Heterologous activation of the actinorhodin biosynthetic pathway in Streptomyces lividans

Identification of a novel unpaired histidine sensor kinase affecting secondary metabolism and morphological differentiation in Streptomyces acidiscabies ATCC 49003

Two-component systems (TCSs) are an important signaling transduction pathway that adapt to changing environments. Commonly, a TCS comprises a sensor kinase that is usually an integral membrane histidine sensor kinase and a response regulator that mediates the cellular responses. Presently, however, we cloned a novel sensor kinase gene (tcsK) that is not adjacent to its cognate response regulator from Streptomyces acidiscabies that produces two secondary metabolites, thaxtomin A and WS5995B, and identified its functional involvement in the production of secondary metabolites and morphological differentiation. The elevated expression and disruption of the tcsK gene enhanced 7.1-fold and almost abolished WS5995B production in S. acidiscabies, respectively, but did not affect the production of thaxtomin A. In addition, spore formation of S. acidiscabies was decreased 120-fold by the disruption of tcsK, and the actinorhodin production of Streptomyces lividans TK24 was increased 5.7-fold by the high expression of tcsK. These results indicate that the novel unpaired tcsK gene may be related to the control of secondary metabolite production and spore formation in actinomycetes.

Activation and silencing of secondary metabolites in Streptomyces albus and Streptomyces lividans after transformation with cosmids containing the thienamycin gene cluster from Streptomyces cattleya

Activation and silencing of antibiotic production was achieved in Streptomyces albus J1074 and Streptomyces lividans TK21 after introduction of genes within the thienamycin cluster from S. cattleya. Dramatic phenotypic and metabolic changes, involving activation of multiple silent secondary metabolites and silencing of others normally produced, were found in recombinant strains harbouring the thienamycin cluster in comparison to the parental strains. In S. albus, ultra-performance liquid chromatography purification and NMR structural elucidation revealed the identity of four structurally related activated compounds: the antibiotics paulomycins A, B and the paulomenols A and B. Four volatile compounds whose biosynthesis was switched off were identified by gas chromatography-mass spectrometry analyses and databases comparison as pyrazines; including tetramethylpyrazine, a compound with important clinical applications to our knowledge never reported to be produced by Streptomyces. In addition, this work revealed the potential of S. albus to produce many others secondary metabolites normally obtained from plants, including compounds of medical relevance as dihydro-β-agarofuran and of interest in perfume industry as β-patchoulene, suggesting that it might be an alternative model for their industrial production. In S. lividans, actinorhodins production was strongly activated in the recombinant strains whereas undecylprodigiosins were significantly reduced. Activation of cryptic metabolites in Streptomyces species might represent an alternative approach for pharmaceutical drug discovery.

Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2)

We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.

Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

Background

The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes.

Results

We identified five large S. coelicolor genomic islands (larger than 25 kb) and 18 smaller islets absent in S. lividans chromosome. Many of these regions show anomalous GC bias and codon usage patterns. Six of them are in close vicinity of tRNA genes while nine are flanked with near perfect repeat sequences indicating that these are probable recent evolutionary acquisitions into S. coelicolor. Embedded within these segments are at least four DNA methylases and two probable methyl-sensing restriction endonucleases. Comparison with S. coelicolor transcriptome and proteome data revealed that some of the missing genes are active during the course of growth and differentiation in S. coelicolor. In particular, a pair of methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor biosynthesis, an acyl-CoA dehydrogenase implicated in timing of actinorhodin synthesis and bldB, a developmentally significant regulator whose mutation causes complete abrogation of antibiotic synthesis belong to this category.

Conclusion

Our findings provide tangible hints for elucidating the genetic basis of important phenotypic differences between these two streptomycetes. Importantly, absence of certain genes in S. lividans identified here could potentially explain the relative ease of DNA transformations and the conditional lack of actinorhodin synthesis in S. lividans.

Transcriptional regulation of Streptomyces coelicolor pathway-specific antibiotic regulators by the absA and absB loci

The four antibiotics produced by Streptomyces coelicolor are all affected by mutations in the absA and absB loci. The absA locus encodes a putative two-component signal transduction system, and the absB locus encodes a homolog of Escherichia coli RNase III. We assessed whether these loci control synthesis of the antibiotics actinorhodin and undecylprodigiosin by regulating transcript abundance from the biosynthetic and regulatory genes specific for each antibiotic. Strains that were Abs- (for antibiotic synthesis deficient) due to mutations in absA or absB were examined. In the Abs- absA mutant strain, transcripts for the actinorhodin biosynthetic genes actVI-ORF1 and actI, and for the pathway-specific regulatory gene actII-ORF4, were substantially lower in abundance than in the parent strain. The level of the transcript for the undecylprodigiosin pathway-specific regulatory gene redD was similarly reduced in this mutant. Additionally, a strain that exhibits precocious hyperproduction of antibiotics (Pha phenotype) due to disruption of the absA locus contained elevated levels of the actVI-ORF1, actII-ORF4, and redD transcripts. In the absB mutant strain, actVI-ORF1, actI, actII-ORF4, and redD transcript levels were also substantially lower than in the parent strain. These results establish that the abs genes affect production of antibiotics through regulation of expression of the antibiotic-specific regulatory genes in S. coelicolor.

abaB, a putative regulator for secondary metabolism in Streptomyces

A chromosomal DNA fragment from Streptomyces antibioticus ATCC11891 was isolated by its ability to stimulate actinorhodin and undecylprodigiosin biosynthesis in Streptomyces lividans TK21. This fragment includes two open reading frames, whose deduced translated products resemble enzymes involved in sulfur metabolism (ORF1) and LysR-type transcriptional regulators (ORF2). The cloning of the promoter region of ORF2 (abaB) in high copy number led to overproduction of both antibiotics suggesting that this phenotype might well be due to titration by this region of one or more proteins. Southern blot analysis revealed that abaB gene is highly conserved among all streptomycetes tested.

Activation of the actinorhodin biosynthetic pathway in Streptomyces lividans

Production of the antibiotic actinorhodin was activated in Streptomyces lividans under conditions in which it is not normally produced when transformed with an activator gene from S. lividans. The gene encodes a 86-nucleotide transcript, responsible for the actinorhodin production phenotype, which is homologous to the 132 nucleotide transcript from S. fradiae, thought to act as a putative antisense RNA.

Functional characterization and transcriptional analysis of the dnrR1 locus, which controls daunorubicin biosynthesis in Streptomyces peucetius

We previously proposed that the adjacent dnrIJ genes represent a two-component regulatory system controlling daunorubicin biosynthesis in Streptomyces peucetius on the basis of the homology of the DnrI and DnrJ proteins to other response regulator proteins and the effect of a dnrI::aphII mutation. In the present paper we report the results of work with the dnrI::aphII mutant in complementation, bioconversion, and transcriptional analysis experiments to understand the function of dnrI. For five putative operons in the sequenced portion of the S. peucetius daunorubicin biosynthesis gene cluster examined, all of the potential transcripts are present in the delta dnrJ mutant and wild-type strains but absent in the dnrI::aphII strain. Since these transcripts code for both early- and late-acting enzymes in daunorubicin biosynthesis, dnrI seems to control all of the daunorubicin biosynthesis genes directly or indirectly. Transcriptional mapping of the 5' and 3' ends of the dnrIJ transcript and the termination site of the convergently transcribed dnrZUV transcript reveals, interestingly, that the two transcripts share extensive complementarity in the regions coding for daunorubicin biosynthesis enzymes. In addition, dnrI may regulate the expression of the drrAB and drrC daunorubicin resistance genes. The delta dnrJ mutant accumulates epsilon-rhodomycinone, the aglycone precursor of daunorubicin. Since this mutant contains transcripts coding for several early- and late-acting enzymes and since dnr mutants blocked in deoxysugar biosynthesis accumulate epsilon-rhodomycinone, we conclude that dnrJ is a daunosamine biosynthesis gene. Moreover, newly available gene sequence data show that the DnrJ protein resembles a group of putative aminotransferase enzymes, suggesting that the role of DnrJ is to add an amino group to an intermediate of daunosamine biosynthesis.

Expression of an heterologous gene activating actinorhodin biosynthesis in Streptomyces lividans and Streptomyces coelicolor

Production of the blue-pigmented antibiotic actinorhodin resulted in activation in the non-producer strain Streptomyces lividans, but not in the natural producer strain Streptomyces coelicolor, when transformed with an heterologous activator gene from Streptomyces fradiae. The gene encodes a 132 nucleotide-long transcript, responsible for the actinorhodin production phenotype, and thought to act as a putative antisense RNA, which has been detected in the transformed S. lividans cultures by reverse transcription followed by cyclic amplification.

Genetic control of polyketide biosynthesis in the genus Streptomyces

The genetic control of polyketide metabolite biosynthesis in Streptomyces sp. producing actinorhodin, daunorubicin, erythromycin, spiramycin, tetracenomycin and tylosin is reviewed. Several examples of positively-acting transcriptional regulators of polyketide metabolism are known, including some two-component sensor kinase-response regulator systems. Translational and posttranslational control mechanisms are only briefly mentioned since very little is known about either of these processes. Examples of how enzyme levels and substrate supply affect polyketide metabolism also are discussed.

Heterologous recognition in vivo of promoter sequences from the Streptomyces coelicolor dagA gene

The Streptomyces coelicolor dagA gene that codes for an extracellular agarase was cloned in the closely related bacterium S. lividans and transferred to the distantly related low G+C Gram-positive bacterium Bacillus subtilis and to the far more distantly related Gram-negative bacterium Escherichia coli. S1 nuclease mapping experiments identified a putative fifth promoter from which transcription of the dagA gene can take place, and accurately mapped the transcription termination site. The transcription terminator was specific for the Streptomyces strains and could terminate transcription initiated by promoters other than those of dagA. The agarase gene is efficiently transcribed in B. subtilis and E. coli, although pulse-chase experiments failed to detect the synthesis of agarase in these two bacteria.