadel, 2010). Since these instruments can discriminate between heavy ( 15 N) and light ( 14 N) peptides, these metabolically labelled samples can be analysed in a single run e.g., control (light) and treatment (heavy). Such an approach considerably reduces run to run variation and enables reliable protein quantification. This Research Topic illustrates two methods that highlight the advantages of 15 N labelling for quantitative proteomics. Shrestha et al. presents a data analysis workflow outlining the steps used to extract quantitative information from a 15 N labelled analysis. Reyes et al. outlines the application of targeted proteomics or parallel reaction monitoring (PRM) to 15 N labelled samples highlighting potential advantages of combining both labelling and PRM for reliable quantification.

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Proteomics and plant biology: contributions to date and a look towards the next decade

Cited by 25 publications

References 133 publications

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops—An Updated Overview

Editorial: Advances in plant proteomics

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