The lab is interested in how bacteria regulate gene expression with a focus on understanding the contribution of non-coding RNAs. It is now apparent that the genomes of all organisms are transcribed into an array of regulatory non-coding RNAs (ncRNAs) and bacterial pathogens have not escaped the ncRNA revolution. Our major challenge now is to understand the functions of these RNA species and high throughput sequencing technologies and bioinformatics are providing the tools that will allow us to address these questions.
Regulatory RNAs and pathogenesis
Our model system is the human pathogen, enterohaemorrhagic E. coli O157 (EHEC), that causes disease ranging from gastroenteritis to life treating haemolytic uremic syndrome. The later is caused by release of Shiga toxins that are expressed from bacteriophage (bacterial viruses) that have inserted into the bacterial genome. We have recently identified large numbers of non-coding RNAs that are encoded in EHEC and are seeking to identify those that regulate virulence. We anticipate that by understanding how bacteria employ ncRNAs to control gene expression and respond to stress we will be able to design interventions that limit bacterial pathogenesis and dissemination.
Regulatory RNAs and antibiotic resistance
Non-coding RNAs play prominent roles in controlling the composition of the bacterial cell wall and membranes. A number of ncRNAs have been shown to control intrinsic antibiotic resistance in bacterial pathogens with 'urgent' or 'serious' levels of antimicrobial resistance. Non-coding RNAs contribute to antibiotic resistance in Methicillin-resistant Staphylococcus aureus (MRSA, designated a 'serious' threat) and we are using high-through put sequencing technologies, bioinformatics, and molecular biology to identify key ncRNAs that mediate antibiotic resistance in MRSA.
More information on the lab's research can be found on the Tree Lab website.
Selected recent publications
- Early termination of the Shiga toxin transcript generates a regulatory small RNA. Sy BM, Lan R, Tree JJ. 2020. PNAS. Accepted.
- Networks of control: small RNA control of antibiotic resistance. Mediati DG, Wu S, Wu W, Tree JJ. 2020. Trends in Genetics. Accepted.
- Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation. Iosub IA, van Nues RW, McKellar SW, et al., Tree JJ, Viero G, Granneman S. eLife. 2020. 9:e54655. link
- An RNA-dependent mechanism for transient expression of bacterial translocation filaments. Wang D, McAteer SP, Wawszczyk AB, Russell CD, Tahoun A, Elmi A, Cockroft SL, Tollervey D, Granneman S, Tree JJ*, Gally DL*. 2018. Nucleic Acids Research. *co-corresponding authors link
- Ribosome maturation by the endoribonuclease YbeY stabilises a type III secretion system transcript required for virulence of enterohemorrhagic Escherichia coli. McAteer SP, Sy BM, Wong JL, Tollervey D, Gally DL*, Tree JJ*. Journal of Biological Chemistry. 2018. *co-corresponding authors link
- Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E. Waters SA, McAteer SP, Kudla G, Pang I, Deshpande NP, Amos TG, Leong KW, Wilkins MR, Strugnell R, Gally DL, Tollervey D, Tree JJ. 2017 Feb 1;36(3):374-387. EMBO Journal. link
- Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL. 2014. 55(2):199-213. Molecular Cell. link
- 2019-2021 NHMRC Project grant CIA New pathways for controlling Shiga toxin expression and virulence in Enterohaemorrhagic E. coli
- 2018-2020 NHMRC Project grant CIA Antibiotic tolerance and sRNA networks in MRSA
- 2014-2016 NHMRC Project grant CIA RNA-based regulation in pathogenic bacteria
- 2018 UNSW Faculty of Science Gold Star
- 2018 UNSW Faculty of Science Tin Star
- 2018 UNSW School of Biotech. & BioSci equipment grant
- 2017 UNSW Faculty of Science Gold Star
- 2015-current Senior Lecturer, School of Biotech & Biomolecular Sciences, UNSW
- 2014-2015 Post Doctoral Researcher, Peter Doherty Institute, University of Melbourne
- 2011-2014 Post-doctoral Researcher, Wellcome Centre for Cell Biology & The Roslin Institute, University of Edinburgh, UK
- 2007-2011 Post-doctoral Researcher, Royal (Dick) School of Veterinary Medicine & The Roslin Institute, University of Edinburgh, UK
- 2007 PhD Microbiology, University of Queensland
- 2001 BScApp (Biotech) Hons I, University of Queensland
- Microbiology 1 MICR2011
- Microbiology 1 MICR2011
- Bacteria and Disease BABS 3081
- Microbial Genetics BABS3021
- Medicine Foundations MFAC1501
- Molecular Frontiers BABS3281
PhD, Honours, and 3rd year Undergraduate projects in Molecular Biology and Microbiology are available in the lab.
Current Lab members:
- Dr Daniel Mediati (Post-doctoral researcher)
- Dr Brandon Sy (Post-docotral researcher)
- Dr Ignatius Pang (Post-doctoral researcher)
- Winton Wu (PhD student)
- Sylvania Wu (PhD student)
- Daniel Neville (Honours student)