Investigating proteome and transcriptome defense response of table grapes induced by Yarrowia lipolytica
Introduction
Postharvest decay caused by pathogen infection in fruits during the process of picking and harvesting have brought tremendous economic losses. Recently, antagonistic yeast has become a research hotspot in controlling postharvest decay of fruits, and has prospective to replace chemical methods (Droby et al., 2009). Yarrowia lipolytica is an antagonistic yeast, our previous research results confirmed that Y. lipolytica could effectively control postharvest diseases of grapes caused by Penicillium rubens (Wang et al., 2019). It was proved that Y. lipolytica could rapidly colonized in the wound or on the surface of grapes and maintained a higher yeast cell count at 20 °C as well as 4 °C (Yang et al., 2017). Y. lipolytica could induce defense-related enzyme activities of grapes, such as polyphenoloxidase (PPO), peroxidase (POD), catalase (CAT), phenylalanine ammonialyase (PAL), ascorbate peroxidase (APX) and β-1,3 glucanase (GLU), and enhance the expression levels of genes encoding these defense-related enzymes (Wang et al., 2019), in order to improve the resistance to pathogens. Induced resistance in plants was an important physiological mechanism of resistance to pathogen. However, there were a few studies about molecular mechanism of induced resistance of fruits.
In order to understand the molecular mechanisms of induced resistance, proteomics and transcriptomics approaches were applied in the studies of postharvest fruit diseases. Proteomics could explore all the expressed proteins after transcription and translation, and can reflect the expression level of proteins under special treatment conditions in specific tissues (Earley et al., 2010). It was reported that when 1 × 108 cells/mL of Y. lipolytica cells were added into apple wounds, after 3 days, the two-dimensional electrophoresis and mass spectrometry study results showed that 35 proteins were identified as differentially expressed, among which the expression levels of pathogenesis-related (PR) proteins (PR10, PR5 and PR9), dehydrin, antiallergic protein and other resistant proteins were up-regulated (Zhang et al., 2017a). Pichia membranefaciens is also an antagonistic yeast, could induce the expression of antioxidant proteins, PRs, antioxidant enzymes and other proteins of peach fruit (Zhang et al., 2017b). The higher expression of these proteins could enhance the resistance of fruits against pathogens. Similar proteomic study also proved that expression of benzoquinone oxidoreductase and streptozotocin 5 were induced in pear fruits treated with P. caribica, which might be related to the disease resistance mechanism of pear fruit (Xu et al., 2013).
Transcriptomics study comprises of information about total RNA extracted from certain tissue. First, the cDNA was synthesized using RNA. Then evaluation of the cDNA library was carried out and finally, the biological analysis was practiced through Next-Generation Sequencing (NGS) platform (Wu et al., 2014). A previous study on the transcriptomics of grapes treated with Metschnikowia fructicola showed that there were 830 differentially expressed genes (DEGs) were identified, of which 539 up-regulated DEGs and 291 down-regulated DEGs. Among the up-regulated DEGs, 6 were related to oxidative stress, including respiratory burst oxidase homologue B, cytochrome B5 isoform B, oxygen transporter, peroxidase, oxidoreductase, l-ascorbate peroxidase, CDSP32; 4 DEGs associated with pathogenesis, including chitinase, trypsin and protease inhibitor family protein, acidic endochitinase, β-1,3-glucanase 3; 4 DEGs involved in signal transduction, including calcium-binding EF hand family protein, mitogen-activated protein kinase kinase, GTP binding, G Protein (Hershkovitz et al., 2012). All of those genes were associated with disease resistance in grapes. Another transcriptomics study in pear fruits treated with M. guilliermondii reported that the expression levels of G-protein coupled receptor 1-like, cationic peroxidase 1-like, β-glucosidase 12-like, WRKY and PR10 were increased and eventually induced by M. guilliermondii (Yan et al., 2018b).
Many researchers have already studied the biological control of postharvest diseases of grapes by antagonistic yeasts, but the explication for the control of postharvest diseases of grapes by yeasts mainly focused on competition for nutrition and space, parasitism, induced resistance, and so on (Wang et al., 2019). Still there were a very few studies available about the molecular mechanism of induced resistance. Therefore, the objectives of this study were to investigate (1) the changes of differentially expressed proteins in grapes after treated with Y. lipolytica or distilled water by proteomics analysis; (2) changes of differentially expressed genes in grapes after treated with Y. lipolytica or distilled water by transcriptomics analysis.
Section snippets
Fruits and yeast
Table grapes (Vitis vinifera L. “Red Globe Grape”) were harvested at commercial maturity from an orchard in Zhenjiang, Jiangsu province. The flowering period of table grapes is from April to May, and in August ripe grapes entered to the market, in the next several months following August, the same colour and lustre, healthy and homogenous fruits were selected for the experiment. Fruits were selected randomly and sterilized with 0.1 % NaClO for 2 min, and then washed with tap water, and used for
2-DE analysis of proteins induced by Y. lipolytica in grapes and identification of differentially expressed proteins with MS/MS
2-DE analysis of proteins induced by Y. lipolytica in grapes is shown in Fig. 1. Differently expressed proteins were assayed by comparing the yeast-treated sample (grapes treated with Y. lipolytica) and the control sample (grapes treated with sterile water) after 3 days incubation. The range of isoelectric point (PI) and the molecular mass for most proteins were 3–10 and 14.4–97.4 kDa, respectively. 47 high abundance protein spots were selected with ImageMaster 7.0 software (ratio >1.5).
Discussion
It has been proved that Y. lipolytica as an antagonistic yeast, could control postharvest decay of grapes caused by P. rubens, reduce OTA content in grapes produced by P. rubens and enhance the defense-related enzyme activities (Wang et al., 2019). It was also reported that Y. lipolytica could efficiently control postharvest decay caused by P. expansum and B. cinerea in apples. In the present study, GO categorization of DEGs in table grapes treated with Y. lipolytica mainly included signal
CRediT authorship contribution statement
Lina Zhao: Writing - original draft, Data curation. Meiyan Wang: Investigation, Validation. Bo Li: Investigation, Validation. Solairaj Dhanasekaran: Writing - review & editing. Kaili Wang: Formal analysis, Methodology. Xiangyu Gu: Formal analysis, Methodology. Xiaoyun Zhang: Software. Hongyin Zhang: Conceptualization, Funding acquisition, Supervision.
Declaration of Competing Interest
The authors declare that there is no conflicts of interest.
Acknowledgments
This work was supported by the National Natural Science Foundation of China (31701971), the China Postdoctoral Science Foundation (2018M630532) and Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake (hzhlab1703).
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