Genome-Guided Investigation Provides New Insights into Secondary Metabolites of Streptomyces parvulus SX6 from Aegiceras corniculatum.

Whole-genome sequencing and genome mining are recently considered an efficient approach to shine more light on the underlying secondary metabolites of Streptomyces. The present study unearths the biosynthetic potential of endophytic SX6 as a promising source of biologically active substances and plant-derived compounds for the first time. Out of 38 isolates associated with Aegiceras corniculatum (L.) Blanco, Streptomyces parvulus SX6 was highly active against Pseudomonas aeruginosa ATCC® 9027™ and methicillin-resistant Staphylococcus epidermidis (MRSE) ATCC® 35984™. Additionally, S. parvulus SX6 culture extract showed strong cytotoxicity against Hep3B, MCF-7, and A549 cell lines at a concentration of 30 µg/ml, but not in non-cancerous HEK-293 cells. The genome contained 7.69 Mb in size with an average G + C content of 72.8% and consisted of 6,779 protein-coding genes. AntiSMASH analysis resulted in the identification of 29 biosynthetic gene clusters (BGCs) for secondary metabolites. Among them, 4 BGCs showed low similarity (28-67% of genes show similarity) to actinomycin, streptovaricin, and polyoxypeptin gene clusters, possibly attributed to antibacterial and anticancer activities observed. In addition, the complete biosynthetic pathways of plant-derived compounds, including daidzein and genistein were identified using genome mining and HPLC-DAD-MS analysis. These findings portray an exciting avenue for future characterization of promising secondary metabolites from mangrove endophytic S. parvulus.

Two new streptovaricin derivatives from mutants of Streptomyces spectabilis CCTCC M2017417.

Two new ansamycin derivatives, damavaricin H (1) and protostreptovaricin VI (2) were isolated from the Streptomyces spectabilis CCTCC M2017417 derived mutants of ΔstvP5 and ΔstvA2, respectively. The structures of 1 and 2 were established by analysis of the HRESIMS as well as 1D and 2D NMR datasets. The minimum inhibitory concentration (MIC) results showed that compounds 1 and 2 possessed the corresponding anti-MRSA bioactivities of 4 ∼ 8 µg/ml and 8 ∼ 16 µg/ml, which confirmed the structure-activity relationships of streptovaricins reported previously and also revealed that addition of the hydroxyl group at C-8 increased the anti-MRSA activity.

Production of 3-desmethyl protostreptovaricin I from the genetically engineered Streptomyces spectabilis CCTCC M2017417.

A new streptovaricin analogue, namely 3-desmethyl protostreptovaricin I (1), was isolated from the culture of the genetically engineered strain ΔstvM2 derived from Streptomyces spectabilis CCTCC M2017417. Its structure was elucidated on the basis of extensive spectroscopic analyses, including 1D and 2D NMR tests, and high resolution mass spectrometry analysis. Compound 1 is the first example of 3-desmethyl streptovaricin analogues reported so far, however, it showed no antibacterial activities against Staphylococcus aureus ATCC 29213.

Uncovering the cytochrome P450-catalyzed methylenedioxy bridge formation in streptovaricins biosynthesis.

Streptovaricin C is a naphthalenic ansamycin antibiotic structurally similar to rifamycins with potential anti-MRSA bioactivities. However, the formation mechanism of the most fascinating and bioactivity-related methylenedioxy bridge (MDB) moiety in streptovaricins is unclear. Based on genetic and biochemical evidences, we herein clarify that the P450 enzyme StvP2 catalyzes the MDB formation in streptovaricins, with an atypical substrate inhibition kinetics. Furthermore, X-ray crystal structures in complex with substrate and structure-based mutagenesis reveal the intrinsic details of the enzymatic reaction. The mechanism of MDB formation is proposed to be an intramolecular nucleophilic substitution resulting from the hydroxylation by the heme core and the keto-enol tautomerization via a crucial catalytic triad (Asp89-His92-Arg72) in StvP2. In addition, in vitro reconstitution uncovers that C6-O-methylation and C4-O-acetylation of streptovaricins are necessary prerequisites for the MDB formation. This work provides insight for the MDB formation and adds evidence in support of the functional versatility of P450 enzymes.

Functional Analysis of Cytochrome P450s Involved in Streptovaricin Biosynthesis and Generation of Anti-MRSA Analogues.

The streptovaricins, chemically related to the rifamycins, are highly effective antibacterial agents, particularly against mycobacteria. Herein, a bioassay-guided investigation of Streptomyces spectabilis CCTCC M2017417 has led to the characterization of streptovaricins as potent compounds against methicillin-resistant Staphylococcus aureus (MRSA). We identified the streptovaricin biosynthetic gene cluster from S. spectabilis CCTCC M2017417 based on genomic sequencing and bioinformatic analysis. Targeted in-frame deletion of five cytochrome P450 genes (stvP1-P5) resulted in the identification of four new streptovaricin analogues and revealed the functions of these genes as follows: stvP1, stvP4, and stvP5 are responsible for the hydroxylation of C-20, Me-24, and C-28, respectively. stvP2 is possibly involved in formation of the methylenedioxy bridge, and stvP3, a conserved gene found in the biosynthetic cluster for naphthalenic ansamycins, might be related to the formation of a naphthalene ring. Biochemical verification of the hydroxylase activity of StvP1, StvP4, and StvP5 was performed, and StvP1 showed unexpected biocatalytic specificity and promiscuity. More importantly, anti-MRSA studies of streptovaricins and derivatives revealed significant structure-activity relationships (SARs): The hydroxyl group at C-28 plays a vital role in antibacterial activity. The hydroxyl group at C-20 substantially enhances activity in the absence of the methoxycarbonyl side chain at C-24, which can increase the activity regardless of the presence of a hydroxyl group at C-20. The inner lactone ring between C-21 and C-24 shows a positive effect on activity. This work provides meaningful information on the SARs of streptovaricins and demonstrates the utility of the engineering of streptovaricins to yield novel anti-MRSA molecules.

Involvement of the beta subunit of RNA polymerase in resistance to streptolydigin and streptovaricin in the producer organisms Streptomyces lydicus and Streptomyces spectabilis.

Streptomyces lydicus NRRL2433 and S. spectabilis NRRL2494 produce two inhibitors of bacterial RNA polymerase: the 3-acyltetramic acid streptolydigin and the naphthalenic ansamycin streptovaricin, respectively. Both strains are highly resistant to their own antibiotics. Independent expression of the S. lydicus and S. spectabilis rpoB and rpoC genes, encoding the beta- and beta'-subunits of RNA polymerase, respectively, in S. albus showed that resistance is mediated by rpoB, with no effect of rpoC. Within the beta-subunit, resistance was confined to an amino acid region harboring the "rif region." Comparison of the beta-subunit amino acid sequences of this region from the producer strains and those of other streptomycetes and site-directed mutagenesis of specific differential residues located in it (L485 and D486 in S. lydicus and N474 and S475 in S. spectabilis) showed their involvement in streptolydigin and streptovaricin resistance. Other amino acids located close to the "Stl pocket" in the S. lydicus beta-subunit (L555, F593, and M594) were also found to exert influence on streptolydigin resistance.

An antimutagenic metabolite, streptovaricin C, isolated from Streptomyces sp.

Streptomyces sp. KM1-30 was isolated from soil as a producer of antimutagens by screening with a modified Ames test. The chemical structure of the antimutagenic metabolite was identified as streptovaricin C, which is known to inhibit DNA dependent RNA polymerase from E. coli and RNA dependent DNA polymerase from RNA tumor viruses, by MS and 1H-, 13C-NMR analyses. Addition of streptovaricin C to the cultures of UV treated Salmonella typhimurium TA100 or Trp-P-2-treated S. typhimurium TA98 decreased the frequency of mutation without a decrease in viable cell counts. The effect of streptovaricin C to the mutation induced by UV and Trp-P-2 was not desmutagenic, but antimutagenic.

Comparative investigation of a streptovaricin-producing strain of Streptomyces spectabilis and its selectant.

Some differences were found in the ultrastructural, cultural and physiological-biochemical properties between the parent strain Streptomyces spectabilis 1000 and its natural selectant S. spectabilis 1011-10, producers of streptovaricin.

Biosynthesis of the streptovaricins: 3-amino-5-hydroxybenzoic acid as a precursor to the meta-C7N unit.

[Carboxy-14C]-3-amino-5-hydroxybenzoic acid (AHBA) has been shown to be incorporated by Streptomyces spectabilis to the extent of greater than 0.1% (35: 1 dilution) in the ansamycin antibiotic streptovaricin C, the major component of the streptovaricin complex. When [carboxy-13C]AHBA was similarly administered, C-21 (quinone methide carbonyl at 188.3 ppm) of streptovaricin C was specifically labeled (at twenty one times natural abundance). In preparation for the 13C incorporation study the 13C NMR spectrum of streptovaricin C was investigated, making extensive use of short- and long-range HETCOR. These assignments revise some of those proposed earlier for streptovaricin C.

Streptomyces species producing the streptovaricin complex.

Morphological, cultural and physiological-biochemical properties of Streptomyces sp. strain 1000 and its antibiotic production were investigated. Antibiotics 1011 (identical with the streptovaricin complex) and 1012 (with antibacterial action) were isolated from the cultural broth of this strain. The overproducing natural variant 1011 was isolated from the population of a strain producing antibiotic 1011 at a concentration of 1000 mg/L (activity of the parent strain represents 41 mg/L only). Comparative taxonomical characteristic of Streptomyces sp. strain 1000 with strains from S. spectabilis showed that the strain 1000 differed in some properties and antibiotic production being considered as a new variant of S. spectabilis. The strain shows an expressed antibiotic activity against G+ as well as G- bacterial and yeasts.

Drug inhibitors of RNA polymerase II transcription.

Transcription by RNA polymerase II occurs after formation of a transcription complex. This complex is assembled in stages by the interaction of transcription factors with the template and/or with each other. We report on the ability of six drugs to inhibit the assembly of the RNA polymerase II transcription complex. Assembly of the complex on the adenovirus major late promoter requires several transcription factors. The normal assembly process requires that the DNA first interact with TFIIA, then with TFIID, and finally with at least four additional transcription factors (one of which is RNA polymerase II). We observed that streptolydigin (10 micrograms/ml) inhibits association of ILA and IID, and at higher concentrations (100 micrograms/ml) inhibits that IIA/IID complex from binding to DNA. Streptovaricin (100 micrograms/ml) appears to inhibit the IIA/IID interaction with DNA and prevents reinitiation (at 500 micrograms/ml). Adriamycin (1 microgram/ml) inhibits the interaction of TFIID with the IIA/DNA complex and inhibits an additional event immediately prior to, or during, elongation. Daunorubicin may be an elongation inhibitor. Heparin at 10 micrograms/ml inhibits further assembly after the IIA/IID/DNA complex has formed, and at 100 micrograms/ml also inhibits a late event in the assembly process and blocks reinitiation. Rifamycin AF/013 (100 micrograms/ml) inhibits the early events necessary to form the IIA/IID/DNA complex and (at 10 micrograms/ml) an assembly event following formation of the IIA/IID/DNA complex. Therefore, these compounds should be useful as probes for further examination of the assembly process.

Selective killing of human T cell lymphotropic virus type I-transformed cell lines by a damavaricin Fc derivative.

n-Pentyl ether of damavaricin Fc (n-pentyl DvFc) preferentially killed human T-cell lymphotropic virus type I (HTLV-I)-transformed cell lines. The mechanism of action of the drug was investigated using MT-4 cells. Cytotoxic action was diminished by the removal of n-pentyl DvFc from the culture or by the addition of sulfhydryl compounds such as 2-mercaptoethanol and dithiothreitol. The killing activity of n-pentyl DvFc was also diminished by membrane-acting agents including quinidine and diphenylhydantoin. Influx and subsequent efflux of Ca2+ were observed when either HTLV-I infected (MT-4 cells) or uninfected cells were treated with n-pentyl DvFc. An efflux of K+ was observed in HTLV-I infected MT-4 cells immediately after the exposure of the cells to n-pentyl DvFc. The K+ efflux, however, was not observed in the uninfected T cells. n-Pentyl DvFc seems to act primarily on the cell surface of MT-4 cells, leading to the perturbation of membrane function. The restoration of cell growth, however, is critically dependent on the presence of dithiothreitol and 2-mercaptoethanol, implying a role for a free sulfhydryl group in the killing activity.

Effects of antibiotics on RNA polymerase III transcription.

We investigated the effects of six drugs on an RNA polymerase III in vitro transcription system. Adriamycin, daunorubicin, heparin, rifamycin AF/013, streptolydigin, and streptovaricin all inhibit RNA synthesis from a tRNA gene or the adenovirus 2 (AD2) VA1 RNA gene. The completed RNA polymerase III transcription complex is formed by the sequential, ordered addition of protein factors. Although both genes reportedly use the same transcription fractions for in vitro RNA synthesis, some of these drugs interfere differentially with these genes. A drug concentration that inhibits transcription from one gene may not inhibit transcription from the other gene. Adriamycin seems to block transcription if added between the binding of the individual transcription fractions. Daunorubicin appears to inhibit VA transcription only if added prior to both transcription fractions, but inhibits tRNA synthesis before and during transcription factor binding. Heparin blocks both genes between factors binding to DNA and after factor binding. Rifamycin blocks VA synthesis more effectively than tRNA synthesis. Streptolydigin blocks transcription of both genes. Streptovaricin probably blocks transcription by inhibiting early transcription complex assembly events. These drugs appear useful as appropriate probes to investigate transcription complexes since several discriminate between complexes formed on different genes during the assembly process.

DNA replication by a DNA-membrane complex extracted from Bacillus subtilis: site of initiation in vitro and initiation potential of subcomplexes.

A DNA-membrane complex extracted from Bacillus subtilis was studied further as a model system for initiation of bacterial DNA replication in vitro. Of three subcomplexes purified from the crude complex by a combination of CsCl and sucrose gradient centrifugation, the synthetic capability of only one was inhibited significantly by streptovaricin, a known inhibitor of RNA primer formation. A selective enrichment in the level of this subcomplex was obtained by manipulating a thymine-requiring mutant. The synthetic capabilities of an enriched and nonenriched DNA-membrane complex were compared in the presence and absence of streptovaricin. Although the rate and extent of DNA synthesis per unit of protein were approximately the same in the absence of the antibiotic, there was a much greater inhibition of synthesis shown by the enriched complex in the presence of streptovaricin. Although the amount of DNA present in the putative initiation subcomplex was less than 0.3 to 0.4% of the total DNA present in the crude complex, such DNA, except for a few quantitative differences, was still representative of genomic DNA. Newly synthesized DNA hybridized to specific origin- and non-origin-derived restriction fragments of the B. subtilis genome. However, when an elongation inhibitor (ddCTP) was added, hybridization of such DNA to almost all of the nonorigin fragments disappeared or was reduced drastically, whereas origin region hybridization patterns remained strong. The highest level of hybridization in the origin region occurred with a BamHI (B7) restriction fragment of 5.6 kilobases that has been implicated by others as one site initiation in vivo (N. Ogasawara, M. Seiki, and H. Yoshikawa, Nature (London) 281:702-704, 1979; S. J. Seror-Laurent and G. Henckes, Proc. Natl. Acad. Sci. USA 82:3586-3590, 1985).

Evaluation of antibacterial agents in a high-volume bovine polymorphonuclear neutrophil Staphylococcus aureus intracellular killing assay.

A bovine polymorphonuclear leukocyte (PMN) monolayer system was used to determine the ability of different antibiotics to kill surviving intracellular Staphylococcus aureus. The following classes of antimicrobial agents were tested in this high-volume assay procedure: aminocyclitol, beta-lactam, coumarin, lincosaminide, macrolide, naphthalenic ansamycin, paulomycin, peptide, quinolone, and tetracycline. The activities of these compounds were compared with those of positive (rifampin), negative (cloxacillin), and non-antibiotic-treated controls. Only oxytetracycline, the ansamycins (rifampin, rifamycin SV, streptovaricin A, C, and D), paulomycin, and paldimycin caused a significant reduction in the viable count of intracellular S. aureus. Of these, however, the intracellular killing by the streptovaricins was directly related to the cytotoxicity (as determined by trypan blue exclusion) of these compounds for the PMNs. Although the paulomycins were cytotoxic for the PMNs, the cytotoxic and the intracellular killing activity of these new compounds could be distinguished. The relevance of these results to the therapeutic effectiveness of these antibiotics in the treatment of bovine staphylococcal mastitis is discussed.