BACKGROUND
fruit softening is a complex process during which a large number of proteins interact in order to achieve the physiological condition that allows fruit to accomplish its final objective, seed dispersion  <cit> .
peaches  from fresh eating melting flesh varieties are characterized as having a short shelf life due to the rapid loss of firmness at the end of the ripening process, the softening of the fruit mesocarp.
changes in the cell wall are particularly important for this phenomenon, especially the dismantling of its structure, the degradation of the polymers of which it is composed and the loss of turgor pressure in the fruit  <cit> .
after softening, fruit is susceptible to physical injury and pathogen attack and can only be stored for a few days  <cit> .
cold storage has been used to increase the postharvest life of peach fruit; however, this procedure leads to undesirable changes in fruit quality.
these symptoms are known as chilling injury and include mealiness or lack of juice, as well as browning, among others  <cit> .
mealiness has been associated with abnormal cell wall dismantling during cold storage and the subsequent ripening.
however, the mechanisms that disrupt the normal fruit cell wall metabolism during this low temperature disorder are not yet clear  <cit> .
the browning phenotype has been linked to interaction between phenols and polyphenol oxidase.
these elements are usually found in different compartments within the cell, but the membrane permeability of deteriorated tissues may cause them to come into contact with one another  <cit> .
other important metabolic processes may be altered in cold injured fruit.
for example, there is evidence that abnormal oxidative metabolism is triggered at low storage temperatures  <cit> .
despite these findings, little is known about the softening process and the molecular events that lead to the physiological disorder observed in cold stored fruit.
in order to increase our understanding of this physiological process, we engaged in a global analysis using a proteomic approach that should provide us with a more accurate representation of the cellular/physiological state of the fruit rather than profiling the expression of mrnas  <cit> .
our aim was to identify proteins that could be differentially accumulated in soften and/or cold injured peaches.
to this end, we utilized two-dimensional gel electrophoresis , a widely used technology that allows for the evaluation of many proteins.
several steps of the process have been optimized during recent years, giving this technique an excellent resolving power  <cit> .
furthermore, the introduction of 2-d difference gel electrophoresis  by Ünlü et al.
<cit> , allows the comparison of different protein samples within the same gel, strengthening the confidence of the 2-d quantitative analysis.
thus, a 2-d dige approach was designed to inspect for proteins that could be differentially accumulated in peach fruit during softening and under conditions that led to chilling injury altered fruit.
RESULTS
physiological response of peach fruit to different postharvest storage conditions
the peaches utilized in this work correspond to those analyzed by campos-vargas et al  <cit> .
in that study four postharvest stages were selected and each group named as: e <dig>  firm fruit taken from packing; e <dig>  fruit soften at 20°c; e <dig>  fruit stored in a cold room at 4°c for three weeks; and e <dig>  fruit stored at cold room and then kept at 20°c to allow for softening .
some of the physiological parameters measured by campos-vargas et al.
<cit>  are summarized in table  <dig>  which also describes the degree of browning of the fruit at each stage.
the results showed that fruit became nearly ten times less firm under normal softening conditions, dropping from  <dig>  n in e <dig> to  <dig>  n in e <dig>  this change is characteristic of peach melting varieties.
fruit stored at 4°c for three weeks  showed a significant decrease in firmness, reaching a value of  <dig>  n. fruit from the e <dig> stage reached a firmness value of  <dig>  n, which is similar to normally softened fruit .
the fruit from the e <dig> stage showed symptoms of chilling injury such as lack of juice  and browning .
peaches that were softened after being stored in the cold  produced more ethylene than fruit softened normally.
as expected, respiration also increased from e <dig> to e <dig>  interestingly, fruit kept in the cold  exhibited a high respiration rate that did not change when the fruit was allowed to soften .
tss - total soluble solids
a,b,c values  followed by different small letters are significantly different within the same column at p =  <dig>
1: no sample available for measurements
<dig> : juice can not be measured in these samples due to the high firmnes they present
3: please refer to additional file  <dig> for further details; + no browning; ++ no browning degree with a color change of the mesocarp; +++ medium browning degree; ++++ high browning degree
the data used in this table have been acquired from campos-vargas et al.
sci hortic-amsterdam  <dig>  110:79-83
2-d map of peach mesocarp fruit developed using dige technology
2-d difference gel electrophoresis  analysis was performed in order to identify changes in the amount of proteins present under different postharvest conditions.
figure  <dig> presents a representative image from cy5/cy <dig> overlapped gels of the four postharvest conditions under evaluation.
a reproducible protein pattern is observed throughout the evaluated stages, and some changes in content can be visually detected.
on average, the gels exhibited  <dig> spots, from which  <dig> well-focused spots were chosen for further analysis because they were present in all of the cy <dig> reference gels.
about 85% of these proteins presented a pi ranging from  <dig>  to  <dig>  and were between  <dig> to  <dig> kda in size .
some of the spots that were highly abundant or had a clear differential protein accumulation were identified by means of lc-ms/ms mass spectrometry .
the results of this analysis showed coverage of over 15% for most proteins.
a complete list of the protein sequences with peptides delivered by mass spectra is presented in the additional file  <dig>
a: spot numbers as assigned in figure  <dig>
b: protein assignment based on lc-ms/ms identification.
c: gene bank accession number.
d: probability that the match is random.
only proteins with scores greater than the minimum value for ms-based identification confidence are reported.
additional data about ms are reported in the additional file  <dig>
the values in the columns  <dig> to  <dig> indicate if the protein accumulation pattern changes between the conditions shown above them.
positive values indicate a higher abundance in the first condition whereas negative values indicate the opposite situation.
the theoretical isoelectric points  and molecular weight  of the proteins were calculated and compared to the experimental data.
most of the spots identified showed a good relationship to their theoretical mw .
only the dehydrin and the glyceraldehyde-3-phosphate dehydrogenase  showed some discrepancies; however, the experimental pi and molecular weight values for the dehydrin match quite well to those described by wisniewski et al.
<cit> .
posttranslational modification, abnormal electrophoretic mobility or a smaller molecular weight for the prunus persica gapdh may explain the differences detected in that regard.
some of the spots identified had matching protein ids but different isoelectrical points and/or molecular weights .
in terms of their accumulation pattern, some displayed the same profile and others showed differences in their isoform.
as table  <dig> demonstrates, these spots include the following proteins: low molecular weight heat shock proteins, annexin, 1-aminocyclopropane-1-carboxylate oxidase, catalase, dehydrin, pyruvate dehydrogenase, actin and nadp-dependent malic enzyme.
overall,  <dig> distinct peach fruit mesocarp proteins were identified in this study.
multivariate analysis of the data through hierarchical clustering and pca
in order to detect real changes in protein accumulation among the four postharvest conditions evaluated, the experimental data from 2-d gels were screened before being used for statistical analysis .
a one-way analysis of variance  followed by a false discovery rate correction  allowed us to determinate that  <dig> -about 18% of the spots analyzed- showed statistically significant changes.
thirty-nine of these proteins could be detected and excised from the gels and then identified by mass spectrometry.
some of the identified proteins that changed during postharvest such as endopolygalacturonase  and the 1-aminocyclopropane-1-carboxylate  had been linked to the peach fruit ripening process  <cit> .
some, like dehydrin-like and thaumatin-like protein, had been detected in cold stressed plant tissues  <cit>  .
a graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis, a technique that cluster together proteins with similar patterns of expression among different postharvest treatments  <cit> .
four general trends in the data could be visualized by this method, as displayed in figure  <dig>  the first group  is represented by sixteen proteins that showed a pronounced increase during the normal softening process  compared to the absence of a noticeable increase in protein accumulation during the softening of cold stored fruit .
this behaviour is exemplified by a group of proteins that cluster with a thioredoxin h, a protein that has an important role in the cellular redox regulation  <cit> .
group ii showed twelve proteins that under the normal postharvest storage presented a decrease in their content between e <dig> and e <dig>  an example of this is observed in the case of a catalase , which showed its higher levels during e <dig> compared to e <dig> and e <dig>  to decline even further in e <dig>  group iii is represented by four proteins that have a pronounced accumulation only in the abnormal ripening that follows the low temperature storage , like an anthocyanidin synthase and other proteins that cluster along with it.
group iv is composed by seven proteins that did not present any change between e <dig> and e <dig> fruit, whereas their level increased in e <dig>  remaining constant in e <dig>  one of those proteins is a dehydrin, which exhibit a clear high level in chilling stressed fruit  compared to healthy fruit .
some proteins did not fit in these four general clusters.
for instance, two pyruvate decarboxylases  were up-regulated in the softening process that leads to the development of chill injured fruit  more than in the normal ripening process .
the protein pectin metilesterase  also had a particular accumulation pattern, since it was up-regulated in the normal ripening process, whereas in the transition from e <dig> to e <dig> this increment was even higher.
no other protein showed a similar trend.
the endopg protein  was also located in a different group, due to the degree of differences among its accumulation levels in the four postharvest conditions.
a principal component analysis  evaluation was performed in order to identify the most relevant features of the data set retrieved from the 2d-dige gels  <cit> .
the pca identifies new variables, called principal components, which are linear combinations of the original variables.
these new features can describe a large amount of data in a lower dimensional space, which makes the pca a useful tool for data categorization.
the analysis of the weight loadings associated with each spot indicates which proteins have the greatest impact on the trends observed in the score plots .
the first component was able to separate mature samples  from ripe ones .
endopolygalacturonase , a thaumatin-like protein  and a small heat shock protein  were among the proteins that had the higher impact in the ripe fruit classification.
a catalase  and an annexin  were important for the trend observed for the mature fruit .
the second component was able to differentiate chilling injured fruit samples  from the ripe healthy fruit samples .
again, the endopg  and the shsp  had a high impact on the ripe healthy fruit trend, along with a nadp-dependent isocitrate dehydrogenase .
the proteins anthocyanidin synthase , thaumatin-like protein , alpha- <dig> -glucan-protein synthase  and phosphoserine aminotransferase  were very relevant in differentiating chilling injured fruit from healthy fruit, which supports the results obtained by the hierarchical clustering.
the third component differentiated between the fruit sample that was stored at low temperature  and the mature fruit sample  .
a pectin methylesterase  and a dehydrin-like protein  played an important role in differentiating between the chilling injured fruit, while a major allergen protein pru p i  displayed the opposite behavior.
interestingly, some proteins that were classified as not statistically differentially accumulated had a high impact on the pca trends .
this difference may be due to a false negative type ii error.
finally, the three principal components represent nearly 56% of the original variance, with values of  <dig> %,  <dig> % and  <dig> %, respectively, for the pc <dig>  pc <dig> and pc <dig> components.
characterization of the differentially accumulated proteins
in order to generate an overview of the most relevant biological processes involved in fruit softening and its response to the low temperature storage, a categorization of differentially accumulated proteins was performed based on the gene ontology  annotation.
this standardized categorization system provides a less subjective and more reproducible assignment of the biological processes underlying the chilling injury development  <cit> .
figure  <dig> displays the results obtained from the quickgo tool.
as expected, almost 25% of the proteins differentially expressed were associated with the biological processes 'response to stress' and 'cellular homeostasis'.
the relevant impact detected in processes related to the metabolism of carbohydrates and amino acid metabolism  is also noteworthy.
discussion
peaches are climacteric fruit that display a decrease in mesocarp texture firmness.
melting varieties present a marked softening of this region.
this process is less pronounced in non-melting varieties  <cit> .
in prunus persica, it forms part of the final stages of a broader phenomenon, the fruit ripening  <cit> .
of the physiological changes that the fruit displays during its ripening, the accumulation of soluble solids and changes in colour and aroma are very relevant for consumer acceptability.
these attributes are severely affected in fruit that has been exposed to low temperatures for a prolonged amount of time  <cit> .
this study identified several proteins that may be related to changes in fruit metabolism during cold storage and the subsequent ripening that leads to the development of chilling injury.
these proteins are mainly linked to processes such as response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism .
our discussion will be guided by those general categories.
cellular component organization - cell wall metabolism
the drastic changes in the texture of the fruit mesocarp in the melting varieties have been associated with a massive solubilization and depolymerization of pectin-derived polyuronides.
these changes correlated with the concerted action of two proteins, endopolygalacturonases  and pectin methylesterases   <cit> .
the main pme function is demethylation of the polyuronides so that they can be degraded by the endopg.
therefore, these proteins play an important role in dismantling the cell wall.
both the endopg and the pme are encoded by multi-gene families.
recently, murayama et al.
identified one member of each that is up-regulated above the other members during peach fruit softening, namely pppg <dig> and pppme <dig>  pppg <dig> is the endopg detected in our 2-d peach fruit gels and pppme <dig> resembles the one we identified .
additionally, they increase as we go from mature  to ripe fruit  .
several groups have reported changes in the degree of methylesterification and size of the homogalacturonans, which are localized to the middle lamella of the wall .
the pme levels that we detected were consistently remarkably higher at the end of cold storage  than they were during normal fruit softening, whereas the levels of pppg <dig> decreased to a minimum  <cit> .
high pme activity during the cold storage could partially de-methylesterify homogalacturonans, which would maintain a high molecular weight due to the lack of endopg, protein that remains low in ripe chilling injured fruit .
it has been suggested that these large polymers are involved in the lack of juiciness characteristic of the mealy fruit  <cit> .
it also has been reported that the arabinose  content of cell wall polysaccharides is different in chilling injured peaches  <cit> .
arabinose is mainly found in the cell wall ara-containing polymers in the furanose ring configuration, though the substrate for this transfer  has not been found in plants  <cit> .
our results showed that accumulation of an α- <dig> -glucan-protein synthase , increased exclusively in chilling injured fruit .
this protein is highly homologous to a rice udp-arabinopyranose mutase , an enzyme that catalyzes the formation of udp-l-arabinofuranose from udp-l-arabinopyranose  <cit> .
this increase suggests that this protein and the arabinans are linked to the development of chilling injury in prunus persica.
the results from the pca  support the relevance of pppg <dig>  pme and uam in the development of the chilling injury.
response to stress and cellular homeostasis
fruit senescence can be considered as an oxidative phenomenon  <cit>  that requires the presence of ros  in order to achieve a degradation state that will allow the seed release to occur.
several enzymes involved in ros metabolism are expressed in early stages of fruit development and ripening and gradually are turned off as the fruit approaches senescence, making it more susceptible to be damaged by these molecules  <cit> .
as shown in figure  <dig>  most of the proteins that are up-regulated in the mature fruit are related to ros metabolism and show a decrease in their accumulation from mature to ripe fruit.
after low temperature storage, their levels decrease in cold stored fruit .
as a result, the fruits' capacity to withstand cold induced stress is perturbed.
one of the most important enzymes involved in the control of ros generation, particularly hydrogen peroxide, is catalase .
at least two catalases have been identified in p. persica  <cit> .
until now, the only isoform detected in the 2-d gels is catalase  <dig>   <cit> , which appears in two spots with the same pi an different mw.
our results show that both spots are more abundant in firm fruit and decreased significantly in healthy soft fruit.
a similar expression trend was found in apricot  <cit>  and in tomato and saskatoon   <cit> .
peach fruit stored at 4°c for three weeks showed reduced catalase accumulation .
this result is supported by wang et al.
<cit> , who measured significantly lower cat activity in peach fruit  stored at 0°c for  <dig> days as compared to controls.
this negative effect on cat accumulation could be harmful to the cold stored fruit due to the higher levels of h2o <dig> that could be present in their cells.
the hydrogen peroxide would not only affect the redox status of the cell, but could influence signal transduction cascades, since this molecule has been postulated as a second messenger for signals generated by means of ros  <cit> .
the content of the iron binding protein ferritin  changed in a manner that is similar to the catalase accumulation pattern.
interestingly, its biological function is also linked to the ros metabolism, though its mechanism of action is somehow different.
ferritin can control the free iron concentration inside the cell and thus reduce its availability for the production of hydrogen peroxide derived hydroxyl radical  <cit> .
moreover, this protein has been shown to play a crucial role in the interaction between the iron homeostasis and oxidative stress in arabidopsis, where its absence increased ros levels as well as the activity of enzymes involved in their detoxification  <cit> .
on the other hand, peach fruit that went soft without being exposed to cold storage accumulated small heat shock proteins.
this seems to be a common ripening regulatory mechanism in fruit  <cit>  as these proteins serve as protein chaperones and membrane stabilizers  <cit> .
a low molecular weight heat shock protein  was identified in four spots with different molecular weight and pi.
this protein shows an identity of 76% with carrot  hsp, whereas a small heat shock protein  was found in two spots and shows an identity of 82% with a  <dig>  kda hsp protein from quercus suber.
both proteins have been linked to the stabilization of cell components when facing stress conditions such as heat and oxidative stress  <cit> .
the lower level of these proteins in the chill injured fruit would reduce their capacity to cope with oxidative stress.
the protein thioredoxin , which was found to increase during softening, plays an important role in cellular redox regulation  <cit> .
trxs are small, widely distributed proteins.
thioredoxin h  has been associated with fruit ripening in several species, including peaches  <cit> .
it has also been found to be responsive to abiotic stress stimuli such as chilling injury and drought  <cit> .
interestingly, both shsps  <cit>  and the cgapdh  <cit> , which cluster together with the trx , have been identified as established or potential targets of this protein.
one of the most abundant proteins in our gels was identified as an abscisic stress ripening-like protein .
it showed a slight, non-statistically significant increase between mature and ripe fruits and a clear down-regulation in mealy fruits .
this protein belongs to the aba/wds induced protein family  which is composed of plant proteins induced by water deficit stress or abscisic acid  stress and ripening.
frankel et al.
<cit>  found that the banana ortholog presented a differential accumulation between two varieties with contrasting susceptibility to dehydration.
it was highly accumulated in the tolerant one and virtually absent in the sensitive variety under normal conditions  <cit> .
a similar situation was reported by riccardi et al.
in maize  <cit> .
this protein may have protective function against dehydration in mature, ripe and cold stored fruit, though this protection is somehow diminished in mealy fruit.
further work must be done in order to determinate the function of this abundant protein in peach fruit and explain its decrease in chilling injured fruit.
the thaumatin-like protein  is an ethylene inducible protein.
its transcript has been shown to be highly expressed in overripe fruit and senescent flowers but not in senescent leaves  <cit> .
this differential expression also has been reported in susceptible and chilled-injury resistant peach fruit varieties, although its relationship to this phenomenon was not established   <cit> .
response to abiotic stimulus
the 1-aminocyclopropane-1-carboxylate oxidase  <dig>  is one of the main enzymes that control ethylene biosynthesis because it is responsible for converting 1-aminocyclopropane-1-carboxylate  into ethylene.
peach physiological measurements indicated that there were a good relationship among the ethylene levels and the aco accumulation pattern at e <dig>  e <dig> and e <dig>  i.e., higher levels of aco correlated with higher levels of ethylene.
however, when peaches stored at low temperatures were allowed to ripen and became chill injured, the ethylene levels where significantly higher than they had been in the healthy fruit.
this behaviour is similar to that which is observed in nectarine fruit ripened upon cold storage  <cit> .
this ethylene increase did not correlate with ppaco <dig> content .
it is known that the main regulatory step in the ethylene synthesis in peaches is related to the prunus persica 1-aminocyclopropane-1-carboxylate synthase  <dig>  transcriptional and/or translational control  <cit> .
however, we did not identify ppacs <dig> in this study and therefore cannot rule out the possibility that the ethylene increase observed in the e <dig> stage is associated to this protein.
the posttranslational regulatory mechanisms that determine its presence in three different spots may help to explain this situation.
it is well known that dehydrins are induced by environmental stress factors like cold stress that result in cellular dehydration  <cit> .
we found that a peach dehydrin-like protein  was accumulated during the cold storage.
this protein was also accumulated in the fruit that softened at room temperature after the exposure to cold.
it is known that ethylene can induce the accumulation of dehydrins  <cit> .
given that ethylene is elevated in chilling injured fruit, it is likely that this could induce the increase of dehydrin .
the presence of another dehydrin  in cold stored fruits also was reported  <cit> .
wisniewski et al.
<cit>  demonstrated that both dehydrins had a different expression pattern in peach bark, leaf and embryo.
however, no one has evaluated their behaviour in fruit mesocarp or the possibility that enhancing their presence in the fruit could improve or protect enzyme activities.
another protein with increased accumulation during cold storage was a glutamate dehydrogenase .
in their study of tobacco and grapevine, skopelitis et al.
<cit>  demonstrated that gdh accumulation was induced under ros generating conditions such as high salt concentration and involved in the formation of glutamate, which in turn was used for proline biosynthesis, a molecule that could have a protective effect on cellular membranes  <cit> .
gdh has also been implicated in cold tolerance  <cit>  and associated with senescing organs.
ogundiwin et al.
<cit>  using a transcriptomic approach detected an increase in the expression of a glutamate dehydrogenase in cold treated peach mesocarp tissue samples as compared to the control material, which is similar to the protein accumulation pattern detected in this publication.
this pattern fits well with its stress responsive regulation .
carbohydrate and amino acid metabolism
cytosolic gapdh  is a protein implicated in the conversion of glyceraldehyde 3-phosphate to  <dig> -bisphosphoglycerate in the glycolytic pathway.
an increase in this protein, which is affected in fruit stored at low temperatures, was detected during the transition from mature to ripe fruit.
experiments in cell suspension cultures of a. thaliana determined that these proteins may be an important target for hydrogen peroxide  <cit> , being inactivated in vitro by h2o <dig>  thus, the authors suggested that cgapdh also may play a role in mediating ros signalling in plants.
nadp-isocitrate dehydrogenase  is another protein that presented a clear increment in its levels during fruit softening .
this protein catalyzes the conversion of isocitrate to 2-oxoglutarate, generating nadph.
it can be implicated in several processes such as the supply of nadph, an important source of reducing power for the antioxidant fruit system  <cit> ; the catabolism of organic acids in peach, with the concomitant decrease in the levels of organic acid content  <cit>  and/or the degradation of stored carbon fuels in ripe fruit, such as sugars  <cit> ; and the synthesis of 2-oxoglutarate, an organic acid involved in the coordination of the carbon-nitrogen metabolism  <cit> .
consequently, a decrease in this protein during the abnormal ripening that follows cold storage could have an important impact on the fruit's ability to withstand its metabolism as well as in its organoleptical characteristics.
this statement is supported by the key role that it plays in separating healthy fruit from chilling injured ripe fruit in the pca analysis .
the accumulation profile of nadp-dependent malic enzyme  is quite different from that of its counterpart nadp-isocitrate dehydrogenase.
the former is preferentially expressed in mature fruit and down-regulated in ripe fruit.
this profile fits with the one detected by western blot in peach fruit cv.
dixiland  <cit> .
this protein, which uses malate to generate pyruvate and nadph, may be relevant for the energy balance in the mature fruit  <cit> .
this function would be affected in cold stored fruit  and would constitute a source of stress.
the protein phosphoserine aminotransferase  is preferentially accumulated in chilling injured fruit.
it catalyzes the reversible formation of 2-oxoglutarate and phosphohydroxypyruvate to phosphoserine in the phosphorylated pathway of serine biosynthesis  <cit> .
therefore, it could be an important source of 2-oxoglutarate for a chilling injured fruit facing a down regulation of the nadp-icdh accumulation.
nevertheless, instead of using the 2-oxoglutarate as a product, the enzyme could be helping the biosynthesis of serine.
this amino acid is involved in the formation of compounds such as glycine betaine, which could have a beneficial effect on chilling stressed plants  <cit> .
there is a need for more exhaustive studies of the metabolic effects of this enzyme on cold stressed fruit.
the accumulation pattern for the pyruvate decarboxylase  proteins  also was detected by a microarray approach and activity assays in peach fruits  <cit> .
during a process known as ethanolic fermentation, pyruvate is decarboxylated to acetaldehyde through the action of pdc.
thereafter, acetaldehyde is converted to ethanol by alcohol dehydrogenase .
the ethanol and acetaldehyde generated could be used for the synthesis of ethyl esters, which are aroma constituents  <cit> .
however, it has been reported that this fermentative pathway could have many others functions and be triggered by environmental stress like chilling  <cit> .
moyano et al.
<cit>  showed that the strawberry fruit pdc <dig> responds to oxidative stress.
something similar could be present in chilling injured peach fruits  <cit> , inducing a higher accumulation of the peach pdcs under this condition as compared to normal fruit.
these higher levels of acetaldehyde could be beneficial for the cold stored fruit due to the inhibition of ethylene production  <cit> .
the possibility of generating energy for the fruit through this pathway when mitochondrial respiration has been hampered may be crucial to the survival of chilling injured fruit  <cit> .
generation of precursor metabolites and energy
chloroplasts of higher plants contain the ndh complex, which catalyzes the transfer of electrons from nadh to plastoquinone.
this complex, together with electron draining reactions, protects plants against photo-oxidative-related stresses through the poise of the redox levels of the cyclic photosynthetic electron transporters  <cit> .
during senescence, the expression of ndh genes and the activity of the ndh complex increase  <cit> .
the higher levels of the subunit f  of this complex in the ripe fruit are consistent with the developmental accumulation pattern.
however, its deregulation, for example, by its over-expression, triggers the production of ros, inducing programmed cell death in leaves  <cit> .
chloroplasts are present in green plant tissues and converted into chromoplasts during fruit ripening.
in tomato  and bell pepper  fruit, chromoplasts accumulate both plastid encoded mrnas and determined proteins at low levels, being translationally active  <cit> .
the same situation seems to be present in peach fruit, which presents an active accumulation of this protein during ripening.
it is plausible that levels of this protein, which is inserted in the thylakoid membrane, could have been affected by exposure to low temperatures, which are known to alter the cell membranes' conformation and structure  <cit> .
this situation would lead to an imbalance in the natural senescence process in cold stored peach fruit and ripe cold injured fruit.
signal transduction and transport
an adp-ribosylation factor  also was accumulated during cold storage and ripening, suggesting that membrane trafficking may be altered during cold storage.
arfs work like gtp-dependent switches for the assembly/disassembly of the coat proteins driving vesicle budding/fusion  <cit> ; however, they are linked to other processes such as alteration of membrane lipid compositions and act in remodelling various cell membrane compartments  <cit> .
changes in membrane composition and structure, with a concomitant increase in permeability, are among the first events triggered by chilling stress  <cit> ; efficient membrane trafficking therefore would be required in fruits under this condition  <cit> .
during ripening, high levels of ros also would damage the membrane.
arfs could be over-expressed under stress to counteract the continuous membrane fruit tissue harm.
annexins are a diverse, multigene family of calcium-dependent, membrane-binding proteins that serve as targets for ca+ <dig> in most eukaryotic cells.
the main property of nearly all annexins is the binding to and possibly holding together of certain biological structures, especially membranes  <cit> .
these proteins thus have the capacity to interact with lipid and protein moieties at the membranes, contributing to stress adaptation via regulation of various signalling pathways  <cit> .
due to its accumulation profile and the characteristics of these proteins, it may be involved in regulating stress-activated signalling pathways.
this role is lost in the fruit which has been stored at low temperatures .
other metabolic processes
the proteins that were up-regulated exclusively in fruit with chilling injury symptoms included an an anthocyanidin synthase .
this protein is one of the four dioxygenases  of the flavonoid biosynthetic pathway that has normally been associated with the conversion of leucoanthocyanidins to anthocyanidins  <cit> , substrates for the synthesis of anthocyanin, a major pigment in fruit and flowers.
even though anthocyanidins are red in colour  <cit> , under certain circumstances they can be enzymatically processed and derive into compounds that can be readily oxidized by polyphenol oxidases  and peroxidases , yielding a brown colour  <cit> .
tissue browning is one of the symptoms associated to chilling injury and the 'o'henry' variety is prone to it  <cit>  .
however, the mechanism that causes this problem is still under investigation  <cit> .
ans accumulation in chilling injured fruit could enhance the synthesis of anthocyanidins in the fruit mesocarp and increase the substrates for pod and/or ppo.
the recent identification of the ans gene as the responsible for a qtl affecting browning in peaches, strongly supports our hypothesis  <cit> .
it also strengthens the use of proteomics as a tool for the identification of markers that could potentially be useful in assisted breeding  <cit> .
a glutathione s-transferase  was detected in the peach fruit 2-d gels and was preferentially expressed in mature  fruit.
this protein belongs to the tau subfamily, which is one of the four subfamilies that have been described.
it is involved in cellular detoxification due to its ability to conjugate endobiotic and xenobiotic compounds to glutathione  <cit> .
its accumulation profile is quite similar to that of the annexin, which suggests fruit has active systems for coping with stress that run parallel to the action of cat .
the down-regulation of these proteins and related metabolic mechanisms may be detrimental for fruit proper softening.
changes in fruit ripening have been assessed mostly using transcriptomics  <cit> .
however, some discrepancies have been found between transcript content analysis and proteins content analysis.
a few proteomics analyses in peaches have been recently reported and their focus has been the analysis of fruit-pathogen interaction  <cit> .
obenland et al.
<cit>  described the comparison between juicy and mealy fruit using 2-d analysis.
they described five proteins as differentially accumulated between both stages.
in addition, borsani et al.
<cit>  used 2-d dige to evaluate the protein changes during postharvest.
they found  <dig> proteins that were differentially accumulated.
our study focused on the analysis of four postharvest stages including firm , soft , cold stored  and chill-injured  fruits.
therefore, we covered a broader set of postharvest conditions, enabling us to identify changes in a larger set of proteins.
thus, we got a deeper outlook of the molecular events that take place during softening and chilling injury.
CONCLUSIONS
using a comparative proteomic approach with 2-d dige allowed us to identify proteins that showed stage-specific changes in their accumulation pattern.
several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated.
finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest.

 fruit softening is a complex process during which a large number of proteins interact in order to achieve the physiological condition that allows fruit to accomplish its final objective, seed dispersion. peaches from fresh eating melting flesh varieties are characterized as having a short shelf life due to the rapid loss of firmness at the end of the ripening process, the softening of the fruit mesocarp. changes in the cell wall are particularly important for this phenomenon, especially the dismantling of its structure, the degradation of the polymers of which it is composed and the loss of turgor pressure in the fruit. after softening, fruit is susceptible to physical injury and pathogen attack and can only be stored for a few days. cold storage has been used to increase the postharvest life of peach fruit; however, this procedure leads to undesirable changes in fruit quality. these symptoms are known as chilling injury and include mealiness or lack of juice, as well as browning, among others. mealiness has been associated with abnormal cell wall dismantling during cold storage and the subsequent ripening. however, the mechanisms that disrupt the normal fruit cell wall metabolism during this low temperature disorder are not yet clear. the browning phenotype has been linked to interaction between phenols and polyphenol oxidase. these elements are usually found in different compartments within the cell, but the membrane permeability of deteriorated tissues may cause them to come into contact with one another. other important metabolic processes may be altered in cold injured fruit. for example, there is evidence that abnormal oxidative metabolism is triggered at low storage temperatures. despite these findings, little is known about the softening process and the molecular events that lead to the physiological disorder observed in cold stored fruit. in order to increase our understanding of this physiological process, we engaged in a global analysis using a proteomic approach that should provide us with a more accurate representation of the cellular/physiological state of the fruit rather than profiling the expression of mrnas. our aim was to identify proteins that could be differentially accumulated in soften and/or cold injured peaches. to this end, we utilized two-dimensional gel electrophoresis, a widely used technology that allows for the evaluation of many proteins. several steps of the process have been optimized during recent years, giving this technique an excellent resolving power. furthermore, the introduction of 2-d difference gel electrophoresis by Ünlü et al., allows the comparison of different protein samples within the same gel, strengthening the confidence of the 2-d quantitative analysis. thus, a 2-d dige approach was designed to inspect for proteins that could be differentially accumulated in peach fruit during softening and under conditions that led to chilling injury altered fruit.  physiological response of peach fruit to different postharvest storage conditions the peaches utilized in this work correspond to those analyzed by campos-vargas et al. in that study four postharvest stages were selected and each group named as: e firm fruit taken from packing; e fruit soften at 20°c; e fruit stored in a cold room at 4°c for three weeks; and e fruit stored at cold room and then kept at 20°c to allow for softening. some of the physiological parameters measured by campos-vargas et al. are summarized in table which also describes the degree of browning of the fruit at each stage. the results showed that fruit became nearly ten times less firm under normal softening conditions, dropping from n in e to n in e this change is characteristic of peach melting varieties. fruit stored at 4°c for three weeks showed a significant decrease in firmness, reaching a value of n. fruit from the e stage reached a firmness value of n, which is similar to normally softened fruit. the fruit from the e stage showed symptoms of chilling injury such as lack of juice and browning. peaches that were softened after being stored in the cold produced more ethylene than fruit softened normally. as expected, respiration also increased from e to e interestingly, fruit kept in the cold exhibited a high respiration rate that did not change when the fruit was allowed to soften. tss - total soluble solids a,b,c values followed by different small letters are significantly different within the same column at p = 1: no sample available for measurements: juice can not be measured in these samples due to the high firmnes they present 3: please refer to additional file for further details; + no browning; ++ no browning degree with a color change of the mesocarp; +++ medium browning degree; ++++ high browning degree the data used in this table have been acquired from campos-vargas et al. sci hortic-amsterdam 110:79-83 2-d map of peach mesocarp fruit developed using dige technology 2-d difference gel electrophoresis analysis was performed in order to identify changes in the amount of proteins present under different postharvest conditions. figure presents a representative image from cy5/cy overlapped gels of the four postharvest conditions under evaluation. a reproducible protein pattern is observed throughout the evaluated stages, and some changes in content can be visually detected. on average, the gels exhibited spots, from which well-focused spots were chosen for further analysis because they were present in all of the cy reference gels. about 85% of these proteins presented a pi ranging from to and were between to kda in size. some of the spots that were highly abundant or had a clear differential protein accumulation were identified by means of lc-ms/ms mass spectrometry. the results of this analysis showed coverage of over 15% for most proteins. a complete list of the protein sequences with peptides delivered by mass spectra is presented in the additional file a: spot numbers as assigned in figure b: protein assignment based on lc-ms/ms identification. c: gene bank accession number. d: probability that the match is random. only proteins with scores greater than the minimum value for ms-based identification confidence are reported. additional data about ms are reported in the additional file the values in the columns to indicate if the protein accumulation pattern changes between the conditions shown above them. positive values indicate a higher abundance in the first condition whereas negative values indicate the opposite situation. the theoretical isoelectric points and molecular weight of the proteins were calculated and compared to the experimental data. most of the spots identified showed a good relationship to their theoretical mw. only the dehydrin and the glyceraldehyde-3-phosphate dehydrogenase showed some discrepancies; however, the experimental pi and molecular weight values for the dehydrin match quite well to those described by wisniewski et al.. posttranslational modification, abnormal electrophoretic mobility or a smaller molecular weight for the prunus persica gapdh may explain the differences detected in that regard. some of the spots identified had matching protein ids but different isoelectrical points and/or molecular weights. in terms of their accumulation pattern, some displayed the same profile and others showed differences in their isoform. as table demonstrates, these spots include the following proteins: low molecular weight heat shock proteins, annexin, 1-aminocyclopropane-1-carboxylate oxidase, catalase, dehydrin, pyruvate dehydrogenase, actin and nadp-dependent malic enzyme. overall, distinct peach fruit mesocarp proteins were identified in this study. multivariate analysis of the data through hierarchical clustering and pca in order to detect real changes in protein accumulation among the four postharvest conditions evaluated, the experimental data from 2-d gels were screened before being used for statistical analysis. a one-way analysis of variance followed by a false discovery rate correction allowed us to determinate that -about 18% of the spots analyzed- showed statistically significant changes. thirty-nine of these proteins could be detected and excised from the gels and then identified by mass spectrometry. some of the identified proteins that changed during postharvest such as endopolygalacturonase and the 1-aminocyclopropane-1-carboxylate had been linked to the peach fruit ripening process. some, like dehydrin-like and thaumatin-like protein, had been detected in cold stressed plant tissues. a graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis, a technique that cluster together proteins with similar patterns of expression among different postharvest treatments. four general trends in the data could be visualized by this method, as displayed in figure the first group is represented by sixteen proteins that showed a pronounced increase during the normal softening process compared to the absence of a noticeable increase in protein accumulation during the softening of cold stored fruit. this behaviour is exemplified by a group of proteins that cluster with a thioredoxin h, a protein that has an important role in the cellular redox regulation. group ii showed twelve proteins that under the normal postharvest storage presented a decrease in their content between e and e an example of this is observed in the case of a catalase, which showed its higher levels during e compared to e and e to decline even further in e group iii is represented by four proteins that have a pronounced accumulation only in the abnormal ripening that follows the low temperature storage, like an anthocyanidin synthase and other proteins that cluster along with it. group iv is composed by seven proteins that did not present any change between e and e fruit, whereas their level increased in e remaining constant in e one of those proteins is a dehydrin, which exhibit a clear high level in chilling stressed fruit compared to healthy fruit. some proteins did not fit in these four general clusters. for instance, two pyruvate decarboxylases were up-regulated in the softening process that leads to the development of chill injured fruit more than in the normal ripening process. the protein pectin metilesterase also had a particular accumulation pattern, since it was up-regulated in the normal ripening process, whereas in the transition from e to e this increment was even higher. no other protein showed a similar trend. the endopg protein was also located in a different group, due to the degree of differences among its accumulation levels in the four postharvest conditions. a principal component analysis evaluation was performed in order to identify the most relevant features of the data set retrieved from the 2d-dige gels. the pca identifies new variables, called principal components, which are linear combinations of the original variables. these new features can describe a large amount of data in a lower dimensional space, which makes the pca a useful tool for data categorization. the analysis of the weight loadings associated with each spot indicates which proteins have the greatest impact on the trends observed in the score plots. the first component was able to separate mature samples from ripe ones. endopolygalacturonase, a thaumatin-like protein and a small heat shock protein were among the proteins that had the higher impact in the ripe fruit classification. a catalase and an annexin were important for the trend observed for the mature fruit. the second component was able to differentiate chilling injured fruit samples from the ripe healthy fruit samples. again, the endopg and the shsp had a high impact on the ripe healthy fruit trend, along with a nadp-dependent isocitrate dehydrogenase. the proteins anthocyanidin synthase, thaumatin-like protein, alpha- -glucan-protein synthase and phosphoserine aminotransferase were very relevant in differentiating chilling injured fruit from healthy fruit, which supports the results obtained by the hierarchical clustering. the third component differentiated between the fruit sample that was stored at low temperature and the mature fruit sample. a pectin methylesterase and a dehydrin-like protein played an important role in differentiating between the chilling injured fruit, while a major allergen protein pru p i displayed the opposite behavior. interestingly, some proteins that were classified as not statistically differentially accumulated had a high impact on the pca trends. this difference may be due to a false negative type ii error. finally, the three principal components represent nearly 56% of the original variance, with values of %, % and %, respectively, for the pc pc and pc components. characterization of the differentially accumulated proteins in order to generate an overview of the most relevant biological processes involved in fruit softening and its response to the low temperature storage, a categorization of differentially accumulated proteins was performed based on the gene ontology annotation. this standardized categorization system provides a less subjective and more reproducible assignment of the biological processes underlying the chilling injury development. figure displays the results obtained from the quickgo tool. as expected, almost 25% of the proteins differentially expressed were associated with the biological processes'response to stress' and'cellular homeostasis'. the relevant impact detected in processes related to the metabolism of carbohydrates and amino acid metabolism is also noteworthy. discussion peaches are climacteric fruit that display a decrease in mesocarp texture firmness. melting varieties present a marked softening of this region. this process is less pronounced in non-melting varieties. in prunus persica, it forms part of the final stages of a broader phenomenon, the fruit ripening. of the physiological changes that the fruit displays during its ripening, the accumulation of soluble solids and changes in colour and aroma are very relevant for consumer acceptability. these attributes are severely affected in fruit that has been exposed to low temperatures for a prolonged amount of time. this study identified several proteins that may be related to changes in fruit metabolism during cold storage and the subsequent ripening that leads to the development of chilling injury. these proteins are mainly linked to processes such as response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism. our discussion will be guided by those general categories. cellular component organization - cell wall metabolism the drastic changes in the texture of the fruit mesocarp in the melting varieties have been associated with a massive solubilization and depolymerization of pectin-derived polyuronides. these changes correlated with the concerted action of two proteins, endopolygalacturonases and pectin methylesterases. the main pme function is demethylation of the polyuronides so that they can be degraded by the endopg. therefore, these proteins play an important role in dismantling the cell wall. both the endopg and the pme are encoded by multi-gene families. recently, murayama et al. identified one member of each that is up-regulated above the other members during peach fruit softening, namely pppg and pppme pppg is the endopg detected in our 2-d peach fruit gels and pppme resembles the one we identified. additionally, they increase as we go from mature to ripe fruit. several groups have reported changes in the degree of methylesterification and size of the homogalacturonans, which are localized to the middle lamella of the wall. the pme levels that we detected were consistently remarkably higher at the end of cold storage than they were during normal fruit softening, whereas the levels of pppg decreased to a minimum. high pme activity during the cold storage could partially de-methylesterify homogalacturonans, which would maintain a high molecular weight due to the lack of endopg, protein that remains low in ripe chilling injured fruit. it has been suggested that these large polymers are involved in the lack of juiciness characteristic of the mealy fruit. it also has been reported that the arabinose content of cell wall polysaccharides is different in chilling injured peaches. arabinose is mainly found in the cell wall ara-containing polymers in the furanose ring configuration, though the substrate for this transfer has not been found in plants. our results showed that accumulation of an α- -glucan-protein synthase, increased exclusively in chilling injured fruit. this protein is highly homologous to a rice udp-arabinopyranose mutase, an enzyme that catalyzes the formation of udp-l-arabinofuranose from udp-l-arabinopyranose. this increase suggests that this protein and the arabinans are linked to the development of chilling injury in prunus persica. the results from the pca support the relevance of pppg pme and uam in the development of the chilling injury. response to stress and cellular homeostasis fruit senescence can be considered as an oxidative phenomenon that requires the presence of ros in order to achieve a degradation state that will allow the seed release to occur. several enzymes involved in ros metabolism are expressed in early stages of fruit development and ripening and gradually are turned off as the fruit approaches senescence, making it more susceptible to be damaged by these molecules. as shown in figure most of the proteins that are up-regulated in the mature fruit are related to ros metabolism and show a decrease in their accumulation from mature to ripe fruit. after low temperature storage, their levels decrease in cold stored fruit. as a result, the fruits' capacity to withstand cold induced stress is perturbed. one of the most important enzymes involved in the control of ros generation, particularly hydrogen peroxide, is catalase. at least two catalases have been identified in p. persica. until now, the only isoform detected in the 2-d gels is catalase, which appears in two spots with the same pi an different mw. our results show that both spots are more abundant in firm fruit and decreased significantly in healthy soft fruit. a similar expression trend was found in apricot and in tomato and saskatoon. peach fruit stored at 4°c for three weeks showed reduced catalase accumulation. this result is supported by wang et al., who measured significantly lower cat activity in peach fruit stored at 0°c for days as compared to controls. this negative effect on cat accumulation could be harmful to the cold stored fruit due to the higher levels of h2o that could be present in their cells. the hydrogen peroxide would not only affect the redox status of the cell, but could influence signal transduction cascades, since this molecule has been postulated as a second messenger for signals generated by means of ros. the content of the iron binding protein ferritin changed in a manner that is similar to the catalase accumulation pattern. interestingly, its biological function is also linked to the ros metabolism, though its mechanism of action is somehow different. ferritin can control the free iron concentration inside the cell and thus reduce its availability for the production of hydrogen peroxide derived hydroxyl radical. moreover, this protein has been shown to play a crucial role in the interaction between the iron homeostasis and oxidative stress in arabidopsis, where its absence increased ros levels as well as the activity of enzymes involved in their detoxification. on the other hand, peach fruit that went soft without being exposed to cold storage accumulated small heat shock proteins. this seems to be a common ripening regulatory mechanism in fruit as these proteins serve as protein chaperones and membrane stabilizers. a low molecular weight heat shock protein was identified in four spots with different molecular weight and pi. this protein shows an identity of 76% with carrot hsp, whereas a small heat shock protein was found in two spots and shows an identity of 82% with a kda hsp protein from quercus suber. both proteins have been linked to the stabilization of cell components when facing stress conditions such as heat and oxidative stress. the lower level of these proteins in the chill injured fruit would reduce their capacity to cope with oxidative stress. the protein thioredoxin, which was found to increase during softening, plays an important role in cellular redox regulation. trxs are small, widely distributed proteins. thioredoxin h has been associated with fruit ripening in several species, including peaches. it has also been found to be responsive to abiotic stress stimuli such as chilling injury and drought. interestingly, both shsps and the cgapdh, which cluster together with the trx, have been identified as established or potential targets of this protein. one of the most abundant proteins in our gels was identified as an abscisic stress ripening-like protein. it showed a slight, non-statistically significant increase between mature and ripe fruits and a clear down-regulation in mealy fruits. this protein belongs to the aba/wds induced protein family which is composed of plant proteins induced by water deficit stress or abscisic acid stress and ripening. frankel et al. found that the banana ortholog presented a differential accumulation between two varieties with contrasting susceptibility to dehydration. it was highly accumulated in the tolerant one and virtually absent in the sensitive variety under normal conditions. a similar situation was reported by riccardi et al. in maize. this protein may have protective function against dehydration in mature, ripe and cold stored fruit, though this protection is somehow diminished in mealy fruit. further work must be done in order to determinate the function of this abundant protein in peach fruit and explain its decrease in chilling injured fruit. the thaumatin-like protein is an ethylene inducible protein. its transcript has been shown to be highly expressed in overripe fruit and senescent flowers but not in senescent leaves. this differential expression also has been reported in susceptible and chilled-injury resistant peach fruit varieties, although its relationship to this phenomenon was not established. response to abiotic stimulus the 1-aminocyclopropane-1-carboxylate oxidase is one of the main enzymes that control ethylene biosynthesis because it is responsible for converting 1-aminocyclopropane-1-carboxylate into ethylene. peach physiological measurements indicated that there were a good relationship among the ethylene levels and the aco accumulation pattern at e e and e i.e., higher levels of aco correlated with higher levels of ethylene. however, when peaches stored at low temperatures were allowed to ripen and became chill injured, the ethylene levels where significantly higher than they had been in the healthy fruit. this behaviour is similar to that which is observed in nectarine fruit ripened upon cold storage. this ethylene increase did not correlate with ppaco content. it is known that the main regulatory step in the ethylene synthesis in peaches is related to the prunus persica 1-aminocyclopropane-1-carboxylate synthase transcriptional and/or translational control. however, we did not identify ppacs in this study and therefore cannot rule out the possibility that the ethylene increase observed in the e stage is associated to this protein. the posttranslational regulatory mechanisms that determine its presence in three different spots may help to explain this situation. it is well known that dehydrins are induced by environmental stress factors like cold stress that result in cellular dehydration. we found that a peach dehydrin-like protein was accumulated during the cold storage. this protein was also accumulated in the fruit that softened at room temperature after the exposure to cold. it is known that ethylene can induce the accumulation of dehydrins. given that ethylene is elevated in chilling injured fruit, it is likely that this could induce the increase of dehydrin. the presence of another dehydrin in cold stored fruits also was reported. wisniewski et al. demonstrated that both dehydrins had a different expression pattern in peach bark, leaf and embryo. however, no one has evaluated their behaviour in fruit mesocarp or the possibility that enhancing their presence in the fruit could improve or protect enzyme activities. another protein with increased accumulation during cold storage was a glutamate dehydrogenase. in their study of tobacco and grapevine, skopelitis et al. demonstrated that gdh accumulation was induced under ros generating conditions such as high salt concentration and involved in the formation of glutamate, which in turn was used for proline biosynthesis, a molecule that could have a protective effect on cellular membranes. gdh has also been implicated in cold tolerance and associated with senescing organs. ogundiwin et al. using a transcriptomic approach detected an increase in the expression of a glutamate dehydrogenase in cold treated peach mesocarp tissue samples as compared to the control material, which is similar to the protein accumulation pattern detected in this publication. this pattern fits well with its stress responsive regulation. carbohydrate and amino acid metabolism cytosolic gapdh is a protein implicated in the conversion of glyceraldehyde 3-phosphate to -bisphosphoglycerate in the glycolytic pathway. an increase in this protein, which is affected in fruit stored at low temperatures, was detected during the transition from mature to ripe fruit. experiments in cell suspension cultures of a. thaliana determined that these proteins may be an important target for hydrogen peroxide, being inactivated in vitro by h2o thus, the authors suggested that cgapdh also may play a role in mediating ros signalling in plants. nadp-isocitrate dehydrogenase is another protein that presented a clear increment in its levels during fruit softening. this protein catalyzes the conversion of isocitrate to 2-oxoglutarate, generating nadph. it can be implicated in several processes such as the supply of nadph, an important source of reducing power for the antioxidant fruit system; the catabolism of organic acids in peach, with the concomitant decrease in the levels of organic acid content and/or the degradation of stored carbon fuels in ripe fruit, such as sugars; and the synthesis of 2-oxoglutarate, an organic acid involved in the coordination of the carbon-nitrogen metabolism. consequently, a decrease in this protein during the abnormal ripening that follows cold storage could have an important impact on the fruit's ability to withstand its metabolism as well as in its organoleptical characteristics. this statement is supported by the key role that it plays in separating healthy fruit from chilling injured ripe fruit in the pca analysis. the accumulation profile of nadp-dependent malic enzyme is quite different from that of its counterpart nadp-isocitrate dehydrogenase. the former is preferentially expressed in mature fruit and down-regulated in ripe fruit. this profile fits with the one detected by western blot in peach fruit cv. dixiland. this protein, which uses malate to generate pyruvate and nadph, may be relevant for the energy balance in the mature fruit. this function would be affected in cold stored fruit and would constitute a source of stress. the protein phosphoserine aminotransferase is preferentially accumulated in chilling injured fruit. it catalyzes the reversible formation of 2-oxoglutarate and phosphohydroxypyruvate to phosphoserine in the phosphorylated pathway of serine biosynthesis. therefore, it could be an important source of 2-oxoglutarate for a chilling injured fruit facing a down regulation of the nadp-icdh accumulation. nevertheless, instead of using the 2-oxoglutarate as a product, the enzyme could be helping the biosynthesis of serine. this amino acid is involved in the formation of compounds such as glycine betaine, which could have a beneficial effect on chilling stressed plants. there is a need for more exhaustive studies of the metabolic effects of this enzyme on cold stressed fruit. the accumulation pattern for the pyruvate decarboxylase proteins also was detected by a microarray approach and activity assays in peach fruits. during a process known as ethanolic fermentation, pyruvate is decarboxylated to acetaldehyde through the action of pdc. thereafter, acetaldehyde is converted to ethanol by alcohol dehydrogenase. the ethanol and acetaldehyde generated could be used for the synthesis of ethyl esters, which are aroma constituents. however, it has been reported that this fermentative pathway could have many others functions and be triggered by environmental stress like chilling. moyano et al. showed that the strawberry fruit pdc responds to oxidative stress. something similar could be present in chilling injured peach fruits, inducing a higher accumulation of the peach pdcs under this condition as compared to normal fruit. these higher levels of acetaldehyde could be beneficial for the cold stored fruit due to the inhibition of ethylene production. the possibility of generating energy for the fruit through this pathway when mitochondrial respiration has been hampered may be crucial to the survival of chilling injured fruit. generation of precursor metabolites and energy chloroplasts of higher plants contain the ndh complex, which catalyzes the transfer of electrons from nadh to plastoquinone. this complex, together with electron draining reactions, protects plants against photo-oxidative-related stresses through the poise of the redox levels of the cyclic photosynthetic electron transporters. during senescence, the expression of ndh genes and the activity of the ndh complex increase. the higher levels of the subunit f of this complex in the ripe fruit are consistent with the developmental accumulation pattern. however, its deregulation, for example, by its over-expression, triggers the production of ros, inducing programmed cell death in leaves. chloroplasts are present in green plant tissues and converted into chromoplasts during fruit ripening. in tomato and bell pepper fruit, chromoplasts accumulate both plastid encoded mrnas and determined proteins at low levels, being translationally active. the same situation seems to be present in peach fruit, which presents an active accumulation of this protein during ripening. it is plausible that levels of this protein, which is inserted in the thylakoid membrane, could have been affected by exposure to low temperatures, which are known to alter the cell membranes' conformation and structure. this situation would lead to an imbalance in the natural senescence process in cold stored peach fruit and ripe cold injured fruit. signal transduction and transport an adp-ribosylation factor also was accumulated during cold storage and ripening, suggesting that membrane trafficking may be altered during cold storage. arfs work like gtp-dependent switches for the assembly/disassembly of the coat proteins driving vesicle budding/fusion; however, they are linked to other processes such as alteration of membrane lipid compositions and act in remodelling various cell membrane compartments. changes in membrane composition and structure, with a concomitant increase in permeability, are among the first events triggered by chilling stress; efficient membrane trafficking therefore would be required in fruits under this condition. during ripening, high levels of ros also would damage the membrane. arfs could be over-expressed under stress to counteract the continuous membrane fruit tissue harm. annexins are a diverse, multigene family of calcium-dependent, membrane-binding proteins that serve as targets for ca+ in most eukaryotic cells. the main property of nearly all annexins is the binding to and possibly holding together of certain biological structures, especially membranes. these proteins thus have the capacity to interact with lipid and protein moieties at the membranes, contributing to stress adaptation via regulation of various signalling pathways. due to its accumulation profile and the characteristics of these proteins, it may be involved in regulating stress-activated signalling pathways. this role is lost in the fruit which has been stored at low temperatures. other metabolic processes the proteins that were up-regulated exclusively in fruit with chilling injury symptoms included an an anthocyanidin synthase. this protein is one of the four dioxygenases of the flavonoid biosynthetic pathway that has normally been associated with the conversion of leucoanthocyanidins to anthocyanidins, substrates for the synthesis of anthocyanin, a major pigment in fruit and flowers. even though anthocyanidins are red in colour, under certain circumstances they can be enzymatically processed and derive into compounds that can be readily oxidized by polyphenol oxidases and peroxidases, yielding a brown colour. tissue browning is one of the symptoms associated to chilling injury and the'o'henry' variety is prone to it. however, the mechanism that causes this problem is still under investigation. ans accumulation in chilling injured fruit could enhance the synthesis of anthocyanidins in the fruit mesocarp and increase the substrates for pod and/or ppo. the recent identification of the ans gene as the responsible for a qtl affecting browning in peaches, strongly supports our hypothesis. it also strengthens the use of proteomics as a tool for the identification of markers that could potentially be useful in assisted breeding. a glutathione s-transferase was detected in the peach fruit 2-d gels and was preferentially expressed in mature fruit. this protein belongs to the tau subfamily, which is one of the four subfamilies that have been described. it is involved in cellular detoxification due to its ability to conjugate endobiotic and xenobiotic compounds to glutathione. its accumulation profile is quite similar to that of the annexin, which suggests fruit has active systems for coping with stress that run parallel to the action of cat. the down-regulation of these proteins and related metabolic mechanisms may be detrimental for fruit proper softening. changes in fruit ripening have been assessed mostly using transcriptomics. however, some discrepancies have been found between transcript content analysis and proteins content analysis. a few proteomics analyses in peaches have been recently reported and their focus has been the analysis of fruit-pathogen interaction. obenland et al. described the comparison between juicy and mealy fruit using 2-d analysis. they described five proteins as differentially accumulated between both stages. in addition, borsani et al. used 2-d dige to evaluate the protein changes during postharvest. they found proteins that were differentially accumulated. our study focused on the analysis of four postharvest stages including firm, soft, cold stored and chill-injured fruits. therefore, we covered a broader set of postharvest conditions, enabling us to identify changes in a larger set of proteins. thus, we got a deeper outlook of the molecular events that take place during softening and chilling injury.  using a comparative proteomic approach with 2-d dige allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest. 
several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. the results showed that the'response to stress','cellular homeostasis','metabolism of carbohydrates' and'amino acid metabolism' biological processes were affected the most during the postharvest. using a comparative proteomic approach with 2-d dige allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. in this study, a 2-d dige approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury. thirty-nine of the proteins could be identified by mass spectrometry. finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest. a categorization of the differentially accumulated proteins was performed using gene ontology annotation. a graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. the analysis allowed us to identify spots -representing about 18% of the total number analyzed- that show statistically significant changes. some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. storing fruit at low temperatures has been widely used to extend its postharvest life. proteins such as endopolygalacturonase, catalase, nadp-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. peach fruit undergoes a rapid softening process that involves a number of metabolic changes.
 peach fruit undergoes a rapid softening process that involves a number of metabolic changes. storing fruit at low temperatures has been widely used to extend its postharvest life. however, this leads to undesired changes, such as mealiness and browning, which affect the quality of the fruit. in this study, a 2-d dige approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury.  the analysis allowed us to identify spots -representing about 18% of the total number analyzed- that show statistically significant changes. thirty-nine of the proteins could be identified by mass spectrometry. some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. however, we identified other proteins that had not been linked to these processes. a graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. proteins such as endopolygalacturonase, catalase, nadp-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. a categorization of the differentially accumulated proteins was performed using gene ontology annotation. the results showed that the'response to stress','cellular homeostasis','metabolism of carbohydrates' and'amino acid metabolism' biological processes were affected the most during the postharvest.  using a comparative proteomic approach with 2-d dige allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest. 