Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection

Abstract

Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it.

Plant Molecular Responses to Potato Virus Y: A Continuum of Outcomes from Sensitivity and Tolerance to Resistance

“…However, these observations are based on changes in transcript abundance. Translation between transcriptomics and proteomics data is not trivial, as transcriptomic data may not necessarily reflect protein abundance in these functional categories [93]. Recently, a proteomic analysis of potato ER response against PVY was published by Szajko et al where the authors showed that the stress-responsive proteins were the most abundant among the qualitative changes induced by PVY in the resistant genotype PW363 [56].…”

iTRAQ-Based Proteomic Analysis of Watermelon Fruits in Response to Cucumber green mottle mosaic virus Infection

“…The mRNAs can still be detected when translation is inhibited, while they cannot be translated into corresponding proteins [56,57]. Our study found that CGMMV infection significantly affected the accumulation levels of many ribosomal proteins and translation initiation factors in watermelon fruits (Table S6), which played important roles in post-transcriptional regulatory mechanisms [24]. These ribosomal proteins could stabilize the formation of ribosome around the start codons as well as affect translation efficiency.…”

“…Due to the limitations in the sensitivity of identification methods of present proteins, changes in abundance of some proteins were usually not detected [13,24]. Additionally, discrepancies between transcript and protein levels might originate from specific biological metabolic processes.…”

“…This technique has been widely applied in proteome sequencing studies with high accuracy and reproducibility in recent years. Moreover, there have been many reports on the utilization of the iTRAQ technique to study changes in plant physiological metabolisms in response to abiotic stresses, such as cold [15][16][17], heat [18], and salt [19], and biotic stresses, including fungi [20,21], bacteria [22,23], and viruses [24,25].…”

Next generation sequencing and proteomics in plant virology: how is Colombia doing?

“…RNA-Seq has been used to find insights in several plant-virus interactions, including model plants such as Arabidopsis thaliana (Sun et al, 2016;Wu et al, 2016), plants of agronomical importance such as Oryza sativa (Blazquez et al, 2013;Wong et al, 2015), Zea mays (Chakrabarty et al, 2018), Manihot esculenta (Fang et al, 2014;Amuge et al, 2017;Anjanappa et al, 2018), Solanum tuberosum (Goyer et al, 2015;Stare et al, 2017) and tropical fruits such as C. papaya (Madroñero et al, 2018). However, to date (04-10-2019), a Google Scholar search, the NCBI PMC database, and the Web of Science using the queries "plant", "virus", "interaction", "transcriptome", "RNA-Seq", and "Colombia" with different combinations did not yield any results for plant-virus interactions research developed in Colombia.…”