Ubiquitin-specific protease UBP14 stabilizes HY5 by deubiquitination to promote photomorphogenesis in Arabidopsis thaliana.

Transcription factor ELONGATED HYPOCOTYL5 (HY5) is the central hub for seedling photomorphogenesis. E3 ubiquitin (Ub) ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) inhibits HY5 protein accumulation through ubiquitination. However, the process of HY5 deubiquitination, which antagonizes E3 ligase-mediated ubiquitination to maintain HY5 homeostasis has never been studied. Here, we identified that Arabidopsis thaliana deubiquitinating enzyme, Ub-SPECIFIC PROTEASE 14 (UBP14) physically interacts with HY5 and enhances its protein stability by deubiquitination. The da3-1 mutant lacking UBP14 function exhibited a long hypocotyl phenotype, and UBP14 deficiency led to the failure of rapid accumulation of HY5 during dark to light. In addition, UBP14 preferred to stabilize nonphosphorylated form of HY5 which is more readily bound to downstream target genes. HY5 promoted the expression and protein accumulation of UBP14 for positive feedback to facilitate photomorphogenesis. Our findings thus established a mechanism by which UBP14 stabilizes HY5 protein by deubiquitination to promote photomorphogenesis in A. thaliana.

Discrete Acyltransferases and Thioesterases in Iso-Migrastatin and Lactimidomycin Biosynthesis.

Iso-Migrastatin (iso-MGS) and lactimidomycin (LTM) are glutarimide-containing polyketide natural products (NPs) that are biosynthesized by homologous acyltransferase (AT)-less type I polyketide synthase (PKS) assembly lines. The biological activities of iso-MGS and LTM have inspired numerous efforts to generate analogues via genetic manipulation of their biosynthetic machinery in both native producers and model heterologous hosts. A detailed understanding of the MGS and LTM AT-less type I PKSs would serve to inspire future engineering efforts while advancing the fundamental knowledge of AT-less type I PKS enzymology. The mgs and ltm biosynthetic gene clusters (BGCs) encode for two discrete ATs of the architecture AT-enoylreductase (AT-ER) and AT-type II thioesterase (AT-TE). Herein, we report the functional characterization of the mgsB and ltmB and the mgsH and ltmH gene products, revealing that MgsB and LtmB function as type II thioesterases (TEs) and MgsH and LtmH are the dedicated trans-ATs for the MGS and LTM AT-less type I PKSs. In vivo and in vitro experiments demonstrated that MgsB was devoid of any AT activity, despite the presence of the conserved catalytic triad of canonical ATs. Cross-complementation experiments demonstrated that MgsH and LtmH are functionally interchangeable between the MGS and LTM AT-less type I PKSs. This work sets the stage for future mechanistic studies of AT-less type I PKSs and efforts to engineer the MGS and LTM AT-less type I PKS assembly lines for novel glutarimide-containing polyketides.

Cofactor-independent C-C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis.

Biosynthesis of atypical angucyclines involves unique oxidative B-ring cleavage and rearrangement reactions, which are catalyzed by AlpJ-family oxygenases, including AlpJ, JadG, and GilOII. Prior investigations established the essential requirement for FADH2/FMNH2 as cofactors when utilizing the quinone intermediate dehydrorabelomycin as a substrate. In this study, we unveil a previously unrecognized facet of these enzymes as cofactor-independent oxygenases when employing the hydroquinone intermediate CR1 as a substrate. The enzymes autonomously drive oxidative ring cleavage and rearrangement reactions of CR1, yielding products identical to those observed in cofactor-dependent reactions of AlpJ-family oxygenases. Furthermore, the AlpJ- and JadG-catalyzed reactions of CR1 could be quenched by superoxide dismutase, supporting a catalytic mechanism wherein the substrate CR1 reductively activates molecular oxygen, generating a substrate radical and the superoxide anion O2 •-. Our findings illuminate a substrate-controlled catalytic mechanism of AlpJ-family oxygenases, expanding the realm of cofactor-independent oxygenases. Notably, AlpJ-family oxygenases stand as a pioneering example of enzymes capable of catalyzing oxidative reactions in either an FADH2/FMNH2-dependent or cofactor-independent manner.

Confirmation of the stereochemistry of spiroviolene.

We confirm the previously revised stereochemistry of spiroviolene by X-ray crystallographically characterizing a hydrazone derivative of 9-oxospiroviolane, which is synthesized by hydroboration/oxidation of spiroviolene followed by oxidation of the resultant hydroxy group. An unexpected thermal boron migration occurred during the hydroboration process of spiroviolene that resulted in the production of a mixture of 1α-hydroxyspiroviolane, 9α- and 9ß-hydroxyspiroviolane after oxidation. The assertion of the cis-orientation of the 19- and 20-methyl groups provided further support for the revised cyclization mechanism of spiroviolene.

Efficient Broadband Near-Infrared CaMgGe2O6:Cr3+ Phosphor for pc-LED.

Broadband near-infrared (NIR) phosphor-converted light-emitting diodes (pc-LEDs) are essential to integrate near-infrared spectrometers into mobile devices for the rapid and noninvasive detection of biological components. However, efficient broadband NIR phosphors with a peak emission wavelength longer than 800 nm are deficient. In this study, CaMgGe2O6:Cr3+ phosphor was prepared by a high-temperature solid-state reaction. The phosphor doped with 0.02Cr3+ showed an emission band at 845 nm with a broad bandwidth of 160 nm and a high quantum yield of 84% under 450 nm excitation. The broadband NIR pc-LED was fabricated using CaMgGe2O6:0.02Cr3+ phosphor based on a blue light-emitting diode (LED) chip. A photoelectric efficiency of 27.2% @ 10 mA and an NIR output power of 57.98 mW @ 100 mA were achieved, which are the highest values reported yet for broadband NIR pc-LEDs with a peak wavelength longer than 800 nm. Using the fabricated NIR pc-LED as the light source, the characteristic absorption spectra of some substances were obtained. All of the results indicated that the CaMgGe2O6:Cr3+ phosphor has considerable potential in near-infrared spectroscopic applications.

Discovery of the leinamycin family of natural products by mining actinobacterial genomes.

Nature's ability to generate diverse natural products from simple building blocks has inspired combinatorial biosynthesis. The knowledge-based approach to combinatorial biosynthesis has allowed the production of designer analogs by rational metabolic pathway engineering. While successful, structural alterations are limited, with designer analogs often produced in compromised titers. The discovery-based approach to combinatorial biosynthesis complements the knowledge-based approach by exploring the vast combinatorial biosynthesis repertoire found in Nature. Here we showcase the discovery-based approach to combinatorial biosynthesis by targeting the domain of unknown function and cysteine lyase domain (DUF-SH) didomain, specific for sulfur incorporation from the leinamycin (LNM) biosynthetic machinery, to discover the LNM family of natural products. By mining bacterial genomes from public databases and the actinomycetes strain collection at The Scripps Research Institute, we discovered 49 potential producers that could be grouped into 18 distinct clades based on phylogenetic analysis of the DUF-SH didomains. Further analysis of the representative genomes from each of the clades identified 28 lnm-type gene clusters. Structural diversities encoded by the LNM-type biosynthetic machineries were predicted based on bioinformatics and confirmed by in vitro characterization of selected adenylation proteins and isolation and structural elucidation of the guangnanmycins and weishanmycins. These findings demonstrate the power of the discovery-based approach to combinatorial biosynthesis for natural product discovery and structural diversity and highlight Nature's rich biosynthetic repertoire. Comparative analysis of the LNM-type biosynthetic machineries provides outstanding opportunities to dissect Nature's biosynthetic strategies and apply these findings to combinatorial biosynthesis for natural product discovery and structural diversity.

Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

P450-Catalyzed Tailoring Steps in Leinamycin Biosynthesis Featuring Regio- and Stereoselective Hydroxylations and Substrate Promiscuities.

Leinamycin (LNM) is a potent antitumor antibiotic produced by Streptomyces atroolivaceus S-140. Both in vivo and in vitro characterization of the LNM biosynthetic machinery have established the formation of the 18-membered macrolactam backbone and the C-3 alkyl branch; the nascent product, LNM E1, of the hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS); and the generation of the thiol moiety at C-3 of LNM E1. However, the tailoring steps converting LNM E1 to LNM are still unknown. Based on gene inactivation and chemical investigation of three mutant strains, we investigated the tailoring steps catalyzed by two cytochromes P450 (P450s), LnmA and LnmZ, in LNM biosynthesis. Our studies revealed that (i) LnmA and LnmZ regio- and stereoselectively hydroxylate the C-8 and C-4' positions, respectively, on the scaffold of LNM; (ii) both LnmA and LnmZ exhibit substrate promiscuity, resulting in multiple LNM analogs from several shunt pathways; and (iii) the C-8 and C-4' hydroxyl groups play important roles in the cytotoxicity of LNM analogs against different cancer cell lines, shedding light on the structure-activity relationships of the LNM scaffold and the LNM-type natural products in general. These studies set the stage for future biosynthetic pathway engineering and combinatorial biosynthesis of the LNM family of natural products for structure diversity and drug discovery.

Discovery and Characterization of 1-Aminocyclopropane-1-carboxylic Acid Synthase of Bacterial Origin.

The guangnanmycins (GNMs) belong to a small group of natural products featuring a 1-aminocyclopropane-1-carboxylic acid (ACC) moiety. While extensively studied in plants, ACC biosynthesis in bacteria remains poorly understood. Here we report inactivation of gnmY in vivo and biochemical characterization of GnmY in vitro, assigning GnmY as the first bacterial free ACC synthase that catalyzes the synthesis of ACC from S-adenosyl methionine. ACC is activated by GnmS and subsequently incorporated into the GNM scaffold by the GNM hybrid nonribosomal peptide synthetase-polyketide synthase system in GNM biosynthesis. GnmS exhibits relaxed substrate specificity, exploitation of which allowed the incorporation of 1-aminocyclobutane-1-carboxylic acid (ACBC) into the GNM scaffold to produce a GNM analogue with a cyclobutane ring at C-17. This study provides new insights into ACC biosynthesis in bacteria. GnmY and GnmS might be portable to engineer other ACC/ACBC-containing natural products.

Highly efficient upconversion emission of Er3+ in δ-Sc4Zr3O12 and broad-range temperature sensing.

Developing optical temperature sensors with a wider range, higher sensitivity and repeatability based on Er3+/Yb3+ doped upconverting phosphors has always been at the forefront of temperature measurement technologies. Here, we report the intense green upconversion luminescence in Er3+/Yb3+ doped δ-Sc4Zr3O12 for the first time and its temperature sensing performance is investigated. The structure of δ-Sc4Zr3O12 is given by Rietveld refinement of XRD data and the site occupancy of Er3+ ions has been determined. Compared with cubic Sc2O3 and ZrO2, under 972 nm excitation, the green emission from Er3+ centers in Sc4Zr3O12 is increased by 59-fold and 264-fold, respectively. By experimental analysis, this enhancement of upconversion luminescence is attributed to the low-symmetrical environment of Er3+, generation of Yb3+ clusters and high internal efficiency of Yb3+ emission in Sc4Zr3O12. In addition, the fluorescence intensity ratio of two green emission bands (2H11/2/4S3/2 → 4I15/2) is studied as a function of temperature ranging from 303 to 793 K in Sc4Zr3O12. The maximum sensitivity observed via calculation is 0.00634 K-1 at 573 K, and the sensitivity is still as high as 0.00534 K-1 at 793 K. The stability of a Sc4Zr3O12 thermometer is also examined via a recycling test. These findings suggest that δ-Sc4Zr3O12 is a promising upconversion host and could achieve high-sensitivity optical temperature sensing with a wide measuring range.

Highly Efficient Green-Emitting Phosphors Ba2Y5B5O17 with Low Thermal Quenching Due to Fast Energy Transfer from Ce3+ to Tb3.

This paper demonstrates a highly thermally stable and efficient green-emitting Ba2Y5B5O17:Ce3+, Tb3+ phosphor prepared by high-temperature solid-state reaction. The phosphor exhibits a blue emission band of Ce3+ and green emission lines of Tb3+ upon Ce3+ excitation in the near-UV spectral region. The effect of Ce3+ to Tb3+ energy transfer on blue to green emission color tuning and on luminescence thermal stability is studied in the samples codoped with 1% Ce3+ and various concentrations (0-40%) of Tb3+. The green emission of Tb3+ upon Ce3+ excitation at 150 °C can keep, on average, 92% of its intensity at room temperature, with the best one showing no intensity decreasing up to 210 °C for 30% Tb3+. Meanwhile, Ce3+ emission intensity only keeps 42% on average at 150 °C. The high thermal stability of the green emission is attributed to suppression of Ce3+ thermal de-excitation through fast energy transfer to Tb3+, which in the green-emitting excited states is highly thermally stable such that no lifetime shortening is observed with raising temperature to 210 °C. The predominant green emission is observed for Tb3+ concentration of at least 10% due to efficient energy transfer with the transfer efficiency approaching 100% for 40% Tb3+. The internal and external quantum yield of the sample with Tb3+ concentration of 20% can be as high as 76% and 55%, respectively. The green phosphor, thus, shows attractive performance for near-UV-based white-light-emitting diodes applications.

The Inductive Effect of Neighboring Cations in Tuning Luminescence Properties of the Solid Solution Phosphors.

Forming solid solutions through cation substitution is an efficient way to improve the luminescence properties of Ce3+ or Eu2+ activated phosphors and even to develop new ones, which is badly needed for phosphor-converted white LEDs. Here, we report new color tunable solid solution phosphors based on Eu2+ activated K2Al2B2O7 as a typical case to demonstrate that, besides crystal field splitting of 5d levels, centroid shift and Stokes shift can be dominant in tuning excitation and emission spectra as well as thermal stability of solid solution phosphors, both of which were previously considered to be negligible. Moreover, a general model involving the inductive effect of neighboring cations is proposed to explain the obvious variations in centroid shift and Stokes shift with cation substitution. Our work is propitious for the construction of more reasonable structure-property relations and thus offers theoretical guidance for designing solid solution phosphors.

Enhanced ∼2 µm Emission of Tm3+ in Lu2O3 by Addition of a Trace Amount of Er3.

Er3+-induced intensity enhancement of ∼2 µm emission is observed in 2 atom % Tm3+ doped Lu2O3 under 782 nm excitation. The maximum enhancement reaches 41.9% with only 0.05 atom % Er3+. Er3+ introduces a new quantum cutting process which is proved to be a Tm3+ → Er3+ → Tm3+ forward-backward energy transfer (FBET) system. The FBET system is observed to work efficiently even at very low Er3+ concentration. Thus, energy loss due to energy migration among Tm3+ ions is suggested to be suppressed by the FBET process. The Tm3+ → Er3+ → Tm3+ FBET system may be a new route to improve the performance of Tm3+ lasers.

Investigation of the Energy-Transfer Mechanism in Ho3+- and Yb3+-Codoped Lu2O3 Phosphor with Efficient Near-Infrared Downconversion.

A high-temperature solid-state method was used to synthesize the Ho3+- and Yb3+-codoped cubic Lu2O3 powders. The crystal structures of the as-prepared powders were characterized by X-ray diffraction. The energy-transfer (ET) phenomenon between Ho3+ ions and Yb3+ ions was verified by the steady-state spectra including visible and near-infrared (NIR) regions. Beyond that, the decay curves were also measured to certify the existence of the ET process. The downconversion phenomena appeared when the samples were excited by 446 nm wavelength corresponding to the transition of Ho3+: 5I8→5G6/5F1. On the basis of the analysis of the relationship between the initial transfer rate of Ho3+: 5F3 level and the Yb3+ doping concentration, it indicates that the ET from 5F3 state of Ho3+ ions to 2F5/2 state of Yb3+ ions is mainly through a two-step ET process, not the long-accepted cooperative ET process. In addition, a 62% ET efficiency can be achieved in Lu2O3: 1% Ho3+/30% Yb3+. Unlike the common situations in which the NIR photons are all emitted by the acceptors Yb3+, the sensitizers Ho3+ also make contributions to the NIR emission upon 446 nm wavelength excitation. Meanwhile, the 5I5→5I8 transition and 5F4/5S2→5I6 transition of Ho3+ as well as the 2F5/2→2F7/2 transition of Yb3+ match well with the optimal spectral response of crystalline silicon solar cells. The current research indicates that Lu2O3: Ho3+/Yb3+ is a promising material to improve conversion efficiency of crystalline silicon solar cell.

Inhomogeneous-Broadening-Induced Intense Upconversion Luminescence in Tm3+ and Yb3+ Codoped Lu2O3-ZrO2 Disordered Crystals.

Near-infrared (980 nm) to near-infrared (800 nm) and blue (490 nm) upconversion has been studied in 0.2% Tm3+ and 10% Yb3+ codoped Lu2O3-ZrO2 solid solutions as a function of the ZrO2 content in the range of 0-50%, prepared by a high-temperature solid-state reaction. The continuous enhancement of upconversion luminescence is observed with increasing ZrO2 content up to 30%. Analyses of the Yb3+ emission intensity and lifetime indicate enlarged absorption of a 980 nm excitation laser and enhanced energy transfer from Yb3+ to Tm3+ with the addition of ZrO2. The spectrally inhomogeneous broadening of the dopants in this disordered solid solution is considered to play the main role in the enhancement by providing better matches with the excitation laser line and increasing the spectral overlap for efficient energy transfer from Yb3+ to Tm3+. In addition, the inhomogeneous broadening is also validated to improve energy migration among Yb3+ ions and energy back transfer from Tm3+ to Yb3+. Hence, it is understandable that a drop in the upconversion luminescence intensity occurs as the concentration of ZrO2 is further increased from 30% to 50%. This work indicates the possibility of disordered crystals to achieve intense upconversion luminescence for biological and optoelectronic applications.

Engineered jadomycin analogues with altered sugar moieties revealing JadS as a substrate flexible O-glycosyltransferase.

Glycosyltransferases (GTs)-mediated glycodiversification studies have drawn significant attention recently, with the goal of generating bioactive compounds with improved pharmacological properties by diversifying the appended sugars. The key to achieving glycodiversification is to identify natural and/or engineered flexible GTs capable of acting upon a broad range of substrates. Here, we report the use of a combinatorial biosynthetic approach to probe the substrate flexibility of JadS, the GT in jadomycin biosynthesis, towards different non-native NDP-sugar substrates, enabling us to identify six jadomycin B analogues with different sugar moieties. Further structural engineering by precursor-directed biosynthesis allowed us to obtain 11 new jadomycin analogues. Our results for the first time show that JadS is a flexible O-GT that can utilize both L- and D- sugars as donor substrates, and tolerate structural changes at the C2, C4 and C6 positions of the sugar moiety. JadS may be further exploited to generate novel glycosylated jadomycin molecules in future glycodiversification studies.

Angucyclines as signals modulate the behaviors of Streptomyces coelicolor.

The angucycline antibiotic jadomycin B (JdB) produced by Streptomyces venezuelae has been found here to induce complex survival responses in Streptomyces coelicolor at subinhibitory concentration. The receptor for JdB was identified as a "pseudo" gamma-butyrolactone receptor, ScbR2, which was shown to bind two previously unidentified target promoters, those of redD (redDp) and adpA (adpAp), thus directly regulating undecylprodigiosin (Red) production and morphological differentiation, respectively. Because AdpA also directly regulates the expression of redD, ScbR2, AdpA, and RedD together form a feed-forward loop controlling both differentiation and Red production phenotypes. Different signal strengths (i.e., JdB concentrations) were shown to induce the two different phenotypes by modulating the relative transcription levels of adpA vs. redD. The induction of morphological differentiation and endogenous antibiotic production by exogenous antibiotic exemplifies an important survival strategy more sophisticated than the induction of antibiotic resistance.

A Long-Range Acting Dehydratase Domain as the Missing Link for C17-Dehydration in Iso-Migrastatin Biosynthesis.

The dehydratase domains (DHs) of the iso-migrastatin (iso-MGS) polyketide synthase (PKS) were investigated by systematic inactivation of the DHs in module-6, -9, -10 of MgsF (i.e., DH6, DH9, DH10) and module-11 of MgsG (i.e., DH11) in vivo, followed by structural characterization of the metabolites accumulated by the mutants, and biochemical characterization of DH10 in vitro, using polyketide substrate mimics with varying chain lengths. These studies allowed us to assign the functions for all four DHs, identifying DH10 as the dedicated dehydratase that catalyzes the dehydration of the C17 hydroxy group during iso-MGS biosynthesis. In contrast to canonical DHs that catalyze dehydration of the ß-hydroxy groups of the nascent polyketide intermediates, DH10 acts in a long-range manner that is unprecedented for type I PKSs, a novel dehydration mechanism that could be exploited for polyketide structural diversity by combinatorial biosynthesis and synthetic biology.