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Julian Davies

Publications and source records attributed to Julian Davies.

At least 19 recordsLinked to original sources
PubMed2006

Small molecules: the lexicon of biodiversity.

The extent of microbial diversity in the Biosphere is not known (and probably never will be!). One aspect of this diversity is the production of biologically active small molecules; within the Streptomycetes alone this may be millions of compounds with an extraordinary diversity and complexity of structure. First recognised as pigments and later, in the 1950s, as antibiotics, it is now clear that the small molecules produced by microbes have many different functions in nature. This huge collection of biologically active compounds with various properties has been used as pharmaceuticals and agriculturals. They also interact with proteins and RNA with high specificity and have been shown to be regulators and effectors of diverse biochemical reactions. The use of small molecules (other than as pharmaceuticals) deserves to be explored in order to exploit microbial biotechnology to the full.

Biodiversity↗
PubMed2006

Transcription modulation of Salmonella enterica serovar Typhimurium promoters by sub-MIC levels of rifampin.

Promoter-lux fusions that showed rifampin-modulated transcription were identified from a Salmonella enterica serovar Typhimurium 14028 reporter library. The transformation of a subset of fusions into mutants that lacked one of six global regulatory proteins or were rifampin resistant showed that transcription modulation was independent of the global regulators, promoter specific, and dependent on the interaction of rifampin with RNA polymerase.

Antibiotics, Antitubercular↗
PubMed2006

Molecular cloning of streptomyces genes encoding vanillate demethylase.

The vanillate demethylase genes from Streptomyces sp. NL15-2K were cloned and sequenced. The vanA and vanB gene homologs, which encode the terminal oxygenase subunit (VanA) and the ferredoxin-type reductase subunit (VanB) of the enzyme respectively, were found in the sequenced 7.5-kb DNA region. Expression of the vanAB genes in Streptomyces lividans 1326 resulted in in vivo demethylation of veratric acid to vanillic acid.

Amino Acid Motifs↗
PubMed2006

The world of subinhibitory antibiotic concentrations.

Although antibiotics have long been known to have multiple effects on bacterial cells at low concentrations, it is only with the advent of genome transcription analyses that these activities have been studied in detail at the level of cell metabolism. It has been shown that all antibiotics, regardless of their receptors and mode of action, exhibit the phenomenon of hormesis and provoke considerable transcription activation at low concentrations. These analyses should be of value in providing information on antibiotic side-effects, in bioactive natural product discovery and antibiotic mode-of-action studies.

Anti-Bacterial Agents↗
PubMed2006

Are antibiotics naturally antibiotics?

Antibiotics have been used for more than 50 years and are the cornerstone of infectious disease treatment; in addition, these low-molecular-weight bioactive compounds have been applied to many other therapeutic purposes. However, there is almost no information on the evolutionary biology or ecology of naturally occurring low-molecular-weight compounds. The large number of different structural types and the extremely broad range of biological activities of organic molecules produced by microbes raise many questions concerning their roles in nature. Recent evidence for the enormous complexity of microbial populations in the environment favors the notion that the principal roles of small molecules in microbial ecology are cell-cell communication and not antibiosis.

Anti-Bacterial Agents↗
PubMed2006

Bacterial single-stranded DNA-binding proteins are phosphorylated on tyrosine.

Single-stranded DNA-binding proteins (SSBs) are required for repair, recombination and replication in all organisms. Eukaryotic SSBs are regulated by phosphorylation on serine and threonine residues. To our knowledge, phosphorylation of SSBs in bacteria has not been reported. A systematic search for phosphotyrosine-containing proteins in Streptomyces griseus by immunoaffinity chromatography identified bacterial SSBs as a novel target of bacterial tyrosine kinases. Since genes encoding protein-tyrosine kinases (PTKs) have not been recognized in streptomycetes, and SSBs from Streptomyces coelicolor (ScSSB) and Bacillus subtilis (BsSSB) share 38.7% identity, we used a B.subtilis protein-tyrosine kinase YwqD to phosphorylate two cognate SSBs (BsSSB and YwpH) in vitro. We demonstrate that in vivo phosphorylation of B.subtilis SSB occurs on tyrosine residue 82, and this reaction is affected antagonistically by kinase YwqD and phosphatase YwqE. Phosphorylation of B.subtilis SSB increased binding almost 200-fold to single-stranded DNA in vitro. Tyrosine phosphorylation of B.subtilis, S.coelicolor and Escherichia coli SSBs occured while they were expressed in E.coli, indicating that tyrosine phosphorylation of SSBs is a conserved process of post-translational modification in taxonomically distant bacteria.

Bacillus subtilis↗
PubMed2006

The truth about antibiotics.

Microbes produce millions of organic compounds of low molecular weight--a world of very diverse chemical and biological ecology. We propose that, at the low concentrations likely to be found in the environment, the majority of these compounds play important roles in the modulation of metabolic function in natural microbial communities. The biological diversity is reflected by distinct target responses affecting a variety of transcription regulatory networks by different mechanisms. This provides the basis of chemical signalling processes in the microbial world and may well extend into many prokaryote-eukaryote interactions.

Anti-Bacterial Agents↗
PubMed2006

Isolation and characterization of Streptomyces sp. NL15-2K capable of degrading lignin-related aromatic compounds.

Strain NL15-2K was isolated from soil by screening for bacteria capable of catabolizing lignin-related aromatic acids. This isolate was identified as a Streptomyces sp. on the basis of morphology and an analysis of its 16S rRNA gene sequence. NL15-2K utilized caffeic acid, coniferyl alcohol, ferulic acid, isovanillic acid, protocatechuic acid, vanillic acid, vanillin, and veratric acid as sole carbon sources.

Benzaldehydes↗
PubMed2005

Uncialamycin, a new enediyne antibiotic.

[structure: see text] Laboratory cultures of an undescribed streptomycete obtained from the surface of a British Columbia lichen produce uncialamycin (1), a new enediyne antibiotic. The structure of uncialamycin (1) has been elucidated by analysis of spectroscopic data. Uncialamycin (1) exhibits potent in vitro antibacterial activity against gram-positive and gram-negative human pathogens, including Burkholderia cepacia, a major cause of morbidity and mortality in patients with cystic fibrosis.

Anthraquinones↗
PubMed2005

Heterologous production of daptomycin in Streptomyces lividans.

Daptomycin and the A21978C antibiotic complex are lipopeptides produced by Streptomyces roseosporus and also in recombinant Streptomyces lividans TK23 and TK64 strains, when a 128 kbp region of cloned S. roseosporus DNA containing the daptomycin gene cluster is inserted site-specifically in the phiC31 attB site. A21978C fermentation yields were initially much lower in S. lividans than in S. roseosporus, and detection was complicated by the production of host metabolites. However A21978C production in S. lividans was improved by deletion of genes encoding the production of actinorhodin and by medium optimization to control the chemical form of the calcium dependent antibiotic (CDA). This latter compound has not previously been chemically characterized as a S. lividans product. Adding phosphate to a defined fermentation medium resulted in formation of only the phosphorylated forms of CDA, which were well separated from A21978C on chromatographic analysis. Adjusting the level of phosphate in the medium led to an improvement in A21978C yield from 20 to 55 mg/l.

Anthraquinones↗
PubMed2005

Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence.

Genomic and proteomic approaches were used to investigate phthalate and benzoate catabolism in Rhodococcus sp. strain RHA1, a polychlorinated biphenyl-degrading actinomycete. Sequence analyses identified genes involved in the catabolism of benzoate (ben) and phthalate (pad), the uptake of phthalate (pat), and two branches of the beta-ketoadipate pathway (catRABC and pcaJIHGBLFR). The regulatory and structural ben genes are separated by genes encoding a cytochrome P450. The pad and pat genes are contained on a catabolic island that is duplicated on plasmids pRHL1 and pRHL2 and includes predicted terephthalate catabolic genes (tpa). Proteomic analyses demonstrated that the beta-ketoadipate pathway is functionally convergent. Specifically, the pad and pat gene products were only detected in phthalate-grown cells. Similarly, the ben and cat gene products were only detected in benzoate-grown cells. However, pca-encoded enzymes were present under both growth conditions. Activity assays for key enzymes confirmed these results. Disruption of pcaL, which encodes a fusion enzyme, abolished growth on phthalate. In contrast, after a lag phase, growth of the mutant on benzoate was similar to that of the wild type. Proteomic analyses revealed 20 proteins in the mutant that were not detected in wild-type cells during growth on benzoate, including a CatD homolog that apparently compensated for loss of PcaL. Analysis of completed bacterial genomes indicates that the convergent beta-ketoadipate pathway and some aspects of its genetic organization are characteristic of rhodococci and related actinomycetes. In contrast, the high redundancy of catabolic pathways and enzymes appears to be unique to RHA1 and may increase its potential to adapt to new carbon sources.

Bacterial Proteins↗
PubMed2004

Dual effects of MLS antibiotics: transcriptional modulation and interactions on the ribosome.

The macrolide-lincosamide-streptogramin (MLS) antibiotics are an important group of translation inhibitors that act on the 50S ribosome. We show that, at subinhibitory concentrations, members of the MLS group modulate specific groups of bacterial promoters, as detected by screening a library of promoter-luxCDABE reporter clones of Salmonella enterica serovar Typhimurium. The patterns of transcription permit identification of classes of promoters having differential responses to antibiotics of related structure and mode-of-action; studies of antibiotic synergy or antagonism showed that eukaryotic translation inhibitors may act on the 50S ribosome. The mechanism of transcriptional modulation is not known but may involve bacterial stress responses and/or the disturbance and subsequent compensation of metabolic networks as a result of subtle interference with ribosome function. Transcriptional patterns detected with promoter-lux clones provide a novel approach to antibiotic discovery and mode-of-action studies.

Anti-Bacterial Agents↗
PubMed2004

Novel pathway of salicylate degradation by Streptomyces sp. strain WA46.

A novel salicylate-degrading Streptomyces sp., strain WA46, was identified by UV fluorescence on solid minimal medium containing salicylate; trace amounts of gentisate were detected by high-pressure liquid chromatography when strain WA46 was grown with salicylate. PCR amplification of WA46 DNA with degenerate primers for gentisate 1,2-dioxygenase (GDO) genes produced an amplicon of the expected size. Sequential PCR with nested GDO primers was then used to identify a salicylate degradation gene cluster in a plasmid library of WA46 chromosomal DNA. The nucleotide sequence of a 13.5-kb insert in recombinant plasmid pWD1 (which was sufficient for the complete degradation of salicylate) showed that nine putative open reading frames (ORFs) (sdgABCDEFGHR) were involved. Plasmid pWD1 derivatives disrupted in each putative gene were transformed into Streptomyces lividans TK64. Disruption of either sdgA or sdgC blocked salicylate degradation; constructs lacking sdgD accumulated gentisate. Cell extracts from Escherichia coli DH5 alpha transformants harboring pUC19 that expressed each of the sdg ORFs showed that conversions of salicylate to salicylyl-coenzyme A (CoA) and salicylyl-CoA to gentisyl-CoA required SdgA and SdgC, respectively. SdgA required CoA and ATP as cofactors, while NADH was required for SdgC activity; SdgC was identified as salicylyl-CoA 5-hydroxylase. Gentisyl-CoA underwent spontaneous cleavage to gentisate and CoA. SdgA behaved as a salicylyl-CoA ligase despite showing amino acid sequence similarity to an AMP-ligase. SdgD was identified as a GDO. These results suggest that Streptomyces sp. strain WA46 degrades salicylate by a novel pathway via a CoA derivative. Two-dimensional polyacrylamide gel electrophoresis and reverse transcriptase-PCR studies indicated that salicylate induced expression of the sdg cluster.

Acyl Coenzyme A↗
PubMed2004

Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1.

Rhodococcus sp. strain RHA1, a potent polychlorinated-biphenyl (PCB)-degrading strain, contains three linear plasmids ranging in size from 330 to 1,100 kb. As part of a genome sequencing project, we report here the complete sequence and characterization of the smallest and least-well-characterized of the RHA1 plasmids, pRHL3. The plasmid is an actinomycete invertron, containing large terminal inverted repeats with a tightly associated protein and a predicted open reading frame (ORF) that is similar to that of a mycobacterial rep gene. The pRHL3 plasmid has 300 putative genes, almost 21% of which are predicted to have a catabolic function. Most of these are organized into three clusters. One of the catabolic clusters was predicted to include limonene degradation genes. Consistent with this prediction, RHA1 grew on limonene, carveol, or carvone as the sole carbon source. The plasmid carries three cytochrome P450-encoding (CYP) genes, a finding consistent with the high number of CYP genes found in other actinomycetes. Two of the CYP genes appear to belong to novel families; the third belongs to CYP family 116 but appears to belong to a novel class based on the predicted domain structure of its reductase. Analyses indicate that pRHL3 also contains four putative "genomic islands" (likely to have been acquired by horizontal transfer), insertion sequence elements, 19 transposase genes, and a duplication that spans two ORFs. One of the genomic islands appears to encode resistance to heavy metals. The plasmid does not appear to contain any housekeeping genes. However, each of the three catabolic clusters contains related genes that appear to be involved in glucose metabolism.

Amino Acid Sequence↗
PubMed2004

Antimicrobial resistance gene delivery in animal feeds.

Avoparcin, a glycopeptide antimicrobial agent related to vancomycin, has been used extensively as a growth promoter in animal feeds for more than 2 decades, and evidence has shown that such use contributed to the development of vancomycin-resistant enterococci. A cluster that includes three genes, vanH, vanA, and vanX, is required for high-level resistance to glycopeptides. In the vancomycin producer Amycolatopsis orientalis C329.2, homologs of these genes are present, suggesting an origin for the cluster. We found substantial bacterial DNA contamination in animal feed-grade avoparcin. Furthermore, nucleotide sequences related to the cluster vanHAX are present in this DNA, suggesting that the prolonged use of avoparcin in agriculture led to the uptake of glycopeptide resistance genes by animal commensal bacteria, which were subsequently transferred to humans.

Animal Feed↗
PubMed2003

Gathering no moss.

I never imagined that I would be asked to write an autobiography in a microbiology tome. For that matter, little did I think that I would consider microbiology the most intriguing subject in the life sciences and the only field I wanted to study. My formal scientific training was in chemistry. This is a recounting of my conversion and the opportunities I have had to work in the microbial sciences with some of the major figures (and characters) during a period of marvelous intensity and productivity. I want to recognize and thank my many distinguished colleagues for the ways in which they have helped me to experience a fruitful and stimulating life as a microbiologist.

France↗
PubMed2002

Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics.

Antibiotics such as erythromycin and rifampicin, at low concentrations, alter global bacterial transcription patterns as measured by the stimulation or inhibition of a variety of promoter-lux reporter constructs in a Salmonella typhimurium library. Analysis of a 6,500-clone library indicated that as many as 5% of the promoters may be affected, comprising genes for a variety of functions, as well as a significant fraction of genes with no known function. Studies of a selection of the reporter clones showed that stimulation varied depending on the nature of the antibiotic, the promoter, and what culture medium was used; the response differed on solid as compared with liquid media. Transcription was markedly reduced in antibiotic-resistant hosts, but the presence of mutations deficient in stress responses such as SOS or universal stress did not prevent antibiotic-induced modulation. The results show that small molecules may have contrasting effects on bacteria depending on their concentration: either the modulation of bacterial metabolism by altering transcription patterns or the inhibition of growth by the inhibition of specific target functions. Both activities could play important roles in the regulation of microbial communities. These studies indicate that the detection of pharmaceutically useful natural product inhibitors could be effectively achieved by measuring activation of transcription at low concentrations in high-throughput assays using appropriate bacterial promoter-reporter constructs.

Anti-Bacterial Agents↗