Ying-Ying Wu

Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L.

A Gram-stain-positive, aerobic and yellow actinobacterial strain, designated SYP-A7303T, was isolated from the root of Ginkgo biloba L. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SYP-A7303T belongs to the genus Nocardioides. The 16S rRNA gene sequence of strain SYP-A7303T showed highest similarity to Nocardioides marinus CL-DD14T (u2009=u2009JCM 15615T) (98.3u200a%) and Nocardioides aquiterrae GW-9T (u2009=u2009JCM 11813T) (97.1u200a%), and less than 96.9u200a% to the type strains of other species of the genus Nocardioides. Strain SYP-A7303T grew optimally at 28u2009°C, pHu20097.0 and in the absence of NaCl. It contained ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, with mannose, ribose, rhamnose, glucose and galactose as whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown lipid. The menaquinone was MK-8(H4) and the predominant cellular fatty acids were iso-C16u200a:u200a0, C18u200a:u200a1ω9c and C17u200a:u200a1ω8c. The DNA G+C content was 72u200amol%. Mean DNA-DNA relatedness values between strain SYP-A7303T and the closely related strains N. marinus JCM 15615T and N. aquiterrae JCM 11813T were 62.5u2009±u20092.4 and 56.5u2009±u20093.5u200a%, respectively. Based on the morphological, physiological, biochemical and chemotaxonomic characteristics presented in this study, strain SYP-A7303T represents a novel species of the genus Nocardioides, for which the name Nocardioides ginkgobilobae sp. nov. is proposed. The type strain is SYP-A7303T (u2009=u2009DSM 100492Tu2009=u2009KCTC 39594T).

Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere soil.

A Gram-staining-negative, yellow-pigmented strain, designated SYP-B804T, was isolated from the rhizosphere of Panax notoginseng. The strain was rod-shaped with a single polar flagellum. The optimum temperature and pH required for growth of the strain were 28-32u2009°C and pHu20097-8, respectively. 16S rRNA gene sequence analysis indicated that strain SYP-B804T showed highest 16S rRNA gene sequence similarity with Luteimonas mephitis DSM 12574T (98.0u2009%). However, the DNA-DNA relatedness value between them (38.1u2009±u20090.6u2009%) was less than the threshold value for the delineation of genomic species. Ubiquinone-8 (Q-8) was the predominant quinone. The major fatty acids were iso-C15u2009:u20090 and iso-C17u2009:u20091ω9c. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 71u2009%. On the basis of phenotypic, chemotaxonomic and molecular characteristics, strain SYP-B804T merits recognition as a representative of a novel species of the genus Luteimonas, for which the name Luteimonas notoginsengisoli sp. nov. is proposed, with SYP-B804T (u2009=u2009KCTC 42211Tu2009=u2009JCM 30329T) as the type strain.

Indole diterpenoids from the endophytic fungus Drechmeria sp. as natural antimicrobial agents

A fungal strain, Drechmeria sp., was isolated from the root of Panax notoginseng. Totally, seven new indole diterpenoids, drechmerins A-G (1-7), were isolated from the fermentation broth of Drechmeria sp. together with four known analogues (8-11). Their structures were determined on the basis of 1D and 2D NMR and electronic circular dichroism (ECD) spectroscopic analyses as well as theoretical calculations. All the isolated compounds were evaluated for their antimicrobial activities against Candida albicans, Staphylococcus aureus, Bacillus cereus, B.xa0subtillis, Pseudomonas aeruginosa, and Klebsiella pneumonia, respectively. Drechmerin B (2) displayed antimicrobial activity against C.xa0albicans with an MIC value of 12.5u202fμg/mL. Molecular docking was used to investigate interactions of peptide deformylase with compounds 1-3, 5-7, 9, and 10.

Drechmerin H, a novel 1(2), 2(18)-di seco indole diterpenoid from the fungus Drechmeria sp. as a natural agonist of human pregnane X receptor

A novel 1(2), 2(18)-diseco indole diterpenoid, drechmerin H (1), was isolated from the fermentation broth of Drechmeria sp. together with a new indole diterpenoid, 2-epi terpendole A (3), and a known analogue, terpendole A (2). Their structures were determined by HRESIMS, 1D and 2D NMR, ECD, and X-ray single crystal diffraction analyses as well as quantum chemical calculation. The abosulte configuration of terpendole A (2) was determined for the first time. Compound 1 displayed the significant agonistic effect on pregnane X receptor (PXR) with EC50 value of 134.91u202f±u202f2.01u202fnM, and its interaction with PXR was investigated by molecular docking. Meantime, a plausible biosynthetic pathway for compounds 1-3 is also discussed in the present work.

New and bioactive natural products from an endophyte of Panax notoginseng

Five new derivatives of macrolide antibiotic Brefeldin A (BFA, 6), named as Brefeldin E1–E5 (1–5), along with Brefeldin A 7-O-acetate (7), mycotoxins (8–9) and mangrovamides A (10) were produced by an endophytic fungus, Penicillium sp., which was isolated from the healthy root of Panax notoginseng. The structures of 1–5 were established on the basis of their spectroscopic data, while the absolute configurations were assigned using a modified Moshers method. All compounds were evaluated for their cytotoxic, antiviral and antimicrobial activities. Compounds 1–5 and 8–10 displayed low or moderate cytotoxicity against a panel of cancer cell lines. Compounds 1, 2, 4, 5, and 8–10 showed moderate antimicrobial activity. Compound 6 showed strong anticancer and antiviral properties. Additionally, it demonstrated broad-spectrum activity against human pathogenic bacteria and fungal pathogens that can cause root-rot disease in Panax notoginseng, including Escherichia coli, Staphylococcus aureus, Bacillus cereus, Klebsiella pneumonia, Candida albicans, Fusarium solani, Cylindrocarpon didynum and Alternaria panax. Compound 7, which could be mediated by 6 through the acetylation at the 7-hydroxyl, showed similar bioactivities to compound 6. Further studies of the cellular mechanism of compounds 6 and 7 showed that they arrested HepG2 cells at the S phase. Due to the similarities in the basic carbon skeleton and the chemical construction correlations between compounds 1–7, the plausible biosynthetic pathway of the BFA series of compounds has been proposed and their structure–activity relationships are also discussed.

Arthrobacter ginkgonis sp. nov., an actinomycete isolated from rhizosphere of Ginkgo biloba L.

A Gram-stain-positive, aerobic actinobacterial strain (designated SYP-A7299T), which displayed a rod-coccus growth lifecycle, was isolated from the rhizosphere of Ginkgo biloba L. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SYP-A7299T belongs to the genus Arthrobacter and is most closely related to Arthrobacter halodurans JSM 078085T (97.4u200a% 16S rRNA gene sequence similarity). The DNA-DNA relatedness value between strain SYP-A7299T and A. halodurans JSM 078085T was 37u200a% ±2.9. The cell-wall peptidoglycan was A4α, and glucose and galactose were whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids and an unknown polar lipid. The major menaquinone were MK-8(H2) (72u200a%) and MK-9(H2) (28u200a%), and the predominant cellular fatty acids were anteiso-C15u2009:u20090, iso-C15u2009:u20090 and anteiso-C17u2009:u20090. The DNA G+C content was 68.9u2009mol%. Based on the morphological, physiological, biochemical and chemotaxonomic characters presented in this study, strain SYP-A7299T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter ginkgonis sp. nov. is proposed. The type strain is SYP-A7299T (=DSM 100491T=KCTC 39u200a592T).

An indole diterpenoid isolated from the fungus Drechmeria sp. and its antimicrobial activity

Abstract One new indole diterpenoid, drechmerin I (1), was isolated from the fermentation broth of Drechmeria sp. isolated from the root of Panax notoginseng. Its structure was elucidated based on 1 D and 2 D nuclear magnetic resonance (NMR), high resolution electrospray ionization mass spectrum (HRESIMS), and electronic circular dichroism (ECD) spectroscopic analyses as well as TD DFT calculations of ECD spectra. Drechmerin I (1) was assayed for its antimicrobial activity against Candida albicans, Staphylococcus aureus, Bacillus cereus, B. subtillis, Pseudomonas aeruginosa, and Klebsiella pneumonia, respectively. Drechmerin I (1) showed antimicrobial activities against B. subtillis with an MIC value of 200 μg/mL. The interaction of S. aureus peptide deformylase with drechmerin I (1) was investigated by molecular docking. Graphical Abstract

An endophytic Fungi of Ginkgo biloba L. produces antimicrobial metabolites as potential inhibitors of FtsZ of Staphylococcus aureus

A total of 58 fungal isolates, belonging to 24 genera, were obtained from the leaves, stems and roots of Ginkgo biloba L.. Among them, one endophytic fungal strain, Penicillium cataractum SYPF 7131, displayed the strongest antibacterial activity. Four new compounds (1-4) were isolated from the strain fermentation broth together with four known compounds (5-8). These structures were determined on the basis of 1D and 2D NMR and [Rh2(OCOCF3)4]-induced electronic circular dichroism (ECD) spectroscopic analyses. All the isolated compounds were screened for their in vitro antimicrobial activities. Compound 3 and 4 showed moderate inhibitory activity against Staphylococcus aureus. Compound 7 exhibited significant inhibitory activity against S. aureus with MIC value of 10u202fμg/mL. Further, the in silico molecular docking studies of the active compounds was used to explore the binding interactions with the active site of filamentous temperature-sensitive protein Z (FtsZ) from Staphylococcus aureus. The docking results revealed that compounds 3, 4 and 7 showed high binding energies, strong H-bond interactions and hydrophobic interactions with FtsZ from S. aureus validating the observed antimicrobial activity. Based on antimicrobial activities and docking studies, compounds 3, 4 and 7 were identified as promising antimicrobial lead molecules.

New antimicrobial compounds produced by endophytic Penicillium janthinellum isolated from Panax notoginseng as potential inhibitors of FtsZ

A total of 180 fungal isolates, belonging to 20 genera and 47 species, were obtained from the roots, stems and leaves of Panax notoginseng. One isolate, the endophytic fungus Penicillium janthinellum SYPF 7899, displayed the strongest antibacterial activity and was studied for its production of secondary metabolites. In total, three new compounds, including rotational isomers 1a, 1b and 2 were isolated from the solid cultures of P. janthinellum, as well as eight known compounds (3-10). These structures were determined on the basis of 1D, 2D NMR and electronic circular dichroism (ECD) spectroscopic analyses as well as theoretical calculations. Compound 1 exhibited significant inhibitory activities against Bacillus subtilis and Staphylococcus aureus with MIC values of 15 and 18u202fμg/ml, respectively. The other compounds showed moderate or weak activities. In addition, morphological observation showed the rod-shaped cells of B. subtilis growing into long filaments, which reached 1.5- to 2-fold of the length of the original cells after treatment with compound 1. The coccoid cells of S. aureus exhibited a similar response and swelled to a 2-fold volume after treatment with compound 1. In silico molecular docking was explored to study the binding interactions between the compounds and the active sites of filamentous temperature-sensitive protein Z (FtsZ) from B. subtilis and S. aureus. Compound 1a, 1b and 2 showed high binding energies, strong H-bond interactions and hydrophobic interactions with FtsZ. Based on the antimicrobial activities, cellular phenotype observation and docking studies, compound 1 is considered to be a promising antimicrobial inhibitor of FtsZ.

Bacillus notoginsengisoli sp. nov., a novel bacterium isolated from the rhizosphere of Panax notoginseng

A Gram-stain-positive, rod-shaped, motile bacterium designated as SYP-B691T was isolated from rhizospheric soil of Panax notoginseng. Phylogenetic analysis indicated that SYP-B691T clearly represented a member of the genus Bacillus and showed 16S rRNA gene similarity lower than 97.0u200a% with the type strains of species of the genus Bacillus, which indicates that it should be considered as a candidate novel species within this genus. The optimum growth of the strain was found to occur at 37u2009°C and pH 7.0-9.0. The genomic DNA G+C content was determined to be 45.2u2009mol%. It contained meso-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid. MK-7 was the only menaquinone identified. The major cellular fatty acids of SYP-B691T were identified as iso-C15u200a:u200a0 and anteiso-C15u200a:u200a0. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, SYP-B691T merits recognition as a representative of a novel species of the genus Bacillus, for which the name Bacillus notoginsengisoli sp. nov. is proposed, with SYP-B691T(=DSM 29196T=JCM 30743T) as the type strain.