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Research program

The lab is interested in how bacteria pathogens cause disease with a strong focus on understanding how non-coding RNAs control virulence gene expression. It is now apparent that the genomes of all organisms are transcribed into an array of regulatory non-coding RNAs (ncRNAs) and our major challenge now is to understand the functions of these RNA species. The lab uses a range of molecular techniques including UV-crosslinking, high throughput sequencing, RNA structure probing, and bioinformatics to understand the functions of regulatory RNAs.

Regulatory RNAs and pathogenesisÌý

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 RNAsÌýandÌýantibiotic resistanceÌý

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 inÌýbacterial pathogens withÌý'urgent' or 'serious' levels of antimicrobial resistance. Non-coding RNAs contribute to antibiotic resistance in Methicillin-resistantÌýStaphylococcus 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. Ìý

More information on the lab's research can be found on the .

Selected recentÌýpublications

1. . Mediati DG, et al. Tree JJ. 2022.ÌýNature Communications. 13(1):3558.
2. McKellar SW, et al. Tree JJ and Granneman S. 2022.ÌýNature Communications.Ìý13(1):3560.
3. . Davies MR, Keller N, Brouwer S, Jespersen MG, Cork AJ, Hayes AJ, Pitt ME, De Oliveira DMP, Harbison-Price N, Bertolla OM, Mediati DG, Curren BF, Taiaroa G, Lacey JA, Smith HV, Fang NX, Coin LJM, Stevens K, Tong SYC, Sanderson-Smith M, Tree JJ, Irwin AD, Grimwood K, Howden BP, Jennison AV, Walker MJ. 2023.ÌýNature Communications.Ìý14(1):1051.
4. ÌýMediati DG, Lalaouna D, Tree JJ. 2021.ÌýmBio. 12(4):e0104121
5. . Sy BM, Lan R, Tree JJ.ÌýPNAS. 2020.Ìý117Ìý(40)Ìý25055-25065
6. . Mediati DG, Wu S, Wu W, Tree JJ. 2020.ÌýTrends in Genetics.Ìý
7. Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation.ÌýIosub IA, van Nues RW, McKellar SW, et al.,ÌýTree JJ, Viero G, Granneman S. eLife. 2020. 9:e54655.
8. ÌýWang D, McAteer SP, Wawszczyk AB, Russell CD, Tahoun A, Elmi A, Cockroft SL, Tollervey D, Granneman S, Tree JJ*, Gally DL*.Ìý2018.ÌýNucleic Acids Research. *co-corresponding authorsÌý
9. ÌýMcAteer SP, Sy BM, Wong JL, Tollervey D, Gally DL*, Tree JJ*.ÌýJournal of Biological Chemistry. 2018. *co-corresponding authorsÌý
10. ÌýWaters 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.ÌýEMBO Journal.
11. ÌýTree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL.Ìý2014. 55(2):199-213.ÌýMolecular Cell.

Professional Experience

• 2022-current Associate Professor, School of Biotech & Biomolecular Sciences, UNSW
• 2015-2021 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,ÌýUniversity of Edinburgh, UK
• 2007 PhD Microbiology, University of Queensland
• 2001 BScApp (Biotech) Hons I,ÌýUniversity of Queensland

Teaching

Coordinator:Ìý

• Microbiology 1 MICR2011

Lecturer:

• Microbiology 1 MICR2011
• Bacteria and Disease BABS 3081
• Microbial Genetics BABS3021
• Medicine Foundations MFAC1501
• Molecular Frontiers BABS3281

Supervision

PhD, Honours, and 3rd yearÌýUndergraduate projects in Molecular Biology and Microbiology are available in the lab.Ìý

Current Lab members:

• Dr Daniel Mediati (Post-doctoral researcher)
• Dr Winton Wu (Post-doctoral researcher)
• Pranita Poudyal (PhD student)
• Thomas Zammit (PhD student)
• Janelle Ramos (PhD student, co-supervised by A/Prof Matthew Baker)
• Christopher Jin (Hons student)
• Monika Vesse (Hons student)