Dr Amy Bottomley obtained her B.Sc (Hons) in microbiology in 2007, before undertaking her PhD studies under the supervision of Prof. Simon Foster at the University of Sheffield, UK. During her PhD she studied the bacterial cell division process in Staphylococcus aureus, the causative agent of ‘golden staph’ infections. After being awarded her PhD in 2011, she continued in Sheffield as a Post-Doctoral Researcher to develop methods for super resolution fluorescence microscopy to study bacterial cell division proteins.
In May 2012, she joined the research group of Prof. Liz Harry at the i3 institute, University of Technology Sydney where she continues to work as a senior research-intensive Post-Doctoral Associate. Her research involves understanding bacterial cell division and how it is regulated in response to a variety of environmental cues, including during infection and in response to nutrient availability.
Australian society of microbiology member: 2012 to present
Can supervise: YES
Dr Amy Bottomley has extensive research experience in the field of molecular microbiology, specifically focussing on bacterial cell division. During her PhD she was the first to identify the interaction network of cell division proteins in S. aureus (Molecular Microbiology 2011), and she further characterised a function for the division protein DivIB, showing its involvement in cell wall binding (Molecular Microbiology, 2014).
Her work at UTS focusses on understanding the regulation of bacterial cell division in response to a variety of environmental cues. She works on a number of projects including studying the importance of temporary inhibition of the division process in E.coli as a survival mechanism, which is particularly important for uropathogenic E.coli (which causes urinary tract infections) during infection. She also studies how the division process is regulated in response to nutrient availability in the model organism Bacillus subtilis.
Dr Amy Bottomley is also part of a cross disciplinary team with Prof Liz Harry and A/Prof Alison Ung to design novel drugs that target the bacterial division process with the aim of development of new antibiotics.
During her research, Dr Bottomley has developed skills in molecular cell biology of bacteria, fluorescence microscopy, protein purification and protein chemistry.
Dr Bottomley is also a member of the Faculty of Science Early Career Researcher committee to promote the outstanding work of ECRs at UTS, and the chair of the School of Life Science and i3 institute presentation (SIP) seminar series committee.
Bottomley, AL, Peterson, E, Iosifidis, G, Yong, AMH, Hartley-Tassell, LE, Ansari, S, McKenzie, C, Burke, C, Duggin, IG, Kline, KA & Harry, EJ 2020, 'The novel E. coli cell division protein, YtfB, plays a role in eukaryotic cell adhesion', Scientific Reports, vol. 10, no. 1.View/Download from: Publisher's site
© 2020, The Author(s). Characterisation of protein function based solely on homology searches may overlook functions under specific environmental conditions, or the possibility of a protein having multiple roles. In this study we investigated the role of YtfB, a protein originally identified in a genome-wide screen to cause inhibition of cell division, and has demonstrated to localise to the Escherichia coli division site with some degree of glycan specificity. Interestingly, YtfB also shows homology to the virulence factor OapA from Haemophilus influenzae, which is important for adherence to epithelial cells, indicating the potential of additional function(s) for YtfB. Here we show that E. coli YtfB binds to N'acetylglucosamine and mannobiose glycans with high affinity. The loss of ytfB results in a reduction in the ability of the uropathogenic E. coli strain UTI89 to adhere to human kidney cells, but not to bladder cells, suggesting a specific role in the initial adherence stage of ascending urinary tract infections. Taken together, our results suggest a role for YtfB in adhesion to specific eukaryotic cells, which may be additional, or complementary, to its role in cell division. This study highlights the importance of understanding the possible multiple functions of proteins based on homology, which may be specific to different environmental conditions.
Phan, M-D, Bottomley, AL, Peters, KM, Harry, EJ & Schembri, MA 2020, 'Uncovering novel susceptibility targets to enhance the efficacy of third-generation cephalosporins against ESBL-producing uropathogenic Escherichia coli.', The Journal of antimicrobial chemotherapy, vol. 75, no. 6, pp. 1415-1423.View/Download from: Publisher's site
BACKGROUND:Uropathogenic Escherichia coli (UPEC) are a major cause of urinary tract infection (UTI), one of the most common infectious diseases in humans. UPEC are increasingly associated with resistance to multiple antibiotics. This includes resistance to third-generation cephalosporins, a common class of antibiotics frequently used to treat UTI. METHODS:We employed a high-throughput genome-wide screen using saturated transposon mutagenesis and transposon directed insertion-site sequencing (TraDIS) together with phenotypic resistance assessment to identify key genes required for survival of the MDR UPEC ST131 strain EC958 in the presence of the third-generation cephalosporin cefotaxime. RESULTS:We showed that blaCMY-23 is the major ESBL gene in EC958 responsible for mediating resistance to cefotaxime. Our screen also revealed that mutation of genes involved in cell division and the twin-arginine translocation pathway sensitized EC958 to cefotaxime. The role of these cell-division and protein-secretion genes in cefotaxime resistance was confirmed through the construction of mutants and phenotypic testing. Mutation of these genes also sensitized EC958 to other cephalosporins. CONCLUSIONS:This work provides an exemplar for the application of TraDIS to define molecular mechanisms of resistance to antibiotics. The identification of mutants that sensitize UPEC to cefotaxime, despite the presence of a cephalosporinase, provides a framework for the development of new approaches to treat infections caused by MDR pathogens.
Valentin, E, Bottomley, AL, Chilambi, GS, Harry, EJ, Amal, R, Sotiriou, GA, Rice, SA & Gunawan, C 2020, 'Heritable nanosilver resistance in priority pathogen: A unique genetic adaptation and comparison with ionic silver and antibiotics', Nanoscale, vol. 12, no. 4, pp. 2384-2392.View/Download from: Publisher's site
© 2020 The Royal Society of Chemistry. The past decade has seen the incorporation of antimicrobial nanosilver (NAg) into medical devices, and, increasingly, in everyday 'antibacterial' products. With the continued rise of antibiotic resistant bacteria, there are concerns that these priority pathogens will also develop resistance to the extensively commercialized nanoparticle antimicrobials. Herein, this work reports the emergence of stable resistance traits to NAg in the WHO-listed priority pathogen Staphylococcus aureus, which has previously been suggested to have no, or very low, capacity for silver resistance. With no native presence of genetically encoded silver defence mechanisms, the work showed that the bacterium is dependent on mutation of physiologically essential genes, including those involved in nucleotide synthesis and oxidative stress defence. While some mutations were uniquely associated with resistance to NAg, the study also found common mutations that could be protective against both NAg and ionic silver. This is consistent with the observation of NAg/ionic silver cross-resistance. These mutations were detected following withdrawal of the silver exposure, denoting heritable characteristics that allow for spread of the resistance traits even with discontinued silver use. Heritable silver resistance in priority pathogen cautions that these nanoparticle antimicrobials should only be used as needed, to preserve their efficacy for treating infections.
Bouzo, D, Cokcetin, NN, Li, L, Ballerin, G, Bottomley, AL, Lazenby, J, Whitchurch, CB, Paulsen, IT, Hassan, KA & Harry, EJ 2020, 'Characterizing the mechanism of action of an ancient antimicrobial, manuka honey, against pseudomonas aeruginosa using modern transcriptomics', mSystems, vol. 5, no. 3.View/Download from: Publisher's site
Copyright © 2020 Bouzo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Manuka honey has broad-spectrum antimicrobial activity, and unlike traditional antibiotics, resistance to its killing effects has not been reported. However, its mechanism of action remains unclear. Here, we investigated the mechanism of action of manuka honey and its key antibacterial components using a transcriptomic approach in a model organism, Pseudomonas aeruginosa. We show that no single component of honey can account for its total antimicrobial action, and that honey affects the expression of genes in the SOS response, oxidative damage, and quorum sensing. Manuka honey uniquely affects genes involved in the explosive cell lysis process and in maintaining the electron transport chain, causing protons to leak across membranes and collapsing the proton motive force, and it induces membrane depolarization and permeabilization in P. aeruginosa. These data indicate that the activity of manuka honey comes from multiple mechanisms of action that do not engender bacterial resistance. IMPORTANCE The threat of antimicrobial resistance to human health has prompted interest in complex, natural products with antimicrobial activity. Honey has been an effective topical wound treatment throughout history, predominantly due to its broad-spectrum antimicrobial activity. Unlike traditional antibiotics, honey-resistant bacteria have not been reported; however, honey remains underutilized in the clinic in part due to a lack of understanding of its mechanism of action. Here, we demonstrate that honey affects multiple processes in bacteria, and this is not explained by its major antibacterial components. Honey also uniquely affects bacterial membranes, and this can be exploited for combination therapy with antibiotics that are otherwise ineffective on their own. We argue that honey should be included as part of the current array ...
Bojer, MS, Wacnik, K, Kjelgaard, P, Gallay, C, Bottomley, AL, Cohn, MT, Lindahl, G, Frees, D, Veening, J-W, Foster, SJ & Ingmer, H 2019, 'SosA inhibits cell division in Staphylococcus aureus in response to DNA damage.', Molecular microbiology, vol. 112, no. 4, pp. 1116-1130.View/Download from: Publisher's site
Inhibition of cell division is critical for viability under DNA-damaging conditions. DNA damage induces the SOS response that in bacteria inhibits cell division while repairs are being made. In coccoids, such as the human pathogen, Staphylococcus aureus, this process remains poorly studied. Here, we identify SosA as the staphylococcal SOS-induced cell division inhibitor. Overproduction of SosA inhibits cell division, while sosA inactivation sensitizes cells to genotoxic stress. SosA is a small, predicted membrane protein with an extracellular C-terminal domain in which point mutation of residues that are conserved in staphylococci and major truncations abolished the inhibitory activity. In contrast, a minor truncation led to SosA accumulation and a strong cell division inhibitory activity, phenotypically similar to expression of wild-type SosA in a CtpA membrane protease mutant. This suggests that the extracellular C-terminus of SosA is required both for cell division inhibition and for turnover of the protein. Microscopy analysis revealed that SosA halts cell division and synchronizes the cell population at a point where division proteins such as FtsZ and EzrA are localized at midcell, and the septum formation is initiated but unable to progress to closure. Thus, our findings show that SosA is central in cell division regulation in staphylococci.
Kusuma, KD, Griffith, R, Harry, EJ, Bottomley, AL & Ung, AT 2019, 'In silico Analysis of FtsZ Crystal Structures Towards a New Target for Antibiotics', Australian Journal of Chemistry, vol. 72, no. 3, pp. 184-196.View/Download from: Publisher's site
© 2018 CSIRO. The bacterial cell division protein FtsZ is conserved in most bacteria and essential for viability. There have been concerted efforts in developing inhibitors that target FtsZ as potential antibiotics. Key to this is an in-depth understanding of FtsZ structure at the molecular level across diverse bacterial species to ensure inhibitors have high affinity for the FtsZ target in a variety of clinically relevant pathogens. In this study, we show that FtsZ structures differ in three ways: (1) the H7 helix curvature; (2) the dimensions of the interdomain cleft; and (3) the opening/closing mechanism of the interdomain cleft, whereas no differences were observed in the dimensions of the nucleotide-binding pocket and T7 loop. Molecular dynamics simulation may suggest that there are two possible mechanisms for the process of opening and closing of the interdomain cleft on FtsZ structures. This discovery highlights significant differences between FtsZ structures at the molecular level and this knowledge is vital in assisting the design of potent FtsZ inhibitors.
Kusuma, KD, Payne, M, Ung, AT, Bottomley, AL & Harry, EJ 2019, 'FtsZ as an Antibacterial Target: Status and Guidelines for Progressing This Avenue.', ACS infectious diseases, vol. 5, no. 8, pp. 1279-1294.View/Download from: Publisher's site
The disturbing increase in the number of bacterial pathogens that are resistant to multiple, or sometimes all, current antibiotics highlights the desperate need to pursue the discovery and development of novel classes of antibacterials. The wealth of knowledge available about the bacterial cell division machinery has aided target-driven approaches to identify new inhibitor compounds. The main division target being pursued is the highly conserved and essential protein FtsZ. Despite very active research on FtsZ inhibitors for several years, this protein is not yet targeted by any commercial antibiotic. Here, we discuss the suitability of FtsZ as an antibacterial target for drug development and review progress achieved in this area. We use hindsight to highlight the gaps that have slowed progress in FtsZ inhibitor development and to suggest guidelines for concluding that FtsZ is actually the target of these molecules, a key missing link in several studies. In moving forward, a multidisciplinary, communicative, and collaborative process, with sharing of research expertise, is critical if we are to succeed.
Productive bacterial cell division and survival of progeny requires tight coordination between chromosome segregation and cell division to ensure equal partitioning of DNA. Unlike rod-shaped bacteria that undergo division in one plane, the coccoid human pathogen Staphylococcus aureus divides in three successive orthogonal planes, which requires a different spatial control compared to rod-shaped cells. To gain a better understanding of how this coordination between chromosome segregation and cell division is regulated in S. aureus, we investigated proteins that associate with FtsZ and the divisome. We found that DnaK, a well-known chaperone, interacts with FtsZ, EzrA
and DivIVA, and is required for DivIVA stability. Unlike in several rod shaped organisms, DivIVA in S. aureus associates with several components of the divisome, as well as the chromosome segregation protein, SMC. This data, combined with phenotypic analysis of mutants, suggests a novel role for S. aureus DivIVA in ensuring cell division and
chromosome segregation are coordinated.
Gorle, AK, Bottomley, AL, Harry, EJ, Collins, JG, Keene, FR & Woodward, CE 2017, 'DNA condensation in live E. coli provides evidence for transertion.', Molecular BioSystems, vol. 13, no. 4, pp. 677-680.View/Download from: Publisher's site
Condensation studies of chromosomal DNA in E. coli with a tetranuclear ruthenium complex are carried out and images obtained with wide-field fluorescence microscopy. Remarkably different condensate morphologies resulted, depending upon the treatment protocol. The occurrence of condensed nucleoid spirals in live bacteria provides evidence for the transertion hypothesis.
Mann, R, Mediati, DG, Duggin, IG, Harry, EJ & Bottomley, AL 2017, 'Metabolic Adaptations of Uropathogenic E. coli in the Urinary Tract.', Frontiers in Cellular and Infection Microbiology, vol. 7, pp. 1-15.View/Download from: Publisher's site
Escherichia coli ordinarily resides in the lower gastrointestinal tract in humans, but some strains, known as Uropathogenic E. coli (UPEC), are also adapted to the relatively harsh environment of the urinary tract. Infections of the urine, bladder and kidneys by UPEC may lead to potentially fatal bloodstream infections. To survive this range of conditions, UPEC strains must have broad and flexible metabolic capabilities and efficiently utilize scarce essential nutrients. Whole-organism (or "omics") methods have recently provided significant advances in our understanding of the importance of metabolic adaptation in the success of UPECs. Here we describe the nutritional and metabolic requirements for UPEC infection in these environments, and focus on particular metabolic responses and adaptations of UPEC that appear to be essential for survival in the urinary tract.
Bottomley, AL, Kabli, AF, Hurd, AF, Turner, RD, Garcia-Lara, J & Foster, SJ 2014, 'Staphylococcus aureus DivIB is a peptidoglycan-binding protein that is required for a morphological checkpoint in cell division.', Molecular Microbiology, vol. 94, no. 5, pp. 1041-1064.View/Download from: Publisher's site
Bacterial cell division is a fundamental process that requires the coordinated actions of a number of proteins which form a complex macromolecular machine known as the divisome. The membrane-spanning proteins DivIB and its orthologue FtsQ are crucial divisome components in Gram-positive and Gram-negative bacteria respectively. However, the role of almost all of the integral division proteins, including DivIB, still remains largely unknown. Here we show that the extracellular domain of DivIB is able to bind peptidoglycan and have mapped the binding to its β subdomain. Conditional mutational studies show that divIB is essential for Staphylococcus aureus growth, while phenotypic analyses following depletion of DivIB results in a block in the completion, but not initiation, of septum formation. Localisation studies suggest that DivIB only transiently localises to the division site and may mark previous sites of septation. We propose that DivIB is required for a molecular checkpoint during division to ensure the correct assembly of the divisome at midcell and to prevent hydrolytic growth of the cell in the absence of a completed septum.
Li, F, Harry, L, Bottomley, AL, Edstein, MD, Birrell, GW, Woodward, CE, Keene, FR & Collins, JG 2014, 'Dinuclear ruthenium(II) antimicrobial agents that selectively target polysomes in vivo', Chemical Science, vol. 5, pp. 685-693.View/Download from: Publisher's site
Wide-field fluorescence microscopy at high magnification was used to study the intracellular binding site of Rubb16 in Escherichia coli. Upon incubation of E. coli cells at the minimum inhibitory concentration, Rubb16 localised at ribosomes with no significant DNA binding observed. Furthermore, Rubb16 condensed the ribosomes when they existed as polysomes. It is postulated that the condensation of polysomes would halt protein production, and thereby inhibit bacterial growth. The results of this study indicate that the family of inert dinuclear ruthenium complexes Rubbn selectively target RNA over DNA in vivo. Selective RNA targeting could be advantageous for the development of therapeutic agents, and because of differences in ribosome structure between bacteria and eukaryotic cells, the Rubbn complexes could be selectively toxic to bacteria. In support of this hypothesis, the toxicity of Rubb16 was found to be significantly less to liver and kidney cell lines than against a range of bacteria.
Monahan, LG, Liew, AT, Bottomley, AL & Harry, L 2014, 'Division site positioning in bacteria: one size does not fit all', Frontiers in Microbiology, vol. 5, no. 19.View/Download from: Publisher's site
Spatial regulation of cell division in bacteria has been a focus of research for decades. It has been well studied in two model rod-shaped organisms, Escherichia coli and Bacillus subtilis, with the general belief that division site positioning occurs as a result of the combination of two negative regulatory systems, Min and nucleoid occlusion. These systems influence division by preventing the cytokinetic Z ring from forming anywhere other than midcell. However, evidence is accumulating for the existence of additional mechanisms that are involved in controlling Z ring positioning both in these organisms and in several other bacteria. In some cases the decision of where to divide is solved by variations on a common evolutionary theme, and in others completely different proteins and mechanisms are involved. Here we review the different ways bacteria solve the problem of finding the right place to divide. It appears that a one-size-fits-all model does not apply, and that individual species have adapted a division-site positioning mechanism that best suits their lifestyle, environmental niche and mode of growth to ensure equal partitioning of DNA for survival of the next generation.
Reichmann, NT, Cassona, CP, Monteiro, JM, Bottomley, AL, Corrigan, RM, Foster, SJ, Pinho, MG & Gründling, A 2014, 'Differential localization of LTA synthesis proteins and their interaction with the cell division machinery in Staphylococcus aureus', Molecular Microbiology, vol. 92, no. 2, pp. 273-286.View/Download from: Publisher's site
Lipoteichoic acid (LTA) is an important cell wall component of Gram-positive bacteria. In Staphylococcus aureus it consists of a polyglycerolphosphate-chain that is retained within the membrane via a glycolipid. Using an immunofluorescence approach, we show here that the LTA polymer is not surface exposed in S.?aureus, as it can only be detected after digestion of the peptidoglycan layer. S.?aureus mutants lacking LTA are enlarged and show aberrant positioning of septa, suggesting a link between LTA synthesis and the cell division process. Using a bacterial two-hybrid approach, we show that the three key LTA synthesis proteins, YpfP and LtaA, involved in glycolipid production, and LtaS, required for LTA backbone synthesis, interact with one another. All three proteins also interacted with numerous cell division and peptidoglycan synthesis proteins, suggesting the formation of a multi-enzyme complex and providing further evidence for the co-ordination of these processes. When assessed by fluorescence microscopy, YpfP and LtaA fluorescent protein fusions localized to the membrane while the LtaS enzyme accumulated at the cell division site. These data support a model whereby LTA backbone synthesis proceeds in S.?aureus at the division site in co-ordination with cell division, while glycolipid synthesis takes place throughout the membrane.
Steele, VR, Bottomley, AL, Garcia-Lara, J, Kasturiarachchi, J & Foster, SJ 2011, 'Multiple essential roles for EzrA in cell division of Staphylococcus aureus', Molecular Microbiology, vol. 80, no. 2, pp. 542-555.View/Download from: Publisher's site
In Bacillus subtilis, EzrA is involved in preventing aberrant formation of FtsZ rings and has also been implicated in the localization cycle of Pbp1. We have identified the orthologue of EzrA in Staphylococcus aureus to be essential for growth and cell division in this organism. Phenotypic analyses following titration of EzrA levels in S. aureus have shown that the protein is required for peptidoglycan synthesis as well as for assembly of the divisome at the midcell and cytokinesis. Protein interaction studies revealed that EzrA forms a complex with both the cytoplasmic components of the division machinery and those with periplasmic domains, suggesting that EzrA may be a scaffold molecule permitting the assembly of the division complex and forming an interface between the cytoplasmic cytoskeletal element FtsZ and the peptidoglycan biosynthetic apparatus active in the periplasm.
Bottomley, AL, Turnbull, L, Whitchurch, CB & Harry, EJ 2017, 'Immobilization Techniques of Bacteria for Live Super-resolution Imaging Using Structured Illumination Microscopy.' in Pontus Nordenfelt and Mattias Collin (ed), Bacterial Pathogenesis, pp. 197-209.View/Download from: Publisher's site
Advancements in optical microscopy technology have allowed huge progression in the ability to understand protein structure and dynamics in live bacterial cells using fluorescence microscopy. Paramount to high-quality microscopy is good sample preparation to avoid bacterial cell movement that can result in motion blur during image acquisition. Here, we describe two techniques of sample preparation that reduce unwanted cell movement and are suitable for application to a number of bacterial species and imaging methods.
Using the crystal structure of S. aureus FtsZ with a co-crystallised known inhibitor, a pharmacophore was developed that could be utilized in the design of novel inhibitors. A library of 19 molecules were synthesized and structurally elucidated that contain a pyrazole linker (Scheme 1). These molecules were screened against S. aureus ATCC 25923 and Escherichia coli (E. coli) MG1556 cells to determine their antibacterial activity.