Professor Colin Smith
Professor of Functional Genomics
Qualifications: B.Sc, PhD
Phone: Work: 01483 68 6937
Room no: 15 AX 02
My first degree, in Microbiology, was obtained from the University of Bristol in 1981 and from 1981-1984 I undertook my PhD research on the molecular genetics of Streptomyces in the labs of Prof Keith Chater and Prof Sir David Hopwood at the John Innes Institute (now the John Innes Centre), Norwich, UK. My graduate research was focused on developing RNA methods for Streptomyces coelicolor and exploiting them to understand gene structure and regulation in this complex antibiotic-producing bacterial group. I subsequently returned to the University of Bristol (to the Biochemistry Department) in 1985 to work as a postdoctoral research associate in the lab of Prof Nigel Brown, continuing to dissect basic transcriptional regulatory mechanisms in Streptomyces.
I took up a Lectureship in Molecular Genetics at the University of Manchester Institute of Science and Technology (UMIST, Manchester) in 1988 and for the following decade studied a range of genetic regulatory networks in Streptomyces, perhaps most notably the heat-shock response, that deploys the molecular chaperone machines and associated proteases. Since 1999 I have embraced multidisciplinarity in my research activities - developing collaborative research projects with physiologists, nutritionists, chemists, mathematicians, engineers, statisticians and computer scientists. In the academic year 2001-2002 I undertook a sabbatical in the Control Systems Centre (Dept. Electronics and Electrical Engineering) at UMIST with Dr Olaf Wolkenhauer. A productive collaboration with Prof Jason Micklefield (UMIST, then Manchester University) produced a number of high impact publications on the biosynthetic engineering of nonribosomally synthesised peptide antibiotics – a major novel class of last line-of-defence antibiotics that are active against Gram-positive superbugs, such as vancomycin-resistant Staphylococcus and Enterococcus strains.
I relocated to the University of Surrey in 2003 to take up a Chair in Functional Genomics, just before UMIST merged with the University of Manchester. Since then my major research areas have focused on the application of genomics technologies to study gene regulation at a global level – both in the context of antibiotic production by Streptomyces and in the investigation of the effects of sleep disruption and nutritional supplementation on human gene expression.
In 2000 we set about establishing a DNA microarray and bioinformatics resource for the national and international Streptomyces communities, largely funded by the BBSRC. This work led ultimately to the development of high density experimentally-optimised commercial Agilent-format microarrays for S. coelicolor [http://genomebiology.com/2009/10/1/R5; http://www.biomedcentral.com/1471-2164/11/682]. The Agilent format microarrays now supersede in house-printed DNA microarrays and we therefore no longer in house production. Bioinformatics resources were also developed as part of this work and can be accessed at: http://strep-microarray.sbs.surrey.ac.uk.
Systems biology of Streptomyces: transcriptional and translational regulatory networks controlling antibiotic production and responses to environmental stress
We combine the use of high density DNA microarrays and next-generation sequencing-based RNA-seq methods to quantify dynamic changes in global gene expression and transcription factor binding under different physiological conditions. These studies have tended to concentrate on transcriptional changes. However, our recent polysome profiling and ‘Ribosome Profiling’ experiments – that reveal all RNAs associated with ribosomes - have revealed extensive control of stress responses and antibiotic production at the level of translation. In some cases translational induction, rather than transcriptional induction, appear to dominate some networks. These ‘translatomic’ findings are providing us with new insights into the mechanisms controlling antibiotic production by Streptomyces and they should enable us to design new ‘synthetic biology’ approaches to activate or enhance antibiotic biosynthetic pathways. This work involves close collaboration with Prof Byung-Kwan Cho at KAIST (Korea). Our current focus is aimed at identifying the proteins and RNA molecules/structures that mediate the translational control. A long term goal is to integrate the translational regulatory networks with the transcriptional networks in order to develop more comprehensive dynamic in silico models of Streptomyces metabolism.
Influences of human sleep disruption on genome wide expression
We are working in collaboration with sleep and circadian biology specialists at the University of Surrey to study the effects of sleep disruption on gene expression. We have undertaken two large scale studies of the effects of sleep deprivation and mistimed sleep (shift work/jet-lag) on global gene expression in human subjects. The first results from these respective studies were recently published as two major articles in PNAS. This work is now being extended to a new study co-funded by the BBSRC and the European Space Agency (commenced August 2015).
The influence of vitamin supplementation on gene expression in human subjects of different ethnicities
We have recently brought our genomics experience to an interdisciplinary human nutrition study led by Prof Sue Lanham-New of the University of Surrey. We investigated the global influence of different forms of vitamin D supplementation on gene expression. The two commonly used forms of vitamin D were assessed in Caucasian and South Asian women: vitamin D2 (a synthetic form generally used by vegetarians and muslims) and vitamin D3 (the native form naturally-produced by our skin and available from animal products). The results of the analysis were striking, with the findings that D3 was far superior in raising serum levels of the active vitamin (25OHD) and the observation that some very different cellular pathways are influenced at the genetic level by the two different forms of vitamin D. The interporetation and further validation of these findings is ongoing. The results of our study are likely to have a high societal impact because they may ultimately influence national and international guidelines on the fortification of foods with vitamin D.
This work is supported by DRINC, a partnership between BBSRC, the Engineering and Physical Sciences Research Council (EPSRC), the Economic and Social Research Council (ESRC), the Medical Research Council (MRC), and a consortium of leading food and drink companies.
Personal genomics and personalized medicine
I am a strong advocate of personal genomics and support the public sharing of such data. Indeed, I had my own genome completely sequenced by Illumina Inc in early 2013 [http://www.theguardian.com/science/2013/jun/08/genome-sequenced]. I follow closely the large scale personal genome projects such as the ‘Personal Genome Project’ [http://www.genomemedicine.com/content/6/2/10] and Genomics England’s 100,000 human genomes project [http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(14)62453-3/fulltext; http://www.nature.com/nature/journal/v524/n7566/full/524503a.html] and I actively engage in outreach activities to raise awareness of the potential of such genome studies for enhancing human health and wellbeing.
- 'Exploiting human and mouse transcriptomic data: Identification of circadian genes and pathways influencing health'.
The power of the application of bioinformatics across multiple publicly available transcriptomic data sets was explored. Using 19 human and mouse circadian transcriptomic data sets, we found that NR1D1 and NR1D2 which encode heme-responsive nuclear receptors are the most rhythmic transcripts across sleep conditions and tissues suggesting that they are at the core of circadian rhythm generation. Analyzes of human transcriptomic data show that a core set of transcripts related to processes including immune function, glucocorticoid signalling, and lipid metabolism is rhythmically expressed independently of the sleep-wake cycle. We also identify key transcripts associated with transcription and translation that are disrupted by sleep manipulations, and through network analysis identify putative mechanisms underlying the adverse health outcomes associated with sleep disruption, such as diabetes and cancer. Comparative bioinformatics applied to existing and future data sets will be a powerful tool for the identification of core circadian- and sleep-dependent molecules.
- 'Exploiting human and mouse transcriptomic data: identification of circadian genes and pathways influencing health'.
BioEssays, 36 Article number 10.1002/bies.201400193
[ Status: Accepted ]
- 'The D2-D3 Study: comparing the efficacy of 15 mu g/d vitamin D2 vs. D3 in raising vitamin D status in both South Asian and Caucasian women, and the ethical implications of placebo treatment'. PROCEEDINGS OF THE NUTRITION SOCIETY, 74 (OCE1), pp. E116-E116. . (2015)
- 'Genome-wide analysis of in vivo binding of the master regulator DasR in Streptomyces coelicolor identifies novel non-canonical targets.'.
PLoS One, United States: 10 (4)Full text is available at: http://epubs.surrey.ac.uk/809060/
Streptomycetes produce a wealth of natural products, including over half of all known antibiotics. It was previously demonstrated that N-acetylglucosamine and secondary metabolism are closely entwined in streptomycetes. Here we show that DNA recognition by the N-acetylglucosamine-responsive regulator DasR is growth-phase dependent, and that DasR can bind to sites in the S. coelicolor genome that have no obvious resemblance to previously identified DasR-responsive elements. Thus, the regulon of DasR extends well beyond what was previously predicted and includes a large number of genes with functions far removed from N-acetylglucosamine metabolism, such as genes for small RNAs and DNA transposases. Conversely, the DasR regulon during vegetative growth largely correlates to the presence of canonical DasR-responsive elements. The changes in DasR binding in vivo following N-acetylglucosamine induction were studied in detail and a possible molecular mechanism by which the influence of DasR is extended is discussed. Discussion of DasR binding was further informed by a parallel transcriptome analysis of the respective cultures. Evidence is provided that DasR binds directly to the promoters of all genes encoding pathway-specific regulators of antibiotic production in S. coelicolor, thereby providing an exquisitely simple link between nutritional control and secondary metabolism.
- 'The D2-D3 Study: a randomised, double-blind, placebo-controlled food-fortification trial in women, comparing the efficacy of 15ug/d vitamin D2 vs vitamin D3 in raising serum 25OHD levels'. PROCEEDINGS OF THE NUTRITION SOCIETY, 74 (OCE1), pp. E16-E16. . (2015)
- 'A terD domain-encoding gene (SCO2368) is involved in calcium homeostasis and participates in calcium regulation of a DosR-like regulon in Streptomyces coelicolor.'.
J Bacteriol, United States: 197 (5), pp. 913-923.doi: 10.1128/JB.02278-14
Although Streptomyces coelicolor is not resistant to tellurite, it possesses several TerD domain-encoding (tdd) genes of unknown function. To elucidate the function of tdd8, the transcriptomes of S. coelicolor strain M145 and of a tdd8 deletion mutant derivative (the Δtdd8 strain) were compared. Several orthologs of Mycobacterium tuberculosis genes involved in dormancy survival were upregulated in the deletion mutant at the visual onset of prodiginine production. These genes are organized in a putative redox stress response cluster comprising two large loci. A binding motif similar to the dormancy survival regulator (DosR) binding site of M. tuberculosis has been identified in the upstream sequences of most genes in these loci. A predicted role for these genes in the redox stress response is supported by the low NAD(+)/NADH ratio in the Δtdd8 strain. This S. coelicolor gene cluster was shown to be induced by hypoxia and NO stress. While the tdd8 deletion mutant (the Δtdd8 strain) was unable to maintain calcium homeostasis in a calcium-depleted medium, the addition of Ca(2+) in Δtdd8 culture medium reduced the expression of several genes of the redox stress response cluster. The results shown in this work are consistent with Tdd8 playing a significant role in calcium homeostasis and redox stress adaptation.
- 'A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.'.
Mol Microbiol, doi: 10.1111/mmi.12810
Streptomyces coelicolor is a model for studying bacteria renowned as the foremost source of natural products used clinically. Post-genomic studies have revealed complex patterns of gene expression and links to growth, morphological development and individual genes. However, the underlying regulation remains largely obscure, but undoubtedly involves steps after transcription initiation. Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. This was achieved by combining RNA-sequencing approaches suited to the analysis of GC-rich organisms. Escherichia coli was analysed in parallel to validate the methodology and allow comparison. Previously, sites of RNA processing and degradation had not been mapped on a transcriptome-wide scale for E. coli. Through examples, we show the value of our approach and data sets. This includes the identification of new layers of transcriptional complexity associated with several key regulators of secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and rRNA processing associated with the generation of specialized ribosomes in E. coli. New regulatory small RNAs were identified for both organisms. Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression.
- 'Deciphering the regulon of Streptomyces coelicolor AbrC3, a positive response regulator of antibiotic production.'.
Appl Environ Microbiol, United States: 80 (8), pp. 2417-2428.doi: 10.1128/AEM.03378-13Full text is available at: http://epubs.surrey.ac.uk/805402/
The atypical two-component system (TCS) AbrC1/C2/C3 (encoded by SCO4598, SCO4597, and SCO4596), comprising two histidine kinases (HKs) and a response regulator (RR), is crucial for antibiotic production in Streptomyces coelicolor and for morphological differentiation under certain nutritional conditions. In this study, we demonstrate that deletion of the RR-encoding gene, abrC3 (SCO4596), results in a dramatic decrease in actinorhodin (ACT) and undecylprodiginine (RED) production and delays morphological development. In contrast, the overexpression of abrC3 in the parent strain leads to a 33% increase in ACT production in liquid medium. Transcriptomic analysis and chromatin immunoprecipitation with microarray technology (ChIP-chip) analysis of the ΔabrC3 mutant and the parent strain revealed that AbrC3 directly controls ACT production by binding to the actII-ORF4 promoter region; this was independently verified by in vitro DNA-binding assays. This binding is dependent on the sequence 5'-GAASGSGRMS-3'. In contrast, the regulation of RED production is not due to direct binding of AbrC3 to either the redZ or redD promoter region. This study also revealed other members of the AbrC3 regulon: AbrC3 is a positive autoregulator which also binds to the promoter regions of SCO0736, bdtA (SCO3328), absR1 (SCO6992), and SCO6809. The direct targets share the 10-base consensus binding sequence and may be responsible for some of the phenotypes of the ΔabrC3 mutant. The identification of the AbrC3 regulon as part of the complex regulatory network governing antibiotic production widens our knowledge regarding TCS involvement in control of antibiotic synthesis and may contribute to the rational design of new hyperproducer host strains through genetic manipulation of such systems.
- 'Mistimed sleep disrupts circadian regulation of the human transcriptome.'.
Proc Natl Acad Sci U S A, United States: 111 (6), pp. E682-E691.Full text is available at: http://epubs.surrey.ac.uk/805147/
Circadian organization of the mammalian transcriptome is achieved by rhythmic recruitment of key modifiers of chromatin structure and transcriptional and translational processes. These rhythmic processes, together with posttranslational modification, constitute circadian oscillators in the brain and peripheral tissues, which drive rhythms in physiology and behavior, including the sleep-wake cycle. In humans, sleep is normally timed to occur during the biological night, when body temperature is low and melatonin is synthesized. Desynchrony of sleep-wake timing and other circadian rhythms, such as occurs in shift work and jet lag, is associated with disruption of rhythmicity in physiology and endocrinology. However, to what extent mistimed sleep affects the molecular regulators of circadian rhythmicity remains to be established. Here, we show that mistimed sleep leads to a reduction of rhythmic transcripts in the human blood transcriptome from 6.4% at baseline to 1.0% during forced desynchrony of sleep and centrally driven circadian rhythms. Transcripts affected are key regulators of gene expression, including those associated with chromatin modification (methylases and acetylases), transcription (RNA polymerase II), translation (ribosomal proteins, initiation, and elongation factors), temperature-regulated transcription (cold inducible RNA-binding proteins), and core clock genes including CLOCK and ARNTL (BMAL1). We also estimated the separate contribution of sleep and circadian rhythmicity and found that the sleep-wake cycle coordinates the timing of transcription and translation in particular. The data show that mistimed sleep affects molecular processes at the core of circadian rhythm generation and imply that appropriate timing of sleep contributes significantly to the overall temporal organization of the human transcriptome.
- 'Effects of insufficient sleep on circadian rhythmicity and expression amplitude of the human blood transcriptome.'.
Proc Natl Acad Sci U S A, United States: 110 (12), pp. E1132-E1141.Full text is available at: http://epubs.surrey.ac.uk/802564/
Insufficient sleep and circadian rhythm disruption are associated with negative health outcomes, including obesity, cardiovascular disease, and cognitive impairment, but the mechanisms involved remain largely unexplored. Twenty-six participants were exposed to 1 wk of insufficient sleep (sleep-restriction condition 5.70 h, SEM = 0.03 sleep per 24 h) and 1 wk of sufficient sleep (control condition 8.50 h sleep, SEM = 0.11). Immediately following each condition, 10 whole-blood RNA samples were collected from each participant, while controlling for the effects of light, activity, and food, during a period of total sleep deprivation. Transcriptome analysis revealed that 711 genes were up- or down-regulated by insufficient sleep. Insufficient sleep also reduced the number of genes with a circadian expression profile from 1,855 to 1,481, reduced the circadian amplitude of these genes, and led to an increase in the number of genes that responded to subsequent total sleep deprivation from 122 to 856. Genes affected by insufficient sleep were associated with circadian rhythms (PER1, PER2, PER3, CRY2, CLOCK, NR1D1, NR1D2, RORA, DEC1, CSNK1E), sleep homeostasis (IL6, STAT3, KCNV2, CAMK2D), oxidative stress (PRDX2, PRDX5), and metabolism (SLC2A3, SLC2A5, GHRL, ABCA1). Biological processes affected included chromatin modification, gene-expression regulation, macromolecular metabolism, and inflammatory, immune and stress responses. Thus, insufficient sleep affects the human blood transcriptome, disrupts its circadian regulation, and intensifies the effects of acute total sleep deprivation. The identified biological processes may be involved with the negative effects of sleep loss on health, and highlight the interrelatedness of sleep homeostasis, circadian rhythmicity, and metabolism.
- 'The ROK-family regulator Rok7B7 pleiotropicaly affects xylose utilization, carbon catabolite repression and antibiotic production in Streptomyces coelicolor.'.
J Bacteriol, 195 (6), pp. 1236-1248.doi: 10.1128/JB.02191-12Full text is available at: http://epubs.surrey.ac.uk/803533/
Members of the ROK family of proteins are mostly transcriptional regulators and kinases that generally relate to the control of primary metabolism, whereby its member glucose kinase acts as the central control protein in carbon control in Streptomyces. Here we show that deletion of SCO6008 (rok7B7) strongly affects carbon catabolite repression (CCR), growth and antibiotic production in Streptomyces coelicolor. Deletion of SCO7543 also affected antibiotic production, while no major changes were observed after deletion of the rok family genes SCO0794, SCO1060, SCO2846, SCO6566 or SCO6600. Global expression profiling of the rok7B7 mutant by proteomics and microarray analysis revealed strong up-regulation of the xylose transporter operon xylFGH, which lies immediately downstream of rok7B7, consistent with the improved growth and delayed development of the mutant on xylose. The enhanced CCR, which was especially obvious on rich or xylose-containing media, correlated with elevated expression of glucose kinase and of the glucose transporter GlcP. In liquid-grown cultures, expression of the biosynthetic enzymes for production of prodigionines (Red), siderophores and calcium dependent antibiotic (Cda) was enhanced in the mutant, and overproduction of Red was corroborated by MALDI-ToF analysis. These data present Rok7B7 as a pleiotropic regulator of growth, CCR and antibiotic production in Streptomyces.
- 'Identification of new developmentally regulated genes involved in Streptomyces coelicolor sporulation.'.
BMC Microbiol, England: 13Full text is available at: http://epubs.surrey.ac.uk/805403/
BACKGROUND: The sporulation of aerial hyphae of Streptomyces coelicolor is a complex developmental process. Only a limited number of the genes involved in this intriguing morphological differentiation programme are known, including some key regulatory genes. The aim of this study was to expand our knowledge of the gene repertoire involved in S. coelicolor sporulation. RESULTS: We report a DNA microarray-based investigation of developmentally controlled gene expression in S. coelicolor. By comparing global transcription patterns of the wild-type parent and two mutants lacking key regulators of aerial hyphal sporulation, we found a total of 114 genes that had significantly different expression in at least one of the two mutants compared to the wild-type during sporulation. A whiA mutant showed the largest effects on gene expression, while only a few genes were specifically affected by whiH mutation. Seven new sporulation loci were investigated in more detail with respect to expression patterns and mutant phenotypes. These included SCO7449-7451 that affect spore pigment biogenesis; SCO1773-1774 that encode an L-alanine dehydrogenase and a regulator-like protein and are required for maturation of spores; SCO3857 that encodes a protein highly similar to a nosiheptide resistance regulator and affects spore maturation; and four additional loci (SCO4421, SCO4157, SCO0934, SCO1195) that show developmental regulation but no overt mutant phenotype. Furthermore, we describe a new promoter-probe vector that takes advantage of the red fluorescent protein mCherry as a reporter of cell type-specific promoter activity. CONCLUSION: Aerial hyphal sporulation in S. coelicolor is a technically challenging process for global transcriptomic investigations since it occurs only as a small fraction of the colony biomass and is not highly synchronized. Here we show that by comparing a wild-type to mutants lacking regulators that are specifically affecting processes in aerial hypha, it is possible to identify previously unknown genes with important roles in sporulation. The transcriptomic data reported here should also serve as a basis for identification of further developmentally important genes in future functional studies.
- 'Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets.'.
Nucleic Acids Res, doi: 10.1093/nar/gks766Full text is available at: http://epubs.surrey.ac.uk/725768/
Streptomycetes sense and respond to the stress of phosphate starvation via the two-component PhoR-PhoP signal transduction system. To identify the in vivo targets of PhoP we have undertaken a chromatin-immunoprecipitation-on-microarray analysis of wild-type and phoP mutant cultures and, in parallel, have quantified their transcriptomes. Most (ca. 80%) of the previously in vitro characterized PhoP targets were identified in this study among several hundred other putative novel PhoP targets. In addition to activating genes for phosphate scavenging systems PhoP was shown to target two gene clusters for cell wall/extracellular polymer biosynthesis. Furthermore PhoP was found to repress an unprecedented range of pathways upon entering phosphate limitation including nitrogen assimilation, oxidative phosphorylation, nucleotide biosynthesis and glycogen catabolism. Moreover, PhoP was shown to target many key genes involved in antibiotic production and morphological differentiation, including afsS, atrA, bldA, bldC, bldD, bldK, bldM, cdaR, cdgA, cdgB and scbR-scbA. Intriguingly, in the PhoP-dependent cpk polyketide gene cluster, PhoP accumulates substantially at three specific sites within the giant polyketide synthase-encoding genes. This study suggests that, following phosphate limitation, Streptomyces coelicolor PhoP functions as a 'master' regulator, suppressing central metabolism, secondary metabolism and developmental pathways until sufficient phosphate is salvaged to support further growth and, ultimately, morphological development.
- 'Comparison of vitamin D2 and vitamin D3 supplementation in raising serum 25-hydroxyvitamin D status: a systematic review and meta-analysis.'.
Am J Clin Nutr, United States: 95 (6), pp. 1357-1364.Full text is available at: http://epubs.surrey.ac.uk/725769/
Currently, there is a lack of clarity in the literature as to whether there is a definitive difference between the effects of vitamins D(2) and D(3) in the raising of serum 25-hydroxyvitamin D [25(OH)D].
- 'Introduction of a Non-Natural Amino Acid into a Nonribosomal Peptide Antibiotic by Modification of Adenylation Domain Specificity'. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 51 (29), pp. 7181-7184. . (2012)
- 'Active site modification of the beta-ketoacyl-ACP synthase FabF3 of Streptomyces coelicolor affects the fatty acid chain length of the CDA lipopeptides'.
CHEMICAL COMMUNICATIONS, 47 (6), pp. 1860-1862.doi: 10.1039/c0cc03444d
- 'Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2).'.
BMC Res Notes, England: 4Full text is available at: http://epubs.surrey.ac.uk/203297/
- 'Vitamin D-2 v. vitamin D-3 supplementation in raising 25OHD status: preliminary findings of a meta-analysis'. PROCEEDINGS OF THE NUTRITION SOCIETY, 70 (OCE3), pp. E94-E94. . (2011)
- 'RankProdIt: A web-interactive Rank Products analysis tool.'.
BMC Res Notes, England: 3Full text is available at: http://epubs.surrey.ac.uk/203303/
- 'Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization.'.
BMC Genomics, England: 11Full text is available at: http://epubs.surrey.ac.uk/203299/
Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type S. lividans 66, a derivative industrial strain, TK24, and S. coelicolor M145.
- 'One of the Two Genes Encoding Nucleoid-Associated HU Proteins in Streptomyces coelicolor Is Developmentally Regulated and Specifically Involved in Spore Maturation'.
JOURNAL OF BACTERIOLOGY, 191 (21), pp. 6489-6500.doi: 10.1128/JB.00709-09
- 'A gene expression profiling approach assessing celecoxib in a randomized controlled trial in prostate cancer.'.
Cancer Genomics Proteomics, Greece: 6 (2), pp. 93-99.Full text is available at: http://epubs.surrey.ac.uk/203293/
We performed a pilot study, looking at the COX-2 inhibitor celecoxib, on newly diagnosed prostate cancer patients in the neo-adjuvant setting using DNA microarray analysis.
- 'NepA is a structural cell wall protein involved in maintenance of spore dormancy in Streptomyces coelicolor'. MOLECULAR MICROBIOLOGY, 71 (6), pp. 1591-1603. . (2009)
- 'Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon'.
GENOME BIOLOGY, 10 (1) Article number ARTN R5 Full text is available at: http://epubs.surrey.ac.uk/203295/
- 'Acidic pH shock induces the expressions of a wide range of stress-response genes'.
BMC GENOMICS, 9 Article number ARTN 604 Full text is available at: http://epubs.surrey.ac.uk/225052/
- 'Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion'. JOURNAL OF BIOLOGICAL CHEMISTRY, 283 (37), pp. 25186-25199. . (2008)
- 'Effects of pH shock on the secretion system in Streptomyces coelicolor A3(2)'. JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY, 18 (4), pp. 658-662. . (2008)
- 'pH shock induces overexpression of regulatory and biosynthetic genes for actinorhodin productionin Streptomyces coelicolor A3(2)'. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 76 (5), pp. 1119-1130. . (2007)
- 'Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics'. BIOMETRICS, 63 (3), pp. 816-823. . (2007)
- 'New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures'.
BMC GENOMICS, 8 Article number ARTN 261 Full text is available at: http://epubs.surrey.ac.uk/203300/
- 'Loss of the controlled localization of growth stage-specific cell-wall synthesis pleiotropically affects developmental gene expression in an ssgA mutant of Streptomyces coelicolor'. MOLECULAR MICROBIOLOGY, 64 (5), pp. 1244-1259. . (2007)
- 'An asparagine oxygenase (AsnO) and a 3-hydroxyasparaginyl phosphotransferase (HasP) are involved in the biosynthesis of calcium-dependent lipopeptide antibiotics'.
MICROBIOLOGY-SGM, 153, pp. 768-776.Full text is available at: http://epubs.surrey.ac.uk/225055/
- 'Engineered biosynthesis of nonribosomal lipopeptides with modified fatty acid side chains'.
Journal of the American Chemical Society, 129 (49), pp. 15182-15192.doi: 10.1021/ja074331o
The biological properties of the calcium-dependent antibiotics (CDAs), daptomycin and related nonribosomal lipopeptides, depend to a large extent on the nature of the N-terminal fatty acid moiety. It is suggested that the chain length of the unusually short (C6) 2,3-epoxyhexanoyl fatty acid moiety of CDA is determined by the specificity of the KAS-II enzyme encoded by fabF3 in the CDA biosynthetic gene cluster. Indeed, deletion of the downstream gene hxcO results in three new lipopeptides, all of which possess hexanoyl side chains (hCDAs). This confirms that HxcO functions as a hexanoyl-CoA or -ACP oxidase. The absence of additional CDA products with longer fatty acid groups further suggests that the CDA lipid chain is biosynthesized on a single ACP and is then transferred directly from this ACP to the first CDA peptide synthetase (CdaPS1). Interestingly, the hexanoyl-containing CDAs retain antibiotic activity. To further modulate the biological properties of CDA by introducing alternative fatty acid groups, a mutasynthesis approach was developed. This involved mutating the key active site Ser residue of the CdaPSI, module 1 PCP domain to Ala, which prevents subsequent phosphopantetheinylation. In the absence of the natural module 1 PCP tethered intermediate, it is possible to effect incorporation of different N-acyl-L-serinyl N-acetylcysteamine (NAC) thioester analogues, leading to CDA products with pentanoyl as well as hexanoyl side chains. © 2007 American Chemical Society.
- 'Analysis of gene expression in operons of Streptomyces coelicolor'.
GENOME BIOLOGY, 7 (6) Article number ARTN R46 Full text is available at: http://epubs.surrey.ac.uk/203294/
- 'Biosynthesis of the (2S,3R)-3-methyl glutamate residue of nonribosomal lipopeptides'.
Journal of the American Chemical Society, 128 (34), pp. 11250-11259.doi: 10.1021/ja062960c
The calcium-dependent antibiotics (CDAs) and daptomycin are therapeutically relevant nonribosomal lipopeptide antibiotics that contain penultimate C-terminal 3-methyl glutamate (3-MeGlu) residues. Comparison with synthetic standards showed that (2S,3R)-configured 3-MeGlu is present in both CDA and daptomycin. Deletion of a putative methyltransferase gene glmT from the cda biosynthetic gene cluster abolished the incorporation of 3-MeGlu and resulted in the production of Glu-containing CDA exclusively. However, the 3-MeGlu chemotype could be re-established through feeding synthetic 3-methyl-2- oxoglutarate and (2S,3R)-3-MeGlu, but not (2S,3S)-3-MeGlu. This indicates that methylation occurs before peptide assembly, and that the module 10 A-domain of the CDA peptide synthetase is specific for the (2S,3R)-stereoisomer. Further mechanistic analyses suggest that GlmT catalyzes the SAM-dependent methylation of α-ketoglutarate to give (3R)-methyl-2-oxoglutarate, which is transaminated to (2S,3R)-3-MeGlu. These insights will facilitate future efforts to engineer lipopeptides with modified glutamate residues, which may have improved bioactivity and/or reduced toxicity. © 2006 American Chemical Society.
- 'MILVA: An interactive tool for the exploration of multidimensional microarray data'. BIOINFORMATICS, 21 (22), pp. 4192-4193. . (2005)
- 'SsgA-like proteins determine the fate of peptidoglycan during sporulation of Streptomyces coelicolor'. MOLECULAR MICROBIOLOGY, 58 (4), pp. 929-944. . (2005)
- 'A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor'. MOLECULAR MICROBIOLOGY, 56 (2), pp. 465-479. . (2005)
- 'An experimental evaluation of a loop versus a reference design for two-channel microarrays'. BIOINFORMATICS, 21 (4), pp. 492-501. . (2005)
- 'Active-site modifications of adenylation domains lead to hydrolysis of upstream nonribosomal peptidyl thioester intermediates'.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126 (16), pp. 5032-5033.doi: 10.1021/ja048778y
- 'Negative feedback regulation of dnaK, clpB and lon expression by the DnaK chaperone machine in Streptomyces coelicolor, identified by transcriptome and in vivo DnaK-depletion analysis'. MOLECULAR MICROBIOLOGY, 50 (1), pp. 153-166. . (2003)
- 'IS VITAMIN D3 MORE EFFECTIVE THAN VITAMIN D2 IN RAISING 25OHD STATUS IN WOMEN WITH OSTEOPOROSIS AND OSTEOPENIA?'. SPRINGER LONDON LTD OSTEOPOROSIS INTERNATIONAL, Birmingham, ENGLAND: Osteoporosis Conference 25, pp. S687-S687. . (2014)
- 'DAILY SUPPLEMENTATION WITH VITAMIN D3 IS COMPREHENSIVELY MORE EFFECTIVE THAN VITAMIN D2 IN RAISING 25OHD STATUS AND CONCOMITANTLY REDUCING PARATHYROID HORMONE LEVELS: IMPLICATIONS FOR BONE HEALTH'. SPRINGER LONDON LTD OSTEOPOROSIS INTERNATIONAL, Birmingham, ENGLAND: Osteoporosis Conference 25, pp. S665-S665. . (2014)
- 'Mistimed sleep disrupts the circadian regulation of the human transcriptome'. WILEY-BLACKWELL JOURNAL OF SLEEP RESEARCH, Tallinn, ESTONIA: 22nd Congress of the European-Sleep-Research-Society 23, pp. 15-15. . (2014)
- 'Reconstructing regulatory networks in Streptomyces using evolutionary algorithms'.
2013 13th UK Workshop on Computational Intelligence, UKCI 2013, , pp. 24-30.
Reconstructing biological networks is vital in developing our understanding of nature. Biological systems of particular interest are bacteria that can produce antibiotics during their life cycle. Such an organism is the soil dwelling bacterium Streptomyces coelicolor. Although some of the genes involved in the production of antibiotics in the bacterium have been identified, how these genes are regulated and their specific role in antibiotic production is unknown. By understanding the network structure and gene regulation involved it may be possible to improve the production of antibiotics from this bacterium. Here we use an evolutionary algorithm to optimise parameters in the gene regulatory network of a sub-set of genes in S. coelicolor involved in antibiotic production. We present some of our preliminary results based on real gene expression data for continuous and discrete modelling techniques. © 2013 IEEE.
- 'Gene expression profiling of human cancers'. NEW YORK ACAD SCIENCES SIGNAL TRANSDUCTION AND COMMUNICATION IN CANCER CELLS, Erice, ITALY: Conference on Signal Transduction and Communication in Cancer Cells 1028, pp. 28-37. . (2004)
I lecture on molecular biology and genetics to undergraduates at all three levels of the degree programme – encompassing all biosciences students.
I lecture on the MSc Medical Microbiology and MSc Veterinary Microbiology courses covering: microbial genome evolution and the role of lateral gene transfer; next generation sequencing technologies; transcriptomics; genomics-based diagnostics and infection surveillance.
Chair: Athena SWAN Self Assessment Team of School of Biosciences and Medicine
Academic Lead: Core Genomics facility
DNA microarray resource
For information on availability of DNA microarrays and their use please access: The Streptomyces coelicolor Microrray Resource.