Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations.

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

Near-infrared imaging for visualizing the synergistic relationship between autophagy and NFS1 protein during multidrug resistance using an ICT-TICT integrated platform.

Drug resistance is a major challenge for cancer treatment, and its identification is crucial for medical research. However, since drug resistance is a multi-faceted phenomenon, it is important to simultaneously evaluate multiple target fluctuations. Recently developed fluorescence-based probes that can simultaneously respond to multiple targets offer many advantages for real-time and in situ monitoring of cellular metabolism, including ease of operation, rapid reporting, and their non-invasive nature. As such we developed a dual-response platform (Vis-H2S) with integrated ICT-TICT to image H2S and viscosity in mitochondria, which could simultaneously track fluctuations in cysteine desulfurase (NFS1 protein and H2S inducer) and autophagy during chemotherapy-induced multidrug resistance. This platform could monitor multiple endogenous metabolites and the synergistic relationship between autophagy and NFS1 protein during multidrug resistance induced by chemotherapy. The results indicated that chemotherapeutic drugs simultaneously up-regulate the levels of NFS1 protein and autophagy. It was also found that the NFS1 protein was linked with autophagy, which eventually led to multidrug resistance. As such, this platform could serve as an effective tool for the in-depth exploration of drug resistance mechanisms.

Single cell glycan-linkages profiling for hepatocellular carcinoma early diagnosis using lanthanide encoded bacteriophage MS2 based ICP-MS.

Early diagnosis is paramount for enhancing survival rates and prognosis in the context of malignant diseases. Hepatocellular carcinoma (HCC), the second leading cause of cancer-related deaths worldwide, poses significant challenges for its early detection. In this study, we present an innovative approach which contributed to the early diagnosis of HCC. By lanthanide encoding signal amplification to map glycan-linkages at the single-cell level, the minute quantities of "soft" glycan-linkages on single cell surface were converted into "hard" elemental tags through the use of an MS2 signal amplifier. Harnessing the power of lanthanides encoded within MS2, we achieve nearly three orders of magnitude signal amplification. These encoded tags are subsequently quantified using single-cell inductively coupled plasma mass spectrometry (SC-ICP-MS). Linear discriminant analysis (LDA) identifies seven specific glycan-linkages (α-2,3-Sia, α-Gal, α-1,2-Fuc, α-1,6-Fuc, α-2,6-Sia, α-GalNAc, and Gal-ß-1,3-GalNAc) as biomarkers. Our methodology is initially validated at the cellular level with 100% accuracy in discriminating between hepatic carcinoma HepG2 cells and their normal HL7702 cells. We apply this approach to quantify and classify glycan-linkages on the surfaces of 55 clinical surgical HCC specimens. Leveraging these seven glycan-linkages as biomarkers, we achieve precise differentiation between 8 normal hepatic specimens, 40 early HCC specimens, and 7 colorectal metastasis HCC specimens. This pioneering work represents the first instance of employing single-cell glycan-linkages as biomarkers promising for the early diagnosis of HCC with a remarkable 100% predictive accuracy rate, which holds immense potential for enhancing the feasibility and precision of HCC diagnosis in clinical practice.

Reinvent Aliphatic Arsenicals as Reversible Covalent Warheads toward Targeted Kinase Inhibition and Non-acute Promyelocytic Leukemia Cancer Treatment.

The success of arsenic in acute promyelocytic leukemia (APL) treatment is hardly transferred to non-APL cancers, mainly due to the low selectivity and weak binding affinity of traditional arsenicals to oncoproteins critical for cancer survival. We present herein the reinvention of aliphatic trivalent arsenicals (As) as reversible covalent warheads of As-based targeting inhibitors toward Bruton's tyrosine kinase (BTK). The effects of As warheads' valency, thiol protection, methylation, spacer length, and size on inhibitors' activity were studied. We found that, in contrast to the bulky and rigid aromatic As warhead, the flexible aliphatic As warheads were well compatible with the well-optimized guiding group to achieve nanomolar inhibition against BTK. The optimized As inhibitors effectively blocked the BTK-mediated oncogenic signaling pathway, leading to elevated antiproliferative activities toward lymphoma cells and xenograft tumor. Our study provides a promising strategy enabling rational design of new aliphatic arsenic-based reversible covalent inhibitors toward non-APL cancer treatment.

The dynamics of B-cell reconstitution post allogeneic hematopoietic stem cell transplantation: A real-world study.

BACKGROUND: The immune reconstitution after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is crucial for preventing infections and relapse and enhancing graft-versus-tumor effects. B cells play an important role in humoral immunity and immune regulation, but their reconstitution after allo-HSCT has not been well studied. METHODS: In this study, we analyzed the dynamics of B cells in 252 patients who underwent allo-HSCT for 2 years and assessed the impact of factors on B-cell reconstitution and their correlations with survival outcomes, as well as the development stages of B cells in the bone marrow and the subsets in the peripheral blood. RESULTS: We found that the B-cell reconstitution in the bone marrow was consistent with the peripheral blood (p = 0.232). B-cell reconstitution was delayed by the male gender, age >50, older donor age, the occurrence of chronic and acute graft-versus-host disease, and the infections of fungi and cytomegalovirus. The survival analysis revealed that patients with lower B cells had higher risks of death and relapse. More importantly, we used propensity score matching to obtain the conclusion that post-1-year B-cell reconstitution is better in females. Meanwhile, using mediation analysis, we proposed the age-B cells-survival axis and found that B-cell reconstitution at month 12 posttransplant mediated the effect of age on patient survival (p = 0.013). We also found that younger patients showed more immature B cells in the bone marrow after transplantation (p = 0.037). CONCLUSION: Our findings provide valuable insights for optimizing the management of B-cell reconstitution and improving the efficacy and safety of allo-HSCT.

A new carbazole based fluorescent probe with AIE characteristic for detecting and imaging hydrazine in living cells, mungbean sprouts, Arabidopsis thaliana, and practical samples.

In this study, we report a new carbazole-malononitrile fluorescent probe CBC with an interesting aggregation-induced emission (AIE) characteristic. Probe CBC could rapidly and selectively detect hydrazine (N2H4) in ～100% aqueous media, and also exhibit an exceedingly low detection limit of 6.3 nM for sensitively detecting N2H4. The sensing mechanism of CBC towards N2H4 has been well demonstrated through the spectra of 1H NMR, HRMS and FTIR. Interestingly, probe CBC was applied to visualize and detect gaseous and aqueous N2H4 with sensitive color changes. Importantly, probe CBC was applied to effectively detect N2H4 in practical samples such as soil, human serum, human urine, plants, foods and beverages, as well as sensitively sense and image N2H4 in biological systems including living mungbean sprouts, Arabidopsis thaliana, and HeLa cells.

Ecological and human health hazards of soil heavy metals after wildfire: A case study of Liangshan Yi autonomous prefecture, China.

Soil samples were collected in at different depths from the conflagration area in Liangshan Yi Autonomous Region, China, to investigate the distribution characteristics and ecological and human health risks of heavy metals after a wildfire. The samples collected comprise wildfire ash (WA) above the soil surface, ash soil (AS) 0-5 cm, and plain soil (PS) 5-15 cm below the soil surface. Additionally, reference soil (RS) was collected from a nearby unburned area at the same latitude as the conflagration area. The results showed that the concentrations of zinc (Zn), copper (Cu), lead (Pb), and cadmium (Cd) in the WA and AS were significantly higher than in reference soil (RS) (p < 0.05). Concentrations of Pb in the PS were 2.52 times higher than that in RS (17.9 mg kg-1) (p < 0.05). The AS and WA had the highest Index of potential ecological risks (RI > 600). In addition, The Cd in AS and WA contributed the most to the highest Improved nemerow index (INI) and RI with a contribution of more than 80%. The concentration of heavy metals was used to establish non-carcinogenic effects and cancer risks in humans via three exposure pathways: accident ingestion of soil, dermal contact with soil, and inhalation of soil particles. Hazard index (HI) values of each sample were all less than 1, indicating the non-carcinogenic risk was within the acceptable range and would not adversely affect the local population's health. The Cancer risk (CR) values of Cr, As, Cd, and Ni were all below 1 × 10-6, indicating that heavy metal pollution from this wildfire did not pose a cancer risk to residents.

D-Limonene Affects the Feeding Behavior and the Acquisition and Transmission of Tomato Yellow Leaf Curl Virus by Bemisia tabaci.

Bemisia tabaci (Gennadius) is an important invasive pest transmitting plant viruses that are maintained through a plant-insect-plant cycle. Tomato yellow leaf curl virus (TYLCV) can be transmitted in a persistent manner by B. tabaci, which causes great losses to global agricultural production. From an environmentally friendly, sustainable, and efficient point of view, in this study, we explored the function of d-limonene in reducing the acquisition and transmission of TYLCV by B. tabaci as a repellent volatile. D-limonene increased the duration of non-feeding waves and reduced the duration of phloem feeding in non-viruliferous and viruliferous whiteflies by the Electrical Penetration Graph technique (EPG). Additionally, after treatment with d-limonene, the acquisition and transmission rate of TYLCV was reduced. Furthermore, BtabOBP3 was determined as the molecular target for recognizing d-limonene by real-time quantitative PCR (RT-qPCR), fluorescence competitive binding assays, and molecular docking. These results confirmed that d-limonene is an important functional volatile which showed a potential contribution against viral infections with potential implications for developing effective TYLCV control strategies.

[Effects of Pre-Transplant CONUT and Post-Transplant MRD on Prognosis of Patients with Multiple Myeloma after Auto-HSCT].

OBJECTIVE: To explore the effects of pre-transplant controlling nutritional status (CONUT) and post-transplant minimal residual disease (MRD) on prognosis of patients with multiple myeloma (MM) after autologous hematopoietic stem cell transplantation (auto-HSCT). METHODS: The clinical data of 79 patients who received auto-HSCT from 2011 to 2020 in The First Affiliated Hospital of Chongqing Medical University were retrospectively analyzed. The patients were divided into Low-CONUT group (n=62) and High-CONUT group (n=17) according to whether the CONUT score was less than 5. The differences in clinical features, hematopoietic reconstruction, adverse reactions, efficacy and survival between the two groups were compared. In addition, the prognostic risk factors were analyzed and verified by time-dependent ROC curve. RESULTS: The proportions of male patients and bone marrow plasma cells>30% at initial diagnosis in High-CONUT group were both higher than those in Low-CONUT group (both P <0.05). While, there were no significant differences in hematopoietic reconstruction and adverse reactions (>grade 2) between the two groups. The complete response (CR) rate and CR+very good partial response (VGPR) rate before transplantation in Low-CONUT group were both significantly higher than those in High-CONUT group (both P <0.05). After 3 months of transplantation, the CR+VGPR rate still remained an advantage in Low-CONUT group compared with High-CONUT group (P <0.01), but CR rate did not(P >0.05). The overall survival (OS) and progression-free survival (PFS) in Low-CONUT group were both superior to those in High-CONUT group (both P <0.05). Low CONUT score (0-4) before transplantation and negative MRD at 6 months after transplantation were favorable factors affecting OS and PFS (both P <0.05), while the International Myeloma Working Group (IMWG) high-risk at initial diagnosis and lactate dehydrogenase (LDH) level>250 U/L before transplantation were only risk factors for PFS (both P <0.05). Time-dependent ROC curve analysis showed that pre-transplant CONUT score and MRD status at 6 months after transplantation could independently or jointly predict 1- and 2-year OS and PFS, and the combined prediction was more effective. CONCLUSION: The combination of pre-transplant CONUT and post-transplant MRD can better predict the prognosis of MM patients.

A conformational selection mechanism of flavivirus NS5 for species-specific STAT2 inhibition.

Flaviviruses, including Zika virus (ZIKV) and Dengue virus (DENV), rely on their non-structural protein 5 (NS5) for both replication of viral genome and suppression of host IFN signaling. DENV and ZIKV NS5s were shown to facilitate proteosome-mediated protein degradation of human STAT2 (hSTAT2). However, how flavivirus NS5s have evolved for species-specific IFN-suppression remains unclear. Here we report structure-function characterization of the DENV serotype 2 (DENV2) NS5-hSTAT2 complex. The MTase and RdRP domains of DENV2 NS5 form an extended conformation to interact with the coiled-coil and N-terminal domains of hSTAT2, thereby promoting hSTAT2 degradation in cells. Disruption of the extended conformation of DENV2/ZIKV NS5, but not the alternative compact state, impaired their hSTAT2 binding. Our comparative structural analysis of flavivirus NS5s further reveals a conserved protein-interaction platform with subtle amino-acid variations likely underpinning diverse IFN-suppression mechanisms. Together, this study uncovers a conformational selection mechanism underlying species-specific hSTAT2 inhibition by flavivirus NS5.

A ratiometric fluorescent probe for imaging the fluctuation of HOBr during endoplasmic reticulum stress.

Endoplasmic reticulum (ER) stress is closely associated with cell apoptosis, autophagy, DNA damage, metabolism, and migration. When ER stress occurs, a large number of reactive oxygen species, including hypobromous acid (HOBr), are generated. The degree of ER stress can be understood by accurately detecting the HOBr concentration in the ER. Unfortunately, no ER-targetable probes for detecting HOBr have been reported to date. To solve this problem, we developed a naphthalimide-based fluorescent probe (ER-NABr) for imaging HOBr in the ER. Upon reaction with HOBr, a red shift in the fluorescence spectrum occurs due to the difference in the molecular conjugation between the original ER-NABr and the reaction product. ER-NABr showed a fast response (within 30 s) and high selectivity towards HOBr, with a ratiometric quantitative response (5-40 µM) and high sensitivity (138 nM). With its excellent biocompatibility and remarkable ER-targetable ability, ER-NABr was successfully utilized to ratiometrically image intracellular HOBr, particularly during ER stress, which is beneficial for revealing the role of HOBr in ER-associated diseases.

Associations of problematic smartphone use with depressive symptoms and suicidal ideation in university students before and after the COVID-19 outbreak: A meta-analysis.

BACKGROUND AND AIM: Problematic smartphone use (PSU) has been suggested to present with depressive symptoms and suicidal ideation (SI) as well as sleep disturbance, lack of social support, and emotional isolation. The aim of this systematic review and meta-analysis was to evaluate the association between PSU with depressive symptoms and SI in university students, and to determine the potential influence of the coronavirus disease 2019 (COVID-19) outbreak. METHODS: Observational studies pertinent to our research were identified through comprehensive searches of the PubMed, Embase, Cochrane Library, and Web of Science databases. To account for potential heterogeneity, the random-effects models were employed to aggregate the findings. RESULTS: Eighteen datasets from 17 case-control studies, including 24,019 university students, were included. Among them, 8,775 (36.5 %) had PSU. A higher prevalence of depressive symptoms (odds ratio [OR]: 2.40, 95 % confidence interval [CI]: 2.19 to 2.63, p < 0.001; prediction interval: 1.95 to 2.96) was observed in university students with higher scores for PSU measures. A subgroup analysis showed a stronger association between PSU and depressive symptoms after the COVID-19 outbreak as compared to that before the outbreak (OR: 2.76 versus 2.16, p for subgroup difference = 0.002), which explained the heterogeneity. The association between PSU and depressive symptoms in university students was similar to those reported in studies from China and other countries, and in studies with different quality scores. Finally, a meta-analysis of three studies suggested that PSU was also associated with the prevalence of SI (OR: 2.18, 95 % CI: 1.77 to 2.68, p < 0.001; I2 = 0 %). CONCLUSION: In university students, PSU may be a risk factor for depressive symptoms and SI, and the association between PSU and depressive symptoms became stronger after the COVID-19 outbreak.

A review on the calculation and application of lignin Hansen solubility parameters.

Hansen solubility parameters (HSPs) play a critical role in the majority of processes involving lignin depolymerization, separation, fractionation, and polymer blending, which are directly related to dissolution properties. However, the calculation of lignin HSPs is highly complicated due to the diversity of sources and the complexity of lignin structures. Despite their important role, lignin HSPs have been undervalued, attracting insufficient attention. This review summarizes the calculation methods for lignin HSPs and proposes a straightforward method based on lignin subunits. Furthermore, it highlights the crucial applications of lignin HSPs, such as identifying ideal solvents for lignin dissolution, selecting suitable solvents for lignin depolymerization and extraction, designing green solvents for lignin fractionation, and guiding the preparation of lignin-based composites. For instance, leveraging HSPs to design a series of solvents could potentially achieve sequential controllable lignin fractionation, addressing issues of low value-added applications of lignin resulting from poor homogeneity. Notably, HSPs serve as valuable tools for understanding the dissolution behavior of lignin. Consequently, we expect this review to be of great interest to researchers specializing in lignin and other macromolecules.

Efficient De Novo Biosynthesis of Curcumin in Escherichia coli by Optimizing Pathway Modules and Increasing the Malonyl-CoA Supply.

Curcumin is a natural phenylpropanoid compound with various biological activities and is widely used in food and pharmaceuticals. A de novo curcumin biosynthetic pathway was constructed in Escherichia coli BL21(DE3). Optimization of the curcumin biosynthesis module achieved a curcumin titer of 26.8 ± 0.6 mg/L. Regulating the metabolic fluxes of the ß-oxidation pathway and fatty acid elongation cycle and blocking the endogenous malonyl-CoA consumption pathway increased the titer to 113.6 ± 7.1 mg/L. Knockout of endogenous curcumin reductase (curA) and intermediate product detoxification by heterologous expression of the solvent-resistant pump (srpB) increased the titer to 137.5 ± 3.0 mg/L. A 5 L pilot-scale fermentation, using a three-stage pH alternation strategy, increased the titer to 696.2 ± 20.9 mg/L, 178.5-fold higher than the highest curcumin titer from de novo biosynthesis previously reported, thereby laying the foundation for efficient biosynthesis of curcumin and its derivatives.

Colorectal cancer subtyping and prognostic model construction based on interleukin-related genes.

BACKGROUND: Members of the interleukin (IL) family are closely linked to cancer development and progression. But research on prognosis of colorectal cancer (CRC) related to IL is still lacking. This study investigated new CRC prognostic markers and offered new insights for CRC prognosis and treatment. METHODS: CRC-related data and IL gene data were collected from public databases. Sample clustering was done with NMF package to divide samples into different subtypes. Differential, enrichment, survival, and immune analyses were conducted on subtypes. A prognostic model was constructed using regression analysis. Drug sensitivity analysis was performed using GDSC database. Western blot was performed to assess effect of IL7 on the JAK/STAT signaling pathway. Flow cytometry was utilized to examine impact of IL7 on CD8+ T cell apoptosis. RESULTS: Two CRC subtypes based on IL-associated genes were obtained. Cluster1 had a higher survival rate than Cluster2, and they showed differences in some immune levels. The two clusters were mainly enriched in the JAK-STAT signaling pathway, Th17 cell differentiation, and IL-17 signaling pathway. An 11-gene signature was built, and Riskscore was an independent prognosticator for CRC. Low-risk group showed higher sensitivity to nine common targeted anticancer drugs. Western blot and flow cytometry results demonstrated that IL7 could phosphorylate STAT5 and promote survival of CD8+ T cells. CONCLUSION: This study divided CRC samples into two IL-associated subtypes and obtained an 11-gene signature. Additionally, targeted drugs that may improve prognosis of CRC patients were identified. These findings are of paramount importance for patient's prognosis and CRC treatment.

Novel cuproptosis-related lncRNAs can predict the prognosis of patients with multiple myeloma.

Background: Cuproptosis-related long-stranded non-coding RNAs (lncRNAs) have several implications for the prognosis of multiple myeloma (MM). This research aimed to construct a prognostic risk model for MM patients and explore the potential signaling pathways in the risk group. Methods: Cuproptosis-related lncRNAs were obtained from the co-expression analysis of cuproptosis-related genes and lncRNAs. Subsequently, twelve cuproptosis-related lncRNAs were selected to construct a prognostic risk model of MM patients by the least absolute shrinkage and selection operator (LASSO) regression. Then, the clinical data of these patients were randomly divided into the training group and the testing group. Next, patients were divided into the low- and high-risk groups according to the median risk score. The Kaplan-Meier survival analysis was performed to clarify the prognostic differences between risk subtypes. Besides, the Cox analysis was conducted to identify whether the risk score can be used as an independent prognostic factor. In addition, the receiver operating characteristic (ROC) curve analysis and the concordance index (C-index) curve analysis were performed to elucidate the value of risk score as a prognostic indicator. Finally, the differential risk analysis and functional enrichment analysis were carried out to identify the potential signaling pathways in the low- and high-risk groups. Results: The results demonstrated that the overall survival (OS) of patients in the high-risk group was shorter than that in the low-risk group. There were significant differences in the expression of genes in MM patients between the high- and low-risk groups. The Gene Ontology (GO) analysis results showed that the differentially expressed risk-related genes (DERGs) were mainly concentrated on the collagen-containing extracellular matrix. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results, the DERGs may be related to the neuroactive ligand-receptor interaction and mitogen-activated protein kinase (MAPK) signaling pathway, indicating that they may be involved in the progression of tumors. Conclusions: The findings of this study suggest that cuproptosis-related lncRNAs may be effective biomarkers for predicting the prognosis of MM patients, which is anticipated to contribute to the improvement of clinical outcomes.

Clinical significance of WT1 in the evaluation of therapeutic effect and prognosis of non-M3 acute myeloid leukemia.

To explore the clinical significance and prognosis of acute myeloid leukemia (AML) patients with WT1 mutations.In total, the clinical data of 269 adult patients with non-M3 AML were considered retrospectively. From these patients, 153 carried WT1 mutation whereas 116 were negative. WT1 mutation positive patients were further divided into WT1 low expression and high expression groups base on the expression level of WT1 by qPCR at diagnosis (cut off: 170500). Survival and therapeutic effect analysis were performed for the above patients with different interfering factors such as co-mutations, the extent of WT1 log reduction and the chemotherapy regimens. Patients with high WT1 expression have higher rate of relapse. We can accurately identify patients with inferior outcomes when we take the following factors into consideration: the WT1 expression level at diagnosis; different prognostic factors including co-mutations (especially NPM1 and FLT3-ITD); the log reduction of WT1 after induction therapy and the risk of stratification. Idarubicin + Cytarabine (IA) regimen could reduce the expression level of WT1 after treatment, and Allo-HSCT played an important role in improving the prognosis of patients with WT1 high expression and patients with WT1 negativity. Among the relapsed patients, there existed a rising trend of WT1-MRD in advance than MFC-MRD and that of patients with continuous complete remission (CR). Different clinical background should be taken into consideration when we judge the prognosis and therapeutic effect of patients with WT1 mutations. In addition, WT1 may be an optional MRD marker, which needs regular monitoring.

DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2.

DNA methylation provides an important epigenetic mechanism that critically regulates gene expression, genome imprinting, and retrotransposon silencing. In plants, DNA methylation is prevalent not only in a CG dinucleotide context but also in non-CG contexts, namely CHG and CHH (H = C, T, or A) methylation. It has been established that plant non-CG DNA methylation is highly context dependent, with the +1- and +2-flanking sequences enriched with A/T nucleotides. How DNA sequence, conformation, and dynamics influence non-CG methylation remains elusive. Here, we report structural and biochemical characterizations of the intrinsic substrate preference of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), a plant DNA methyltransferase responsible for establishing all cytosine methylation and maintaining CHH methylation. Among nine CHH motifs, the DRM2 methyltransferase (MTase) domain shows marked substrate preference toward CWW (W = A or T) motifs, correlating well with their relative abundance in planta. Furthermore, we report the crystal structure of DRM2 MTase in complex with a DNA duplex containing a flexible TpA base step at the +1/+2-flanking sites of the target nucleotide. Comparative structural analysis of the DRM2-DNA complexes provides a mechanism by which flanking nucleotide composition impacts DRM2-mediated DNA methylation. Furthermore, the flexibility of the TpA step gives rise to two alternative DNA conformations, resulting in different interactions with DRM2 and consequently temperature-dependent shift of the substrate preference of DRM2. Together, this study provides insights into how the interplay between the conformational dynamics of DNA and temperature as an environmental factor contributes to the context-dependent CHH methylation by DRM2.

Promoting FADH2 Regeneration of Hydroxylation for High-Level Production of Hydroxytyrosol from Glycerol in Escherichia coli.

Hydroxytyrosol is a natural polyphenolic compound widely used in the food and drug industries. The current commercial production of hydroxytyrosol relies mainly on plant extracts, which involve long extraction cycles and various raw materials. Microbial fermentation has potential value as an environmentally friendly and low-cost method. Here, a de novo biosynthetic pathway of hydroxytyrosol has been designed and constructed in an Escherichia coli strain with released tyrosine feedback inhibition. By introduction of hpaBC from E. coli and ARO10 and ADH6 from Saccharomyces cerevisiae, the de novo biosynthesis of hydroxytyrosol was achieved. An important finding in cofactor engineering is that the introduction of L-amino acid deaminase (LAAD) promotes not only cofactor regeneration but also metabolic flow redistribution. To further enhance the hydroxylation process, different 4-hydroxyphenylacetate 3-monooxygenase (hpaB) mutants and HpaBC proteins from different sources were screened. Finally, after optimization of the carbon source, pH, and seed medium, the optimum engineered strain produced 9.87 g/L hydroxytyrosol in a 5 L bioreactor. This represents the highest titer reported to date for de novo biosynthesis of hydroxytyrosol in microorganisms.

Efficient Production of Chlorogenic Acid in Escherichia coli Via Modular Pathway and Cofactor Engineering.

Chlorogenic acid is a natural phenolic compound widely used in the food and daily chemical industries. Compared to plant extraction, microbial cell factories provide a green and sustainable production method for the production of chlorogenic acid. However, complex metabolic flux distribution and potential byproducts limited the biosynthesis of chlorogenic acid in microorganisms. A de novo biosynthesis pathway for chlorogenic acid was constructed in Escherichia coli via modular engineering. Increasing the shikimate pathway flux greatly promoted chlorogenic acid production, and the influence of pyruvate metabolism on chlorogenic acid synthesis was also explored. The supply of cofactors for the key enzymes quinate/shikimate 5-dehydrogenase (YdiB) and 4-hydroxyphenylacetate 3-monooxygenase (HpaBC) was enhanced by a cofactor regeneration system. Furthermore, mutants of YdiB were verified for chlorogenic acid production in vivo. Chlorogenic acid browning occurred when the buffer pH of the buffer exceeded 6.0, but two-stage pH control achieved a chlorogenic acid titer of 2789.2 mg/L in a 5 L fermenter, the highest reported to date. This study provided a strategy for the efficient production of chlorogenic acid from simple carbon sources.