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 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

1. RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance. Mediati DG, et al. Tree JJ. 2022. Nature Communications. 13(1):3558.
2. RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression. McKellar SW, et al. Tree JJ and Granneman S. 2022. Nature Communications. 13(1):3560.
3. Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1_UK. 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. Nature Communications. 14(1):1051.
4. Burning the candle at both ends: Have exoribonucleases driven divergence of regulatory RNA mechanisms in bacteria? Mediati DG, Lalaouna D, Tree JJ. 2021. mBio. 12(4):e0104121
5. Early termination of the Shiga toxin transcript generates a regulatory small RNA. Sy BM, Lan R, Tree JJ. PNAS. 2020. 117 (40) 25055-25065
6. Networks of control: small RNA control of antibiotic resistance. Mediati DG, Wu S, Wu W, Tree JJ. 2020. Trends in Genetics. 
7. 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.
8. 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 
9. 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 
10. 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.
11. 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.

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, University of Edinburgh, UK
• 2007 PhD Microbiology, University of Queensland
• 2001 BScApp (Biotech) Hons I, University of Queensland

Teaching

Coordinator: 

• 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 year Undergraduate projects in Molecular Biology and Microbiology are available in the lab. 

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)