Construction and application of a promoter-probe plasmid that allows chromogenic identification in Streptomyces lividans

A visualization reporter system for characterizing antibiotic biosynthetic gene clusters expression with high-sensitivity

The crisis of antibiotic resistance has become an impending global problem. Genome sequencing reveals that streptomycetes have the potential to produce many more bioactive compounds that may combat the emerging pathogens. The existing challenge is to devise sensitive reporter systems for mining valuable antibiotics. Here, we report a visualization reporter system based on Gram-negative bacterial acyl-homoserine lactone quorum-sensing (VRS-bAHL). AHL synthase gene (cviI) of Chromobacterium violaceum as reporter gene is expressed in Gram-positive Streptomyces to synthesize AHL, which is detected with CV026, an AHL deficient mutant of C. violaceum, via its violacein production upon AHL induction. Validation assays prove that VRS-bAHL can be widely used for characterizing gene expression in Streptomyces. With the guidance of VRS-bAHL, a novel oxazolomycin derivative is discovered to the best of our knowledge. The results demonstrate that VRS-bAHL is a powerful tool for advancing genetic regulation studies and discovering valuable active metabolites in microorganisms.

A quorum sensing based visualization reporter system is presented for the characterization of promoters in Gram-positive bacteria, utilizing violacein production, especially for use in the identification of secondary metabolites.

Engineering diverse eubacteria promoters for robust Gene expression in Streptomyces lividans

Due to the lack of powerful gene regulation elements, the engineering development of Streptomyces is often limited. Here, we disclosed that the heterologous σ⁷⁰ -dependent promoters, which have been reported as inefficient tools for gene expression in Streptomyces, could be efficiently recognized by Streptomyces housekeeping factor σ^hrdB. Therefore, an effective strategy was developed to engineer these promoters for robust gene expression in Streptomyces by fusing them with optimized 5'-untranslation regions (5'-UTRs). As a proof of concept, the widely used Ptac in E. coli was engineered by fusing its core promoter region with the 5'-UTR_R15 from a relatively powerful Streptomyces promoter PkasO*_R15 and resulted in Ptac*, the activity of which was 8.1-fold that of Ptac and 1.7-fold that of PkasO*_R15 in S. lividans TK24. Next, the 5'-UTR_R15 was optimized by randomizing the ribosome binding site (RBS). Based on the base biases of those RBSs with higher activity, eight artificial RBSs were rationally designed, and the optimal resulting promoter Ptac*_RBS3 showed about 2.1, 3.6, and 17.6 times the activity of Ptac*, PkasO*_R15, and Ptac, respectively, demonstrating that the heterologous Ptac was converted into a type of robust Streptomyces promoters. This study thus greatly expands promoter diversity for the engineering of Streptomyces.

Directly utilizing an endogenous gene to dissect regulatory elements in the biosynthetic gene cluster of nosiheptide

Coupling the deletion of an endogenous gene and a non-integrative promoter-probe vector allowed reliable identification of biosynthetic promoters of nosiheptide.

Actinomycetes biosynthetic potential: how to bridge in silico and in vivo?

Actinomycetes genome sequencing and bioinformatic analyses revealed a large number of "cryptic" gene clusters coding for secondary metabolism. These gene clusters have the potential to increase the chemical diversity of natural products. Indeed, reexamination of well-characterized actinomycetes strains revealed a variety of hidden treasures. Growing information about this metabolic diversity has promoted further development of strategies to discover novel biologically active compounds produced by actinomycetes. This new task for actinomycetes genetics requires the development and use of new approaches and tools. Application of synthetic biology approaches led to the development of a set of strategies and tools to satisfy these new requirements. In this review, we discuss strategies and methods to discover small molecules produced by these fascinating bacteria and also discuss a variety of genetic instruments and regulatory elements used to activate secondary metabolism cryptic genes for the overproduction of these metabolites.

Integrative, xylE-based promoter probe vectors for use in Streptomyces

Two promoter probe plasmid vectors, designated pIPP1 and pIPP2, were constructed from the existing plasmids pXE4 and pSET152. pIPP1 and 2 use the xylE gene of Pseudomonas putida as a reporter and can be transferred to streptomycetes by conjugation from Escherichia coli. The function of these plasmids as promoter probes was demonstrated in Streptomyces antibioticus and Streptomyces coelicolor using the phenoxazinone synthase and polynucleotide phosphorylase promoters from S. antibioticus. xylE activity could be detected in colonies on agar plates or via the in vitro assay for catechol dioxygenase. The integration into the S. antibioticus chromosome of the constructs containing the phsA promoter was verified by Southern blotting. The presence of the bla locus in pIPP1 allows the recovery of putative promoters by marker rescue.

Cross-talk of global nutritional regulators in the control of primary and secondary metabolism in Streptomyces

Limitation of different nutrients in Streptomyces coelicolor A3(2) triggers nutrient‐stress responses, mediated by PhoP, GlnR, AfsR and other regulators, that are integrated at the molecular level and control secondary metabolite biosynthesis and differentiation. In addition, utilization of chitin or N‐acetylglucosamine regulates secondary metabolite biosynthesis by a mechanism mediated by DasR. Phosphate control of primary and secondary metabolism in Streptomyces species is mediated by the two‐component PhoR–PhoP system. In S. coelicolor, PhoP controls secondary metabolism by binding to a PHO box in the afsS promoter overlapping with the AfsR binding site. Therefore, the afsS promoter serves to integrate the PhoP‐mediated response to phosphate limitation and AfsR‐mediated responses to other unknown environmental stimuli. Interestingly, phosphate control oversees nitrogen regulation but not vice versa. In ΔphoP mutants, expression of some nitrogen metabolism genes including glnA, glnII and glnK is increased. Phosphate control of these genes is exerted through binding of PhoP to the promoters of glnR (the global nitrogen regulator), glnA, glnII and the amtB–glnK–glnD operon. This regulation allows a ‘metabolic homeostasis’ of phosphate and nitrogen utilization pathways, preventing nutritional unbalances. Similar mechanisms of interaction between phosphate control and carbon catabolite regulation or between phosphate and DasR‐mediated N‐acetylglucosamine regulation appear to exist. Transport of N‐acetylglucosamine by the NagE2 permease and, therefore, regulation of secondary metabolism, is dependent upon the balance of phosphorylated/dephosphorylated proteins of the N‐acetylglucosamine phosphotransferase system. These findings provide the bases for understanding the mechanisms underlying systems biology of Streptomyces species.

Cross-talk between two global regulators in Streptomyces: PhoP and AfsR interact in the control of afsS, pstS and phoRP transcription

The regulatory proteins AfsR and PhoP control expression of the biosynthesis of actinorhodin and undecylprodigiosin in Streptomyces coelicolor. Electrophoretic mobility shift assays showed that PhoP(DBD) does not bind directly to the actII-ORF4, redD and atrA promoters, but it binds to the afsS promoter, in a region overlapping with the AfsR operator. DNase I footprinting studies revealed a PhoP protected region of 26 nt (PHO box; two direct repeats of 11 nt) that overlaps with the AfsR binding sequence. Binding experiments indicated a competition between AfsR and PhoP; increasing concentrations of PhoP(DBD) resulted in the disappearance of the AfsR-DNA complex. Expression studies using the reporter luxAB gene coupled to afsS promoter showed that PhoP downregulates afsS expression probably by a competition with the AfsR activator. Interestingly, AfsR binds to other PhoP-regulated promoters including those of pstS (a component of the phosphate transport system) and phoRP (encoding the two component system itself). Analysis of the AfsR-protected sequences in each of these promoters allowed us to distinguish the AfsR binding sequence from the overlapping PHO box. The reciprocal regulation of the phoRP promoter by AfsR and of afsS by PhoP suggests a fine interplay of these regulators on the control of secondary metabolism.

Genetic regulation of secondary metabolic pathways in Streptomyces

Streptomyces species are (along with the fungi) the best-known antibiotic-producing organisms. Often, they make several different antibiotics. The biosynthesis of each antibiotic is encoded by a complex gene cluster that usually also contains regulatory and resistance genes. Typically, there may be more than one such pathway-specific regulatory gene per cluster. Both activator and repressor genes are known. Some of the regulatory genes for different pathways are related. In S. coelicolor, expression of several such biosynthetic gene clusters also depends on at least 11 globally acting genes, at least one of which is involved in the translation of a rare codon (UUA). A protein phosphorylation cascade also seems to be involved. Gene clusters closely similar to those for the biosynthesis of aromatic polyketide antibiotics determine spore pigment in some species. These genes show different regulation from antibiotic production genes. The evolution of gene clusters for polyketide antibiotics, and the possible adaptive benefits of secondary metabolism, are discussed.

Identification and characterization of the afsR homologue regulatory gene from Streptomyces peucetius ATCC 27952

We have isolated an afsR homologue, called afsR-p, through genome analysis of Streptomyces peucetius ATCC 27952. AfsR-p shares 60% sequence identity with AfsR from Streptomyces coelicolor A3 (2). afsR-p was expressed under the control of the ermE* promoter in its hosts S. peucetius, Streptomyces lividans TK 24, Streptomyces clavuligerus and Streptomyces griseus. We observed overproduction of doxorubicin (4-fold) in S. peucetius, gamma-actinorhodin (2.6-fold) in S. lividans, clavulanic acid (1.5-fold) in S. clavuligerus and streptomycin (slight) in S. griseus. Overproduction was due to expression of the gene in these strains as compared to the wild-type strains harboring the vector only. Comparative study of the expression of afsR-p revealed that regulatory networking in Streptomyces is not uniform. We speculate that phosphorylated AfsR-p becomes bound to the promoter region of afsS. The latter activates other regulatory genes, including pathway regulatory genes, and induces the production of secondary metabolites including antibiotics. We identified specific conserved amino acids and exploited them for the isolation of the partial sequence of the afsR homologue from S. clavuligerus and Streptomyces achromogens (rubradirin producer). Such findings provide additional evidence for the presence of a serine/threonine and tyrosine kinase-dependent global regulatory network in Streptomyces.

Genomewide insertional mutagenesis in Streptomyces coelicolor reveals additional genes involved in morphological differentiation

The filamentous soil bacterium Streptomyces coelicolor undergoes a complex cycle of morphological differentiation involving the formation of an aerial mycelium and the production of pigmented antibiotics. We have developed a procedure for generating insertional mutants of S. coelicolor based on in vitro transposition of a plasmid library of cloned S. coelicolor DNAs. The insertionally mutated library was introduced into S. coelicolor, and transposon insertions were recovered at widely scattered locations around the chromosome. Many of the insertions revealed previously uncharacterized genes, and several caused novel mutant phenotypes, such as altered pigment production, enhanced antibiotic sensitivity, delayed or impaired formation of aerial hyphae, and a block in spore formation. The sporulation mutant harbored an insertion in one of three adjacent genes that are apparently unique to Streptomyces but are each represented by at least 20 paralogs at dispersed locations in the chromosome. Individual members of the three families often are found grouped together in a characteristic arrangement, suggesting that they have a common function.

The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus

A new Sulfolobus islandicus strain, REY15/4, harboured both a novel fusellovirus, SSV2, and a small plasmid, pSSVx. The plasmid spread in S. solfataricus P1 together with the virus after infection with either the supernatant of a culture of REY15/4 or purified virus. Spreading of the plasmid required co-transfection with either SSV2 or the related SSV1 as helpers. Virus purified from REY15/4 constituted a mixture of two sizes of particles, one with the dimensions of a normal fusellovirus and the other smaller. Cloned SSV2 produced only the larger particles and only SSV2 DNA, indicating that the smaller particles contained pSSVx packaged into capsids made up of SSV2 components. The 5.7 kb genome of pSSVx revealed regions of high sequence similarity to the cryptic Sulfolobales plasmids pRN1, pRN2 and pDL10. Thus, pSSVx belongs to the family of pRN plasmids that share a highly conserved region, which probably constitutes the minimal replicon. They also contain a variable region showing no sequence similarity. In pSSVx, this region contains three open reading frames (ORFs), two of which are juxtapositioned and show high sequence similarity to a tandem of ORFs in fusellovirus genomes. Neither pRN1 nor pRN2, which lack this tandem, spread in the presence of the fuselloviruses, which implies that the sequences of these ORFs enable pSSVx to use the packaging system of the viral helpers for spreading.

Isolation and purification of two novel streptomycete RNase inhibitors, SaI14 and SaI20, and cloning, sequencing, and expression in Escherichia coli of the gene coding for SaI14

Two new RNase inhibitors, SaI14 (Mr, approximately 14,000) and SaI20 (Mr, approximately 20,000), were isolated and purified from a Streptomyces aureofaciens strain. The gene sai14, coding for SaI14 protein, was cloned and expressed in Escherichia coli. The alignment of the deduced amino acid sequence of SaI14 with that of barstar, the RNase inhibitor from Bacillus amyloliquefaciens, showed significant similarity between them, especially in the region which contains most of the residues involved in barnase-barstar complex formation.

A method for the identification of promoters recognized by RNA polymerase containing a particular sigma factor: cloning of a developmentally regulated promoter and corresponding gene directed by the Streptomyces aureofaciens sigma factor RpoZ

We have developed a method for the identification of promoters recognized by a particular sigma factor of RNA polymerase, based on a two-compatible plasmid system in Escherichia coli (Ec). Using the method, a DNA fragment containing the promoter, PREN40, recognized by sporulation-specific Streptomyces aureofaciens (Sa) sigma factor RpoZ, was cloned. High-resolution S1 nuclease mapping using RNA prepared from Ec, and Sa from various developmental stages has shown a high degree of similarity of PREN40 to consensus sequence of flagellar and chemotaxis promoters. The promoter was induced at the time of aerial mycelium formation, and was off in the Sa strain with the rpoZ-disrupted gene. A promoter-bearing DNA fragment was inserted into the promoter-probe plasmid pARC1 to give expression patterns consistent with the results of direct RNA analysis. The region downstream of the promoter was cloned in Sa. Sequence analysis revealed an open reading frame (ORF) of 283 amino acids (Mr 30006), encoding a highly basic (pI 12.35) protein with high percentage of serine, threonine and alanine (41.8%).

The Streptomyces aureofaciens homologue of the whiB gene is essential for sporulation; its expression correlates with the developmental stage

In previous experiments, a Streptomyces aureofaciens gene highly similar to the sporulation-specific whiB gene of Streptomyces coelicolor was identified. By integrative transformation, via double cross-over, a stable null mutant of the whiB-homologous gene of S. aureofaciens was obtained. The disruption blocked differentiation at a stage between the formation of aerial mycelium and the development of mature spores, producing white aerial hyphae without septation. Expression of the whiB gene was investigated during differentiation by S1 nuclease mapping, using RNA prepared from S. aureofaciens in various developmental stages. Two putative promoters were identified upstream of the whiB coding region. The stronger promoter, whiB-P2, was induced at the beginning of aerial mycelium formation, and the weaker promoter, whiB-P1, was expressed fairly constantly during differentiation. No differences in the expression of the whiB promoters were detected in an rpoZ-disrupted S. aureofaciens strain. The promoter bearing DNA fragment was inserted into the promoter-probe vector pARC1 to produce an expression pattern consistent with the results of direct RNA analysis.

Expression of the Streptomyces aureofaciens glyceraldehyde-3-phosphate dehydrogenase gene (gap) is developmentally regulated and induced by glucose

In previous experiments, the Streptomyces aureofaciens gap gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified. To investigate expression of the gene, S1 nuclease mapping and Northern blot hybridization were performed using RNA prepared from S. aureofaciens cultivated under various conditions. These studies suggested monocistronic organization and developmental regulation of the gene. A single promoter, gap-P, was identified upstream of the gap coding region. In cultures grown on solid medium in the absence of glucose, its transcription was induced at the time of aerial mycelium formation. In addition, gap transcription was also induced in substrate mycelium by glucose. A promoter-bearing DNA fragment was inserted into two promoter-probe vectors, to give expression patterns consistent with the results of direct RNA analysis.

Differential expression of two sporulation specific sigma factors of Streptomyces aureofaciens correlates with the developmental stage

In previous experiments, the Streptomyces aureofaciens (Sa) rpoZ, and sigF genes have been shown to encode putative sigma factors essential in differentiation. In an attempt to investigate expression of these genes during differentiation, we have performed S1 nuclease mapping using RNA prepared from Sa in various developmental stages. Two putative promoters were identified upstream of the rpoZ coding region. The promoters significantly differed in their strength, and were active in distinct developmental stages; the weaker, rpoZ-P1, was active only in substrate mycelium, and the stronger, rpoZ-P2, was induced at the beginning of aerial mycelium formation. Transcriptional analysis of sigF revealed two apparent transcription start points, both being detectable only in the late phase of aerial mycelium formation. No sigF transcription was detected in an rpoZ-disrupted Sa strain. Promoter-bearing DNA fragments from rpoZ and sigF were inserted into several promoter-probe vectors, to give expression patterns consistent with the results of direct RNA analysis. The results implicate temporally different expression of rpoZ and sigF during the differentiation of Sa, and direct or indirect dependence of sigF expression on the rpoZ-encoded putative sigma factor, thus indicating a cascade of sigma factors in Streptomyces development.

Repeated sequences from the Arabidopsis thaliana genome function as enhancers in transgenic tobacco

Sixteen segments of Arabidopsis thaliana DNA that function as enhancers in transgenic tobacco plants were isolated using the pROA97 enhancer cloning vehicle and library transformation of Nicotiana tabacum. The sequences were compared for AT content, homology, repeated motifs, and expression pattern in transgenic N. tabacum. The sequences were average with respect to the AT content of A. thaliana DNA. They could be placed into seven homology groups. Five of the sequences are single-copy sequences. The remaining eleven sequences represent two homology groups. Homology Group I contains seven sequences with minor differences. Homology Group II contains four sequences with minor differences. Two repeated motifs were identified (5'-CCTCT-3' and 5'-AAGGAT-3'). Both repeated motifs are found in other plant enhancers, and in the promoter region of the cauliflower mosaic virus 35S gene. In the 35S gene TATA region, the motifs can form two alternative stem-loop structures. The TATATAA sequence is located in the loop region of both stem-loop structures.

Development of a temperature-inducible expression system for Streptomyces spp

PCR mutagenesis of a 0.9-kbp fragment, containing a repressor gene, traR, and its target promoter, Ptra, from Streptomyces nigrifaciens plasmid pSN22, produced Streptomyces lividans clones with temperature-inducible Ptra expression. Using the promoterless gene for the thermostable Thermus flavus malate dehydrogenase as an indicator, an induction of enzyme activity of as much as was observed in a temperature shift from 28 to 37 degrees C. Temperature downshift reestablished repression of Ptra, making these promoter cassettes very attractive for the temporally regulated expression of cloned genes in Streptomyces spp.

The aerial mycelium-defective phenotype of Streptomyces griseus resulting from A-factor deficiency is suppressed by a Ser/Thr kinase of S. coelicolor A3(2)

A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) is essential for aerial mycelium formation and streptomycin (Sm) production in Streptomyces griseus. A protein Ser/Thr kinase (AfsK), the product of the Streptomyces coelicolor A3(2) afsK gene, controlling secondary metabolism in this strain, reversed the aerial mycelium-negative phenotype of an A-factor-deficient mutant strain, S. griseus HH1, and induced sporulation without affecting A-factor productivity or Sm production. A mutant AfsK protein lacking kinase activity failed to induce aerial mycelium formation which indicates the importance of the kinase activity for suppression in S. griseus. These data suggest that a Ser/Thr kinase functionally similar to S. coelicolor A3(2) AfsK plays a regulatory role in aerial mycelium formation in S. griseus, either as a member in the A-factor regulatory network or independently of this network.

Regulation of the transfer genes of Streptomyces plasmid pSN22: in vivo and in vitro study of the interaction of TraR with promoter regions

Expression of the tra operon, essential for conjugative transfer of the 11-kb Streptomyces nigrifaciens plasmid pSN22, is negatively regulated by traR, which is located upstream of the tra operon and transcribed in the opposite orientation. The transcriptional start points for the tra and traR mRNAs were determined by primer extension; they are 72 bp apart and have identical -10 promoter sequences. The TraR protein was overexpressed in Escherichia coli and used for gel retardation and DNase I protection experiments. It bound specifically to the bidirectional tra-traR promoter region and protected four DNA regions, each of which contains a similar 12-bp sequence. The binding was strongest to the region downstream of the tra promoter, probably ensuring that expression of the potentially lethal traB gene is turned off before traR. The efficiency of intramycelial plasmid transfer was decreased by the mutation at the downstream region.

A hydroxylase-like gene product contributes to synthesis of a polyketide spore pigment in Streptomyces halstedii

A gene, schC, adjacent to the sch gene cluster encoding the biosynthesis of a polyketide spore pigment in Streptomyces halstedii was sequenced. Its deduced product resembled flavin adenine nucleotide-containing hydroxylases involved in the biosynthesis of polycyclic aromatic polyketide antibiotics and in catabolic pathways of aromatic compounds. When schC was disrupted, the normally green spores of S. halstedii became lilac. An schC-like gene was located in an equivalent position next to a large gene cluster (whiE) known to determine spore pigment in Streptomyces coelicolor A3(2).

Hybridization and DNA sequence analyses suggest an early evolutionary divergence of related biosynthetic gene sets encoding polyketide antibiotics and spore pigments in Streptomyces spp

The whiE gene cluster of Streptomyces coelicolor, which is related to gene sets encoding the biosynthesis of polycyclic aromatic polyketide antibiotics, determines a spore pigment. Southern blotting using probes from three different parts of the whiE cluster revealed related gene sets in about half of a collection of diverse Streptomyces strains. A 5.2-kb segment of one such cluster, sch, previously shown to determine spore pigmentation in Streptomyces halstedii, was sequenced. Seven open reading frames (ORFs), two of them incomplete, were found. Six of the ORFs resemble the known part of the whiE cluster closely. The derived gene products include a ketosynthase (= condensing enzyme) pair, acyl carrier protein and cyclase, as well as two of unidentified function. The seventh ORF diverges from the main cluster and encodes a protein that resembles a dichlorophenol hydroxylase. Comparison with sequences of related gene sets for the biosynthesis of antibiotics suggests that gene clusters destined to specify pigment production diverged from those destined to specify antibiotics early in the evolution of the Streptomyces genus.

Differential expression of principal sigma factor homologues of Streptomyces aureofaciens correlates with the developmental stage

In previous experiments, Streptomyces aureofaciens has been shown to contain four genes hrdA, hrdB, hrdD, and hrdE, encoding polypeptides very similar to principal sigma factors of RNA polymerase. Two apparent tandem promoters were identified for each of the hrdA, hrdB and hrdD genes by S1 nuclease mapping using RNA prepared of S. aureofaciens in various developmental stages. Under all the conditions studied, tandem promoters of each gene differed significantly in their respective strengths. Transcription from the hrd promoters depended on developmental stage. While hrdB is transcribed from both promoters in all developmental stages, both tandem promoters of the hrdD gene are active only in vegetative stage and transcription of the hrdA tandem promoters temporally correlates with the aerial mycelium formation. In addition to a promoter, hrdB-P2, which lies upstream of the open reading frame, the hrdB gene, proposed to encode functional principal factor, appeared to contain at least one internal promoter, hrdB-P1. Activity of all promoters was consistent with S1 mapping experiments after insertion of promoter-bearing DNA fragments to promoter-probe vectors pIJ486 and pARC1. The results implicate temporally different expression of the hrd genes during the differentiation of S. aureofaciens.

Tn4556 and luciferase: synergistic tools for visualizing transcription in Streptomyces

Progress in understanding genetic regulatory controls in the Actinomycetes has been rate limited by the properties of in vivo transcriptional probes. We have developed a set of plasmid- and transposon-based promoter-probe vectors that employ the Vibrio harveyi luciferase-encoding luxAB cassette as a reporter of transcription. The primary advantages of luciferase (Lux) over other reporter gene products are: (i) unsurpassed sensitivity; (ii) utility during stationary-phase gene expression; and (iii) the ability to localize promoter activity spatially within developing colonies. We have used these vectors to screen for Streptomyces coelicolor promoters that exhibit developmental phenotypes or that are induced by various environmental stimuli. The plasmid-based probes have proved invaluable for identifying cis- and trans-acting elements that are required for stationary-phase expression of the S. coelicolor sapA gene. A collection of novel bld and whi insertion mutants has been obtained by use of the Lux-encoding transposon, Tn5353.

Inducible expression of ribosomal clindamycin resistance in Bacteroides vulgatus

The abilities of erythromycin and clindamycin to act as inducers of clindamycin resistance in the strain Bacteroides vulgatus RYC18F6 is evaluated in vivo (efficiency of plating of inhibitory clindamycin concentrations) and in vitro [efficiency of poly(U)-directed polypeptide synthesis by ribosomes]. Uninduced cells failed to grow during the first 72 h, even at a very low clindamycin concentration (0.1 microgram/ml); after induction with erythromycin or clindamycin, cells were able to form colonies at 32 micrograms/ml after 48 h. The in vitro polymerization test with B. vulgatus RYC18F6 ribosomes (S-30 extract) showed that ribosomes from uninduced cells were fully sensitive to the inhibitory effect of clindamycin. Ribosomes obtained from erythromycin- or clindamycin-induced cells presented a reduced sensitivity to clindamycin inhibition. These results show that resistance to clindamycin in B. vulgatus RYC18F6 is an inducible phenomenon involving a ribosomal modification, probably similar to that previously described for gram-positive bacteria.

Transcriptional analysis of the isopenicillin N synthase-encoding gene of Streptomyces clavuligerus

The gene (pcbC) encoding isopenicillin N synthase of Streptomyces clavuligerus is separated from an upstream open reading frame (ORF) by a 31-bp intergenic region. Inspection of the sequence of this intergenic region did not identify a promoter sequence. The promoter probe plasmid, pIJ4083, which contains the promoter-less catechol-2,3-dioxygenase (C23O)-encoding gene (xylE) as a reporter gene, was used to analyze the sequence upstream from the pcbC gene for promoter activity. Introduction of an SphI site at the start codon of pcbC by site-directed mutagenesis allowed the cloning of a 335-bp fragment (-334 to +1 in relation to the pcbC start codon) immediately upstream from xylE in pIJ4083. C23O activity was detected in both Streptomyces lividans and S. clavuligerus cultures that contained the upstream fragment, suggesting the presence of a promoter sequence. Northern analysis of total RNA extracted from S. clavuligerus identified a monocistronic 1.2-kb transcript hybridizing to a pcbC-specific probe. When RNA was isolated at various times during growth in liquid culture, the presence of a transcript was first detected during stationary phase. Analysis of the pcbC transcript by primer extension located the transcription start point to a C residue within the upstream ORF, 91 bp upstream from the pcbC start codon.

Construction and application of plasmid- and transposon-based promoter-probe vectors for Streptomyces spp. that employ a Vibrio harveyi luciferase reporter cassette

Several versatile promoter-probe vectors have been constructed for Streptomyces strains which utilize the production of blue-green light as a measure of transcription activity. Three plasmid vectors (two high and one low copy number) and two transposons are described. The multicopy plasmids pRS1106 and pRS1108 contain a transcription terminator and multiple-cloning polylinker upstream of promoterless luciferase (lux) and neomycin resistance reporter genes. Plasmid pHI90 is similar in structure to the pRS vectors except that its single copy number is an advantage for regulation studies or situations in which overexpression is otherwise toxic to the cell. The two transposons carry a promoterless lux cassette cloned such that transposition into a target DNA and fusion to the target's transcription unit occur simultaneously. Tn5351 was created by inserting the luciferase genes near the right end of the viomycin resistance transposon Tn4563. Tn5353 carries the luciferase genes near the right end of a neomycin resistance transposon derived from Tn4556. The size of Tn5353 was minimized by deleting nonessential transposon sequences, making this element small enough to be cloned into phi C31 bacteriophages for efficient transposon delivery to target cells of Streptomyces strains. The two Tnlux transposons have been used to generate Streptomyces coelicolor morphological mutants and to monitor transcription from chromosomal promoters during development.

Regulation and function of the Streptomyces plasmid pSN22 genes involved in pock formation and inviability

pSN22 is an 11-kb multicopy plasmid from Streptomyces nigrifaciens which is being studied in Streptomyces lividans. A segment of about 7 kb of pSN22 contains five genes involved in conjugation. Three of them, traA, traB, and traR, are essential for plasmid transfer and for the mobilization of chromosomal markers (fertility), while the remaining two genes, spdA and spdB, merely enhance the efficiency of plasmid transfer, resulting in the formation of larger pocks. In vitro promoter-probing experiments identified a 550-bp BglII-SmaI DNA fragment with promoter activity in both orientations; Northern (RNA blot) hybridization identified corresponding divergent transcripts of 1 and 5.2 kb for traR and the traA-traB-spdB operon, respectively. The traR gene product repressed its own transcription and also the transcription of the traA-traB-spdB operon. Plasmids containing a functional traB gene could not "survive" without traR being present in the same cell either in cis or in trans, presumably because unregulated expression of traB is lethal to the host. Plasmids with a functional traA gene but without traR had a low transformation efficiency and inhibited the growth of host cells.

Phage Vectors that Allow Monitoring of Transcription of Secondary Metabolism Genes in Streptomyces

We describe a bacteriophage phi C31-based system that permits the transcriptional fusion of the convenient reporter gene xylE to chromosomally located promoters in Streptomyces hosts. Applicability of the system to genes for secondary metabolism is demonstrated in an experiment showing that transcription of genes for actinorhodin production in Streptomyces coelicolor A3(2) depends on a transfer RNA gene (bldA) for the rare UUA codon. Two other phi C31::xylE vectors are described that allow detection of promoter activity away from their natural location, either at single copy in a prophage or during lytic infections in plaques.

Bacterial resistance to macrolide, lincosamide, and streptogramin antibiotics by target modification

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Cloning, nucleotide sequence, and transcriptional analysis of the NAD(P)-dependent cholesterol dehydrogenase gene from a Nocardia sp. and its hyperexpression in Streptomyces spp

NAD(P)-dependent cholesterol dehydrogenases [NAD(P)-CDH], which allow easier quantification of cholesterol by means of directly measuring the A340 of NAD(P)H, are useful for clinical purposes. The amino acid sequences of the NH2 terminus and the fragments obtained by CNBr decomposition of the NAD(P)-CDH from a Nocardia sp. were determined for preparation of synthetic oligonucleotides as hybridization probes. A 4.4-kbp BamHI fragment hybridizing to these probes was cloned on pUC19 in Escherichia coli. The nucleotide sequence together with the determined amino acid sequences revealed that this enzyme consists of 364 amino acids (Mr, 39,792) and contains an NAD(P)-binding consensus sequence at its NH2-terminal portion. High-resolution S1 nuclease mapping suggested that in NAD(P)-CDH of both Nocardia and Streptomyces spp. transcription initiates at the adenine residue, which is the first position of the translational initiation triplet (AUG) of this protein. The S1 mapping experiments also showed that cholesterol-dependent regulation in the Nocardia sp. occurred at the level of transcription. In Streptomyces lividans containing the cloned fragment, however, this promoter was expressed constitutively. DNA manipulation of the cloned gene in E. coli, including the generation of a ribosome-binding sequence at an appropriate position by oligonucleotide-directed mutagenesis, led to production of this protein in a very large amount but in the enzymatically inactive form of inclusion bodies. On the other hand, a Streptomyces host-vector system was successfully used for producing 40 times as much enzymatically active NAD(P)-CDH as that produced by the original Nocardia sp.

Localization and characterization of a temporally regulated promoter from the Streptomyces aureofaciens 2201 plasmid pSA 2201

An RNA polymerase-binding 167 bp HinfI fragment from a low-copy Streptomyces plasmid pSA 2201 has been shown to have promoter activity in vivo using a promoter-probe vector. This promoter (A1) is probably involved in expression of the genes responsible for the production of an antibiotic compound, found to be located on this plasmid. A 2600 nucleotides (nt) long transcript starting from this promoter has been identified by Northern hybridization analysis. The transcription start point has been determined using high-resolution S1 mapping and confirmed by in vitro transcription analysis with purified S. aureofaciens 2201 RNA polymerase. The A1 promoter shows no homology in the -10 and -35 consensus sequence of the typical bacterial promoters, and expression from this promoter is temporally dependent on the phase of growth having the maximum transcription activity in the stationary phase.

Transcriptional and translational features of a sporulation gene of Streptomyces griseus

The nucleotide (nt) sequence of a 2.8-kb fragment of DNA that restores sporulation to one class of bald mutants of Streptomyces griseus revealed an open reading frame (ORF) with the potential to encode a 55.5-kDa polypeptide. The presence of an in-frame TTA in the coding sequence indicated that translation is likely to require the tRNA(Leu)UUA encoded by the bldA gene. Two overlapping transcripts are initiated at transcriptional start points (tsp) separated by 258 nt and are transcribed in the same direction. The downstream tsp lies within the ORF and is followed by a second potential translation initiation site, which would encode a 49.5-kDa polypeptide in the same reading frame as the 55.5-kDa polypeptide. Transcription assays suggested that both tsp functioned during vegetative growth, but the relative abundance of the shorter transcript decreased during the early stages of submerged sporulation. Analysis of sequentially deleted subclones indicated that expression of the longer ORF was necessary to complement bald mutants. The presence of two tsp alternating with potential translation start codons suggests the temporally regulated synthesis of two polypeptides that have identical C termini but different N termini.

Primary structure of AfsR, a global regulatory protein for secondary metabolite formation in Streptomyces coelicolor A3(2)

The afsR gene of Streptomyces coelicolor A3(2) complements afsB mutations affecting production of pigmented antibiotics. It also directs pigment production in Streptomyces lividans when carried on a plasmid vector. Nucleotide sequencing of the afsR gene revealed that it codes for a 993-amino acid protein (Mr 105,600) with A- and B-type ATP-binding consensus sequences at its N-terminal portion and two DNA-binding consensus sequences with a helix-turn-helix motif at its C-terminal portion. Each of the N- and C-terminal halves was capable of conferring pigment production, to some extent, in S. lividans, when carried separately on a multicopy plasmid. In addition, expression in trans of the two regions on the same plasmid conferred pigment production to almost the same extent as did the intact afsR gene. Mutations at the two ATP-binding consensus sequences, that were generated by in vitro site-directed mutagenesis, revealed their functional importance. Disruption of the S. coelicolor A3(2) chromosomal afsR gene in either the N- or C-terminal half using phage phi C31 KC515 resulted in significant, but not complete, loss of pigment production. These data suggest that the AfsR protein comprises two domains, viz., an ATP-binding and a DNA-binding domain, each of which could function as a positive regulator for pigment production. These afsR mutants sporulate normally. In addition to an internal promoter, which we previously detected in the middle of the AfsR coding region, S1 nuclease mapping revealed two tandem transcriptional start points, separated by 64 bp, upstream from a putative ATG start codon of the AfsR product.

Spore colour in Streptomyces coelicolor A3(2) involves the developmentally regulated synthesis of a compound biosynthetically related to polyketide antibiotics

Streptomyces coelicolor produces spores whose development of a grey colour requires the activity of the whiE locus. The cloned whiE locus was identified after mobilization into a whiE mutant of a library of S. coelicolor DNA inserted into a transmissible plasmid vector. The whiE region of the cloned DNA was localized both by subcloning and by mutagenesis of the cloned DNA with the Streptomyces transposon Tn4560. Nucleotide sequencing of this region revealed seven open reading frames, of which six show homology at the level of deduced gene products with genes involved in the synthesis of polyketide antibiotics. A previously described S. coelicolor DNA segment encoding biosynthesis of a brown pigment (Horinouchi and Beppu, 1985) corresponds to the cloned whiE DNA. It is proposed that whiE is normally expressed only in the aerial hyphae, where the biosynthetic product is responsible for spore colour.

Enhancer sequences from Arabidopsis thaliana obtained by library transformation of Nicotiana tabacum

In this paper we report on the use of a bidirectional enhancer cloning vehicle to isolate and characterize new enhancer sequences from Arabidopsis thaliana. A library of A. thaliana genomic Sau3A segments was constructed in Escherichia coli in the binary plasmid enhancer cloning vehicle pROA97. The T-DNA based vector carries abbreviated TATA regions from the cauliflower mosaic virus 35S transcription unit upstream of two genes. The library was transferred via triparental mating into Agrobacterium tumefaciens. The neomycin phosphotransferase II gene was used for selection of kanamycin-resistant transformed tobacco callus cells. Approximately 1100 transgenic plants were regenerated and assayed for expression of the E. coli beta-glucuronidase (GUS) gene in leaves, stems, roots, or seeds. Plasmids carrying putative enhancer sequences were rescued from the genomes of transgenic plants and the cloned sequences were assayed for enhancer function in genetic selection experiments. Plants were regenerated from the kanamycin-resistant calli obtained in the secondary transformation experiments. Histochemical analysis of GUS activity in the leaf, stem, and root tissues of transgenic plants showed a variety of expression patterns. The DNA sequences are presented of five Arabidopsis segments which confer enhancer function.

The ermC leader peptide: amino acid alterations leading to differential efficiency of induction by macrolide-lincosamide-streptogramin B antibiotics

The inducibility of ermC by erythromycin, megalomicin, and celesticetin was tested with both wild-type ermC and several regulatory mutants altered in the 19-amino-acid-residue leader peptide, MGIFSIFVISTVHYQP NKK. In the model test system that was used, the ErmC methylase was translationally fused to beta-galactosidase. Mutational alterations that mapped in the interval encoding Phe-4 through Ile-9 of the leader peptide not only affected induction by individual antibiotics, but did so differentially. The subset of mutations that affected inducibility by the two macrolides erythromycin and megalomicin overlapped and were distinct from the subset of mutations that affected induction by celesticetin. These studies provide a model system for experimentally varying the relative efficiencies with which different antibiotics induce the expression of ermC. The possibility that antibiotics with inducing activity interact directly with the nascent leader peptide was tested by using a chemically synthesized decapeptide, MGIFSIFVIS--, attached at its C-terminus to a solid-phase support. This peptide, however, failed to bind erythromycin in vitro.

Use of the tyrosinase gene from Streptomyces to probe promoter sequences for Escherichia coli

We have constructed a promoter-probe vector utilizing the expression of a promoter-less tyrosinase derived from Streptomyces plasmid pIJ702. The vector, pMX100, has single sites for EcoRI, KpnI, BamHI, XbaI, SalI, and SphI for cloning promoter sequences. When the tac promoter was inserted into pMX100, E. coli harboring the chimeric plasmid produced the melanin pigment.

xylE functions as an efficient reporter gene in Streptomyces spp.: use for the study of galP1, a catabolite-controlled promoter

We describe the development of a convenient and sensitive reporter gene system for Streptomyces spp. based on the use of a promoterless copy of the xylE gene of Pseudomonas putida. The xylE gene product is a catechol dioxygenase, which converts the colorless substrate catechol to an intensely yellow hydroxymuconic semialdehyde. A promoterless copy of xylE was placed under the transcriptional control of galP1, a glucose-repressed and galactose-induced promoter from Streptomyces lividans, and its expression was examined in bacterial colonies on agar plates or in liquid cultures grown in the presence of glucose or galactose as the sole carbon source. On plates, colonies of bacteria grown on galactose turned bright yellow within a few minutes of being sprayed with a solution of catechol, whereas colonies on glucose-containing plates remained white or only slightly colored, even after extensive incubation. Activity of galP1-xylE fusions was conveniently measured in crude cell extracts with a simple colorimetric assay and was shown to faithfully reflect intracellular RNA levels, as determined by quantitative dot blots. Moreover, differences in expression levels of xylE fusions driven by mutant galP1 promoters were readily apparent in color reactions on plates. The properties of xylE as a reporter gene thus make it suitable not only for quantitatively monitoring expression of regulated promoters in Streptomyces spp. but also for recovering mutations that alter the expression levels of promoters of interest.

An improved plasmid for the isolation and analysis of Streptomyces promoters

A Streptomyces promoter-probe plasmid vector was developed to isolate and characterize nucleotide sequences involved in transcriptional regulation. This pCLL34 vector was derived from plasmid pARC1 carrying the SLP1.2 origin of replication [Horinouchi and Beppu, J. Bacteriol. 162 (1985) 406-412]. Important features of the new vector include moderate host range, low copy number, simple identification of promoter activity by brown pigment production, an upstream transcriptional terminator, and a polylinker sequence containing a unique BamHI site for flexible cloning and fragment reisolation. The vector also provides the capability to directly determine the sequence of promoter-active inserts by dideoxy chain-termination sequencing methods using double-stranded plasmid templates and the appropriate oligodeoxynucleotide primers.

Cloning and nucleotide sequence of a cellulase gene, casA, from an alkalophilic Streptomyces strain

A gene encoding an endo-type semi-alkaline cellulase was cloned from an alkalophilic Streptomyces strain in Streptomyces lividans, and its nucleotide sequence was determined. Downstream from the transcriptional start point, which was determined by high-resolution S1 mapping, an open reading frame of 388 amino acids (aa) was present. The N-terminal amino acid sequence of the mature enzyme determined by an Edman degradation procedure suggested that the cellulase had an extraordinarily long leader sequence of about 70 aa. Comparison with the leader sequences of endoglucosidase H from Streptomyces plicatus and the cellulase from Cellulomonas fimi suggested that the semi-alkaline cellulase was processed in two steps during maturation.

Construction and characterization of multicopy expression-vectors in Streptomyces spp

A strong transcriptional signal previously cloned from the Streptomyces griseus genome in S. lividans was subcloned and its nucleotide sequence was determined. Upstream of the transcriptional start point which was determined by high-resolution S1 nuclease mapping, -35 (5'-TTGCCG-3') and -10 (5'-TAGCGT-3') sequences, separated by 18 nucleotides, were present. By replacing the tet promoter of pBR322 with the Streptomyces promoter, no expression of the tet gene was observed in Escherichia coli cells. The result suggests that notwithstanding a similarity to the E. coli -35 and -10 sequences, the Streptomyces promoter is not functional in E. coli. The strong promoter was inserted in multi-copy and wide host range plasmids pIJ702 and pKS11, resulting in the pSEV series of expression-vectors with several unique restriction endonuclease cleavage sites downstream of the promoter for cloning of foreign genes. The extremely heat-stable malate dehydrogenase of Thermus flavus, when its coding sequence with a ribosome-binding site was located downstream of the strong promoter in pSEV2, was produced in large quantities in S. lividans throughout growth. When an extracellular cellulase from Bacillus subtilis was expressed in a cellulase-negative S. lividans strain, virtually all of the cellulase activity was found in the culture supernatant.

Chromogenic identification of promoters in Streptomyces lividans by using an ampC beta-lactamase promoter-probe vector

A promoter-probe system, based on the ampC beta-lactamase gene of Escherichia coli, has been developed for the isolation and characterization of transcriptional signals in the gram-positive bacterium Streptomyces lividans. The promoter-probe vector, denoted pJAS14, has the SLP1.2 replicon with a copy number of four-five plasmids per cell. It contains a unique BamHI site just in front of the ampC ribosome-binding site, and upstream of this BamHI site a transcriptional terminator signal that prevents readthrough transcription from plasmid-borne promoters has been inserted. Using pJAS14, we have shot-gun cloned chromosomal DNA from S. lividans and S. lavendulae into the BamHI site, and isolated a number of promoter containing DNA fragments by the use of the chromogenic cephalosporin nitrocefin. On plates, we identified promoters of varying strengths and also with differences in nutritional and temporal expression. Using liquid cultures of S. lividans, it has been demonstrated that one promoter, denoted P1 (SEP8), as well as the ampC gene of E. coli, show activity corresponding to the vegetative growth of the cells. The P1 (SEP8) promoter was shown to be expressed also in E. coli, and it initiates RNA synthesis at exactly the same nucleotides in both S. lividans and E. coli. The promoter shows good homology to the E. coli promoter consensus sequence in both the -35 and -10 regions. Thus, this promoter is a representative of the SEP (Streptomyces E. coli-type promoter) class of promoters recently described (Jaurin and Cohen 1985). This indicates that an S. lividans RNA polymerase recognizes the same sequence determinants and chooses the point of initiation of RNA synthesis in the same way as the corresponding E. coli enzyme.

The impact of genetic engineering on the commercial production of antibiotics by Streptomyces and related bacteria

Developments in Streptomyces genetics that have laid a foundation for this field over the past ten years are reviewed and discussed to suggest how this knowledge might useful for improving the commercial production of antibiotics. This brief analysis predicts a bright future for the application of Streptomyces genetics in antibiotic production.

Nucleotide sequence of the streptothricin acetyltransferase gene from Streptomyces lavendulae and its expression in heterologous hosts

The nucleotide sequence of the streptothricin acetyltransferase (STAT) gene from streptothricin-producing Streptomyces lavendulae predicts a 189-amino-acid protein of molecular weight 20,000, which is consistent with that determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme. The amino acid composition and the NH2-terminal sequence determined by using the purified protein are in good agreement with those predicted from the nucleotide sequence, except for the absence of the NH2-terminal methionine in the mature protein. High-resolution S1 nuclease protection mapping suggests that transcription initiates at or near the adenine residue which is the first position of the translational initiation triplet (AUG) of STAT. Another open reading frame located just upstream of the STAT gene was detected and contains a region bearing a strong resemblance to DNA-binding domains which are conserved in known DNA-binding proteins. By addition of promoter signals and a synthetic ribosome-binding (Shine-Dalgarno) sequence at an appropriate position upstream of the STAT translational start codon, the STAT gene confers streptothricin resistance on Escherichia coli and Bacillus subtilis. The STAT coding sequence with both the promoter of a B. subtilis cellulase gene and a synthetic Shine-Dalgarno sequence was functionally expressed in Streptomyces lividans, which suggests that the addition of an artificial leader upstream of the translational initiation codon (AUG) does not significantly influence the translation of STAT.