BackgroundThe secreted Meloidogyne javanica fatty acid- and retinol-binding (FAR) protein Mj-FAR-1 is involved in nematode development and reproduction in host tomato roots. To gain further insight into the role of Mj-FAR-1 in regulating disease development, local transcriptional changes were monitored in tomato hairy root lines with constitutive mj-far-1 expression compared with control roots without inoculation, and 2, 5 and 15 days after inoculation (DAI), using mRNA sequencing analysis.ResultsGene-expression profiling revealed a total of 3970 differentially expressed genes (DEGs) between the two lines. Among the DEGs, 1093, 1039, 1959, and 1328 genes were up- or downregulated 2-fold with false discovery rate < 0.001 in noninoculated roots, and roots 2, 5, and 15 DAI compared with control roots, respectively. Four main groups of genes that might be associated with Mj-FAR-1-mediated susceptibility were identified: 1) genes involved in biotic stress responses such as pathogen-defense mechanisms and hormone metabolism; 2) genes involved in phenylalanine and phenylpropanoid metabolism; 3) genes associated with cell wall synthesis, modification or degradation; and 4) genes associated with lipid metabolism. All of these genes were overrepresented among the DEGs. Studying the distances between the treatments, samples from noninoculated roots and roots at 2 DAI clustered predominantly according to the temporal dynamics related to nematode infection. However, at the later time points (5 and 15 DAI), samples clustered predominantly according to mj-far-1 overexpression, indicating that at these time points Mj-FAR-1 is more important in defining a common transcriptome.ConclusionsThe presence of four groups of DEGs demonstrates a network of molecular events is mediated by Mj-FAR-1 that leads to highly complex manipulation of plant defense responses against nematode invasion. The results shed light on the in vivo role of secreted FAR proteins in parasitism, and add to the mounting evidence that secreted FAR proteins play a major role in nematode parasitism.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1426-3) contains supplementary material, which is available to authorized users.

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Plant-parasitic nematodes are extremely destructive pathogens with a cosmopolitan distribution and a host range that affects most crops. They are characterized by distinct parasitic lifestyles, e.g., as sedentary or migratory endo-or ectoparasites, resulting in high losses in yield and revenue. Possessing limited lipid metabolism, they produce one or two structurally unique classes of small α-helix-rich fatty acid and retinol binding (FAR) proteins that have no counterpart in other organisms. We investigated the sequence and structural characteristics of the FAR protein of the root-knot nematode Meloidogyne javanica (Mj-FAR-1) in comparison to other studied FAR proteins. Protein sequence analyses enabled phylogenetic clustering according to trophic groups and lifestyles. Bioinformatics analysis of the FAR protein sequences revealed ten likely core amino acids representing the trophic-group clustering. Clear modifications of four of these amino acids from less reactive (nonpolar, with aliphatic R group) to more reactive (positively or negatively charged R groups, or uncharged polar R groups) might distinguish free-living from parasitic nematode species. Structural predictions of the mature Mj-FAR-1 protein and its ligand-binding pockets, suggest that adaptation toward parasitism is associated with increased reactivity of the second pocket residues, as well as those on the protein surface. Subcellular localization of Mj-FAR-1 with or without its signal peptide was determined by Agrobacterium infiltration of N-terminal mCherrytagged protein into Nicotiana benthamiana leaves. Intact Mj-FAR-1 with its signal peptide was predominantly localized along the plasma membrane surrounding plant cells while removing the signal peptide resulted in additional localization within the cell nucleus. The nuclear localization agreed with in-silico analysis of the Mj-FAR-1 sequence and sheds new light on its function in manipulating the plant response. Our study provides the first basic structural information and subcellular localization of the plant-parasitic Mj-FAR-1 protein.Keywords Fatty acid and retinol binding (FAR) protein .Plant-parasitic nematode . Root-knot nematode . Meloiodgyne javanica . Parasitism . Effector protein Abbreviations MjMeloidogyne javanica FAR Fatty acid and retinol binding (protein) Eur J Plant Pathol

Aims Microstructure plays an important role in biological systems. Microstructural features are critical in the interaction between two biological organisms, for example, a microorganism and the surface of a plant. However, isolating the structural effect of the interaction from all other parameters is challenging when working directly with the natural system. Replicating microstructure of leaves was recently shown to be a powerful research tool for studying leaf-environment interaction. However, no such tool exists for roots. Roots present a special challenge because of their delicacy (specifically Plant Soil (2020) 447:157-168 https://doi. ConclusionsThis newly developed tool may be used to study the effect of microstructure, isolated from all other effects, on the interaction of roots with their environment.

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