Development of a dual fluorescent reporter system to identify inhibitors of Staphylococcus aureus virulence factors.

IMPORTANCE: Staphylococcus aureus is a formidable pathogen responsible for a wide range of infections, and the emergence of antibiotic-resistant strains has posed significant challenges in treating these infections. In this study, we have established a novel dual reporter system capable of concurrently monitoring the activities of two critical virulence regulators in S. aureus. By incorporating both reporters into a single screening platform, we provide a time- and cost-efficient approach for assessing the activity of compounds against two distinct targets in a single screening round. This innovative dual reporter system presents a promising strategy for the identification of molecules capable of modulating virulence gene expression in S. aureus, potentially expediting the development of antivirulence therapies.

Flavone inhibits Staphylococcus aureus virulence via inhibiting the sae two component system.

The rising prevalence of antibiotic resistance in Staphylococcus aureus calls for the development of innovative antimicrobial agents targeting novel pathways. S. aureus generates various virulence factors that compromise host defense mechanisms. Flavone, a core structure of flavonoids, has been shown to diminish the production of staphyloxanthin and alpha-hemolysin. Nonetheless, the influence of flavone on the majority of other virulence factors in S. aureus and its underlying molecular mechanism remain elusive. In this study, we examined the impact of flavone on the transcriptional profile of S. aureus using transcriptome sequencing. Our findings revealed that flavone substantially downregulated the expression of over 30 virulence factors implicated in immune evasion by the pathogen. Gene set enrichment analysis of the fold change-ranked gene list in relation to the Sae regulon indicated a robust association between flavone-induced downregulation and membership in the Sae regulon. Through the analysis of Sae target promoter-gfp fusion expression patterns, we observed a dose-dependent inhibition of Sae target promoter activity by flavone. Moreover, we discovered that flavone protected human neutrophils from S. aureus-mediated killing. Flavone also decreased the expression of alpha-hemolysin and other hemolytic toxins, resulting in a reduction in S. aureus' hemolytic capacity. Additionally, our data suggested that the inhibitory effect of flavone on the Sae system operates independently of its capacity to lower staphyloxanthin levels. In conclusion, our study proposes that flavone exhibits a broad inhibitory action on multiple virulence factors of S. aureus by targeting the Sae system, consequently diminishing the bacterium's pathogenicity.

Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments.

Members of the genus Novosphingobium were frequently isolated from polluted environments and possess great bioremediation potential. Here, three species, designated B2637T, B2580T and B1949T, were isolated from mangrove sediments and might represent novel species in the genus Novosphingobium based on a polyphasic taxonomy study. Phylogenomic analysis revealed that strains B2580T, B1949T and B2637T clustered with Novosphingobium naphthalenivorans NBRC 102051T, 'N. profundi' F72 and N. decolorationis 502str22T, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolates and their closely related species were less than 94 and 54 %, respectively, all below the threshold of species discrimination. The sizes of the genomes of isolates B2580T, B2637T and B1949T ranged from 4.4 to 4.6 Mb, containing 63.3-66.4 % G+C content. Analysis of their genomic sequences identified genes related to pesticide degradation, heavy-metal resistance, nitrogen fixation, antibiotic resistance and sulphur metabolism, revealing the biotechnology potential of these isolates. Except for B2637T, B1949T and B2580T were able to grow in the presence of quinalphos. Results from these polyphasic taxonomic analyses support the affiliation of these strains to three novel species within the genus Novosphingobium, for which we propose the name Novosphingobium album sp. nov. B2580T (=KCTC 72967T=MCCC 1K04555T), Novosphingobium organovorum sp. nov. B1949T (=KCTC 92158T=MCCC 1K03763T) and Novosphingobium mangrovi sp. nov. B2637T (KCTC 72969T=MCCC 1K04460T).

Taxonomy and anticancer potential of Streptomyces niphimycinicus sp. nov. against nasopharyngeal carcinoma cells.

Streptomyces species are ubiquitous, Gram-positive, spore-forming bacteria with the ability to produce various clinically relevant compounds. The strain 4503 T was isolated from mangrove sediments, showing morphological and chemical properties which were consistent with those of members of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was primarily identified as members of the genus Streptomyces, sharing more than 99% sequence identity to Streptomyces yatensis DSM 41771 T, S. antimycoticus NBRC 12839 T, and S. melanosporofaciens NBRC 13061 T. Average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values between strain 4503 T and its close relatives were all below 95-96% and 75% of the novel species threshold, respectively. Results from phylogenetic, genomic, phenotypic, and chemotaxonomic characteristics analyses confirmed that the isolate represented a novel species of the genus Streptomyces, for which the name Streptomyces niphimycinicus sp. nov. 4503 T (= MCCC 1K04557T = JCM 34996 T) is proposed. The bioassay-guided fractionation of the extract of strain 4503 T resulted in the isolation of a known compound niphimycin C, which showed cytotoxic activity against nasopharyngeal carcinoma (NPC) cell lines TW03 and 5-8F with half maximal inhibitory concentration (IC50) values of 12.24 µg/mL and 9.44 µg/mL, respectively. Further experiments revealed that niphimycin C not only exhibited the capacity of anti-proliferation, anti-metastasis, induction of cell cycle arrest, and apoptosis, but was also able to increase the reactive oxygen species (ROS) production and regulate several signaling pathways in NPC cells. KEY POINTS: • Strain 4503 T was classified as a novel species of Streptomyces. • Niphimycin C correlates with the cytotoxic effect of strain 4503 T against NPC cells. • Niphimycin C induces apoptosis, autophagic flux disruption and cell cycle arrest.

Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments.

Two novel actinobacteria with the ability to degrade kerosene, designated as B3033T and Y57T, were isolated from mangrove sediments in Tieshan Harbour, South China Sea. Both strains are Gram-staining-positive, non-spore forming, slow-growing, oxidase-positive, non-motile and aerobic. Their major cellular fatty acids were C16 : 0 and C18 : 1ω9c. Analysis of 16S rRNA gene sequences revealed the close relationship of strain B3033T to Mycobacterium kyogaense DSM 107316T (99.4 % nucleotide identity) and strain Y57T to Mycolicibacterium chubuense ATCC 27278T (98.7 %) and Mycolicibacterium rufum JS14T (98.7 %). Whole genome average nucleotide blast identity (ANI) and the digital DNA-DNA hybridization (dDDH) values between the two isolates and the type strains of species of the genus Mycolicibacterium were lower than 94 and 45 %, respectively, which were below the threshold values of 95 % (for ANI) and 70 % (for dDDH) recommended for bacterial species differentiation. The genome sequence of B3033T comprised a circular 11.0 Mb chromosome with a DNA G+C content of 68.1 mol%. Y57T had a genome size of 5.6 Mb and a DNA G+C content of 68.7 mol%. Genes involved in degradation of aromatic compounds and copper resistance were identified in the genomes of both strains that could improve their adaptive capacity to the mangrove environment. These results combined with those of chemotaxonomic analyses, MALDI-TOF MS profiles and phenotypic analyses support the affiliation of these strains to two novel species within the genus Mycolicibacterium, for which we propose the names Mycolicibacterium aurantiacum sp. nov. B3033T (=KCTC 49712T=MCCC 1K04526T) and Mycolicibacterium xanthum sp. nov. Y57T (=KCTC 49711T=MCCC 1K04875T) as type strains.

Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment.

A Gram-stain-negative, aerobic, milky white bacterium, designated B2012T, was isolated from mangrove sediment collected at Beibu Gulf, South China Sea. Antimicrobial activity assay revealed that the isolate possesses the capability of producing antibacterial compounds. Strain B2012T shared the highest 16S rRNA gene sequence relatedness (96.9-95.5 %) with members of the genus Acuticoccus. The isolate and all known Acuticoccus species contain Q-10 as the main respiratory quinone and have the same polar lipid components (phosphatidylcholine, unidentified glycolipid, unidentified lipid, unidentified amino lipid and phosphatidylglycerol). However, genomic relatedness referred by values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and the percentage of conserved proteins between strain B2012T and other type strains of the genus Acuticoccus were below the proposed thresholds for species discrimination. The genome of strain B2012T was assembled into 65 scaffolds with an N50 size of 244239 bp, resulting in a 5.5 Mb genome size. Eight secondary metabolite biosynthetic gene clusters were detected in this genome, including three non-ribosomal peptide biosynthetic loci encoding yet unknown natural products. Strain B2012T displayed moderately halophilic and alkaliphilic properties, growing optimally at 2-3 % (w/v) NaCl concentration and at pH 8-9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, C16 : 0 dimethyl aldehyde (DMA) and C16 : 0. Combined data from phenotypic, genotypic and chemotaxonomic analyses suggested that strain B2012T represents a novel species of the genus Acuticoccus, for which the name Acuticoccus mangrovi sp. nov. is proposed. The type strain of the type species is B2012T (=MCCC 1K04418T=KCTC 72962T).

Probing the Kinetic Anabolism of Poly-Beta-Hydroxybutyrate in Cupriavidus necator H16 Using Single-Cell Raman Spectroscopy.

Poly-beta-hydroxybutyrate (PHB) can be formed in large amounts in Cupriavidus necator and is important for the industrial production of biodegradable plastics. In this investigation, laser tweezers Raman spectroscopy (LTRS) was used to characterize dynamic changes in PHB content-as well as in the contents of other common biomolecule-in C. necator during batch growth at both the population and single-cell levels. PHB accumulation began in the early stages of bacterial growth, and the maximum PHB production rate occurred in the early and middle exponential phases. The active biosynthesis of DNA, RNA, and proteins occurred in the lag and early exponential phases, whereas the levels of these molecules decreased continuously during the remaining fermentation process until the minimum values were reached. The PHB content inside single cells was relatively homogenous in the middle stage of fermentation; during the late growth stage, the variation in PHB levels between cells increased. In addition, bacterial cells in various growth phases could be clearly discriminated when principle component analysis was performed on the spectral data. These results suggest that LTRS is a valuable single-cell analysis tool that can provide more comprehensive information about the physiological state of a growing microbial population.

[Baseline correction of Raman spectrum based on piecewise linear fitting].

The baseline drifts of Raman spectra occur in many types of instrumental measurements. It is an important part and a routine step to correct the baseline drift for the data preprocessing. In the present work, the limitations of the baseline correction method based on polynomial fitting were highlighted and a modified polynomial fitting method, i. e. piecewise linear fitting method, was proposed. Combined with the computer, this method could eliminate the baseline automatically. A series of Raman spectra of single polystyrene bead, red blood cell or yeast cell acquired by laser tweezers Raman spectroscopy were preprocessed by this method and its efficiency was verified. The results demonstrated that piecewise linear fitting can correct the baseline shifts effectively and provides more accurate information for further data analysis. It is a feasible method for correction of Raman spectrum.

[Analysis of pigments from Rhodotorula glutinis by Raman spectroscopy and thin layer chromatography].

The pigments from Rhodotorula glutinis were separated by using thin layer chromatography, and the result showed that Rhodotorula glutinis cells could synthesize at least three kinds of pigments, which were beta-carotene, torulene, and torularhodin. The Raman spectra based on the three pigments were acquired, and original spectra were preprocessed by background elimination, baseline correction, and three-point-smoothing, then the averaged spectra from different pigments were investigated, and the result indicated that Raman shift which represents C-C bond was different, and the wave number of beta-carotene demonstrated the largest deviation, finally torulene and torularhodin in Rhodotorula glutinis had more content than beta-carotene. Quantitative analysis of Raman peak height ratio revealed that peak height ratio of pigments showed little difference, which could be used as parameters for further research on living cells, providing reference content of pigments. The above results suggest that Raman spectroscopy combined with thin layer chromatography can be applied to analyze pigments from Rhodotorula glutinis, provides abundant information about pigments, and serves as an effective method to study pigments.

[Analysis of astaxanthin in Phaffia rhodozyma using laser tweezers raman spectroscopy].

In the present paper, a method was established based on laser tweezer Raman spectroscopy for rapid quantification of astaxanthin in Phaffia rhodozyma cells. First, the Raman spectra of astaxanthin standard solution with different concentrations were determined and the standard curve for astaxanthin with the peak intensity at 1 520 cm- was plotted; And then the Phaffia yeast cells cultivated in different nitrogen source and carbon source medium were divided into two parts, one for the detection of Raman spectra, and the other for the determination of ultraviolet visible spectrophotometry; Finally the relationship between the two methods was analyzed. The correlation coefficient of standard curve for astaxanthin is 0.998 3. Comparing laser tweezers Raman spectroscopy method with traditional ultraviolet visible spectrophotometry in analyzing the content of astaxanthin in unit mass Phaffia rhodozyma and the yield of astaxanthin in unit volume fermentation broth of Phaffia rhodozyma, the authors found that the data obtained have good linear relationship. And the correlation coefficients are 0.917 7 and 0.905 4, respectively. Therefore, both methods have almost the same effect of measuement. But laser tweezers Raman spectroscopy method is more efficient in the quantitative analysis of astaxanthin in Phaffia rhodozyma cells.

[Raman tweezers-based analysis of carotenoid synthesis in Rhodotorula glutinis].

Carotenoid synthesis in Rhodotorula glutinis was investigated with Raman tweezers in order to find the effect of nitrogen and carbon resource on carotenoid yield. The cells in fermentation terminus were harvested, and then divided into two parts, one for UV analysis, the other for Raman tweezers detection. Original spectra were preprocessed by carrying out background elimination and baseline correction, and the averaged spectra of cells cultivated in different fermentation medium were analyzed qualitatively. The results showed that the Raman intensity of carotenoid were obviously different. There was a high correlation between UV results and Raman peak height data, the correlation coefficients of fitted parameters were 0.907 8 and 0.912 1, respectively. Quantitative analysis of 1 508 cm(-1) peak height indicated that the appropriate nitrogen and carbon resources for the growth of Rhodotorula glutinis cells and synthesis of carotenoid were yeast extract + tryptone, and glucose, respectively. The above results suggest that Raman tweezers can provide information about carotenoids in Rhodotorula glutinis cells and serve as an effective tool for real time measurement of carotenoid synthesis and optimization of fermentation medium.

[Identification of Cortex Phellodendri by Fourier-transform infrared spectroscopy and principal component analysis].

Fourier transform infrared spectrometer was used to collect infrared spectra of Cortex Phellodendri from six different regions. Original spectra were preprocessed by carrying out appropriate baseline correction and five-points smoothing, and the averaged spectra of Cortex Phellodendri from the six origins were analyzed. As a result, the averaged spectra looked quite similar. The normalized spectra were selected to construct principal component analysis model in the range of fingerprint region 1800 - 500 cm(-1), and according to the model, the first three principal components accounted for 98% of the variance information in the fingerprint region, and each sample was able to form distinct cluster in the principal component space, then the identification of Cortex Phellodendri from the six regions was basically achieved; besides, to some extent, the sparse density of the samples distribution reflected the genetic relationship. The loading factors of the model were analyzed, and the results indicated that the differences between Cortex Phellodendri samples mostly depended on the contents of protein, carbohydrates, lipids, alkaloids, sterols, obaculactone, oba-cunone, and obacunonlc acid. On the whole, combined with principal component analysis, FTIR provides an effective way to evaluate the herbal Cortex Phellodendri rapidly and nondestructively, which also reflects the content difference of material composition.

[Using Raman spectroscopy to analyze apoptosis of gastric cancer cells induced by cisplatin].

Apoptosis of gastric cancer cells induced by cisplatin was investigated using laser Raman spectroscopy. Gastric cancer cells (SGC7901) were treated with 10 microg x mL(-1) cisplatin for 24, 48 and 72 hours, then were divided into two parts, one for fluorescence staining, the other for collection of Raman spectra by means of scanning. The acquired spectra were then preprocessed by background elimination, smoothing, normalization, baseline correction, and peak fitting. Fluorescence staining result showed that the nucleuses from untreated group were uniformly stained, while those from the group treated for 72 hours were densely stained and broken. The spectra results revealed that the intensity of peaks associated with nucleic acid and protein decreased after the cells were incubated with cisplatin for 24, 48 and 72 hours. The intensity of peaks at 783, 1002 and 1343 cm(-1) respectively fell to 52, 64 and 76 percent of the original value after 72 h of treatment, which indicated that cisplatin could induce apoptosis of gastric cancer cells and reduce the amount of nucleic acid and protein in the cells. The above results suggest that Raman spectra can provide abundant information about the changes in materials in cells and serve as an effective method for real time measurement of apoptosis.

Poly(3-hydroxybutyrate) anabolism in Cupriavidus necator cultivated at various carbon-to-nitrogen ratios: insights from single-cell Raman spectroscopy.

Cupriavidus necator accumulates large amounts of poly(3-hydroxybutyrate) (PHB), a biodegradable substitute for petroleum-based plastics, under certain nutrient conditions. Conventional solvent-extraction-based methods for PHB quantification only obtain average information from cell populations and, thus, mask the heterogeneity among individual cells. Laser tweezers Raman spectroscopy (LTRS) was used to monitor dynamic changes in the contents of PHB, nucleic acids, and proteins in

Monitoring and rapid quantification of total carotenoids in Rhodotorula glutinis cells using laser tweezers Raman spectroscopy.

Rhodotorula glutinis is known to accumulate large amounts of carotenoids under certain culture conditions, which have very important industrial applications. So far, the molecular mechanism of regulating carotenogenesis is still not well understood. To better understand the carotenogenesis process, it requires methods that can detect carotenogenesis rapidly and reliably in single live cells. In this paper, a method based on laser tweezers Raman spectroscopy (LTRS) was developed to directly detect carotenoids, as well as other important biological molecules in single live R. glutinis cells. The data showed that the accumulation of carotenoids and lipids occurred mainly in the late exponential and stationary phases when the cell growth was inhibited by nutrient limitation. Meanwhile, the carotenoid concentration changed together with the concentration of nucleic acids, which increased in the first phase and decreased in the last phase of the culture. These data demonstrate that LTRS is a rapid, convenient, and reliable method to study the carotenogenesis process in vivo.