Proteomics as a way to identify extra-radicular fungal proteins from Glomus intraradices– RiT-DNA carrot root mycorrhizas

Proteome adaptations under contrasting soil phosphate regimes of Rhizophagus irregularis engaged in a common mycorrhizal network

For many plants, their symbiosis with arbuscular mycorrhizal fungi plays a key role in the acquisition of mineral nutrients such as inorganic phosphate (Pi), in exchange for assimilated carbon. To study gene regulation and function in the symbiotic partners, we and others have used compartmented microcosms in which the extra-radical mycelium (ERM), responsible for mineral nutrient supply for the plants, was separated by fine nylon nets from the associated host roots and could be harvested and analysed in isolation. Here, we used such a model system to perform a quantitative comparative protein profiling of the ERM of Rhizophagus irregularis BEG75, forming a common mycorrhizal network (CMN) between poplar and sorghum roots under a long-term high- or low-Pi fertilization regime. Proteins were extracted from the ERM and analysed by liquid chromatography-tandem mass spectrometry. This workflow identified a total of 1301 proteins, among which 162 displayed a differential amount during Pi limitation, as monitored by spectral counting. Higher abundances were recorded for proteins involved in the mobilization of external Pi, such as secreted acid phosphatase, 3',5'-bisphosphate nucleotidase, and calcium-dependent phosphotriesterase. This was also the case for intracellular phospholipase and lysophospholipases that are involved in the initial degradation of phospholipids from membrane lipids to mobilize internal Pi. In Pi-deficient conditions. The CMN proteome was especially enriched in proteins assigned to beta-oxidation, glyoxylate shunt and gluconeogenesis, indicating that storage lipids rather than carbohydrates are fuelled in ERM as the carbon source to support hyphal growth and energy requirements. The contrasting pattern of expression of AM-specific fatty acid biosynthetic genes between the two plants suggests that in low Pi conditions, fatty acid provision to the fungal network is mediated by sorghum roots but not by poplar. Loss of enzymes involved in arginine synthesis coupled to the mobilization of proteins involved in the breakdown of nitrogen sources such as intercellular purines and amino acids, support the view that ammonium acquisition by host plants through the mycorrhizal pathway may be reduced under low-Pi conditions. This proteomic study highlights the functioning of a CMN in Pi limiting conditions, and provides new perspectives to study plant nutrient acquisition as mediated by arbuscular mycorrhizal fungi.

Polymicrobial Multi-functional Approach for Enhancement of Crop Productivity

There is an increasing global need for enhancing the food production to meet the needs of the fast-growing human population. Traditional approach to increasing agricultural productivity through high inputs of chemical nitrogen and phosphate fertilizers and pesticides is not sustainable because of high costs and concerns about global warming, environmental pollution, and safety concerns. Therefore, the use of naturally occurring soil microbes for increasing productivity of food crops is an attractive eco-friendly, cost-effective, and sustainable alternative to the use of chemical fertilizers and pesticides. There is a vast body of published literature on microbial symbiotic and nonsymbiotic nitrogen fixation, multiple beneficial mechanisms used by plant growth-promoting rhizobacteria (PGPR), the nature and significance of mycorrhiza-plant symbiosis, and the growing technology on production of efficacious microbial inoculants. These areas are briefly reviewed here. The construction of an inoculant with a consortium of microbes with multiple beneficial functions such as N(2) fixation, biocontrol, phosphate solubilization, and other plant growth-promoting properties is a positive new development in this area in that a single inoculant can be used effectively for increasing the productivity of a broad spectrum of crops including legumes, cereals, vegetables, and grasses. Such a polymicrobial inoculant containing several microorganisms for each major function involved in promoting the plant growth and productivity gives it greater stability and wider applications for a range of major crops. Intensifying research in this area leading to further advances in our understanding of biochemical/molecular mechanisms involved in plant-microbe-soil interactions coupled with rapid advances in the genomics-proteomics of beneficial microbes should lead to the design and development of inoculants with greater efficacy for increasing the productivity of a wide range of crops.

The influence of the fungal pathogen Mycocentrospora acerina on the proteome and polyacetylenes and 6-methoxymellein in organic and conventionally cultivated carrots (Daucus carota) during post harvest storage

Many carrots are discarded during post harvest cold storage due to development of fungal infections, caused by, e.g., Mycocentrospora acerina (liquorice rot). We compared the susceptibility of carrots grown under conventional and organic agricultural practices. In one year, organically cultivated carrots showed 3× to 7× more symptoms than conventionally cultivated, when studying naturally occurring disease at 4 and 6 months, respectively. On the other hand, we have developed a bioassay for infection studies of M. acerina on carrots and observed that organic roots were more susceptible after one month of storage than conventional ones, but no differences were apparent after four or six months storage. Levels of polyacetylenes (falcarinol, falcarindiol and falcarindiol-3-acetate) did not change, whereas the isocoumarin phytoalexin (6-methoxymellein) accumulated in infected tissue as well as in healthy tissue opposite the infection. The proteomes of carrot and M. acerina were characterized, the intensity of 33 plant protein spots was significantly changed in infected roots including up regulation of defence and stress response proteins but also a decrease of proteins involved in energy metabolism. This combined metabolic and proteomic study indicates that roots respond to fungal infection through altered metabolism: simultaneous induction of 6-methoxymellein and synthesis of defence related proteins.

Arbuscular mycorrhizal symbiosis elicits proteome responses opposite of P-starvation in SO4 grapevine rootstock upon root colonisation with two Glomus species

Although plant biotisation with arbuscular mycorrhizal fungi (AMF) is a promising strategy for improving plant health, a better knowledge regarding the molecular mechanisms involved is required. In this context, we sought to analyse the root proteome of grapevine rootstock Selection Oppenheim 4 (SO4) upon colonisation with two AMF. As expected, AMF colonisation stimulates plant biomass. At the proteome level, changes in protein amounts due to AMF colonisation resulted in 39 differentially accumulated two-dimensional electrophoresis spots in AMF roots relative to control. Out of them, 25 were co-identified in SO4 roots upon colonisation by Glomus irregulare and Glomus mosseae supporting the existence of conserved plant responses to AM symbiosis in a woody perennial species. Among the 18 proteins whose amount was reduced in AMF-colonised roots were proteins involved in glycolysis, protein synthesis and fate, defence and cell rescue, ethylene biosynthesis and purine and pyrimidine salvage degradation. The six co-identified proteins whose amount was increased had functions in energy production, signalling, protein synthesis and fate including proteases. Altogether these data confirmed that a part of the accommodation program of AMF previously characterized in annual plants is maintained within roots of the SO4 rootstock cuttings. Nonetheless, particular responses also occurred involving proteins of carbon metabolism, development and root architecture, defence and cell rescue, anthocyanin biosynthesis and P remobilization, previously reported as induced upon P-starvation. This suggests the occurrence of P reprioritization upon AMF colonization in a woody perennial plant species with agronomical interest.

Medicago truncatula proteomics

Legumes (Fabaceae) are unique in their ability to enter into an elaborate symbiosis with nitrogen-fixing rhizobial bacteria. Rhizobia-legume (RL) symbiosis represents one of the most productive nitrogen-fixing systems and effectively renders the host plants to be more or less independent of other nitrogen sources. Due to high protein content, legumes are among the most economically important crop families. Beyond that, legumes consist of over 16,000 species assigned to 650 genera. In most cases, the genomes of legumes are large and polyploid, which originally did not predestine these plants as genetic model systems. It was not until the early 1990 th that Medicago truncatula was selected as the model plant for studying Fabaceae biology. M. truncatula is closely related to many economically important legumes and therefore its investigation is of high relevance for agriculture. Recently, quite a number of studies were published focussing on in depth characterizations of the M. truncatula proteome. The present review aims to summarize these studies, especially those which focus on the root system and its dynamic changes induced upon symbiotic or pathogenic interactions with microbes.

Identification of bacterial proteins mediating the interactions between Pseudomonas putida UW4 and Brassica napus (Canola)

The influence of canola root exudates on the proteome of Pseudomonas putida UW4 and the mutant strain P. putida UW4/AcdS(-), which lacks a functional 1-aminocyclopropane-1-carboxylate deaminase gene, was examined using two-dimensional difference in-gel electrophoresis. Seventy-two proteins with significantly altered expression levels in the presence of canola root exudates were identified by mass spectrometry. Many of these proteins are involved in nutrient transport and utilization, cell envelope synthesis, and transcriptional or translational regulation and, hence, may play important roles in plant-bacterial interactions. Four proteins showing large changes in expression in response to canola root exudates in both the wild-type and mutant strains of P. putida UW4 (i.e., outer membrane protein F, peptide deformylase, transcription regulator Fis family protein, and a previously uncharacterized protein) were both overexpressed and disrupted in P. putida UW4 in an effort to better understand their functions. Functional studies of these modified strains revealed significantly enhanced or inhibited plant-growth-promoting abilities compared with the wild-type P. putida UW4, in agreement with the suggested involvement of three of these four proteins in plant-bacterial interactions. The work reported here suggests strategies to both identify potential antibacterial agents and develop bacterial strains that might be useful adjuncts to agriculture. This approach may be an effective means of identifying key proteins mediating the interactions of bacteria with their rhizosphere environment.

Mutations in DMI3 and SUNN modify the appressorium-responsive root proteome in arbuscular mycorrhiza

Modification of the Medicago truncatula root proteome during the early stage of arbuscular mycorrhizal symbiosis was investigated by comparing, using two-dimensional electrophoresis, the protein patterns obtained from non-inoculated roots and roots synchronized for Glomus intraradices appressorium formation. This approach was conducted in wild-type (J5), mycorrhiza-defective (TRV25, dmi3), and autoregulation-defective (TR122, sunn) M. truncatula genotypes. The groups of proteins that responded to appressorium formation were further compared between wild-type and mutant genotypes; few overlaps and major differences were recorded, demonstrating that mutations in DMI3 and SUNN modified the appressorium-responsive root proteome. Except for a chalcone reductase, none of the differentially displayed proteins that could be identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry previously was known as appressorium responsive. A DMI3-dependent increased accumulation of signal transduction-related proteins (dehydroascorbate reductase, cyclophilin, and actin depolymerization factor) was found to precede mycorrhiza establishment. Differences in the accumulation of proteins related to plant defense reactions, cytoskeleton rearrangements, and auxin signaling upon symbiont contact were recorded between wild-type and hypermycorrhizal genotypes, pointing to some putative pathways by which SUNN may regulate very early arbuscule formation.

Identification of membrane-associated proteins regulated by the arbuscular mycorrhizal symbiosis

A sub-cellular proteomic approach was carried out to monitor membrane-associated protein modifications in response to the arbuscular mycorrhizal (AM) symbiosis. Membrane proteins were extracted from Medicago truncatula roots either inoculated or not with the AM fungus Glomus intraradices. Comparative two-dimensional electrophoresis revealed that 36 spots were differentially displayed in response to the fungal colonization including 15 proteins induced, 3 up-regulated and 18 down-regulated. Among them, seven proteins were found to be commonly down-regulated in AM-colonized and phosphate-fertilized roots. Twenty-five spots out of the 36 of interest could be identified by matrix assisted laser desorption/ionisation-time of flight and/or tandem mass spectrometry analyses. Excepting an acid phosphatase and a lectin, none of them was previously reported as being regulated during AM symbiosis. In addition, this proteomic approach allowed us for the first time to identify AM fungal proteins in planta.