What Is New in (Plant) Proteomics Methods and Protocols: The 2015–2019 Quinquennium

Jorrín‐Novo, Jesús V.

doi:10.1007/978-1-0716-0528-8_1

Cited by 10 publications

(7 citation statements)

References 43 publications

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“…Besides gel based, gel free [116], antibody chips [13] and MS-imaging [117] are also available for analyzing plant sample proteome contents. However, the most promising approaches are related to how validated and integrate proteomics data with other omics approaches in order to get a more systemic vision of the processes under evaluation [118]. In this work we integrated proteomics data generated by us and others, as well as different sets of transcriptomic data publicly available to unveil information regarding critical molecular processes involved in the peach fruit ripening.…”

Section: Future Perspectivesmentioning

confidence: 99%

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

et al. 2021

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Background Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences between the mesocarp of mature and ripe fruit, it would be possible to highlight critical molecular processes involved in the fruit ripening. Results To accomplish this goal, the proteome from mature and ripe fruit was assessed from the variety O’Henry through shotgun proteomics using 1D-gel (PAGE-SDS) as fractionation method followed by LC/MS-MS analysis. Data from the 131,435 spectra could be matched to 2740 proteins, using the peach genome reference v1. After data pre-treatment, 1663 proteins could be used for comparison with datasets assessed using transcriptomic approaches and for quantitative protein accumulation analysis. Close to 26% of the genes that code for the proteins assessed displayed higher expression at ripe fruit compared to other fruit developmental stages, based on published transcriptomic data. Differential accumulation analysis between mature and ripe fruit revealed that 15% of the proteins identified were modulated by the ripening process, with glycogen and isocitrate metabolism, and protein localization overrepresented in mature fruit, as well as cell wall modification in ripe fruit. Potential biomarkers for the ripening process, due to their differential accumulation and gene expression pattern, included a pectin methylesterase inhibitor, a gibbellerin 2-beta-dioxygenase, an omega-6 fatty acid desaturase, a homeobox-leucine zipper protein and an ACC oxidase. Transcription factors enriched in NAC and Myb protein domains would target preferentially the genes encoding proteins more abundant in mature and ripe fruit, respectively. Conclusions Shotgun proteomics is an unbiased approach to get deeper into the proteome allowing to detect differences in protein abundance between samples. This technique provided a resolution so that individual gene products could be identified. Many proteins likely involved in cell wall and sugar metabolism, aroma and color, change their abundance during the transition from mature to ripe fruit.

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Section: Future Perspectivesmentioning

confidence: 99%

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

et al. 2021

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“…Therefore, old protocols for in vivo and in vitro experiments have been progressively optimized or substituted by new ones. In other cases, a synergic combination of more approaches has been useful to elucidate many biological processes [ 91 , 92 , 93 , 94 , 95 ]. The great advancement in the fields of genomics, bioinformatics, structural biology, and immunology offered new tools to improve the efficacy of new vaccine formulations against the AMR.…”

Section: Next Generation Vaccinesmentioning

confidence: 99%

The Potential Role of Vaccines in Preventing Antimicrobial Resistance (AMR): An Update and Future Perspectives

Costanzo

Roviello²

2023

Vaccines

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In the modern era, the consumption of antibiotics represents a revolutionary weapon against several infectious diseases, contributing to the saving of millions of lives worldwide. However, the misuse of antibiotics for human and animal purposes has fueled the process of antimicrobial resistance (AMR), considered now a global emergency by the World Health Organization (WHO), which significantly increases the mortality risk and related medical costs linked to the management of bacterial diseases. The current research aiming at developing novel efficient antibiotics is very challenging, and just a few candidates have been identified so far due to the difficulties connected with AMR. Therefore, novel therapeutic or prophylactic strategies to fight AMR are urgently needed. In this scenario, vaccines constitute a promising approach that proves to be crucial in preventing pathogen spreading in primary infections and in minimizing the usage of antibiotics following secondary bacterial infections. Unfortunately, most of the vaccines developed against the main resistant pathogens are still under preclinical and clinical evaluation due to the complexity of pathogens and technical difficulties. In this review, we describe not only the main causes of AMR and the role of vaccines in reducing the burden of infectious diseases, but we also report on specific prophylactic advancements against some of the main pathogens, focusing on new strategies that aim at improving vaccine efficiency.

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“…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%

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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What Is New in (Plant) Proteomics Methods and Protocols: The 2015–2019 Quinquennium

Cited by 10 publications

References 43 publications

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

Shotgun proteomics of peach fruit reveals major metabolic pathways associated to ripening

The Potential Role of Vaccines in Preventing Antimicrobial Resistance (AMR): An Update and Future Perspectives

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

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