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Chinese cabbage (Brassica rapa ssp. pekinensis) is a globally cultivated and consumed leafy vegetable due to its abundant plant secondary metabolites and antioxidant compounds, including flavonoids, ascorbic acids, glucosinolates, and vitamins, which have been reported to confer health-promoting effects. Glucosinolates components in leaves of Chinese cabbage plantlets under different concentrations of sodium selenite (0, 30, and 50 μmol/L) were analyzed. Seven glucosinolates were identified and quantified using UHPLC-QTOF-MS. Finally, treatments with 30 and 50 μmol/L Na2SeO3 solution significantly increased the levels of total selenium content as well as total phenols, flavonoids, anthocyanins, and DPPH free radical scavenging ability in Chinese cabbage seedlings. Our results revealed that 30 μmol/L Na2SeO3 effectively enhanced aliphatic glucosinolate levels and total glucosinolate content while causing a significant reduction in indole glucosinolates. Furthermore, downregulation was observed for BrCYP79F1, BrBCAT4, and BrMAM1 genes associated with aliphatic glucosinolate synthesis. Conversely, BrMYB28 and BrCYP83A1 genes exhibited significant upregulation. Thus, the positive influence of Na2SeO3 on glucosinolate biosynthesis in Chinese cabbage can be attributed to the upregulation of key genes related to this process. [ABSTRACT FROM AUTHOR]

【Objective】Lithocarols are a novel class of polyisoprenyl diphenylketone compounds, which have a good antitumor activity. The lithocarols biosynthesis gene litI was cloned, expressed and purified, the promoter of the gene litI was functionally identified, which will lay a molecular foundation for the biosynthesis and transcriptional regulation of lithocarols.【Method】The biosynthetic gene litI was cloned and expressed in Escherichia coli, and the expressed protein LitI was preliminarily purified by nickel affinity chromatography column. The properties and structure of the protein were analyzed by bioinformatics method. The litI gene promoter fragment was amplified, the luciferase expression system was constructed to analyze the transcriptional activity of the promoter, and its functional components were predicted by the PlantCARE promoter analysis website.【Result】LitI protein is a hydrophilic protein, which has a relative molecular weight of 51 kD and a secondary structure including 51.32% α-helix, 8.99% extended chain, 3.95% β-angle, and 35.75% irregular curling. The gene litI promoter shows strong transcription activity, and it could initiate the transcription of ampicillin resistance gene in E. coli, and litI promoter contained TATA box and CAAT box.【Conclusion】LitI protein is obtained by heterologous expression, its properties and structure are analyzed, and the promoter fragment of litI gene with strong transcription activity is identified. [ABSTRACT FROM AUTHOR]

Chemical study of the nematicidal biocontrol fungus Pochonia chlamydosporia PC-170 led to discovery of six resorcylic acid lactones (RALs), including three nematicidal glycosylated RALs, monocillin VI glycoside (1), colletogloeolactone A (2) and monocillin II glycoside (3), and three antibacterial non-glycosylated RALs, monocillin VI (4), monocillin IV (5) and monocillin II (6). The planar structure of the new compound monocillin VI glycoside (1) was elucidated using HRESIMS and NMR data, and its monosaccharide configuration was further determined through sugar hydrolysis experiment and GC--MS analysis method. Furthermore, their two biosynthetic-related PKS genes, pchE and pchI, were identified through the gene knockout experiment. The glycosylated RALs 1--3 exhibited nematicidal activity against Meloidogyne incognita, with LC50 values of 94, 152 and 64 μg/mL, respectively, and thus had great potential in the development of new nematicidal natural products to control M. incognita in the future. [ABSTRACT FROM AUTHOR]

Functional cosmetics industries using skin microbiome screening and beneficial materials isolated from key microorganisms are receiving increasing attention. Since Epidermidibacterium keratini EPI-7T was first discovered in human skin, previous studies have confirmed that it can produce a new pyrimidine compound, 1,1′-biuracil, having anti-aging effects on human skin. Therefore, we conducted genomic analyses to judge the use value of E. keratini EPI-7T and provide up-to-date information. Whole-genome sequencing analysis of E. keratini EPI-7T was performed to generate new complete genome and annotation information. E. keratini EPI-7T genome was subjected to comparative genomic analysis with a group of closely-related strains and skin flora strains through bioinformatic analysis. Furthermore, based on annotation information, we explored metabolic pathways for valuable substances that can be used in functional cosmetics. In this study, the whole-genome sequencing (WGS) and annotation results of E. keratini EPI-7T were improved, and through comparative analysis, it was confirmed that the E. keratini EPI-7T has more metabolite-related genes than comparison strains. In addition, we annotated the vital genes for biosynthesis of 20 amino acids, orotic acid, riboflavin (B2) and chorismate. In particular, we were able to prospect that orotic acid could accumulate inside E. keratini EPI-7T under uracil-enriched conditions. Therefore, through a genomics approach, this study aims to provide genetic information for the hidden potential of E. keratini EPI-7T and the strain development and biotechnology utilization to be conducted in further studies. [ABSTRACT FROM AUTHOR]

Functional cosmetics industries using skin microbiome screening and beneficial materials isolated from key microorganisms are receiving increasing attention. Since Epidermidibacterium keratini EPI-7T was first discovered in human skin, previous studies have confirmed that it can produce a new pyrimidine compound, 1,1′-biuracil, having anti-aging effects on human skin. Therefore, we conducted genomic analyses to judge the use value of E. keratini EPI-7T and provide up-to-date information. Whole-genome sequencing analysis of E. keratini EPI-7T was performed to generate new complete genome and annotation information. E. keratini EPI-7T genome was subjected to comparative genomic analysis with a group of closely-related strains and skin flora strains through bioinformatic analysis. Furthermore, based on annotation information, we explored metabolic pathways for valuable substances that can be used in functional cosmetics. In this study, the whole-genome sequencing (WGS) and annotation results of E. keratini EPI-7T were improved, and through comparative analysis, it was confirmed that the E. keratini EPI-7T has more metabolite-related genes than comparison strains. In addition, we annotated the vital genes for biosynthesis of 20 amino acids, orotic acid, riboflavin (B2) and chorismate. In particular, we were able to prospect that orotic acid could accumulate inside E. keratini EPI-7T under uracil-enriched conditions. Therefore, through a genomics approach, this study aims to provide genetic information for the hidden potential of E. keratini EPI-7T and the strain development and biotechnology utilization to be conducted in further studies.

Chemical study of the nematicidal biocontrol fungus Pochonia chlamydosporia PC-170 led to discovery of six resorcylic acid lactones (RALs), including three nematicidal glycosylated RALs, monocillin VI glycoside (1) , colletogloeolactone A (2) and monocillin II glycoside (3) , and three antibacterial non-glycosylated RALs, monocillin VI (4) , monocillin IV (5) and monocillin II (6) . The planar structure of the new compound monocillin VI glycoside (1) was elucidated using HRESIMS and NMR data, and its monosaccharide configuration was further determined through sugar hydrolysis experiment and GC-MS analysis method. Furthermore, their two biosynthetic-related PKS genes, pchE and pchI , were identified through the gene knockout experiment. The glycosylated RALs 1-3 exhibited nematicidal activity against Meloidogyne incognita , with LC 50 values of 94, 152 and 64  μ g/mL, respectively, and thus had great potential in the development of new nematicidal natural products to control M. incognita in the future., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Li, Luo, Zhang, Khan, Ling, Zhao, Yang, Mao, Xie, Zhou and Li.)

Streptomyces sp. N11-34 is a producer of bicyclic peptides named nyuzenamides A and B. We elucidated its taxonomic position and surveyed its nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters by whole genome analysis. Streptomyces sp. N11-34 showed 16S rRNA gene sequence similarities of 99.9% and 99.8% to Streptomyces hygroscopicus NBRC 13472T and Streptomyces demainii NRRL B-1478T, respectively. Although these members formed a clade in a phylogenetic tree based on 16S rRNA gene sequences, the clade split into two closely related subclades in multilocus sequence analysis (MLSA). One included Streptomyces sp. N11-34, S. demainii NRRL B-1478T, S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867 and the other comprised S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859. These phylogenetic relationships were supported by phylogenomic analysis. Although Streptomyces sp. N11-34 was classified to S. hygroscopicus at the species level based on MLSA evolutionary distances and DNA–DNA relatedness, these distances and relatedness of members between the two subclades were comparatively far (0.004–0.006) and low (75.4–76.4%), respectively. Streptomyces sp. N11-34 possessed six NRPS, seven PKS and four hybrid PKS/NRPS gene clusters in the genome. Among the seventeen, ten were identified to be biosynthetic gene clusters (BGCs) of nyuzenamide, echoside, coelichelin, geldanamycin, mediomycin, nigericin, azalomycin, spore pigment, alchivemycin and totopotensamide, whereas the remaining seven were orphan in our bioinformatic analysis. All seventeen are conserved in S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867. In contrast, S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859 lacked the BGCs of alchivemycin, totopotensamide, a nonribosomal peptide and a hybrid polyketide/nonribosomal peptide compound. This difference was in a good accordance with the abovementioned phylogenetic relationship. Based on phenotypic differences in addition to phylogenetic relationship, DNA–DNA relatedness and BGCs, strains of S. hygroscopicus should be reclassified to two subspecies: S. hygroscopicus subsp. hygroscopicus and a new subspecies, for which we proposed S. hygroscopicus subsp. sporocinereus subsp. nov. The type strain is NBRC 100766T (=ATCC 43692T = DSM 41460T = INMI 32T = JCM 9093T = NRRL B-16376T = VKM Ac-312T). S. demainii was classified in this subspecies.

Jiangxienone produced by Cordyceps jiangxiensis exhibits significant cytotoxicity and good selectivity against various human cancer cells, especially gastric cancer cells. In this work, the effect of nitrogen deficiency on the accumulation of jiangxienone and the transcription levels of jiangxienone biosynthesis genes was studied in submerged fermentation of C. jiangxiensis. Results showed that accumulation of jiangxienone was improved under nitrogen deficiency condition. A maximal jiangxienone content of 3.2 µg/g cell dry weight was reached at 5 mM glutamine, and it was about 8.9-fold higher than that obtained at 60 mM glutamine (control). The transcription levels of the biosynthetic pathway genes hmgr and sqs and the nitrogen regulatory gene areA were upregulated by 7-, 14-, and 28-fold, respectively, in culture with 5 mM glutamine compared to the control. It was hypothesized that the jiangxienone biosynthesis may involve the mevalonate pathway in C. jiangxiensis. Taken together, our study indicated that nitrogen deficiency is an efficient strategy for enhancing jiangxienone accumulation in submerged fermentation of C. jiangxiensis, which is useful for further understanding the regulation of jiangxienone biosynthesis. [ABSTRACT FROM AUTHOR]

Endophytic actinomycetes are one of the primary groups that share symbiotic relationships with medicinal plants and are key reservoir of biologically active compounds. In this study, six selective medicinal plants were targeted for the first time for endophytic actinomycetes isolation from Gibbon Wild Life Sanctuary, Assam, India, during winter and summer and 76 isolates were obtained. The isolates were found to be prevalent in roots followed by stem and leaves. 16S rRNA gene sequence analysis revealed 16 genera, including rare genera, Verrucosispora, Isoptericola and Kytococcus, which have never been previously reported as endophytic. The genus Streptomyces (66%) was dominant in both seasons. Shannon's diversity index showed that Azadirachta indica (1.49), Rauwolfia serpentina (1.43) and Emblica officinalis (1.24) were relatively good habitat for endophytic actinomycetes. Antimicrobial strains showed prevalence of polyketide synthase (PKS) type-II (85%) followed by PKS type-I (14%) encoded in the genomes. Expression studies showed 12-fold upregulation of PKSII gene in seventh day of incubation for Streptomyces antibioticus (EAAG90). Our results emphasize that the actinomycetes assemblages within plant tissue exhibited biosynthetic systems encoding for important biologically active compounds. [ABSTRACT FROM AUTHOR]

Streptomyces sp. TP-A0598, isolated from seawater, produces lydicamycin, structurally unique type I polyketide bearing two nitrogen-containing five-membered rings, and four congeners TPU-0037-A, -B, -C, and -D. We herein report the 8 Mb draft genome sequence of this strain, together with classification and features of the organism and generation, annotation and analysis of the genome sequence. The genome encodes 7,240 putative ORFs, of which 4,450 ORFs were assigned with COG categories. Also, 66 tRNA genes and one rRNA operon were identified. The genome contains eight gene clusters involved in the production of polyketides and nonribosomal peptides. Among them, a PKS/NRPS gene cluster was assigned to be responsible for lydicamycin biosynthesis and a plausible biosynthetic pathway was proposed on the basis of gene function prediction. This genome sequence data will facilitate to probe the potential of secondary metabolism in marine-derived Streptomyces. [ABSTRACT FROM AUTHOR]

The article presents a study on the significance of amino glycoside of biosynthetic genes exploration in deep-sea environment. It says that 2-deoxy-scyllo-inosose (DOI) synthase is engaged in aminoglycoside biosynthesis and was demonstrated in genetic engineering. It states that environmental DNA is an effective source of novel genes due to its undiscovered domain which was cloned for aminoglycosides biosythesis. Furthermore, low diversity of genes was obtained from deep-sea environment.

Streptomyces sp. N11-34 is a producer of bicyclic peptides named nyuzenamides A and B. We elucidated its taxonomic position and surveyed its nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters by whole genome analysis. Streptomyces sp. N11-34 showed 16S rRNA gene sequence similarities of 99.9% and 99.8% to Streptomyces hygroscopicus NBRC 13472T and Streptomyces demainii NRRL B-1478T, respectively. Although these members formed a clade in a phylogenetic tree based on 16S rRNA gene sequences, the clade split into two closely related subclades in multilocus sequence analysis (MLSA). One included Streptomyces sp. N11-34, S. demainii NRRL B-1478T, S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867 and the other comprised S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859. These phylogenetic relationships were supported by phylogenomic analysis. Although Streptomyces sp. N11-34 was classified to S. hygroscopicus at the species level based on MLSA evolutionary distances and DNA–DNA relatedness, these distances and relatedness of members between the two subclades were comparatively far (0.004–0.006) and low (75.4–76.4%), respectively. Streptomyces sp. N11-34 possessed six NRPS, seven PKS and four hybrid PKS/NRPS gene clusters in the genome. Among the seventeen, ten were identified to be biosynthetic gene clusters (BGCs) of nyuzenamide, echoside, coelichelin, geldanamycin, mediomycin, nigericin, azalomycin, spore pigment, alchivemycin and totopotensamide, whereas the remaining seven were orphan in our bioinformatic analysis. All seventeen are conserved in S. hygroscopicus NBRC 100766, S. hygroscopicus NBRC 16556 and S. hygroscopicus TP-A0867. In contrast, S. hygroscopicus NBRC 13472T and S. hygroscopicus NBRC 12859 lacked the BGCs of alchivemycin, totopotensamide, a nonribosomal peptide and a hybrid polyketide/nonribosomal peptide compound. This difference was in a good accordance with the abovementioned phylogenetic relationship. Based on phenotypic differences in addition to phylogenetic relationship, DNA–DNA relatedness and BGCs, strains of S. hygroscopicus should be reclassified to two subspecies: S. hygroscopicus subsp. hygroscopicus and a new subspecies, for which we proposed S. hygroscopicus subsp. sporocinereus subsp. nov. The type strain is NBRC 100766T (=ATCC 43692T = DSM 41460T = INMI 32T = JCM 9093T = NRRL B-16376T = VKM Ac-312T). S. demainii was classified in this subspecies. [ABSTRACT FROM AUTHOR]

The article reports on the organization of the biosynthetic gene cluster for the polyketide antitumor macrolide, pladienolide, in Streptomyces plantensis Mer-11107. It states that pladienolides are novel 12-membered macrolides produced by Streptomyces plantensis Mer-11107 and show strong antitumor activity which can be a lead in the search for novel antitumor agents.

The article presents a study on the diversity and identification of putative aminotransferase genes involved in biosynthesis of aminoglycoside antibiotics from deep sea environmental DNA using nested polymerase chain reaction (PCR). The study shows the similarity of almost half of the deep-sea sequence with aminoglycoside-producers genes while others are deep-sea specific genes. Further, temperature-gradient gel electrophoresis (TGGE) is determined as an effective tool in DNA fragment analysis.

The article discusses the results of a study identifying novel aminoglycoside-producing non-actinomycete from soil. The industrial potential of the 2-Deoxy-scyllo-inosose synthase in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics is explored. The enzyme is industrially useful because of its ability to convert sugar into 6-membered carbocyle.

Examines the cloning of aminoglycoside-biosynthetic genes from soil DNA for accumulation of genetic information. Identification of aminotransferase genes; Phylogenetic analysis of the genes; Occurrence of horizontal gene transfer in the soil; Biosynthesis of aminoglycoside antibiotics.

Examines the construction of a bacterial artificial chromosome library to isolate the biosynthetic gene cluster for the polyketide/peptide hybrid-type antibiotic cystothiazole A from the myxobacerium Cystobacter fuscus. Cloning of the gene; DNA sequences; Genes responsible for the final methyl ester formation in the cystothiazole A biosynthesis.

j.r. nair, g. narasimman and v. sekar. 2004. The study seeks to shed light on the aminopolyol, broad-spectrum antibiotic zwittermicin A gene cluster of Bacillus thuringiensis subsp. kurstaki HD1 and to identify any new uncharacterized genes with an eventual goal to establish a better understanding of the resistance gene cluster. We screened 51 serovars of B. thuringiensis by PCR and identified 12 zmaR-positive strains. The zmaR-positive B. thuringiensis subsp. kurstaki HD1 strain displayed inhibition zones against indicator fungal strain Phytophthora meadii and bacterial strain Erwinia herbicola as well as against Rhizopus sp., Xanthomonas campestris and B. thuringiensis subsp. finitimus. The zmaR gene cluster of strain HD1 was partially cloned using a lambda library and was extensively characterized based on the information available from a study performed on a similar group of genes in Bacillus cereus. Three of the five genes in the zwittermicin gene cluster, including the zmaR gene, had counterparts in B. cereus, and the other two were new members of the B. thuringiensis zmaR gene cluster. The two new genes were extensively analysed and the data is presented. Understanding antifungal activity of B. thuringiensis may help us to design suitable Cry toxin delivery agents with antifungal activity as well as enhanced insecticidal activity. [ABSTRACT FROM AUTHOR]

The CRISPR/Cas9 technology allows fast and marker-less genome engineering that can be employed to study secondary metabolism in actinobacteria. Here, we report a standard experimental protocol for the deletion of a biosynthetic gene in a Streptomyces species, using the vector pCRISPomyces-2 developed by Huimin Zhao and collaborators. We also describe how carrying out metabolite analysis can reveal the putative biosynthetic function of the inactivated gene., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)