Developing the E. coli platform for efficient production of UMP-derived chemicals.

5-Methyluridine (5-MU) is a prominent intermediate for industrial synthesis of several antiviral-drugs, however, its availability over the past decades has overwhelmingly relied on chemical and enzymatic strategies. Here, we have realized efficient production of 5-MU in E. coli, for the first time, via a designer artificial pathway consisting of a two-enzyme cascade (UMP 5-methylase and phosphatase). More importantly, we have engineered the E. coli cell factory to boost 5-MU production by systematic evaluation of multiple strategies, and as a proof of concept, we have further developed an antibiotic-free fermentation strategy to realize 5-MU production (10.71 g/L) in E. coli MB229 (a ΔthyA strain). Remarkably, we have also established a versatile and robust platform with exploitation of the engineered E. coli for efficient production of diversified UMP-derived chemicals. This study paves the way for future engineering of E. coli as a synthetic biology platform for acceleratively accessing UMP-derived chemical diversities.

Reshaping immunometabolism in the tumour microenvironment to improve cancer immunotherapy.

The evolving understanding of cellular metabolism has revealed a the promise of strategies aiming to modulate anticancer immunity by targeting metabolism. The combination of metabolic inhibitors with immune checkpoint blockade (ICB), chemotherapy and radiotherapy may offer new approaches to cancer treatment. However, it remains unclear how these strategies can be better utilized despite the complex tumour microenvironment (TME). Oncogene-driven metabolic changes in tumour cells can affect the TME, limiting the immune response and creating many barriers to cancer immunotherapy. These changes also reveal opportunities to reshape the TME to restore immunity by targeting metabolic pathways. Further exploration is required to determine how to make better use of these mechanistic targets. Here, we review the mechanisms by which tumour cells reshape the TME and cause immune cells to transition into an abnormal state by secreting multiple factors, with the ultimate goal of proposing targets and optimizing the use of metabolic inhibitors. Deepening our understanding of changes in metabolism and immune function in the TME will help advance this promising field and enhance immunotherapy.

Retraction notice to "A novel circular RNA circ-ZNF652 promotes hepatocellular carcinoma metastasis through inducing snail-mediated epithelial-mesenchymal transition by sponging miR-203/miR-502-5p" [YBBRC 513(4) (2019) 812-819].

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). The authors claim that other members of their lab attempted to repeat the experiments in this study several times and found that the activation ability of snail on circ-znf652 was significantly lower than reported, indicating that this regulation loop does not exist. The authors' incorrect experimental method and lack of reasonable control, coupled with the lack of experimental experience of the first author, led to the mistakes and mean the results cannot be relied upon. In order not to mislead other scientists, they requested to retract their manuscript. The Editor-in-Chief has approved this retraction. The authors apologise to the readership of the journal for these errors.

Elucidation of the Late Steps during Hexacosalactone A Biosynthesis in Streptomyces samsunensis OUCT16-12.

Hexacosalactone A (1) is a polyene macrolide compound featuring a 2-amino-3-hydroxycyclopent-2-enone (C5N)-fumaryl moiety. While compound 1 has been proposed to be assembled via a type I modular polyketide synthase (PKS) system, most of the putative biosynthetic steps lack experimental evidence. In this study, we elucidated the post-PKS tailoring steps of compound 1 through in vivo gene inactivation and in vitro biochemical assays. We demonstrated that the amide synthetase HexB and O-methyltransferase HexF are responsible for the installations of the C5N moiety and the methyl group at 15-OH of compound 1, respectively; two new hexacosalactone analogs, named hexacosalactones B (4) and C (5), were purified and structurally characterized, followed by anti-multidrug resistance (anti-MDR) bacterial assays, revealing that the C5N ring and the methyl group are necessary for the antibacterial bioactivities. Through database mining of C5N-forming proteins HexABC, six uncharacterized biosynthetic gene clusters (BGCs), putatively encoding compounds with different types of backbones, were identified, providing potentials to discover novel bioactive compounds with C5N moiety. IMPORTANCE In this study, we elucidate the post-PKS tailoring steps during the biosynthesis of compound 1 and demonstrate that both C5N and 15-OMe groups are critical for the antibacterial activities of compound 1, paving the way for generation of hexacosalactone derivatives via synthetic biology strategy. In addition, mining of HexABC homologs from the GenBank database revealed their wide distribution across the bacterial world, facilitating the discovery of other bioactive natural products with C5N moiety.

Potential to mitigate nitrogen emissions from paddy runoff: A microbiological perspective.

Ditches and ponds are the basic units of agroecosystems that serve irrigation and drainage and also perform the natural ecological function of reducing nitrogen (N) emissions. To better enhance the design and advance management strategies in the paddy field ecosystem to minimize N emission, the N cycling microorganism in the paddy field ecosystem including interconnected fields with rice-wheat rotation, ditches, and ponds in central China was investigated by metagenomic techniques. Our results showed that ditches and ponds may be N removal hotspots by microorganisms in the rice and wheat seasons respectively. Given seasonal variation, the abundance of N-related microorganisms was high during the rice season. However, the Shannon and Simpson indices were lower and the microbial co-occurrence network was destabilized, which could make microbes in the rice season fragile and sensitive. Phytoplankton as key environmental factors affecting the N cycling microbial could promote more stable microbial communities through maintaining a good mutualistic symbiosis. While high algae concentration significantly promotes the abundance of norB than nosZ (P < 0.05), which may result in more N2O production. To trade off N removal and N2O emission, the algae concentration needs to be controlled. Our findings provide a systematic profile of N-related microorganisms in the paddy field ecosystem, and it would benefit in developing effective strategies for limiting N pollution in agriculture.

Correlation between RASSF1A Methylation in Cell-Free DNA and the Prognosis of Cancer Patients: A Systematic Review and Meta-Analysis.

Background: Although the effects of methylation of the Ras association domain-containing protein 1 isoform A (RASSF1A) gene in cell-free DNA on the outcomes of patients with different types of cancer have been reported, the results are inconsistent. Objective: : To explore the relationships between RASSF1A methylation in cell-free DNA and the outcomes of cancer patients. Methods: The PubMed, Embase, and Web of Science databases were searched for papers related to this topic on December 8, 2021. The retrieved articles were screened by two independent researchers, following which the methodological quality of the selected studies was evaluated using the Newcastle-Ottawa Scale. Additionally, hazard ratios were calculated, and publication bias of the studies was determined using Egger's test. Results: Nine relevant publications involving a combined total of 1254 patients with different types of cancer were included in this study. The combined results of the random effects models yielded a hazard ratio of 1.73 (95% confidence interval: 1.31, 2.29; P < 0.001), which suggested there was a significant association between RASSF1A methylation and overall survival, and patients with an RASSF1A methylation status had a significantly increased risk of total death. Moreover, the Egger test result suggested there was no significant publication bias among the included studies. Conclusions: The methylation of RASSF1A in cell-free DNA in cancer patients was observably associated with an increased risk of poor overall survival.

Association of has_circ_0001944 upregulations with prognosis and cancer progression in patients with colorectal cancer.

BACKGROUND: CircRNAs are functional in cancer-related processes and are promising candidates for cancer prognostic biomarkers. The study aimed to evaluate the functional and clinical significance of has_circ_0001944 in colorectal cancer (CRC), including predictive value for overall survival (OS) and recurrence-free survival (RFS), and its effect on cell growth and metastasis. METHODS: This retrospective study included 133 patients with CRC. The expression of has_circ_0001944 in tissues and cells was quantified by real-time quantitative reverse transcription PCR. Receiver operating characteristics and Kaplan-Meier survival analysis were used to assess the significance of has_circ_0001944 as a prognostic marker, and its reliability was validated using multivariate regression analysis. Subsequently, XTT, transwell migration, and modified-transwell invasion assays were used to determine the behavior of the CRC cells in response to has_circ_0001944 inhibition. RESULTS: Results of the qRT-PCR showed upregulation of has_circ_0001944 in the CRC samples compared to the normal samples. High has_circ_0001944 expression indicated shorter OS and RFS, comes down to poor prognosis. Multivariate regression analysis showed that elevated has_circ_0001944 increased the risk of death or recurrence and is a valuable prognostic factor. Following the has_circ_0001944 inhibition, the proliferation, migration and invasion of the CRC cells were reduced. miR-548b-3p was target miRNA of has_circ_0001944. CONCLUSION: Up-regulation of has_circ_0001944 is associated with a poor prognosis of CRC. has_circ_0001944 downregulation can slow the progression of CRC partly by targeting miR-548b-3p.

Genome-Guided Discovery of Antifungal Filipins from a Deep-Sea-Derived Streptomyces antibioticus.

Nine new (1-3, 5-8, 11, and 12; named filipins VI-XIV) and three known (4, 9, and 10) filipin-type polyene macrolides were isolated from the deep-sea-derived Streptomyces antibioticus OUCT16-23 using a genome-guided strategy coupled with bioassay. Their structures were elucidated based on the extensive MS and NMR spectroscopic analyses together with ECD calculations. In an antifungal assay, compounds 4, 5, and 7-10 showed different degrees of growth inhibition against Candida albicans with minimum inhibitory concentrations (MICs) of 1.56-12.5 µg/mL, by which the alkyl side-chain substitution affecting the activity was preliminarily studied. A biosynthetic pathway to 1-12 in S. antibioticus OUCT16-23 is also proposed.

MgMoO4 as an anode material for lithium ion batteries and its multi-electron reaction mechanism.

Single-phase magnesium molybdate, MgMoO4, is successfully synthesized by a facile sol-gel method. Attributed to the multielectron reaction and the synergistic effect of the elements molybdenum (Mo) and magnesium (Mg), the MgMoO4 electrode exhibits excellent electrochemical properties. After activation, benefiting from the decrease in particle size and the uniform nanosphere morphology, the MgMoO4 electrodes can deliver a stable high specific capacity of about 1060 mA h g-1 at a current density of 100 mA g-1 after 600 cycles. Based on the important role of the activation process, electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM) and scan rate cyclic voltammetry (CV) measurement methods were employed to reveal the effect of the activation process on the electrochemical behavior of the electrode material. Furthermore, by combining the in situ X-ray diffraction (XRD) and ex situ X-ray photoelectron spectroscopy (XPS) results, we illustrate the lithium storage mechanism of the MgMoO4 electrode in detail.

Profiling and Characterization of microRNAs Responding to Sodium Butyrate Treatment in Gastric Cancer Cells.

BACKGROUND: Short-chain fatty acids exert anti-cancer effects on tumor cells. OBJECTIVE: We aimed to reveal the signaling network altered by butyrate in Gastric Cancer (GC) using small RNA sequencing (sRNA-seq). METHODS: The effects of butyrate on the biological behavior of NCI-N87 and KATO III cells in vitro were assessed by functional assays and half-maximal inhibitory concentrations (IC50) of butyrate in KATO III cells were calculated. sRNA-seq was performed on KATO III cells. Differentially expressed miRNAs (DE-miRNAs) were identified between butyrate treatment and control groups using DESeq2, and miRNA targets were predicted. A protein-protein interaction (PPI) network of DE-miRNA targets was created using Metascape. Key MCODE complexes were identified using the MCODE algorithm and cluster Profiler. The relationship between DE-miRNA and GC overall survival (OS) was evaluated using Kaplan-Meier curves. RESULTS: Butyrate dose-dependently inhibited NCI-N87 and KATO III cell viability. KATO III cells were more sensitive to butyrate than NCI-N87 cells. Butyrate promoted apoptosis and inhibited KATO III cell migration. Total 324 DE-miRNAs were identified in KATO III cells, and 459 mRNAs were predicted as targets of 83 DE-miRNAs. Two key protein complexes were identified in a PPI network of the 459 targets. A key signaling network responding to butyrate was generated using targets in these key complexes and their miRNA regulators. The DE-miRNAs in the key signaling network were related to the OS of GC. CONCLUSION: Butyrate altered the biological behavior of GC cells, which may be achieved by regulating miRNAs and related oncogenic pathways.

Synthesis of a full range Fe-doped ZnFexCo2-xO4 and its application as anode material for lithium-ion battery.

Fe-Doped ZnFexCo2-xO4 (x = 0.00, 0.17, 0.33, 0.47, 0.67, 0.87, 1.17, 1.37, 1.67, 1.87, 2.00) compounds were prepared by a sol-gel method. X-ray diffraction measurements show that Fe-doping does not change the crystal structure of ZnCo2O4 and dopant Fe successfully occupies the 16c Co site. Because of the bigger radius of the doping ion, the cell parameters and cell volumes of ZnFexCo2-xO4 compounds present an obvious linear increase with increasing Fe content. In addition, attributed to the similar crystal structures for ZnFe2O4 and ZnCo2O4, a full range (0 ≤ x ≤ 2) of ZnFexCo2-xO4 solid solution phases was obtained. V/I measurement results show that a small Fe doping content obviously improved the electronic conductivity of the sample. In addition, due to the smaller particles size and uniform particle distribution caused by Fe doping, the lithium ion diffusion coefficient of the sample was increased by 2 orders of magnitude. Based on the improved electronic conductivity combined with the significantly increased lithium-ion diffusion coefficient, a sample with Fe doping content of x = 0.33, ZnFe0.33Co1.67O4, presents a high reversible specific capacity and excellent rate cycle stability. At a rate of 100 mA g-1, a relatively high discharge capacity of 850 mA h g-1 can still be obtained after 100 cycles, which is obviously higher than that of pure ZnCo2O4 (only 295 mA h g-1). Even at a higher discharge rate of 500 mA g-1, a discharge capacity of 450 mA h g-1 with a capacity retention of nearly 100% was obtained. Based on its excellent electrochemical properties, ZnFe0.33Co1.67O4 will be a promising anode material for rechargeable lithium-ion batteries.

Prognostic Score Model Based on Ten Differentially Methylated Genes for Predicting Clinical Outcomes in Patients with Adenocarcinoma of the Colon.

PURPOSE: We aimed to screen novel genetic biomarkers for use in a prognostic score (PS) model for the accurate prediction of survival outcomes for patients with colon adenocarcinoma (COAD). METHODS: Gene expression and methylation data were downloaded from The Cancer Genome Atlas database, and the samples were randomly divided into training and validation sets for the screening of differentially methylated genes (DMGs) and differentially expressed genes (DEGs). Co-methylated genes were screened using weighted gene co-expression network analysis. Functional enrichment analysis was performed using the Database for Annotation, Visualization, and Integrated Discovery. Univariate and multivariate Cox regression analyses were performed to identify prognosis-related genes and clinical factors. Receiver operating characteristic curve analysis was carried out to evaluate the predictive performance of the PS model. RESULTS: In total, 1434 DEGs and 1038 DMGs were screened in the training set, among which 284 were found to be overlapping genes. For 127 of these overlapping genes, the methylation and expression levels were significantly negatively correlated. An optimal signature from 10 DMGs was identified to construct the PS model. Patients with a high PS seemed to have worse outcomes than those with a low PS. Moreover, cancer recurrence and the PS model status were independent prognostic factors. CONCLUSION: This PS model based on an optimal 10-gene signature would help in the stratification of patients with COAD and improve the assessment of their clinical outcomes.

Expression and prognostic analysis of Rho GTPase-activating protein 11A in lung adenocarcinoma.

BACKGROUND: Rho GTPase-activating protein 11A (ARHGAP11A) is a member of the Rho GTPase-activating protein (RhoGAP) subfamily. However, its expression, prognostic significance and clinicopathologic factors correlation in lung adenocarcinoma is still unclear. METHODS: The original gene expression profile, survival data, and clinical information of patients with lung adenocarcinoma (LUAD) were downloaded from The Cancer Genome Atlas (TCGA) database. The expression difference of ARHGAP11A between LUAD tissues and adjacent normal tissues in the TCGA database was analyzed by using R software, and verified by the Oncomine database and immunohistochemical (IHC) assay of LUAD sections. Logistic regression was applied to analyze the relationship between the expression of ARHGAP11A and clinicopathological factors of LUAD. Kaplan-Meier (KM) survival curves and a Cox proportional-hazards model were selected to evaluate the prognostic significance of ARHGAP11A expression. Gene set enrichment analysis (GSEA) software was applied to screen the tumor signaling pathways associated with the low and high expression group of ARHGAP11A in LUAD. RESULTS: The TCGA database showed that the expression of ARHGAP11A was significantly higher in LUAD tissues than in normal tissues (P<0.001). The up-regulation of ARHGAP11A in LUAD was verified by the Oncomine database (P<0.001) and IHC assay (P<0.001). Logistic regression analysis revealed the high expression of ARHGAP11A to be closely related to age, sex, advanced pathological stage, advanced T stage, and lymph node metastasis. The KM plots based on the TCGA and KM plotter databases indicated that patients with LUAD highly expressing ARHGAP11A had a poorer overall survival (OS) than patients with low expression of ARHGAP11A. Multivariate Cox regression analysis showed that the high expression of ARHGAP11A could be an important independent predictor of a poor prognosis of LUAD [hazards ratio (HR) =1.385; P<0.001]. GSEA indicated that 10 signal pathways were significantly enriched in LUAD samples with the ARHGAP11A expression phenotype. CONCLUSIONS: ARHGAP11A may play a carcinogenic role in the malignant progression of LUAD, and it can be considered as a new independent prognostic factor and potential therapeutic target for LUAD.

The facile synthesis and electrochemical performance of Ni2V2O7 as a novel anode material for lithium-ion batteries.

The single-phase binary nickel vanadate Ni2V2O7 was successfully synthesized by a simple solid-state method to explore novel anode materials for lithium-ion batteries. After an activation process, the Ni2V2O7 electrode exhibited excellent electrochemical performance with a stable, high specific capacity of about 960 mA h g-1 at a current density of 100 mA g-1, which is attributed to the multiple valence states and the synergistic effect of the transition elements V and Ni. Even at a high current density of 2000 mA g-1, a stable specific capacity of about 400 mA h g-1 was still obtained. Considering the influence of the activation process on the electrochemical performance of the Ni2V2O7 electrode, we studied the origin of the excellent electrochemical performance, where the improved lithium diffusion coefficient and increased pseudocapacitive contribution caused by the activation process led to a significant improvement in the electrochemical performance, including rate capacity and cycle stability. By combining in situ X-ray diffraction (XRD) and ex situ X-ray photoelectron spectroscopy (XPS) methods, for the first time, we illustrate the detailed lithium storage mechanism of the Ni2V2O7 electrode during the lithium insertion/extraction process.

Metformin Suppresses the Proliferation and Promotes the Apoptosis of Colon Cancer Cells Through Inhibiting the Expression of Long Noncoding RNA-UCA1.

PURPOSE: LncRNA-UCA1 has been proven to facilitate the proliferation and metastasis of colon cancer. Whether metformin inhibits the progression of colon cancer by suppressing lncRNA-UCA1 remains unknown. In this research, we aimed to explore the role of Metformin playing in pathogenesis of colon cancer. MATERIALS AND METHODS: Using qRT-PCR, we measured the expression of five tumor-promoting lncRNAs in SW480 and SW620 colon cancer cells. Then, we conducted Western blotting and immunohistochemistry to evaluate the effects of MET or UCA1 knockdown or the combined MET+ UCA1 knockdown on the activities of the PI3K/AKT and ERK pathways in vitro and in tumor tissues obtained from tumor-bearing nude mice. RESULTS: The results from CCK-8 assays showed that MET dose-dependently and time-dependently inhibited the viability of the colon cancer cells in vitro. Flow cytometry revealed that MET promoted the apoptosis of the SW480 and SW620 cells. qRT-PCR showed that lncRNA-UCA1 had the highest expression among the five lncRNAs. Suppressing UCA1 expression by siRNA or shRNA could further enhance the metformin-mediated anticancer effects against colon cancer in vitro and in vivo. Metformin decreased the UCA1 expression and further inhibited the proliferation and promoted the apoptosis of the colon cancer cells, which were associated with inactivation of the PI3K/AKT and ERK signaling pathways in vitro and in the tumor tissues obtained from the mice. CONCLUSION: These results indicated that metformin has potential anticancer properties and revealed the anticancer mechanisms of metformin against colon cancer via regulating lncRNA-UCA1.

LncRNA TUBA4B functions as a competitive endogenous RNA to inhibit gastric cancer progression by elevating PTEN via sponging miR-214 and miR-216a/b.

BACKGROUND: Emerging evidence demonstrates that long non-coding RNA (lncRNA) is an important regulator in tumorigenesis and development. Tubulin Alpha 4B (TUBA4B), a novel lncRNA, was recently proposed as a tumor suppressor in several human cancers. However, its role in gastric cancer (GC) remains unclear. In this study, we aimed to investigate the expression level, clinical implication, biological function and potential regulatory mechanism of TUBA4B in GC. METHODS: qRT-PCR was employed to detect the expression of TUBA4B in GC tissues, cell lines and plasma. In vitro and in vivo experiments were carried out using colony formation/CCK-8/transwell invasion/cell apoptosis assay and xenograft tumor model, respectively. mRNA sequencing was used to identify the TUBA4B-related downstream genes. RESULTS: TUBA4B was significantly decreased in GC tissues, cells and plasma. Low TUBA4B was positively correlated with larger tumor size, lymph node metastasis and advanced TNM stage. Moreover, TUBA4B was identified as an effective biomarker for the diagnosis and prognosis of patients with GC. Functionally, ectopic expression of TUBA4B inhibited GC cell proliferation, invasion and induced apoptosis in vitro as well as dampened tumor growth and metastasis in vivo. Furthermore, TUBA4B was found to be a competitive endogenous RNA (ceRNA) that could physically bind to and sequester miR-214 and miR-216a/b to increase the expression of their common downstream target PTEN, resulting in inactivation of PI3K/AKT signaling pathway, thereby retarding GC progression. CONCLUSION: Our data highlight the compelling regulatory role of TUBA4B in GC, and reactivation of TUBA4B may be a promising therapeutic avenue for GC patients.

A novel circular RNA circ-ZNF652 promotes hepatocellular carcinoma metastasis through inducing snail-mediated epithelial-mesenchymal transition by sponging miR-203/miR-502-5p.

Circular RNA (circRNA), a special class of non-coding RNA, is increasingly being realized as a critical regulator in human diseases, including carcinomas. However, its role in hepatocellular carcinoma (HCC) metastasis remains largely unknown. Herein, we enrolled three Gene Expression Omnibus (GEO) databases and screened and identified a novel circRNA, circ-ZNF652 (hsa_circ_0003258), which was significantly upregulated in HCC tissues and cell lines. Importantly, HCC patients with high circ-ZNF652 expression were more prone to vascular invasion, intrahepatic metastasis, distant metastasis, and poor outcome. Subsequent functional experiments showed that depletion of circ-ZNF652 dramatically suppressed the migratory and invasive capabilities of HCC cells in vitro as well as tumor metastasis in vivo by inhibiting the process of epithelial-mesenchymal transition (EMT). Mechanistically, circ-ZNF652 could physically interact with miR-203 and miR-502-5p to increase the expression of their common target gene Snail (a key transcription factor that triggers EMT), thereby promoting the metastasis of HCC. In turn, the upregulated Snail was capable of binding to the E-box motif (CAGGTG) on the promoter of circ-ZNF652 to elevate circ-ZNF652 expression. Collectively, our findings suggest that circ-ZNF652 is a novel driver of EMT and unveil the important regulatory role of circ-ZNF652/miR-203/miR-502-5p/Snail feedback loop in HCC metastasis.

Diagnostic Assessment of septin9 DNA Methylation for Colorectal Cancer Using Blood Detection: A Meta-Analysis.

This meta-analysis aimed to assess the diagnostic efficiency of blood-based septin 9 (SEPT9) methylation assay for the detection of colorectal cancer (CRC). Studies were searched in the Springer, Wiley, Cochrane Library, PubMed, Ovid, Embase, Web of Science, China BioMedicine, Wanfang and China National Knowledge Infrastructure databases until July 2017. Methodological quality assessment was performed based on the guidelines of the Quality Assessment of Diagnostic Accuracy Studies. According to 1/3 and 2/3 algorithms, the meta-analyses for the diagnostic effect of SEPT9 in CRC were compared with healthy subjects and subjects with polyps, adenoma, and non-CRC, respectively. The random effects model was applied and publication bias was evaluated. The included 29 studies comprised 10,486 subjects (3202 patients with CRC and 7284 controls). In comparison with healthy subjects, the pooled sensitivity with 95% confidence intervals (CIs) of SEPT9 methylation for the diagnosis of CRC was 0.74 (95% CI: 0.61-0.84) in the 1/3 algorithm group, whereas the specificity was 0.96 (95% CI: 0.95-0.97) in the 2/3 algorithm group. Additionally, positive likelihood ratio was less than 10 and negative likelihood ratio more than 0.1 in the 2/3 algorithm group for patients with CRC vs. polyps and adenoma. The P value of Deeks' funnel plot was 0.36, suggesting that there was no publication bias. SEPT9 methylation can be used to diagnose CRC in healthy individuals under the 2/3 algorithm. The determination of SEPT9 methylation does not distinguish well between CRC and polyps or adenoma.

An ATP-Dependent Ligase with Substrate Flexibility Involved in Assembly of the Peptidyl Nucleoside Antibiotic Polyoxin.

Polyoxin (POL) is an unusual peptidyl nucleoside antibiotic, in which the peptidyl moiety and nucleoside skeleton are linked by an amide bond. However, their biosynthesis remains poorly understood. Here, we report the deciphering of PolG as an ATP-dependent ligase responsible for the assembly of POL. A polG mutant is capable of accumulating multiple intermediates, including the peptidyl moiety (carbamoylpolyoxamic acid [CPOAA]) and the nucleoside skeletons (POL-C and the previously overlooked thymine POL-C). We further demonstrate that PolG employs an ATP-dependent mechanism for amide bond formation and that the generation of the hybrid nucleoside antibiotic POL-N is also governed by PolG. Finally, we determined that the deduced ATP-binding sites are functionally essential for PolG and that they are highly conserved in a number of related ATP-dependent ligases. These insights have allowed us to propose a catalytic mechanism for the assembly of peptidyl nucleoside antibiotic via an acyl-phosphate intermediate and have opened the way for the combinatorial biosynthesis/pathway engineering of this group of nucleoside antibiotics.IMPORTANCE POL is well known for its remarkable antifungal bioactivities and unusual structural features. Actually, elucidation of the POL assembly logic not only provides the enzymatic basis for further biosynthetic understanding of related peptidyl nucleoside antibiotics but also contributes to the rational generation of more hybrid nucleoside antibiotics via synthetic biology strategy.