Purification and structure determination of four bioactive molecules from a newly isolated Streptomyces sp. TN97 strain

Characterization of Streptomyces sp. KB1 and its cultural optimization for bioactive compounds production

Background

Bioactive compounds (BCs) from natural resources have been extensively studied because of their use as models in the development of novel and important medical and biopreservative agents. One important source of BCs is microorganisms, particularly terrestrial bacteria of the order Actinomycetales.

Methods

We characterized Streptomyces sp. KB1 by observing its morphology, physiology, and growth on different media using biochemical tests, optimizing cultural conditions by changing one independent variable at a time.

Results

Streptomyces sp. KB1 (TISTR 2304) is a gram-positive and long filamentous bacteria that forms straight to flexuous (rectiflexibile) chains of globose-shaped and smooth-surfaced spores. It can grow under aerobic condition s only at a temperature range of 25-37 °C and initial pH range of 5-10 in the presence of sodium chloride 4% (w/v). Therefore, it is considered an obligate aerobe, mesophilic, neutralophilic, and moderately halophilic bacteria. The isolate grew well on peptone-yeast extract iron, Luria Bertani (LB), and a half-formula of LB (LB/2), but could not grow on MacConkey agar. It utilized fructose, mannose, glucose, and lactose as its carbon source along with acid production and showed positive reactions to casein hydrolysis, gelatin liquefaction, nitrate reduction, urease, and catalase production. Streptomyces sp. KB1 (TISTR 2304) could produce the maximum number of BCs when 1% of its starter was cultivated in a 1,000 ml baffled flask containing 200 ml of LB/2 broth with its initial pH adjusted to 7 with no supplemental carbon source, nitrogen source, NaCl, or trace element at 30 °C, shaken at 200 rpm in an incubator for 4 days.

Marine Natural Product Antimycin A Suppresses Wheat Blast Disease Caused by Magnaporthe oryzae Triticum

The application of chemical pesticides to protect agricultural crops from pests and diseases is discouraged due to their harmful effects on humans and the environment. Therefore, alternative approaches for crop protection through microbial or microbe-originated pesticides have been gaining momentum. Wheat blast is a destructive fungal disease caused by the Magnaporthe oryzae Triticum (MoT) pathotype, which poses a serious threat to global food security. Screening of secondary metabolites against MoT revealed that antimycin A isolated from a marine Streptomyces sp. had a significant inhibitory effect on mycelial growth in vitro. This study aimed to investigate the inhibitory effects of antimycin A on some critical life stages of MoT and evaluate the efficacy of wheat blast disease control using this natural product. A bioassay indicated that antimycin A suppressed mycelial growth (62.90%), conidiogenesis (100%), germination of conidia (42%), and the formation of appressoria in the germinated conidia (100%) of MoT at a 10 µg/mL concentration. Antimycin A suppressed MoT in a dose-dependent manner with a minimum inhibitory concentration of 0.005 μg/disk. If germinated, antimycin A induced abnormal germ tubes (4.8%) and suppressed the formation of appressoria. Interestingly, the application of antimycin A significantly suppressed wheat blast disease in both the seedling (100%) and heading stages (76.33%) of wheat at a 10 µg/mL concentration, supporting the results from in vitro study. This is the first report on the inhibition of mycelial growth, conidiogenesis, conidia germination, and detrimental morphological alterations in germinated conidia, and the suppression of wheat blast disease caused by a Triticum pathotype of M. Oryzae by antimycin A. Further study is required to unravel the precise mode of action of this promising natural compound for considering it as a biopesticide to combat wheat blast.

Drought Exposed Burkholderia seminalis JRBHU6 Exhibits Antimicrobial Potential Through Pyrazine-1,4-Dione Derivatives Targeting Multiple Bacterial and Fungal Proteins

The present study aimed to explore the antimicrobial potentials of soil bacteria and identify the bioactive compounds and their likely targets through in silico studies. A total 53 bacterial isolates were screened for their antimicrobial potential of which the strain JRBHU6 showing highest antimicrobial activity was identified as Burkholderia seminalis (GenBank accession no. MK500868) based on 16S ribosomal RNA (rRNA) gene sequencing and phylogenetic analysis. B. seminalis JRBHU6 also produced hydrolytic enzymes chitinases and cellulase of significance in accrediting its antimicrobial nature. The bioactive metabolites produced by the isolate were extracted in different organic solvents among which methanolic extract showed best growth-suppressing activities toward multidrug resistant Staphylococcus aureus and fungal strains, viz Fusarium oxysporum, Aspergillus niger, Microsporum gypseum, Trichophyton mentagrophytes, and Trichoderma harzianum. The antimicrobial compounds were purified using silica gel thin layer chromatography and high-performance liquid chromatography (HPLC). On the basis of spectroscopic analysis, the bioactive metabolites were identified as pyrrolo(1,2-a)pyrazine-1,4-dione,hexahydro (PPDH) and pyrrolo(1,2-a)pyrazine-1,4-dione, hexahydro-3(2-methylpropyl) (PPDHMP). In silico molecular docking studies showed the bioactive compounds targeting fungal and bacterial proteins, among which PPDHMP was multitargeting in nature as reported for the first time through this study.

Purification and characterization of seven bioactive compounds from the newly isolated Streptomyces cavourensis TN638 strain via solid-state fermentation

The strain TN638 was isolated from Tunisian soil contaminated with industrial wastewater and selected for its potent antimicrobial activity against the tested Gram positive bacteria: Staphylococcus aureus (S. aureus) ATCC 6538 and Listeria monocytogenes (L. monocytogenes) ATCCC 19117, and Gram negative bacteria: Agrobacterium tumefaciens (A. tumefaciens) ATCC 23308 and Salmonella typhimurium (S. typhimurium) ATCC 14028 and fungi: Candida albicans (C. albicans) ATCC 10231, Rhizoctonia solani (R. solani) ATCC 58938 and Fusarium sp. Solide-state fermentation (SSF) dry crude extract of the TN638 strain presents a strong inhibitory activity notably against the phytopathogenic microorganism A. tumefaciens ATCC 23308 and the two pathogenic bacteria S. aureus ATCC 6538 and L. monocytogenes ATCCC 19117 with a zone of inhibition of 48, 34 and 34 mm respectively. According to the morphological characteristic, the complete 16S rRNA gene nucleotide sequence determination [1492 bp deposited in National Center of Biotechnology Information (NCBI) database under the accession no. LN854629.1; https://www.ncbi.nlm.nih.gov/nuccore/LN854629.1/], and the phylogenetic analysis, we can deduce that our isolate is an actinomycete bacterium belonging to the genus Streptomyces and the most closely related strain was Streptomyces cavourensis (S. cavourensis) NRRL 2740T (99.9%). We propose the assignment of our strain as Streptomyces cavourensis (S. cavourensis) TN638 strain. Work-up and purification of the strain extract using different chromatographic techniques afforded seven bio-compounds namely: Cyclo-(Leu-Pro) (1), Cyclo-(Val-Pro) (2), Cyclo-(Phe-Pro) (3), nonactin (4), monactin (5), dinactin (6) and trinactin (7). The chemical structures of compounds 1-7 were confirmed by nuclear magnetic resonance (NMR) 1D and 2D spectroscopy, mass spectrometry, and comparison with literature data. The three purified diketopiperazine (DKP) derivatives (1-3), demonstrated significant antibacterial activity against A. tumefaciens ATCC 23308 and S. typhimurium ATCC 14028. The four pure macrotetrolides (4-7), exhibited strong inhibitory effect against all tested Gram positive and Gram negative bacteria notably against A. tumefaciens ATCC 23308 and S. typhimurium ATCC 14028 with a minimum inhibitory concentration (MIC) around 8 μg/mL quite similar to that of ampicillin. Thus, we propose the use of the (SSF) active extract of the S. cavourensis TN638 strain as safe biological product to control disease caused by plant pathogen A. tumefaciens. Also, the purified active molecules produced by this strain could be used in pharmaceutical field.

Purification and structural elucidation of three bioactive compounds isolated from Streptomyces coelicoflavus BC 01 and their biological activity

The strain Streptomyces coelicoflavus BC 01 was isolated from mangrove soil and used as inoculum for submerged fermentation. The fermented broth was extracted with ethyl acetate, the crude extract was subjected to silica gel column chromatography and the homogeneity of the isolated fractions was determined by TLC and then subjected to RP-HPLC for their purity. The purification steps led to the isolation of three pure bioactive compounds named as BC 01_C1, BC 01_C2 and BC 01_C3. The chemical structure of these three compounds was established on the basis of their spectroscopic studies like UV, IR, ¹H and ¹³C NMR and GC–MS data by comparison with reference data from literature. The structure of the compound BC 01_C1 was established as 5-amino-2-(6-(2-hydroxyethyl)-3-oxononyl) cyclohex-2-enone. The compound BC 01_C2 was established as8-(aminomethyl)-7-hydroxy-1-(1-hydroxy-4-(hydroxylmethoxy)-2,3-dimethylbutyl)-2-methyl dodecahydro phenanthren-9(1H)-one and the compound BC 01_C3 was established as1-((E)-2-ethylhex-1-en-1-yl)2-((E)-2-ethylidenehexyl)cyclohexane-1,2-dicarboxylate. The MIC values of the three isolated compounds (BC 01_C1, BC 01_C2 and BC 01_C3) were found between 12.5–75 μg/ml for bacteria and 50–125 μg/ml for fungi used in this study. These compounds also possess in vitro antioxidant and anti-inflammatory activities.

Optimization of antifungal production by an alkaliphilic and halotolerant actinomycete, Streptomyces sp. SY-BS5, using response surface methodology

OBJECTIVE

Optimization of medium components and physicochemical parameters for antifungal production by an alkaliphilic and salt-tolerant actinomycete designated Streptomyces sp. SY-BS5; isolated from an arid region in south of Algeria.

MATERIALS AND METHODS

The strain showed broad-spectrum activity against pathogenic and toxinogenic fungi. Identification of the actinomycete strain was realized on the basis of 16S rRNA gene sequencing. Antifungal production was optimized following one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. The most suitable medium for growth and antifungal production was found using one-factor-at-a-time methodology. The individual and interaction effects of three nutritional variables, carbon source (glucose), nitrogen source (yeast extract) and sodium chloride (NaCl) were optimized by Box-Behnken design. Finally, culture conditions for the antifungal production, pH and temperature were studied and determined.

RESULTS

Analysis of the 16S rRNA gene sequence (1454 nucleotides) assigned this strain to Streptomyces genus with 99% similarity with Streptomyces cyaneofuscatus JCM4364(T), the most closely related. The results of the optimization study show that concentrations 3.476g/L of glucose, 3.876g/L of yeast extract and 41.140g/L of NaCl are responsible for the enhancement of antifungal production by Streptomyces sp. SY-BS5. The preferable culture conditions for antifungal production were pH 10, temperature 30°C for 09 days.

CONCLUSION

This study proved that RSM is usual and powerful tool for the optimization of antifungal production from actinomycetes.

Novel 1,5,7-trihydroxy-3-hydroxy methyl anthraquinone isolated from terrestrial Streptomyces sp. (eri-26) with antimicrobial and molecular docking studies

Streptomyces sp. isolate ERI-26 was obtained from the Nilgiris forest soil of Western Ghats, Tamil Nadu, India. Novel anthraquinone compound was isolated from the active fraction 5; it was identified by spectroscopical data using UV, IR, NMR and MASS. The isolated compound 1,5,7-trihydroxy-3-hydroxy methyl anthraquinone was tested against bacteria and fungi at minimum inhibitory concentration level. The compound showed significant antimicrobial activity against bacteria, Staphylococcus aureus at 125 μg/ml, Staphylococcus epidermidis at 62.5 μg/m, Bacillus subtilis at 31.25 μg/ml, fungi; Epidermophyton floccosum at 62.5 μg/ml, Aspergillus niger at 31.25 μg/ml, Aspergiller flavus at 31.25 μg/ml, Trichophyton rubrum at 62.5 μg/ml and Botrytis cinerea at 62.5 μg/ml. The isolated compound was subjected to molecular docking studies for the inhibition of TtgR, topoisomerase IV and AmpC β-lactamase enzymes which are targets for antimicrobials. Docking studies of the compound showed low docking energy indicating its usefulness as antimicrobial agent. 1,5,7-Trihydroxy-3-hydroxy methyl anthraquinone is new, and its antimicrobial and molecular docking properties are reported for the first time.

Purification of protein AP-toxin from Arthrinium phaeospermum causing blight in Bambusa pervariabilis × Dendrocalamopisis grandis and its metabolic effects on four bamboo varieties

Bambusa pervariabilis × Dendrocalamopisis grandis blight is caused by a toxin produced by the fungus Arthrinium phaeospermum. In this study, a toxin fraction (P1-2-2) with an estimated molecular mass of 31 kDa was purified from a culture filtrate of this fungus by ammonium sulfate precipitation, Sephadex G-50 gel chromatography, Q Sepharose Fast Flow anion exchange resin, and Sephadex G-75 chromatography. The N-terminal amino acid sequence (i.e., H(2)N-Gln-Val-Arg-Asp-Arg-Leu-Glu-Ser-Thr) determined by Edman degradation showed homology to known serine alkaline proteases. The purified protein was named AP-toxin. Effects of the purified protein toxin on total phenol, flavonoid, total nucleic acid, DNA, RNA, soluble protein, and soluble sugar content, as well as DNase and RNase activities and disease index, were analyzed in different bamboo varieties by the impregnation method. The toxin had a significant effect on each parameter tested. In addition, a significant correlation was observed among the metabolic index, treatment time, bamboo resistance, and disease index. These data suggest that AP-toxin plays an important role in mediating the phytotoxic activities of A. phaeospermum. This study also indicates that metabolic indices could reflect the resistance indices of hybrid bamboo to blight.

Streptomyces lunalinharesii strain 235 shows the potential to inhibit bacteria involved in biocorrosion processes

Four actinomycete strains previously isolated from Brazilian soils were tested for their antimicrobial activity against Bacillus pumilus LF-4 and Desulfovibrio alaskensis NCIMB 13491, bacteria that are well known to be involved in biofilm formation and biocorrosion. Strain 235, belonging to the species Streptomyces lunalinharesii, inhibited the growth of both bacteria. The antimicrobial activity was seen over a wide range of pH, and after treatment with several chemicals and heat but not with proteinase K and trypsin. The antimicrobial substances present in the concentrated supernatant from growth media were partially characterized by SDS-PAGE and extracellular polypeptides were seen. Bands in the size range of 12 to 14.4 kDa caused antimicrobial activity. Transmission electron microscopy of D. alaskensis cells treated with the concentrated supernatant containing the antimicrobial substances revealed the formation of prominent bubbles, the spherical double-layered structures on the cell membrane, and the periplasmic space completely filled with electron-dense material. This is the first report on the production of antimicrobial substances by actinomycetes against bacteria involved in biocorrosion processes, and these findings may be of great relevance as an alternative source of biocides to those currently employed in the petroleum industry.

Taxonomy, purification and chemical characterization of four bioactive compounds from new Streptomyces sp. TN256 strain

A new actinomycete strain designated TN256, producing antimicrobial activity against pathogenic bacteria and fungi, was isolated from a Tunisian Saharan soil. Morphological and chemical studies indicated that strain TN256 belonged to the genus Streptomyces. Analysis of the 16S rDNA sequence of strain TN256 showed a similarity level ranging between 99.79 and 97.8% within Streptomyces microflavus DSM 40331(T) and Streptomyces griseorubiginosus DSM 40469(T) respectively. The comparison of its physiological characteristics showed significant differences with the nearest species. Combined analysis of the 16 S rRNA gene sequences (FN687758), fatty acids profile, and results of physiological and biochemical tests indicated that there were genotypic and phenotypic differentiations of that isolate from other Streptomyces species neighbours. These date strongly suggest that strain TN256 represents a novel species with the type strain Streptomyces TN256 (=CTM50228(T)). Experimental validation by DNA-DNA hybridization would be required for conclusive confirmation. Four active products (1-4) were isolated from the culture broth of Streptomyces TN256 using various separation and purification steps and procedures. 1: N-[2-(1H-indol-3-yl)-2 oxo-ethyl] acetamide 'alkaloid' derivative; 2: di-(2-ethylhexyl) phthalate, a phthalate derivative; 3: 1-Nonadecene and 4: Cyclo (L: -Pro-L: -Tyr) a diketopiperazine 'DKP' derivative. The chemical structure of these four active compounds was established on the basis of spectroscopic studies NMR and by comparing with data from the literature. According to our biological studies, we showed in this work that the pure compounds (1-4) possess antibacterial and antifungal activities.

Nematicidal activity of fervenulin isolated from a nematicidal actinomycete, Streptomyces sp. CMU-MH021, on Meloidogyne incognita

An isolate of the actinomycete, Streptomyces sp. CMU-MH021 produced secondary metabolites that inhibited egg hatch and increased juvenile mortality of the root-knot nematode Meloidogyne incognita in vitro. 16S rDNA gene sequencing showed that the isolate sequence was 99% identical to Streptomyces roseoverticillatus. The culture filtrates form different culture media were tested for nematocidal activity. The maximal activity against M. incognita was obtained by using modified basal (MB) medium. The nematicidal assay-directed fractionation of the culture broth delivered fervenulin (1) and isocoumarin (2). Fervenulin, a low molecular weight compound, shows a broad range of biological activities. However, nematicidal activity of fervenulin was not previously reported. The nematicidal activity of fervenulin (1) was assessed using the broth microdilution technique. The lowest minimum inhibitory concentrations (MICs) of the compound against egg hatch of M. incognita was 30 μg/ml and juvenile mortality of M. incognita increasing was observed at 120 μg/ml. Moreover, at the concentration of 250 μg/ml fervenulin (1) showed killing effect on second-stage nematode juveniles of M. incognita up to 100% after incubation for 96 h. Isocoumarin (2), another bioactive compound produced by Streptomyces sp. CMU-MH021, showed weak nematicidal activity with M. incognita.

Two new compounds from the broth of the marine fungus Penicillium griseofulvum Y19-07

Two new compounds, 4-hydroxyphenethyl methyl succinate (1) and 4-hydroxyphenethyl 2-(4-hydroxyphenyl)acetate (2), were isolated from the EtOAc extract of the broth of the marine fungus Penicillium griseofulvum Y19-07. Five known compounds were also obtained in this study. The structures of the new compounds were elucidated by 1D and 2D NMR spectroscopy and mass spectrometry. All of the isolates were evaluated for their scavenging properties toward the 2,2-diphenyl-1-picrylhydrazyl free radical by spectroscopic assays. Also, in the cytotoxicity assay of the two new compounds against HL-60 and PC-3 prostate cancer cell lines, compound 2 showed potential activity with an IC(50) value of 64.5 microM against human HL-60 cancer cells.

Optimization and production of novel antimicrobial agents from sponge associated marine actinomycetes Nocardiopsis dassonvillei MAD08

The sponge-associated actinomycetes were isolated from the marine sponge Dendrilla nigra, collected from the southwest coast of India. Eleven actinomycetes were isolated depending upon the heterogeneity and stability in subculturing. Among these, Nocardiopsis dassonvillei MAD08 showed 100% activity against the multidrug resistant pathogens tested. The culture conditions of N. dassonvillei MAD08 was optimized under submerged fermentation conditions for enhanced antimicrobial production. The unique feature of MAD08 includes extracellular amylase, cellulase, lipase, and protease production. These enzymes ultimately increase the scope of optimization using broad range of raw materials which might be efficiently utilized. The extraction of the cell free supernatant with ethyl acetate yielded bioactive crude extract that displayed activity against a panel of pathogens tested. Analysis of the active thin layer chromatography fraction by Fourier transform infrared and gas chromatography-mass spectrometry evidenced 11 compounds with antimicrobial activity. The ammonium sulfate precipitation of the culture supernatant at 80% saturation yielded an anticandidal protein of molecular weight 87.12 kDa. This is the first strain that produces both organic solvent and water soluble antimicrobial compounds. The active extract was non-hemolytic and showed surface active property envisaging its probable role in inhibiting the attachment of pathogens to host tissues, thus, blocking host-pathogen interaction at an earlier stage of pathogenesis.

The antifungal activity of the terrestrial Streptomyces US80 strain is induced by heat-killed fungi

Study of the influence of different concentrations of glucose, as carbon source, and magnesium, as chemical additive, on production by the Streptomyces sp. US80 strain of the three antifungal molecules (irumamycin, X-14952 B and 17-hydroxy-venturicidin A) showed that the highest antifungal activity was obtained at 5 g/L and 3.5 mM for glucose and magnesium, respectively. Environmental factors for maximum antifungal activity production are: temperature of growth 30 degrees C, pH 7, incubation time 72 h and agitation rate of 200 rpm. To further enhance the production of the three antifungal compounds, which possess a real potential application in the agriculture domain, and to explore the possibility of obtaining other active molecules from the Streptomyces sp. US80, we investigated the effect of the addition of heat-killed fungi to the culture media. Biochemical, microbiological and spectroscopic studies of the cultures of the Streptomyces sp. US80 strain in absence (control) and in presence of heat-killed fungus cells indicate an increase of 70% in the production of the three antifungal molecules, compared to the control culture.