in-vesiculo-synthesis-peptide-membrane-precursors-for-autonomous

In Vesiculo Synthesis of Peptide Membrane Precursors for Autonomous Vesicle Growth

Compartmentalization of biochemical reactions is a central aspect of synthetic cells. For this purpose, peptide-based reaction compartments serve as an ...

Two low phytic acid (lpa) rice mutant lines, Os-lpa-XS110-1 and Os-lpa-XS110-2, were grown together with their parent wild-type variety Xiushui 110 in four field trials. HPLC analysis of inositol phosphates in the seeds produced demonstrated that compared to the wild-type, the reduction in phytic acid content in Os-lpa-XS110-1 (-46%) was more pronounced than that in Os-lpa-XS110-2 (-23%). Lower inositol phosphates (InsP 3, InsP 4, InsP 5) were not detected in the mutants. The lpa mutants and the wild-type rice were subjected to comparative metabolite profiling by capillary gas chromatography. On average, 34% (Os-lpa-XS110-1) and 42% (Os-lpa-XS110-2) of the detected peaks were statistically significantly different between wild-type and mutants. However, only a few of these differences could be consistently observed for all field trials. Identification and quantification of the consistently different metabolites revealed that contents of myo-inositol and raffinose were increased in Os-lpa-XS110-1 but decreased in Os-lpa-XS110-2 compared to the wild-type. In addition, Os-lpa-XS110-1 exhibited increased levels of galactose and galactinol. Consideration of these metabolic changes in light of the routes involved in the biosynthesis of phytic acid indicated a disturbance in the early biosynthetic pathway of phytic acid in Os-lpa-XS110-2 (similar to the lpa-1 type mutation in maize) and a mutation event affecting phosphorylation of myo-inositol in Os-lpa-XS110-1 (similar to the lpa-3-type mutation).

Metabolite profiling of two low phytic acid (lpa) rice mutants.

A metabolite profiling approach based on gas chromatography-mass spectrometry (GC-MS) was used to investigate time-dependent metabolic changes in the course of the germination of rice. Brown rice kernels were soaked and incubated for a total of 96 h under ambient conditions. Samples taken during the germination process were subjected to an extraction and fractionation procedure covering a broad spectrum of lipophilic (e.g., fatty acid methyl esters, hydrocarbons, fatty alcohols, sterols) and hydrophilic (e.g., sugars, acids, amino acids, amines) low molecular weight rice constituents. Investigation of the obtained fractions by GC resulted in the detection of 615 distinct peaks, of which 174 were identified by means of MS. Statistical assessment of the data via principal component analysis demonstrated that the metabolic changes during the germination process are reflected by time-dependent shifts of the scores, which were similar for the three rice materials investigated. Analysis of the corresponding loadings showed that polar metabolites were major contributors to the separation along the first principal component. Relative quantifications based on standardized peak heights revealed dynamic changes of the metabolites in the course of the germination.

Metabolite profiling of germinating rice seeds.

A GC-based approach was applied to compare the metabolite profiles of two low phytic acid (lpa) soybean mutants and their respective wild-types. The lpa mutants (Gm-lpa-TW75-1 and Gm-lpa-ZC-2) were grown together with the wild-types (Taiwan 75 and Zhechun no. 3) in three and four field trials, respectively. HPLC analysis revealed a phytic acid reduction of -53% for Gm-lpa-TW75-1 and of -46% for Gm-lpa-ZC-2. For Gm-lpa-TW75-1, no accumulation of lower inositol phosphates was observed, whereas Gm-lpa-ZC-2 exhibited significantly increased contents of the lower inositol phosphates InsP(3), InsP(4), and InsP(5) compared to the corresponding wild-type. The metabolite profiling revealed that compared to the wild-types, 40% (Gm-lpa-TW75-1) and 21% (Gm-lpa-ZC-2) of the detected peaks were statistically significantly different in the lpa mutants grown at one field trial. However, the majority of these differences were shown to be related to environmental impact and natural variability rather than to the mutation event. Identification of consistent metabolic changes in the lpa mutants revealed decreased contents of myo-inositol, galactinol, raffinose, stachyose, and the galactosyl cyclitols galactopinitol A, galactopinitol B, and fagopyritol B1 compared to the wild-type. These consistently pronounced changes in Gm-lpa-TW75-1 confirmed the suggested mutation target. Consideration of the metabolic changes observed for Gm-lpa-ZC-2 (accumulation of lower inositol phosphates and increased myo-inositol contents) indicated a mutation event affecting the latter biosynthetic steps leading to phytic acid. The study demonstrated the applicability of metabolite profiling for the detection of changes in the metabolite phenotype induced by mutation breeding and its power in assisting in the elucidation of mutation events.

Metabolite profiling of two novel low phytic acid (lpa) soybean mutants.

A metabolite profiling approach based on gas chromatography-mass spectrometry (GC-MS) was applied to investigate the metabolite profiles of genetically modified (GM) Bt-maize (DKC78-15B, TXP 138F) and Roundup Ready-maize (DKC78-35R). For the comparative investigation of the impact of genetic modification versus environmental influence on the metabolite profiles, GM maize was grown together with the non-GM near-isogenic comparators under different environmental conditions, including several growing locations and seasons in Germany and South Africa. Analyses of variance (ANOVA) revealed significant differences between GM and non-GM maize grown in Germany and South Africa. For the factor genotype, 4 and 3%, respectively, of the total number of peaks detected by GC-MS showed statistically significant differences (p < 0.01) in peak heights as compared to the respective isogenic lines. However, ANOVA for the factor environment (growing location, season) revealed higher numbers of significant differences (p < 0.01) between the GM and the non-GM maize grown in Germany (42%) and South Africa (10%), respectively. This indicates that the majority of differences observed are related to natural variability rather than to the genetic modifications. In addition, multivariate data assessment by means of principal component analysis revealed that environmental factors, that is, growing locations and seasons, were dominant parameters driving the variability of the maize metabolite profiles.

Metabolite profiling of maize kernels--genetic modification versus environmental influence.

Metabolic challenge protocols, such as the oral glucose tolerance test, can uncover early alterations in metabolism preceding chronic diseases. Nevertheless, most metabolomics data accessible today reflect the fasting state. To analyze the dynamics of the human metabolome in response to environmental stimuli, we submitted 15 young healthy male volunteers to a highly controlled 4 d challenge protocol, including 36 h fasting, oral glucose and lipid tests, liquid test meals, physical exercise, and cold stress. Blood, urine, exhaled air, and breath condensate samples were analyzed on up to 56 time points by MS- and NMR-based methods, yielding 275 metabolic traits with a focus on lipids and amino acids. Here, we show that physiological challenges increased interindividual variation even in phenotypically similar volunteers, revealing metabotypes not observable in baseline metabolite profiles; volunteer-specific metabolite concentrations were consistently reflected in various biofluids; and readouts from a systematic model of β-oxidation (e.g., acetylcarnitine/palmitylcarnitine ratio) showed significant and stronger associations with physiological parameters (e.g., fat mass) than absolute metabolite concentrations, indicating that systematic models may aid in understanding individual challenge responses. Due to the multitude of analytical methods, challenges and sample types, our freely available metabolomics data set provides a unique reference for future metabolomics studies and for verification of systems biology models.

The dynamic range of the human metabolome revealed by challenges.

Different sources of folate may have different bioavailability and hence may impact the standard definition of folate equivalents. In order to examine this, a short term human study was undertaken to evaluate the relative native folate bioavailabilities from spinach, Camembert cheese and wheat germs compared to pteroylmonoglutamic acid as the reference dose. The study had a single-centre, randomised, four-treatment, four-period, four-sequence, cross-over design, i.e. the four (food) items to be tested (referred to as treatments) were administered in sequences according to the Latin square, so that each experimental treatment occurred only once within each sequence and once within each study period. Each of the 24 subjects received the four experimental items separated by a 14-day equilibrium phase and received a pteroylmonoglutamic acid supplement for 14 days before the first testing and between the testings for saturation of body pools. Folates in test foods, plasma and urine samples were determined by stable isotope dilution assays, and in urine and plasma, the concentrations of 5-methyltetrahydrofolate were evaluated. Standard non-compartmental methods were applied to determine the biokinetic parameters C(max), t(max) and AUC from baseline corrected 5-methyltetrahydrofolate concentrations within the interval from 0 to 12 hours. The variability of AUC and C(max) was moderate for spinach and oral solution of pteroylmonoglutamic acid but high for Camembert cheese and very high for wheat germs. The median t(max) was lowest for spinach, though t(max) showed a high variability among all treatments. When comparing the ratio estimates of AUC and C(max) for the different test foods, highest bioavailability was found for spinach followed by that for wheat germs and Camembert cheese. The results underline the dependence of folate bioavailability on the type of food ingested. Therefore, the general assumption of 50% bioavailability as the rationale behind the definition of folate equivalents has to be questioned and requires further investigation.

Folate bioavailability from foods rich in folates assessed in a short term human study using stable isotope dilution assays.

To investigate cultivar-specific metabolite changes upon drought stress in barley grain, differently adapted cultivars were field-grown under drought conditions using a rain-out shelter and under normal weather conditions (2010-2012). The grain was subjected to a gas chromatography-mass spectrometry-based metabolite profiling approach allowing the analyses of a broad spectrum of lipophilic and hydrophilic low molecular weight constituents. Multi- and univariate analyses demonstrated that there are grain metabolites which were significantly changed upon drought stress, either decreased or increased in all cultivars. On the other hand, for proteinogenic free amino acids increased concentrations were consistently observed in all seasons only in cultivars for which no drought resistance/tolerance had been described. Consistent decreases were seen only in the group of stress tolerant/resistant cultivars. These cultivar-specific correlations were particularly pronounced for branched-chain amino acids. The results indicate that free amino acids may serve as potential markers for cultivars differently adapted to drought stress. 

Metabolite profiling of barley grain subjected to induced drought stress: responses of free amino acids in differently adapted cultivars.

Different dietary sources of folate have differing bioavailabilities, which may affect their nutritional "value." In order to examine if these differences also occur within the same food products, a short-term human pilot study was undertaken as a follow-up study to a previously published human trial to evaluate the relative native folate bioavailabilities from low-fat Camembert cheese compared to pteroylmonoglutamic acid as the reference dose. Two healthy human subjects received the test foods in a randomized cross-over design separated by a 14-day equilibrium phase. Folate body pools were saturated with a pteroylmonoglutamic acid supplement before the first testing and between the testings. Folates in test foods and blood plasma were analyzed by stable isotope dilution assays. The biokinetic parameters C max, t max, and area under the curve (AUC) were determined in plasma within the interval of 0-12 h. When comparing the ratio estimates of AUC and C max for the different Camembert cheeses, a higher bioavailability was found for the low-fat Camembert assessed in the present study (≥64%) compared to a different brand in our previous investigation (8.8%). It is suggested that these differences may arise from the different folate distribution in the soft dough and firm rind as well as differing individual folate vitamer proportions. The results clearly underline the importance of the food matrix, even within the same type of food product, in terms of folate bioavailability. Moreover, our findings add to the increasing number of studies questioning the general assumption of 50% bioavailability as the rationale behind the definition of folate equivalents. However, more research is needed to better understand the interactions between individual folate vitamers and other food components and the potential impact on folate bioavailability and metabolism. 

Pilot Study on Folate Bioavailability from a Camembert Cheese Reveals Contradictory Findings to Recent Results from a Human Short-term Study.

Two low phytic acid (lpa) mutants have been developed previously with the aim to improve the nutritional value of rice (Oryza sativa) grains. In the present study, the impacts of lpa mutations on grain composition and underlying molecular mechanisms were investigated. Comparative compositional analyses and metabolite profiling demonstrated that concentrations of both phytic acid (PA) and total phosphorus (P) were significantly reduced in lpa brown rice, accompanied by changes in other metabolites and increased concentrations of nutritionally relevant compounds. The lpa mutations modified the expression of a number of genes involved in PA metabolism, as well as in sulfate and phosphate homeostasis and metabolism. Map-based cloning and complementation identified the underlying lpa gene to be OsSULTR3;3. The promoter of OsSULTR3;3 is highly active in the vascular bundles of leaves, stems and seeds, and its protein is localized in the endoplasmic reticulum. No activity of OsSULTR3;3 was revealed for the transport of phosphate, sulfate, inositol or inositol 1,4,5 triphosphate by heterologous expression in either yeast or Xenopus oocytes. The findings reveal that OsSULTR3;3 plays an important role in grain metabolism, pointing to a new route to generate value-added grains in rice and other cereal crops.

Disruption of OsSULTR3;3 reduces phytate and phosphorus concentrations and alters the metabolite profile in rice grains.

Membrane compartmentalization and growth are central aspects of living cells, and are thus encoded in every cell's genome. For the creation of artificial cellular systems, genetic information and production of membrane building blocks will need to be coupled in a similar manner. However, natural biochemical reaction networks and membrane building blocks are notoriously difficult to implement in vitro. Here, we utilized amphiphilic elastin-like peptides (ELP) to create self-assembled vesicular structures of about 200 nm diameter. In order to genetically encode the growth of these vesicles, we encapsulate a cell-free transcription-translation system together with the DNA template inside the peptide vesicles. We show in vesiculo production of a functioning fluorescent RNA aptamer and a fluorescent protein. Furthermore, we implement in situ expression of the membrane peptide itself and finally demonstrate autonomous vesicle growth due to the incorporation of this ELP into the membrane.

Towards synthetic cells using peptide-based reaction compartments.

Managing agricultural landscapes to support biodiversity and ecosystem services is a key aim of a sustainable agriculture. However, how the spatial arrangement of crop fields and other habitats in landscapes impacts arthropods and their functions is poorly known. Synthesising data from 49 studies (1515 landscapes) across Europe, we examined effects of landscape composition (% habitats) and configuration (edge density) on arthropods in fields and their margins, pest control, pollination and yields. Configuration effects interacted with the proportions of crop and non-crop habitats, and species' dietary, dispersal and overwintering traits led to contrasting responses to landscape variables. Overall, however, in landscapes with high edge density, 70% of pollinator and 44% of natural enemy species reached highest abundances and pollination and pest control improved 1.7- and 1.4-fold respectively. Arable-dominated landscapes with high edge densities achieved high yields. This suggests that enhancing edge density in European agroecosystems can promote functional biodiversity and yield-enhancing ecosystem services.

Article	Year
Metabolite profiling of two low phytic acid (lpa) rice mutants. Journal of agricultural and food chemistry\| PubMed ID: 18052121	2007
Metabolite profiling of germinating rice seeds. Journal of agricultural and food chemistry\| PubMed ID: 19053355	2008
Metabolite profiling of two novel low phytic acid (lpa) soybean mutants. Journal of agricultural and food chemistry\| PubMed ID: 19601673	2009
Metabolite profiling of maize kernels--genetic modification versus environmental influence. Journal of agricultural and food chemistry\| PubMed ID: 22375597	2012
The dynamic range of the human metabolome revealed by challenges. FASEB journal : official publication of the Federation of American Societies for Experimental Biology\| PubMed ID: 22426117	2012
Folate bioavailability from foods rich in folates assessed in a short term human study using stable isotope dilution assays. Food & function\| PubMed ID: 25407846	2015
Metabolite profiling of barley grain subjected to induced drought stress: responses of free amino acids in differently adapted cultivars. Journal of agricultural and food chemistry\| PubMed ID: 25867895	2015
Pilot Study on Folate Bioavailability from a Camembert Cheese Reveals Contradictory Findings to Recent Results from a Human Short-term Study. Frontiers in nutrition\| PubMed ID: 27092303	2016
Disruption of OsSULTR3;3 reduces phytate and phosphorus concentrations and alters the metabolite profile in rice grains. The New phytologist\| PubMed ID: 27110682	2016
Towards synthetic cells using peptide-based reaction compartments. Nature communications\| PubMed ID: 30242152	2018
The interplay of landscape composition and configuration: new pathways to manage functional biodiversity and agroecosystem services across Europe. Ecology letters\| PubMed ID: 30957401	2019

Thomas Frank

Biography

JoVE Journal Publications

Other Publications