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Suberin, a polymer composed of both aliphatic and aromatic domains, is deposited as a rough matrix upon plant surface damage and during normal growth in the root endodermis, bark, specialized organs (e.g., potato [ Solanum tuberosum ] tubers), and seed coats. To identify genes associated with the developmental control of suberin deposition, we investigated the chemical composition and transcriptomes of suberized tomato ( Solanum lycopersicum ) and russet apple ( Malus x domestica ) fruit surfaces. Consequently, a gene expression signature for suberin polymer assembly was revealed that is highly conserved in angiosperms. Seed permeability assays of knockout mutants corresponding to signature genes revealed regulatory proteins (i.e., AtMYB9 and AtMYB107) required for suberin assembly in the Arabidopsis thaliana seed coat. Seeds of myb107 and myb9 Arabidopsis mutants displayed a significant reduction in suberin monomers and altered levels of other seed coat-associated metabolites. They also exhibited increased permeability, and lower germination capacities under osmotic and salt stress. AtMYB9 and AtMYB107 appear to synchronize the transcriptional induction of aliphatic and aromatic monomer biosynthesis and transport and suberin polymerization in the seed outer integument layer. Collectively, our findings establish a regulatory system controlling developmentally deposited suberin, which likely differs from the one of stress-induced polymer assembly recognized to date., (© 2016 American Society of Plant Biologists. All rights reserved.)

MADS-box genes have been shown to play a role in the formation of fruits, both in Arabidopsis and in tomato. In peach, two C-class MADS-box genes have been isolated. Both of them are expressed during flower and mesocarp development. Here a detailed analysis of a gene that belongs to the PLENA subfamily of MADS-box genes is shown. The expression of this PLENA-like gene (PpPLENA) increases during fruit ripening, and its ectopic expression in tomato plants causes the transformation of sepals into carpel-like structures that become fleshy and ripen like real fruits. Interestingly, the transgenic berries constitutively expressing the PpPLENA gene show an accelerated ripening, as judged by the expression of genes that are important for tomato fruit ripening. It is suggested that PpPLENA might interfere with the endogenous activity of TAGL1, thereby activating the fruit ripening pathway earlier compared with wild-type tomato plants.

Peach (Prunus persica L. Batsch) was chosen as a model to shed light on the physiological role of jasmonates (JAs) during fruit ripening. To this aim, the effects of methyl jasmonate (MJ, 0.40 mM) and propyl dihydrojasmonate (PDJ, 0.22 mM), applied in planta at different fruit developmental stages, on the time-course of ethylene production and fruit quality traits were evaluated. MJ-induced changes in fruit transcriptome at harvest and the expression profiling of relevant JA-responsive genes were analysed in control and JA-treated fruit. Exogenously applied JAs affected the onset of ripening depending upon the fruit developmental stage, with PDJ being more active than MJ. Both compounds enhanced the transcription of allene oxide synthase (PpAOS1), the first specific enzyme in the biosynthesis of jasmonic acid, and altered the pattern of jasmonic acid accumulation. Microarray transcriptome profiling showed that MJ down-regulated some ripening-related genes, such as 1-aminocyclopropane-1-carboxylic acid oxidase (PpACO1) and polygalacturonase (PG), and the transcriptional modulator IAA7. MJ also altered the expression of cell wall-related genes, namely pectate lyase (PL) and expansins (EXPs), and up-regulated several stress-related genes, including some of those involved in JA biosynthesis. Time-course expression profiles of PpACO1, PL, PG, PpExp1, and the transcription factor LIM confirmed the array results. Thus, in peach fruit, exogenous JAs led to a ripening delay due to an interference with ripening- and stress/defence-related genes, as reflected in the transcriptome of treated fruit at harvest.

Ethylene has long been regarded as the main regulator of ripening in climacteric fruits. The characterization of a few tomato mutants, unable to produce climacteric ethylene and to ripen their fruits even following treatments with exogenous ethylene, has shown that other factors also play an important role in the control of climacteric fruit ripening. In climacteric peach and tomato fruits it has been shown that, concomitant with ethylene production, increases in the amount of auxin can also be measured. In this work a genomic approach has been used in order to understand if such an auxin increase is functional to an independent role played by the hormone during ripening of the climacteric peach fruits. Besides the already known indirect activity on ripening due to its up-regulation of climacteric ethylene synthesis, it has been possible to show that auxin plays a role of its own during ripening of peaches. In fact, the hormone has shown the ability to regulate the expression of a number of different genes. Moreover, many genes involved in biosynthesis and transport and, in particular, the signalling (receptors, Auxin Response Factors and Aux/IAA) of auxin had increased expression in the mesocarp during ripening, thus strengthening the idea that this hormone is actively involved in the ripening of peaches. This study has also demonstrated the existence of an important cross-talk between auxin and ethylene, with genes in the auxin domain regulated by ethylene and genes in the ethylene domain regulated by auxin.

In peach (Prunus persica L. Batsch.) the degradation of the pectic compounds of the cell wall is considered to be the principal component responsible for fruit softening. Many genes encoding enzymes acting on the different polymers of the pectic matrix have been shown to be highly expressed during the late phases of softening, with polygalacturonase being the most important. Nevertheless, it is known that softening starts well before the ethylene climacteric rise which occurs concomitant with the maximal expression of the pectolytic enzymes. The cloning and characterization of PpEG4, an endo-beta-1,4-glucanase (EGase) gene preferentially expressed in preclimacteric fruits, are presented here. PpEG4 belongs to the group of EGases containing, at their carboxy-terminus, a peptide similar to the cellulose binding domain of microbial origin. This EGase is also expressed during abscission of both leaves and fruits. The effect of exogenous ethylene treatments on PpEG4 transcription is null in young fruits and negative in preclimacteric ones, while it is positive in abscission zones. Thus, the expression of PpEG4 seems to be more dependent on the type of separation process rather than being influenced by a direct hormone action. The ability of the PpEG4 regulatory sequences to drive transcription in cells undergoing separation events is also maintained in tomato, where about 3 kb of the gene promoter could drive the expression of gusA in preclimacteric fruits and in the fruit abscission zones.

Notwithstanding the economic importance of non-climacteric fruits like grape and strawberry, little is known about the mechanisms that regulate their ripening. Up to now no growth regulator has emerged with a primary role similar to that played by ethylene in the ripening of the climacteric fruits. Strawberries can produce ethylene, although in limited amounts. Two cDNAs coding for enzymes of the ethylene biosynthetic pathway (i.e. FaACO1 and FaACO2), and three cDNAs encoding different ethylene receptors have been isolated. Two receptors (i.e. FaEtr1 and FaErs1) belong to the type-I while the third (i.e. FaEtr2) belongs to the type-II group. The expression of both the ACO and the receptor-encoding genes has been studied in fruits at different stages of development and in fruits treated with hormones (i.e. ethylene and the auxin analogue NAA). All the data thus obtained have been correlated to the known data about ethylene production by strawberry fruits. Interestingly, a good correlation has resulted between the expression of the genes described in this work and the data of ethylene production. In particular, similarly to what occurs during climacteric fruit ripening, there is an increased synthesis of receptors concomitant with the increased synthesis of ethylene in strawberries as well. Moreover, the receptors mostly expressed in ripening strawberries are the type-II ones, that is those with a degenerate histidine-kinase domain. Since the latter domain is thought to establish a weaker link to the CTR1 proteins, even the little ethylene produced by ripening strawberries might be sufficient to trigger ripening-related physiological responses.

During ripening, fleshy fruits undergo textural changes that lead to loss of tissue firmness and consequent softening. It is a common idea that this process is the consequence of cell wall dismantling carried out by different and orderly expressed enzymes. For this purpose, by using a single enzyme family approach many enzymes and related genes have been characterized in different fruits. In this work, the softening of the climacteric peach fruits (Prunus persica (L.) Batsch.) has been studied by using a genomic approach, and the results obtained are novel and partly unexpected. The genes analysed encode proteins involved in the main metabolic aspects of a primary cell wall: degradation, synthesis, structure. In addition, some genes encoding cell-wall-related proteins with an unknown function have been studied. The gene expression profiles show that the softening actually begins well before the climacteric rise and continues thereafter. Genes whose expression starts before the climacteric rise are mostly down-regulated by ethylene, while genes with a ripening-specific expression are mostly up-regulated by the hormone. A few other genes are apparently insensitive to ethylene. Besides the expected parietal degradation, the softening that results from this study also comprises some repairing of the cell wall performed by enzymes involved in the synthesis of parietal polysaccharides and, especially, by proteins with structural functions. The newly synthesized polysaccharides and the structural proteins would thus help to hold together the fruit cell wall while not preventing the softening.

Two endo-beta-1,4-glucanase (EGase; EC 3.2.1.4.) genes, highly expressed during ripening of the non-climacteric strawberries (Fragariaxananassa Duch. cv. Chandler), were isolated. Serial promoter deletions of both genes (i.e. FaEG1 and FaEG3) fused to GUS were transiently assayed in strawberry fruits by using a technique recently developed in this laboratory. Although differences were observed with the short fragments, GUS activity became comparable with the largest fragments of both promoters. The apparently similar strength of the two largest promoter fragments was in contrast with previous results of Northern analyses which demonstrated different transcripts amounts for the two genes. The inclusion of the 3' flanking region of both genes in the transient assays showed that, in the case of FaEG3, the 3' region had a down-regulating effect on the expression of GUS, and this might account for the lower amount of FaEG3 mRNA usually observed in ripe fruits compared to that of FaEG1. Downstream instability elements might be involved in such down-regulation.

Strawberry fruits (Fragaria x ananassa Duch.) undergo a marked softening during their ripening, and the process is accompanied by a release of free sugars with galactose among them. In this work total beta-galactosidase activity was measured in cell wall proteins from strawberry fruits at different developmental stages. Three full-length cDNAs (Fa beta gal1, Fa beta gal2 and Fa beta gal3, respectively) encoding different beta-galactosidases (EC 3.2.1.23) were isolated from a library representing red fruit transcripts. All of them could be detected both in fruits and in vegetative tissues. However, only Fa beta gal1 showed an increasing expression during the ripening stages up to a maximum in the red fruits, while the other two (Fa beta gal2 and Fa beta gal3) were mostly found in green fruits and became barely detectable during ripening proper. The three beta-galactosidase-encoding cDNAs were expressed in the yeast Pichia pastoris, and it was thus possible to demonstrate that each of them encode a beta-galactosidase. The expression of the three beta-galactosidase genes appears to be down-regulated by auxin, as already observed for other ripening-related genes of the non-climacteric strawberry. An unusual characteristic of two strawberry beta-galactosidases (Fa beta gal1 and Fa beta gal2) is that at the C-terminus of the enzymes a domain is found which is structurally related to known animal peptides with a sugar-binding ability.

Fleshy fruits represent a very important economic resource and, therefore, they are an ideal target for biotechnological ameliorations. However, because of their physiological and anatomical characteristics, ripe fleshy fruits represent an extremely difficult material for transient gene expression assays aimed at the study of gene promoters in a short time. To this purpose, a fast and efficient Agrobacterium-mediated transient gene expression system was developed for ripe fleshy fruits. A beta-glucuronidase reporter gene interrupted by an intron was used in order to prevent the possible expression of GUS activity by the Agrobacterium cells. The contemporary use of another reporter gene was used to check the transformation efficiency. This method is based on the injection of an Agrobacterium suspension into the fruits, and allows both qualitative and quantitative assays in a wide range of fruits to be carried out.