Esaú Bojórquez-Velázquez

Cryopreservation is an effective strategy for the long-term conservation of plant germplasm. However, the metabolic responses of cryoderived plants under ex vitro conditions have been little studied. This work evaluates the proteomic profile of Vanilla planifolia plants regenerated from shoot tips recovered after cryopreservation using the Droplet-vitrification (D-V), D-Cryoplate (D-Cp), and V-Cryoplate (V-Cp) methods. The plants were maintained under greenhouse conditions for four years, and protein expression was analyzed using nano-LC-MS/MS. A total of 3523 proteins were identified, and 1019 showed differential expression compared to non-cryopreserved control plants. Nine proteins were consistently upregulated across all cryopreservation methods, including chalcone-flavanone isomerase, Glucose-Methanol-Choline oxidoreductase, calreticulin, glutamine synthetase, 3-ketoacyl-CoA synthase, pectinesterase, BAHD acyltransferase, α/β-hydrolase, and peroxidases. These proteins are associated with stress protection, primary metabolism, cell wall remodeling, and lipid and nitrogen metabolism. Conversely, down-regulation was observed in EG45-type expansin and in proteins containing RNA recognition motifs involved in growth regulation. Functional enrichment analysis revealed enhanced photosynthetic capacity and structural reinforcement in cryoderived plants compared to non-cryopreserved control plants. Among the procedures evaluated, the D-Cp technique, followed by the D-V technique, proved to be the most effective, demonstrating that cryopreservation enabled stable metabolic reprogramming during the greenhouse development of V. planifolia plants.

Amaranth is a promising staple food that produces seeds with excellent nutritional quality. Although cultivated species intended for grain production have interesting agronomic traits, relatively little is known about wild species, which can prosper in diverse environments and could be a rich genetic source for crop improvement. This work focuses on the proteomic comparison between the seeds of wild and cultivated amaranth species using polarity-based protein extraction and two-dimensional gel electrophoresis. Differentially accumulated proteins (DAPs) showed changes in granule-bound starch synthases and a wide range of 11S globulin isoforms. The electrophoretic profile of these proteins suggests that they may contain significant phosphorylation as post-translational modifications (PTMs), which were confirmed via immunodetection. These PTMs may impact the physicochemical functionality of storage proteins, with potential implications for seed agronomic traits and food system applications. Low-abundant DAPs with highly variable accumulation patterns are also discussed; these were involved in diverse molecular processes, such as genic regulation, lipid storage, and stress response.

In recent years, avocados have gained worldwide popularity as a nutritive food. This trend is causing a rise in the production of this fruit, which is accompanied by several problems associated with monocultural practices. Despite massive economic gains, limited molecular and structural information has been generated about avocado ripening. In fact, limited studies have attempted to unravel the proteome complexity dynamics of avocado fruit. We therefore conducted a comparative proteomics study on avocado peel and pulp during the postharvest shelf life using tandem mass tag synchronous precursor selection triple-stage mass spectrometry. We identified 3161 and 1128 proteins in the peel and pulp, respectively. Peels exhibited major over-accumulation of proteins associated with water deprivation and oxidative stress, along with abscisic acid biosynthesis. Ethylene, jasmonic acid, phenylpropanoid, and flavonoid biosynthesis pathways were activated. Structurally, we observed the accumulation of lignin and a reduction in cuticular thickness, which coincides with the reduction in the levels of long-chain acyl-coenzyme A synthetase and a marginal increase in 10,16-dihydroxyhexadecanoic acid. Our study sheds light on the association of proteome modulation with the structural features of Hass avocado. Its detailed characterization will provide an alternative for better preservation during the postharvest period.

Plant growth regulators (PGR) are essential for somatic embryogenesis (SE) in different species, and Coffea canephora is no exception. In our study model, previously, we have been able to elucidate the participation of various genes involved in SE by using different strategies; however, until now, we have not used a proteomic approach. This research seeks to contribute to understanding the primary cellular pathways involved in developing SE in C. canephora. The process of our model consists of two stages: (1) preconditioning in MS medium with auxin (NAA) and cytokinin (KIN), and (2) induction in Yasuda liquid medium added with cytokinin (BA). Therefore, in this study, we analyzed different days of the SE induction process using shotgun label-free proteomics. An amount of 1630 proteins was found among different sampling days of the process, of which the majority were accumulated during the induction stage. We found that some of the most enriched pathways during this process were the biosynthesis of amino acids and secondary metabolites. Eighteen proteins were found related to auxin homeostasis and two to cytokinin metabolism, such as ABC, BIG, ILR, LOG, and ARR. Ten proteins and transcription factors related to SE were also identified, like SERK1, SKP1, nuclear transcription factor Y, MADS-box, and calreticulin, and 19 related to other processes of plant development, among which the 14-3-3 and PP2A proteins stand out. This is the first report on the proteomic approach to elucidate the mechanisms that operate during the induction of SE in C. canephora. So, our findings provide the groundwork for future, more in-depth research. Data are available via ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD047172.

Despite substantial advances in the use of proteomic technologies, their widespread application in fruit tissues of non‐model and recalcitrant species remains limited. This hampers the understanding of critical molecular events during the postharvest period of fleshy tropical fruits. Therefore, we evaluated label‐free quantitation (LFQ) and TMT‐SPS‐MS3 (TMT) approaches to analyse changes in the protein profile of mango peels during postharvest period. We compared two extraction methods (phenol and chloroform/methanol) and two peptide fractionation schemes (SCX and HPRP). We accurately identified 3065 proteins, of which, 1492 were differentially accumulated over at 6 days after harvesting (DAH). Both LFQ and TMT approaches share 210 differential proteins including cell wall proteins associated with fruit softening, as well as aroma and flavour‐related proteins, which were increased during postharvest period. The phenolic protein extraction and the high‐pH reverse‐phase peptide fractionation was the most effective pipeline for relative quantification. Nevertheless, the information provided by the other tested strategies was significantly complementary. Besides, LFQ spectra allowed us to track down intact N‐glycopeptides corroborating N‐glycosylations on the surface of a desiccation‐related protein. This work represents the largest proteomic comparison of mango peels during postharvest period made so far, shedding light on the molecular foundation of edible fruit during ripening.

Glyphosate is one of the most widely used herbicides around the world. Over the past decade, the use of glyphosate and related molecules has significantly risen despite its suggested harmful effects on human health. Therefore, it is of great interest to establish reliable and scalable extraction and quantification pipelines for glyphosate in food-associated products. This herbicide is difficult to detect in foods and related matrices because of its chemical features. In this work, we tested different concentrations of solvents and various extraction protocols for recovering this pesticide. For quantification, we used a dynamic multiple reaction monitoring (dMRM) method in an ultra-high resolution liquid chromatograph coupled to a triple quadrupole mass spectrometer (UPLC-MS-QqQ). We determined that 20 % (v/v) methanol in water was the best solvent for extraction. Accelerated solvent extraction (ASE) and ultrasonication approach allowed better recovery values. However, extraction with the energized dispersive extraction system (EDGE) exhibited a more efficient result in half of the time compared to the other automated protocol tested in our study. Our investigation provides valuable information for the extraction, identification, and quantification of glyphosate-2-13C, which will contribute to monitoring the level of this herbicide in corn flour. Resumen. El glifosato es uno de los herbicidas más utilizados en todo el mundo. Durante la última década, el uso del glifosato y las moléculas derivadas de este compuesto ha aumentado significativamente a pesar de los efectos nocivos que se han indicado para la salud humana. Por lo tanto, es de gran interés establecer herramientas de extracción y cuantificación confiables y escalables para glifosato en los productos asociados con alimentos. Este plaguicida es difícil de detectar en alimentos y otras matrices afines debido a sus características químicas. En este estudio probamos diferentes concentraciones de solventes y varios protocolos de extracción para la recuperación de este herbicida. Para la cuantificación utilizamos un método de monitoreo dinámico de múltiples reacciones (dMRM) en un cromatógrafo de líquidos de ultra alta resolución acoplado a un espectrómetro de masas de triple cuadrupolo (UPLC-MS-QqQ). Determinamos que 20 % (v/v) de metanol en agua era el mejor solvente para la extracción. Las herramientas de extracción acelerada por solventes (ASE) y ultrasonicación permitieron los mejores valores de recuperación. Sin embargo, la extracción con el sistema de extracción dispersiva energizada (EDGE) mostró resultados eficientes en la mitad del tiempo, en comparación con el otro protocolo automatizado probado en nuestro estudio. Nuestra investigación provee información valiosa para la extracción y cuantificación de glifosato-2-13C, lo que contribuirá a monitorear niveles de este herbicida en harina de maíz.

Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.

Amaranth 11S globulins (Ah11Sn) are an excellent source of essential amino acids; however, there have been no investigations on the characterization of their techno-functional properties at different pH conditions and NaCl concentrations, which are necessary for food formulations. In this work, we report a new two-step purification method for native Ah11Sn with purity levels of ~95%. LC–MS/MS analysis revealed the presence of three different Ah11Sn paralogs named Ah11SB, A11SC, and Ah11SHMW, and their structures were predicted with Alphafold2. We carried out an experimental evaluation of Ah11Sn surface hydrophobicity, solubility, emulsifying properties, and assembly capacity to provide an alternative application of these proteins in food formulations. Ah11Sn showed good surface hydrophobicity, solubility, and emulsifying properties at pH values of 2 and 3. However, the emulsions became unstable at 60 min. The assembly capacity of Ah11Sn evaluated by DLS analysis showed mainly the trimeric assembly (~150–170 kDa). This information is beneficial to exploit and utilize Ah11Sn rationally in food systems.