Proteomic analysis of papaya (Carica papaya L.) displaying typical sticky disease symptoms

The Role of Plant Latex in Virus Biology

At least 20,000 plant species produce latex, a capacity that appears to have evolved independently on numerous occasions. With a few exceptions, latex is stored under pressure in specialized cells known as laticifers and is exuded upon injury, leading to the assumption that it has a role in securing the plant after mechanical injury. In addition, a defensive effect against insect herbivores and fungal infections has been well established. Latex also appears to have effects on viruses, and laticifers are a hostile environment for virus colonization. Only one example of successful colonization has been reported: papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2) in Carica papaya. In this review, a summary of studies that support both the pro- and anti-viral effects of plant latex compounds is provided. The latex components represent a promising natural source for the discovery of new pro- and anti-viral molecules in the fields of agriculture and medicine.

A Capsid Protein Fragment of a Fusagra-like Virus Found in Carica papaya Latex Interacts with the 50S Ribosomal Protein L17

Papaya sticky disease is caused by the association of a fusagra-like and an umbra-like virus, named papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), respectively. Both viral genomes are encapsidated in particles formed by the PMeV ORF1 product, which has the potential to encode a protein with 1563 amino acids (aa). However, the structural components of the viral capsid are unknown. To characterize the structural proteins of PMeV and PMeV2, virions were purified from Carica papaya latex. SDS-PAGE analysis of purified virus revealed two major proteins of ~40 kDa and ~55 kDa. Amino-terminal sequencing of the ~55 kDa protein and LC-MS/MS of purified virions indicated that this protein starts at aa 263 of the deduced ORF1 product as a result of either degradation or proteolytic processing. A yeast two-hybrid assay was used to identify Arabidopsis proteins interacting with two PMeV ORF1 product fragments (aa 321-670 and 961-1200). The 50S ribosomal protein L17 (AtRPL17) was identified as potentially associated with modulated translation-related proteins. In plant cells, AtRPL17 co-localized and interacted with the PMeV ORF1 fragments. These findings support the hypothesis that the interaction between PMeV/PMeV2 structural proteins and RPL17 is important for virus-host interactions.

Analysis of proteomic changes in cassava cv. Kasetsart 50 caused by Sri Lankan cassava mosaic virus infection

BACKGROUND

Sri Lankan cassava mosaic virus (SLCMV) is a plant virus causing significant economic losses throughout Southeast Asia. While proteomics has the potential to identify molecular markers that could assist the breeding of virus resistant cultivars, the effects of SLCMV infection in cassava have not been previously explored in detail.

RESULTS

Liquid Chromatography-Tandem Mass Spectrometry (LC/MS-MS) was used to identify differentially expressed proteins in SLCMV infected leaves, and qPCR was used to confirm changes at mRNA levels. LC/MS-MS identified 1,813 proteins, including 479 and 408 proteins that were upregulated in SLCMV-infected and healthy cassava plants respectively, while 109 proteins were detected in both samples. Most of the identified proteins were involved in biosynthetic processes (29.8%), cellular processes (20.9%), and metabolism (18.4%). Transport proteins, stress response molecules, and proteins involved in signal transduction, plant defense responses, photosynthesis, and cellular respiration, although present, only represented a relatively small subset of the detected differences. RT-qPCR confirmed the upregulation of WRKY 77 (A0A140H8T1), WRKY 83 (A0A140H8T7), NAC 6 (A0A0M4G3M4), NAC 35 (A0A0M5JAB4), NAC 22 (A0A0M5J8Q6), NAC 54 (A0A0M4FSG8), NAC 70 (A0A0M4FEU9), MYB (A0A2C9VER9 and A0A2C9VME6), bHLH (A0A2C9UNL9 and A0A2C9WBZ1) transcription factors. Additional upregulated transcripts included receptors, such as receptor-like serine/threonine-protein kinase (RSTK) (A0A2C9UPE4), Toll/interleukin-1 receptor (TIR) (A0A2C9V5Q3), leucine rich repeat N-terminal domain (LRRNT_2) (A0A2C9VHG8), and cupin (A0A199UBY6). These molecules participate in innate immunity, plant defense mechanisms, and responses to biotic stress and to phytohormones.

CONCLUSIONS

We detected 1,813 differentially expressed proteins infected cassava plants, of which 479 were selectively upregulated. These could be classified into three main biological functional groups, with roles in gene regulation, plant defense mechanisms, and stress responses. These results will help identify key proteins affected by SLCMV infection in cassava plants.

Cellular Growth Arrest and Efflux Pumps Are Associated With Antibiotic Persisters in Streptococcus pyogenes Induced in Biofilm-Like Environments

Streptococcus pyogenes (group A Streptococcus-GAS) is an important pathogen for humans. GAS has been associated with severe and invasive diseases. Despite the fact that these bacteria remain universally susceptible to penicillin, therapeutic failures have been reported in some GAS infections. Many hypotheses have been proposed to explain these antibiotic-unresponsive infections; however, none of them have fully elucidated this phenomenon. In this study, we show that GAS strains have the ability to form antimicrobial persisters when inoculated on abiotic surfaces to form a film of bacterial agglomerates (biofilm-like environment). Our data suggest that efflux pumps were possibly involved in this phenomenon. In fact, gene expression assays by real-time qRT-PCR showed upregulation of some genes associated with efflux pumps in persisters arising in the presence of penicillin. Phenotypic reversion assay and whole-genome sequencing indicated that this event was due to non-inherited resistance mechanisms. The persister cells showed downregulation of genes associated with protein biosynthesis and cell growth, as demonstrated by gene expression assays. Moreover, the proteomic analysis revealed that susceptible cells express higher levels of ribosome proteins. It is remarkable that previous studies have reported the recovery of S. pyogenes viable cells from tissue biopsies of patients presented with GAS invasive infections and submitted to therapy with antibiotics. The persistence phenomenon described herein brings new insights into the origin of therapeutic failures in S. pyogenes infections. Multifactorial mechanisms involving protein synthesis inhibition, cell growth impairment and efflux pumps seem to play roles in the formation of antimicrobial persisters in S. pyogenes.

Plant Cell Wall as a Key Player During Resistant and Susceptible Plant-Virus Interactions

The cell wall is a complex and integral part of the plant cell. As a structural element it sustains the shape of the cell and mediates contact among internal and external factors. We have been aware of its involvement in both abiotic (like drought or frost) and biotic stresses (like bacteria or fungi) for some time. In contrast to bacterial and fungal pathogens, viruses are not mechanical destructors of host cell walls, but relatively little is known about remodeling of the plant cell wall in response to viral biotic stress. New research results indicate that the cell wall represents a crucial active component during the plant’s response to different viral infections. Apparently, cell wall genes and proteins play key roles during interaction, having a direct influence on the rebuilding of the cell wall architecture. The plant cell wall is involved in both susceptibility as well as resistance reactions. In this review we summarize important progress made in research on plant virus impact on cell wall remodeling. Analyses of essential defensive wall associated proteins in susceptible and resistant responses demonstrate that the components of cell wall metabolism can affect the spread of the virus as well as activate the apoplast- and symplast-based defense mechanisms, thus contributing to the complex network of the plant immune system. Although the cell wall reorganization during the plant-virus interaction remains a challenging task, the use of novel tools and methods to investigate its composition and structure will greatly contribute to our knowledge in the field.

Battle of Three: The Curious Case of Papaya Sticky Disease

Among the most serious problems in papaya production are the viruses associated with papaya ringspot and papaya sticky disease (PSD). PSD concerns producers worldwide because its symptoms are extremely aggressive and appear only after flowering. As no resistant cultivar is available, several disease management strategies have been used in affected countries, such as the use of healthy seeds, exclusion of the pathogen, and roguing. In the 1990s, a dsRNA virus, papaya meleira virus (PMeV), was identified in Brazil as the causal agent of PSD. However, in 2016 a second virus, papaya meleira virus 2 (PMeV2), with an ssRNA genome, was also identified in PSD plants. Only PMeV is detected in asymptomatic plants, whereas all symptomatic plants contain both viral RNAs separately packaged in particles formed by the PMeV capsid protein. PSD also affects papaya plants in Mexico, Ecuador, and Australia. PMeV2-like viruses have been identified in the affected plants, but the partner virus(es) in these countries are still unknown. In Brazil, PMeV and PMeV2 reside in laticifers that promote spontaneous latex exudation, resulting in the affected papaya fruit's sticky appearance. Genes modulated in plants affected by PSD include those involved in reactive oxygen species and salicylic acid signaling, proteasomal degradation, and photosynthesis, which are key plant defenses against PMeV complex infection. However, the complete activation of the defense response is impaired by the expression of negative effectors modulated by the virus. This review presents a summary of the current knowledge of the Carica papaya-PMeV complex interaction and management strategies.

Comparative proteomic analysis provides novel insights into the regulation mechanism underlying papaya (Carica papaya L.) exocarp during fruit ripening process

BACKGROUND

Papaya (Carica papaya L.) is a popular climacteric fruit, undergoing various physico-chemical changes during ripening. Although papaya is widely cultivated and consumed, few studies on the changes in metabolism during its ripening process at the proteasome level have been performed. Using a newly developed TMT-LCMS analysis, proteomes of papaya fruit at different ripening stages were investigated.

RESULTS

In total, 3220 proteins were identified, of which 2818 proteins were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. The KEGG enrichment analysis showed that various metabolic pathways were significantly altered, particularly in flavonoid and fatty acid metabolisms. The up-regulation of several flavonoid biosynthesis-related proteins may provide more raw materials for pigment biosynthesis, accelerating the color variation of papaya fruit. Variations in the fatty acid metabolism- and cell wall degradation-related proteins were investigated during the ripening process. Furthermore, the contents of several important fatty acids were determined, and increased unsaturated fatty acids may be associated with papaya fruit volatile formation.

CONCLUSIONS

Our data may give an intrinsic explanation of the variations in metabolism during the ripening process of papaya fruit.

Peanut Stunt Virus and Its Satellite RNA Trigger Changes in Phosphorylation in N. benthamiana Infected Plants at the Early Stage of the Infection

Signaling in host plants is an integral part of a successful infection by pathogenic RNA viruses. Therefore, identifying early signaling events in host plants that play an important role in establishing the infection process will help our understanding of the disease process. In this context, phosphorylation constitutes one of the most important post-translational protein modifications, regulating many cellular signaling processes. In this study, we aimed to identify the processes affected by infection with Peanut stunt virus (PSV) and its satellite RNA (satRNA) in Nicotiana benthamiana at the early stage of pathogenesis. To achieve this, we performed proteome and phosphoproteome analyses on plants treated with PSV and its satRNA. The analysis of the number of differentially phosphorylated proteins showed strong down-regulation in phosphorylation in virus-treated plants (without satRNA). Moreover, proteome analysis revealed more down-regulated proteins in PSV and satRNA-treated plants, which indicated a complex dependence between proteins and their modifications. Apart from changes in photosynthesis and carbon metabolism, which are usually observed in virus-infected plants, alterations in proteins involved in RNA synthesis, transport, and turnover were observed. As a whole, this is the first community (phospho)proteome resource upon infection of N. benthamiana with a cucumovirus and its satRNA and this resource constitutes a valuable data set for future studies.

Photosynthetic and Stress Responsive Proteins Are Altered More Effectively in Nicotiana benthamiana Infected with Plum pox virus Aggressive PPV-CR versus Mild PPV-C Cherry-Adapted Isolates

Plum pox virus (PPV, family Potyviridae) is one of the most important viral pathogens of Prunus spp. causing considerable damage to stone-fruit industry worldwide. Among the PPV strains identified so far, only PPV-C, PPV-CR, and PPV-CV are able to infect cherries under natural conditions. Herein, we evaluated the pathogenic potential of two viral isolates in herbaceous host Nicotiana benthamiana. Significantly higher accumulation of PPV capsid protein in tobacco leaves infected with PPV-CR (RU-30sc isolate) was detected in contrast to PPV-C (BY-101 isolate). This result correlated well with the symptoms observed in the infected plants. To further explore the host response upon viral infection at the molecular level, a comprehensive proteomic profiling was performed. Using reverse-phase ultra-high-performance liquid chromatography followed by label-free mass spectrometry quantification, we identified 38 unique plant proteins as significantly altered due to the infection. Notably, the abundances of photosynthesis-related proteins, mainly from the Calvin-Benson cycle, were found more aggressively affected in plants infected with PPV-CR isolate than those of PPV-C. This observation was accompanied by a significant reduction in the amount of photosynthetic pigments extracted from the leaves of PPV-CR infected plants. Shifts in the abundance of proteins that are involved in stimulation of photosynthetic capacity, modification of amino acid, and carbohydrate metabolism may affect plant growth and initiate energy formation via gluconeogenesis in PPV infected N. benthamiana. Furthermore, we suggest that the higher accumulation of H2O2 in PPV-CR infected leaves plays a crucial role in plant defense and development by activating the glutathione synthesis.

Spatiotemporal Changes in Xylan-1/Xyloglucan and Xyloglucan Xyloglucosyl Transferase (XTH-Xet5) as a Step-In of Ultrastructural Cell Wall Remodelling in Potato⁻Potato Virus Y (PVYNTN) Hypersensitive and Susceptible Reaction

One type of monitoring system in a plant cell is the cell wall, which intensively changes its structure during interaction with pathogen-stress factors. The wall plays a role as a dynamic and controlled structure, although it is not fully understood how relevant these modifications are to the molecular mechanisms during plant–virus interactions. In this work we localise the non-cellulosic polysaccharides such as xyloglucan, xylan (xylan-1) and xyloglucosyl transferase (XTH-Xet5), the enzyme that participates in the metabolism of xyloglucan. This provided us with information about the in situ distribution of the components of the hemicellulotic cell wall matrix in hypersensitive and susceptible potato–PVY^NTN interactions. The loosening of the cell wall was accompanied by an increase in xylan depositions during susceptible interactions, whereas, during the hypersensitive response, when the cell wall was reinforced, the xylan content decreased. Moreover, the PVY inoculation significantly redirected XTH-Xet5 depositions, regardless of types of interactions, compared to mock-inoculated tissues. Furthermore, the immunogold localisation clearly revealed the domination of Xet5 in the cell wall and in vesicles in the susceptible host. In contrast, in the resistant host increased levels of Xet5 were observed in cytoplasm, in the cell wall and in the trans-Golgi network. These findings show that the hypersensitive reaction activated XTH-Xet5 in the areas of xyloglucan endo-transglycosylase (XET) synthesis, which was then actively transported to cytoplasm, cell wall and to vacuoles. Our results provide novel insight into cell wall reorganisation during PVY^NTN infection as a response to biotic stress factors. These novel findings help us to understand the mechanisms of defence responses that are incorporated into the cell wall signalling network.

Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya

Global gene expression analysis indicates host stress responses, mainly those mediated by SA, associated to the tolerance to sticky disease symptoms at pre-flowering stage in Carica papaya. Carica papaya plants develop the papaya sticky disease (PSD) as a result of the combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), or PMeV complex. PSD symptoms appear only after C. papaya flowers. To understand the mechanisms involved in this phenomenon, the global gene expression patterns of PMeV complex-infected C. papaya at pre-and post-flowering stages were assessed by RNA-Seq. The result was 633 and 88 differentially expressed genes at pre- and post-flowering stages, respectively. At pre-flowering stage, genes related to stress and transport were up-regulated while metabolism-related genes were down-regulated. It was observed that induction of several salicylic acid (SA)-activated genes, including PR1, PR2, PR5, WRKY transcription factors, ROS and callose genes, suggesting SA signaling involvement in the delayed symptoms. In fact, pre-flowering C. papaya treated with exogenous SA showed a tendency to decrease the PMeV and PMeV2 loads when compared to control plants. However, pre-flowering C. papaya also accumulated transcripts encoding a NPR1-inhibitor (NPR1-I/NIM1-I) candidate, genes coding for UDP-glucosyltransferases (UGTs) and several genes involved with ethylene pathway, known to be negative regulators of SA signaling. At post-flowering, when PSD symptoms appeared, the down-regulation of PR-1 encoding gene and the induction of BSMT1 and JA metabolism-related genes were observed. Hence, SA signaling likely operates at the pre-flowering stage of PMeV complex-infected C. papaya inhibiting the development of PSD symptoms, but the induction of its negative regulators prevents the full-scale and long-lasting tolerance.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

Proteomics offers insight to the mechanism behind Pisum sativum L. response to pea seed-borne mosaic virus (PSbMV)

Pea seed-borne mosaic virus (PSbMV) significantly reduces yields in a broad spectra of legumes. The eukaryotic translation initiation factor has been shown to confer resistance to this pathogen, thus implying that translation and proteome dynamics play a role in resistance. This study presents the results of a proteome-wide analysis of Pisum sativum L. response to PSbMV infection. LC-MS profiling of two contrasting pea cultivars, resistant (B99) and susceptible (Raman) to PSbMV infection, detected >2300 proteins, 116 of which responded to PSbMV ten and/or twenty days post-inoculation. These differentially abundant proteins are involved in number of processes that have previously been reported in the plant-pathogen response, including protein and amino acid metabolism, stress signaling, redox homeostasis, carbohydrate metabolism, and lipid metabolism. We complemented our proteome-wide analysis work with targeted analyses of free amino acids and selected small molecules, fatty acid profiling, and enzyme activity assays. Data from these additional experiments support our findings and validate the biological relevance of the observed proteome changes. We found surprising similarities in the resistant and susceptible cultivars, which implies that a seemingly unaffected plant, with no detectable levels of PSbMV, actively suppresses viral replication.

BIOLOGICAL SIGNIFICANCE

Plant resistance to PSbMV is connected to translation initiation factors, yet the processes involved are still poorly understood at the proteome level. To the best of our knowledge, this is the first survey of the global proteomic response to PSbMV in plants. The combination of label-free LC-MS profiling and two contrasting cultivars (resistant and susceptible) provided highly sensitive snapshots of protein abundance in response to PSbMV infection. PSbMV is a member of the largest family of plant viruses and our results are in accordance with previously characterized potyvirus-responsive proteomes. Hence, the results of this study can further extend our knowledge about these pathogens. We also show that even though no viral replication is detected in the PSbMV-resistant cultivar B99, it is still significantly affected by PSbMV inoculation.

Label-free quantitative proteomic analysis of pre-flowering PMeV-infected Carica papaya L

Papaya meleira virus (PMeV) infects papaya (Carica papaya L.) and leads to Papaya Sticky Disease (PSD) or "Meleira", characterized by a spontaneous exudation of latex from fruits and leaves only in the post-flowering developmental stage. The latex oxidizes in contact with air and accumulates as a sticky substance on the plant organs, impairing papaya fruit's marketing and exportation. To understand pre-flowering C. papaya resistance to PMeV, an LC-MS/MS-based label-free proteomics approach was used to assess the differential proteome of PMeV-infected pre-flowering C. papaya vs. uninfected (control) plants. In this study, 1333 proteins were identified, of which 111 proteins showed a significant abundance change (57 increased and 54 decreased) and supports the hypothesis of increased photosynthesis and reduction of 26S-proteassoma activity and cell-wall remodeling. All of these results suggest that increased photosynthetic activity has a positive effect on the induction of plant immunity, whereas the reduction of caspase-like activity and the observed changes in the cell-wall associated proteins impairs the full activation of defense response based on hypersensitive response and viral movement obstruction in pre-flowering C. papaya plants.

BIOLOGICAL SIGNIFICANCE

The papaya (Carica papaya L.) fruit's production is severely limited by the occurrence of Papaya meleira virus (PMeV) infection, which causes Papaya Sticky Disease (PSD). Despite the efforts to understand key features involved with the plant×virus interaction, PSD management is still largely based on the observation of the first disease symptoms in the field, followed by the elimination of the diseased plants. However, C. papaya develops PSD only after flowering, i.e. about six-months after planting, and the virus inoculum sources are kept in field. The development of PMeV resistant genotypes is impaired by the limited knowledge about C. papaya resistance against viruses. The occurrence of a resistance/tolerance mechanism to PSD symptoms development prior to C. papaya flowering is considered in this study. Thus, field-grown and PMeV-infected C. papaya leaf samples were analyzed using proteomics, which revealed the modulation of photosynthesis-, 26S proteasome- and cell-wall remodeling-associated proteins. The data implicate a role for those systems in C. papaya resistance to viruses and support the idea of a partial resistance induction in the plants at pre-flowering stage. The specific proteins presented in the manuscript represent a starting point to the selection of key genes to be used in C. papaya improvement to PMeV infection resistance. The presented data also contribute to the understanding of virus-induced disease symptoms development in plants, of interest to the plant-virus interaction field.

Partially resistant Cucurbita pepo showed late onset of the Zucchini yellow mosaic virus infection due to rapid activation of defense mechanisms as compared to susceptible cultivar

Zucchini yellow mosaic virus (ZYMV) is an emerging viral pathogen in cucurbit-growing areas wordwide. Infection causes significant yield losses in several species of the family Cucurbitaceae. To identify proteins potentially involved with resistance toward infection by the severe ZYMV-H isolate, two Cucurbita pepo cultivars (Zelena susceptible and Jaguar partially resistant) were analyzed using a two-dimensional gel electrophoresis-based proteomic approach. Initial symptoms on leaves (clearing veins) developed 6-7 days post-inoculation (dpi) in the susceptible C. pepo cv. Zelena. In contrast, similar symptoms appeared on the leaves of partially resistant C. pepo cv. Jaguar only after 15 dpi. This finding was confirmed by immune-blot analysis which showed higher levels of viral proteins at 6 dpi in the susceptible cultivar. Leaf proteome analyses revealed 28 and 31 spots differentially abundant between cultivars at 6 and 15 dpi, respectively. The variance early in infection can be attributed to a rapid activation of proteins involved with redox homeostasis in the partially resistant cultivar. Changes in the proteome of the susceptible cultivar are related to the cytoskeleton and photosynthesis.

A current overview of the Papaya meleira virus, an unusual plant virus

Papaya meleira virus (PMeV) is the causal agent of papaya sticky disease, which is characterized by a spontaneous exudation of fluid and aqueous latex from the papaya fruit and leaves. The latex oxidizes after atmospheric exposure, resulting in a sticky feature on the fruit from which the name of the disease originates. PMeV is an isometric virus particle with a double-stranded RNA (dsRNA) genome of approximately 12 Kb. Unusual for a plant virus, PMeV particles are localized on and linked to the polymers present in the latex. The ability of the PMeV to inhabit such a hostile environment demonstrates an intriguing interaction of the virus with the papaya. A hypersensitivity response is triggered against PMeV infection, and there is a reduction in the proteolytic activity of papaya latex during sticky disease. In papaya leaf tissues, stress responsive proteins, mostly calreticulin and proteasome-related proteins, are up regulated and proteins related to metabolism are down-regulated. Additionally, PMeV modifies the transcription of several miRNAs involved in the modulation of genes related to the ubiquitin-proteasome system. Until now, no PMeV resistant papaya genotype has been identified and roguing is the only viral control strategy available. However, a single inoculation of papaya plants with PMeV dsRNA delayed the progress of viral infection.

Carica papaya microRNAs are responsive to Papaya meleira virus infection

MicroRNAs are implicated in the response to biotic stresses. Papaya meleira virus (PMeV) is the causal agent of sticky disease, a commercially important pathology in papaya for which there are currently no resistant varieties. PMeV has a number of unusual features, such as residence in the laticifers of infected plants, and the response of the papaya to PMeV infection is not well understood. The protein levels of 20S proteasome subunits increase during PMeV infection, suggesting that proteolysis could be an important aspect of the plant defense response mechanism. To date, 10,598 plant microRNAs have been identified in the Plant miRNAs Database, but only two, miR162 and miR403, are from papaya. In this study, known plant microRNA sequences were used to search for potential microRNAs in the papaya genome. A total of 462 microRNAs, representing 72 microRNA families, were identified. The expression of 11 microRNAs, whose targets are involved in 20S and 26S proteasomal degradation and in other stress response pathways, was compared by real-time PCR in healthy and infected papaya leaf tissue. We found that the expression of miRNAs involved in proteasomal degradation increased in response to very low levels of PMeV titre and decreased as the viral titre increased. In contrast, miRNAs implicated in the plant response to biotic stress decreased their expression at very low level of PMeV and increased at high PMeV levels. Corroborating with this results, analysed target genes for this miRNAs had their expression modulated in a dependent manner. This study represents a comprehensive identification of conserved miRNAs inpapaya. The data presented here might help to complement the available molecular and genomic tools for the study of papaya. The differential expression of some miRNAs and identifying their target genes will be helpful for understanding the regulation and interaction of PMeV and papaya.

Comparative proteomic analysis of somatic embryo maturation in Carica papaya L

Background

Somatic embryogenesis is a complex process regulated by numerous factors. The identification of proteins that are differentially expressed during plant development could result in the development of molecular markers of plant metabolism and provide information contributing to the monitoring and understanding of different biological responses. In addition, the identification of molecular markers could lead to the optimization of protocols allowing the use of biotechnology for papaya propagation and reproduction. This work aimed to investigate the effects of polyethylene glycol (PEG) on somatic embryo development and the protein expression profile during somatic embryo maturation in papaya (Carica papaya L.).

Results

The maturation treatment supplemented with 6% PEG (PEG6) resulted in the greatest number of somatic embryos and induced differential protein expression compared with cultures grown under the control treatment. Among 135 spots selected for MS/MS analysis, 76 spots were successfully identified, 38 of which were common to both treatments, while 14 spots were unique to the control treatment, and 24 spots were unique to the PEG6 treatment. The identified proteins were assigned to seven categories or were unclassified. The most representative class of proteins observed in the control treatment was associated with the stress response (25.8%), while those under PEG6 treatment were carbohydrate and energy metabolism (18.4%) and the stress response (18.4%).

Conclusions

The differential expression of three proteins (enolase, esterase and ADH3) induced by PEG6 treatment could play an important role in maturation, and these proteins could be characterized as candidate biomarkers of somatic embryogenesis in papaya.

Proteomics in the fruit tree science arena: new insights into fruit defense, development, and ripening

Fruit tree crops are agricultural commodities of high economic importance, while fruits also represent one of the most vital components of the human diet. Therefore, a great effort has been made to understand the molecular mechanisms covering fundamental biological processes in fruit tree physiology and fruit biology. Thanks to the development of cutting-edge "omics" technologies such as proteomic analysis, scientists now have powerful tools to support traditional fruit tree research. Such proteomic analyses are establishing high-density 2DE reference maps and peptide mass fingerprint databases that can lead fruit science into a new postgenomic research era. Here, an overview of the application of proteomics in key aspects of fruit tree physiology as well as in fruit biology, including defense responses to abiotic and biotic stress factors, is presented. A panoramic view of ripening-related proteins is also discussed, as an example of proteomic application in fruit science.

New insights on the Golgi complex of Tritrichomonas foetus

Tritrichomonas foetus is a protist that causes bovine trichomoniasis and presents a well-developed Golgi. There are very few studies concerning the Golgi in trichomonads. In this work, monoclonal antibodies were raised against Golgi of T. foetus and used as a tool on morphologic and biochemical studies of this organelle. Among the antibodies produced, one was named mAb anti-Golgi 20.3, which recognized specifically the Golgi complex by fluorescence and electron microscopy. By immunoblotting this antibody recognized two proteins with 60 and 66 kDa that were identified as putative beta-tubulin and adenosine triphosphatase, respectively. The mAb 20.3 also recognized the Golgi complex of the Trichomonas vaginalis, a human parasite. In addition, the nucleotide coding sequences of these proteins were identified and included in the T. foetus database, and the 3D structure of the proteins was predicted. In conclusion, this study indicated: (1) adenosine triphosphatase is present in the Golgi, (2) ATPase is conserved between T. foetus and T. vaginalis, (3) there is new information concerning the nucleic acid sequences and protein structures of adenosine triphosphatase and beta-tubulin from T. foetus and (4) the mAb anti-Golgi 20.3 is a good Golgi marker and can be used in future studies.

Comparative proteomic analysis of the plant-virus interaction in resistant and susceptible ecotypes of maize infected with sugarcane mosaic virus

Sugarcane mosaic virus (SCMV) is an important viral pathogen and has caused serious losses in grain and forage yield. To identify candidate SCMV resistance proteins and to explore the molecular mechanisms involved in the plant-SCMV interaction, we conducted proteomic analyses of leaf samples from resistant and susceptible ecotypes of maize infected with SCMV. Proteins were analyzed by quantitative two-dimensional differential gel electrophoresis (2D-DIGE), and 93 protein spots showed statistically significant differences after virus inoculation. Functional categorization showed that SCMV-responsive proteins were mainly involved in energy and metabolism, stress and defense responses, photosynthesis, and carbon fixation. The majority of the identified proteins were located in chloroplast and cytoplasm based on bioinformatic analysis. Among these identified proteins, 17 have not been identified previously as virus-responsive proteins, and 7 were new and did not have assigned functions. Western blotting analyses confirmed the expression patterns of proteins of specific interest, and the genes encoding these proteins were further analyzed by real-time PCR. The results of this study showed overlapping and specific proteomic responses to SCMV infection between resistant and susceptible maize ecotypes. This study provides further insight into the molecular events during compatible and incompatible interactions between viruses and host plants.

BIOLOGICAL SIGNIFICANCE

Sugarcane mosaic virus (SCMV) is an important viral pathogen and has caused serious losses in grain and forage yield. However, little is known about host-SCMV interactions from the proteome perspective. This study analyzed proteomic changes in resistant and susceptible plants that are infected with SCMV using DIGE based proteomics. We identified 17 proteins that have not been identified previously as virus-responsive proteins, and 7 new proteins without assigned functions. These proteins are interesting candidates for future research, as they may be associated with new biological functions and play important roles in plant-virus interactions. Real-time RT-PCR analysis of genes encoding several proteins of interest provided indication on whether the changes in protein abundance were regulated at the mRNA level. The results of this study showed overlapping and specific proteomic responses to SCMV infection between resistant and susceptible ecotypes. After inoculation, the proteins involved in energy and metabolism, stress and defense responses, photosynthesis and other four functional groups showed significant changes in both ecotypes, which suggested that SCMV infection influenced these physiological processes in both the resistant Siyi and the susceptible Mo17. However, the oxidative burst was more pronounced during incompatible plant-SCMV interactions, as compared to those defined as compatible. We also observed an increase of enzymes involved in glycolysis and gluconeogenesis pathways in the resistant maize ecotype Siyi, while decrease in the susceptible maize ecotype Mo17. In addition, there is a marked increase of guanine nucleotide-binding protein beta submit in the resistant Siyi, which suggests a possible involvement of G-protein associated pathways in the resistant responses of maize to SCMV. These observations may possibly reveal protein targets/markers that are useful in the design of future diagnosis or plant protection strategies and provide new insights into the molecular mechanism of plant-virus interactions.

Recent insights into plant-virus interactions through proteomic analysis

Plant viruses represent a major threat for a wide range of host species causing severe losses in agricultural practices. The full comprehension of mechanisms underlying events of virus-host plant interaction is crucial to devise novel plant resistance strategies. Until now, functional genomics studies in plant-virus interaction have been limited mainly on transcriptomic analysis. Only recently are proteomic approaches starting to provide important contributions to this area of research. Classical two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) is still the most widely used platform in plant proteome analysis, although in the last years the application of quantitative "second generation" proteomic techniques (such as differential in gel electrophoresis, DIGE, and gel-free protein separation methods) are emerging as more powerful analytical approaches. Apparently simple, plant-virus interactions reveal a really complex pathophysiological context, in which resistance, defense and susceptibility, and direct virus-induced reactions interplay to trigger expression responses of hundreds of genes. Given that, this review is specifically focused on comparative proteome-based studies on pathogenesis of several viral genera, including some of the most important and widespread plant viruses of the genus Tobamovirus, Sobemovirus, Cucumovirus and Potyvirus. In all, this overview reveals a widespread repression of proteins associated with the photosynthetic apparatus, while energy metabolism/protein synthesis and turnover are typically up-regulated, indicating a major redirection of cell metabolism. Other common features include the modulation of metabolisms concerning sugars, cell wall, and reactive oxigen species as well as pathogenesis-related (PR) proteins. The fine-tuning between plant development and antiviral defense mechanisms determines new patterns of regulation of common metabolic pathways. By offering a 360-degree view of protein modulation, all proteomic tools reveal the extraordinary intricacy of mechanisms with which a simple viral genome perturbs the plant cell molecular networks. This "omic" approach, while providing a global perspective and useful information to the understanding of the plant host-virus interactome, may possibly reveal protein targets/markers useful in the design of future diagnosis and/or plant protection strategies.

Label-free quantitative proteomics reveals differentially regulated proteins in the latex of sticky diseased Carica papaya L. plants

Papaya meleira virus (PMeV) is so far the only described laticifer-infecting virus, the causal agent of papaya (Carica papaya L.) sticky disease. The effects of PMeV on the laticifers' regulatory network were addressed here through the proteomic analysis of papaya latex. Using both 1-DE- and 1D-LC-ESI-MS/MS, 160 unique papaya latex proteins were identified, representing 122 new proteins in the latex of this plant. Quantitative analysis by normalized spectral counting revealed 10 down-regulated proteins in the latex of diseased plants, 9 cysteine proteases (chymopapain) and 1 latex serine proteinase inhibitor. A repression of papaya latex proteolytic activity during PMeV infection was hypothesized. This was further confirmed by enzymatic assays that showed a reduction of cysteine-protease-associated proteolytic activity in the diseased papaya latex. These findings are discussed in the context of plant responses against pathogens and may greatly contribute to understand the roles of laticifers in plant stress responses.