Identification of mRNAs with enhanced expression in ripening strawberry fruit using polymerase chain reaction differential display

Fruit ripening is a complex developmental process that involves specific changes in gene expression and cellular metabolism. In climateric fruits these events are coordinated by the gaseous hormone ethylene, which is synthesized autocatalytically in the early stages of ripening. Nonclimacteric fruits do not synthesize or respond to ethylene in this manner, yet undergo many of the same physiological and biochemical changes associated with the production of a ripe fruit. To gain insight into the molecular determinants associated with nonclimacteric fruit ripening, we examined mRNA populations in ripening strawberry fruit using polymerase chain reaction (PCR) differential display. Five mRNAs with ripening-enhanced expression were identified using this approach. Three of the mRNAs appear to be fruit-specific, with little or no expression detected in vegetative tissues. Sequence analysis of cDNA clones revealed positive identities for three of the five mRNAs based on homology to known proteins. These results indicate that the differential display technique can be a useful tool to study fruit ripening and other developmental processes in plants at the RNA level.     

Molecular and genetic regulation of fruit ripening

Fleshy fruit undergo a novel developmental program that ends in the irreversible process of ripening and eventual tissue senescence. During this maturation process, fruit undergo numerous physiological, biochemical and structural alterations, making them more attractive to seed dispersal organisms. In addition, advanced or over-ripening and senescence, especially through tissue softening and eventual decay, render fruit susceptible to invasion by opportunistic pathogens. While ripening and senescence are often used interchangeably, the specific metabolic activities of each would suggest that ripening is a distinct process of fleshy fruits that precedes and may predispose the fruit to subsequent senescence.     

Metabolic profiling of strawberry (Fragaria x ananassa Duch.) during fruit development and maturation

Strawberry (Fragaria × ananassa Duch), a fruit of economic and nutritional importance, is also a model species for fleshy fruits and genomics in Rosaceae. Strawberry fruit quality at different harvest stages is a function of the fruit's metabolite content, which results from physiological changes during fruit growth and ripening. In order to investigate strawberry fruit development, untargeted (GC-MS) and targeted (HPLC) metabolic profiling analyses were conducted. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were employed to explore the non-polar and polar metabolite profiles from fruit samples at seven developmental stages. Different cluster patterns and a broad range of metabolites that exerted influence on cluster formation of metabolite profiles were observed. Significant changes in metabolite levels were found in both fruits turning red and fruits over-ripening in comparison with red-ripening fruits. The levels of free amino acids decreased gradually before the red-ripening stage, but increased significantly in the over-ripening stage. Metabolite correlation and network analysis revealed the interdependencies of individual metabolites and metabolic pathways. Activities of several metabolic pathways, including ester biosynthesis, the tricarboxylic acid cycle, the shikimate pathway, and amino acid metabolism, shifted during fruit growth and ripening. These results not only confirmed published metabolic data but also revealed new insights into strawberry fruit composition and metabolite changes, thus demonstrating the value of metabolomics as a functional genomics tool in characterizing the mechanism of fruit quality formation, a key developmental stage in most economically important fruit crops.     

Banana harvest maturity and fruit position on the quality of ripe fruit

There is an increasing market demand for smaller banana fruit. The way that this is being addressed involves harvesting some fruits on a bunch at a less advanced stage of maturity. Experiments were carried out to investigate the effect of age of fruit at harvest, position of the fruit on the bunch and different banana varieties on the speed of ripening and the quality of the ripe fruit at two different ripening temperatures after being exposed to exogenous ethylene. The maturity of bananas at harvest affected both the speed of ripening and the quality of the ripe fruit. Speed of ripening of fruit at 13°C was slower the more immature the fruit at harvest, but there was no effect on the speed of ripening of harvest maturity at a ripening temperature of 16°C. The effects of harvest maturity and position of the fruit on the bunch on peel colour and texture were significant but so small that they would be unlikely to affect the consumers' perception in a commercial situation. The higher soluble solids, flavour, sweetness and acceptability after ripening of the more mature fruit at harvest was sufficiently high that consumers could probably detect them.     

Developmental regulation of phospholipase D in tomato fruits

The catabolism of phospholipids initiated by phospholipase D (PLD, EC 3.1.4.4) is an inherent feature of developmental processes that include fruit growth and ripening. In cherry tomatoes (Lycopersicon esculentum Mill.), soluble and membrane-associated PLD activities increased during fruit development, which peaked at the mature green and orange stages. The increase in PLD activity was associated with a similar increase in the intensity of a 92 kDa band as demonstrated by western blot analysis. A full-length cDNA having 2430 bp and encoding a putative polypeptide with 809 amino acids, was isolated using tomato RNA, RT-PCR and 5' and 3' rapid amplification of cloned ends (RACE). Analysis of the primary and secondary structures showed the presence of the C2 domain, the PLD domain and several other features characteristic of PLD alpha. Microtom tomato plants transformed with antisense PLD alpha cDNA, were similar to untransformed plants and showed normal fruit set and development. The ethylene climacteric was delayed by over 7 d in the antisense PLD fruits, indicative of a slower ripening process. The leaves and unripened fruits of antisense PLD microtom plants possessed lowered PLD activity and PLD protein, as demonstrated by western blotting. However, during ripening, PLD activity in the transgenic fruits was maintained at a higher level than that in the untransformed control. Immunolocalization of PLD in microtom tomato fruits revealed the cytosol-membrane translocation of PLD during fruit development. The ripe fruits of antisense PLD celebrity plants possessed lowered PLD expression and activity and showed increased firmness and red colour. These results suggest that the expression of antisense PLD cDNA could be variable in different tomato varieties. The potential role of PLD in ethylene signal transduction events is discussed.     

Changes in structural features of free N-glycan and endoglycosidase activity during tomato fruit ripening

In developing plants, free N-glycans occur ubiquitously at micromolar concentrations. Such oligosaccharides have been proposed to be signaling molecules in plant development. As a part of a study to elucidate the physiological roles of de-N-glycosylation machinery involved in fruit ripening, we analyzed changes in the amounts and structural features of free N-glycans in tomato fruits at four ripening stages. The amount of high-mannose type free N-glycans increased significantly in accordance with fruit ripening, and the relative amounts of high-molecular size N-glycans, such as Man(8-9)GlcNAc(1), became predominant. These observations suggest that the de-N-glycosylation machinery, including endo-beta-N-acetylglucosaminidase (ENGase) activity, is stimulated in the later stages of fruit ripening. But contrary to expectation, we found that total ENGase activities in the tomato fruits did not vary significantly with the ripening process, suggesting that ENGase activity must be maintained at a certain level, and that the expression of alpha-mannosidase involved in the clearance of free N-glycans decreases during tomato fruit ripening.     

Effect of seed on ripening control components during avocado fruit development

Seedless avocado fruit are produced alongside seeded fruit in the cultivar Arad, and both reach maturity at the same time. Using this system, it was possible to show that avocado seed inhibits the ripening process: seedless fruits exhibited higher response to exogenous ethylene already at the fruitlet stage, and also at the immature and mature fruit stages. They produced higher CO₂ levels, and the ethylene peak was apparent at the fruitlet stage of seedless fruit, but not of seeded ones. The expression levels of PaETR, PaERS1 and PaCTR1 on the day of harvest at all developmental stages were very similar between seeded and seedless fruit, except that PaCTR1 was higher in seedless fruit only at very early stages. This expression pattern suggests that the seed does not have an effect on components of the ethylene response pathway when fruits are just picked. The expression of MADS-box genes, PaAG1 and PaAGL9, preceded the increase in ethylene production of mature seeded fruit, but not at earlier stages. However, only PaAGL9 was induced in seedless fruit at early stages of development. Taken together, these data suggest that these genes are perhaps involved in climacteric response in seeded fruit, and the seed is responsible for their induction at normal fruit ripening.     

Phenological variation in fruit characteristics in vertebrate-dispersed plants

Summary We investigated inter-specific variation in fruit characteristics — fruit size, seed number per fruit, seed weight, nutritional content, fruit persistence, and fruit synchronization — in relation to flowering and fruiting phenology in 34 species of fleshy fruited plants. Except for aspects of fruit synchrony and persistence, the results in general were inconsistent with previous suggestions about adaptive variation in phenologically related fruit traits. The main results were as follows: (1) Late flowering, late fruiting, lengthy development time from flower to fruit, and highly persistent fruits constitute a complex of correlated characteristics among the species. (2) Synchronization of fruiting within individuals increased from early ripening fruits to late ripening fruits. Fruiting synchrony was more pronounced in species with a small crop size than in species with a large fruit crop, whereas synchrony was not significantly related to flowering synchronization, nor to life form. (3) Nitrogen and carbohydrate content of fruit pulp did not vary in relation to phenology, whereas lipid content decreased from early to late ripening fruits. (4) No seasonal trends were found for variation in seed size or seed number per fruit. (5) Interactions with flowering phenology and developmental constraints are important in phenological fruiting patterns. Temporal variation in start of fruiting was partly (36%) explained by variation in flowering time. Seed weight variation explained 17% of variation in development time from flower to fruit. (6) Despite constraints from flowering and seed development, some adaptive adjustment in fruiting phenology is likely to be allowed for among the investigated species. Such an adaptive variation in fruiting phenology was suggested by intra-generic comparisons of Prunus and Vaccinium species.     

Activity and expression of polygalacturonase vary at different fruit ripening stages of sweet pepper cultivars

Activity and expression of polygalacturonase (PG), a hydrolytic enzyme involved in ultrastructural changes in the pericarp of sweet pepper (Capsicum annaum), were investigated at different ripening stages of the pepper cultivars Mandi and Talanduo. Molecular cloning of CaPG was carried out by constructing a cDNA library from three stages of fruit ripening. Morphological determination, PG assay, RT-PCR, and ultrastructural studies were used to quantify changes in CaPG gene expression in the pericarp from green, color change and fully ripened stages. We found that CaPG gene expression, PG activity and striking changes in the structure of the cell wall occurred with the transition of ripening stages. CaPG gene expression was high (obvious PCR products) in mature and ripened stages of both cultivars; however, the CaPG gene was not expressed in preclimacteric fruits or vegetative tissues. We conclude that developmental regulation of CaPG gene expression is instrumental for sweet pepper fruit ripening; its expression during development leads to dissolution of middle lamella and eventually disruption of the fully ripened cell wall.     

Extensive transcriptomic studies on the roles played by abscisic acid and auxins in the development and ripening of strawberry fruits

Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. Hormonal regulation of gene expression along all these processes in strawberries is still to be fully elucidated. Although auxins and ABA have been pointed out as the major regulatory hormones, few high-throughput analyses have been carried out to date. The role for ethylene and gibberellins as regulatory hormones during the development and ripening of the strawberry fruit remain still elusive. By using a custom-made and high-quality oligo microarray platform done with over 32,000 probes including all of the genes actually described in the strawberry genome, we have analysed the expression of genes during the development and ripening in the receptacles of these fruits. We classify these genes into two major groups depending upon their temporal and developmental expression. First group are genes induced during the initial development stages. The second group encompasses genes induced during the final maturation and ripening processes. Each of these two groups has been also divided into four sub-groups according their pattern of hormonal regulation. By analyzing gene expression, we clearly show that auxins and ABA are the main and key hormones that combined or independently are responsible of the development and ripening process. Auxins are responsible for the receptacle fruit development and, at the same time¸ prevent ripening by repressing crucial genes. ABA regulates the expression of the vast majority of genes involved in the ripening. The main genes expressed under the control of these hormones are presented and their physiological rule discussed. We also conclude that ethylene and gibberellins do not seem to play a prominent role during these processes.     

Mitochondrial enzymes in mango fruit during ripening

Mitochondria isolated from immature (developing), mature (unripe), and ripe mango pulp actively oxidized the intermediates of the Krebs cycle. The oxidation of citrate, oxoglutarate, succinate and malate by both unripe and ripe fruit mitochondria was several fold greater than that by mitochondria from immature fruit. The levels of malic dehydrogenase and succinic dehydrogenase increased with the onset of ripening, whereas the level of citrate synthase increased several fold on maturation but decreased six-fold on ripening. Isocitrate dehydrogenase and malic enzyme were very high in the immature fruit but after a sudden decrease in the matured fruit showed a considerable rise thereafter. The ratio of the activities of isocitrate lyase to isocitrate dehydrogenase is considerably higher in the immature fruit and greatest in the unripe (mature) fruit. This, together with a higher concentration of glyoxylate at these stages, indicate the operation of the glyoxylate bypass. Oxidized and reduced forms of pyridine nucleotides were estimated.     

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

Plants feature a particularly diverse population of short (s)RNAs, the central component of all RNA silencing pathways. Next generation sequencing techniques enable deeper insights into this complex and highly conserved mechanism and allow identification and quantification of sRNAs. We employed deep sequencing to monitor the sRNAome of developing tomato fruits covering the period between closed flowers and ripened fruits by profiling sRNAs at 10 time-points. It is known that microRNAs (miRNAs) play an important role in development but very little information is available about the majority of sRNAs that are not miRNAs. Here we show distinctive patterns of sRNA expression that often coincide with stages of the developmental process such as flowering, early and late fruit maturation. Moreover, thousands of non-miRNA sRNAs are differentially expressed during fruit development and ripening. Some of these differentially expressed sRNAs derived from transposons but many derive from protein coding genes or regions that show homology to protein coding genes, several of which are known to play a role in flower and fruit development. These findings raise the possibility of a regulative role of these sRNAs during fruit onset and maturation in a crop species. We also identified six new miRNAs and experimentally validated two target mRNAs. These two mRNAs are targeted by the same miRNA but do not belong to the same gene family, which is rare for plant miRNAs. Expression pattern and putative function of these targets indicate a possible role in glutamate accumulation, which contributes to establishing the taste of the fruit.     

Translocation and the alternative D-galacturonate pathway contribute to increasing the ascorbate level in ripening tomato fruits together with the D-mannose/L-galactose pathway

The D-mannose/L-galactose pathway for the biosynthesis of vitamin C (L-ascorbic acid; AsA) has greatly improved the understanding of this indispensable compound in plants, where it plays multifunctional roles. However, it is yet to be proven whether the same pathway holds for all the different organs of plants, especially the fruit-bearing plants, at different stages of development. Micro-Tom was used here to elucidate the mechanisms of AsA accumulation and regulation in tomato fruits. The mRNA expression of the genes in the D-mannose/L-galactose pathway were inversely correlated with increasing AsA content of Micro-Tom fruits during ripening. Feeding L-[6-(14)C]AsA to Micro-Tom plants revealed that the bulk of the label from AsA accumulated in the source leaf was transported to the immature green fruits, and the rate of translocation decreased as ripening progressed. L-Galactose feeding, but neither D-galacturonate nor L-gulono-1,4-lactone, enhanced the content of AsA in immature green fruit. On the other hand, L-galactose and D-galacturonate, but not L-gulono-1,4-lactone, resulted in an increase in the AsA content of red ripened fruits. Crude extract prepared from insoluble fractions of green and red fruits showed D-galacturonate reductase- and aldonolactonase-specific activities, the antepenultimate and penultimate enzymes, respectively, in the D-galacturonate pathway, in both fruits. Taken together, the present findings demonstrated that tomato fruits could switch between different sources for AsA supply depending on their ripening stages. The translocation from source leaves and biosynthesis via the D-mannose/L-galactose pathway are dominant sources in immature fruits, while the alternative D-galacturonate pathway contributes to AsA accumulation in ripened Micro-Tom fruits.