Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere.

Phosphorus (P) deficiency is a predominant constraint on plant growth in acidified soils, largely due to the sequestration of P by toxic aluminum (Al) compounds. Indigenous phosphorus-solubilizing bacteria (PSBs) capable of mobilizing Al-P in these soils hold significant promise. A novel Al-P-solubilizing strain, Al-P Nguyenibacter sp. L1, was isolated from the rhizosphere soil of healthy Lespedeza bicolor plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus Nguyenibacter remains in its infancy. To further explore its biotechnological potentialities, we sequenced the complete genome of this strain, employing an amalgamation of Oxford Nanopore ONT and Illumina sequencing platforms. The resultant genomic sequence of Nguyenibacter sp. L1 manifests as a singular, circular chromosome encompassing 4,294,433 nucleotides and displaying a GC content of 66.73%. The genome was found to host 3,820 protein-coding sequences, 12 rRNAs, and 55 tRNAs. Intriguingly, annotations derived from the eggNOG and KEGG databases indicate the presence of genes affiliated with phosphorus solubilization and nitrogen fixation, including iscU, glnA, and gltB/D associated with nitrogen fixation, and pqqBC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including pqqCDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to Nguyenibacter sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of Nguyenibacter sp. L1 at the molecular level through genetic screening and analysis. The insights gleaned from this study offer strategic guidance for future strain enhancement and establish a strong foundation for the potential incorporation of this bacterium into agricultural practices.

Circular RNA circTTBK2 facilitates non-small-cell lung cancer malignancy through the miR-873-5p/TEAD1/DERL1 axis.

Aim: The underlying mechanisms by which circular RNAs (circRNAs) regulate non-small-cell lung cancer (NSCLC) progression remain elusive. This study investigated the role of circRNA circTTBK2 in NSCLC tumorigenesis. Materials & methods: Quantitative reverse transcriptase polymerase chain reaction analysis of circTTBK2 in NSCLC tissues and cell lines was performed. Cell proliferation, migration, invasion and tumorigenesis were confirmed in vitro and in vivo using CCK-8, EdU incorporation, Transwell assays and xenograft technique. The circTTBK2/miR-873-5p/TEAD1/DERL1 axis was verified by RNA immunoprecipitation, chromatin immunoprecipitation and luciferase reporter assays. Results: Overexpressed circTTBK2 in NSCLC tissues indicates poor prognosis of NSCLC patients. circTTBK2 harbors miR-873-5p, and miR-873-5p directly targets TEAD1. TEAD1 transcriptionally activates DERL1. Conclusion: This study revealed a novel machinery of circTTBK2/miR-873-5p/TEAD1/DERL1 for NSCLC tumorigenesis.

Enzymatic Synthesis of Puerarin Glucosides Using Cyclodextrin Glucanotransferase with Enhanced Antiosteoporosis Activity.

Puerarin (PU) is the most abundant isoflavone from the root of Pueraria lobata and exhibits a broad range of pharmacological activities. However, poor water solubility and low bioavailability limit its use. Enzymatic transglycosylation is emerging as a new strategy to improve the pharmacodynamic and pharmacokinetic properties of natural products for drug development. In this study, three PU glucosides (PU-G, PU-2G, and PU-3G) were synthesized by using a cyclodextrin glucanotransferase from Bacillus licheniformis with PU as the acceptor and α-cyclodextrin as the sugar donor. The transglycosylation products were isolated and structurally identified by mass spectrometry and nuclear magnetic resonance. The water solubilities of PU-G, PU-2G, and PU-3G were 15.6, 100.9, and 179.1 times higher than that of PU, respectively. Moreover, the antiosteoporosis activities of these glucosides were tested, and PU-G was found to show much more potent antiosteoporosis activity as compared to the original PU.

Transcriptome analysis reveals that barnyard grass exudates increase the allelopathic potential of allelopathic and non-allelopathic rice (Oryza sativa) accessions.

BACKGROUND: Allelopathy in rice (Oryza sativa) is a chemically induced response that is elevated by the exogenous application of chemical compounds and barnyard grass root exudates. An in-depth understanding of the response mechanisms of rice to chemical induction is necessary for the identification of target genes for increasing the allelopathic potential of rice. However, no previous studies have evaluated the transcriptomic changes associated with allelopathy in rice in response to barnyard grass exudates treatment. Thus, the aim of the present study was to reveal differentially expressed genes (DEGs) in allelopathic and non-allelopathic rice seedlings treated with barnyard grass exudates to identify target allelopathy genes. RESULTS: The inhibitory effect of the culture solutions on the allelopathic rice accession PI312777 (PI) and the non-allelopathic rice accession Lemont (LE) significantly increased (P < 0.05) after treatment with barnyard grass root exudates. The RNA sequencing results revealed that 14,891 genes in PI(+B) vs. LE(+B), 12,505 genes in PI(+B) vs. PI(-B), and 5857 genes in LE(+B) vs. LE(-B) were differentially expressed following root exudates treatment. These DEGs were classified into three categories and 32 functional groups, i.e., 12 groups in the biological process category, 12 groups in the cellular component category, and eight groups in the molecular function category. There were 5857 and 2846 upregulated genes and 135 and 50 upregulated Gene Ontology terms (P < 0.05) in the biological process category in PI(+B) vs. PI(-B) and LE(+B) vs. LE(-B), respectively. These results indicated that the allelopathic accession PI is more sensitive than the non-allelopathic accession LE to exogenous root exudates treatment. Genes related to rice allelochemical-related biosynthesis pathways, particularly the shikimic acid and acetic acid pathways, were significantly differentially expressed in both rice accessions. These findings suggested that phenolic acids, fatty acids, and flavonoids, which constitute the downstream metabolites of the shikimic acid and acetic acid pathways, are significantly expressed in response to root exudates of barnyard grass. CONCLUSIONS: The allelopathic potential of both rice accessions could be significantly enhanced by barnyard grass root exudates application. Furthermore, genes related to the biosynthesis pathways of reported rice allelochemicals were significantly differentially expressed in both accessions. Phenylalanine ammonia lyase was determined to be a potential target for the regulation of chemical induction.

Separation of allelopathy from resource competition using rice/barnyardgrass mixed-cultures.

Plant-plant interference is the combined effect of allelopathy, resource competition, and many other factors. Separating allelopathy from resource competition is almost impossible in natural systems but it is important to evaluate the relative contribution of each of the two mechanisms on plant interference. Research on allelopathy in natural and cultivated plant communities has been hindered in the absence of a reliable method that can separate allelopathic effect from resource competition. In this paper, the interactions between allelopathic rice accession PI312777, non-allelopathic rice accession Lemont and barnyardgrass were explored respectively by using a target (rice)-neighbor (barnyardgrass) mixed-culture in hydroponic system. The relative competitive intensity (RCI), the relative neighbor effect (RNE) and the competitive ratio (CR) were used to quantify the intensity of competition between each of the two different potentially allelopathic rice accessions and barnyardgrass. Use of hydroponic culture system enabled us to exclude any uncontrolled factors that might operate in the soil and we were able to separate allelopathy from resource competition between each rice accession and barnyardgrass. The RCI and RNE values showed that the plant-plant interaction was positive (facilitation) for PI312777 but that was negative (competition) for Lemont and barnyardgrass in rice/barnyardgrass mixed-cultures. The CR values showed that one PI312777 plant was more competitive than 2 barnyardgrass plants. The allelopathic effects of PI312777 were much more intense than the resource competition in rice/barnyardgrass mixed cultures. The reverse was true for Lemont. These results demonstrate that the allelopathic effect of PI312777 was predominant in rice/barnyardgrass mixed-cultures. The most significant result of our study is the discovery of an experimental design, target-neighbor mixed-culture in combination with competition indices, can successfully separate allelopathic effects from competition.

Carboxymethylpachymaran enhances immunologic function of dendritic cells cultured in two kinds of hepatoma carcinoma cell line's supernatant via nuclear factor κ B/Rel pathway.

OBJECTIVE: To study the immunologic function of dendritic cells (DCs) cultured in two kinds of hepatoma cell line's supernatant and the enhancing effects of carboxymethylpachymaran (CMP) on DCs. METHODS: DCs were harvested after stimulation by granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin (IL)-4 from umbilical cord blood using density-gradient centrifugation method. Cultured supernatant of two hepatoma cell lines (HepG2 and HepG2.2.15) were collected for condition medium (CM) according to a volume ratio of supernatant to incomplete RPMI-1640 medium, which was 3:1. CMP was dissolved in incomplete RPMI-1640 medium. Experimental groups were divided according to the culture medium, either CM or with CMP in it. DCs subsets CD83, CD86, CD1a, and d-related human leukocyte antigens (HLA-DR) were analyzed by flow cytometry. The proliferation ability of allogeneic T cells in mixed lymphocyte reaction (MLR) stimulated by DCs was examined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) analysis. IL-12p70, interferon-γ (IFN-γ), and nuclear factor κB (NF-κB) were detected by enzyme-linked immunosorbent assay analysis. RESULTS: The proliferation of lymphocytes and secreting level of IL-12 and expression of phenotype of DCs cultured in two kinds of CM were lower than those of normal group (P <0.01). Compared with the normal group, groups treated with CMP showed a higher expression level of DCs subsets, lymphocyte reproductive activity, as well as IL-12 and IFN-γ secretion levels. Groups treated with CMP also demonstrated higher levels of DCs phenotype expression and IL-12 and IFN-γ secretion in supernatant of MLR and higher lymphocyte reproductive activity compared with CM group (P <0.05). Compared with the normal group, the expression level of NF-κB in DCs nuclear was higher in CMP groups but lower in two CM groups (P <0.05). After CMP was added, the NF-κB expression levels of two CM groups were increased compared with levels before CMP was added (P <0.05). However, there was no significant difference between the two CM groups (P >0.05). CONCLUSIONS: Two kinds of hepatoma cell line's supernatant can inhibit the immunologic function of DCs. This suppressive effect may be related to the inhibition of NF-κB/Rel pathway. CMP may up-regulate the DCs function by activating the NF-κB/Rel pathway.

The effect of desacetyluvaricin on the expression of TLR4 and P53 protein in Hepg 2.2.15.

BACKGROUND: Previous studies suggest that annonaceous may cause permeability glycoprotein (P-gp) function to abate, leading to cell apoptosis. It has also been reported that annonaceous acetogenins affect hepatocellular carcinoma (HCC) cells in the G1 phase, leading to apoptosis. Desacetyluvaricin (Des), a new type of annonaceous acetogenin monomer, has a significant effect on HCC, with few side effects. OBJECTIVES: To investigate the effect of Des on the expression of Toll-like receptor 4 (TLR4) and P53 protein in HCC. MATERIALS AND METHODS: HCC HepG2.2.15 cell was cultured by routine method. HepG2.2.15 cells were divided into three groups: control group, treated with Des and DDP (cisplatin) which were examined by immunofluorescence flow cytometry for expression of TLR4 and P53. RESULTS: TLR4 was expressed by more cells in the Des group than in the cisplatin or serum-only groups (71.94%, 42.64%, and 37.16%, respectively; Des vs.cisplatin: p < 0.05; Des vs. serum only: p < 0.05), with no difference between the cisplatin and serum-only groups (p > 0.05). P53 was expressed by more cells in the Des and cisplatin groups than in the serum-only group (32.6%, 31.5% and 3.3%, respectively; Des vs. serum only, p < 0.05; cisplatin vs. serum only, p < 0.05), with no difference between the Des and cisplatin groups (p > 0.05). CONCLUSIONS: Des increases TLR4 and P53 expression in HCC cells. Improved immune recognition by the former effect and induction of apoptosis by the latter could be the mechanisms of Des's clinical effects on HCC.

Characterization of metaproteomics in crop rhizospheric soil.

Soil rhizospheric metaproteomics is a powerful scientific tool to uncover the interactions between plants and microorganisms in the soil ecosystem. The present study established an extraction method suitable for different soils that could increase the extracted protein content. Close to 1000 separate spots with high reproducibility could be identified in the stained 2-DE gels. Among the spots, 189 spots representing 122 proteins on a 2-DE gel of rice soil samples were successfully identified by MALDI-TOF/TOF-MS. These proteins mainly originated from rice and microorganisms. They were involved in protein, energy, nucleotide, and secondary metabolisms, as well as signal transduction and resistance. Three characteristics of the crop rhizospheric metaproteomics seemed apparent: (1) approximately one-third of the protein spots could not be identified by MALDI-TOF/TOF/MS, (2) the conservative proteins from plants formed a feature distribution of crop rhizospheric metaproteome, and (3) there were very complex interactions between plants and microorganisms existing in a crop rhizospheric soil. Further functional analysis on the identified proteins unveiled various metabolic pathways and signal transductions involved in the soil biotic community. This study provides a paradigm for metaproteomic research on soil biology.

[Regulation effect of exogenous salicylic acid on weed suppression and molecular physiological characteristics of allelopathic rice].

To investigate the feasibility of using exogenous salicylic acid (SA) to regulate the allelopathic weed suppression of rice, this paper studied the effects of different concentrations exogenous SA on the weed-suppression and physiological-biochemical characteristics of allelopathic rice PI312777, and the relative expression quantity of gene ZB8 in the rice by real time quantitative RT-PCR (FQ-PCR). The results showed that exogenous SA induced the enhancement of the allelopathic potential of donor rice in suppressing target weed plants, and this inducing effect was SA dose and treatment time dependent. After foliar spraying SA, the inhibitory effect of PI312777 on barnyardgrass increased significantly, and the root vigor and superoxide dismutase (SOD) and peroxidase (POD) activities of PI312777 increased, while its catalase (CAT) activity decreased. The reverse was true for the target weed barnyardgrass. At the same time, the phenylalanine ammonialyase (PAL) activity of PI312777 increased significantly, leading to an increase of the total content of phenols. Among the test concentrations of SA, 0.2 mmol x L(-1) had the best inducing effect, under which, the relative expression quantity of ZB8 increased first and decreased then, with a peak at 24 hours after treatment.

[The differential expression of the genes of the key enzymes involved in phenolic compound metabolism in rice (Oryza sativa L.) under different nitrogen supply].

Differential expression of the key genes controlling phenolic metabolism in allelopathic and non-allelopathic rice accessions was investigated under two nitrogen supply levels (lower and normal) using fluorescence quantitative-polymerase chain reaction (FQ-PCR) (Figs.2, 3). The results indicated that 9 key enzyme genes concerned were mediated by lower nitrogen level (Table 2). All of the nine genes (Table 1, Fig.4), were up-regulated by 1.9-5.4 times of the relative gene expression amounts in allelopathic rice accession, 'PI312777' under the lower nitrogen condition compared with their controls, of which PAL gene showed the highest relative gene expression amount with 5.4 times of the relative gene expressions compared with the control, while in non-allelopathic rice Lemont, seven genes were down-regulated by 29%-72% under lower nitrogen supplies compared with their controls and only two genes, i.e., phenylalanine ammonia-lyase and cinnamoyl-CoA genes were up-regulated, which however were a decrease of 22% and 74% over those in allelopathic rice accession (Table 2). These findings strongly suggest that the increase of allelopathic potential induced by 1/4 nutrient stress was responsible for enhanced phenolic compound synthesis metabolism.