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.
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.View/Download from: UTS OPUS or 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.
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: UTS OPUS or 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, Kusuma, K & Harry, E 2017, 'Coordination of chromosome segregation and cell division in Staphylococcus aureus', Frontiers in Microbiology, vol. 8.View/Download from: UTS OPUS or Publisher's site
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: UTS OPUS or 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.
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: UTS OPUS or 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: UTS OPUS or 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: UTS OPUS or 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: UTS OPUS or 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: UTS OPUS or 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: UTS OPUS or 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.