iTRAQ-based analysis of leaf proteome identifies important proteins in secondary metabolite biosynthesis and defence pathways crucial to cross-protection against TMV

Transcriptome analysis of the synergistic mechanisms between two strains of potato virus Y in Solanum tuberosum L

Many viruses employ a process known as superinfection exclusion (SIE) to block subsequent entry or replication of the same or closely related viruses in the cells they occupy. SIE is also referred to as Cross-protection refers to the situation where a host plant infected by a mild strain of a virus or viroid gains immunity against a more severe strain closely related to the initial infectant. The mechanisms underlying cross-protection are not fully understood. In this study, we performed a comparative transcriptomic analysis of potato (Solanum tuberosum L.) leaves. The strains PVYN-Wi-HLJ-BDH-2 and PVYNTN-NW-INM-W-369-12 are henceforth designated as BDH and 369, respectively. In total, 806 differentially expressed genes (DEGs) were detected between the Control and JZ (preinfected with BDH and challenge with 369) treatment. Gene Ontology (GO) analysis showed that the response to external biological stimulation, signal transduction, kinase, immunity, redox pathways were significantly enriched. Among these pathways, we identified numerous differentially expressed metabolites related to virus infection. Moreover, our data also identified a small set of genes that likely play important roles in the establishment of cross-protection. Specifically, we observed significant differential expression of the A1-II gamma-like gene, elongation factor 1-alpha-like gene, and subtilisin-like protease StSBT1.7 gene, with StSBT1.7 being the most significant in our transcriptome data. These genes can stimulate the expression of defense plant genes, induce plant chemical defense, and participate in the induction of trauma and pathogenic bacteria. Our findings provided insights into the mechanisms underlying the ability of mild viruses to protect host plants against subsequent closely related virus infection in Solanum tuberosum L.

Cyberlindnera jadinii yeast as a functional protein source: Modulation of immunoregulatory pathways in the intestinal proteome of zebrafish (Danio rerio)

Yeasts contain bioactive components that can enhance fish immune robustness and disease resistance. Our study focused on analyzing intestinal immunoregulatory pathways in zebrafish (Danio rerio) using iTRAQ and 2D LC-MS/MS to quantify intestinal proteins. Zebrafish were fed either control diet (C) or diet supplemented with autolyzed Cyberlindnera jadinii (ACJ). KEGG analysis revealed that ACJ yeast diet induced increased abundance of proteins related to arginine and proline metabolism, phagosome, C-lectin receptor signaling, ribosome and PPAR signaling pathways, which can modulate and enhance innate immune responses. ACJ yeast diet also showed decreased abundance of proteins associated with inflammatory pathways, including apoptosis, necroptosis and ferroptosis. These findings indicate boosted innate immune response and control of inflammation-related pathways in zebrafish intestine. Our findings in the well annotated proteome of zebrafish enabled a detailed investigation of intestinal responses and provide insight into health-beneficial effects of yeast species C. jadinii, which is relevant for aquaculture species.

iTRAQ-based proteomics identifies proteins associated with betaine accumulation in Lycium barbarum L

In order to better understand the mechanism of betaine accumulation in Lycium barbarum L. (LBL), we used iTRAQ (Isotope relative and absolute quantitative labeling) proteomics to screen and identify differentially abundant proteins (DAPs) at five stages (S1-young fruit stage, S2-green fruit stage, S3-early yellowing stage, S4-late yellowing stage, S5-ripening stage). A total of 1799 DAPs and 171 betaine-related DAPs were identified, and phosphatidylethanolamine N-methyltransferase (NMT), choline monooxygenase (CMO), and betaine aldehyde dehydrogenase (BADH) were found to be the key enzymes related to betaine metabolism. These proteins are mainly involved in carbohydrates, amino acids and their derivatives, fatty acids, carboxylic acids, photosynthesis and photoprotection, isoquinoline alkaloid biosynthesis, peroxisomes, and glycine, serine, and threonine metabolism. Three of the key enzymes were also up- and down-regulated to different degrees at the mRNA level. The study provide new insights into the of mechanism of betaine accumulation in LBL. SIGNIFICANCE: Betaine, a class of naturally occurring, water-soluble alkaloids, has been found to be widespread in animals, higher plants, and microbes. In addition to being an osmotic agent, betaine has biological functions such as hepatoprotection, neuroprotection, and antioxidant activity. Betaine metabolism (synthesis and catabolism) is complexly regulated by developmental and environmental signals throughout the life cycle of plant fruit maturation. As a betaine-accumulating plant, little has been reported about the regulatory mechanisms of betaine metabolism during the growth and development of Lycium barbarum L. (LBL) fruit. Therefore, this study used iTRAQ quantitative proteomics technology to investigate the abundance changes of betaine-related proteins in LBL fruit, screen and analyze the differential abundance proteins related to betaine metabolism, and provide theoretical references for the in-depth study of the mechanism of betaine metabolism in LBL fruit.

Potato Virus Y Strain N-Wi Offers Cross-Protection in Potato Against Strain NTN-NW by Superior Competition

Potato virus Y (PVY) is one of the most economically important pathogens of potato. PVY exhibits different phenotypes in dissimilar potato cultivars. Previously, we observed that two recombinant isolates, PVY^N-Wi-HLJ-BDH-2 (BDH) and PVY^NTN-NW(SYR-II)-INM-W-369-12 (369), exhibited different virulence levels in potato cultivar Kexin 13 despite high genome sequence identity. Indeed, 369 induced severe necrosis and plant death in severe cases in Kexin 13 and severe mosaic in cultivar Yanshu 8, whereas BDH caused mainly mosaic symptoms on the plants of both cultivars. We hypothesized that preinfection of plants with BDH could cross-protect them from 369 infection, and not vice versa. Challenge inoculation, either by mechanical wounding or through grafting, with 369 on plants that were preinfected with BDH did not augment the symptom expression in both cultivars. Reverse transcription quantitative PCR analysis showed that, after challenge inoculation with 369, the titer of the isolate on BDH-preinfected plants remained at a low level (about 3 × 10⁴ copy/µl) during the tested time course (0 h to 30 days). In contrast, in plants that were preinoculated with buffer (mock) and challenge inoculated with 369, the titer of 369 increased continuously until reaching its highest level of about 2 × 10⁷ (Yanshu 8) and about 4 × 10⁸ (Kexin 13) during the time course. Surprisingly, in plants that were preinfected with 369 and challenge inoculated with BDH, the accumulation of BDH reached nearly the same level as that in plants that were preinoculated with buffer and challenge inoculated with BDH. Taken together, these results suggest that PVY^N-Wi mediated cross-protection against PVY^NTN-NW(SYR-II) by superior competition and better fitness.

Presence of a Mitovirus Is Associated with Alteration of the Mitochondrial Proteome, as Revealed by Protein–Protein Interaction (PPI) and Co-Expression Network Models in Chenopodium quinoa Plants

Simple Summary

Plants often harbor persistent plant virus infection transmitted only vertically through seeds, resulting in no obvious symptoms (cryptic infections). Several studies have shown that such cryptic infections provide resilience against abiotic (and biotic) stress. We have recently discovered a new group of cryptic plant viruses infecting mitochondria (plant mitovirus). Mitochondria are cellular organelles displaying a pivotal role in protecting cells from the stress of nature . Here, we look at the proteomic alterations caused by the mitovirus cryptic infection of Chenopodium quinoa by Systems Biology approaches allowing one to evaluate data at holistic level. Quinoa is a domesticated plant species with many exciting features of abiotic stress resistance, and it is distinguished by its exceptional nutritional characteristics, such as the content and quality of proteins, minerals, lipids, and tocopherols. These features determined the growing interest for the quinoa crop by the scientific community and international organizations since they provide opportunities to produce high-value grains in arid, high-salt and high-UV agroecological environments. We discovered that quinoa lines hosting mitovirus activate some metabolic processes that might help them face drought. These findings present a new perspective for breeding crop plants through the augmented genome provided by accessory cryptic viruses to be investigated in the future.

Abstract

Plant mitoviruses belong to Mitoviridae family and consist of positive single-stranded RNA genomes replicating exclusively in host mitochondria. We previously reported the biological characterization of a replicating plant mitovirus, designated Chenopodium quinoa mitovirus 1 (CqMV1), in some Chenopodium quinoa accessions. In this study, we analyzed the mitochondrial proteome from leaves of quinoa, infected and not infected by CqMV1. Furthermore, by protein–protein interaction and co-expression network models, we provided a system perspective of how CqMV1 affects mitochondrial functionality. We found that CqMV1 is associated with changes in mitochondrial protein expression in a mild but well-defined way. In quinoa-infected plants, we observed up-regulation of functional modules involved in amino acid catabolism, mitochondrial respiratory chain, proteolysis, folding/stress response and redox homeostasis. In this context, some proteins, including BCE2 (lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex), DELTA-OAT (ornithine aminotransferase) and GR-RBP2 (glycine-rich RNA-binding protein 2) were interesting because all up-regulated and network hubs in infected plants; together with other hubs, including CAT (catalase) and APX3 (L-ascorbate peroxidase 3), they play a role in stress response and redox homeostasis. These proteins could be related to the higher tolerance degree to drought we observed in CqMV1-infected plants. Although a specific causative link could not be established by our experimental approach at this stage, the results suggest a new mechanistic hypothesis that demands further in-depth functional studies.

iTRAQ-based protein analysis provides insight into heterologous superinfection exclusion with TMV-43A against CMV in tobacco (Nicotiana benthamiana) plants

Heterologous superinfection exclusion (HSE) is a phenomenon of an initial virus infection which prevents reinfection by a distantly related or unrelated challenger virus strain in the same host. Here, we demonstrate that a mild strain mutant of Tobacco mosaic virus (TMV-43A) can protect Nicotiana benthamiana plants against infection by a challenger Cucumber mosaic virus (CMV)-Fny strain. The isobaric tags for relative and absolute quantification (iTRAQ) technique was used to investigate proteome of N. benthamiana plant during HSE. Our results indicated that in superinfected plants, the PSI and PSII proteins in the photosynthetic pathway increased in abundance, providing sufficient energy to plants for survival. The fatty acid synthesis-related proteins acetyl-CoA carboxylase 1-like and fatty acid synthase were decreased in abundance, affecting the formation of virus replication complex, which in turn reduced CMV replication and lessen hijacking of basic building blocks of RNA transcription and protein synthesis required for normal host functions. This is the first analyses of host proteins that are correlated to HSE between two unrelated plant viruses TMV-43A and CMV in N. benthamiana plants. BIOLOGICAL SIGNIFICANCE: CMV is one of the most studied host-virus interaction models in plants. It infects both monocot and dicot crop plants, causing significant economic losses. Superinfection exclusion (also known as cross protection) is one of the methods to combat virus infection. However, there is lack of proteome information of heterologous superinfection exclusion between two taxonomically unrelated plant viruses (such as between CMV and TMV). An iTRAQ-based quantitative approach was used to study proteomics of superinfection, where TMV-43A acts as a protector of N. benthamiana plants against its challenger CMV. Results showed that TMV-43A protects host plants and prevents plant death from CMV infection. This study provided insights into host responses involving multiple host pathways: photosynthesis, plant defence, carbon metabolism, translation and protein processing, fatty acid metabolism and amino acid biosynthesis. The findings provide a reference database for other viruses and increase our knowledge in host proteins that are correlated to superinfection.

Advances of proteomics technologies for multidrug-resistant mechanisms

Multidrug resistance (MDR) is a vital issue in cancer treatment. Drug resistance can be developed through a variety of mechanisms, including increased drug efflux, activation of detoxifying systems and DNA repair mechanisms, and escape of drug-induced apoptosis. Identifying the exact mechanism related in a particular case is a difficult task. Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. In recent years, comparative proteomic methods have been performed to analyze MDR mechanisms in drug-selected model cancer cell lines. In this paper, we review the recent developments and progresses by comparative proteomic approaches to identify potential MDR mechanisms in drug-selected model cancer cell lines, which may help understand and design chemical sensitizers.

Identification of a Novel NtLRR-RLK and Biological Pathways That Contribute to Tolerance of TMV in Nicotiana tabacum

Tobacco mosaic virus (TMV) infection can causes serious damage to tobacco crops. To explore the approach of preventing TMV infection of plants, two tobacco cultivars with different resistances to TMV were used to analyze transcription profiling before and after TMV infection. The involvement of biological pathways differed between the tolerant variety (Yuyan8) and the susceptible variety (NC89). In particular, the plant-virus interaction pathway was rapidly activated in Yuyan8, and specific resistance genes were enriched. Liquid chromatography tandem mass spectrometry analysis detected large quantities of antiviral substances in the tolerant Yuyan8. A novel Nicotiana tabacum leucine-rich repeat receptor kinase (NtLRR-RLK) gene was identified as being methylated and this was verified using bisulfite sequencing. Transient expression of TMV-green fluorescent protein in pRNAi-NtLRR-RLK transgenic plants confirmed that NtLRR-RLK was important for susceptibility to TMV. The specific protein interaction map generated from our study revealed that levels of BIP1, E3 ubiquitin ligase, and LRR-RLK were significantly elevated, and all were represented at node positions in the protein interaction map. The same expression tendency of these proteins was also found in pRNAi-NtLRR-RLK transgenic plants at 24 h after TMV inoculation. These data suggested that specific genes in the infection process can activate the immune signal cascade through different resistance genes, and the integration of signal pathways could produce resistance to the virus. These results contribute to the overall understanding of the molecular basis of plant resistance to TMV and in the long term could identify new strategies for prevention and control virus infection.

iTRAQ-based proteomic analysis reveals several key metabolic pathways associated with male sterility in Salvia miltiorrhiza

Male sterility is a common phenomenon in flowering plants, and it has been widely used in hybrid seed production in a number of economically important crops. In 2002, our team discovered a natural male sterile mutant of Salvia miltiorrhiza. It provided us with the possibility of obtaining stable and controllable quality. To study the molecular mechanism of male sterility in S. miltiorrhiza, we generated proteomic profiles comparing the male sterile mutant type (MT) and wild type (WT) using iTRAQ sequencing. We found a total of 639 differential abundant proteins (DAPs) between MT and WT buds. The DAPs associated with male sterility were mainly involved in (1) carbohydrate and energy metabolism, and (2) protein synthesis and degradation. Based on a comparison between the protein expression profiles of MT and WT, we elucidated a potential protein interaction network involved in male sterility. These results provide new potential biomarkers and insights into the molecular mechanism of male sterility in S. miltiorrhiza.

Male sterility is a common phenomenon in flowering plants, and it has been widely used in hybrid seed production in a number of economically important crops.

Cucumber mosaic virus resistance: Comparative proteomics of contrasting Cucumis sativus cultivars after long-term infection

Plant viruses are a significant threat to a wide range of host species, causing substantial losses in agriculture. Particularly, Cucumber mosaic virus (CMV) evokes severe symptoms, thus dramatically limiting yield. Activation of plant defense reactions is associated with changes in the cellular proteome to ensure virus resistance. Herein, we studied two cultivars of cucumber (Cucumis sativus) resistant host Heliana and susceptible host Vanda. Plant cotyledons were mechanically inoculated with CMV isolate PK1, and systemic leaves were harvested at 33 days post-inoculation. Proteome was profiled by ultrahigh-performance liquid chromatography and comprehensively quantified by ion mobility enhanced mass spectrometry. From 1516 reproducibly quantified proteins using a label-free approach, 133 were differentially abundant among cultivars or treatments by strict statistic and effect size criteria. Pigments and hydrogen peroxide measurements corroborated proteomic findings. Comparison of both cultivars in the uninfected state highlighted more abundant photosynthetic and development-related proteins in resistant cucumber cultivar. Long-term CMV infection caused worse preservation of energy processes and less robust translation in the susceptible cultivar. Contrary, compatible plants had numerous more abundant stress and defense-related proteins. We proposed promising targets for functional validation in transgenic lines: A step toward durable virus resistance in cucurbits and other crops. SIGNIFICANCE: Sustainable production of crops requires an understanding of natural mechanisms of resistance/susceptibility to ubiquitous viral infections. We report original findings of comparative analysis of plant genotypes exposed to CMV. Deep discovery proteomics of resistant and susceptible cucumber cultivars, inoculated with widespread phytovirus, allowed to suggest several novel molecular targets for functional testing in plant protection strategies.

Proteomic Changes during MCMV Infection Revealed by iTRAQ Quantitative Proteomic Analysis in Maize

Maize chlorotic mottle virus (MCMV) has been occurring frequently worldwide and causes severe yield losses in maize (Zea mays). To better investigate the destructive effects of MCMV infection on maize plants, isobaric tagging for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed on MCMV infected maize cv. B73. A total of 972 differentially abundant proteins (DAPs), including 661 proteins with increased abundance and 311 proteins with reduced abundance, were identified in response to MCMV infection. Functional annotations of DAPs and measurement of photosynthetic activity revealed that photosynthesis was decreased, while the abundance of ribosomal proteins, proteins related to stress responses, oxidation-reduction and redox homeostasis was altered significantly during MCMV infection. Two DAPs, disulfide isomerases like protein ZmPDIL-1 and peroxiredoxin family protein ZmPrx5, were further analyzed for their roles during MCMV infection through cucumber mosaic virus-based virus-induced gene silencing (CMV-VIGS). The accumulation of MCMV was suppressed in ZmPDIL-1-silenced or ZmPrx5-silenced B73 maize, suggesting ZmPDIL-1 and ZmPrx5 might enhance host susceptibility to MCMV infection.

iTRAQ-based mitochondrial proteome analysis of the molecular mechanisms underlying postharvest senescence of Zizania latifolia

To explore the molecular mechanisms underlying postharvest senescence of Zizania latifolia, the changes in the mitochondrial proteome of plants treated with or without (control) 1-methyleyelopropene and ethylene during storage at room temperature for 0, 3 and 6 days were investigated using isobaric tags for relative and absolute quantitation (iTRAQ) labeling combined with two-dimensional liquid chromatography-tandem mass spectrometry. A total of 1,390 proteins with two or more peptides were identified, of which 211 showed a significant (p < .05) change (at least twofold) in relative abundance. Monitoring the parallel reaction validated the reliability and accuracy of the iTRAQ results. Bioinformatics and functional analysis of these differentially expressed proteins (DEPs) revealed that postharvest senescence of Z. latifolia could be attributed to (a) strengthened pentose phosphate pathway, (b) imbalanced protein, amino acid, organic acid, and fatty acid metabolism, (c) disordered energy homeostasis, (d) exacerbated oxidative damage, (e) RNA degradation, (f) activation of the Ca²⁺ , mitogen-activated protein kinase, and jasmonic acid signaling pathways, (g) programed cell death, (h) excessive biosynthesis of secondary metabolites, or (i) degradation of cell structure. Our findings provide integrated insight into the molecular mechanisms of postharvest senescence during storage as well as the DEPs that show promise as targets for controlling senescence-induced quality deterioration of Z. latifolia. PRACTICAL APPLICATIONS: Postharvest senescence is the most important factor that causes fast quality deterioration of Zizania latifolia. The understanding of the processes leading to postharvest senescence of Z. latifolia is essential in enhancing the commercial value and extending the shelf life of the product. It is currently believed that the mitochondrial metabolism is closely related to postharvest senescence. For this, the changes of proteome in Z. latifolia mitochondria treated with or without (control) 1-MCP and ETH during storage at room temperature were investigated. Results showed that a variety of physiobiochemical responses occur during postharvest senescence of Z. latifolia. 1-MCP treatment significantly inhibited the changes of these physiobiochemical processes, finally, retarding the postharvest senescence of Z. latifolia. ETH treatment had opposite effects on proteome changes compared with 1-MCP treatment. Taken together, these results enrich the understanding of the molecular mechanisms of postharvest senescence of Z. latifolia.

In planta proximity-dependent biotin identification (BioID) identifies a TMV replication co-chaperone NbSGT1 in the vicinity of 126 kDa replicase

Tobacco mosaic virus (TMV) is a positive, single-stranded RNA virus. It encodes two replicases (126 kDa and 183 kDa), a movement protein and a coat protein. These proteins interact with host proteins for successful infection. Some host proteins such as eEF1α, Tm-1, TOM1, 14-3-3 proteins directly interact with Tobamovirus replication proteins. There are host proteins in the virus replication complex which do not interact with viral replicases directly, such as pyruvate kinase and glyceraldehyde-3-phosphate dehydrogenase. We have used Proximity-dependent biotin identification (BioID) technique to screen for transient or weak protein interactions of host proteins and viral replicase in vivo. We transiently expressed BirA* tagged TMV 126 kDa replicase in TMV infected Nicotiana benthamiana plants. Among 18 host proteins, we identified NbSGT1 as a potential target for further characterization. Silencing of NbSGT1 in N. benthamiana plants increased its susceptibility to TMV infection, and overexpression of NbSGT1 increased resistance to TMV infection. There were weak interactions between NbSGT1 and TMV replicases but no interaction between them was found in Y2H assay. It suggests that the interaction might be transient or indirect. Therefore, the BioID technique is a valuable method to identify weak or transient/indirect interaction(s) between pathogen proteins and host proteins in plants. BIOLOGICAL SIGNIFICANCE: TMV is a well characterized positive-strand RNA virus model for study of virus-plant host interactions. It infects >350 plant species and is one of the significant pathogens of crop loss globally. Many host proteins are involved in TMV replication complex formation. To date there are few techniques available for identifying interacting host proteins to viral proteins. There is limited knowledge on transient or non-interacting host proteins during virus infection/replication. In this study, we used agroinfiltration-mediated in planta BioID technique to identify transiently or non-interacting host proteins to viral proteins in TMV-infected N. benthamiana plants. This technique allowed us to identify potential candidate proteins in the vicinity of TMV 126 kDa replicase. We have selected NbSGT1 and its overexpression suppresses TMV replication and increase plant resistance. NbSGT1 is believed to interact transiently or indirectly with TMV replicases in the presence of Hsp90/Hsp70. BioID is a novel and powerful technique to identify transiently or indirectly interacting proteins in the study of pathogen-host interactions.

A New Era for Mild Strain Cross-Protection

Societal and environmental pressures demand high-quality and resilient cropping plants and plant-based foods grown with the use of low or no synthetic chemical inputs. Mild strain cross-protection (MSCP), the pre-immunization of a plant using a mild strain of a virus to protect against subsequent infection by a severe strain of the virus, fits with future-proofing of production systems. New examples of MSCP use have occurred recently. New technologies are converging to support the discovery and mechanism(s) of action of MSCP strains thereby accelerating the popularity of their use.