Molecular cloning of resistance genes and architecture of a linked gene cluster involved in biosynthesis of oxytetracycline by Streptomyces rimosus

Summary The isolation of mutants of Streptomyces rimosus which were blocked in oxytetracycline (OTC) production was described previously. The genes for the early steps of antibiotic biosynthesis mapped together. Genomic DNA fragments of S. rimosus which conferred resistance to OTC and complemented all of these non-producing mutants have been cloned. The cloned DNA is physically linked within approximately 30 kb of the genome of S. rimosus. The gene cluster is flanked at each end by a resistance gene each of which, independently, can confer resistance to the antibiotic. In OTC-sensitive strains of S. rimosus, the entire gene cluster including both resistance genes has been deleted. Complementation of blocked mutants by cloned DNA fragments in multi-copy vectors was often masked by a secondary effect of switching off antibiotic productions in strains othersise competent to produce OTC. This adverse effect on OTC production was not observed with recombinants using low copy-number vectors.     

Genetics of Streptomyces rimosus, the oxytetracycline producer.

From a genetic standpoint, Streptomyces rimosus is arguably the best-characterized industrial streptomycete as the producer of oxytetracycline and other tetracycline antibiotics. Although resistance to these antibiotics has reduced their clinical use in recent years, tetracyclines have an increasing role in the treatment of emerging infections and noninfective diseases. Procedures for in vivo and in vitro genetic manipulations in S. rimosus have been developed since the 1950s and applied to study the genetic instability of S. rimosus strains and for the molecular cloning and characterization of genes involved in oxytetracycline biosynthesis. Recent advances in the methodology of genome sequencing bring the realistic prospect of obtaining the genome sequence of S. rimosus in the near term.     

Influence of Inorganic Phosphorus on Oxytetracycline Formation by Streptomyces rimosus

Production of oxytetracycline by Streptomyces rimosus in several chemically defined media containing graded concentrations of inorganic phosphorus was studied in shake flasks. Although high levels of inorganic phosphate have been reported to inhibit oxytetracycline formation, this study indicated that composition of the medium is an important factor in determining whether antibiotic production will be stimulated or inhibited by specific concentrations of inorganic phosphate.     

Purification and chemical characterization of antimicrobial compounds from a new soil isolate Streptomyces rimosus MTCC 10792

A new isolate of Streptomyces sp. from soil of state Chhattisgarh (India) having broad spectrum antibacterial and antifungal activity was obtained. The active strain was identified as Streptomyces rimosus subsp. rimosus with accession number MTCC 10792 based on physiological, biochemical characteristics and 16S rRNA sequence homology studies. Antimicrobial compound produced by S. rimosus was tested against the drug resistance pathogens by the Bauer and Kirby method. The crude active metabolite was extracted using solvent n-butanol and purified by silica column chromatography and HPLC method. The physicochemical characteristics of the one purified compound viz. color, melting point, solubility, elemental analysis, ESIMS, IR, UV, 1HNMR, ¹³CNMR and chemical reactions have been investigated. Purified antimicrobial compound produced by S. rimosus MTCC 10792 at concentration 25 μg/mL showed antitubercular activity against Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis H37R as well as broad activity against all tested bacterial and fungal pathogens.     

A New Hybrid Strain of an Oxytetracycline-producing Organism, Streptomyces rimosus

A new strain, Streptomyces rimosus LS-T hybrid, characterized by a lower level of foaming and higher antibiotic activity as compared to the other active strains of S. rimosus, is obtained as a result of selection among prototrophic recombinant forms of strains LS-T293 and BS-21. The studies on strain LS-T hybrid show the possibilities of combining properties of different strains of S. rimosus in the hybrid forms. The occurrence of new properties in the hybrid forms is detected.     

Cloning and expression of the α-amylase gene and oxytetracycline production in Streptomyces rimosus

An 8.4 kb Sau3AI DNA fragment containing the Streptomyces rimosus TM-55 -amylase gene (amy) was ligated to a vector pIJ702, named pCYL01, and cloned into amylase deficient mutant S. lividans M2 (amy ^–). Subcloning study showed that the amy gene was localized in 3.3 kbKpnI-PstI fragment. The molecular weight of the purified -amylases of S. lividans M2/pCYL01 and S. rimosus TM-55 were estimated to be 65.7 kDa. Different sizes of recombinant plasmids carrying the amy gene had been retransferred into the parental strain of S. rimosus TM-55. Among these S. rimosus transformants, TM-55/pCYL01, TM-55/pCYL12 and TM-55/pCYL36 showed amylase activity 1.36- to 2.05-fold at the seventh day (1.61 to 2.42 units vs 1.18 units), and oxytetracycline (OTC) production 2.00- to 2.50-fold at the ninth day (approximate 140 to 170 g ml^–1 vs 72 g ml^–1), higher than that of S. rimosus TM-55 alone, respectively. These results showed that industrial microorganisms could be improved by genetic and metabolic engineering.     

Exploitation of the Streptomyces coelicolor A3(2) genome sequence for discovery of new natural products and biosynthetic pathways

Streptomyces, and related genera of Actinobacteria, are renowned for their ability to produce antibiotics and other bioactive natural products with a wide range of applications in medicine and agriculture. Streptomyces coelicolor A3(2) is a model organism that has been used for more than five decades to study the genetic and biochemical basis for the production of bioactive metabolites. In 2002, the complete genome sequence of S. coelicolor was published. This greatly accelerated progress in understanding the biosynthesis of metabolites known or suspected to be produced by S. coelicolor and revealed that streptomycetes have far greater potential to produce bioactive natural products than suggested by classical bioassay-guided isolation studies. In this article, efforts to exploit the S. coelicolor genome sequence for the discovery of novel natural products and biosynthetic pathways are summarized.     

Identification of phosphorylation sites in aminoglycoside phosphotransferase VIII from Streptomyces rimosus

We demonstrate for the first time the role of phosphorylation in the regulation of activities of enzymes responsible for inactivation of aminoglycoside antibiotics. The aminoglycoside phosphotransferase VIII (APHVIII) from the actinobacterial strain Streptomyces rimosus ATCC 10970 is an enzyme regulated by protein kinases. Two serine residues in APHVIII are shown to be phosphorylated by protein kinases from extracts of the kanamycin-resistant strain S. rimosus 683 (a derivative of strain ATCC 10970). Using site-directed mutagenesis and molecular modeling, we have identified the Ser146 residue in the activation loop of the enzyme as the key site for Ca²⁺-dependent phosphorylation of APHVIII. Comparison of the kanamycin kinase activities of the unphosphorylated and phosphorylated forms of the initial and mutant APHVIII shows that the Ser146 modification leads to a 6–7-fold increase in the kanamycin kinase activity of APHVIII. Thus, Ser146 in the activation loop of APHVIII is crucial for the enzyme activity. The resistance of bacterial cells to kanamycin increases proportionally. From the practical viewpoint, our results increase prospects for creation of highly effective test systems for selecting inhibitors of human and bacterial serine/threonine protein kinases based on APHVIII constructs and corresponding human and bacterial serine/threonine protein kinases.     

Development of an intergeneric conjugal transfer system for rimocidin‐producing Streptomyces rimosus

Aims: To develop an intergeneric conjugation system for rimocidin‐producing Streptomyces rimosus. Methods and Results: High efficiencies of conjugation [10^?2–10^?3 transconjugants/recipient colony forming units (CFU)] were obtained when spores of S. rimosus were heat treated at 40°C for 10 min prior to mixing with E. coli ET12567(pUZ8002/pIJ8600) as donor. Mycelium from liquid grown cultures of S. rimosus could also be used as recipient instead of spores, with 24‐h cultures giving optimal results. TSA (Oxoid) medium containing 10 m mol l^?1 MgCl₂ was the preferred medium for conjugation. Southern hybridization was used to confirm that transconjugants of S. rimosus contained a single copy of pIJ8600 integrated at a unique chromosomal attachment site (attB). The transconjugants exhibited a high stability of plasmid integration and showed strong expression of green fluorescent protein when using pIJ8655 as the conjugative vector. Conclusion: Intergeneric conjugation between E. coli and S. rimosus was achieved at high efficiency using both spores and mycelium. Significance and Impact of the Study: The conjugation system developed provides a convenient gene expression system for S. rimosus R7 and will enable the genetic manipulation of the rimocidin gene cluster.     

Improved oxytetracycline production in Streptomyces rimosus M4018 by metabolic engineering of the G6PDH gene in the pentose phosphate pathway

The aromatic polyketide antibiotic, oxytetracycline (OTC), is produced by Streptomyces rimosus as an important secondary metabolite. High level production of antibiotics in Streptomycetes requires precursors and cofactors which are derived from primary metabolism; therefore it is exigent to engineer the primary metabolism. This has been demonstrated by targeting a key enzyme in the oxidative pentose phosphate pathway (PPP) and nicotinamide adenine dinucleotide phosphate (NADPH) generation, glucose-6-phosphate dehydrogenase (G6PDH), which is encoded by zwf1 and zwf2. Disruption of zwf1 or zwf2 resulted in a higher production of OTC. The disrupted strain had an increased carbon flux through glycolysis and a decreased carbon flux through PPP, as measured by the enzyme activities of G6PDH and phosphoglucose isomerase (PGI), and by the levels of ATP, which establishes G6PDH as a key player in determining carbon flux distribution. The increased production of OTC appeared to be largely due to the generation of more malonyl-CoA, one of the OTC precursors, as observed in the disrupted mutants. We have studied the effect of zwf modification on metabolite levels, gene expression, and secondary metabolite production to gain greater insight into flux distribution and the link between the fluxes in the primary and secondary metabolisms.     

Continuous production of oxytetracycline by immobilized growing Streptomyces rimosus cells

Summary Streptomyces rimosus cells were immobilized with urethane prepolymers and used in the production of oxytetracycline. Based on the criteria for oxytetracycline productivity, cell growth in gels, cell leakage from gels and mechanical strength of gel, a hydrophilic prepolymer, PU-1, the main chain of which was polyethylene glycol (molecular weight, approximately 1500) was employed as gel material among 11 kinds of urethane prepolymers. Use of glucose-free medium for cultivation of PU-1-entrapped cells increased the production rate of oxytetracycline and minimized cell leakage from the gels. When the gel-entrapped cells lost activity, treatment of the cell-entrapping gels with saline or 70% ethanol resulted in recovery of the oxytetracycline productivity. Continuous oxytetracycline fermentation using PU-1-entrapped growing cells was successfully achieved in air-bubbled reactor for at least 35 days with reactivation of the cells.     

Studies on Streptomycetes

Investigation was made on the mycological properties of a strain No. 45449 isolated from a sample of soil collected in Fukuchiyama. Since the antibiotics produced by the strain resembled hydroxymycin and paromomycin, the strain was compared with the hydroxymycin and paromomycin-producing strains, S. paucisporogenes and S. rimosus forma paromomycinus, and as a result the strain No. 45449 was found to be different from the latter two strains. Among known strains, S. flavogriseus resembles the present strain, but they are different morphologically and in the kind of the antibiotics they produce. Thus, as the strain No. 45449 was found to be a new strain, it was named S. pulveraceus nov. sp. The antibiotics produced by the present strain are physiologically basic substances active against Gram-positive and negative bacteria and acid fast bacteria, and they are considered to belong to the neomycin-kanamycin group.     

A Type IV Pilus Mediates DNA Binding during Natural Transformation in Streptococcus pneumoniae

Natural genetic transformation is widely distributed in bacteria and generally occurs during a genetically programmed differentiated state called competence. This process promotes genome plasticity and adaptability in Gram-negative and Gram-positive bacteria. Transformation requires the binding and internalization of exogenous DNA, the mechanisms of which are unclear. Here, we report the discovery of a transformation pilus at the surface of competent Streptococcus pneumoniae cells. This Type IV-like pilus, which is primarily composed of the ComGC pilin, is required for transformation. We provide evidence that it directly binds DNA and propose that the transformation pilus is the primary DNA receptor on the bacterial cell during transformation in S. pneumoniae. Being a central component of the transformation apparatus, the transformation pilus enables S. pneumoniae, a major Gram-positive human pathogen, to acquire resistance to antibiotics and to escape vaccines through the binding and incorporation of new genetic material.     

The Use of Phase Inversion Temperature (PIT) Microemulsion Technology to Enhance Oil Utilisation during <Emphasis Type="Italic">Streptomyces rimosus</Emphasis> Fed-batch Fermentations to Produce Oxytetracycline

The use of a rapeseed oil emulsion feed, produced by a phase inversion temperature (PIT) process, produced more biomass, gave a 3-fold increase in oil utilisation and a higher oxytetracycline titre but a higher residual oil concentration when compared to a conventional fed-batch Streptomyces rimosus process fed with crude rapeseed oil. Importantly, microbial utilisation of the surfactant was confirmed for the first time.     

Engineered Biosynthesis of a Novel Amidated Polyketide, Using the Malonamyl-Specific Initiation Module from the Oxytetracycline Polyketide Synthase

Tetracyclines are aromatic polyketides biosynthesized by bacterial type II polyketide synthases (PKSs). Understanding the biochemistry of tetracycline PKSs is an important step toward the rational and combinatorial manipulation of tetracycline biosynthesis. To this end, we have sequenced the gene cluster of oxytetracycline (oxy and otc genes) PKS genes from Streptomyces rimosus. Sequence analysis revealed a total of 21 genes between the otrA and otrB resistance genes. We hypothesized that an amidotransferase, OxyD, synthesizes the malonamate starter unit that is a universal building block for tetracycline compounds. In vivo reconstitution using strain CH999 revealed that the minimal PKS and OxyD are necessary and sufficient for the biosynthesis of amidated polyketides. A novel alkaloid (WJ35, or compound 2) was synthesized as the major product when the oxy-encoded minimal PKS, the C-9 ketoreductase (OxyJ), and OxyD were coexpressed in CH999. WJ35 is an isoquinolone compound derived from an amidated decaketide backbone and cyclized with novel regioselectivity. The expression of OxyD with a heterologous minimal PKS did not afford similarly amidated polyketides, suggesting that the oxy-encoded minimal PKS possesses novel starter unit specificity.     

Enhancement of oxytetracycline production in a Streptomyces rimosus strain after treatment with acriflavine

Summary A strain ofStreptomyces rimosus was treated with acriflavine as curing agent; morphological and physiologically altered variants were isolated, and changes in sporulation, aerial and substrate mycelia, pigment formation, oxytetracycline (OTC) resistance and biosynthesis are discussed.     

Oxytetracycline production by Streptomyces rimosus in solid-state fermentation of corncob

Corn-cob was used as a substrate in the production of oxytetracycline by Streptomyces rimosus TM-55 in a solidstate fermentation. Oxytetracycline was detected on day 4, and reached its maximum on day 8. Optimal conditions for oxytetracycline production were an initial pH of 5.2 to 6.3, an initial moisture content of 64% to 67%, supplementation with 20% (w/w) rice bran or 1.5% to 2.5% (w/w) (NH₄)₂SO₄ as sole N source, 1.0% (w/w) CaCO₃, 2% (w/w) MgSO₄.7H₂O, and 0.5% (w/w) KH₂PO₄, with incubation for 8 days at 25 to 30°C. Each g substrate produced 7 to 8 mg oxytetracycline.     

Oil feeding during the oxytetracycline biosynthesis

The ability of utilization of vegetal oils belongs to common properties of Streptomycetes. During the cultivation of Streptomyces rimosus and biosynthesis of oxytetracycline in 15 m³ fermenters, a fixed regime of soya bean oil feeds as antifoam agent and partial carbon source according to subjectively designed mechanism was investigated and further also feeding regime after exhausting starch as main carbon source and finally his dosing with ammonia sulphate in accordance with physiological activity of the culture. In the second case with semicontinuous supplements of soya bean oil it was possible to prevent premature autolysis of mycelia and to extend the biosynthetic process with keeping the oxytetracycline production rate. The third approach, the most progressive one, represents besides the automatisation of control loop the necessity of assurance continuous pH adjustment for elevation of the process production rate.     

Oxytetracycline production by Streptomyces rimosus: gas and temperature patterns in a solid-state column reactor

During oxytetracycline production by Streptomyces rimosus TM-55 on sweet potato residue in a solid-state column reactor, the moisture content increased by between 2 and 5% (w/w) during incubation, from an initial content of 70 to 73%, and pH initially increased from 6.0 to 7.3, followed by a gradual decrease to 6.2. Appropriate aeration enhanced oxytetracycline production, while mixing only once daily decreased it. The temperatures in the centre and upper layers of each reactor were higher than elsewhere in static non-aerated cultures. The maximum CO₂ concentration ranged from 2.9 to 3.2% (v/v) and the minimum O₂ concentration was 11.0 to 17.2% (v/v) in static cultures. Under optimal conditions, each gram of dry substrate produced the equivalent potency of 12 mg oxytetracycline.The authors are with the Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan 10617, Republic of China