Metabolic Engineering of Escherichia coli for Bioproduction of (R)-3-Hydroxybutyric Acid through a Three-Pronged Approach.

(R)-3-Hydroxybutyric acid (R-3HB) is an important chiral chemical with extensive applications in the agricultural, food, and chemical industries. The synthesis of R-3HB by microbial fermentation is of interest due to its remarkable stereoselectivity and economy. However, the low production of R-3HB failed to meet the needs of large-scale industrial production. In this study, an engineered strain for the efficient biosynthesis of R-3HB was constructed through a three-pronged approach encompassing biosynthetic pathway optimization, engineering of NADPH regenerators, and central metabolism regulation. The engineered strain Q5081 produced 75.7 g/L R-3HB, with a productivity of 1.26 g/L/h and a yield of 0.34 g/g glucose in fed-batch fermentation, showing the highest reported titer and productivity of R-3HB to date. We also performed transcriptome sequencing and annotation to illustrate the mechanism underlying the enhanced R-3HB production. The systematic metabolic engineering by a three-pronged approach demonstrated the feasibility of improving the biosynthesis, and the engineered strain Q5081 has the potential for widespread applications in the industrial production of R-3HB.

Self-Powered Traffic Lights Through Wind Energy Harvesting Based on High-Performance Fur-Brush Dish Triboelectric Nanogenerators.

Traffic lights play vital roles in urban traffic management systems, providing clear directional guidance for vehicles and pedestrians while ensuring traffic safety. However, the vast quantity of traffic lights widely distributed in the transportation system aggravates energy consumption. Here, a self-powered traffic light system is proposed through wind energy harvesting based on a high-performance fur-brush dish triboelectric nanogenerator (FD-TENG). The FD-TENG harvests wind energy to power the traffic light system continuously without needing an external power supply. Natural rabbit furs are applied to dish structures, due to their outstanding characteristics of shallow wear, high performance, and resistance to humidity. Also, the grid pattern of the dish structure significantly impacts the TENG outputs. Additionally, the internal electric field and the influences of mechanical and structural parameters on the outputs are analyzed by finite element simulations. After optimization, the FD-TENG can achieve a peak power density of 3.275 W m-3. The portable and miniature features of FD-TENG make it suitable for other natural environment systems such as forests, oceans, and mountains, besides the traffic light systems. This study presents a viable strategy for self-powered traffic lights, establishing a basis for efficient environmental energy harvesting toward big data and Internet of Things applications.

Serotype distribution, antimicrobial resistance, and molecular characterization of group B Streptococcus isolates from Chinese pregnant woman.

OBJECTIVE: This study was aimed to investigate the serotypes, antibiotic susceptibilities, and multi-locus sequence type (MLST) profiles of group B Streptococcus (GBS) in the Beijing area. METHODS: Lower vaginal and rectal swabs were obtained from pregnant women of 35-37 gestational weeks (GWs) who attended the Beijing Obstetrics and Gynecology Hospital. All GBS isolates were identified with Gram staining, catalase reaction assays, and CAMP tests, followed by antibiotic susceptibility testing, serotype identification, multilocus sequence typing and erythromycin resistance gene analysis (ermB and mefE). RESULTS: From July 2020 to June 2022, 311 (5.17%) of 6012 pregnant women that were screened for GBS colonization were detected positive. Of the eight serotypes identified (III, Ia, Ib, IV, II, VIII, V, and NT), serotypes III (43.09%), Ia (34.08%) and Ib (17.04%) were the predominant species. In the antimicrobial susceptibility experiments, the resistant rates measured for erythromycin, clindamycin, levofloxacin, and tetracycline were 76.21%, 63.99%, 50.80%, and 81.03%, respectively, and 7.6% of GBS isolates showed inducible clindamycin in resistance (D-test phenotype). Meanwhile, the multilocus sequence typing analysis showed that sequence type 19 (ST19) (30.34%) and ST10 (18.62%) were the dominant sequence types. Among the 237 erythromycin-resistant isolates, 176 harbored ermB (128, 54.00%) or mefE (48, 20.30%) gene alone. CONCLUSION: The infection rates, serotypes or MSLT distribution, and antimicrobial resistance of GBS in Beijing area were investigated, which may be applied in analyses of the epidemiological characteristics of GBS. This contributes to the basic knowledge required for successful GBS vaccine development suited for disease prevention and treatment in China, as well as the implementation of effective clinical antimicrobials.

Naturalization of an alien ancient fruit tree at a fine scale: Community structure and population dynamics of Cydonia oblonga in China.

Naturalized plants play pivotal roles in local plant biodiversity and ecological functions; however, the drivers of naturalization remain poorly understood at a fine scale. Thus, understanding the processes of the development and dominance of alien plants in local natural habitats is of paramount importance. In the present study, we report for the first time the naturalization of Cydonia oblonga in China based on community structure and population dynamics at a fine scale. We conducted a comprehensive survey of the species through field community investigations, interviews, and a literature review. Cydonia oblonga is an ancient fruit tree with a long introduction history of over 4500 years worldwide and a cultivation history of over 2500 years in China. We analyzed C. oblonga community structure using the spatiotemporal substitution method and quantitatively analyzed population dynamics using a static life table, survivorship curve, and time series model to explore the naturalization processes. The following results were obtained. (i) The community comprised 31 coexisting vascular plant species (16 woody and 15 herbaceous species) belonging to 28 genera in 20 families. Rosaceae and Asteraceae were the two most dominant families. (ii) All individuals in the shrub layer as well as the C. oblonga population exhibited a roughly inverted J-shaped basal diameter distribution. A complete age structure was noted, and the survival curve was classified as Deevey type II. According to time series analysis, the population is estimated to increase in the future, specifically of medium and large individuals. (iii) Religious exchange, potent resource competitiveness, and similarity with the native habitat may be the major drivers of the introduction and successful naturalization of C. oblonga. These results suggest that alien species closely related to native ones are more likely to invade, naturalize, and dominate communities in local habitats.

Integrative analysis reveals structural basis for transcription activation of Nurr1 and Nurr1-RXRα heterodimer.

Orphan nuclear receptor Nurr1 plays important roles in the progression of various diseases, including Parkinson's disease, neuroinflammation, Alzheimer's disease, and multiple sclerosis. It can recognize DNA as a monomer or heterodimer with retinoid X receptor α (RXRα). But the molecular mechanism of its transcriptional activity regulation is still largely unknown. Here we obtained a crystal structure of monomer Nurr1 (DNA- and ligand-binding domains, DBD and LBD) bound to NGFI-B response element. The structure exhibited two different forms with distinct DBD orientations, unveiling the conformational flexibility of nuclear receptor monomer. We then generated an integrative model of Nurr1-RXRα heterodimer. In the context of heterodimer, the structural flexibility of Nurr1 would contribute to its transcriptional activity modulation. We demonstrated that the DNA sequence may specifically modulate the transcriptional activity of Nurr1 in the absence of RXRα agonist, but the modulation can be superseded when the agonist binds to RXRα. Together, we propose a set of signaling pathways for the constitutive transcriptional activation of Nurr1 and provide molecular mechanisms for therapeutic discovery targeting Nurr1 and Nurr1-RXRα heterodimer.

Architectural roles of Cren7 in folding crenarchaeal chromatin filament.

Archaea have evolved various strategies in chromosomal organization. While histone homologues exist in most archaeal phyla, Cren7 is a chromatin protein conserved in the Crenarchaeota. Here, we show that Cren7 preferentially binds DNA with AT-rich sequences over that with GC-rich sequences with a binding size of 6~7 bp. Structural studies of Cren7 in complex with either an 18-bp or a 20-bp double-stranded DNA fragment reveal that Cren7 binds to the minor groove of DNA as monomers in a head-to-tail manner. The neighboring Cren7 monomers are located on the opposite sides of the DNA duplex, with each introducing a single-step sharp kink by intercalation of the hydrophobic side chain of Leu28, bending the DNA into an S-shape conformation. A structural model for the chromatin fiber folded by Cren7 was established and verified by the analysis of cross-linked Cren7-DNA complexes by atomic force microscopy. Our results suggest that Cren7 differs significantly from Sul7, another chromatin protein conserved among Sulfolobus species, in both DNA binding and deformation. These data shed significant light on the strategy of chromosomal DNA organization in crenarchaea.

Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA.

Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologs, intercalates into the kinked DNA step. In the present study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e. L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain. Structural analysis shows that L28A induces a kink (∼43°), nearly as sharp as that produced by wild-type Cren7 (∼48°), in the bound DNA fragment despite the lack of side chain intercalation. In another duplex DNA fragment, L28F inserts a large hydrophobic side chain deep into the DNA step, but introduces a smaller kink (∼39°) than that formed by the wild-type protein (∼50°). Mutation of Leu28 into methionine yields two protein conformers differing in loop ß3-ß4 orientation, DNA-binding surface and DNA geometry in the protein-DNA structure. Our results indicate that side chain intercalation is not directly responsible for DNA kinking or bending by Cren7, but plays a critical role in the stabilization of the Cren7-DNA complex. In addition, the flexibility of loop ß3-ß4 in Cren7, as revealed in the crystal structure of L28M-DNA, may serve a role in the modulation of chromosomal organization and function in the cell.

Au nanoclusters suppress chronic lymphocytic leukaemia cells by inhibiting thioredoxin reductase 1 to induce intracellular oxidative stress and apoptosis.

Chronic lymphocytic leukaemia (CLL) is a rare blood cancer that always relapses as refractory disease and eventually leads to death. To date, therapeutic options for CLL patients are scarce and there is an urgent need to develop novel chemotherapeutics that are both effective and safe. Gold-containing compounds induce a lethal oxidative and endoplasmic reticulum stress response in cultured and primary CLL cells via inhibition of thioredoxin reductase (TrxR). However, traditional gold-containing medicines have revealed side effects during clinical applications. Therefore, safer gold-containing drugs are needed to overcome this challenge. In this study, a novel peptide templated gold cluster Au25Sv9 was synthesized and its therapeutic effect on CLL cells was evaluated. This nanocluster could induce cell apoptosis in MEC-1 cells in a dose-dependent manner which correlated with the uptake amount of clusters in cells. As expected, increasing intracellular reactive oxidative species (ROS) in MEC-1 cells was exhibited with the increase of cluster dosage. Further analyses demonstrated the underlying mechanism that the nanoclusters suppress the activity of TrxR1, increase the level of intracellular ROS, destroy the mitochondrial membrane potential and finally trigger the mitochondrial apoptotic pathway in MEC-1 cells. Furthermore, the direct interaction between Au25Sv9 clusters and TrxR1 was confirmed for the first time by isothermal titration calorimetry. These findings explored the preclinical efficacy and potential mechanism of gold clusters in CLL therapy and provided a fundamental reference for the development of other novel gold-containing chemotherapeutics to treat CLL.

Structural Insights into the Methylation of C1402 in 16S rRNA by Methyltransferase RsmI.

RsmI and RsmH are conserved S-Adenosylmethionine (AdoMet)-dependent methyltransferases (MTases) that are responsible for the 2'-O-methylation and N4-methylation of C1402 in bacterial 16S rRNA, respectively. Methylation of m4Cm1402 plays a role in fine-tuning the shape and functions of the P-site to increase the decoding fidelity, and was recently found to contribute to the virulence of Staphylococcus aureus in host animals. Here we report the 2.20-Å crystal structure of homodimeric RsmI from Escherichia coli in complex with the cofactor AdoMet. RsmI consists of an N-terminal putative RNA-binding domain (NTD) and a C-terminal catalytic domain (CTD) with a Rossmann-like fold, and belongs to the class III MTase family. AdoMet is specifically bound into a negatively charged deep pocket formed by both domains by making extensive contacts. Structure-based mutagenesis and isothermal titration calorimetry (ITC) assays revealed Asp100 and Ala124 are vital for AdoMet-binding. Although the overall fold of RsmI shows remarkable similarities to the characterized MTases involved in vitamin B12 biosynthesis, it exhibits a distinct charge distribution especially around the AdoMet-binding pocket because of different substrate specificity. The docking model of RsmI-AdoMet-RNA ternary complex suggested a possible base-flipping mechanism of the substrate RNA that has been observed in several known RNA MTases. Our structural and biochemical studies provide novel insights into the catalytic mechanism of C1402 methylation in 16S rRNA.

Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea.

T:G base pair arising from spontaneous deamination of 5mC or polymerase errors is a great challenge for DNA repair of hyperthermophilic archaea, especially Crenarchaea. Most strains in this phylum lack the protein homologues responsible for the recognition of the mismatch in the DNA repair pathways. To investigate whether Cren7, a highly conserved chromatin protein in Crenarchaea, serves a role in the repair of T:G mispairs, the crystal structures of Cren7-GTAATTGC and Cren7-GTGATCGC complexes were solved at 2.0 Å and 2.1 Å. In our structures, binding of Cren7 to the AT-rich DNA duplex (GTAATTGC) induces opening of T2:G15 but not T10:G7 base pair. By contrast, both T:G mispairs in the GC-rich DNA duplex (GTGATCGC) retain the classic wobble type. Structural analysis also showed DNA helical changes of GTAATTGC, especially in the steps around the open T:G base pair, as compared to GTGATCGC or the matched DNAs. Surface plasmon resonance assays revealed a 4-fold lower binding affinity of Cren7 for GTAATTGC than that for GTGATCGC, which was dominantly contributed by the decrease of association rate. These results suggested that binding of Cren7 to DNA leads to T:G mispair opening in a sequence dependent manner, and therefore propose the potential roles of Cren7 in DNA repair.

Purification, crystallization and preliminary crystallographic analysis of the 16S rRNA methyltransferase RsmI from Escherichia coli.

RsmI and RsmH are AdoMet-dependent methyltransferases that are responsible for the 2'-O-methylation and N(4)-methylation of C1402 of Escherichia coli 16S rRNA, respectively. Modification of this site has been found to play a role in fine-tuning the shape and function of the P-site to increase the decoding fidelity. It is interesting to study the mechanism by which C1402 can be methylated by both RsmI and RsmH. The crystal structure of RsmH in complex with AdoMet and cytidine has recently been determined and provided some implications for N(4)-methylation of this site. Here, the purification and crystallization of RsmI as well as its preliminary crystallographic analysis are reported. Co-crystallization of RsmI with AdoMet was carried out by the sitting-drop vapour-diffusion method and X-ray diffraction data were collected to 2.60 Šresolution on beamline 1W2B at BSRF. The crystal contained three molecules per asymmetric unit and belonged to space group C2, with unit-cell parameters a = 121.9, b = 152.5, c = 54.2 Å, ß = 93.4°.