A proteomic approach to studying plant response to crenate broomrape (Orobanche crenata) in pea (Pisum sativum)

Pea Breeding for Resistance to Rhizospheric Pathogens

Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.

Parasitic Plants: An Overview of Mechanisms by Which Plants Perceive and Respond to Parasites

In contrast to most autotrophic plants, which produce carbohydrates from carbon dioxide using photosynthesis, parasitic plants obtain water and nutrients by parasitizing host plants. Many important crop plants are infested by these heterotrophic plants, leading to severe agricultural loss and reduced food security. Understanding how host plants perceive and resist parasitic plants provides insight into underlying defense mechanisms and the potential for agricultural applications. In this review, we offer a comprehensive overview of the current understanding of host perception of parasitic plants and the pre-attachment and post-attachment defense responses mounted by the host. Since most current research overlooks the role of organ specificity in resistance responses, we also summarize the current understanding and cases of cross-organ parasitism, which indicates nonconventional haustorial connections on other host organs, for example, when stem parasitic plants form haustoria on their host roots. Understanding how different tissue types respond to parasitic plants could provide the potential for developing a universal resistance mechanism in crops against both root and stem parasitic plants.

Biological and Transcriptomic Characterization of Pre-Haustorial Resistance to Sunflower Broomrape (Orobanche cumana W.) in Sunflowers (Helianthus annuus)

Infestations with sunflower broomrape (Orobanche cumana Wallr.), an obligatory root parasite, constitute a major limitation to sunflower production in many regions around the world. Breeding for resistance is the most effective approach to reduce sunflower broomrape infestation, yet resistance mechanisms are often broken by new races of the pathogen. Elucidating the mechanisms controlling resistance to broomrape at the molecular level is, thus, a desirable way to obtain long-lasting resistance. In this study, we investigated broomrape resistance in a confectionery sunflower cultivar with a robust and long-lasting resistance to sunflower broomrape. Visual screening and histological examination of sunflower roots revealed that penetration of the broomrape haustorium into the sunflower roots was blocked at the cortex, indicating a pre-haustorial mechanism of resistance. A comparative RNA sequencing between broomrape-resistant and -susceptible accessions allowed the identification of genes that were significantly differentially expressed upon broomrape infestation. Among these genes were β-1,3-endoglucanase, β-glucanase, and ethylene-responsive transcription factor 4 (ERF4). These genes were previously reported to be pathogenesis-related in other plant species. This transcriptomic investigation, together with the histological examinations, led us to conclude that the resistance mechanism involves the identification of the broomrape and the consequent formation of a physical barrier that prevents the establishment of the broomrape into the sunflower roots.

A comparative proteomic study of cold responses in potato leaves

The potato is an important food crop worldwide. While potatoes are rich in nutrition, the production suffers from yield loss caused by frost and freezing. This study used a common potato cultivar, ‘Zhengshu 6’, as the study system to measure the changes in the contents of soluble protein, malondialdehyde (MDA), proline, and chlorophyll after 1, 3, 5, and 7 days of low temperature treatment. We performed two-dimensional electrophoresis (2-DE) in combination with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) technology and identified 52 differentially expressed protein spots among these timepoints. Results showed that levels of soluble protein, MDA, and proline increased as the duration of the low temperature treatment increased, and the chlorophyll content decreased. The 52 identified protein spots were classified by function as involved in defense response, energy metabolism, photosynthesis, protein degradation, ribosome formation, signal transduction, cell movement, nitrogen metabolism, and other physiological processes, thus allowing potato plants to achieve metabolic balance at low temperatures.

Quantitative Analysis of Target Peptides Related to Resistance Against Ascochyta Blight (Peyronellaea pinodes) in Pea

Peyronellaea pinodes causes Ascochyta blight, one of the major diseases in pea worldwide. Cultivated pea plants have a low resistance to this disease. Although quantitative trait loci (QTLs) involved in the resistance to Ascochyta blight have been identified, the specific genes associated with these QTLs remain unknown, which makes marker-assisted selection difficult. Complex traits alter proteins and their abundance. Quantitative estimation of proteins in pea might therefore be useful in selecting potential markers for breeding. In this work, we developed a strategy using a combination of shotgun proteomics (viz., high performance liquid chromatography-mass spectrometry data-dependent acquisition) and data-independent acquisition (DIA) analysis, to identify putative protein markers associated with resistance to Ascochyta blight and explored its use for breeding selection. For this purpose, an initial list of target peptides based on proteins closely related to resistance to P. pinodes was compiled by using two genotypes with contrasting responses to the disease. Then, targeted data analysis (viz., shotgun proteomics-DIA) was used for constitutive quantification of the target peptides in a representative number of the recombinant inbred line population segregated for resistance as derived from a cross between the two genotypes. Finally, a peptide panel of potential markers for resistance to P. pinodes was built. The results thus obtained are discussed and compared with those of previous gene expression studies using the same parental pea genotypes responding to the pathogen. Also, a molecular defense mechanism against Ascochyta blight in pea is proposed. To the authors' knowledge, this is the first time a targeted proteomics approach based on data analysis has been used to identify peptides associated with resistance to this disease.

iTRAQ-based proteomics of sunflower cultivars differing in resistance to parasitic weed Orobanche cumana

Orobanche cumana is an obligate root parasite causing severe damage to many economically important crops, including sunflowers worldwide. For efficient control measures, it is necessary to understand the resistant mechanism during interaction at molecular level. The present study emphasizes on comparative proteomics to investigate the mechanistic basis of compatible and incompatible interaction of O. cumana with resistant (JY207) and susceptible (TK0409) sunflowers. More than 3500 proteins were identified from two cultivars by iTRAQ analysis. Identified proteins associated with general functions, posttranslational modification, energy production and conversion, carbohydrate transport and metabolism, and signal transduction mechanisms were the most represented category of induced proteins in both cultivars. The resistant interaction was characterized by alteration of defense-related proteins involved in recognition of parasites, accumulation of pathogenesis-related proteins, biosynthesis of lignin, and detoxification of toxic metabolites in JY207 after inoculation. The susceptible interaction was characterized by decreased abundance of proteins involved in biosynthesis and signaling of plant growth regulators including auxin, gibberellin, brassinosteroid, and ethylene in TK0409 after inoculation. The present study provides comprehensive details of proteins and differential modulation of pathways regulated under compatible and incompatible interaction, allowing the identification of important molecular components for development of sustainable resistance against this parasite.

Proteomic Analysis Reveals Coordinated Regulation of Anthocyanin Biosynthesis through Signal Transduction and Sugar Metabolism in Black Rice Leaf

Black rice (Oryza sativa L.) is considered to be a healthy food due to its high content of anthocyanins in the pericarp. The synthetic pathway of anthocyanins in black rice grains has been identified, however, the proteomic profile of leaves during grain development is still unclear. Here, isobaric Tags Relative and Absolute Quantification (iTRAQ) MS/MS was carried out to identify statistically significant changes of leaf proteome in the black rice during grain development. Throughout three sequential developmental stages, a total of 3562 proteins were detected and 24 functional proteins were differentially expressed 3–10 days after flowering (DAF). The detected proteins are known to be involved in various biological processes and most of these proteins were related to gene expression regulatory (33.3%), signal transduction (16.7%) and developmental regulation and hormone-like proteins (12.5%). The coordinated changes were consistent with changes in regulatory proteins playing a leading role in leaves during black rice grain development. This indicated that signal transduction between leaves and grains may have an important role in anthocyanin biosynthesis and accumulation during grain development of black rice. In addition, four identified up-regulated proteins associated with starch metabolism suggested that the remobilization of nutrients for starch synthesis plays a potential role in anthocyanin biosynthesis of grain. The mRNA transcription for eight selected proteins was validated with quantitative real-time PCR. Our results explored the proteomics of the coordination between leaf and grain in anthocyanins biosynthesis of grain, which might be regulated by signal transduction and sugar metabolism in black rice leaf.

The Role of Endogenous Strigolactones and Their Interaction with ABA during the Infection Process of the Parasitic Weed Phelipanche ramosa in Tomato Plants

The root parasitic plant species Phelipanche ramosa, branched broomrape, causes severe damage to economically important crops such as tomato. Its seed germination is triggered by host-derived signals upon which it invades the host root. In tomato, strigolactones (SLs) are the main germination stimulants for P. ramosa. Therefore, the development of low SL-producing lines may be an approach to combat the parasitic weed problem. However, since SLs are also a plant hormone controlling many aspects of plant development, SL deficiency may also have an effect on post-germination stages of the infection process, during the parasite-host interaction. In this study, we show that SL-deficient tomato plants (Solanum lycopersicum; SlCCD8 RNAi lines), infected with pre-germinated P. ramosa seeds, display an increased infection level and faster development of the parasite, which suggests a positive role for SLs in the host defense against parasitic plant invasion. Furthermore, we show that SL-deficient tomato plants lose their characteristic SL-deficient phenotype during an infection with P. ramosa through a reduction in the number of internodes and the number and length of secondary branches. Infection with P. ramosa resulted in increased levels of abscisic acid (ABA) in the leaves and roots of both wild type and SL-deficient lines. Upon parasite infection, the level of the conjugate ABA-glucose ester (ABA-GE) also increased in leaves of both wild type and SL-deficient lines and in roots of one SL-deficient line. The uninfected SL-deficient lines had a higher leaf ABA-GE level than the wild type. Despite the high levels of ABA, stomatal aperture and water loss rate were not affected by parasite infection in the SL-deficient line, while in wild type tomato stomatal aperture and water loss increased upon infection. Future studies are needed to further underpin the role that SLs play in the interaction of hosts with parasitic plants and which other plant hormones interact with the SLs during this process.

Dynamic expression analysis of early response genes induced by potato virus Y in PVY-resistant Nicotiana tabacum

KEY MESSAGE

Dynamic transcriptional changes of the host early responses genes were detected in PVY-resistant tobacco varieties infected with Potato virus Y; PVY resistance is a complex process that needs series of stress responses. Potato virus Y (PVY) causes a severe viral disease in cultivated crops, especially in Solanum plants. To understand the molecular basis of plant responses to the PVY stress, suppression subtractive hybridization (SSH) and microarray approaches were combined to identify the potentially important or novel genes that were involved in early stages (12 h, 1, 2, 3, 5, 8 days) of tobacco response to PVY infection. Dynamic changes of the host plant early responses to PVY infection on a transcriptional level were detected. In total, 167 different expressed ESTs were identified. The majority of genes involved in the metabolic process were found to be down-regulated at 12 h and 1 day, and then up-regulated at least one later period. Genes related to signaling and transcriptions were almost up-regulated at 12 h, 1 or 2 days, while stress response genes were almost up-regulated at a later stage. Genes involved in transcription, transport, cell wall, and several stress responses were found to have changed expression during the PVY infection stage, and numbers of these genes have not been previously reported to be associated with tobacco PVY infection. The diversity expression of these genes indicated that PVY resistance is a complex process that needs a series of stress responses. To resist the PVY infection, the tobacco plant has numerous active and silent responses.

Phenotypical and biochemical characterisation of resistance for parasitic weed (Orobanche foetida Poir.) in radiation-mutagenised mutants of chickpea

BACKGROUND

Some radiation-mutagenised chickpea mutants potentially resistant to the broomrape, Orobanche foetida Poir., were selected through field trials. The objectives of this work were to confirm resistance under artificial infestation, in pots and mini-rhizotron systems, and to determine the developmental stages of broomrape affected by resistance and the relevant resistance mechanisms induced by radiation mutagenesis.

RESULTS

Among 30 mutants tested for resistance to O. foetida, five shared strong resistance in both pot experiments and mini-rhizotron systems. Resistance was not complete, but the few individuals that escaped resistance displayed high disorders of shoot development. Results demonstrated a 2-3-fold decrease in stimulatory activity of root exudates towards broomrape seed germination in resistant mutants in comparison with non-irradiated control plants and susceptible mutants. Resistance was associated with an induction of broomrape necrosis early during infection. When infested, most of the resistant mutants shared enhanced levels of soluble phenolic contents, phenylalanine ammonia lyase activity, guaiacol peroxidase activity and polyphenol oxidase activity, in addition to glutathione and notably ascorbate peroxidase gene expression in roots.

CONCLUSION

Results confirmed enhanced resistance in chickpea radiation-mutagenised mutants, and demonstrated that resistance is based on alteration of root exudation, presumed cell-wall reinforcement and change in root oxidative status in response to infection. © 2016 Society of Chemical Industry.

Pre-fractionation strategies to resolve pea (Pisum sativum) sub-proteomes

Legumes are important crop plants and pea (Pisum sativum L.) has been investigated as a model with respect to several physiological aspects. The sequencing of the pea genome has not been completed. Therefore, proteomic approaches are currently limited. Nevertheless, the increasing numbers of available EST-databases as well as the high homology of the pea and medicago genome (Medicago truncatula Gaertner) allow the successful identification of proteins. Due to the un-sequenced pea genome, pre-fractionation approaches have been used in pea proteomic surveys in the past. Aside from a number of selective proteome studies on crude extracts and the chloroplast, few studies have targeted other components such as the pea secretome, an important sub-proteome of interest due to its role in abiotic and biotic stress processes. The secretome itself can be further divided into different sub-proteomes (plasma membrane, apoplast, cell wall proteins). Cell fractionation in combination with different gel-electrophoresis, chromatography methods and protein identification by mass spectrometry are important partners to gain insight into pea sub-proteomes, post-translational modifications and protein functions. Overall, pea proteomics needs to link numerous existing physiological and biochemical data to gain further insight into adaptation processes, which play important roles in field applications. Future developments and directions in pea proteomics are discussed.

Comparative proteomic analysis of oil palm leaves infected with Ganoderma boninense revealed changes in proteins involved in photosynthesis, carbohydrate metabolism, and immunity and defense

The basidiomycete fungal pathogen Ganoderma boninense is the causative agent for the incurable basal stem rot (BSR) disease in oil palm. This disease causes significant annual crop losses in the oil palm industry. Currently, there is no effective method for disease control and elimination, nor is any molecular marker for early detection of the disease available. An understanding of how BSR affects protein expression in plants may help identify and/or assist in the development of an early detection protocol. Although the mode of infection of BSR disease is primarily via the root system, defense-related genes have been shown to be expressed in both the root and leafs. Thus, to provide an insight into the changes in the global protein expression profile in infected plants, comparative 2DE was performed on leaf tissues sampled from palms with and without artificial inoculation of the Ganoderma fungus. Comparative 2DE revealed that 54 protein spots changed in abundance. A total of 51 protein spots were successfully identified by LC-QTOF MS/MS. The majority of these proteins were those involved in photosynthesis, carbohydrate metabolism as well as immunity and defense.

Apoplastic interactions between plants and plant root intruders

Numerous pathogenic or parasitic organisms attack plant roots to obtain nutrients, and the apoplast including the plant cell wall is where the plant cell meets such organisms. Root parasitic angiosperms and nematodes are two distinct types of plant root parasites but share some common features in their strategies for breaking into plant roots. Striga and Orobanche are obligate root parasitic angiosperms that cause devastating agricultural problems worldwide. Parasitic plants form an invasion organ called a haustorium, where plant cell wall degrading enzymes (PCWDEs) are highly expressed. Plant-parasitic nematodes are another type of agriculturally important plant root parasite. These nematodes breach the plant cell walls by protruding a sclerotized stylet from which PCWDEs are secreted. Responding to such parasitic invasion, host plants activate their own defense responses against parasites. Endoparasitic nematodes secrete apoplastic effectors to modulate host immune responses and to facilitate the formation of a feeding site. Apoplastic communication between hosts and parasitic plants also contributes to their interaction. Parasitic plant germination stimulants, strigolactones, are recently identified apoplastic signals that are transmitted over long distances from biosynthetic sites to functioning sites. Here, we discuss recent advances in understanding the importance of apoplastic signals and cell walls for plant-parasite interactions.

Comparative proteomic analysis of BTH and BABA-induced resistance in pea (Pisum sativum) toward infection with pea rust (Uromyces pisi)

Systemic acquired resistance (SAR) to Uromyces pisi in pea was studied by using a proteomic approach. Two-dimensional electrophoresis (2-DE) was used in order to compare the leaf proteome of two pea genotypes displaying different phenotypes (susceptible and partial resistance to the fungus), and in response to parasite infection under the effect of two inducers of SAR, BTH and BABA. Multivariate statistical analysis identified 126 differential protein spots under the experimental conditions (genotypes/treatments). All of these 126 protein spots were subjected to MALDI-TOF/TOF mass spectrometry to deduce their possible functions. A total of 50 proteins were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the identified proteins corresponded to enzymes belonging to photosynthesis, metabolism, biosynthesis, binding and defense response, whose behavior pattern was different in relation to susceptibility/resistance of the genotypes studied and to the BTH/BABA induction to pathogen response. Results obtained in this work suggested that plants could reduce their photosynthesis and other energy metabolism and enhance the production of defense-related proteins to cope the stress. On the other side, we postulated that resistance induced by the chemicals operates via different mechanisms: BABA inducer could act via phenolic biosynthesis pathway, whereas resistance provided by BTH inducer seems to be mediated by defense and stress-related proteins. The results are discussed in terms of response to rust under the effect of inducers.

Proteomic analysis by two-dimensional differential in gel electrophoresis (2D DIGE) of the early response of Pisum sativum to Orobanche crenata

Crenate broomrape (Orobanche crenata) is considered to be the major constraint for legume crops in Mediterranean countries. Strategies of control have been developed, but only marginal successes have been achieved. For the efficient control of the parasite, a better understanding of its interaction and associated resistance mechanisms at the molecular level is required. The pea response to this parasitic plant and the molecular basis of the resistance was studied using a proteomic approach based on 2D DIGE and MALDI-MSMS analysis. For this purpose, two genotypes showing different levels of resistance to O. crenata, as well as three time points (21, 25, and 30 d after inoculation) have been compared. Multivariate statistical analysis identified 43 differential protein spots under the experimental conditions (genotypes/treatments), 22 of which were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the proteins identified were metabolic and stress-related proteins and a high percentage of them (86%) matched with specific proteins of legume species. The behaviour pattern of the identified proteins suggests the existence of defence mechanisms operating during the early stages of infection that differed in both genotypes. Among these, several proteins were identified with protease activity which could play an important role in preventing the penetration and connection to the vascular system of the parasite. Our data are discussed and compared with those previously obtained in pea and Medicago truncatula.

Two-dimensional electrophoresis based proteomic analysis of the pea (Pisum sativum) in response to Mycosphaerella pinodes

Responses to Mycosphaerella pinodes in pea were studied by using a proteomics approach. Two-dimensional electrophoresis (2-DE) was used in order to compare the leaf proteome of two pea cultivars displaying different phenotypes (susceptible and partial resistance to the fungus), as well as in response to the inoculation. Multivariate statistical analysis identified 84 differential protein spots under the experimental conditions (cultivars/treatments). All of these 84 protein spots were subjected to MALDI-TOF/TOF mass spectrometry to deduce their possible functions. A total of 31 proteins were identified using a combination of peptide mass fingerprinting (PMF) and MSMS fragmentation. Most of the identified proteins corresponded to enzymes belonging to photosynthesis, metabolism, transcription/translation and defense and stress categories. Results are discussed in terms of responses to pathogens.

Analysis of cell wall proteins regulated in stem of susceptible and resistant tomato species after inoculation with Ralstonia solanacearum: a proteomic approach

Proteomics approach was used to elucidate the molecular interactions taking place at the stem cell wall level when tomato species were inoculated with Ralstonia solanacearum, a causative agent of bacterial wilt. Cell wall proteins from both resistant and susceptible plants before and after the bacterial inoculation were extracted from purified cell wall with salt buffers and separated with 2-D IEF/SDS-PAGE and with 3-D IEF/SDS/SDS-PAGE for basic proteins. The gels stained with colloidal Coomassie revealed varied abundance of protein spots between two species (eight proteins in higher abundance in resistant and six other in susceptible). Moreover, proteins were regulated differentially in response to bacterial inoculation in resistant (seven proteins increased and eight other decreased) as well as in susceptible plants (five proteins elevated and eight other suppressed). Combination of MALDI-TOF/TOF MS and LC-ESI-IonTrap MS/MS lead to the identification of those proteins. Plants responded to pathogen inoculation by elevating the expression of pathogenesis related, other defense related and glycolytic proteins in both species. However, cell wall metabolic proteins in susceptible, and antioxidant, stress related as well as energy metabolism proteins in resistant lines were suppressed. Most of the proteins of the comparative analysis and other randomly picked spots were predicted to have secretion signals except some classical cytosolic proteins.

Pathogenesis and stress related, as well as metabolic proteins are regulated in tomato stems infected with Ralstonia solanacearum

A comparative proteome analysis was initiated to systematically investigate the physiological response of tomato (Solanum lycopersicum) to infection with Ralstonia solanacearum, causal agent of bacterial wilt. Plants of the susceptible tomato recombinant inbred line NHG3 and the resistant NHG13 were either infected or not infected with R. solanacearum and subsequently used for proteome analysis. Two-dimensional isoelectric focussing/sodium dodecyl-sulphate polyacrylamide gel electrophoresis (2-D IEF/SDS-PAGE) allowed the separation of about 650-690 protein spots per analysis. Twelve proteins were of differential abundance in susceptible plants in response to bacterial infection, while no differences were observed in the resistant genotype. LC-MS/MS analysis of these spots revealed 12 proteins, six of which were annotated as plant and six as bacterial proteins. Among the plant proteins, two represent pathogenesis related (PR) proteins, one stress response protein, one enzyme of carbohydrate and energy metabolism, and one hypothetical protein. A constitutive difference between resistant and susceptible lines was not found.

Differential expression proteomics to investigate responses and resistance to Orobanche crenata in Medicago truncatula

BACKGROUND

Parasitic angiosperm Orobanche crenata infection represents a major constraint for the cultivation of legumes worldwide. The level of protection achieved to date is either incomplete or ephemeral. Hence, an efficient control of the parasite requires a better understanding of its interaction and associated resistance mechanisms at molecular levels.

RESULTS

In order to study the plant response to this parasitic plant and the molecular basis of the resistance we have used a proteomic approach. The root proteome of two accessions of the model legume Medicago truncatula displaying differences in their resistance phenotype, in control as well as in inoculated plants, over two time points (21 and 25 days post infection), has been compared. We report quantitative as well as qualitative differences in the 2-DE maps between early- (SA 27774) and late-resistant (SA 4087) genotypes after Coomassie and silver-staining: 69 differential spots were observed between non-inoculated genotypes, and 42 and 25 spots for SA 4087 and SA 27774 non-inoculated and inoculated plants, respectively. In all, 49 differential spots were identified by peptide mass fingerprinting (PMF) following MALDI-TOF/TOF mass spectrometry. Many of the proteins showing significant differences between genotypes and after parasitic infection belong to the functional category of defense and stress-related proteins. A number of spots correspond to proteins with the same function, and might represent members of a multigenic family or post-transcriptional forms of the same protein.

CONCLUSION

The results obtained suggest the existence of a generic defense mechanism operating during the early stages of infection and differing in both genotypes. The faster response to the infection observed in the SA 27774 genotype might be due to the action of proteins targeted against key elements needed for the parasite's successful infection, such as protease inhibitors. Our data are discussed and compared with those previously obtained with pea 1 and transcriptomic analysis of other plant-pathogen and plant-parasitic plant systems.

Jasmonate- and salicylate-mediated plant defense responses to insect herbivores, pathogens and parasitic plants

While extensive research has examined plant defense responses to attack by herbivores and pathogens, plant responses to parasitism by other plants are not well characterized. The expression of induced plant defenses is mediated by complex signaling networks in which the plant hormones jasmonic acid (JA) and salicylic acid (SA) play key roles. In general, JA-mediated signaling pathways are implicated in the regulation of antiherbivore defenses, while the SA pathway is associated with defense responses against pathogens. However, there are many exceptions to this basic framework, and recent work suggests that interactions between the JA and SA pathways may play important roles in fine-tuning defense responses. The few studies that have addressed plant responses to parasitism by other plants suggest that both salicylates and jasmonates can mediate effective defenses. Here, a review is given of recent work on these defense signaling molecules with relevance for understanding their role in plant responses to parasitism.

Breeding approaches for crenate broomrape (Orobanche crenata Forsk.) management in pea (Pisum sativum L.)

BACKGROUND

Pea cultivation is strongly hampered in Mediterranean and Middle East farming systems by the occurrence of Orobanche crenata Forsk. Strategies of control have been developed, but only marginal successes have been achieved. Most control methods are either unfeasible, uneconomical, hard to achieve or result in incomplete protection. The integration of several control measures is the most desirable strategy.

RESULTS

[corrected] Recent developments in control are presented and re-evaluated in light of recent developments in crop breeding and molecular genetics. These developments are placed within a framework that is compatible with current agronomic practices.

CONCLUSION

The current focus in applied breeding is leveraging biotechnological tools to develop more and better markers to speed up the delivery of improved cultivars to the farmer. To date, however, progress in marker development and delivery of useful markers has been slow. The application of knowledge gained from basic genomic research and genetic engineering will contribute to more rapid pea improvement for resistance against O. crenata and/or the herbicide.

Soybean proteomics and its application to functional analysis

Complete genome sequences, which are available for rice and Arabidopsis, provide insights into many fundamental aspects of plant biology; they do not, however, address some important aspects of legume biology. Legumes are important for maintenance of human health and as crops for sustainable agriculture. Two model species of legume, Lotus japonicus and Medicago truncatula, have been the focus of projects on genome sequencing and functional genomics. A project aimed at sequencing the genome of the agricultural legume soybean recently began, but functional genomics studies of this plant are in their infancy, and therefore proteomics approaches could be a powerful tool for functional analysis. In this review, we discuss the strengths and weaknesses of proteomics technologies in soybean biology and we examine the limitations of current techniques.

Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica

Striga hermonthica is a root hemiparasite of cereals that causes devastating loss of yield. Recently, a rice cultivar, Nipponbare, was discovered, which exhibits post-attachment resistance to this parasite and quantitative trait loci (QTL) associated with the resistance were identified. Changes in gene expression in susceptible (IAC 165) and resistant (Nipponbare) rice cultivars were profiled using rice whole-genome microarrays. In addition to a functional categorization of changes in gene expression, genes that were significantly up-regulated within resistance QTL were identified. The resistance reaction was characterized by up-regulation of defence genes, including pathogenesis-related proteins, pleiotropic drug resistance ABC transporters, genes involved in phenylpropanoid metabolism and WRKY transcription factors. These changes in gene expression resemble those associated with resistance to microbial pathogens. Three genes encoding proteins of unknown function, within a major resistance QTL on chromosome 12, were highly up-regulated and are excellent candidate resistance genes. The susceptible interaction was characterized by large-scale down-regulation of gene expression, particularly within the functional categories plant growth regulator signalling and metabolism, biogenesis of cellular components and cell division. Up-regulated genes included nutrient transporters, enzymes of amino acid metabolism and some abiotic stress genes.

Environmental proteomics and metallomics

Monitoring environmental pollution using biomarkers requires detailed knowledge about the markers, and many only allow a partial assessment of pollution. New proteomic methods (environmental proteomics) can identify proteins that, after validation, might be useful as alternative biomarkers, although this approach also has its limitations, derived mainly from their application to non-model organisms. Initial studies using environmental proteomics were carried out in animals exposed to model pollutants, and led to the concept of protein expression signatures. Experiments have been carried out in model organisms (yeast, Arabidopsis, rat cells, or mice) exposed to model contaminants. Over the last few years, proteomics has been applied to organisms from ecosystems with different pollution levels, forming the basis of an environmental branch in proteomics. Another focus is connected with the presence of metals bound to biomolecules, which adds an additional dimension to metal-biomolecule and metalloprotein characterization - the field of metallomics. The metallomic approach considers the metallome: a whole individual metal or metalloid species within a cell or tissue. A metallomic analytical approach (MAA) is proposed as a new tool to study and identify metalloproteins.

A diffusible signal from germinating Orobanche ramosa elicits early defense responses in suspension-cultured Arabidopsis thaliana

In plant/parasitic plant interaction, little is known about the host plant response before the establishment of the parasite within the host. In the present work, we focused on host responses to parasitic plant, O. ramosa in the early stage of infection. We used a co-culture system of A. thaliana suspension cells and O. ramosa germinated-seeds to avoid parasite attachment. We showed that O. ramosa induced H(2)O(2) generation and camalexin synthesis by A. thaliana followed by a drastic increase in cell death. We further demonstrated that a heat sensitive diffusible signal is responsible for this cell death. These data indicate that recognition of O. ramosa occurs before the attachment of the parasite and initiates plant defence responses.

Plant resistance to parasitic plants: molecular approaches to an old foe

Parasitic weeds pose severe constraint on major agricultural crops. Varying levels of resistance have been identified and exploited in the breeding programmes of several crops. However, the level of protection achieved to date is either incomplete or ephemeral. Resistance is mainly determined by the coexistence of several mechanisms controlled by multigenic and quantitative systems. Efficient control of the parasite requires a better understanding of the interaction and their associated resistance mechanisms at the histological, genetic and molecular levels. Application of postgenomic technologies and the use of model plants should improve the understanding of the plant-parasitic plant interaction and drive not only breeding programmes through either marker-assisted selection (MAS) or transgenesis but also the development of alternative methods to control the parasite. This review presents the current approaches targeting the characterization of resistance mechanisms and explores their potentiality to control parasitic plants.

Plant proteome analysis: A 2004–2006 update

Since the appearance of the review entitled "Plant Proteome Analysis" in Proteomics in February 2004 (Cánovas, F. M., Dumas-Gaudot, E., Recorbert, G., Jorrín, J. et al., Proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. Although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. These papers concern the proteome of at least 35 plant species but have concentrated mainly on thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The scientific objectives have ranged from a proteomic analysis of organs, tissues, cell suspensions, or subcellular fractions to the study of plant development and response to various stresses. A number of contributions have covered PTMs and protein interactions. The dominant analytical platform has been 2-DE coupled to MS, but "second generation" techniques such as DIGE, multidimensional protein identification technology, isotope-coded affinity tags, and stable isotope labeling by amino acids in cell culture have begun to make an impact. This review aims to provide an update of the contribution of proteomics to plant biology during the period 2004-2006, and is divided into six sections: introduction, subcellular proteomes, plant development, responses to biotic and abiotic stresses, PTMs, and protein interactions. The conclusions summarize a view of the major pitfalls and challenges of plant proteomics.

A proteomic approach to study pea (Pisum sativum) responses to powdery mildew (Erysiphe pisi)

As a global approach to gain a better understanding of the mechanisms involved in pea resistance to Erysiphe pisi, changes in the leaf proteome of two pea genotypes differing in their resistance phenotype were analyzed by a combination of 2-DE and MALDI-TOF/TOF MS. Leaf proteins from control non-inoculated and inoculated susceptible (Messire) and resistant (JI2480) plants were resolved by 2-DE, with IEF in the 5-8 pH range and SDS-PAGE on 12% gels. CBB-stained gels revealed the existence of quantitative and qualitative differences between extracts from: (i) non-inoculated leaves of both genotypes (77 spots); (ii) inoculated and non-inoculated Messire leaves (19 spots); and (iii) inoculated and non-inoculated JI2480 leaves (12 spots). Some of the differential spots have been identified, after MALDI-TOF/TOF analysis and database searching, as proteins belonging to several functional categories, including photosynthesis and carbon metabolism, energy production, stress and defense, protein synthesis and degradation and signal transduction. Results are discussed in terms of constitutive and induced elements involved in pea resistance against Erysiphe pisi.

Peroxidases have more functions than a Swiss army knife

Plant peroxidases (class III peroxidases) are present in all land plants. They are members of a large multigenic family. Probably due to this high number of isoforms, and to a very heterogeneous regulation of their expression, plant peroxidases are involved in a broad range of physiological processes all along the plant life cycle. Due to two possible catalytic cycles, peroxidative and hydroxylic, peroxidases can generate reactive oxygen species (ROS) (*OH, HOO*), polymerise cell wall compounds, and regulate H2O2 levels. By modulating their activity and expression following internal and external stimuli, peroxidases are prevalent at every stage of plant growth, including the demands that the plant meets in stressful conditions. These multifunctional enzymes can build a rigid wall or produce ROS to make it more flexible; they can prevent biological and chemical attacks by raising physical barriers or by counterattacking with a large production of ROS; they can be involved in a more peaceful symbiosis. They are finally present from the first hours of a plant's life until its last moments. Although some functions look paradoxical, the whole process is probably regulated by a fine-tuning that has yet to be elucidated. This review will discuss the factors that can influence this delicate balance.