Complete biosynthesis of QS-21 in engineered yeast.

QS-21 is a potent vaccine adjuvant and remains the only saponin-based adjuvant that has been clinically approved for use in humans1,2. However, owing to the complex structure of QS-21, its availability is limited. Today, the supply depends on laborious extraction from the Chilean soapbark tree or on low-yielding total chemical synthesis3,4. Here we demonstrate the complete biosynthesis of QS-21 and its precursors, as well as structural derivatives, in engineered yeast strains. The successful biosynthesis in yeast requires fine-tuning of the host's native pathway fluxes, as well as the functional and balanced expression of 38 heterologous enzymes. The required biosynthetic pathway spans seven enzyme families-a terpene synthase, P450s, nucleotide sugar synthases, glycosyltransferases, a coenzyme A ligase, acyl transferases and polyketide synthases-from six organisms, and mimics in yeast the subcellular compartmentalization of plants from the endoplasmic reticulum membrane to the cytosol. Finally, by taking advantage of the promiscuity of certain pathway enzymes, we produced structural analogues of QS-21 using this biosynthetic platform. This microbial production scheme will allow for the future establishment of a structure-activity relationship, and will thus enable the rational design of potent vaccine adjuvants.

Source-Supported Suspect Screening (4S) of Phytotoxins in Terrestrial and Aquatic Environments: A Field Study of Lupinus angustifolius L. (Blue Lupin).

Phytotoxins (PTs) are bioactive secondary metabolites produced by plants. More recently, they have been recognized as important aquatic micropollutants. Despite that, only a few PTs have been detected and reported in terrestrial and aquatic environments, while their source and leaching pathways remain largely unclear. Herein, we established a novel approach named source-supported suspect screening (4S) to discover PTs in different environments, investigate their environmental occurrences, identify their sources, and initiate discussions on their leaching mechanisms. The 4S-approach was demonstrated on a five-month Lupinus angustifolius L. (L. angustifolius) crop field experiment, where plant, topsoil, drainage water, and surface water were sampled and analyzed. As a result, 72 PTs (flavonoids and alkaloids) were identified at high confidence, with 10 PTs fully confirmed. Fifty-three PTs detected in soil or water were linked to L. angustifolius, among which 26 PTs were coherently detected in all three environmental compartments. The occurrence and abundance of PTs in terrestrial soil and aquatic environments were influenced by the plant growth stage and precipitation. Soil served as an intermedium when PTs leached from L. angustifolius to the drainage water, while the degree of retardation and eventual occurrence in the aquatic environment depended on both PTs and soil physico-chemical properties.

Does sulfur application continue to reduce cadmium accumulation and increase the seed yield of oilseed rape (Brassica napus L.) at the maturity stage?

BACKGROUND: Oilseed rape requires sulfur (S) fertilization. Cadmium (Cd) differs dramatically in agricultural soils. Rice-oilseed rape rotation distributes widely and contributes the majority of rapeseeds in Asian countries. It was reported that S metabolism was involved in Cd uptake in seedlings of oilseed rape, although the effects of S on Cd accumulation and seed yield at maturity are still unclear. RESULTS: We performed a pot experiment including two Cd rates (0.35 and 10.35 mg kg-1 , as low and high Cd soil) and four S levels (0, 30, 60 and 120 mg kg-1 ). The results showed that low S application (30 mg kg-1 ) resulted in two-fold higher seed-Cd concentration irrespective of soil Cd levels. The responsible mechanism might be that Cd translocation into rapeseeds was involved in sulfate transporters, which could be strongly expressed in shoots and roots when supplying sulfate under S-starvation conditions, but depressed under a S-sufficient environment. For high Cd soil, seed yield decreased by 36%, 48% and 72% at 30, 60 and 120 mg S kg-1 compared to non-S treatment, whereas there were no differences for low Cd soil. Antagonistic effects of S and Cd existed for seed yield according to structure equation model analysis. CONCLUSION: Oilseed rape can be grown in low-Cd fields as a safe food crop with high levels of sulfur fertilizers (>60 mg S kg-1 ). In high-Cd fields, oilseed rape is recommended as a Cd-remediation crop, and rapeseeds should only be used for industrial purposes and not for food. © 2021 Society of Chemical Industry.

Residual effects of sulfur application prior to oilseed rape cultivation on cadmium accumulation in brown rice under an oilseed rape-rice rotation pot experiment.

We aimed to investigate how sulfur (S) application prior to oilseed rape cultivation influences the uptake of cadmium (Cd) by rice grown in low- and high-Cd soils. A pot experiment involving four S levels (0, 30, 60, 120 mg S kg-1) combined with two Cd rates (low and high-0.35 and 10.35 mg Cd kg-1, respectively) was conducted. Soil pore water during rice growth and plant tissues at maturity were analyzed. The soil pore water results indicated that S application decreased Cd solubility under submergence due to the S-induced increase of soil pH and the enhancement of sulfide formation in soil micropores. When S was applied at rates of 30, 60 and 120 mg S kg-1, brown rice Cd concentrations decreased by 18%, 18%, and 55% (p < 0.05) in the low-Cd soil but increased by 20%, 40%, and 40% in the high-Cd soil compared with those in the non-S treatment. The different effects of S on Cd accumulation in brown rice were related to Cd-induced oxidative stress in the rice plants. In low-Cd soils, a S-induced increase in phytochelatins in rice roots restricted and inhibited Cd translocation in brown rice. In high-Cd soils, the Cd-induced oxidative stress in rice plants weakened the protective effects of S, while highlighted the promotion of Cd uptake by S. Overall, S fertilizer is recommended for oilseed rape-rice rotations in low-Cd paddy fields. In high Cd-contaminated fields, oilseed rape-rice rotations are suitable for the simultaneous remediation by oilseed rape and production of rice without S fertilization.

Zinc Photocages with Improved Photophysical Properties and Cell Permeability Imparted by Ternary Complex Formation.

Photocaged complexes can control the availability of metal ions to interrogate cellular signaling pathways. We describe a new photocage, {bis[(2-pyridyl)methyl]amino}(9-oxo-2-xanthenyl)acetic acid (XDPAdeCage, 1), which utilizes a 2-xanthone acetic acid group to mediate a photodecarboxylation reaction. XDPAdeCage photolyzes with a quantum yield of 27%, and binds Zn2+ with 4.6 pM affinity, which decreases by over 4 orders of magnitude after photolysis. For comparison to our previous approach to Zn2+ release via photodecarboxylation, the analogous photocage {bis[(2-pyridyl)methyl]amino}(m-nitrophenyl)acetic acid (DPAdeCage, 2), which uses a m-nitrobenzyl chromophore, was also prepared and characterized. The advantages of the 2-xanthone acetic acid chromophore include red-shifted excitation and a higher extinction coefficient at the preferred uncaging wavelength. The neutral ternary complex of [Zn(XDPAdeCage)]+ with the anionic ligand pyrithione is membrane permeable, which circumvents the need to utilize invasive techniques to introduce intracellular Zn2+ fluctuations. Using fluorescent imaging, we have confirmed transport of Zn2+ across membranes; in addition, RT-PCR experiments demonstrate changes in expression of Zn2+-responsive proteins after photolysis.

Stable Isotopes and Bayesian Modeling Methods of Tracking Sources and Differentiating Bioavailable and Recalcitrant Phosphorus Pools in Suspended Particulate Matter.

Understanding the sources of different phosphorus (P) pools and their bioavailability under imposed biogeochemical environments in a watershed is limited largely due to the lack of appropriate methods. In this research, phosphate oxygen isotope ratios and Bayesian modeling on fingerprinting elements were applied as two novel methods to identify sources and relative recalcitrancy of particulate P pools suspended in water in the continuum of sources from land to the mouth of a coastal estuary to the Chesapeake Bay. Comparative analyses of sizes, relative ratios, and oxygen isotope values of particulate P pools in the creek water suggested that the NaHCO3-P pool was bioavailable, whereas NaOH-P and HCl-P pools were recalcitrant during P transport along the creek. Agricultural field soil, streambank, and river bottom sediments were major sources of particulate P and their contributions varied significantly at the headwater and downstream regions of the creek. Bayesian modeling based on fingerprinting elements suggested that tides played a major role in forming particulate matter from estuarine sources at the creek mouth region and importing it upstream. These findings provide new insights into the origin and fate of particulate P and the fidelity of isotope and fingerprinting methods in source tracking of P in tidally influenced watersheds.

Extra-pituitary prolactin (PRL) and prolactin-like protein (PRL-L) in chickens and zebrafish.

It is generally believed that in vertebrates, prolactin (PRL) is predominantly synthesized and released by pituitary lactotrophs and plays important roles in many physiological processes via activation of PRL receptor (PRLR), including water and electrolyte balance, reproduction, growth and development, metabolism, immuno-modulation, and behavior. However, there is increasing evidence showing that PRL and the newly identified 'prolactin-like protein (PRL-L)', a novel ligand of PRL receptor, are also expressed in a variety of extra-pituitary tissues, such as the brain, skin, ovary, and testes in non-mammalian vertebrates. In this brief review, we summarize the recent research progress on the structure, biological activities, and extra-pituitary expression of PRL and PRL-L in chickens (Gallus gallus) and zebrafish (Danio rerio) from our and other laboratories and briefly discuss their potential paracrine/autocrine roles in non-mammalian vertebrates, which may promote us to rethink the broad spectrum of PRL actions previously attributed to pituitary PRL only.

Swimming Motility Reduces Deposition to Silica Surfaces.

The transport and fate of bacteria in porous media is influenced by physicochemical and biological properties. This study investigated the effect of swimming motility on the attachment of cells to silica surfaces through comprehensive analysis of cell deposition in model porous media. Distinct motilities were quantified for different strains using global and cluster-based statistical analyses of microscopic images taken under no-flow condition. The wild-type, flagellated strain DJ showed strong swimming as a result of the actively swimming subpopulation whose average speed was 25.6 µm/s; the impaired swimming of strain DJ77 was attributed to the lower average speed of 17.4 µm/s in its actively swimming subpopulation; and both the nonflagellated JZ52 and chemically treated DJ cells were nonmotile. The approach and deposition of these bacterial cells were analyzed in porous media setups, including single-collector radial stagnation point flow cells (RSPF) and two-dimensional multiple-collector micromodels under well-defined hydrodynamic conditions. In RSPF experiments, both swimming and nonmotile cells moved with the flow when at a distance ≥20 µm above the collector surface. Closer to the surface, DJ cells showed both horizontal and vertical movement, limiting their contact with the surface, while chemically treated DJ cells moved with the flow to reach the surface. These results explain how wild-type swimming reduces attachment. In agreement, the deposition in micromodels was also lowest for DJ compared with those for DJ77 and JZ52. Wild-type swimming specifically reduced deposition on the upstream surfaces of the micromodel collectors. Conducted under environmentally relevant hydrodynamic conditions, the results suggest that swimming motility is an important characteristic for bacterial deposition and transport in the environment.

Design, synthesis and structure-activity relationship studies of morpholino-1H-phenalene derivatives that antagonize Mcl-1/Bcl-2.

We report herein characteristic studies of Mcl-1 and Bcl-2 dual inhibitors. It was found that a protruding carbonyl group forming hydrogen bond with R263 plays a predominant role compared with the hydrophobic group that occupies the p2 pocket. A series of dual inhibitors representing different parts of the morpholino-1H-phenalene were designed, synthesized and evaluated.

Design, synthesis and structure­activity relationship studies of morpholino-1H-phenalene derivatives that antagonize Mcl-1/Bcl-2.

We report herein characteristic studies of Mcl-1 and Bcl-2 dual inhibitors. It was found that a protruding carbonyl group forming hydrogen bond with R263 plays a predominant role compared with the hydrophobic group that occupies the p2 pocket. A series of dual inhibitors representing different parts of the morpholino-1H-phenalene were designed, synthesized and evaluated.

3-Thiomorpholin-8-oxo-8H-acenaphtho [1,2-b] pyrrole-9-carbonitrile (S1) derivatives as pan-Bcl-2-inhibitors of Bcl-2, Bcl-xL and Mcl-1.

Based on the binding mode of our previously discovered dual inhibitor of Bcl-2 and Mcl-1, 3-thiomorpholin-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile (3, S1), a library of 9-substituted 3 derivatives was synthesized to further probe the p4 pocket of the two targets. By NMR, structure-activity relationship study, and site-directed mutation, compound 6d (3-(4-aminophenylthio)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-3-phenyl)propylamine) was identified to span p2-p4 pockets of Mcl-1, Bcl-2 and Bcl-x(L), and then exhibited 9- to 35-fold better affinity to the three targets than 3 (IC(50)=10, 20 and 18 nM, respectively), which led to greater activity in induction of apoptosis in multiple cancer cell lines. Different contribution of p4 pocket to binding Bcl-2 and Mcl-1 was also investigated by plotting the potency and the HAC of the derivatives.

Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.

Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1.

Establishment of Highly Efficient Plant Regeneration, Callus Transformation and Analysis of Botrytis cinerea-Responsive PR Promoters in Lilium brownii var. viridulum.

Lilium brownii var. viridulum, commonly called Longya lily, is a well-known flower and vegetable plant in China that has poor tolerance to Botrytis fungal disease. The molecularimprovement has mainly been restricted to an efficient regeneration and transformation system. In this study, the highly efficient regeneration of Longya lily was established through the optimization of embryogenic callus, adventitious shoot and rooting induction. The major factors influencing transformation (antibiotics, Agrobacterium concentration, infection time, suspension solution and coculture medium) were examined. The expression responses of PR promoters (ZmPR4 and BjCHI1) to B. cinerea were assessed in transgenic calli. The results showed that Murashige and Skoog (MS) medium with 1.0 mg·L-1 picloram (PIC) and 0.2 mg·L-1 1-naphthaleneacetic acid (NAA) under light conditions and MS with 0.5 mg·L-1 6-benzylaminopurine (6-BA) and 1.0 mg·L-1 NAA under darkness were optimal for embryogenic callus induction (64.67% rate) and proliferation (3.96 coefficient). Callus inoculation into MS containing 2.0 mg·L-1 thidiazuron (TDZ), 0.4 mg·L-1 NAA, 1.0 mg·L-1 TDZ and 0.5 mg·L-1 NAA led to shooting induction (92.22 of rate) and proliferation (3.28 of coefficient) promotion, respectively. The rooting rate reached 99.00% on MS with 0.3 mg·L-1 NAA. Moreover, a transformation rate of 65.56% was achieved by soaking the callus in Agrobacterium at an OD600 of 0.4 for 10 min in modified MS without NH4NO3 as the suspension solution and coculture medium before selecting 75 mg·L-1 hygromycin and 300 mg·L-1 cefotaxime. Only the BjCHI1 promoter was obviously expressed in transgenic calli. These results could facilitate the generation of Longya lily transgenic plants with improved B. cinerea resistance.

An AIE luminogen self-assembled nanoprobe for efficient monitoring of the concentration and structural transition of human serum albumin.

Monitoring the content and structural transition of human serum albumin (HSA) is valuable for diagnosing hypoalbuminemia and albuminuria and elucidating its transport function, respectively. Herein, we developed a multifunctional and efficient nanoprobe based on the self-assembly of an amphiphilic aggregation-induced emission luminogen, TPNN, for HSA detection and structure monitoring. TPNN molecules formed loose self-assembly in aqueous media and emitted faint fluorescence due to vigorous intramolecular motion. In the presence of HSA, a remarkable fluorescence enhancement accompanied by dissociation of TPNN assembly was observed due to the site-specific binding of TPNN to the middle long-narrow pocket of HSA. This binding blocked the intramolecular motion while producing a sensitive, selective, fast and stable fluorescence turn-on response to HSA, making TPNN assembly suitable for the HSA assay. TPNN assemblies also showed superior selectivity to HSA than bovine serum albumin (BSA) due to the distinct binding modes, and enabled us to distinguish the two homologous proteins. Furthermore, the generated TPNN-HSA complex underwent stepwise fluorescence quenching in the presence of protein denaturants and proteases, which revealed the process and kinetics of HSA unfolding and cleavage. TPNN assembly provides a powerful tool for accurate quantification of HSA in serum and urine and real-time monitoring of HSA structural transition.

Obtaining clean and informative mass spectra from complex chromatographic and high-resolution all-ions-fragmentation data by nonnegative parallel factor analysis 2.

A major challenge in processing of complex data obtained from chromatography hyphenated to mass spectrometry is to resolve chromatographically co-eluting compounds. In this study, we present a workflow for the resolution of ultra-high pressure liquid chromatography high-resolution mass spectrometry data obtained by the broadband data-independent acquisition MSE operation (UHPLCHRMSE). The workflow is based on a recently introduced algorithm for Parallel Factor Analysis 2 (PARAFAC2) that allows to enforce non-negativity on all the model coefficients. The workflow was tested on three sets of UHPLC-HRMSE measurements from a Lupinus angustifolius L. crop field study, which included plant tissue samples, soil samples and samples from drainage water as well as stream water close to the field. The three datasets included 93, 59, and 75 chromatographic runs in total for the plant, soil and water batches, respectively. Nonnegative-PARAFAC2 models were fitted on the summed high and low energy (HE and LE) traces on chromatographic intervals corresponding to spiked standard for the three sample sets independently. In soil and plant samples, 13 out of 14 spiked standards were resolved by NN-PARAFAC2 even in presence of chromatographic co-elution, and their mass spectral loadings could be matched to a reference spectrum. In contrast, only seven spiked standards were correctly resolved and matched for the water samples because a higher chromatographic baseline rendered the data noisier. The results show that the workflow we present can provide improved mass spectral selectivity for data-independent acquisition compared to using the raw mass spectra and can be used to match fragment ions from the HE trace, and precursor and adduct ions from the LE trace even in presence of co-eluting compounds.

Enhancing the power of liquid chromatography-Mass spectrometry for chemical fingerprinting of phytotoxins in the environment.

Phytotoxins are plant secondary metabolites. They have recently been considered as chemicals of emerging concern (CECs) and there is a growing interest in their environmental fate and potential threat to public health. Dedicated target and non-target screening (NTS) analysis of phytotoxins in environmental samples are sparse, meanwhile phytotoxins are rarely detected in NTS-based analysis due to lack of an efficient methodology. Development of new analytical measurement methods is therefore highly needed. In this study, we for the first time investigated key parameters of reversed phase liquid chromatography-high resolution mass spectrometry (RPLC-HRMS) for five major classes of phytotoxins (alkaloids, steroids, terpenoids, flavonoids and aromatic polyketides) in environmental matrices; the investigation included analytical conditions which have not yet been explored by others, e.g. ionization at alkaline pH above 9. As the outcome we established a new analytical method for target/suspect screening and NTS of phytotoxins in the environment, which significantly improved the detection sensitivity with up to 40 times compared to previous methods, and enabled the discovery of over 30 phytotoxins in a NTS-based environmental study. We also observed that the negative ionization of phenols could be facilitated by the number of hydroxyl groups on the ring rather than their position of substitution. This study is of interest for a better fundamental understanding of the behavior of phytotoxins in LC-MS. Dedicated target/suspect screening and NTS methods will facilitate a better risk characterization of phytotoxins in the environment and stimulate implementation of new public regulation on phytotoxins.

Selective pressurized liquid extraction of plant secondary metabolites: Convallaria majalis L. as a case.

A fast and efficient selective pressurized liquid extraction (sPLE) method was developed to extract secondary metabolites from complex plant matrix. Convallaria majalis L., a plant producing toxic steroids, was used as proof-of-concept. The method was optimized in the aspects of preheating, dispersant, extraction temperature and solvent, and the use of C18 as in-cell cleanup sorbent. Eight authentic natural steroids with diverse sugar moieties and hydrophobicities were selected as reference analytes and spiked to 0.1 g dried leaves. The extraction performance was evaluated based on the analytes' stability, recovery, matrix effect in the electrospray interface and the level of co-extractives. With the optimal method, the extraction was finished in 10 min. A colorless extract was obtained with recoveries ranging from 63% to 107% and absolute matrix effects ranging from 3% to 27%. The optimized method was validated by extracting 0.1 g, 0.2 g and 0.4 g spiked plant samples; method accuracy and precision were assessed by recoveries and relative standard deviations of the combined extraction-analysis workflow. The method was also tested on soil samples and indicated its suitability for measuring secondary metabolites in multiple environmental matrices. To our knowledge, this is the first time sPLE has been reported to extract plant secondary metabolites from a complex plant matrix, with satisfactory recoveries and low matrix effects. This is also the first time (s)PLE has been reported to extract plant secondary metabolites from soil. We envision the method be coupled with liquid chromatography-electrospray ionization-high resolution mass spectrometry in a standard metabolomics workflow to facilitate plant metabolomics studies.

Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.

Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.

Evaluation of bacterial run and tumble motility parameters through trajectory analysis.

In this paper, a method for extraction of the behavior parameters of bacterial migration based on the run and tumble conceptual model is described. The methodology is applied to the microscopic images representing the motile movement of flagellated Azotobacter vinelandii. The bacterial cells are considered to change direction during both runs and tumbles as is evident from the movement trajectories. An unsupervised cluster analysis was performed to fractionate each bacterial trajectory into run and tumble segments, and then the distribution of parameters for each mode were extracted by fitting mathematical distributions best representing the data. A Gaussian copula was used to model the autocorrelation in swimming velocity. For both run and tumble modes, Gamma distribution was found to fit the marginal velocity best, and Logistic distribution was found to represent better the deviation angle than other distributions considered. For the transition rate distribution, log-logistic distribution and log-normal distribution, respectively, was found to do a better job than the traditionally agreed exponential distribution. A model was then developed to mimic the motility behavior of bacteria at the presence of flow. The model was applied to evaluate its ability to describe observed patterns of bacterial deposition on surfaces in a micro-model experiment with an approach velocity of 200 µm/s. It was found that the model can qualitatively reproduce the attachment results of the micro-model setting.