Dry Stamping Coral Powder: An Effective Method for Isolating Coral Symbiotic Actinobacteria.

Actinobacteria are important sources of antibiotics and have been found repeatedly in coral core microbiomes, suggesting this bacterial group plays important functional roles tied to coral survival. However, to unravel coral-actinobacteria ecological interactions and discover new antibiotics, the complex challenges that arise when isolating symbiotic actinobacteria must be overcome. Moreover, by isolating unknown actinobacteria from corals, novel biotechnological applications may be discovered. In this study, we compared actinobacteria recovery from coral samples between two widely known methods for isolating actinobacteria: dry stamping and heat shock. We found that dry stamping was at least three times better than heat shock. The assembly of isolated strains by dry stamping was unique for each species and consistent across same-species samples, highlighting that dry stamping can be reliably used to characterize coral actinobacteria communities. By analyzing the genomes of the closest related type strains, we were able to identify several functions commonly found among symbiotic organisms, such as transport and quorum sensing. This study provides a detailed methodology for isolating coral actinobacteria for ecological and biotechnological purposes.

Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism.

Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.

CAM Models: Lessons and Implications for CAM Evolution.

The evolution of Crassulacean acid metabolism (CAM) by plants has been one of the most successful strategies in response to aridity. On the onset of climate change, expanding the use of water efficient crops and engineering higher water use efficiency into C3 and C4 crops constitute a plausible solution for the problems of agriculture in hotter and drier environments. A firm understanding of CAM is thus crucial for the development of agricultural responses to climate change. Computational models on CAM can contribute significantly to this understanding. Two types of models have been used so far. Early CAM models based on ordinary differential equations (ODE) reproduced the typical diel CAM features with a minimal set of components and investigated endogenous day/night rhythmicity. This line of research brought to light the preponderant role of vacuolar malate accumulation in diel rhythms. A second wave of CAM models used flux balance analysis (FBA) to better understand the role of CO2 uptake in flux distribution. They showed that flux distributions resembling CAM metabolism emerge upon constraining CO2 uptake by the system. We discuss the evolutionary implications of this and also how CAM components from unrelated pathways could have integrated along evolution.

Knockdown of the plastid-encoded acetyl-CoA carboxylase gene uncovers functions in metabolism and development.

De novo fatty acid biosynthesis in plants relies on a prokaryotic-type acetyl-CoA carboxylase (ACCase) that resides in the plastid compartment. The enzyme is composed of four subunits, one of which is encoded in the plastid genome, whereas the other three subunits are encoded by nuclear genes. The plastid gene (accD) encodes the ß-carboxyltransferase subunit of ACCase and is essential for cell viability. To facilitate the functional analysis of accD, we pursued a transplastomic knockdown strategy in tobacco (Nicotiana tabacum). By introducing point mutations into the translational start codon of accD, we obtained stable transplastomic lines with altered ACCase activity. Replacement of the standard initiator codon AUG with UUG strongly reduced AccD expression, whereas replacement with GUG had no detectable effects. AccD knockdown mutants displayed reduced ACCase activity, which resulted in changes in the levels of many but not all species of cellular lipids. Limiting fatty acid availability caused a wide range of macroscopic, microscopic, and biochemical phenotypes, including impaired chloroplast division, reduced seed set, and altered storage metabolism. Finally, while the mutants displayed reduced growth under photoautotrophic conditions, they showed exaggerated growth under heterotrophic conditions, thus uncovering an unexpected antagonistic role of AccD activity in autotrophic and heterotrophic growth.

Metabolomic markers and physiological adaptations for high phosphate utilization efficiency in rice.

Utilizing phosphate more efficiently is crucial for sustainable crop production. Highly efficient rice (Oryza sativa) cultivars have been identified and this study aims to identify metabolic markers associated with P utilization efficiency (PUE). P deficiency generally reduced leaf P concentrations and CO2 assimilation rates but efficient cultivars were reducing leaf P concentrations further than inefficient ones while maintaining similar CO2 assimilation rates. Adaptive changes in carbon metabolism were detected but equally in efficient and inefficient cultivar groups. Groups furthermore did not differ with respect to partial substitutions of phospholipids by sulfo- and galactolipids. Metabolites significantly more abundant in the efficient group, such as sinapate, benzoate and glucoronate, were related to antioxidant defence and may help alleviating oxidative stress caused by P deficiency. Sugar alcohols ribitol and threitol were another marker metabolite for higher phosphate efficiency as were several amino acids, especially threonine. Since these metabolites are not known to be associated with P deficiency, they may provide novel clues for the selection of more P efficient genotypes. In conclusion, metabolite signatures detected here were not related to phosphate metabolism but rather helped P efficient lines to keep vital processes functional under the adverse conditions of P starvation.

Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves.

Upon exposure to light, plant cells quickly acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. This developmental transition involves the de novo biogenesis of the thylakoid system and requires reprogramming of metabolism and gene expression. Etioplast-to-chloroplast differentiation involves massive changes in plastid ultrastructure, but how these changes are connected to specific changes in physiology, metabolism, and expression of the plastid and nuclear genomes is poorly understood. Here, we describe a new experimental system in the dicotyledonous model plant tobacco (Nicotiana tabacum) that allows us to study the leaf deetiolation process at the systems level. We have determined the accumulation kinetics of photosynthetic complexes, pigments, lipids, and soluble metabolites and recorded the dynamic changes in plastid ultrastructure and in the nuclear and plastid transcriptomes. Our data describe the greening process at high temporal resolution, resolve distinct genetic and metabolic phases during deetiolation, and reveal numerous candidate genes that may be involved in light-induced chloroplast development and thylakoid biogenesis.

The metabolic (under)groundwork of the lily bulb toward sprouting.

Large bulbs of Lilium longiflorum have an obligatory cold requirement to flower. Bulb cooling is widely used to induce and accelerate flowering. However, in-depth investigations of the effect of bulb cooling on major landmarks of plant development are lacking. It has been demonstrated that low temperature induces carbohydrate degradation, yet integrative studies on metabolic changes occurring in the bulb are not available. We detected that cold exposure mainly hastened bulb sprouting, rather than floral transition or blooming. Metabolite profiling of cooled and non-cooled bulbs was carried out, revealing cold-induced accumulation of soluble sugars, lipids and specific amino acids, and a significant reduction in tricarboxylic acid (TCA)-cycle elements. We observed that metabolic pathways located in the cytosol - including glycolysis, lipid synthesis and part of the gamma-Aminobutyric acid (GABA) shunt - were enhanced by cold exposure, while mitochondrial metabolism - namely the TCA cycle - was reduced by cold. We suggest a physiological model accounting for this metabolic discrepancy.

Lipidomics analysis unravels the effect of nitrogen fertilization on lipid metabolism in tea plant (Camellia sinensis L.).

BACKGROUND: Nitrogen (N) plays an important role in the formation of tea quality-related compounds, like amino acids and flavor/aroma origin compounds. Lipids, which have been reported to be affected by N deficiency, are precursors to the generation of flavor/aroma origin compounds in tea plant. However, there is no literature about the lipid profiles of tea plant affected by N fertilization. Hence, we hypothesize that the biosynthesis of flavor-related compounds in tea was affected by N through its regulation of lipid metabolism. RESULTS: In this study, mature leaves and new shoots of tea plant grown under three N levels at the rates of 0, 285 and 474 kg/ha were applied for ultra-performance liquid chromatography-mass spectrometry (UPLC/MS) based lipidomic analysis. Totally, 178 lipid species were identified. The results showed that the composition of lipid compounds in mature leaves and new shoots varied dramatically, which was also affected by N levels. The higher content of the storage lipid TAG and higher carbon (C)/N ratio in mature leaves than that of new shoots in tea plants grown under low N level (0 kg/ha) suggested that tea plants could remobilize the C stored in TAG to maintain their C/N balance and help to improve the quality of tea. N fertilization resulted in a higher content of the compounds 36:6 MGDG and 36:6 DGDG. Since these compounds contain linolenic acid (18:3), a precursor to the formation of aroma origin compounds, we suggested their increase could contribute to the quality of tea. CONCLUSIONS: Taken together, the present work indicated that appropriate application of N fertilizer could balance the lipid metabolism and the formation of flavor/aroma origin compounds, which help to improve the quality of tea. Moreover, excess N fertilization might deteriorate the aroma quality of made tea due to increases of precursors leading to grassy odor.

Using lipidomics for expanding the knowledge on lipid metabolism in plants.

Lipids are a crucial and diverse class of biomolecules. Their structural heterogeneity in plants is staggering, and many aspects of plant life are manifested and mediated by lipids. Recent advances in metabolomic and lipidomic technologies and analysis have immensely increased our knowledge of the plant lipidome, its biosynthesis, regulation, adaptation, remodeling, functions, roles, and interactions. Here we review the recent literature and trends in lipidomics, and discuss specific issues pertaining to lipidomic research in plants, and how lipidomics has helped elucidate key issues in plant cell biology, immunity, response to stress, evolution, crop enhancement-to name but a few.

Reproductive failure in Arabidopsis thaliana under transient carbohydrate limitation: flowers and very young siliques are jettisoned and the meristem is maintained to allow successful resumption of reproductive growth.

The impact of transient carbon depletion on reproductive growth in Arabidopsis was investigated by transferring long-photoperiod-grown plants to continuous darkness and returning them to a light-dark cycle. After 2 days of darkness, carbon reserves were depleted in reproductive sinks, and RNA in situ hybridization of marker transcripts showed that carbon starvation responses had been initiated in the meristem, anthers and ovules. Dark treatments of 2 or more days resulted in a bare-segment phenotype on the floral stem, with 23-27 aborted siliques. These resulted from impaired growth of immature siliques and abortion of mature and immature flowers. Depolarization of PIN1 protein and increased DII-VENUS expression pointed to rapid collapse of auxin gradients in the meristem and inhibition of primordia initiation. After transfer back to a light-dark cycle, flowers appeared and formed viable siliques and seeds. A similar phenotype was seen after transfer to sub-compensation point irradiance or CO2 . It also appeared in a milder form after a moderate decrease in irradiance and developed spontaneously in short photoperiods. We conclude that Arabidopsis inhibits primordia initiation and aborts flowers and very young siliques in C-limited conditions. This curtails demand, safeguarding meristem function and allowing renewal of reproductive growth when carbon becomes available again.

The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation.

Lipid remodeling is one of the most dramatic metabolic responses to phosphorus (P) starvation. It consists of the degradation of phospholipids to release the phosphate needed by the cell and the accumulation of glycolipids to replace phospholipids in the membranes. It is shown that PHR1, a well-described transcriptional regulator of P starvation of the MYB family, largely controls this response. Glycerolipid composition and the expression of most lipid-remodeling gene transcripts analysed were altered in the phr1 mutant under phosphate starvation in comparison to wild-type plants. In addition to these results, the lipidomic characterization of wild-type plants showed two novel features of the lipid response to P starvation for Arabidopsis. Triacylglycerol (TAG) accumulates dramatically under P starvation (by as much as ~20-fold in shoots and ~13-fold in roots), a response known to occur in green algae but hardly known in plants. Surprisingly, there was an increase in phosphatidylglycerol (PG) in P-starved roots, a response that may be adaptive as it was suppressed in the phr1 mutant.

Liquid chromatography high-resolution mass spectrometry for fatty acid profiling.

Quantification of fatty acids has been crucial to elucidate lipid biosynthesis pathways in plants. To date, fatty acid identification and quantification has relied mainly on gas chromatography (GC) coupled to flame ionization detection (FID) or mass spectrometry (MS), which requires the derivatization of samples and the use of chemical standards for annotation. Here we present an alternative method based on a simple procedure for the hydrolysis of lipids, so that fatty acids can be quantified by liquid chromatography mass spectrometry (LC-MS) analysis. Proper peak annotation of the fatty acids in the LC-MS-based methods has been achieved by LC-MS measurements of authentic standard compounds and elemental formula annotation supported by (13)C isotope-labeled Arabidopsis. As a proof of concept, we have compared the analysis by LC-MS and GC-FID of two previously characterized Arabidopsis thaliana knock-out mutants for FAD6 and FAD7 desaturase genes. These results are discussed in light of lipidomic profiles obtained from the same samples. In addition, we performed untargeted LC-MS analysis to determine the fatty acid content of two diatom species. Our results indicate that both LC-MS and GC-FID analyses are comparable, but that because of higher sensitivity and selectivity the LC-MS-based method allows for a broader coverage and determination of novel fatty acids.

Systems Analysis of the Response of Photosynthesis, Metabolism, and Growth to an Increase in Irradiance in the Photosynthetic Model Organism Chlamydomonas reinhardtii.

We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.

Plasma membrane lipid-protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana.

The plasma membrane is an important organelle providing structure, signaling and transport as major biological functions. Being composed of lipids and proteins with different physicochemical properties, the biological functions of membranes depend on specific protein-protein and protein-lipid interactions. Interactions of proteins with their specific sterol and lipid environment were shown to be important factors for protein recruitment into sub-compartmental structures of the plasma membrane. System-wide implications of altered endogenous sterol levels for membrane functions in living cells were not studied in higher plant cells. In particular, little is known how alterations in membrane sterol composition affect protein and lipid organization and interaction within membranes. Here, we conducted a comparative analysis of the plasma membrane protein and lipid composition in Arabidopsis sterol-biosynthesis mutants smt1 and ugt80A2;B1. smt1 shows general alterations in sterol composition while ugt80A2;B1 is significantly impaired in sterol glycosylation. By systematically analyzing different cellular fractions and combining proteomic with lipidomic data we were able to reveal contrasting alterations in lipid-protein interactions in both mutants, with resulting differential changes in plasma membrane signaling status.

Analysis of short-term changes in the Arabidopsis thaliana glycerolipidome in response to temperature and light.

Although the influence of temperature, particularly cold, on lipid metabolism is well established, previous studies have focused on long-term responses and have largely ignored the influence of other interacting environmental factors. Here, we present a time-resolved analysis of the early responses of the glycerolipidome of Arabidopsis thaliana plants exposed to various temperatures (4, 21 and 32°C) and light intensities (darkness, 75, 150 and 400 µmol m(-2) s(-1)), including selected combinations. Using a UPLC/MS-based lipidomic platform, we reproducibly measured most glycerolipid species reported for Arabidopsis leaves, including the classes phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI) phosphatidylglycerol (PG), monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol (SQDG). In addition to known lipids, we have identified previously unobserved compounds, such as 36-C PGs and eukaryotic phospholipids containing 16:3 acyl chains. Occurrence of these lipid species implies the action of new biochemical mechanisms. Exposition of Arabidopsis plants to various light and temperature regimes results in two major effects. The first is the dependence of the saturation level of PC and MGDG pools on light intensity, likely arising from light regulation of de novo fatty acid synthesis. The second concerns an immediate decrease in unsaturated species of PG at high-temperature conditions (32°C), which could mark the first stages of adaptation to heat-stress conditions. Observed changes are discussed in the context of current knowledge, and new hypotheses have been formulated concerning the early stages of the plant response to changing light and temperature conditions.

Development of a novel virtual screening cascade protocol to identify potential trypanothione reductase inhibitors.

The implementation of a novel sequential computational approach that can be used effectively for virtual screening and identification of prospective ligands that bind to trypanothione reductase (TryR) is reported. The multistep strategy combines a ligand-based virtual screening for building an enriched library of small molecules with a docking protocol (AutoDock, X-Score) for screening against the TryR target. Compounds were ranked by an exhaustive conformational consensus scoring approach that employs a rank-by-rank strategy by combining both scoring functions. Analysis of the predicted ligand-protein interactions highlights the role of bulky quaternary amine moieties for binding affinity. The scaffold hopping (SHOP) process derived from this computational approach allowed the identification of several chemotypes, not previously reported as antiprotozoal agents, which includes dibenzothiepine, dibenzooxathiepine, dibenzodithiepine, and polycyclic cationic structures like thiaazatetracyclo-nonadeca-hexaen-3-ium. Assays measuring the inhibiting effect of these compounds on T. cruzi and T. brucei TryR confirm their potential for further rational optimization.