By Associate Professor Jai Tree

Books

, 2018, Systems Biology, Rajewsky N; Jurga S; Barciszewski J, (eds.), Springer International Publishing, http://dx.doi.org/10.1007/978-3-319-92967-5

Book Chapters

Wu W; Pang CNI; Tree JJ; Mediati DG, 2023, 'Profiling the in vivo RNA interactome associated with the endoribonuclease RNase III in Staphylococcus aureus', in Enzymes in RNA Science and Biotechnology: Part B, Elsevier, pp. 299 - 324, http://dx.doi.org/10.1016/bs.mie.2023.05.001

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

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

Journal articles

Mediati DG; Dan W; Lalaouna D; Dinh H; Pokhrel A; Rowell KN; Michie KA; Stinear TP; Cain AK; Tree JJ, 2024, 'The 3′ UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions', Cell Reports, 43, http://dx.doi.org/10.1016/j.celrep.2024.114082

Wu W; Pang CNI; Mediati DG; Tree JJ, 2024, 'The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerant Staphylococcus aureus', mSystems, 9, http://dx.doi.org/10.1128/msystems.00971-23

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, 'Detection of Streptococcus pyogenes M1UK in Australia and characterization of the mutation driving enhanced expression of superantigen SpeA', Nature Communications, 14, http://dx.doi.org/10.1038/s41467-023-36717-4

Mediati DG; Wong JL; Gao W; McKellar S; Pang CNI; Wu S; Wu W; Sy B; Monk IR; Biazik JM; Wilkins MR; Howden BP; Stinear TP; Granneman S; Tree JJ, 2022, 'Publisher Correction: RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance (Nature Communications, (2022), 13, 1, (3558), 10.1038/s41467-022-31177-8)', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-33167-2

McKellar SW; Ivanova I; Arede P; Zapf RL; Mercier N; Chu LC; Mediati DG; Pickering AC; Briaud P; Foster RG; Kudla G; Ross Fitzgerald J; Caldelari I; Carroll RK; Tree JJ; Granneman S, 2022, 'RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-31173-y

Mediati DG; Wong JL; Gao W; McKellar S; Pang CNI; Wu S; Wu W; Sy B; Monk IR; Biazik JM; Wilkins MR; Howden BP; Stinear TP; Granneman S; Tree JJ, 2022, 'RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-31177-8

Tree J; Hassan K; Jefferies T; Sanderson-Smith M, 2022, 'ASM2022 Sydney conference review', Microbiology Australia, 43, pp. 135 - 136, http://dx.doi.org/10.1071/MA22040

Gulliver EL; Sy BM; Wong JL; Deveson Lucas DS; Powell DR; Harper M; Tree JJ; Boyce JD, 2022, 'The Role and Targets of the RNA-Binding Protein ProQ in the Gram-Negative Bacterial Pathogen Pasteurella multocida', Journal of Bacteriology, 204, http://dx.doi.org/10.1128/jb.00592-21

Sy BM; Tree JJ, 2022, 'The Small RNA CyaR Activates Translation of the Outer Membrane Haem Receptor chuA in Enterohemorrhagic Escherichia coli', Frontiers in Microbiology, 13, http://dx.doi.org/10.3389/fmicb.2022.821196

Mediati DG; Lalaouna D; Tree JJ, 2021, 'Burning the candle at both ends: Have exoribonucleases driven divergence of regulatory rna mechanisms in bacteria?', mBio, 12, http://dx.doi.org/10.1128/mBio.01041-21

Sy BM; Tree JJ, 2021, 'Small RNA Regulation of Virulence in Pathogenic Escherichia coli', Frontiers in Cellular and Infection Microbiology, 10, http://dx.doi.org/10.3389/fcimb.2020.622202

Mediati DG; Wu S; Wu W; Tree JJ, 2021, 'Networks of Resistance: Small RNA Control of Antibiotic Resistance', Trends in Genetics, 37, pp. 35 - 45, http://dx.doi.org/10.1016/j.tig.2020.08.016

Fernandez-Brando RJ; McAteer SP; Montanez-Culma J; Cortes-Araya Y; Tree J; Bernal A; Fuentes F; Fitzgerald S; Pineda GE; Ramos MV; Gally DL; Palermo MS, 2020, 'Mechanisms involved in the adaptation of Escherichia coli O157:H7 to the host intestinal microenvironment', Clinical Science, 134, pp. 3283 - 3301, http://dx.doi.org/10.1042/CS20200971

Sy BM; Lan R; Tree JJ, 2020, 'Early termination of the Shiga toxin transcript generates a regulatory small RNA', Proceedings of the National Academy of Sciences of the United States of America, 117, pp. 25055 - 25065, http://dx.doi.org/10.1073/pnas.2006730117

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, 9, pp. 1 - 33, http://dx.doi.org/10.7554/eLife.54655

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, 5, http://dx.doi.org/10.1128/mSystems.00665-19

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, 293, pp. 9506 - 9519, http://dx.doi.org/10.1074/jbc.RA118.002592

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, 293, pp. 9006 - 9016, http://dx.doi.org/10.1074/jbc.RA117.000300

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, 46, pp. 3366 - 3381, http://dx.doi.org/10.1093/nar/gky096

Tree JJ; Gerdes K; Tollervey D, 2018, 'Transcriptome-Wide Analysis of Protein–RNA and RNA–RNA Interactions in Pathogenic Bacteria', Methods in Enzymology, 612, pp. 467 - 488, http://dx.doi.org/10.1016/bs.mie.2018.08.009

Iosub I; Marchioretto M; Sy B; McKellar S; Nieken K; van Nues R; Tree J; Viero G; Granneman S, 2018, 'Hfq CLASH uncovers sRNA-target interaction networks involved in adaptation to nutrient availability', , http://dx.doi.org/10.1101/481986

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, 36, pp. 374 - 387, http://dx.doi.org/10.15252/embj.201694639

Winther K; Tree J; tollervey D; Gerdes G, 2016, 'VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation', Nucleic Acids Research, 44, pp. 9860 - 9871, http://dx.doi.org/10.1093/nar/gkw781

Monk IR; Tree JJ; Howden BP; Stinear TP; Foster TJ, 2016, 'Erratum for Monk et al., Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages.', mBio, 7, pp. e00171, http://dx.doi.org/10.1128/mBio.00171-16

Monk IR; Tree JJ; Howden BP; Stinear TP; Foster TJ, 2015, 'Complete bypass of restriction systems for major staphylococcus aureus lineages', mBio, 6, pp. 1 - 12, http://dx.doi.org/10.1128/mBio.00308-15

Tree JJ; Granneman S; McAteer SP; Tollervey D; Gally DL, 2014, 'Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli', Molecular Cell, 55, pp. 199 - 213, http://dx.doi.org/10.1016/j.molcel.2014.05.006

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, 8, http://dx.doi.org/10.1371/journal.ppat.1002672

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, 83, pp. 208 - 223, http://dx.doi.org/10.1111/j.1365-2958.2011.07927.x

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, 79, pp. 4716 - 4729, http://dx.doi.org/10.1128/IAI.00023-11

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, 286, pp. 29922 - 29931, http://dx.doi.org/10.1074/jbc.M111.233858

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, 80, pp. 1349 - 1365, http://dx.doi.org/10.1111/j.1365-2958.2011.07650.x

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, 2, http://dx.doi.org/10.3389/fmicb.2011.00168

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, 78, pp. 2312 - 2319, http://dx.doi.org/10.1128/IAI.01208-09

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, 78, pp. 1659 - 1669, http://dx.doi.org/10.1128/IAI.01010-09

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, 77, pp. 4209 - 4220, http://dx.doi.org/10.1128/IAI.00562-09

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, 17, pp. 361 - 370, http://dx.doi.org/10.1016/j.tim.2009.06.001

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, 11, pp. 121 - 137, http://dx.doi.org/10.1111/j.1462-5822.2008.01244.x

Mabbett AN; Ulett GC; Watts RE; Tree JJ; Totsika M; Ong CLY; Wood JM; Monaghan W; Looke DF; Nimmo GR; Svanborg C; Schembri MA, 2009, 'Virulence properties of asymptomatic bacteriuria Escherichia coli', International Journal of Medical Microbiology, 299, pp. 53 - 63, http://dx.doi.org/10.1016/j.ijmm.2008.06.003

Tree JJ; Ulett GC; Ong CLY; 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, 190, pp. 6909 - 6912, http://dx.doi.org/10.1128/JB.00451-08

Wells TJ; Tree JJ; Ulett GC; Schembri MA, 2007, 'Autotransporter proteins: Novel targets at the bacterial cell surface', FEMS Microbiology Letters, 274, pp. 163 - 172, http://dx.doi.org/10.1111/j.1574-6968.2007.00833.x

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, 9, pp. 2110 - 2116, http://dx.doi.org/10.1111/j.1462-2920.2007.01320.x

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, 328, pp. 1205 - 1210, http://dx.doi.org/10.1016/j.bbrc.2005.01.084

Preprints

Wu W; Pang CNI; Mediati D; Tree JJ, 2023, The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerantStaphylococcus aureus, http://dx.doi.org/10.1101/2023.08.23.554412

Mediati DG; Dan W; Lalaouna D; Dinh H; Pokhrel A; Stinear TP; Cain AK; Tree JJ, 2023, The 3’ UTR ofvigRis required for virulence inStaphylococcus aureusand has expanded through STAR sequence repeat insertions, http://dx.doi.org/10.1101/2023.05.16.541063

Sy BM; Tree JJ, 2021, Enterohaemorrhagic E. coli utilizes an AND-OR logic gate to regulate expression of an outer membrane haem receptor, http://dx.doi.org/10.1101/2021.08.24.457593

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