Dynamic changes in proteins during apple (Malus x domestica) fruit ripening and storage

The effect of cold plasma treatment on the fruit quality and aroma components of winter jujubes (Ziziphus jujuba Mill. 'Dongzao')

Cold plasma (CP) is a novel environmental-friendly preservation technology that causes minimal damage to fruits. The flavor and quality of winter jujubes have decreased with the extended storage time. Currently, the research on the use of CP on winter jujubes (Ziziphus jujuba Mill. 'Dongzao') mainly focuses on the effect of the treatment on storage quality. There is limited research on the effect of CP treatment on the flavor of winter jujubes. This study used different CP (80 kV) treatment durations (0, 5, and 10 min) to treat winter jujubes. The appropriate treatment time was selected by observing the changes in color, respiratory intensity, soluble sugar content, total acid content, and vitamin C (VC) content of winter jujubes. Amino acid analyzer and headspace solid-phase microextraction in combination with gas chromatography coupled with mass spectrometric detection were used to analyze the effect of CP treatment on the flavor compounds of winter jujubes. The results showed that the 5-min CP treatment could significantly slow down the red coloration of winter jujube while maintaining high soluble sugar, total acid, and VC content. At the respiration peak, the respiratory intensity of the 5-min CP treatment group was 0.74 mg CO2·kg-1·h-1 lower than that of the control group (p < 0.05). CP treatment slowed down the decrease in the content of amino acids and volatile organic compounds (such as 2-methyl-4-pentenal, 2-hexenal, and 3-hexenal) in winter jujubes. This study will provide basic data for applying CP preservation technology in postharvest winter jujubes.

Impact of Cultivation and Storage Conditions on Total Mal d 1 Content and Isoallergen Profile in Apples

The allergen Mal d 1 is often responsible for adverse allergic reactions to fresh apples in northern and central Europe. The Mal d 1 content and isoallergen profile are proposed to have an impact on the allergenic potential of the fruit. Therefore, we investigated the impact of the cropping system on the Mal d 1 content and the isoallergen profile of apples by mass spectrometry for the varieties 'Jonagored' and 'Topaz'. To monitor the impact of storage time and conditions, apples of the varieties 'Santana' and 'Jonagold' were stored for up to 12 weeks under regular air (RA), under RA in combination with 1-methylcyclopropene (1-MCP) treatment, and under a controlled atmosphere (CA). The impact of the cropping system (integrated production vs organic production) was negligible. However, a significant increase in the Mal d 1 content during storage was observed, being higher when stored under CA conditions than under RA conditions. An additional treatment with 1-MCP prior to RA storage drastically reduced the level of Mal d 1 expression in the flesh of the apples by ∼50%. Furthermore, the content of isoallergens 1.03 and 1.06 increased disproportionately under CA conditions, while under RA conditions, only isoallergen 1.06 was affected. With the 1-MCP treatment, no changes in the isoallergen profile were obvious.

Identification of allergenomic signatures in allergic and well-tolerated apple genotypes using LC-MS/MS

The apple fruit (Malus domestica L. Borkh) is one of the most popular fruits worldwide. Beyond their beneficial properties, apples contain proteins that trigger allergic reactions in susceptible consumers. Mal d1 to d4 are allergens present in a variety of different isoforms in apples. In this study, we used proteomics to quantify all four Mal d proteins in 52 apple genotypes with varying allergenic potentials. A total of 195, 17, 14, and 18 peptides were found to be related to Mal d1, d2, d3, and d4 proteins, respectively of which 25 different Mal d proteins could be unambiguously identified. The allergenic potential of the Mal d isoforms was characterized by comparing the isoform abundance with the allergenic score of genotypes from oral challenge tests. The detected Mal d peptides presumably have different IgE binding properties and could be used as potential molecular markers to discriminate between hypoallergenic and hyperallergenic cultivars.

The Fruit Proteome Response to the Ripening Stages in Three Tomato Genotypes

The tomato is a horticultural crop that appears in various colors as it ripens. Differences in the proteome expression abundance of a tomato depend on its genotype and ripening stage. Thus, this study aimed to confirm the differences in changes in the proteome according to four ripening stages (green, breaker, turning, and mature) of three tomato genotypes, i.e., yellow, black, and red tomatoes, using a gel-based proteomic technique. The number of protein spots shown as two-dimensional electrophoresis (2-DE) gels differed according to tomato genotype and ripening stage. A total of 286 variant proteins were determined using matrix-assisted laser desorption-time of flight (MALDI-TOF) mass spectrometry (MS) analysis, confirming 233 identified protein functions. In three tomato genotypes in each ripening stage, grouping according to the Munich Information Center for Protein Sequences (MIPS) functional categories confirmed the variant proteins involved in the following: energy processes (21%); metabolism (20%); protein fate (15%); protein synthesis (10%); a protein with a binding function or cofactor requirement (8%); cell rescue, defense, and virulence (8%); cellular transport, transport facilitation, and transport routes (6%); the biogenesis of cellular components (5%); cell cycle and DNA processing (2%); others (5%). Among the identified protein spots in the function category, two proteins related to metabolism, four related to energy, four related to protein synthesis, and two related to interaction with the cellular environment showed significantly different changes according to the fruit color by the ripening stage. This study reveals the physiological changes in different types of tomatoes according to their ripening stage and provides information on the proteome for further improvement.

MLP-PG1, a major latex-like protein identified in Cucurbita pepo, confers resistance through the induction of pathogenesis-related genes

MAIN CONCLUSION

MLP-PG1, identified in Cucurbita pepo, plays a crucial role in resistance against fungal pathogens through the induction of pathogenesis-related genes.

ASTRACT

MLP-PG1, a major latex-like protein (MLP) from zucchini (Cucurbita pepo), was identified as a transporting factor for hydrophobic organic pollutants. MLPs are members of the Bet v 1 family, similar to pathogenesis-related class 10 proteins (PR-10s). However, the biological functions of MLPs remain unclear. Herein, we show that MLP-PG1 induces the expression of pathogenesis-related (PR) genes and indirectly promotes resistance against pathogens. The activity of the MLP-PG1 promoter in leaves of transgenic tobacco plants was significantly enhanced by inoculation with Pseudomonas syringae pv. tabaci. However, MLP-PG1 did not induce direct resistance through RNase activity. Therefore, we examined the possibility that MLP-PG1 is indirectly involved in resistance; indeed, we found that MLP-PG1 induced the expression of defense-related genes. Overexpression of MLP-PG1 highly upregulated PR-2 and PR-5 and decreased the area of lesions caused by Botrytis cinerea in the leaves of transgenic tobacco plants. Our results demonstrate that MLP-PG1 is involved in indirect resistance against plant diseases, especially caused by fungal pathogens, through the induction of PR genes. This study is the first report to show the induction of PR genes by the expression of MLP from the RNA sequencing analysis and the involvement of MLP-PG1 in the resistance.

Label-free quantitative proteomics analysis of jujube (Ziziphus jujuba Mill.) during different growth stages

Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.

Effect of heat treatment on the quality and energy metabolism in "Golden Delicious" apple fruit

The effect of heat treatment on fruit firmness and related enzymes, acidity and related enzymes, and energy metabolism on postharvest apple fruit was investigated. Results showed that heat treatment prevented softening at the early stage and maintained acidity. Compared with the control, heat treatment markedly inhibited the transcript level of MdcyME1-3 but improved the transcript level of MdPG3 and MdGAL1, thus heat-treated fruit exhibited higher activity of polygalacturonase (PG) and β-galactosidase (β-Gal). Moreover, levels of energy charge in heat-treated fruit were significantly higher than that in the control fruit. These results suggested that β-Gal played an important role in apple fruit softening at the later storage, and heat treatment maintained acidity and energy metabolism while enhanced the activity of cell wall enzymes. PRACTICAL APPLICATIONS: To reveal the mechanism of energy metabolism affecting fruit softening and change in fruit acidity, the enzyme activity and gene expression of apple fruits after heat treatment were studied. By comparing the heat treatment group with the control group, this study successfully explained the genomic mechanism controlling apple fruit acidity and softening in the fruit mature period at high level of energy charge, found key cell wall enzymes and candidate genes, and supplied theoretical guidance for maintaining the fruit quality of "Golden Delicious" fruit.

Review: Biological functions of major latex-like proteins in plants

Major latex-like proteins (MLPs) have been identified in dicots and monocots. They are members of the birch pollen allergen Bet v 1 family as well as pathogenesis-related proteins class 10. MLPs have two main features. One is binding affinity toward various hydrophobic compounds, such as long-chain fatty acids, steroids, and systemic acquired resistance signals, via its internal hydrophobic cavity or hydrophobic residues on its surface. MLPs transport such compounds to other organs via phloem and xylem vessels and contribute to the expression of physiologically important ligands' activity in the particular organs. The second feature is responses to abiotic and biotic stresses. MLPs are involved in drought and salt tolerance through the mediation of plant hormone signaling pathways. MLPs generate resistance against pathogens by the induction of pathogenesis-related protein genes. Therefore, MLPs play crucial roles in drought and salt tolerance and resistance against pathogens. However, knowledge of MLPs is fragmented, and an overview of them is needed. Herein, we summarize the current knowledge of the biological functions of MLPs, which to our knowledge, is the first review about MLPs that has been reported.

Non-destructive methods for fruit quality evaluation

This work studies the evolution in time of several varieties of apples with application in quality storage maintenance. Two different methods were used to evaluate long-stored apples for better sorting and degradation assessment. The first method was laser photoacoustic spectroscopy for the detection of ethylene and ethanol compounds from the internal atmosphere of apples. The second method was multispectral imaging that measures the image and the spectrum combined and also can be used to address features such as ripening and external defects. The experiments showed that, the ethylene value decreases and the value of ethanol increases, which sometimes we may associate with a drift of the images toward darker tones, because the apple is slowly degrading. Non-invasive, real-time inspection can reveal when the degradation process begins, improving the capability of sorting, maintaining their quality and storability.

Unraveling Interactions of the Necrotrophic Fungal Species Botrytis cinerea With 1-Methylcyclopropene or Ozone-Treated Apple Fruit Using Proteomic Analysis

Gray mold caused by the necrotrophic fungus Botrytis cinerea is one of the major postharvest diseases of apple fruit. The exogenous application of 1-methylcyclopropene (1-MCP) and gaseous ozone (O 3) is commonly used to ensure postharvest fruit quality. However, the effect of these treatments on the susceptibility of apple fruit to postharvest pathogens remains largely unknown. Herein, the effect of O 3 and 1-MCP treatments on the development of gray mold on apple fruit (cv. "Granny Smith") was investigated. Artificially inoculated apple fruits, treated or not with 1-MCP, were subjected for 2 months to cold storage [0°C, relative humidity (RH) 95%] either in an O3-enriched atmosphere or in a conventional cold chamber. Minor differences between 1-MCP-treated and control fruits were found in terms of disease expression; however, exposure to ozone resulted in a decrease of disease severity by more than 50% compared with 1-MCP-treated and untreated fruits. Proteomic analysis was conducted to determine proteome changes in the mesocarp tissue of control and 1-MCP- or O3-treated fruits in the absence or in the presence of inoculation with B. cinerea. In the non-inoculated fruits, 26 proteins were affected by 1-MCP, while 51 proteins were altered by ozone. Dynamic changes in fruit proteome were also observed in response to B. cinerea. In O3-treated fruits, a significant number of disease/defense-related proteins were increased in comparison with control fruit. Among these proteins, higher accumulation levels were observed for allergen, major allergen, ACC oxidase, putative NBS-LRR disease resistance protein, major latex protein (MLP)-like protein, or 2-Cys peroxiredoxin. In contrast, most of these proteins were down-accumulated in 1-MCP-treated fruits that were challenged with B. cinerea. These results suggest that ozone exposure may contribute to the reduction of gray mold in apple fruits, while 1-MCP was not effective in affecting this disease. This is the first study deciphering differential regulations of apple fruit proteome upon B. cinerea infection and postharvest storage treatments, underlying aspects of host response related to the gray mold disease.

Investigations of changes in the arabinogalactan proteins (AGPs) structure, size and composition during the fruit ripening process

Arabinogalactan proteins (AGPs) are ubiquitous cell wall and plasma membrane components and are characterised by extensive glycosylation and heterogeneity of their carbohydrate and protein units. The aim of the study was to evaluate the structural features of AGPs present in apple fruits at different stages of the ripening process. AGPs were extracted using the Yariv reagent and examined using SDS-PAGE, immunoblotting, FT-IR, and AFM. In situ analysis, immunofluorescence (CLSM) and immunogold-labelling (TEM), were performed. We demonstrated that AGPs were indeed present in apple fruits at the different stages of the ripening process. The changes in the amount (1.52–2.08 mg g⁻¹), diameter (152.73–75.05 nm), molecular mass (50–250 kDa), and distribution in the cell of AGPs demonstrate their variable presence and changeable structure during the ripening process. We propose specific wavenumbers, i.e. 1265 cm⁻¹, 1117 cm⁻¹, and 960 cm⁻¹, which could be assigned to AGPs. The immunofluorescence and immunogold-labelling results indicate that the JIM13 antibody is the most characteristic for AGPs in apple fruits. This study quantitatively demonstrated for the first time that AGP accumulation occurs in ripe fruits, which is supported by the highest AGPs content, the highest molecular mass, and the appearance of a specific distribution pattern at the cellular level.

Metabolomic and transcriptomic analyses highlight the influence of lipid changes on the post-harvest softening of Pyrus ussurian Max. 'Zaoshu Shanli'

How lipids influence post-harvest softening in pears is not well understood. LC-MS/MS (Liquid chromatography-tandem mass spectrometry) and RNA-Seq analyses of 'Zaoshu Shanli' (ZSSL) pears were conducted during post-harvest storage. This approach enabled the identification of 98 different metabolites that upregulated and 95 that downregulated at 18 days post-harvest in ZSSL fruits to day 0. Metabolites were significantly enriched in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways including glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis. When comparing fruits from day 18 to those from day 0 post-harvest, RNA-seq analyses further highlighted 6496 differentially expressed genes (DEGs) in ZSSL fruits that were significantly enriched in KEGG pathways including glycerophospholipid metabolism and fatty acid degradation. Overall, these results suggested that glycerophospholipid metabolism is closely related to the post-harvest softening of pears. Further research will be essential in order to fully explore the functional implications of and mechanistic basis for these findings.

Tiered approach for the identification of Mal d 1 reduced, well tolerated apple genotypes

A rising proportion of the world population suffers from food-related allergies, including incompatibilities to apples. Although several allergenic proteins have been found in apples, the most important proteins that cause allergic reactions to apples in Central-Northern Europe, and North America are the Mal d 1 proteins, which are homologues of the birch pollen allergen Bet v 1. As the demand for hypoallergenic fruits is constantly increasing, we selected apple genotypes with a low total content of Mal d 1 by enzyme-linked immunosorbent assay analysis from segregating populations and tested the tolerability of these fruits through a human provocation study. This tiered approach, which exploited the natural diversity of apples, led to the identification of fruits, which were tolerated by allergic patients. In addition, we found a significant correlation (coefficient >0.76) between the total Mal d 1 content and flavan-3-ol amount and show that the isoform composition of the Mal d 1 proteins, which was determined by LC-MS/MS has a decisive effect on the tolerability of apple genotypes. The approach presented can be applied to other types of fruit and to other allergenic proteins. Therefore, the strategy can be used to reduce the allergen content of other plant foods, thereby improving food safety for allergy subjects.

Primary Metabolism in Fresh Fruits During Storage

The extension of commercial life and the reduction of postharvest losses of perishable fruits is mainly based on storage at low temperatures alone or in combination with modified atmospheres (MAs) and controlled atmospheres (CAs), directed primarily at reducing their overall metabolism thus delaying ripening and senescence. Fruits react to postharvest conditions with desirable changes if appropriate protocols are applied, but otherwise can develop negative and unacceptable traits due to the onset of physiological disorders. Extended cold storage periods and/or inappropriate temperatures can result in development of chilling injuries (CIs). The etiology, incidence, and severity of such symptoms vary even within cultivars of the same species, indicating the genotype significance. Carbohydrates and amino acids have protective/regulating roles in CI development. MA/CA storage protocols involve storage under hypoxic conditions and high carbon dioxide concentrations that can maximize quality over extended storage periods but are also affected by the cultivar, exposure time, and storage temperatures. Pyruvate metabolism is highly reactive to changes in oxygen concentration and is greatly affected by the shift from aerobic to anaerobic metabolism. Ethylene-induced changes in fruits can also have deleterious effects under cold storage and MA/CA conditions, affecting susceptibility to chilling and carbon dioxide injuries. The availability of the inhibitor of ethylene perception 1-methylcyclopropene (1-MCP) has not only resulted in development of a new technology but has also been used to increase understanding of the role of ethylene in ripening of both non-climacteric and climacteric fruits. Temperature, MA/CA, and 1-MCP alter fruit physiology and biochemistry, resulting in compositional changes in carbon- and nitrogen-related metabolisms and compounds. Successful application of these storage technologies to fruits must consider their effects on the metabolism of carbohydrates, organic acids, amino acids and lipids.

Primary Metabolism in Avocado Fruit

Avocado (Persea americana Mill) is rich in a variety of essential nutrients and phytochemicals; thus, consumption has drastically increased in the last 10 years. Avocado unlike other fruit is characterized by oil accumulation during growth and development and presents a unique carbohydrate pattern. There are few previous and current studies related to primary metabolism. The fruit is also quite unique since it contains large amounts of C7 sugars (mannoheptulose and perseitol) acting as transportable and storage sugars and as potential regulators of fruit ripening. These C7 sugars play a central role during fruit growth and development, but still confirmation is needed regarding the biosynthetic routes and the physiological function during growth and development of avocado fruit. Relatively recent transcriptome studies on avocado mesocarp during development and ripening have revealed that most of the oil is synthesized during early stages of development and that oil synthesis is halted when the fruit is harvested (pre-climacteric stage). Most of the oil is accumulated in the form of triacylglycerol (TAG) representing 60-70% in dry basis of the mesocarp tissue. During early stages of fruit development, high expression of transcripts related to fatty acid and TAG biosynthesis has been reported and downregulation of same genes in more advanced stages but without cessation of the process until harvest. The increased expression of fatty acid key genes and regulators such as PaWRI1, PaACP4-2, and PapPK-β-1 has also been reported to be consistent with the total fatty acid increase and fatty acid composition during avocado fruit development. During postharvest, there is minimal change in the fatty acid composition of the fruit. Almost inexistent information regarding the role of organic acid and amino acid metabolism during growth, development, and ripening of avocado is available. Cell wall metabolism understanding in avocado, even though crucial in terms of fruit quality, still presents severe gaps regarding the interactions between cell wall remodeling, fruit development, and postharvest modifications.

Disassembly of the fruit cell wall by the ripening-associated polygalacturonase and expansin influences tomato cracking

Fruit cracking is an important problem in horticultural crop production. Polygalacturonase (SlPG) and expansin (SlEXP1) proteins cooperatively disassemble the polysaccharide network of tomato fruit cell walls during ripening and thereby, enable softening. A Golden 2-like (GLK2) transcription factor, SlGLK2 regulates unripe fruit chloroplast development and results in elevated soluble solids and carotenoids in ripe fruit. To determine whether SlPG, SlEXP1, or SlGLK2 influence the rate of tomato fruit cracking, the incidence of fruit epidermal cracking was compared between wild-type, Ailsa Craig (WT) and fruit with suppressed SlPG and SlEXP1 expression (pg/exp) or expressing a truncated nonfunctional Slglk2 (glk2). Treating plants with exogenous ABA increases xylemic flow into fruit. Our results showed that ABA treatment of tomato plants greatly increased cracking of fruit from WT and glk2 mutant, but not from pg/exp genotypes. The pg/exp fruit were firmer, had higher total soluble solids, denser cell walls and thicker cuticles than fruit of the other genotypes. Fruit from the ABA treated pg/exp fruit had cell walls with less water-soluble and more ionically and covalently-bound pectins than fruit from the other lines, demonstrating that ripening-related disassembly of the fruit cell wall, but not elimination of SlGLK2, influences cracking. Cracking incidence was significantly correlated with cell wall and wax thickness, and the content of cell wall protopectin and cellulose, but not with Ca2+ content.

A New Insight into Biospeckle Activity in Apple Tissues

The monitoring and characterization of agricultural products before harvest or during ripening, storage, and shelf life has recently been increasingly explored in the literature. The analysis of biospeckle activity has potential for the determination of the optimal harvest window, the monitoring of the fruit ripening process, and the detection of diseases and bruising. In this technique, the specimen is illuminated with coherent light and speckle intensity fluctuations are analyzed using diverse methodologies. Prior work shows that biospeckle activity is strongly correlated to physiological indexes conventionally used to evaluate fruit texture and composition. Here, we scrupulously investigate the biospeckle activity of Gala apple fruits during postharvest stages. We simulate realistic conditions for shelf-life monitoring, namely an unknown history of the fruit and storage in an uncontrolled atmosphere. Scattering spot images are acquired with multiple exposure times using a simple optical setup. The contrast, reflecting biospeckle activity, is computed after eliminating inhomogeneous zones. The results show, for the first time, speckle activity at short time scales. The retrieved correlations between speckle parameters and the ratio of apples’ firmness to their soluble solids content reveal significant links despite the unknown fruit’s origin, harvest date, and storage history.

Distribution of arabinogalactan proteins and pectins in the cells of apple (Malus × domestica) fruit during post-harvest storage

BACKGROUND AND AIMS

Changes in the arrangement of cell wall components determine cell wall properties (integrity, stiffness), thereby affecting the macro-scale properties of fruits, which are important for consumers and industry. Arabinogalactan proteins (AGPs) are ubiquitous components of the plant cell, in which they have various functions. Currently, AGPs are considered to be one of the less well-known, enigmatic proteoglycans, a consequence of their heterogeneous structure and unclear mechanism of activity.

METHODS

An immunocytochemical study was conducted to elucidate the distribution of AGPs and pectic polysaccharides contained in apple (Malus × domestica) fruit during senescence. De-esterified homogalacturonan (LM19), methyl-esterified homogalacturonan (LM20), processed arabinan (LM16) and three AGP epitopes (JIM13, JIM15, MAC207) were identified in the fruit at three stages: fresh fruit, and fruit at 1 and 3 months of post-harvest storage.

KEY RESULTS

Microscopy revealed spatio-temporal changes in the localization of all examined epitopes. Changes of fruit cell wall assembly and its degradation were confirmed by determination of the galacturonic acid content in the WSP (water soluble pectins), CSP (chelator soluble pectins) and DASP (dilute alkali soluble pectins) fractions.

CONCLUSIONS

The results revealed dependencies between AGPs, arabinan and homogalacturonan distribution in apple fruit, which are correlated with changes in microstructure during senescence. We propose that AGPs are involved in establishment of the cell wall - plasma membrane continuum.

Elaboration and Characterization of Active Apple Starch Films Incorporated with Ellagic Acid

Apple starch films were obtained from apples harvested at 60, 70, 80 and 90 days after full bloom (DAFB). Mechanical properties and water vapor permeability (WVP) were evaluated. The apple starch films at 70 DAFB presented higher values in the variables of tensile strength (8.12 MPa), elastic modulus (3.10 MPa) and lower values of water vapor permeability (6.77 × 10−11 g m−1 s−1 Pa−1) than apple starch films from apples harvested at 60, 80 and 90 DAFB. Therefore, these films were chosen to continue the study incorporating ellagic acid (EA). The EA was added at three concentrations [0.02% (FILM-EA0.02%), 0.05% (FILM-EA0.05%) and 0.1% (FILM-EA0.1%) w/w] and compared with the apple starch films without EA (FILM-Control). The films were characterized by their physicochemical, optical, morphological and mechanical properties. Their thermal stability and antioxidant capacity were also evaluated. The FILM-Control and FILM-EA0.02% showed a uniform surface, while FILM-EA0.05% and FILM-EA0.1% showed a rough surface and insoluble EA particles. Compared to FILM-Control, EA modified the values of tensile strength, elasticity modulus and elongation at break. The antioxidant capacity increased as EA concentration did. EA incorporation allowed obtaining films with higher antioxidant capacity, capable of blocking UV light with better mechanical properties than film without EA.

Structural network of arabinogalactan proteins (AGPs) and pectins in apple fruit during ripening and senescence processes

The cell wall is an essential framework determining the overall form of the plant cell. Our study was focused on the distribution of arabinogalactan proteins (AGPs), arabinan, and homogalacturonan in fruit cells during ripening and storage with emphasis on quantitative analysis of their presence in particular regions of the cell wall - plasma membrane. The localization of the examined compounds was determined with immunohistochemistry techniques and immunogold labelling. Spatio-temporal colocalization between AGPs epitopes - [βGlcA(1→3)-αGalA(1→2)Rha] recognized by JIM13 and MAC207 antibodies, and arabinan labelled by the LM16 antibody was detected in the inner cell wall layer, in association with the plasma membrane. The specific arrangement of AGP and arabinan epitopes differentiated them from homogalacturonan epitopes, consisting of GalA residues recognized by LM19 and LM20 antibodies in all the examined fruit maturity stages. The disruption of cell wall - plasma membrane continuum, observed during ripening-associated softening process, was associated with both the substantial decrease of AGPs, pectins content and with remodeling of their arrangement. The results indicate that the textural properties of fruit during growth and postharvest storage, an attribute of fruit quality becoming selection criteria for consumers, depend on the existence of dynamic network organizing polysaccharides and glycoproteins in the extracellular matrix.

Impact of the Ripening Stage of Wax Apples on Chemical Profiles of Juice and Cider

Wax apple fruit (Syzygium aqueum Alston cv. Taaptimjan) is a tropical fruit with many nutritional bioactive compounds and high economic value. However, when fully ripe, the thin-skinned fruit is highly susceptible to physical damage and microbial spoilage that significantly reduce its commercial value. The present study was aimed to find a suitable ripening stage between the ripe and overripe wax apple fruits for developing a value-added beverage specifically cider. The chemical profiles of ripe and overripe wax apple juice and cider were determined by measuring sugar, acid, alcohol, mineral, proximate, ascorbic acid, amino acid, antioxidant, and volatile levels. Overall, the results showed significant variations. The physicochemical and proximate analysis showed highest values for ripe fruit juice than overripe fruit juice and the cider samples. The amino acids in the samples were found almost at similar levels. Polyphenolic content and antioxidant activities were higher in ciders than in unfermented juices. In addition, the overripe fruit cider had more volatile compounds than ripe fruit cider and unfermented juices. Overall, the overripe fruit is suitable for producing cider, whereas the ripe fruit is more suitable for the unfermented beverages.

An Electronic Nose for Royal Delicious Apple Quality Assessment - A Tri-layer Approach

Foodborne pathogens cause serious health issues and have a strong impact on the economy of the country. In this context, quality testing of royal delicious apple by detecting pathogen contamination using an electronic nose, which contains an array of six ready-made sensors, has been proposed. To estimate the types of pathogens, fresh, half and completely contaminated apple samples were considered for bacterial studies. This study revealed the presence of Staphylococcus, Salmonella and Shigella bacteria, which were in the order of zero, 10², 10³-10⁴ CFU/mL. Further, the recorded headspace GC-MS spectra of contaminated samples confirmed the presence of bacterial spoilage markers namely acetone, ethyl acetate, ethyl alcohol and acetaldehyde. Voltage swing of 0.2 and 0.5 V was observed for half and completely contaminated apple samples respectively with reference to the fresh sample. Voltage responses of the sensors fed to Principal component analysis and Ward's method of hierarchical cluster algorithms helped to assess the quality of apple samples. By correlating the results of tri-layers namely bacterial count, GCMS data and classification results, reference table was developed and embedded in the ATmega processor of the electronic nose for real-time quality estimation of apple samples.

Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome

Indian sandalwood (Santalum album) is an important tropical evergreen tree known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements. In-depth proteome analysis revealed the identities of 72,325 unique peptides, which confirmed 10,076 of the predicted genes. The addition of transcriptomic and proteogenomic approaches resulted in the identification of 53 novel proteins and 34 gene-correction events that were missed by genomic approaches. Proteogenomic analysis also helped in reassigning 1,348 potential noncoding RNAs as bona fide protein-coding messenger RNAs. Gene expression patterns at the RNA and protein levels indicated that peptide sequencing was useful in capturing proteins encoded by nuclear and organellar genomes alike. Mass spectrometry-based proteomic evidence provided an unbiased approach toward the identification of proteins encoded by organellar genomes. Such proteins are often missed in transcriptome data sets due to the enrichment of only messenger RNAs that contain poly(A) tails. Overall, the use of integrated omic approaches enhanced the quality of the assembly and annotation of this nonmodel plant genome. The availability of genomic, transcriptomic, and proteomic data will enhance genomics-assisted breeding, germplasm characterization, and conservation of sandalwood trees.

Targeted quantitative profiling of metabolites and gene transcripts associated with 4-aminobutyrate (GABA) in apple fruit stored under multiple abiotic stresses

4-Aminobutyrate accumulates in plants under abiotic stress. Here, targeted quantitative profiling of metabolites and transcripts was conducted to monitor glutamate- and polyamine-derived 4-aminobutyrate production and its subsequent catabolism to succinate or 4-hydroxybutyrate in apple (Malus x domestica Borkh.) fruit stored at 0 °C with 2.5 kPa O₂ and 0.03 or 5 kPa CO₂ for 16 weeks. Low-temperature-induced protein hydrolysis appeared to be responsible for the enhanced availability of amino acids during early storage, and the resulting higher glutamate level stimulated 4-aminobutyrate levels more than polyamines. Elevated CO₂ increased the levels of polyamines, as well as succinate and 4-hydroxybutyrate, during early storage, and 4-aminobutyrate and 4-hydroxybutyrate over the longer term. Expression of all of the genes likely involved in 4-aminobutyrate metabolism from glutamate/polyamines to succinate/4-hydroxybutyrate was induced in a co-ordinated manner. CO₂-regulated expression of apple GLUTAMATE DECARBOXYLASE 2, AMINE OXIDASE 1, ALDEHYDE DEHYDROGENASE 10A8 and POLYAMINE OXIDASE 2 was evident with longer term storage. Evidence suggested that respiratory activities were restricted by the elevated CO₂/O₂ environment, and that decreasing NAD⁺ availability and increasing NADPH and NADPH/NADP⁺, respectively, played key roles in the regulation of succinate and 4-hydroxybutyate accumulation. Together, these findings suggest that both transcriptional and biochemical mechanisms are associated with 4-aminobutyrate and 4-hydroxybutyrate metabolism in apple fruit stored under multiple abiotic stresses.

Proteomic analysis reveals dynamic regulation of fruit development and sugar and acid accumulation in apple

Understanding the fruit developmental process is critical for fruit quality improvement. Here, we report a comprehensive proteomic analysis of apple fruit development over five growth stages, from young fruit to maturity, coupled with metabolomic profiling. A tandem mass tag (TMT)-based comparative proteomics approach led to the identification and quantification of 7098 and 6247 proteins, respectively. This large-scale proteomic dataset presents a global view of the critical pathways involved in fruit development and metabolism. When linked with metabolomics data, these results provide new insights into the modulation of fruit development, the metabolism and storage of sugars and organic acids (mainly malate), and events within the energy-related pathways for respiration and glycolysis. We suggest that the key steps identified here (e.g. those involving the FK2, TST, EDR6, SPS, mtME and mtMDH switches), can be further targeted to confirm their roles in accumulation and balance of fructose, sucrose and malate. Moreover, our findings imply that the primary reason for decreases in amino acid concentrations during fruit development is related to a reduction in substrate flux via glycolysis, which is mainly regulated by fructose-bisphosphate aldolase and bisphosphoglycerate mutase.

Metabolomic-Based Strategy for Fingerprinting of Sambucus nigra L. Berry Volatile Terpenoids and Norisoprenoids: Influence of Ripening and Cultivar

The integration of plant metabolomics to support preharvest fruit development studies can provide important insights into the biochemical mechanisms involved and lately support producers on harvesting management. A metabolomic-based strategy for fingerprinting of volatile terpenoids and norisoprenoids from Sambucus nigra L. berries from three cultivars, through ripening, was established. From 42 monoterpenic, 20 sesquiterpenic, and 14 norisoprenoid compounds, 48 compounds are reported for the first time as S. nigra berries components. Chemometric tools revealed that ripening was the factor that influenced more the volatile fraction profile and physicochemical parameters (pH, TS, and TSS), followed by cultivar. For the unripe stages, a higher overall content of the studied metabolites was observed, which gradually decreased over the ripening stages, being consistent for the three cultivars. These trends were mainly ruled by limonene, p-cymene, aromadendrene, β-caryophyllene, and dihydroedulan, which might therefore be used by producers as an additional simple decision making tool in conjunction with physicochemical parameters.

The Omics Revolution in Agricultural Research

The Agrochemicals Division cosponsored the 13th International Union of Pure and Applied Chemistry International Congress of Pesticide Chemistry held as part of the 248th National Meeting and Exposition of the American Chemical Society in San Francisco, CA, USA, August 10-14, 2014. The topic of the Congress was Crop, Environment, and Public Health Protection; Technologies for a Changing World. Over 1000 delegates participated in the Congress with interactive scientific programming in nine major topic areas including the challenges and opportunities of agricultural biotechnology. Plenary speakers addressed global issues related to the Congress theme prior to the daily technical sessions. The plenary lecture addressing the challenges and opportunities that omic technologies provide agricultural research is presented here. The plenary lecture provided the diverse audience with information on a complex subject to stimulate research ideas and provide a glimpse of the impact of omics on agricultural research.

Proteomics and SSH Analyses of ALA-Promoted Fruit Coloration and Evidence for the Involvement of a MADS-Box Gene, MdMADS1

Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA), a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control) were identified by complementary gel-based and gel-free separation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control) and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related genes. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX, and MdUFGT) in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin-related verification in apple calli suggested that the regulation of MdMADS1 on anthocyanin biosynthesis was partially independent of fruit ripening process. Taken together, our findings provide insight into the mechanism how ALA regulates anthocyanin accumulation and add new information on transcriptase regulators of fruit coloration.

Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics

Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.

Transcriptomic events associated with internal browning of apple during postharvest storage

BACKGROUND

Postharvest ripening of apple (Malus x domestica) can be slowed down by low temperatures, and a combination of low O2 and high CO2 levels. While this maintains the quality of most fruit, occasionally storage disorders such as flesh browning can occur. This study aimed to explore changes in the apple transcriptome associated with a flesh browning disorder related to controlled atmosphere storage using RNA-sequencing techniques. Samples from a browning-susceptible cultivar ('Braeburn') were stored for four months under controlled atmosphere. Based on a visual browning index, the inner and outer cortex of the stored apples was classified as healthy or affected tissue.

RESULTS

Over 600 million short single-end reads were mapped onto the Malus consensus coding sequence set, and differences in the expression profiles between healthy and affected tissues were assessed to identify candidate genes associated with internal browning in a tissue-specific manner. Genes involved in lipid metabolism, secondary metabolism, and cell wall modifications were highly modified in the affected inner cortex, while energy-related and stress-related genes were mostly altered in the outer cortex. The expression levels of several of them were confirmed using qRT-PCR. Additionally, a set of novel browning-specific differentially expressed genes, including pyruvate dehydrogenase and 1-aminocyclopropane-1-carboxylate oxidase, was validated in apples stored for various periods at different controlled atmosphere conditions, giving rise to potential biomarkers associated with high risk of browning development.

CONCLUSIONS

The gene expression data presented in this study will help elucidate the molecular mechanism of browning development in apples at controlled atmosphere storage. A conceptual model, including energy-related (linked to the tricarboxylic acid cycle and the electron transport chain) and lipid-related genes (related to membrane alterations, and fatty acid oxidation), for browning development in apple is proposed, which may be relevant for future studies towards improving the postharvest life of apple.

Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress

Tea [Camellia sinensis (L.) O. Kuntze] is an important economic crop, and drought is the most important abiotic stress affecting yield and quality. Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance. Increased understanding of ABA effects on tea plant under drought stress is essential to develop drought-tolerant tea genotypes, along with crop management practices that can mitigate drought stress. The objective of the present investigation is evaluation of effects of exogenous ABA on the leaf proteome in tea plant exposed to drought stress. Leaf protein patterns of tea plants under simulated drought stress [(polyethylene glycol (PEG)-treated] and exogenous ABA treatment were analyzed in a time-course experiment using two-dimensional electrophoresis (2-DE), followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Among the 72 protein spots identified by MALDI-TOF MS, 16 proteins were downregulated and two were upregulated by exogenous ABA. The upregulated proteins have roles in glycolysis and photosystem II stabilization. Twenty-one protein spots were responsive to drought stress and most participate in carbohydrate and nitrogen metabolism, control of reactive oxygen species (ROS), defense, signaling or nucleic acid metabolism. The combined treatments of exogenous ABA and drought showed upregulation of 10 protein spots at 12 h and upregulation of 11 proteins at 72 h after initiation of drought stress. The results support the importance of the role that ABA plays in the tea plant during drought stress, by improving protein transport, carbon metabolism and expression of resistance proteins.

Dynamic changes in the date palm fruit proteome during development and ripening

Date palm (Phoenix dactylifera) is an economically important fruit tree in the Middle East and North Africa and is characterized by large cultivar diversity, making it a good model for studies on fruit development and other important traits. Here in gel comparative proteomics combined with tandem mass spectrometry were used to study date fruit development and ripening. Total proteins were extracted using a phenol-based protocol. A total of 189 protein spots were differentially regulated (p≤0.05). The identified proteins were classified into 14 functional categories. The categories with the most proteins were 'disease and defense' (16.5%) and 'metabolism' (15.4%). Twenty-nine proteins have not previously been identified in other fleshy fruits and 64 showed contrasting expression patterns in other fruits. Abundance of most proteins with a role in abiotic stress responses increased during ripening with the exception of heat shock proteins. Proteins with a role in anthocyanin biosynthesis, glycolysis, tricarboxylic acid cycle and cell wall degradation were upregulated particularly from the onset of ripening and during ripening. In contrast, expression of pentose phosphate- and photosynthesis-related proteins decreased during fruit maturation. Although date palm is considered a climacteric species, the analysis revealed downregulation of two enzymes involved in ethylene biosynthesis, suggesting an ethylene-independent ripening of 'Barhi' fruits. In summary, this proteomics study provides insights into physiological processes during date fruit development and ripening at the systems level and offers a reference proteome for the study of regulatory mechanisms that can inform molecular and biotechnological approaches to further improvements of horticultural traits including fruit quality and yield.

Understanding development and ripening of fruit crops in an 'omics' era

Next generation sequencing has revolutionized plant biology. Not only has our understanding of plant metabolism advanced using model systems and modern chromatography, but application of 'omics'-based technology has been widely extended to non-model systems as costs have plummeted and efficiency increased. As a result, important fundamental questions relating to important horticultural crops are being answered, and novel approaches with application to industry are in progress. Here we review recent research advances on development and ripening of fruit crops, how next generation sequencing approaches are driving this advance and the emerging future landscape.