Jai Tree

Senior Lecturer

Research program

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

  1. Early termination of the Shiga toxin transcript generates a regulatory small RNA. Sy BM, Lan R, Tree JJ. 2020. PNASAccepted.
  2. Networks of control: small RNA control of antibiotic resistance. Mediati DG, Wu S, Wu W, Tree JJ. 2020. Trends in GeneticsAccepted.
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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 Celllink

Grants

NHMRC funding

  • 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

University funding

  • 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

Professional Experience

  • 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

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 Brandon Sy (Post-docotral researcher)
  • Dr Ignatius Pang (Post-doctoral researcher)
  • Winton Wu (PhD student)
  • Sylvania Wu (PhD student)
  • Daniel Neville (Honours student)

PUBLICATIONS

Journal articles
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Iosub IA; van Nues RW; McKellar SW; Nieken KJ; Marchioretto M; Sy B; Tree JJ; Viero G; Granneman S, 2020, 'Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation', eLife, vol. 9, pp. 1 - 33, http://dx.doi.org/10.7554/eLife.54655
2020
Gao W; Guérillot R; Lin YH; Tree J; Beaume M; François P; Monk IR; Seemann T; Schrenzel J; Howden BP; Stinear TP, 2020, 'Comparative Transcriptomic and Functional Assessments of Linezolid-Responsive Small RNA Genes in Staphylococcus aureus', mSystems, vol. 5, http://dx.doi.org/10.1128/mSystems.00665-19
2020
Tree JJ; Gerdes K; Tollervey D, 2018, 'Transcriptome-Wide Analysis of Protein–RNA and RNA–RNA Interactions in Pathogenic Bacteria', Methods in Enzymology, vol. 612, pp. 467 - 488, http://dx.doi.org/10.1016/bs.mie.2018.08.009
2018
Wang D; McAteer S; Wawszczyk AB; Russel CD; Tahoun A; Elmi A; Cockroft SL; Tollervey D; Granneman S; Tree J; Gally D, 2018, 'An RNA-dependent mechanism for transient expression of bacterial translocation filaments', Nucliec Acids Research, vol. 46, pp. 3366 - 3381, http://dx.doi.org/10.1093/nar/gky096
2018
McAteer SP; Sy BM; Wong JL; Tollervey D; Gally DL; Tree JJ, 2018, 'Ribosome maturation by the endoribonuclease YbeY stabilizes a type 3 secretion system transcript required for virulence of enterohemorrhagic Escherichia coli', Journal of Biological Chemistry, vol. 293, pp. 9006 - 9016, http://dx.doi.org/10.1074/jbc.RA117.000300
2018
Husna AU; Wang N; Cobbold SA; Newton HJ; Hocking DM; Wilksch JJ; Scott TA; Davies MR; Hinton JC; Tree JJ; Lithgow T; McConville MJ; Strugnell RA, 2018, 'Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium', Journal of Biological Chemistry, vol. 293, pp. 9506 - 9519, http://dx.doi.org/10.1074/jbc.RA118.002592
2018
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, 'Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E', EMBO Journal, vol. 36, pp. 374 - 387, http://dx.doi.org/10.15252/embj.201694639
2017
Winther K; Tree J; tollervey D; Gerdes G, 2016, 'VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation', Nucleic Acids Research, vol. 44, pp. 9860 - 9871, http://dx.doi.org/10.1093/nar/gkw781
2016
Monk IR; Tree JJ; Howden BP; Stinear TP; Foster TJ, 2015, 'Complete bypass of restriction systems for major staphylococcus aureus lineages', mBio, vol. 6, pp. 1 - 12, http://dx.doi.org/10.1128/mBio.00308-15
2015
Tree JJ; Granneman S; McAteer SP; Tollervey D; Gally DL, 2014, 'Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli', Molecular Cell, vol. 55, pp. 199 - 213, http://dx.doi.org/10.1016/j.molcel.2014.05.006
2014
Flockhart AF; Tree JJ; Xu X; Karpiyevich M; McAteer SP; Rosenblum R; Shaw DJ; Low CJ; Best A; Gannon V; Laing C; Murphy KC; Leong JM; Schneiders T; La Ragione R; Gally DL, 2012, 'Identification of a novel prophage regulator in Escherichia coli controlling the expression of type III secretion', Molecular Microbiology, vol. 83, pp. 208 - 223, http://dx.doi.org/10.1111/j.1365-2958.2011.07927.x
2012
Xu X; McAteer SP; Tree JJ; Shaw DJ; Wolfson EBK; Beatson SA; Roe AJ; Allison LJ; Chase-Topping ME; Mahajan A; Tozzoli R; Woolhouse MEJ; Morabito S; Gally DL, 2012, 'Lysogeny with Shiga toxin 2-encoding bacteriophages represses type III secretion in enterohemorrhagic Escherichia coli', PLoS Pathogens, vol. 8, http://dx.doi.org/10.1371/journal.ppat.1002672
2012
Tree JJ; Roe AJ; Flockhart A; Mcateer SP; Xu X; Shaw D; Mahajan A; Beatson SA; Best A; Lotz S; Woodward MJ; La Ragione R; Murphy KC; Leong JM; Gally DL, 2011, 'Transcriptional regulators of the GAD acid stress island are carried by effector protein-encoding prophages and indirectly control type III secretion in enterohemorrhagic Escherichia coli O157:H7', Molecular Microbiology, vol. 80, pp. 1349 - 1365, http://dx.doi.org/10.1111/j.1365-2958.2011.07650.x
2011
Wang D; Zetterström CE; Gabrielsen M; Beckham KSH; Tree JJ; Macdonald SE; Byron O; Mitchell TJ; Gally DL; Herzyk P; Mahajan A; Uvell H; Burchmore R; Smith BO; Elofsson M; Roe AJ, 2011, 'Identification of bacterial target proteins for the salicylidene acylhydrazide Class of virulence-blocking compounds', Journal of Biological Chemistry, vol. 286, pp. 29922 - 29931, http://dx.doi.org/10.1074/jbc.M111.233858
2011
Bail J; McAteer SP; Paxton E; Mahajan A; Gally DL; Tree JJ, 2011, 'Screening of an E. Coli O157: H7 bacterial artificial chromosome library by comparative genomic hybridization to identify genomic regions contributing to growth in bovine gastrointestinal mucus and epithelial cell colonization', Frontiers in Microbiology, vol. 2, http://dx.doi.org/10.3389/fmicb.2011.00168
2011
Tahoun A; Siszler G; Spears K; McAteer S; Tree J; Paxton E; Gillespie TL; Martinez-Argudo I; Jepson MA; Shaw DJ; Koegl M; Haas J; Gally DL; Mahajan A, 2011, 'Comparative analysis of EspF variants in inhibition of Escherichia coli phagocytosis by macrophages and inhibition of E. Coli translocation through human- and bovine-derived M cells', Infection and Immunity, vol. 79, pp. 4716 - 4729, http://dx.doi.org/10.1128/IAI.00023-11
2011
Achard MES; Tree JJ; Holden JA; Simpfendorfer KR; Wijburg OLC; Strugnell RA; Schembri MA; Sweet MJ; Jennings MP; McEwan AG, 2010, 'The multi-copper-ion oxidase CueO of Salmonella enterica serovar typhimurium is required for systemic virulence', Infection and Immunity, vol. 78, pp. 2312 - 2319, http://dx.doi.org/10.1128/IAI.01208-09
2010
Allsopp LP; Totsika M; Tree JJ; Ulett GC; Mabbett AN; Wells TJ; Kobe B; Beatson SA; Schembri MA, 2010, 'UpaH is a newly identified autotransporter protein that contributes to biofilm formation and bladder colonization by uropathogenic Escherichia coli CFT073', Infection and Immunity, vol. 78, pp. 1659 - 1669, http://dx.doi.org/10.1128/IAI.01010-09
2010
Tree JJ; Wang D; McInally C; Mahajan A; Layton A; Houghton I; Elofsson M; Stevens MP; Gally DL; Roe AJ, 2009, 'Characterization of the effects of salicylidene acylhydrazide compounds on type III secretion in Escherichia coli O157:H7', Infection and Immunity, vol. 77, pp. 4209 - 4220, http://dx.doi.org/10.1128/IAI.00562-09
2009
Mahajan A; Currie CG; Mackie S; Tree J; Mcateer S; Mckendrick I; Mcneilly TN; Roe A; La Ragione RM; Woodward MJ; Gally DL; Smith DGE, 2009, 'An investigation of the expression and adhesin function of H7 flagella in the interaction of Escherichia coli O157: H7 with bovine intestinal epithelium', Cellular Microbiology, vol. 11, pp. 121 - 137, http://dx.doi.org/10.1111/j.1462-5822.2008.01244.x
2009
Tree JJ; Wolfson EB; Wang D; Roe AJ; Gally DL, 2009, 'Controlling injection: regulation of type III secretion in enterohaemorrhagic Escherichia coli', Trends in Microbiology, vol. 17, pp. 361 - 370, http://dx.doi.org/10.1016/j.tim.2009.06.001
2009
MABBETT A; ULETT G; WATTS R; TREE J; TOTSIKA M; ONG C; WOOD J; MONAGHAN W; LOOKE D; NIMMO G, 2009, 'Virulence properties of asymptomatic bacteriuria Escherichia coli', International Journal of Medical Microbiology, vol. 299, pp. 53 - 63, http://dx.doi.org/10.1016/j.ijmm.2008.06.003
2009
Tree JJ; Ulett GC; Ong C-LY; Trott DJ; McEwan AG; Schembri MA, 2008, 'Trade-Off between Iron Uptake and Protection against Oxidative Stress: Deletion of cueO Promotes Uropathogenic Escherichia coli Virulence in a Mouse Model of Urinary Tract Infection', Journal of Bacteriology, vol. 190, pp. 6909 - 6912, http://dx.doi.org/10.1128/jb.00451-08
2008
Wells TJ; Tree JJ; Ulett GC; Schembri MA, 2007, 'Autotransporter proteins: novel targets at the bacterial cell surface', FEMS Microbiology Letters, vol. 274, pp. 163 - 172, http://dx.doi.org/10.1111/j.1574-6968.2007.00833.x
2007
Tree JJ; Ulett GC; Hobman JL; Constantinidou C; Brown NL; Kershaw C; Schembri MA; Jennings MP; McEwan AG, 2007, 'The multicopper oxidase (CueO) and cell aggregation in Escherichia coli', Environmental Microbiology, vol. 9, pp. 2110 - 2116, http://dx.doi.org/10.1111/j.1462-2920.2007.01320.x
2007
Tree JJ; Kidd SP; Jennings MP; McEwan AG, 2005, 'Copper sensitivity of cueO mutants of Escherichia coli K-12 and the biochemical suppression of this phenotype', Biochemical and Biophysical Research Communications, vol. 328, pp. 1205 - 1210, http://dx.doi.org/10.1016/j.bbrc.2005.01.084
2005
Book Chapters
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Wong J; Pang I; Wilkins M; Tree J, 2018, 'Systems-level analysis of bacterial regulatory small RNA networks', in Systems Biology, Springer, pp. 97 - 127
2018
Sy B; Wong J; Granneman S; Tollervey D; Gally D; Tree JJ, 2018, 'High-resolution, high-throughput analysis of Hfq-binding sites using UV crosslinking and analysis of cDNA (CRAC)', in Bacterial regulatory RNA, pp. 251 - 272, http://dx.doi.org/10.1007/978-1-4939-7634-8_15
2018