Critical Review on Proteomics of Fruit Development

Question: Discuss about the Critical Review on Proteomics of Fruit Development. Answer: Introduction: Carbohydrate is an essential element for the growth and development of human body along with restoring the building blocks of life. Fruits and vegetable contribute to a massive chunk of the carbohydrate along with vitamins and minerals into the daily food intake that we do. Fruits have high nutritional value and are first choice of dietary intake of physicians and nutritionists. Fruits are infused with variety of vitamins, fibre and phytochemicals that are highly beneficial to the human body (Kuang et al. 2013). Therefore the value of fruits in the needs of the human population is paramount with the rapidly decreasing life style standards and feeding habits of the society. According to a lot of physicians increasing the daily fruit intake can have a profound beneficial effect on the health and wellbeing of the individuals (Lin et al. 2012). Furthermore, fruits are considered to be the most abundant source of natural sugars and are beneficial for the horde of diabetics as well. So it has become a mandate for the scientific research to focus on improving the fruit quality in terms of taste, firmness and nutrition. Along the years there have been a myriad of scientific research committed to the betterment of the fruit quality and its nutritional value, some have been successful and some not very successful. The focus of this critical review is on the proteomic analysis of two fruits with very high market value across the globe and is consumed by a vast majority. The purpose behind proteomic study to determine fruit quality and ways to improve it lies in the interlinked genetic mechanisms and the protein expression background. It has to be considered that fruit quality is a decisive factor in determining the market value of the fruits considered and affects not only the consumers but also the retailers and the taste and quality attributes are governed by intricate genetic pathways and altering these pathways or even just attempting to alter them would require thorough genomic and proteomic analysis of the genera (McAtee, Karim and Schaffer 2013). This essay attempts to criticize two such attempt s, focusing on the genetics and proteomics of fruit quality development taking the aid of two articles and evaluate the achievements and drawbacks of both of them. The first article under the spotlight for this critical review is on the proteomic analysis of apple, by Mingjun Li and his co-authors (Li et al. 2016). This research study focuses on identification of the proteomic analysis of all the regulatory pathways associated with fruit development and sugar and acid accumulation in the apples during the developmental stages. In more detail, the research paper explains the proteomics of the apple fruit development across five growth stages along with metabolomic profiling. In this research study the researchers have applied the TMI (tandem mass tag) proteomic analysis approach to identify and quantify a variety of proteins (Li et al. 2016). This research study has identified some key switches in the signalling cascades that will prove to be instrumental in constructing a global view on the proteomics of fruit development (Li et al. 2016). The study by Li et al. 2016 focussed primarily on the proteomics and metabolomics of the fruit development phenomenon. Where a proteomic analysis gives a clear idea of the protein sequence of the genera, the metabolomic study gives the details of the metabolites produced, a thorough idea of both the aspects are critical to find ways to exploit the fruit development pathway according to our benefits. Previous studies suggest that the metabolic pathways and accumulation of carbohydrates in apple and genera alike are strictly developmental stage dependent (Nogueira et al. 2012). In the early developmental stages very low levels of sugars and high levels of organic acids accumulate in the fruit (Razzaq et al., 2013). As the developmental stages progress the rate of carbohydrate metabolism slows down and the sugar concentration inside the fruit increases exponentially, which elevates the taste and sweetness of the fruit at the maturation stage. It has to be considered that the solids accumulated throughout the developmental stages contribute largely to the taste of the fruit, a vital element of fruit quality. For the entire study by Li et al. 2016, the first variable evaluated was the fresh weight or soluble solid content, the soluble sugars and organic acids accumulated inside the fruit were analysed via GC-MS (Chagn et al. 2012). The next assessment was of the free amino acids using the liquid chromatography and fluorescence detection technique by Li. The proteomic analysis demands the optimal extraction and characterization of the proteins accumulated, which in the study was done using HPLC technique and statistical analysis of the data collected was done by BLAST alignment (Li et al. 2016). Their results showed some key factors in the developmental genetics of the apple fruit family; the experiment quantified 6247 proteins out of which 3713 were in overlapped sequences, contributing to particular gene products. The ANOVA analysis identified 7785 genes out of approximately 63541 genes that are expressed during the fruit development. Appreciation is due for this research to identify almost 12.3% of the entire transcriptome of apple (Li et al. 2016). Now their next initiative was to assign the proteins identified with annotated transcriptome. The dynamic genetic reprogramming yielded the identification of 8 clusters having differential expression pattern. The study discovered four clusters out of them to have no effect on the development stages and found K1 and K2 cluster to have profound role in the development procedure (Li et al. 2016). Hormonal signalling also plays a vital role in the quality and taste of the fruit, and the study shed light on the hormonal regulation involved in the developmental pathway as well, furthermore, the study discovered 132 proteins to be involved in cell wall construction and 275 to be related to internal barrier development and found 94 proteins in total to be involved in sugar transport and accumulation cycle. The fruit quality is heavily dependent on the taste and nutritional value of it therefore this discovery no doubt is commendable (Eccher et al. 2014). The next study under consideration for this critical review is the iTRAQ based protein profiling of oriental melon by Guo et al. 2017. Despite this study focussing on oriental melon as a sample, which is a popular exotic fruit for its nutritional properties, the study bears a lot of similarities to the previous study. In this study the technique chosen for protein profiling is iTRAQ, using isobaric labelling to obtain relative and absolute quantification of the protein sequence. Similar to the previous research study this study was also focussed on protein profiling at different developmental stages, however the variables analysed were different (Guo et al. 2017). Soluble solid content also contributes to the sweetness of the fruit, a key factor rightly capture by the second article, along with its soluble sugar content using refractometer like the previous study (Guo et al. 2017). The study nest analysed the ethylene content of the fruit via extraction using chromatography. Volatile compound analysis was the next step in line in this study followed by the protein extraction using acetone precipitation technique. The last few step that completed this protein profiling study were iTRAQ analysis, LC-MS analysis and protein identification and bioinformatic analysis followed by real time PCR to replicate the coded cDNA (Guo et al. 2017). Their attempt was to evaluate the protein profiling for the genera of oriental melon and find out key switches in the developmental procedure that will improve the fruit quality if manipulated. The results of the study was very simplified and articulated, the SSC count increased in the early developmental period and then gradually decreased as the fruit progressed towards ripening and maturation. Hence it can be concluded from the study that the key genetic switches are in the early developmental processes, and manipulation of any of the genetic pathway later on will do nothing to improve the taste or nutritional value of the fruit. The volatile compound analysis revealed 17 esters, 12 alcohols, 4 aldehydes and 4 acidic compounds to be present in the fruit that contributed to the exotic aroma of the melon. The protein analysis study revealed the presence of differentially expressing proteins across four developmental stages, and to further investigate the protein profiling for these about 1694 proteins were analysed using hierarchical clustering. This study analysed 4 clusters of proteins each showing different functions at different stages (Guo et al. 2017). Now a thorough understanding of the expression pattern of these protein clusters can reveal key information can aid in exploiting the fruit quality, hence it can be concluded that it is a step in the right direction for the study. In order to critically compare the efficacy and drawbacks of both articles any further, it is important to tally their findings, and the conclusion each study has drawn based on the findings reflecting the quality development. The first article on Malus could successfully identify that cell production progresses on a vigorous rate in early developmental stages, they could also identify that the protein expression at this stage is much higher than the rest of the stages. The authors described that the protein expression and changes to the core cell cycle progresses with fruit development, a conclusion very similar to the previous studies (Li, Feng and Cheng 2012). The study could identify key kinases and auxin response factor involved with the fruit development procedure but could not assign QTLs to these key proteins, so that it becomes easier for them to characterize the expression pattern of that particular sequence. Both articles verified the role of proteins expressing in the ear ly stages of development as expected, but there are hardly any significant similarities in the proteins. The study attempted to explain the genetic trajectory associated with Malus in intricate detail that can be instrumental in improving the fruit quality quite commendably. As the previous studies suggested the predominant two sugars that are generally accumulated in the fruit are sorbitol and sucrose as explained by Ma 2012. The study could describe with clarity the protein expression involved in the phloem transport and accumulation of these two sugars. However, not enough information was available on the signalling mechanism of the key enzymes of metabolism of these sugars (Ma 2012). However the protein expression details were well articulated in the thesis paper encompassing all the key proteins involved in the procedures which can be really helpful in the conduction of further studies. On the other hand the second article on oriental melon discussed only about the metabolic pathway, completely neglecting the genetic and signalling aspect of the development and maturation procedure. The first segment in the discussion was focussed around alpha linolenic acid metabolism, a key organic acid that is first accumulated in the melon fruit. However, we could gather substantial information about the key enzymes involve with metabolic pathway of the said acid like the ADH or AAT, enzymes vital for the alcohol and ester formation that contribute to the volatile properties for the fruit (Cohen, Elkabetz and Edelstein 2016). The role of ADH in the coloration of the fruit was another verification of the research study, however previous articles suggest that this particular hydrogenase is responsible for colour development of a number of berries as well, therefore we can assume this hydrogenase can be a conserved sequence, and the vital information curated by the paper will be us eful in determining the pathways of colour development of many other fruit families (Cohen, Elkabetz and Edelstein 2016). Apart from the detailed description of alpha Linolenic acid, the study further diversifies into starch and sucrose metabolism, another decisive factor in fruit quality. As the fruit quality heavily depends on fruit taste, a transparent understanding about the sugar accumulation is of much importance to scientific research. As the previous studies suggest, the very first carbohydrates to be accumulated in the fruits are glucose and fructose, along with sucrose (Cohen, Elkabetz and Edelstein 2016). Sucrose is considered the most valuable sugar present in the fruits for not only its contribution to the taste and flavour of the fruit but is also a catalyst to the production of other valuable components of a ripened fruit. The study focussed on the Sucrose synthetase and sucrose phosphate synthetase enzyme, vital for sucrose synthesis to better understand the molecular mechanism of sucrose synthesis and transport (Cohen, Elkabetz and Edelstein 2016). The mechanism of up and down-regulatio n of the SPS protein was clearly explained in the study however, the transcriptomic switches were not discussed in detail. The glycolytic pathway was also critically analysed which gave a clear insight on the ATP generation and it contribution to sugar accumulation in the fruit but the study heavily lacked the genetic and trancriptome analysis with the thesis paper being focussing on protein profiling as the title suggested (Guo et al. 2017). The first article however provided vital information about the genetic network of the carbohydrate accumulation in the fruit during the development, that can be vital for exploiting their pathways to improve the fruit quality. Two comprehensive studies on the efficacy of SUC4 protein showed that the protein is crucially involved in the phloem unloading by Wei et al., 2014 and Li et al., 2012, this study further enhanced the knowledge on this mechanism by validating that the SUC4 expression surges parallel with the progression of the developmental stages of the fruit (Wei et al. 2014). Another remarkable discovery of the paper was the discovery of analogues of the hexose transporters, SOT1 and SOT2, involved with the post phloem loading of sorbitol. The study proved true to its claim by discussing a substantial amount about the genetics of the fruit development however, it similarly lacked in discussion about the metabolomics (Guo et al. 2017). Although the paper was able to discuss a bout the glycolytic pathway and the enzymes involved in general but did not provide any specific information about the accumulation of the sugars and its metabolic pathways (Monforte et al. 2014). On a concluding note it can be said that both the papers lacked one or the other section to be discussed. Where the first article on apple explained all the details on the proteomic level, characterizing the proteins that are instrumental in the fruit development and with careful manipulation can contribute to the improved quality of the fruit, vastly neglected the metabolomic analysis. The second article in spite of being on protein profiling, was more focussed on explaining the metabolic pathways of the different sugars and organic acids that are accumulated in the fruit responsible for the colour and taste development of the fruit than evaluating the protein expression patterns. However the information provided by both the papers are appreciable and can prove to be instrumental in further research studies that could shed light on the expression patterns of the proteins in the early developmental stages of the fruit development, and can be instrumental in the manipulation of these protein expression pathways to improve the quality of such fruits with high market value exponentially. References: Chagn, D., Crowhurst, R.N., Troggio, M., Davey, M.W., Gilmore, B., Lawley, C., Vanderzande, S., Hellens, R.P., Kumar, S., Cestaro, A. and Velasco, R., 2012. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple.PLoS one,7(2), p.e31745. Chagn, D., Krieger, C., Rassam, M., Sullivan, M., Fraser, J., Andr, C., Pindo, M., Troggio, M., Gardiner, S.E., Henry, R.A. and Allan, A.C., 2012. QTL and candidate gene mapping for polyphenolic composition in apple fruit.BMC Plant Biology,12(1), p.12. Cohen, R., Elkabetz, M. and Edelstein, M., 2016. Variation in the responses of melon and watermelon to Macrophomina phaseolina.Crop Protection,85, pp.46-51. Eccher, G., Ferrero, S., Populin, F., Colombo, L. and Botton, A., 2014. Apple (Malus domestica L. Borkh) as an emerging model for fruit development.Plant Biosystems-An International Journal Dealing with all Aspects of Plant Biology,148(1), pp.157-168. Gambino, G. and Gribaudo, I., 2012. Genetic transformation of fruit trees: current status and remaining challenges.Transgenic research,21(6), pp.1163-1181. Guo, X., Xu, J., Cui, X., Chen, H. and Qi, H., 2017. iTRAQ-based Protein Profiling and Fruit Quality Changes at Different Development Stages of Oriental Melon.BMC Plant Biology,17(1), p.28. Ireland, H.S., Yao, J.L., Tomes, S., Sutherland, P.W., Nieuwenhuizen, N., Gunaseelan, K., Winz, R.A., David, K.M. and Schaffer, R.J., 2013. Apple SEPALLATA1/2?like genes control fruit flesh development and ripening.The Plant Journal,73(6), pp.1044-1056. Kuang, J.F., Chen, L., Shan, W., Yang, S., Lu, W.J. and Chen, J.Y., 2013. Molecular characterization of two banana ethylene signaling component MaEBFs during fruit ripening.Postharvest Biology and Technology,85, pp.94-101. Li, M., Feng, F. and Cheng, L., 2012. Expression patterns of genes involved in sugar metabolism and accumulation during apple fruit development.PLoS One,7(3), p.e33055. Li, M., Li, D., Feng, F., Zhang, S., Ma, F. and Cheng, L., 2016. Proteomic analysis reveals dynamic regulation of fruit development and sugar and acid accumulation in apple.Journal of experimental botany, p.erw277. Lin, C.Y., Ku, H.M., Chiang, Y.H., Ho, H.Y., Yu, T.A. and Jan, F.J., 2012. Development of transgenic watermelon resistant to Cucumber mosaic virus and Watermelon mosaic virus by using a single chimeric transgene construct.Transgenic research,21(5), pp.983-993. Ma, F., 2012.Carbon and nitrogen metabolism in transgenic apple leaves with decreased sorbitol synthesis. CORNELL UNIVERSITY. McAtee, P., Karim, S. and Schaffer, R.J., 2013. A dynamic interplay between phytohormones is required for fruit development, maturation, and ripening.Frontiers in plant science,4, p.79. Monforte, A.J., Diaz, A., Cao-Delgado, A. and van der Knaap, E., 2014. The genetic basis of fruit morphology in horticultural crops: lessons from tomato and melon.Journal of Experimental Botany,65(16), pp.4625-4637. Nogueira, S.B., Labate, C.A., Gozzo, F.C., Pilau, E.J., Lajolo, F.M. and do Nascimento, J.R.O., 2012. Proteomic analysis of papaya fruit ripening using 2DE-DIGE.Journal of proteomics,75(4), pp.1428-1439. Razzaq, K., Khan, A.S., Malik, A.U. and Shahid, M., 2013. Ripening period influences fruit softening and antioxidative system of Samar Bahisht Chaunsamango.Scientia Horticulturae,160, pp.108-114. Verde, I., Abbott, A.G., Scalabrin, S., Jung, S., Shu, S., Marroni, F., Zhebentyayeva, T., Dettori, M.T., Grimwood, J., Cattonaro, F. and Zuccolo, A., 2013. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.Nature genetics,45(5), pp.487-494. Wei, X., Liu, F., Chen, C., Ma, F. and Li, M., 2014. The Malus domestica sugar transporter gene family: identifications based on genome and expression profiling related to the accumulation of fruit sugars.Frontiers in plant science,5, p.569.