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MGB-BP-3 is a potential first-in-class antibiotic, a Strathclyde Minor Groove Binder (S-MGB), that has successfully completed Phase IIa clinical trials for the treatment of

Here, we characterize an uncommon set of telomeres from Streptomyces rimosus ATCC 10970, the parental strain of a lineage of one of the earliest-discovered antibiotic producers. Following the closure of its genome sequence, we compared unusual telomeres from this organism with the other five classes of replicon ends found amongst streptomycetes. Closed replicons of streptomycete chromosomes were organized with respect to their phylogeny and physical orientation, which demonstrated that different telomeres were not associated with particular clades and are likely shared amongst different strains by plasmid-driven horizontal gene transfer. Furthermore, we identified a ~50 kb origin island with conserved synteny that is located at the core of all streptomycete chromosomes and forms an axis around which symmetrical chromosome inversions can take place. Despite this chromosomal bilateral symmetry, a bias in parS sites to the right of oriC is maintained across the family Streptomycetaceae and suggests that the formation of ParB/parS nucleoprotein complexes on the right replichore is a conserved feature in streptomycetes. Consequently, our studies reveal novel features of linear bacterial replicons that, through their manipulation, may lead to improvements in growth and productivity of this important industrial group of bacteria.

Rising levels of antibiotic resistance dictate that new antibiotics with novel modes of action must be found. Here, we investigated the mode of action of a novel antibiotic that is a member of a family of synthetic DNA minor groove binding (MGB) molecules. MGB-BP-3 has successfully completed a Phase II clinical trial in humans as an orally administered drug for the treatment of chronic Clostridioides (Clostridium) difficile infections, where it outperformed the existing benchmark (vancomycin). MGB-BP-3 is active against a variety of Gram-positive pathogens including Staphylococcus aureus, which was used as the model for this study. The transcriptomic response of S. aureus to MGB-BP-3 identified downregulated promoters. DNase I and permanganate footprinting demonstrated binding to essential SigA promoters and the inhibition of promoter isomerisation by RNA polymerase holoenzyme. Promoters controlling DNA replication and peptidoglycan biosynthesis are amongst those affected by MGB-BP-3. Thus, MGB-BP-3 binds to and inhibits multiple essential promoters on the S. aureus chromosome, suggesting that evolution of resistance by drug target mutation should be unlikely. In confirmation, laboratory-directed evolution against sub-inhibitory concentrations of MGB-BP-3 resulted in no resistance whereas resistance to the single target RNA-polymerase inhibitor rifampicin arose rapidly.

Actinobacteriaare a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic. These are made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last twenty years, the large size and complexity of many Actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large scale comparative genomics and evolutionary studies. To enable greater understanding and exploitation of Actinobacterial genomes, specialist genomic databases must be linked to high-quality genome sequences. Here we provide a curated database of 612 high-quality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome reannotation. Utilising this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution.Significance as a bioresource to the communityTheActinobacteriaare a large diverse phylum of bacteria, often with large, complex genomes with a high G+C content. Sequence databases have great variation in the quality of sequences, equivalence of annotation and phylogenetic representation, which makes it challenging to undertake evolutionary and phylogenetic studies. To address this, we have assembled a curated, taxa-specific, non-redundant database to aid detailed comparative analysis of Actinobacteria. ActDES constitutes a novel resource for the community of Actinobacterial researchers that will be useful primarily for two types of analyses: (i) comparative genomic studies – facilitated by reliable identification of orthologs across a set of defined, phylogenetically-representative genomes, and (ii) phylogenomic studies which will be improved by identification of gene subsets at specified taxonomic level. These analyses can then act as a springboard for the studies of the evolution of virulence genes, the evolution of metabolism and identification of targets for metabolic engineering.Data summaryAll genome sequences used in this study can be found in the NCBI taxonomy browserhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/www.tax.cgiand are summarised along with Accession numbers in Table S1All other data are available on Figsharehttps://doi.org/10.6084/m9.figshare.12167529andhttps://doi.org/10.5281/zenodo.3830391Perl script files available on GitHubhttps://github.com/nselem/ActDESincluding details of how to batch annotate genomes in RAST from the terminalhttps://github.com/nselem/myrastSupp. Table S1List of genomes from NCBI (Actinobacteria database.xlsx)https://doi.org/10.6084/m9.figshare.12167529CVS genome annotation files including the FASTA files of nucleotide and amino acids sequences (individual .cvs files)https://doi.org/10.6084/m9.figshare.12167880BLAST nucleotide database (.fasta file)https://doi.org/10.6084/m9.figshare.12167724BLAST protein database (.fasta file)https://doi.org/10.6084/m9.figshare.12167724Supp. Table S2 Expansion table genus level (Expansion table.xlsx Tab Genus level)https://doi.org/10.6084/m9.figshare.12167529Supp. Table S2 Expansion table species level (Expansion table.xlsx Tab species level)https://doi.org/10.6084/m9.figshare.12167529All GlcP and Glk data – blast hits from ActDES database, MUSCLE Alignment files and .nwk tree files can be found athttps://doi.org/10.6084/m9.figshare.12167529Interactive trees in Microreact for Glk treehttps://microreact.org/project/w_KDfn1xA/90e6759eand associated files can be found athttps://doi.org/10.6084/m9.figshare.12326441.v1Interactive trees in Microreact for GlcP treehttps://microreact.org/project/VBUdiQ5_k/0fc4622band associated files can be found athttps://doi.org/10.6084/m9.figshare.12326441.v1

Background. Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source. Results. RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source. Conclusions. Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.

Background Streptomycete bacteria are prolific producers of specialized metabolites, many of which have clinically relevant bioactivity. A striking feature of their genomes is the expansion of gene families that encode the same enzymatic function. Genes that undergo expansion events, either by horizontal gene transfer or duplication, can have a range of fates: genes can be lost, or they can undergo neo-functionalization or sub-functionalization. To test whether expanded gene families in Streptomyces exhibit differential expression, an RNA-Seq approach was used to examine cultures of wild-type Streptomyces coelicolor grown with either glucose or tween as the sole carbon source. Results RNA-Seq analysis showed that two-thirds of genes within expanded gene families show transcriptional differences when strains were grown on tween compared to glucose. In addition, expression of specialized metabolite gene clusters (actinorhodin, isorenieratane, coelichelin and a cryptic NRPS) was also influenced by carbon source. Conclusions Expression of genes encoding the same enzymatic function had transcriptional differences when grown on different carbon sources. This transcriptional divergence enables partitioning to function under different physiological conditions. These approaches can inform metabolic engineering of industrial Streptomyces strains and may help develop cultivation conditions to activate the so-called silent biosynthetic gene clusters.

Multi-locus sequencing typing (MLST) is widely used to monitor the phylogeny of microbial outbreaks. However, several strains of vancomycin-resistant Enterococcus faecium (VREfm) with a missing MLST locus (pstS) have recently emerged in Australia, with a few cases also reported in England. Here, we identified similarly distinct strains circulating in two closely located hospitals in Scotland. Whole genome sequencing of five VREfm strains isolated from these hospitals identified four pstS-null strains across both hospitals, while the fifth was of a multi-locus sequence type (ST) 262, which is the first documented in the UK. All five Scottish isolates had an insertion in the tetM gene, which is associated with increased susceptibility to tetracyclines, providing no other tetracycline-resistant gene is present. Such an insertion, which encompasses a dfrG gene and two currently uncharacterised genes, was additionally identified in all tested VanA-type pstS-null VREfm strains (5 English and 18 Australian). Phylogenetic comparison with other VREfm genomes indicates that the four pstS-null Scottish isolates sequenced in this study are more closely related to pstS-null strains from Australia rather than the English pstS-null isolates. Given how rapidly such pstS-null strains have expanded in Australia, the emergence of this clone in Scotland raises concerns for a potential outbreak.

MGB-BP-3 (MGB) is a novel synthetic antibiotic inspired by Distamycin – a natural product that is capable of binding to the minor groove of DNA. MGB has a high bactericidal activity against a broad range of Gram-positive bacteria without the toxicity associated with the natural products that it was inspired by. Its oral formulation, developedfor the treatment of Clostridium difficile infections, is currently progressing through a phase 2 clinical trial. This study investigatesthe mode of action of this novel antibiotic. To allow better understanding of MGB’s mode of action, RNA-Seq analysis was undertaken on S. aureus following challenge with 0.5 x MIC (0.1 µg ml−1) MGB-BP-3. Triplicate samples of RNA were extracted at 10 min after challenge. RNA-Seq analysis identified 698 transcripts showing significant changes in expression profile, which were confirmed by quantitative RT-PCR. Amongst these, 62 essential genes showed transcriptional arrest. Glycolysis, pentose phosphate pathway and the TCA cycle were affected. In addition, biosynthesis of nucleotides and certain amino acids were altered and Biolog phenotype arrays were performed in the presence of MGB to confirm this. DNA binding assays demonstrated MGB binding to intergenic regions upstream of strongly down-regulated essential genes (mraY and dnaD). Attempts to evolve resistance to MGB have so far been unsuccessful unlike with the rifampicin control. In conclusion our findings are consistent with a bactericidal mode of action of MGB at the transcriptional level of multiple essential genes.

The genus Streptomyces is comprised of soil-dwelling Gram-positive Actinobacteria that are widely used for the industrial production of antibiotics. S. clavuligerus is used for the industrial production of clavulanic acid, which is a potent b-lactamase inhibitor, and is, therefore, able to restore the sensitivity of b-lactamase-producing bacteria penicillins and cephalosporins. In fermentations, the carbon sources available for utilisation by the producing organism have profoundly impact central carbon and specialised metabolic pathways. We have a long-term goal of using carbon sources from food waste to produce clavulanic acid with a view to developing more sustainable fermentations. To achieve this, the carbon utilisation profile of S. clavuligerus has to be diversified. Wildtype S. clavuligerus is a natural glucose auxotroph and has adapted to utilise glycerol most efficiently. It has been shown that the lack of glucose utilisation by S. clavuligerus is due to the insufficient expression of genes whose products are required for glucose uptake (glcP) and phosphorylation (glk). To enable glucose utilisation by S. clavuligerus strains, we have constructed strains for heterologous expression of either glcP or glk from different Streptomyces species. Further, the range of utilisable carbon sources for growth and clavulanic acid production has been investigated. Growth on solid media has revealed interplay between carbon and nitrogen metabolism, with extracellular protease production being regulated in a carbon source-dependent manner. Therefore, the role of protease secretion and its relationship with clavulanic acid production has been examined, revealing a complex role between carbon catabolite repression, protease production and clavulanic acid biosynthesis.

Antimicrobial resistance and the shortage of novel antibiotics have led to an urgent need for new antibacterial drug leads. Several existing natural product scaffolds (including chelocardins) have not been developed because their suboptimal pharmacological properties could not be addressed at the time. It is demonstrated here that reviving such compounds through the application of biosynthetic engineering can deliver novel drug candidates. Through a rational approach, the carboxamido moiety of tetracyclines (an important structural feature for their bioactivity) was introduced into the chelocardins, which are atypical tetracyclines with an unknown mode of action. A broad-spectrum antibiotic lead was generated with significantly improved activity, including against all Gram-negative pathogens of the ESKAPE panel. Since the lead structure is also amenable to further chemical modification, it is a platform for further development through medicinal chemistry and genetic engineering.

Production of biofuels is a significant technical and commercial challenge To compete effectively with fossil fuels the efficiency of processes that convert sustainable feedstocks to biofuel has to be improved Ideally the ultimate aim is a single process that degrades the renewable feedstock quickly and delivers high titers of biofuel at a price that is competitive with equivalent fuel from fossil sources However the microbes that are currently being investigated for biofuel production fall into two categories those that degrade cellulosic feedstock but cannot make biofuels effectively and those that do make biofuels but are poor at degrading the cellulosic feedstock When biofuel production is engineered into cellulose degraders or cellulose degradation engineered into microbes with capability to produce biofuel another factor lignin content a toxic component in most sustainable feedstocks comes into play This review considers the latent opportunity to harness Streptomyces bacteria to address this issue

The challenge of antimicrobial resistance is well understood and extensive research is underway worldwide to find effective, new antibacterial agents that will be less susceptible to the emergence of resistance than those of previous generations. The challenge of combining potency with resilience is unlikely to be met using the standard medicinal chemistry paradigm of single drug, single target, single effect. Our approach using specially designed minor groove binders for DNA (Strathclyde MGBs), whilst formally attacking a single molecular target, in practice disrupts many biological processes such that the emergence of resistance can be expected to be low. The first example of this approach to reach the clinic, MGB-BP-3, is highly effective against Gram positive bacteria and has been successfully taken through a Phase 1 clinical trial for the treatment of Clostridium difficile infections by our development partner, MGB Biopharma. Mechanism of action studies with S. aureus as the target organism have provided evidence consistent with the expectation. RNAseq experiments have shown that there are substantial changes in gene expression, some upregulated and others downregulated, such that the bacterium faces multiple metabolic challenges to its survival. In particular processes associated with cell wall integrity and energy production are affected, the latter being consistent with the steep dose response kill curve observed with this type of drug. Moreover attempts to generate resistant strains have failed. Taken together, these properties identify Strathclyde minor groove binders as significant new compounds in the fight against antibacterial resistance.

Introductory paragraphExpanding the genetic repertoire of an organism by gene duplication or horizontal gene transfer (HGT) can aid adaptation. Streptomyces species are prolific producers of bioactive specialised metabolites with adaptive functions in nature and some have found utility in human medicine such as antibiotics. Whilst the biosynthesis of these specialised metabolites is directed by dedicated biosynthetic gene clusters (BGCs), little attention has been focussed on how these organisms have evolved robustness into their genomes to facilitate the metabolic plasticity required to provide chemical precursors for biosynthesis. Here we show that specific expansions of gene families in central carbon metabolism have evolved and become fixed in Streptomyces bacteria to enable plasticity and robustness that maintain cell functionality whilst costly specialised metabolites are produced. These expanded gene families, in addition to being a metabolic adaptation, make excellent targets for metabolic engineering of industrial specialised metabolite producing bacteria.

The fluid mosaic model has recently been amended to account for the existence of membrane domains enriched in certain phospholipids. In rod-shaped bacteria, the anionic phospholipid cardiolipin is enriched at the cell poles but its role in the morphogenesis of the filamentous bacterium Streptomyces coelicolor is unknown. It was impossible to delete clsA (cardiolipin synthase; SCO1389) unless complemented by a second copy of clsA elsewhere in the chromosome. When placed under the control of an inducible promoter, clsA expression, phospholipid profile and morphogenesis became inducer dependent. TLC analysis of phospholipid showed altered profiles upon depletion of clsA expression. Analysis of cardiolipin by mass spectrometry showed two distinct cardiolipin envelopes that reflected differences in acyl chain length; the level of the larger cardiolipin envelope was reduced in concert with clsA expression. ClsA-EGFP did not localize to specific locations, but cardiolipin itself showed enrichment at hyphal tips, branch points and anucleate regions. Quantitative analysis of hyphal dimensions showed that the mycelial architecture and the erection of aerial hyphae were affected by the expression of clsA. Overexpression of clsA resulted in weakened hyphal tips, misshaped aerial hyphae and anucleate spores and demonstrates that cardiolipin synthesis is a requirement for morphogenesis in Streptomyces.

The hospital environment is particularly susceptible to contamination by bacterial pathogens that grow on surfaces in biofilms. The effects of hospital biocides on two nosocomial pathogens, meticillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa, growing as free-floating (planktonic) and adherent biofilm populations (sessile) were examined. Clinical isolates of MRSA and P. aeruginosa were grown as biofilms on discs of materials found in the hospital environment (stainless steel, glass, polyethylene and Teflon) and treated with three commonly used hospital biocides containing benzalkonium chloride (1 % w/v), chlorhexidine gluconate (4 % w/v) and triclosan (1 % w/v). Cell viability following biocide treatment was determined using an XTT assay and the LIVE/DEAD BacLight Bacterial Viability kit. The minimum bactericidal concentration (MBC) of all biocides for planktonic populations of both organisms was considerably less than the concentration recommended for use by the manufacturer. However, when isolates were grown as biofilms, the biocides were ineffective at killing bacteria at the concentrations recommended for use. Following biocide treatment, 0-11 % of cells in MRSA biofilms survived, and up to 80 % of cells in P. aeruginosa biofilms survived. This study suggests that although biocides may be effective against planktonic populations of bacteria, some biocides currently used in hospitals are ineffective against nosocomial pathogens growing as biofilms attached to surfaces and fail to control this reservoir for hospital-acquired infection.

Streptomycetes are prolific producers of a plethora of medically useful metabolites. These compounds are made by complex secondary (specialized) metabolic pathways, which utilize primary metabolic intermediates as building blocks. In this review we discuss the evolution of specialized metabolites and how expansion of gene families in primary metabolism has lead to the evolution of diversity in these specialized metabolic pathways and how developing a better understanding of expanded primary metabolic pathways can help enhance synthetic biology approaches to industrial pathway engineering.

Endophytic bacteria, such as Streptomyces, have the potential to act as a source for novel bioactive molecules with medicinal properties. The present study was aimed at assessing the antimalarial activity of crude extract isolated from various strains of actinobacteria living endophytically in some Malaysian medicinal plants. Using the four day suppression test method on male ICR strain mice, compounds produced from three strains of Streptomyces (SUK8, SUK10, and SUK27) were tested in vivo against Plasmodium berghei PZZ1/100 in an antimalarial screen using crude extracts at four different concentrations. One of these extracts, isolated from Streptomyces SUK10 obtained from the bark of Shorea ovalis tree, showed inhibition of the test organism and was further tested against P. berghei-infected mice for antimalarial activity at different concentrations. There was a positive relationship between the survival of the infected mouse group treated with 50 µg/kg body weight (bw) of ethyl acetate-SUK10 crude extract and the ability to inhibit the parasites growth. The parasite inhibition percentage for this group showed that 50% of the mice survived for more than 90 days after infection with the parasite. The nucleotide sequence and phylogenetic tree suggested that Streptomyces SUK10 may constitute a new species within the Streptomyces genus. As part of the drug discovery process, these promising finding may contribute to the medicinal and pharmaceutical field for malarial treatment.

Streptomycetes are prolific producers of a plethora of medically useful metabolites. These compounds are made by complex secondary (specialized) metabolic pathways, which utilize primary metabolic intermediates as building blocks. In this review we discuss the evolution of specialized metabolites and how expansion of gene families in primary metabolism has lead to the evolution of diversity in these specialized metabolic pathways and how developing a better understanding of expanded primary metabolic pathways can help enhance synthetic biology approaches to industrial pathway engineering.

Three novel polyketide metabolites were isolated from laboratory-scale fermentation of the Streptomyces rimosus mutant strain R1059. Structural elucidation of the compounds was based on NMR experiments. The compounds were characterized as naphthalene derivatives: (rel)-4beta,8-dihydroxy-3alpha-hydroxymethyl-4alpha-methyl-1,2,3,4-tetrahydronaphthalene1-one (1), 4xi8-dihydroxy-3-hydroxymethyl-4xi-methyl-1,4-dihydronaphthalene-1-one (2) and (rel)-4beta,8-dihydroxy-3alpha-O-[alpha-glucopyranosyl]hydroxymethyl-4alpha-methyl-1,2,3,4-tetrahydronaphthalene-1-one (3). The compounds isolated appear to be derived via a shorter polyketide backbone than oxytetracycline (4), the normal end-product made by the parent of this strain. Compound 3 was the glucoside of 1 and must be formed as a post-PKS reaction by the activation of a glycosyl transferase, which has not been reported in this species before.

With the exceptions of Bacillus cereus and Bacillus anthracis , Bacillus species are generally perceived to be inconsequential. However, the relevance of other Bacillus species as food poisoning organisms and etiological agents in nongastrointestinal infections is being increasingly recognized. Eleven Bacillus species isolated from veterinary samples associated with severe nongastrointestinal infections were assessed for the presence and expression of diarrheagenic enterotoxins and other potential virulence factors. PCR studies revealed the presence of DNA sequences encoding hemolysin BL (HBL) enterotoxin complex and B. cereus enterotoxin T (BceT) in five B. cereus strains and in Bacillus coagulans NB11. Enterotoxin HBL was also harbored by Bacillus polymyxa NB6. After 18 h of growth in brain heart infusion broth, all seven Bacillus isolates carrying genes encoding enterotoxin HBL produced this toxin. Cell-free supernatant fluids from all 11 Bacillus isolates demonstrated cytotoxicity toward human HEp-2 cells; only one Bacillus licheniformis strain adhered to this test cell line, and none of the Bacillus isolates were invasive. This study constitutes the first demonstration that Bacillus spp. associated with serious nongastrointestinal infections in animals may harbor and express diarrheagenic enterotoxins traditionally linked to toxigenic B. cereus .

Microbial metabolites, especially the antibiotics, have contributed enormously to the improvement in quality of healthcare over the last fifty years. However, the efficacy of such medicines has been eroded continually by the speed with which clinical infections acquire resistance to antibiotics. It is therefore necessary to continue to discover and develop new drugs to combat the ‘antibiotic resistance problem’. Recent discoveries reinforce the view that some microbes make metabolites that have other useful therapeutic properties, e.g. immune-suppressants, cholesterol-lowering drugs and anti-parasitics. This adds to the momentum to drive the discovery of new microbial metabolites. The filamentous soil bacteria, Streptomyces, are the source of over half of all clinically useful microbial metabolites. The molecular genetics of this important genus has developed rapidly over the last 20 years – to the point where molecular techniques can now be used to subvert strains into making novel metabolites, not seen previously in nature.

The oxidation of 3-alkyl benzofurans, indoles, and a benzothiophene by the chloroperoxidase from Caldariomyces fumago has been investigated. Under conditions in which the catalase activity of chloroperoxidase was minimised in the presence of chloride and hydrogen peroxide, 3-methylbenzothiophene was oxidised at sulfur but the indoles (5-9) and benzofurans (1-4) gave 2,3-diols as initial products. In the case of N-unsubstituted indoles, these tautomerised to give the corresponding lactam. In contrast, the diols (predominantly trans) formed from the benzofurans were sufficiently stable for isolation and full characterisation. This novel reaction has the potential to be developed into a useful synthetic biotransformation.

Oxytetracycline is a polyketide antibiotic made by Streptomyces rimosus. From DNA sequencing, the gene product of otcD1 is deduced to function as a bifunctional cyclase/aromatase involved in ring closure of the polyketide backbone. Although otcD1 is contiguous with the ketoreductase gene, they are located an unusually large distance from the genes encoding the “minimal polyketide synthase” of the oxytetracycline gene cluster. A recombinant, disrupted in the genomic copy ofotcD1, made four novel polyketides, all of shorter chain length (by up to 10 carbons) than oxytetracycline. All four novel structures contained the unusual carboxamido group, typical of oxytetracycline. This implies that the carboxamido group is present at the start of biosynthesis of oxytetracycline, a topic that has been debated in the literature. Loss of the cyclase protein has a profound influence on the length of polyketide chain assembled, implying that OtcD1 plays a greater role in the overall integrity of the quaternary structure of the polyketide complex than hitherto imagined.

Tetracyclines (TCs) are medically important antibiotics from the polyketide family of natural products. Chelocardin (CHD), produced by Amycolatopsis sulphurea, is a broad-spectrum tetracyclic antibiotic with potent bacteriolytic activity against a number of Gram-positive and Gram-negative multi-resistant pathogens. CHD has an unknown mode of action that is different from TCs. It has some structural features that define it as 'atypical' and, notably, is active against tetracycline-resistant pathogens. Identification and characterization of the chelocardin biosynthetic gene cluster from A. sulphurea revealed 18 putative open reading frames including a type II polyketide synthase. Compared to typical TCs, the chd cluster contains a number of features that relate to its classification as 'atypical': an additional gene for a putative two-component cyclase/aromatase that may be responsible for the different aromatization pattern, a gene for a putative aminotransferase for C-4 with the opposite stereochemistry to TCs and a gene for a putative C-9 methylase that is a unique feature of this biosynthetic cluster within the TCs. Collectively, these enzymes deliver a molecule with different aromatization of ring C that results in an unusual planar structure of the TC backbone. This is a likely contributor to its different mode of action. In addition CHD biosynthesis is primed with acetate, unlike the TCs, which are primed with malonamate, and offers a biosynthetic engineering platform that represents a unique opportunity for efficient generation of novel tetracyclic backbones using combinatorial biosynthesis., This research was supported in part by grants from the Slovenian Research Agency (7-576-1/2004), the Slovene Human Resources and Scholarship Fund (Ad futura Programs 2006/523-17), the Socrates/Erasmus Program (2006/07420), the British Council (Partnership in Science Award RNP 7/2008), Slovenian Technology Agency TIA (VALOR08-02) and SPIRIT Slovenija (P-MR-09/104).

This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.-- et al., We report the draft genome of Streptomyces rimosus (ATCC 10970), a soil isolate that produces oxytetracycline, a commercially important and clinically useful antibiotic., We acknowledge financial support from the National Yang-Ming University, Taiwan, for the sequencing project (R.K.), a British Council for Research Projects Network grant (P.A.H. and H.P.), and the British Council/CUC for a Scotland-China Higher Education Research Partnership for PhD Studies (Z.T.).

Catalase was purified from the Gram-positive bacterium Streptomyces coelicolor A3(2) in a three-step purification procedure comprising (NH4)2SO4, fractionation, Phenyl-Sepharose chromatography and Mono Q chromatography. The purification of catalase, as judged by the final specific activity of 110000 U mg-1 was 250-fold with a 35% yield. The native protein was a homotetramer with a subunit M r 55000. N-terminal and internal peptide sequence analyses showed that there was a high degree of sequence similarity between the S. coelicolor catalase and other microbial and mammalian catalases. Southern blot analysis indicated that there was a single catalase gene in S. coelicolor. The specific activity of catalase throughout the growth of batch cultures was investigated and elevated catalase activity was found in stationary-phase cells.

Infection control is a key aspect of wound management strategies. Infection results in chemical imbalances and inflammation in the wound and may lead to prolonged healing times and degradation of the wound surface. Frequent changing of wound dressings may result in damage to healing tissues and an increased risk of infection. This paper presents the first results from a monitoring system that is being developed to detect presence and growth of bacteria in real time. It is based on impedance sensors that could be placed at the wound-dressing interface and potentially monitor bacterial growth in real time. As wounds can produce large volumes of exudate, the initial system reported here was developed to test for the presence of bacteria in suspension. Impedance was measured using disposable silver-silver chloride electrodes. The bacteria Staphylococcus aureus were chosen for the study as a species commonly isolated from wounds. The growth of bacteria was confirmed by plate counting methods and the impedance data were analysed for discernible differences in the impedance profiles to distinguish the absence and/or presence of bacteria. The main findings were that the impedance profiles obtained by silver-silver chloride sensors in bacterial suspensions could detect the presence of high cell densities. However, the presence of the silver-silver chloride electrodes tended to inhibit the growth of bacteria. These results indicate that there is potential to create a real time infection monitor for wounds based upon impedance sensing.

The fluid mosaic model has recently been amended to account for the existence of membrane domains enriched in certain phospholipids. In rod-shaped bacteria, the anionic phospholipid cardiolipin is enriched at the cell poles but its role in the morphogenesis of the filamentous bacterium Streptomyces coelicolor is unknown. It was impossible to delete clsA (cardiolipin synthase; SCO1389) unless complemented by a second copy of clsA elsewhere in the chromosome. When placed under the control of an inducible promoter, clsA expression, phospholipid profile and morphogenesis became inducer dependent. TLC analysis of phospholipid showed altered profiles upon depletion of clsA expression. Analysis of cardiolipin by mass spectrometry showed two distinct cardiolipin envelopes that reflected differences in acyl chain length; the level of the larger cardiolipin envelope was reduced in concert with clsA expression. ClsA-EGFP did not localize to specific locations, but cardiolipin itself showed enrichment at hyphal tips, branch points and anucleate regions. Quantitative analysis of hyphal dimensions showed that the mycelial architecture and the erection of aerial hyphae were affected by the expression of clsA. Overexpression of clsA resulted in weakened hyphal tips, misshaped aerial hyphae and anucleate spores and demonstrates that cardiolipin synthesis is a requirement for morphogenesis in Streptomyces.

Smart video analytics algorithms can be embedded within surveillance sensors for fast in-camera processing. This paper presents a DSP embedded video analytics system for object and people tracking, using a PTZ camera. The tracking algorithm is based on adaptive template matching and it employs a novel Sum of Weighted Absolute Differences. The video analytics is implemented on the DSP board DM6437 EVM and it automatically controls the PTZ camera, to keep the target central to the field of view. The EVM is connected to the network and the tracking algorithm can be remotely activated, so that the PTZ enhanced with the DSP embedded video analytics becomes a smart surveillance sensor. The system runs in real-time and simulation results demonstrate that the described SWAD outperforms other template matching measures in terms of efficiency and accuracy.

In order to enable microorganisms to manifest their intracellular oxygen levels we constructed a genetic sensor circuitry which converts signals impinging on the cellular redox balance into a reporter gene expression readout. Based on the newly found Streptomyces rimosus redox control system, consisting of Rex modulating Retinopathy of prematurity (ROP)-containing promoters in a NADH-dependent manner, we designed an Escherichia coli sensor transcription control system, which constitutes a Rex transactivator (REDOX) with the ability to bind and activate promoters. When oxygen levels were high and resulted in depleted NADH pools, Rex-specific target promoter (cydP1) driven from the expression of secreted (Green fluorscent protein, GFP) reporter gene was low as a consequence of increased Rex-ROP affinity. Conversely, at hypoxic conditions, it led to high intracellular NADH levels, strongly reduced Rex-ROP interaction and increased GFP expression in E. coli cells. The sensor capacity (oxygen levels) of redox system enabled monitoring of the population's metabolic state in vivo. Our research will not only help to understand the molecular mechanism of the Rex family but also foster progresses in biosensor development.

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.

Recent advances in the molecular genetics of Streptomyces have increased our understanding of polyketide antibiotic biosynthesis, to the point where recombinant DNA approaches to generate novel structures are possible. Our understanding of how antibiotic pathways are regulated and integrated into central metabolism also provides the opportunity for strain manipulation to enhance productivity.

Objectives: The MBCs of three commonly used hospital biocides [containing quaternary ammonium compounds (QACs), chlorhexidine gluconate and triclosan] were determined for clinical isolates of Staphylococcus aureus, which were also screened for genes encoding Qac efflux pumps. Methods: MBCs were determined by broth microdilution for 94 clinical isolates of S. aureus, including 38 hospital-acquired methicillin-resistant S. aureus (HA-MRSA), 25 community-associated methicillinresistant S. aureus (CA-MRSA), 25 methicillin-susceptible S. aureus (MSSA) and 6 with intermediate resistance to vancomycin (VISA). All isolates were screened by PCR for the presence of qacA, B, C, G, H and J. Results: Biocides had MBCs 10‐1000-fold lower than the concentration recommended for use by the manufacturer. HA-MRSA isolates developed significantly enhanced tolerance to QACs following repeat exposure to subinhibitory concentrations. Ten HA-MRSA and four VISA isolates carried qacA .T wo HA-MRSA isolates, one MSSA isolate and one VISA isolate carried qacC. One VISA isolate carried qacA and qacC. The CA-MRSA isolates did not carry qac genes. qacG, H and J were not detected in any HA-MRSA. Isolates with qac genes had significantly (P < 0.0001) higher MBCs for biocides containing QACs and chlorhexidine gluconate. These biocides induced expression of qac genes when assayed with a luciferase reporter. Conclusions: Biocides commonly used in the hospital environment should be effective against clinical isolates of S. aureus if used at concentrations recommended by the manufacturer. However, isolates have the potential to develop increased tolerance to these agents and the expression of Qac efflux pumps results in isolates with a selective advantage when challenged with biocides containing QACs and chlorhexidine gluconate.

DNA/DNA genome microarray analysis together with genome sequencing suggests that the genome of members of the genus Streptomyces would seem to have a common structure including a linear genomic structure, a core of common syntenous Actinomycete genes, the presence of species specific terminal regions and two intermediate group of syntenous genes that seem to be genus specific. We analyzed Streptomyces species using DNA/DNA microarray comparative genome analysis. Only Streptomyces rimosus failed to give a congruent genome pattern for the genes found in Streptomyces coelicolor. We expanded the analysis to include a number of strains related to the type strain of S. rimosus and obtained a similar divergence from the main body of Streptomyces species. These strains showed very close identity to the original strain with no gene deletion or duplication detected. The 16S rRNA sequences of these S. rimosus strains were confirmed as very similar to the S. rimosus sequences available from the Ribosomal Database Project. When the SSU ribosomal RNA phylogeny of S. rimosus is analyzed, the species is positioned at the edge of the Streptomyces clade. We conclude that S. rimosus represents a distinct evolutionary lineage making the species a worthy possibility for genome sequencing.

The synthesis and properties of 80 short minor groove binders related to distamycin and the thiazotropsins are described. The design of the compounds was principally predicated upon increased affinity arising from hydrophobic interactions between minor groove binders and DNA. The introduction of hydrophobic aromatic head groups, including quinolyl and benzoyl derivatives, and of alkenes as linkers led to several strongly active antibacterial compounds with MIC for Staphylococcus aureus, both methicillin-sensitive and -resistant strains, in the range of 0.1-5 microg mL-1, which is comparable to many established antibacterial agents. Antifungal activity was also found in the range of 20-50 microg mL-1 MIC against Aspergillus niger and Candida albicans, again comparable with established antifungal drugs. A quinoline derivative was found to protect mice against S. aureus infection for a period of up to six days after a single intraperitoneal dose of 40 mg kg-1.

Streptomyces are mycelial, soil-dwelling, differentiating bacteria that are renowned for the production of many clinically-useful antibiotics (e.g. streptomycin, erythromycin, tetracyclines, and a number of the third-generation penicillin-like antibiotics). They also make other useful metabolites (e.g. anticancer agents, immunosuppressants, antihelmintics, growth promoters, herbicides, and insecticides). Their status as simple microbial models of differentiation is well established and, because they are taxonomically related to pathogens such as mycobacteria that cause tuberculosis and leprosy (but are themselves “safe” organisms), they are being cited increasingly as informative models for these life-threatening pathogens. Much effort has gone into investigating the fundamental biology of Streptomyces . In recent years, the dissection of the architecture and regulation of antibiotic production gene clusters has been undertaken, together with studies on the regulatory circuits that control production and integrate with the signaling pathways of the differentiation processes. As clinical infections invariably develop resistance to antibiotics, there is an ongoing need to discover new drugs to combat this problem. The Streptomyces are viewed as a rich source of such drugs and contemporary effort, using recombinant technologies, is aimed at altering the genes for antibiotic production pathways so that they produce new, potentially useful metabolites that may keep them one step ahead of the resistance problem. Recent advances in the molecular biological techniques applicable to streptomycetes have assisted greatly in this task. The genome sequence of the model streptomycete, Streptomyces coelicolor , was published in 2002, followed recently by that of Streptomyces avermitilis . In 2004, a number of other sequencing projects were in progress, so that these resources will grow significantly in the near future. The Streptomyces are remarkable in that their genomes are among the largest (8–9 Mb, compared with E. coli at 4.6 Mb) reported so far for any bacteria. Bioinformatics, combined with postgenomic techniques such as microarrays and proteome gels, are now being used to define and characterize global gene expression under a variety of conditions. Rapid methods have been developed to create mutants for any gene, using its genome-derived DNA sequence to guide the strategy. Mutant libraries generated by random transposon insertion, are also becoming available. These aim to provide a collection of mutants in which each of the almost 8000 genes in Streptomyces is mutated individually. With these recent postgenomic resources building on the robust genetic systems that have been set up for Streptomyces , the next few years promise to be an exciting phase in our understanding of these unique bacteria. Keywords: Auxotroph; Complementation; Cosmid; Generalized Transduction; Lysogeny; Open Reading Frame (ORF); Proteome; Protoplast; Secondary Metabolite; Transcriptome; Sigma (σ) Factor; Transformation/Transformant; Transposition; Transposon

SUMMARY 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.

Oxytetracycline (OTC) is a 19-carbon polyketide antibiotic made by Streptomyces rimosus. The otcC gene encodes an anhydrotetracycline oxygenase that catalyzes a hydroxylation of the anthracycline structure at position C-6 after biosynthesis of the polyketide backbone is completed. A recombinant strain of S. rimosus that was disrupted in the genomic copy of otcC synthesized a novel C-17 polyketide. This result indicates that the absence of the otcC gene product significantly influences the ability of the OTC "minimal" polyketide synthase to make a polyketide product of the correct chain length. A mutant copy of otcC was made by site-directed mutagenesis of three essential glycine codons located within the putative NADPH-binding domain. The mutant gene was expressed in Escherichia coli, and biochemical analysis confirmed that the gene product was catalytically inactive. When the mutant gene replaced the ablated gene in the chromosome of S. rimosus, the ability to make a 19-carbon backbone was restored, indicating that OtcC is an essential partner in the quaternary structure of the synthase complex.

The search for novel anti-infective and anticancer drugs ranges over many types of compound. Following earlier work into the synthesis of compounds that bind into the minor groove of DNA (based upon the well-known N-methylpyrrole amino acid monomer), we have extended our studies to develop compounds including a wide range of alternative heterocyclic rings and alkyl substituents (with Professor Roger Waigh, Pharmaceutical Sciences). [see references] For reasons of commercial significance, the detailed structures of these compounds cannot be disclosed until early 2003 but Scheme2 is illustrative. However we have been gratified to find that some of our compounds containing novel structural features have antibacterial activity against such key organisms as MRSA and Cryptosporidium as well as against a number of fungi including Aspergillus and Candida. Moreover, nmr studies have given us strong insight into the detailed binding of our compounds with DNA. The chief synthetic chemical problems to be solved relate to the efficient solid phase synthesis of compounds containing the new heterocyclic monomers and, in some cases, to the monomers themselves. These problems are being addressed in partnership with LINK Technologies, a local biotech company, through the Teaching Company Scheme. There are also major structural and biochemical problems to be tackled. Some of our active compounds have very potent and specific binding patterns to DNA; in order to make further progress in targeting specific genes, the structural basis for this must be understood. Having discovered significant antibacterial and antifungal activity we are also keen to confirm and extend preliminary results that indicate interference with the action of cytokines in some cell types.

The genome sequence of Mycobacterium tuberculosis has revealed the presence of 20 different cytochrome P450 mono-oxygenases (P450s) within this organism, and subsequent genome sequences of other mycobacteria and of Streptomyces coelicolor have indicated that these actinomycetes also have large complements of P450s, pointing to important physiological roles for these enzymes. The actinomycete P450s include homologues of 14alpha-sterol demethylases, the targets for the azole class of drugs in yeast and fungi. Previously, this type of P450 was considered to be absent from bacteria. When present at low concentrations in growth medium, azole antifungal drugs were shown to be potent inhibitors of the growth of Mycobacterium smegmatis and of Streptomyces strains, indicating that one or more of the P450s in these bacteria were viable drug targets. The drugs econazole and clotrimazole were most effective against M. smegmatis (MIC values of

Forty-seven strains representing 14 different Bacillus species isolated from clinical and food samples were grown in reconstituted infant milk formulae (IMF) and subsequently assessed for adherence to, invasion of, and cytotoxicity toward HEp-2 and Caco-2 cells. Cell-free supernatant fluids from 38 strains (81%) were shown to be cytotoxic, 43 strains (91%) adhered to the test cell lines, and 23 strains (49%) demonstrated various levels of invasion. Of the 21 Bacillus cereus strains examined, 5 (24%) were invasive. A larger percentage of clinically derived Bacillus species (20%) than of similar species tested from the food environment were invasive. Increased invasion occurred after growth of selected Bacillus species in reconstituted IMF containing glucose. While PCR primer studies revealed that many different Bacillus species contained DNA sequences encoding the hemolysin BL (HBL) enterotoxin complex and B. cereus enterotoxin T, not all of these isolates expressed these diarrheagenic genes after growth in reconstituted IMF. Of the 47 Bacillus isolates examined, 3 isolates of B. cereus and 1 isolate of B. subtilis produced the HBL enterotoxin after 18 h of growth in brain heart infusion broth. However, eight isolates belonging to the species B. cereus , B. licheniformis , B. circulans , and B. megaterium were found to produce this enterotoxin after growth in reconstituted IMF when assessed with the B. cereus enterotoxin (diarrheal type) reversed passive latex agglutination (RPLA) kit. It is concluded that several Bacillus species occurring occasionally in clinical specimens and food samples are of potential medical significance due to the expression of putative virulence factors.

Physiological studies have shown that Streptomyces rimosus produces the polyketide antibiotic oxytetracycline abundantly when its mycelial growth is limited by phosphate starvation. We show here that transcripts originating from the promoter for one of the biosynthetic genes, otcC (encoding anhydrotetracycline oxygenase), and from a promoter for the divergent otcX genes peak in abundance at the onset of antibiotic production induced by phosphate starvation, indicating that the synthesis of oxytetracycline is controlled, at least in part, at the level of transcription. Furthermore, analysis of the sequences of the promoters for otcC , otcX , and the polyketide synthase ( otcY ) genes revealed tandem repeats having significant similarity to the DNA-binding sites of ActII-Orf4 and DnrI, which are Streptomyces antibiotic regulatory proteins (SARPs) related to the OmpR family of transcription activators. Together, the above results suggest that oxytetracycline production by S. rimosus requires a SARP-like transcription factor that is either produced or activated or both under conditions of low phosphate concentrations. We also provide evidence consistent with the otrA resistance gene being cotranscribed with otcC as part of a polycistronic message, suggesting a simple mechanism of coordinate regulation which ensures that resistance to the antibiotic increases in proportion to production.

Oxytetracycline (CTC) is a member of the tetracycline family of broad spectrum antibiotics produced by the filamentous bacteria. These antibiotics have maintained their importance in aspects of human health care (especially the semi-synthetic, doxycycline), but they are also used increasingly in animal healthcare and animal feed supplements.