Deciphering the structural and biological properties of the lipid A moiety of lipopolysaccharides from Burkholderia cepacia strain ASP B 2D, in Arabidopsis thaliana

Genome-wide association mapping highlights candidate genes and immune genotypes for net blotch and powdery mildew resistance in barley

Net blotch (NB) and powdery mildew (PM) are major barley diseases with the potential to cause a dramatic loss in grain yield. Breeding for resistant barley genotypes in combination with identifying candidate resistant genes will accelerate the genetic improvement for resistance to NB and PM. To address this challenge, a set of 122 highly diverse barley genotypes from 34 countries were evaluated for NB and PM resistance under natural infection for in two growing seasons. Moreover, four yield traits; plant height (Ph), spike length (SL), spike weight (SW), and the number of spikelets per spike (NOS) were recorded. High genetic variation was found among genotypes in all traits scored in this study. No significant phenotypic correlation was found in the resistance between PM and NB. Immune genotypes for NB and PM were identified. A total of 21 genotypes were immune to both diseases. Of the 21 genotypes, the German genotype HOR_9570 was selected as the most promising genotype that can be used for future breeding programs. Furthermore, a genome-wide association study (GWAS) was used to identify resistant alleles to PM and NB. The results of GWAS revealed a set of 14 and 25 significant SNPs that were associated with increased resistance to PM and NB, respectively. This study provided very important genetic resources that are highly resistant to the Egyptian PM and NB pathotypes and revealed SNP markers that can be utilized to genetically improve resistance to PM and NB.

Lipopolysaccharides from Ralstonia solanacearum induce a broad metabolomic response in Solanum lycopersicum

Ralstonia solanacearum, one of the most destructive crop pathogens worldwide, causes bacterial wilt disease in a wide range of host plants. The major component of the outer membrane of Gram-negative bacteria, lipopolysaccharides (LPS), has been shown to function as elicitors of plant defense leading to the activation of signaling and defense pathways in several plant species. LPS from a R. solanacearum strain virulent on tomato (LPSR. sol.), were purified, chemically characterized, and structurally elucidated. The lipid A moiety consisted of tetra- to hexa-acylated bis-phosphorylated disaccharide backbone, also decorated by aminoarabinose residues in minor species, while the O-polysaccharide chain consisted of either linear tetrasaccharide or branched pentasaccharide repeating units containing α-L-rhamnose, N-acetyl-β-D-glucosamine, and β-L-xylose. These properties might be associated with the evasion of host surveillance, aiding the establishment of the infection. Using untargeted metabolomics, the effect of LPSR. sol. elicitation on the metabolome of Solanum lycopersicum leaves was investigated across three incubation time intervals with the application of UHPLC-MS for metabolic profiling. The results revealed the production of oxylipins, e.g., trihydroxy octadecenoic acid and trihydroxy octadecadienoic acid, as well as several hydroxycinnamic acid amide derivatives, e.g., coumaroyl tyramine and feruloyl tyramine, as phytochemicals that exhibit a positive correlation to LPSR. sol. treatment. Although the chemical properties of these metabolite classes have been studied, the functional roles of these compounds have not been fully elucidated. Overall, the results suggest that the features of the LPSR. sol. chemotype aid in limiting or attenuating the full deployment of small molecular host defenses and contribute to the understanding of the perturbation and reprogramming of host metabolism during biotic immune responses.

Effects of LPS from Rhodobacter sphaeroides, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root

The effects of lipopolysaccharide (LPS) from Rhodobacter sphaeroides, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (Oryza sativa) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from Rhodobacter sphaeroides NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of R. sphaeroides NBRC 12203^T at the concentration of 10¹ cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r² = 0.6333, p < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.

Plasma Membrane-Associated Proteins Identified in Arabidopsis Wild Type, lbr2-2 and bak1-4 Mutants Treated with LPSs from Pseudomonas syringae and Xanthomonas campestris

Plants recognise bacterial microbe-associated molecular patterns (MAMPs) from the environment via plasma membrane (PM)-localised pattern recognition receptor(s) (PRRs). Lipopolysaccharides (LPSs) are known as MAMPs from gram-negative bacteria that are most likely recognised by PRRs and trigger defence responses in plants. The Arabidopsis PRR(s) and/or co-receptor(s) complex for LPS and the associated defence signalling remains elusive. As such, proteomic identification of LPS receptors and/or co-receptor complexes will help to elucidate the molecular mechanisms that underly LPS perception and defence signalling in plants. The Arabidopsis LPS-binding protein (LBP) and bactericidal/permeability-increasing protein (BPI)-related-2 (LBR2) have been shown to recognise LPS and trigger defence responses while brassinosteroid insensitive 1 (BRI1)-associated receptor kinase 1 (BAK1) acts as a co-receptor for several PRRs. In this study, Arabidopsis wild type (WT) and T-DNA knock out mutants (lbr2-2 and bak1-4) were treated with LPS chemotypes from Pseudomonas syringae pv. tomato DC3000 (Pst) and Xanthomonas campestris pv. campestris 8004 (Xcc) over a 24 h period. The PM-associated protein fractions were separated by liquid chromatography and analysed by tandem mass spectrometry (LC-MS/MS) followed by data analysis using Byonic^TM software. Using Gene Ontology (GO) for molecular function and biological processes, significant LPS-responsive proteins were grouped according to defence and stress response, perception and signalling, membrane transport and trafficking, metabolic processes and others. Venn diagrams demarcated the MAMP-responsive proteins that were common and distinct to the WT and mutant lines following treatment with the two LPS chemotypes, suggesting contributions from differential LPS sub-structural moieties and involvement of LBR2 and BAK1 in the LPS-induced MAMP-triggered immunity (MTI). Moreover, the identification of RLKs and RLPs that participate in other bacterial and fungal MAMP signalling proposes the involvement of more than one receptor and/or co-receptor for LPS perception as well as signalling in Arabidopsis defence responses.

Bacterial lipopolysaccharide induces settlement and metamorphosis in a marine larva

How larvae of the many phyla of marine invertebrates find places appropriate for settlement, metamorphosis, growth, and reproduction is an enduring question in marine science. Biofilm-induced metamorphosis has been observed in marine invertebrate larvae from nearly every major marine phylum. Despite the widespread nature of this phenomenon, the mechanism of induction remains poorly understood. The serpulid polychaete Hydroides elegans is a well established model for investigating bacteria-induced larval development. A broad range of biofilm bacterial species elicit larval metamorphosis in H. elegans via at least two mechanisms, including outer membrane vesicles (OMVs) and complexes of phage-tail bacteriocins. We investigated the interaction between larvae of H. elegans and the inductive bacterium Cellulophaga lytica, which produces an abundance of OMVs but not phage-tail bacteriocins. We asked whether the OMVs of C. lytica induce larval settlement due to cell membrane components or through delivery of specific cargo. Employing a biochemical structure–function approach with a strong ecological focus, the cells and OMVs produced by C. lytica were interrogated to determine the class of the inductive compounds. Here, we report that larvae of H. elegans are induced to metamorphose by lipopolysaccharide produced by C. lytica. The widespread prevalence of lipopolysaccharide and its associated taxonomic and structural variability suggest it may be a broadly employed cue for bacterially induced larval settlement of marine invertebrates.

Antimicrobial peptide activity is anticorrelated with lipid a leaflet affinity

The activity of antimicrobial peptides (AMPs) has significant bacterial species bias, the mechanisms of which are not fully understood. We employed single-molecule tracking to measure the affinity of three different AMPs to hybrid supported bilayers composed of lipid A extracted from four different Gram negative bacteria and observed a strong empirical anticorrelation between the affinity of a particular AMP to a given lipid A layer and the activity of that AMP towards the bacterium from which that lipid A was extracted. This suggested that the species bias of AMP activity is directly related to AMP interactions with bacterial outer membranes, despite the fact that the mechanism of antimicrobial activity occurs at the inner membrane. The trend also suggested that the interactions between AMPs and the outer membrane lipid A (even in the absence of other components, such as lipopolysaccharides) capture effects that are relevant to the minimum inhibitory concentration.

Lipopolysaccharide perception in Arabidopsis thaliana: Diverse LPS chemotypes from Burkholderia cepacia, Pseudomonas syringae and Xanthomonas campestris trigger differential defence-related perturbations in the metabolome

Lipopolysaccharides (LPSs) are microbe-associated molecular pattern molecules (MAMPs) from Gram-negative bacterial pathogens that potentially contain three different MAMPs (the O-polysaccharide chain, the oligosaccharide core and lipid A). LPSs was purified from Burkholderia cepacia, Pseudomonas syringae and Xanthomonas campestris and electrophoretically profiled. Outcomes of the interactions of the three different LPS chemotypes with Arabidopsis thaliana, as reflected in the induced defence metabolites, profiled at 12 h and 24 h post elicitation, were investigated. Plants were pressure-infiltrated with LPS solutions and methanol-based extractions at different time points were performed for untargeted metabolomics using ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. Multivariate data modelling and chemometric analysis were applied to generate interpretable biochemical information from the multidimensional data sets. The three LPSs triggered differential metabolome changes in the plants as apparent from chromatographically distinct MS chromatograms. Unsupervised and supervised multivariate data models exhibited time- and treatment-related variations, and revealed discriminating metabolite variables. Heat map models comparatively displayed the up-regulated pathways affecting the metabolomes and Venn diagrams indicated up-regulated and shared metabolites among the three LPS treatments. The altered metabolomes reflect the up-regulation of metabolites from not only the glucosinolate pathway, but also from the shikimate-phenylpropanoid-flavonoid -, terpenoid - and indolic/alkaloid pathways, as well as oxygenated fatty acids. Distinct phytochemical profiles, especially at the earlier time point, suggest differences in the perception of the three LPS chemotypes, associated with the molecular patterns within the tripartite lipoglycans.

Adaptive defence-related changes in the metabolome of Sorghum bicolor cells in response to lipopolysaccharides of the pathogen Burkholderia andropogonis

Plant cell suspension culture systems are valuable for the study of complex biological systems such as inducible defence responses and aspects of plant innate immunity. Perturbations to the cellular metabolome can be investigated using metabolomic approaches in order to reveal the underlying metabolic mechanism of cellular responses. Lipopolysaccharides from the sorghum pathogen, Burkholderia andropogonis (LPSB.a.), were purified, chemically characterised and structurally elucidated. The lipid A moiety consists of tetra- and penta-acylated 1,4'-bis-phosphorylated disaccharide backbone decorated by aminoarabinose residues, while the O-polysaccharide chain consists of linear trisaccharide repeating units of [→2)-α-Rha3CMe-(1 → 3)-α-Rha-(1 → 3)-α-Rha-(1 → ]. The effect of LPSB.a. in triggering metabolic reprogramming in Sorghum bicolor cells were investigated using untargeted metabolomics with liquid chromatography coupled to mass spectrometry detection. Cells were treated with LPSB.a. and the metabolic changes monitored over a 30 h time period. Alterations in the levels of phytohormones (jasmonates, zeatins, traumatic-, azelaic- and abscisic acid), which marked the onset of defence responses and accumulation of defence-related metabolites, were observed. Phenylpropanoids and indole alkaloids as well as oxylipins that included di- and trihydroxyoctadecedienoic acids were identified as signatory biomarkers, with marked secretion into the extracellular milieu. The study demonstrated that sorghum cells recognise LPSB.a. as a 'microbe-associated molecular pattern', perturbing normal cellular homeostasis. The molecular features of the altered metabolome were associated with phytohormone-responsive metabolomic reconfiguration of primary and secondary metabolites originating from various metabolic pathways, in support of defence and immunity.

Prospects of Gene Knockouts in the Functional Study of MAMP-Triggered Immunity: A Review

Plants depend on both preformed and inducible defence responses to defend themselves against biotic stresses stemming from pathogen attacks. In this regard, plants perceive pathogenic threats from the environment through pattern recognition receptors (PRRs) that recognise microbe-associated molecular patterns (MAMPs), and so induce plant defence responses against invading pathogens. Close to thirty PRR proteins have been identified in plants, however, the molecular mechanisms underlying MAMP perception by these receptors/receptor complexes are not fully understood. As such, knockout (KO) of genes that code for PRRs and co-receptors/defence-associated proteins is a valuable tool to study plant immunity. The loss of gene activity often causes changes in the phenotype of the model plant, allowing in vivo studies of gene function and associated biological mechanisms. Here, we review the functions of selected PRRs, brassinosteroid insensitive 1 (BRI1) associated receptor kinase 1 (BAK1) and other associated defence proteins that have been identified in plants, and also outline KO lines generated by T-DNA insertional mutagenesis as well as the effect on MAMP perception—and triggered immunity (MTI). In addition, we further review the role of membrane raft domains in flg22-induced MTI in Arabidopsis, due to the vital role in the activation of several proteins that are part of the membrane raft domain theory in this regard.

Polysaccharides from Burkholderia species as targets for vaccine development, immunomodulation and chemical synthesis

Covering: up to 2018 Burkholderia species are a vast group of human pathogenic, phytopathogenic, and plant- or environment-associated bacteria. B. pseudomallei, B. mallei, and B. cepacia complex are the causative agents of melioidosis, glanders, and cystic fibrosis-related infections, respectively, which are fatal diseases in humans and animals. Due to their high resistance to antibiotics, high mortality rates, and increased infectivity via the respiratory tract, B. pseudomallei and B. mallei have been listed as potential bioterrorism agents by the Centers for Disease Control and Prevention. Burkholderia species are able to produce a large network of surface-exposed polysaccharides, i.e., lipopolysaccharides, capsular polysaccharides, and exopolysaccharides, which are virulence factors, immunomodulators, major biofilm components, and protective antigens, and have crucial implications in the pathogenicity of Burkholderia-associated diseases. This review provides a comprehensive and up-to-date account regarding the structural elucidation and biological activities of surface polysaccharides produced by Burkholderia species. The chemical synthesis of oligosaccharides mimicking Burkholderia polysaccharides is described in detail. Emphasis is placed on the recent research efforts toward the development of glycoconjugate vaccines against melioidosis and glanders based on synthetic or native Burkholderia oligo/polysaccharides.

miR393 regulation of lectin receptor-like kinases associated with LPS perception in Arabidopsis thaliana

microRNAs regulate dynamic aspects of innate immunity in Arabidopsis thaliana in response to lipopolysaccharides. Lectin-domain receptor-like kinases function as surveillance proteins and miR393 targets transcripts of an L-type LecRK (LECRK-V.7, At3g59740). This study investigated miR393 regulation of LecRLKs associated with LPS perception. Following pre-treatment of wild type -, miR393 ab double mutant - and miR393 overexpressor plants with LPS, the expression of miR393 and two other LecRLK genes (G-type lectin S-receptor-like protein kinases, SD1-13 (At1g11330) and SD1-29 (At1g61380) were evaluated. Overexpression and repression of miR393 respectively suppressed and induced transcripts of the LecRLK genes. The results indicate that miR393 regulates the three LecRLKs following perception of bacterial LPS, in support of immunity and basal resistance.

Single-Molecule Resolution of Antimicrobial Peptide Interactions with Supported Lipid A Bilayers

The molecular interactions between antimicrobial peptides (AMPs) and lipid A-containing supported lipid bilayers were probed using single-molecule total internal reflection fluorescence microscopy. Hybrid supported lipid bilayers with lipid A outer leaflets and phospholipid (1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)) inner leaflets were prepared and characterized, and the spatiotemporal trajectories of individual fluorescently labeled LL37 and Melittin AMPs were determined as they interacted with the bilayer surfaces comprising either monophosphoryl or diphosphoryl lipid A (from Escherichia coli) to determine the impact of electrostatic interactions. Large numbers of trajectories were obtained and analyzed to obtain the distributions of surface residence times and the statistics of the spatial trajectories. Interestingly, the AMP species were sensitive to subtle differences in the charge of the lipid, with both peptides diffusing more slowly and residing longer on the diphosphoryl lipid A. Furthermore, the single-molecule dynamics indicated a qualitative difference between the behavior of AMPs on hybrid Lipid A bilayers and on those composed entirely of DOPE. Whereas AMPs interacting with a DOPE bilayer exhibited two-dimensional Brownian diffusion with a diffusion coefficient of ∼1.7 μm2/s, AMPs adsorbed to the lipid A surface exhibited much slower apparent diffusion (on the order of ∼0.1 μm2/s) and executed intermittent trajectories that alternated between two-dimensional Brownian diffusion and desorption-mediated three-dimensional flights. Overall, these findings suggested that bilayers with lipid A in the outer leaflet, as it is in bacterial outer membranes, are valuable model systems for the study of the initial stage of AMP-bacterium interactions. Furthermore, single-molecule dynamics was sensitive to subtle differences in electrostatic interactions between cationic AMPs and monovalent or divalent anionic lipid A moieties.

Trans-envelope multidrug efflux pumps of Gram-negative bacteria and their synergism with the outer membrane barrier

Antibiotic resistance is a serious threat to public health. Significant efforts are currently directed toward containment of the spread of resistance, finding new therapeutic options concerning resistant human and animal pathogens, and addressing the gaps in the fundamental understanding of mechanisms of resistance. Experimental data and kinetic modeling revealed a major factor in resistance, the synergy between active efflux and the low permeability barrier of the outer membrane, which dramatically reduces the intracellular accumulation of many antibiotics. The structural and mechanistic particularities of trans-envelope efflux pumps amplify the effectiveness of cell envelopes as permeability barriers. An important feature of this synergism is that efflux pumps and the outer membrane barriers are mechanistically independent and select antibiotics based on different physicochemical properties. The synergism amplifies even weak polyspecificity of multidrug efflux pumps and creates a major hurdle in the discovery and development of new therapeutics against Gram-negative pathogens.

Characterization of complex, heterogeneous lipid A samples using HPLC-MS/MS technique III. Positive-ion mode tandem mass spectrometry to reveal phosphorylation and acylation patterns of lipid A

In this study, we report the detailed analysis of the fragmentation patterns of positively charged lipid A species based on their tandem mass spectra obtained under low-energy collision-induced dissociation conditions of an electrospray quadrupole time-of-flight mass spectrometer. The tandem mass spectrometry experiments were performed after the separation of the compounds with a reversed-phase high performance liquid chromatography method. We found that both, phosphorylated and nonphosphorylated lipid A molecules can be readily ionized in the positive-ion mode by adduct formation with triethylamine added to the eluent. The tandem mass spectra of the lipid A triethylammonium adduct ions showed several product ions corresponding to inter-ring glycosidic cleavages of the sugar residues, as well as consecutive and competitive eliminations of fatty acids, phosphoric acid, and water following the neutral loss of triethylamine. Characteristic product ions provided direct information on the phosphorylation site(s), also when phosphorylation isomers (ie, containing either a C1 or a C4' phosphate group) were simultaneously present in the sample. Continuous series of high-abundance B-type and low-abundance Y-type inter-ring fragment ions were indicative of the fatty acyl distribution between the nonreducing and reducing ends of the lipid A backbone. The previously reported lipid A structures of Proteus morganii O34 and Escherichia coli O111 bacteria were used as standards. Although, the fragmentation pathways of the differently phosphorylated lipid A species significantly differed in the negative-ion mode, they were very similar in the positive-ion mode. The complementary use of positive-ion and negative-ion mode tandem mass spectrometry was found to be essential for the full structural characterization of the C1-monophosphorylated lipid A species.

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties. In addition, different neutralizing ion types (Ca²⁺, K⁺, and Na⁺) are considered to examine the ion's influence on the membrane properties. The trajectory analysis shows that (1) the area per lipid is mostly correlated to the acyl chain number, and the area per lipid increases as a function of the acyl chain number; (2) the hydrophobic thickness is mainly determined by the average acyl chain length with slight dependence on the acyl chain number, and the hydrophobic thickness generally increases with the average acyl chain length; (3) a good correlation is observed among the area per lipid, hydrophobic thickness, and acyl chain order; and (4) although the influence of neutralizing ion types on the area per lipid and hydrophobic thickness is minimal, Ca²⁺ stays longer on the membrane surface than K⁺ or Na⁺, consequently leading to lower lateral diffusion and a higher compressibility modulus, which agrees well with available experiments.

Proteomic analysis of Arabidopsis plasma membranes reveals lipopolysaccharide-responsive changes

Plant plasma membranes (PMs) contain pattern recognition receptors (PRRs), lately believed to be associated within multicomponent complexes, which perceive microbe-associated molecular pattern (MAMP) molecules like lipopolysaccharides (LPSs) and result in signal transduction events that lead to activated immune defense responses. As such, Arabidopsis thaliana leaves were treated with LPS from Escherichia coli (LPS_E.coli) over time, and PM fractions isolated and evaluated using gel-based and subsequent mass spectrometry approaches for identification of LPS-responsive proteins. From the identified protein bands and spots, it is concluded that perception of hexaacylated LPS and resulting signal transduction occurs via PM-associated protein(s), amongst others, receptor-like kinases (RLKs) including G-type lectin S-receptor kinase and BAK1, and mostly likely within specialized perception domains.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012

This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.

Structure, biosynthesis and function of unusual lipids A from nodule-inducing and N2-fixing bacteria

This review focuses on the chemistry and structures of (Brady)rhizobium lipids A, indispensable parts of lipopolysaccharides. These lipids contain unusual (ω-1) hydroxylated very long chain fatty acids, which are synthesized by a very limited group of bacteria, besides rhizobia. The significance and requirement of the very long chain fatty acids for outer membrane stability as well as the genetics of the synthesis pathway are discussed. The biological role of these fatty acids for bacterial life in extremely different environments (soil and intracellular space within nodules) is also considered.

Lipopolysaccharide perception leads to dynamic alterations in the microtranscriptome of Arabidopsis thaliana cells and leaf tissues

BACKGROUND

MicroRNAs (miRNAs) are non-coding RNA molecules which have recently emerged as important gene regulators in plants and their gene expression analysis is becoming increasingly important. miRNAs regulate gene expression at the post-transcriptional level by translational repression or target degradation of specific mRNAs and gene silencing. In order to profile the microtranscriptome of Arabidopsis thaliana leaf and callus tissues in response to bacterial lipopolysaccharide (LPS), small RNA libraries were constructed at 0 and 3 h post induction with LPS and sequenced by Illumina sequencing technology.

RESULTS

Differential regulation of subset of miRNAs in response to LPS treament was observed. Small RNA reads were mapped to the miRNA database and 358 miRNAs belonging to 49 miRNA families in the callus tissues and 272 miRNAs belonging to 40 miRNA families in the leaf tissues were identified. Moreover, target genes for all the identified miRNAs families in the leaf tissues and 44 of the 49 miRNAs families in the callus tissues were predicted. The sequencing analysis showed that in both callus and leaf tissues, various stress regulated-miRNAs were differentially expressed and real time PCR validated the expression profile of miR156, miR158, miR159, miR169, miR393, miR398, miR399 and miR408 along with their target genes.

CONCLUSION

A. thaliana callus and leaf callus tissues respond to LPS as a microbe-associated molecular pattern molecule through dynamic changes to the microtranscriptome associated with differential transcriptional regulation in support of immunity and basal resistance.

Comparative conventional- and quantum dot-labeling strategies for LPS binding site detection in Arabidopsis thaliana mesophyll protoplasts

Lipopolysaccharide (LPS) from Gram-negative bacteria is recognized as a microbe-associated molecular pattern (MAMP) and not only induces an innate immune response in plants, but also stimulates the development of characteristic defense responses. However, identification and characterization of a cell surface LPS-receptor/binding site, as described in mammals, remains elusive in plants. As an amphiphilic, macromolecular lipoglycan, intact LPS potentially contains three MAMP-active regions, represented by the O-polysaccharide chain, the core and the lipid A. Binding site studies with intact labeled LPS were conducted in Arabidopsis thaliana protoplasts and quantified using flow cytometry fluorescence changes. Quantum dots (Qdots), which allow non-covalent, hydrophobic labeling were used as a novel strategy in this study and compared to covalent, hydrophilic labeling with Alexa 488. Affinity for LPS-binding sites was clearly demonstrated by concentration-, temperature-, and time-dependent increases in protoplast fluorescence following treatment with the labeled LPS. Moreover, this induced fluorescence increase was convincingly reduced following pre-treatment with excess unlabeled LPS, thereby indicating reversibility of LPS binding. Inhibition of the binding process is also reported using endo- and exocytosis inhibitors. Here, we present evidence for the anticipated presence of LPS-specific binding sites in Arabidopsis protoplasts, and furthermore propose Qdots as a more sensitive LPS-labeling strategy in comparison to the conventional Alexa 488 hydrazide label for binding studies.

Ergosterol, an orphan fungal microbe-associated molecular pattern (MAMP)

Fungal pathogens continue to pose a significant threat to crop production and food supply. The early stages of plant-fungus interactions are mostly mediated by microbe-associated molecular pattern (MAMP) molecules, perceived by plant pattern recognition receptors (PRRs). Currently, the identified fungal MAMP molecules include chitin, chitosan, β-glucans, elicitins and ergosterol. Although the molecular battles between host plants and infecting fungal phytopathogens have been studied extensively, many aspects still need to be investigated to obtain a holistic understanding of the intrinsic mechanisms, which is paramount in combating fungal plant diseases. Here, an overview is given of the most recent findings concerning an 'orphan' fungal MAMP molecule, ergosterol, and we present what is currently known from a synopsis of different genes, proteins and metabolites found to play key roles in induced immune responses in plant-fungus interactions. Clearly, integrative investigations are still needed to provide a comprehensive systems-based understanding of the dynamics associated with molecular mechanisms in plant-ergosterol interactions and associated host responses.

Membrane lipids in Agrobacterium tumefaciens: biosynthetic pathways and importance for pathogenesis

Many cellular processes critically depend on the membrane composition. In this review, we focus on the biosynthesis and physiological roles of membrane lipids in the plant pathogen Agrobacterium tumefaciens. The major components of A. tumefaciens membranes are the phospholipids (PLs), phosphatidylethanolamine (PE), phosphatidylglycerol, phosphatidylcholine (PC) and cardiolipin, and ornithine lipids (OLs). Under phosphate-limited conditions, the membrane composition shifts to phosphate-free lipids like glycolipids, OLs and a betaine lipid. Remarkably, PC and OLs have opposing effects on virulence of A. tumefaciens. OL-lacking A. tumefaciens mutants form tumors on the host plant earlier than the wild type suggesting a reduced host defense response in the absence of OLs. In contrast, A. tumefaciens is compromised in tumor formation in the absence of PC. In general, PC is a rare component of bacterial membranes but amount to ~22% of all PLs in A. tumefaciens. PC biosynthesis occurs via two pathways. The phospholipid N-methyltransferase PmtA methylates PE via the intermediates monomethyl-PE and dimethyl-PE to PC. In the second pathway, the membrane-integral enzyme PC synthase (Pcs) condenses choline with CDP-diacylglycerol to PC. Apart from the virulence defect, PC-deficient A. tumefaciens pmtA and pcs double mutants show reduced motility, enhanced biofilm formation and increased sensitivity towards detergent and thermal stress. In summary, there is cumulative evidence that the membrane lipid composition of A. tumefaciens is critical for agrobacterial physiology and tumor formation.

Fortifying the barrier: the impact of lipid A remodelling on bacterial pathogenesis

Gram-negative bacteria decorate their outermost surface structure, lipopolysaccharide, with elaborate chemical moieties, which effectively disguises them from immune surveillance and protects them from the onslaught of host defences. Many of these changes occur on the lipid A moiety of lipopolysaccharide, a component that is crucial for host recognition of Gram-negative infection. In this Review, we describe the regulatory mechanisms controlling lipid A modification and discuss the impact of modifications on pathogenesis, bacterial physiology and bacterial interactions with the host immune system.

Microbial recognition and evasion of host immunity

Plants are able to detect microbes by pattern recognition receptors in the host cells that, upon recognition of the enemy, activate effective immune responses in the invaded tissue. Recognition of microbes occurs by common conserved structures called microbe-associated molecular patterns (MAMPs). Plant pathogens and beneficial soil-borne microbes live in close contact with their host. Hence, prevention of the host's defence programme is essential for their survival. Active suppression of host defences by microbial effector proteins is a well-known strategy employed by many successful plant-associated microbes. Evasion of host immune recognition is less well studied but is emerging as another important strategy. Escape from recognition by the host's immune system can be caused by alterations in the structure of the recognized MAMPs, or by active intervention of ligand-receptor recognition. This paper reviews the structure and recognition of common MAMPs and the ways that plant-associated microbes have evolved to prevent detection by their host.

MAMP (microbe-associated molecular pattern) triggered immunity in plants

Plants are sessile organisms that are under constant attack from microbes. They rely on both preformed defenses, and their innate immune system to ward of the microbial pathogens. Preformed defences include for example the cell wall and cuticle, which act as physical barriers to microbial colonization. The plant immune system is composed of surveillance systems that perceive several general microbe elicitors, which allow plants to switch from growth and development into a defense mode, rejecting most potentially harmful microbes. The elicitors are essential structures for pathogen survival and are conserved among pathogens. The conserved microbe-specific molecules, referred to as microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs), are recognized by the plant innate immune systems pattern recognition receptors (PRRs). General elicitors like flagellin (Flg), elongation factor Tu (EF-Tu), peptidoglycan (PGN), lipopolysaccharides (LPS), Ax21 (Activator of XA21-mediated immunity in rice), fungal chitin, and β-glucans from oomycetes are recognized by plant surface localized PRRs. Several of the MAMPs and their corresponding PRRs have, in recent years, been identified. This review focuses on the current knowledge regarding important MAMPs from bacteria, fungi, and oomycetes, their structure, the plant PRRs that recognizes them, and how they induce MAMP-triggered immunity (MTI) in plants.

Agrobacteria lacking ornithine lipids induce more rapid tumour formation

Ornithine lipids (OLs) are phosphorus-free membrane lipids that are widespread among Gram-negative bacteria. Their basic structure consists of a 3-hydroxy fatty acyl group attached in amide linkage to the α-amino group of ornithine and a second fatty acyl group ester-linked to the 3-hydroxy position of the first fatty acid. It has been shown that OLs can be hydroxylated within the amide-linked fatty acyl moiety, the secondary fatty acyl moiety or within the ornithine moiety. These modifications have been related to increased stress tolerance and symbiotic proficiency in different organisms such as Rhizobium tropici or Burkholderia cenocepacia. Analysing the membrane lipid composition of the plant pathogen Agrobacterium tumefaciens we noticed that it forms two different OLs. In the present work we studied if OLs play a role in stress tolerance and pathogenicity in A. tumefaciens. Mutants deficient in the OLs biosynthesis genes olsB or olsE were constructed and characterized. They either completely lack OLs (ΔolsB) or only form the unmodified OL (ΔolsE). Here we present a characterization of both OL mutants under stress conditions and in a plant transformation assay using potato tuber discs. Surprisingly, the lack of agrobacterial OLs promotes earlier tumour formation on the plant host.

Activation of camalexin biosynthesis in Arabidopsis thaliana in response to perception of bacterial lipopolysaccharides: a gene-to-metabolite study

Lipopolysaccharides (LPS), as lipoglycan microbe-associated molecular pattern molecules, trigger activation of signal transduction pathways involved in defence that generate an enhanced defensive capacity in plants. The transcriptional regulation of the genes for tryptophan synthase B, TSB1, and the cytochrome P450 monooxygenases CYP79B2 and CYP71B15, involved in the camalexin biosynthetic pathway, were investigated in response to LPS treatment. GUS-reporter assays for CYP71B15 and CYP79B2 gene promoter activation were performed on transgenic plants and showed positive histochemical staining in response to LPS treatment, indicating activation of the promoters. Quantitative PCR revealed that transcripts of TSB1, CYP79B2 and CYP71B15 exhibited differential, transient up-regulation. TSB1 transcript levels were up-regulated between 6 and 9 h after LPS-induction, while CYP71B15 and CYP79B2 both exhibited maxima at 12 h. To obtain information on the gene-to-metabolite network, the effect of the transcriptome changes on the metabolome was correlated to camalexin production. Increases in camalexin concentration were quantified by ultra pressure liquid chromatography-mass spectrometry and both absorbance spectra and elemental composition confirmed its identity. The concentrations increased from 0.03 to 3.7 μg g(-1) fresh weight over a 24-h time period, thus indicating that the up-regulation of the biosynthetic pathway in response to LPS was accompanied by a time-dependent increase in camalexin concentration. Metabolomic analysis through principal component analysis-derived scores plots revealed clusters of sample replicates for 0, 6, 12, 18 and 24 h while loadings plots for LPS data identified camalexin as a biomarker that clearly demonstrated the variability between samples.

The role of lipopolysaccharide and peptidoglycan, two glycosylated bacterial microbe-associated molecular patterns (MAMPs), in plant innate immunity

In an environment that is rich in potentially pathogenic microorganisms, the survival of higher eukaryotic organisms depends on efficient pathogen sensing and rapidly mounted defence responses. Such protective mechanisms are found in all multicellular organisms, and are collectively referred to as 'innate immunity'. Innate immunity is the first line of defence against invading microorganisms in vertebrates and the only line of defence in invertebrates and plants. Bacterial glycoconjugates, such as lipopolysaccharides (LPSs) from the outer membrane of Gram-negative bacteria and peptidoglycan (PGN) from the cell walls of both Gram-positive and Gram-negative bacteria, have been found to act as elicitors of plant innate immunity. These conserved, indispensable, microbe-specific molecules are also referred to as 'microbe-associated molecular patterns' (MAMPs). MAMPs are recognized by the plant innate immune system through the action of pattern recognition receptors (PRRs). A greater insight into the mechanisms of MAMP recognition and the description of PRRs for different microbial glycoconjugates will have considerable impact on the improvement of plant health and disease resistance. Here, the current knowledge about LPS and PGN as MAMPs is reviewed.

Distinct carbohydrate and lipid-based molecular patterns within lipopolysaccharides from Burkholderia cepacia contribute to defense-associated differential gene expression in Arabidopsis thaliana

Lipopolysaccharides are structural components within the cell walls of Gram-negative bacteria. The LPSs as microbe-associated molecular pattern (MAMP) molecules can trigger defense-related responses involved in MAMP-triggered immunity and basal resistance in plants, presumably from an initial perception event. LPS from Burkholderia cepacia as well as two fragments, the glycolipid, lipid A and the polysaccharide (OPS-core) chain, were used to treat Arabidopsis thaliana seedlings to evaluate the eliciting activities of the individual LPS sub-domains by means of Annealing Control Primer-based Differential Display transcript profiling. Genes found to be up-regulated encode for proteins involved in signal perception and transduction, transcriptional regulation and defense - and stress responses. Furthermore, genes encoding proteins involved in chaperoning, secretion, protein-protein interactions and protein degradation were differentially expressed. It is concluded that intact LPS, as well as the two sub-components, induced the expression of a broad range of genes associated with perception and defense as well as metabolic reprogramming of cellular activities in support of immunity and basal resistance. Whilst the lipid A and OPS moieties were able to up-regulate sub-sets of defense-associated genes over the same spectrum of categories as intact LPS, the up-regulation observed with intact LPS was the more comprehensive, suggesting that the lipid A and glycan molecular patterns of the molecule act as partial agonists, but that the intact LPS structure is required for full agonist activity.