ORCID Profile
0000-0003-4846-6566
Current Organisations
NHS Greater Glasgow and Clyde
,
Royal Edinburgh Hospital
,
Gartnavel Royal Hospital
,
Dykebar Hospital
,
Leverndale Hospital
,
Gogarburn Hospital
,
CRC Scotland & London
,
University of Glasgow
,
The University of Edinburgh
,
University of Queensland
,
Jadavpur University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Infectious Agents | Microbial Genetics | Microbiology | Bacteriology
ANZSRC Socio-Economic Objective (SEO)
Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Expanding Knowledge in the Biological Sciences | Veterinary Pharmaceutical Treatments (e.g. Antibiotics) |
Related Links
Publications
Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum
Publisher: eLife Sciences Publications, Ltd
Date: 30-06-2023
Abstract: Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multi-drug resistant clones both alarmingly associated with high mortality. The molecular microbial genetics underpinning these recalcitrant K. pneumoniae infections is unclear, coupled with the emergence of lineages resistant to nearly all present day clinically important antimicrobials. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani medium), human urine and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. Genome-wide functional studies like these provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
Author response: Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation
Publisher: eLife Sciences Publications, Ltd
Date: 07-12-2020
Structure of dual-BON domain protein DolP identifies phospholipid binding as a new mechanism for protein localization
Publisher: eLife Sciences Publications, Ltd
Date: 14-12-2020
DOI: 10.7554/ELIFE.62614
Abstract: The Gram-negative outer-membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents, and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here, we reveal DolP is a lipoprotein functionally conserved amongst Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for Escherichia coli DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds anionic phospholipids through an extensive membrane:protein interface. This interaction is essential for DolP function and is required for sub-cellular localisation of the protein to the cell ision site, providing evidence of subcellular localisation of these phospholipids within the outer membrane. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.
Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum
Publisher: eLife Sciences Publications, Ltd
Date: 30-06-2023
DOI: 10.7554/ELIFE.88971
Abstract: Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multi-drug resistant clones both alarmingly associated with high mortality. The molecular microbial genetics underpinning these recalcitrant K. pneumoniae infections is unclear, coupled with the emergence of lineages resistant to nearly all present day clinically important antimicrobials. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani medium), human urine and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. Genome-wide functional studies like these provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
Transposon mutagenesis screen inKlebsiella pneumoniaeidentifies genetic determinants required for growth in human urine and serum
Publisher: Cold Spring Harbor Laboratory
Date: 06-2023
DOI: 10.1101/2023.05.31.543172
Abstract: Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multi-drug resistant clones both alarmingly associated with high mortality. The molecular microbial genetics underpinning these recalcitrant K. pneumoniae infections is unclear, coupled with the emergence of lineages resistant to nearly all present day clinically important antimicrobials. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani medium), human urine and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. Genome-wide functional studies like these provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
Pathogenic Differences of Type 1 Restriction-Modification Allele Variants in Experimental Listeria monocytogenes Meningitis
Publisher: Frontiers Media SA
Date: 30-10-2020
Transposon-Directed Insertion-Site Sequencing Reveals Glycolysis Gene gpmA as Part of the H2O2 Defense Mechanisms in Escherichia coli
Publisher: MDPI AG
Date: 18-10-2022
Abstract: Hydrogen peroxide (H2O2) is a common effector of defense mechanisms against pathogenic infections. However, bacterial factors involved in H2O2 tolerance remain unclear. Here we used transposon-directed insertion-site sequencing (TraDIS), a technique allowing the screening of the whole genome, to identify genes implicated in H2O2 tolerance in Escherichia coli. Our TraDIS analysis identified 10 mutants with fitness defect upon H2O2 exposure, among which previously H2O2-associated genes (oxyR, dps, dksA, rpoS, hfq and polA) and other genes with no known association with H2O2 tolerance in E. coli (corA, rbsR, nhaA and gpmA). This is the first description of the impact of gpmA, a gene involved in glycolysis, on the susceptibility of E. coli to H2O2. Indeed, confirmatory experiments showed that the deletion of gpmA led to a specific hypersensitivity to H2O2 comparable to the deletion of the major H2O2 scavenger gene katG. This hypersensitivity was not due to an alteration of catalase function and was independent of the carbon source or the presence of oxygen. Transcription of gpmA was upregulated under H2O2 exposure, highlighting its role under oxidative stress. In summary, our TraDIS approach identified gpmA as a member of the oxidative stress defense mechanism in E. coli.
Plasmids Can Shift Bacterial Morphological Response against Antibiotic Stress
Publisher: Wiley
Date: 24-11-2022
Abstract: Bacterial cell filamentation is a morphological change wherein cell ision is blocked, which can improve bacterial survival under unfavorable conditions (e.g., antibiotic stress that causes DNA damage). As an extrachromosomal DNA molecule, plasmids can confer additionally advantageous traits including antibiotic resistance on the host. However, little is known about whether plasmids could shift bacterial morphological responses to antibiotic stress. Here, it is reported that plasmid‐free cells, rather than plasmid‐bearing cells, exhibit filamentation and asymmetrical cell ision under exposure to sub‐inhibitory concentrations of antibiotics (ciprofloxacin and cephalexin). The underlying mechanism is revealed by investigating DNA damage, cell ision inhibitor sulA , the SOS response, toxin‐antitoxin module ( parDE ) located on plasmids, and efflux pumps. Significantly higher expression of sulA is observed in plasmid‐free cells, compared to plasmid‐bearing cells. Plasmid carriage enables the hosts to suffer less DNA damage, exhibit stronger efflux pump activities, and thus have a higher antibiotic tolerance. These benefits are attributed to the parDE module that mediates stress responses from plasmid‐bearing cells and mainly contributes to cell morphological changes. Collectively, the findings demonstrate that plasmids can confer additional innate defenses on the host to antibiotics, thus advancing the understanding of how plasmids affect bacterial evolution in hostile environments.
Transposon mutagenesis reveals differential essential pathways in modelSalmonellaTyphimurium strains SL1344 and SL3261
Publisher: Cold Spring Harbor Laboratory
Date: 03-10-2023
Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319
Publisher: American Society for Microbiology
Date: 02-2018
Abstract: The genome sequence of the human pathogen Corynebacterium diphtheriae bv. mitis strain ISS 3319 was determined and closed in this study. The genome is estimated to have 2,404,936 bp encoding 2,257 proteins. This strain also possesses a plasmid of 1,960 bp.
Dpaa detaches braun’s lipoprotein from peptidoglycan
Publisher: American Society for Microbiology
Date: 29-06-2021
Abstract: Gram-negative bacteria have a complex cell envelope with two membranes and a periplasm containing the peptidoglycan layer. The outer membrane is firmly connected to the peptidoglycan by highly abundant proteins.
Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth
Publisher: Public Library of Science (PLoS)
Date: 23-12-2021
DOI: 10.1371/JOURNAL.PGEN.1009586
Abstract: The cell envelope is essential for viability in all domains of life. It retains enzymes and substrates within a confined space while providing a protective barrier to the external environment. Destabilising the envelope of bacterial pathogens is a common strategy employed by antimicrobial treatment. However, even in one of the best studied organisms, Escherichia coli , there remain gaps in our understanding of how the synthesis of the successive layers of the cell envelope are coordinated during growth and cell ision. Here, we used a whole-genome phenotypic screen to identify mutants with a defective cell envelope. We report that loss of yhcB , a conserved gene of unknown function, results in loss of envelope stability, increased cell permeability and dysregulated control of cell size. Using whole genome transposon mutagenesis strategies, we report the comprehensive genetic interaction network of yhcB , revealing all genes with a synthetic negative and a synthetic positive relationship. These genes include those previously reported to have a role in cell envelope biogenesis. Surprisingly, we identified genes previously annotated as essential that became non-essential in a Δ yhcB background. Subsequent analyses suggest that YhcB functions at the junction of several envelope biosynthetic pathways coordinating the spatiotemporal growth of the cell, highlighting YhcB as an as yet unexplored antimicrobial target.
YhcB coordinates peptidoglycan and LPS biogenesis with phospholipid synthesis during Escherichia coli cell growth
Publisher: Cold Spring Harbor Laboratory
Date: 18-04-2021
DOI: 10.1101/2021.04.16.440158
Abstract: The cell envelope is essential for viability in all kingdoms of life. It retains enzymes and substrates within a confined space while providing a protective barrier to the external environment. Destabilising the envelope of bacterial pathogens is a common strategy employed by antimicrobial treatment. However, even in one of the most well studied organisms, Escherichia coli , there remain gaps in our understanding of how the synthesis of the successive layers of the cell envelope are coordinated during growth and cell ision. Here, we used a whole genome phenotypic screen to identify mutants with a defective cell envelope. We report that loss of yhcB , a conserved gene of unknown function, results in loss of envelope stability, increased cell permeability and dysregulated control of cell size. Using whole genome transposon mutagenesis strategies we report the complete genetic interaction network of yhcB , revealing all genes with a synthetic negative and a synthetic positive relationship. These genes include those previously reported to have a role in cell envelope biogenesis. Surprisingly, we identified genes previously annotated as essential that became non-essential in a Δ yhcB background. Subsequent analyses suggest that YhcB sits at the junction of several envelope biosynthetic pathways coordinating the spatiotemporal growth of the cell, highlighting YhcB as an as yet unexplored antimicrobial target.
The Essential Genome of Escherichia coli K-12
Publisher: American Society for Microbiology
Date: 07-03-2018
Abstract: Transposon-directed insertion site sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries, and therefore, it remains unclear whether the two methodologies are comparable. To address this, a high-density transposon library was constructed in Escherichia coli K-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false-positive identification of essential genes, statistical data analysis included corrections for both gene length and genome length. Through this analysis, new essential genes and genes previously incorrectly designated essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Ex les include short essential regions within genes, orientation-dependent effects, and fine-resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis data sets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry. IMPORTANCE Incentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes in Escherichia coli , we constructed a transposon mutant library of unprecedented density. Initial automated analysis of the resulting data revealed many discrepancies compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high-density TraDIS sequencing data for each putative essential gene for the E. coli model laboratory organism. This paper is important because it provides a better understanding of the essential genes of E. coli , reveals the limitations of relying on automated analysis alone, and provides a new standard for the analysis of TraDIS data.
A multiomic approach to defining the essential genome of the globally important pathogen Corynebacterium diphtheriae
Publisher: Public Library of Science (PLoS)
Date: 26-04-2023
DOI: 10.1371/JOURNAL.PGEN.1010737
Abstract: Diphtheria is a respiratory disease caused by Corynebacterium diphtheriae . While the toxin-based vaccine has helped control outbreaks of the disease since the mid-20 th century there has been an increase in cases in recent years, including systemic infections caused by non-toxigenic C . diphtheriae strains. Here we describe the first study of gene essentiality in C . diphtheriae , providing the most-dense Tra nsposon D irected I nsertion S equencing (TraDIS) library in the phylum Actinobacteriota. This high-density library has allowed the identification of conserved genes across the genus and phylum with essential function and enabled the elucidation of essential domains within the resulting proteins including those involved in cell envelope biogenesis. Validation of these data through protein mass spectrometry identified hypothetical and uncharacterized proteins in the proteome which are also represented in the vaccine. These data are an important benchmark and useful resource for the Corynebacterium , Mycobacterium , Nocardia and Rhodococcus research community. It enables the identification of novel antimicrobial and vaccine targets and provides a basis for future studies of Actinobacterial biology.
TraDIS-validate: a method for curating ordered gene-replacement libraries
Publisher: Cold Spring Harbor Laboratory
Date: 16-02-2022
DOI: 10.1101/2022.02.16.479736
Abstract: In recent years the availability of genome sequence information has grown logarithmically resulting in the identification of a plethora of uncharacterised genes. To address this gap in functional annotation, many high-throughput screens have been devised with the goal of uncovering novel gene functions. Gene-replacement libraries are one such tool that can be screened in a high-throughput way to link genotype and phenotype and are key community resources. However, for a phenotype to be attributed to a specific gene, there needs to be confidence in the genotype. Construction of large libraries can be laborious and occasionally errors will arise. Here, we present a rapid and accurate method for the validation of any ordered gene-replacement library. We applied our method (TraDIS-Validate) to the well-known Keio library of Escherichia coli gene-deletion mutants. Our method identified 3,718 constructed mutants out of a total of 3,728 confirmed isolates. TraDIS-validate therefore had a success rate of 99.7% for identifying the correct kanamycin cassette position. This dataset provides a benchmark for the purity of the Keio mutants and a screening method for mapping the position of an antibiotic resistance cassette in any ordered library.
LI-Detector: a Method for Curating Ordered Gene-Replacement Libraries
Publisher: American Society for Microbiology
Date: 31-08-2022
DOI: 10.1128/SPECTRUM.00833-22
Abstract: The construction of ordered gene replacement libraries requires significant investment of time and resources to create a valuable community resource. During construction, technical errors may result in a limited number of incorrect mutants being made. Such mutants may confound the output of subsequent experiments. Here, using the remarkable E. coli Keio knockout library, we describe a method to rapidly validate the construction of every mutant.
Oxidative & nitrosative stress in depression: Why so much stress?
Publisher: Elsevier BV
Date: 09-2014
DOI: 10.1016/J.NEUBIOREV.2014.05.007
Abstract: Many studies support a crucial role for oxidative & nitrosative stress (O&NS) in the pathophysiology of unipolar and bipolar depression. These disorders are characterized inter alia by lowered antioxidant defenses, including: lower levels of zinc, coenzyme Q10, vitamin E and glutathione increased lipid peroxidation damage to proteins, DNA and mitochondria secondary autoimmune responses directed against redox modified nitrosylated proteins and oxidative specific epitopes. This review examines and details a model through which a complex series of environmental factors and biological pathways contribute to increased redox signaling and consequently increased O&NS in mood disorders. This multi-step process highlights the potential for future interventions that encompass a erse range of environmental and molecular targets in the treatment of depression.
Related Organisations
NHS Greater Glasgow And Clyde
Location: United Kingdom of Great Britain and Northern Ireland
Royal Edinburgh Hospital
Location: United Kingdom of Great Britain and Northern Ireland
Gartnavel Royal Hospital
Location: United Kingdom of Great Britain and Northern Ireland
Dykebar Hospital
Location: United Kingdom of Great Britain and Northern Ireland
Leverndale Hospital
Location: United Kingdom of Great Britain and Northern Ireland
Gogarburn Hospital
Location: United Kingdom of Great Britain and Northern Ireland
CRC Scotland & London
Location: United Kingdom of Great Britain and Northern Ireland
University Of Glasgow
Location: United Kingdom of Great Britain and Northern Ireland
The University Of Edinburgh
Location: United Kingdom of Great Britain and Northern Ireland
Related Funding Activities
YhcB, A Crucial Player In The Control Of Bacterial Cell Envelope Biogenesis
Start Date: 2022
End Date: 2024
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP220101960
Start Date: 01-2022
End Date: 01-2025
Amount: $489,000.00
Funder: Australian Research Council
View Funded Activity