Publications

Research Highlights:

  • Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK. Davies MR et al., Walker M. 2023. Nature Communications. link.
  • RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance. Mediati DG, Wong JL, Geo 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. Nature Communications. link.
  • RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression. McKellar SW, Ivanova I, Rei PA, Zapf R, Mediati DG, Mercier M, Pickering AC, Foster R, Kudla G, Caldelari I, Fitzgerald R, O’Caroll R, Tree JJ and Granneman S. 2022. Nature Communications. link.
  • Networks of resistance: small RNA control of antibiotic resistance. Mediati DG, Wu S, Wu W, Tree JJ. 2020. Trends in Genetics. link.

All research articles:

Characterisation of the genetic mutation driving enhanced superantigen SpeA expression in Streptococcus pyogenes M1UK. Mark R. Davies, Nadia Keller, Stephan Brouwer, Magnus G. Jesperson, Amanda J. Cork, Andrew J. Hayes, Miranda E. Pitt, David M. P. O. de Oliveir, Nichaela Harbison Price, Daniel G. Mediati, Bodie Curren, George Taiaroa, Jake A. Lacey, Helen V. Smith, Ning-Xia Fang, Lachlan J. M. Coin, Kerrie Stevens, Martina Sanderson-Smith, Jai J. Tree, Adam D. Irwin, Keith Grimwood, Benjamin P. Howden, Amy V. Jennison, Mark J. Walker. 2023. Nature Communications. link.

RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance. Mediati DG, Wong JL, Geo 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. Nature Communications. link.

RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression. McKellar SW, Ivanova I, Rei PA, Zapf R, Mediati DG, Mercier M, Pickering AC, Foster R, Kudla G, Caldelari I, Fitzgerald R, O’Caroll R, Tree JJ and Granneman S. 2022. Nature Communications. link.

The Small RNA CyaR Activates Translation of the Outer Membrane Haem Receptor chuA in Enterohemorrhagic Escherichia coli. Sy BM & Tree JJ. 2022. Frontiers in Microbiology.

The Role and Targets of the RNA-Binding Protein ProQ in the Gram-Negative Bacterial Pathogen Pasteurella multocida. Gulliver EL, Sy BM, Wong JL, Lucas DSD, Powell DR, Harper M , Tree JJ, Boyce JD. 2022. Journal of Bacteriology. e0059221.

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

Small RNA regulation of virulence in pathogenic Escherichia coli. Sy BM & Tree JJ. 2021. Frontiers in Cellular and Infection Microbiology. link.

Early termination of the Shiga toxin transcript generates a regulatory small RNA. Sy BM, Lan R, Tree JJ. 2020. PNAS. link.

Networks of resistance: small RNA control of antibiotic resistance. Mediati DG, Wu S, Wu W, Tree JJ. 2020. Trends in Genetics. link.

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation. Iosub IA, van Nues RW, McKellar SW, Nieken KJ, Marchioretto M, Sy B, Tree JJ, Viero G, Granneman S. eLife. 2020. link

Comparative Transcriptomic and Functional Assessments of Linezolid-Responsive Small RNA Genes in Staphylococcus aureus. Gao W, Guérillot R, Lin YH, Tree JJ, Beaume M, François P, Monk IR, Seemann T, Schrenzel J, Howden BP, Stinear TP. 2020. mSystems. link

Mechanisms involved in the adaption of Escherichia coli to O157:H7 to the host intestinal environment. Fernandez-Brando RJ, McAteer SP, Montañez-Culma J,  Cortés-Araya Y, Tree JJ, Bernal A, Fuentes F, Fitzgerald S, Pineda GE; Ramos MV, Gally DL, Palermo MS. 2020. Clinical Sciences. link.

Transcriptome-wide analysis of protein-RNA and RNA-RNA interactions in pathogenic bacteria. Tree, JJ.*, Gerdes, K., Tollervey D*. 2018. Methods in Enzymology. *co-corresponding authors. link

Systems-level analysis of bacterial regulatory small RNA networks. Wong J, Pang I, Wilkins M, Tree JJ. Systems Biology. In RNA Technologies. Ed Rajewski N, Jurga S, Barciszewski J. 2018. p97-127. 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

High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC). Sy B, Wong J, Granneman S, Tollervey D, Gally D, Tree JJ. Methods in Molecular Biology. 2018. 1737:251-272.  link

Methionine biosynthesis and transport are functionally redundant for the growth and virulence of Salmonella Typhimurium. Husna A, Wang N, Cobbold S, Newton H, Hocking D, Wilksch J, Scott T, Davies M, Hinton J, Tree J, Lithgow T, McConville M, Strugnell R. 2018. Journal of Biological Chemistry. 293(24):9506-9519. 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

VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation. Winther K, Tree JJ, Tollervey D, Gerdes K. 2016. 44(20):9860-9871. Nucleic Acids Research. link

Complete Bypass of Restriction Systems for Major Staphylococcus aureus Lineages. Monk IR, Tree JJ, Howden BP, Stinear TP, Foster TJ. 2015 6(3):e00308-15. MBio. 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

Lysogeny with Shiga toxin 2-encoding bacteriophages represses type III secretion in enterohemorrhagic Escherichia coli. Xu X, McAteer SP, Tree JJ, Shaw DJ, Wolfson EB, Beatson SA, Roe AJ, Allison LJ, Chase-Topping ME, Mahajan A, Tozzoli R, Woolhouse ME, Morabito S, Gally DL. 2012. 8(5):e1002672. PLoS Pathogens. link

Identification of a novel prophage regulator in Escherichia coli controlling the expression of type III secretion. 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 83(1):208-23. Molecular Microbiology. link

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. 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 80(5):1349-65. Molecular Microbiology. link

Identification of bacterial target proteins for the salicylidene acylhydrazide class of virulence-blocking compounds. Wang D, Zetterström CE, Gabrielsen M, Beckham KS, 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. 286(34):29922-31. Journal of Biological Chemistry. link

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. 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 79(11):4716-29. Infection & Immunity. link

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. Bai J, McAteer SP, Paxton E, Mahajan A, Gally DL, Tree JJ. 2011. 2:168. Frontiers in Microbiology. link

The multi-copper-ion oxidase CueO of Salmonella enterica serovar Typhimurium is required for systemic virulence. Achard ME, Tree JJ, Holden JA, Simpfendorfer KR, Wijburg OL, Strugnell RA, Schembri MA, Sweet MJ, Jennings MP, McEwan AG. 2010. 78(5):2312-9. Infection and Immunity. link

UpaH is a newly identified autotransporter protein that contributes to biofilm formation and bladder colonization by uropathogenic Escherichia coli CFT073. Allsopp LP, Totsika M, Tree JJ, Ulett GC, Mabbett AN, Wells TJ, Kobe B, Beatson SA, Schembri MA. 2010. 78(4):1659-69. Infection & Immunity. link

An investigation of the expression and adhesin function of H7 flagella in the interaction of Escherichia coli O157 : H7 with bovine intestinal epithelium. Mahajan A, Currie CG, Mackie S, Tree J, McAteer S, McKendrick I, McNeilly TN, Roe A, La Ragione RM, Woodward MJ, Gally DL, Smith DG. 2009. 11(1):121-37. Cellular Microbiology. link

Controlling injection: regulation of type III secretion in enterohaemorrhagic Escherichia coli. Tree JJ, Wolfson EB, Wang D, Roe AJ, Gally DL. 2009. 17(8):361-70. Trends in Microbiology. link

Characterization of the effects of salicylidene acylhydrazide compounds on type III secretion in Escherichia coli O157:H7. Tree JJ, Wang D, McInally C, Mahajan A, Layton A, Houghton I, Elofsson M, Stevens MP, Gally DL, Roe AJ. 2009. 77(10):4209-20. Infection & Immunity. link

Virulence properties of asymptomatic bacteriuria Escherichia coli. Mabbett AN, Ulett GC, Watts RE, Tree JJ, Totsika M, Ong CL, Wood JM, Monaghan W, Looke DF, Nimmo GR, Svanborg C, Schembri MA. 2009.299(1):53-63. doi: 10.1016/j.ijmm.2008.06.003. International Journal of Medical Microbiology. link

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. Tree JJ, Ulett GC, Ong CL, Trott DJ, McEwan AG, Schembri MA. 2008 190(20):6909-12. Journal of Bacteriology. link

Autotransporter proteins: novel targets at the bacterial cell surface. Wells TJ, Tree JJ, Ulett GC, Schembri MA. 2007. 274(2):163-72. FEMS Microbiology Letters  link

The multicopper oxidase (CueO) and cell aggregation in Escherichia coli. Tree JJ, Ulett GC, Hobman JL, Constantinidou C, Brown NL, Kershaw C, Schembri MA, Jennings MP, McEwan AG. 2007. 9(8):2110-6. Environmental Microbiology.  link

Copper sensitivity of cueO mutants of Escherichia coli K-12 and the biochemical suppression of this phenotype. Tree JJ, Kidd SP, Jennings MP, McEwan AG. 2005. 328(4):1205-10. Biochemical and Biophysical Research Communications. link

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