University of Dundee

Dr. Robert Ryan

Bacterial signalling and pathogenesis
Position: 
Wellcome Trust Senior Research Fellow and Reader in Molecular Bacteriology
Address: 
College of Life Sciences, University of Dundee, Dundee
Full Telephone: 
+44 (0) 1382 384272, int ext 84272
Email: 

Research

Bacterial signalling and pathogenesis

Research

(i) Bacterial interactions and interspecies signalling

The research efforts in my group are directed towards understanding the molecular basis of pathogenesis of human infections caused by opportunistic gram-negative bacteria. The main focus of the group is concerned with understanding the role that interspecies signalling plays in influencing both bacterial virulence and response to therapy in polymicrobial infections. Understanding the complex interplay between pathogens during infection is becoming crucial for improving the therapy of polymicrobial diseases such as cystic fibrosis lung. Many pathogenic bacteria use cell-cell signalling to regulate expression of factors contributing to virulence.

Bacteria produce signals of diverse structural classes. The signal molecule DSF (diffusible signal factor) is a cis-unsaturated fatty acid that was first described in the plant pathogen Xanthomonas campestris. Recent work has shown that structurally related molecules are produced by the unrelated bacteria Burkholderia cenocepacia, Stenotrophomonas maltophilia and Pseudomonas aeruginosa to regulate virulence, formation of biofilms and antibiotic tolerance in these important human pathogens. Furthermore, DSF family signals have been shown to be involved in interspecies signalling that modulates bacterial behavior. The group has made a substantial contribution to the understanding of how a number of key sensor kinase proteins perceive the DSF family of signal molecules and how they are involved in regulation of biofilm formation and bacterial virulence in a number of human pathogens. This work is becoming increasingly important with the growing challenge of antimicrobial resistance and the paucity of novel antibiotics. This study is utilizing state of the art techniques such as next-generation transcriptome analysis and proteomics to shed light on the novel signal transduction systems involved in the regulation of bacterial virulence and biofilm formation. This should lead to the identification of new drug targets and new opportunities for the control of bacterial disease.

Figure 1. Mutation of genes encoding BCAM0581 and BCAM0227 has similar effects on biofilm architecture within biofilms of Burkholderia cenocepacia.

 

(ii) Bacterial intracellular signalling

My laboratory also has another major effort aimed at determining the role the intracellular second messenger, cyclic di-GMP, has in co-ordinating expression and function of factors involved in the formation of biofilms, regulation of antibiotic resistance and virulence determinants expressed in gram-negative bacteria.

The level of cyclic di-GMP in bacterial cells is influenced by both synthesis and degradation. The GGDEF protein domain synthesizes cyclic di-GMP, whereas EAL and HD-GYP domains are involved in cyclic di-GMP hydrolysis. Studies of the function and role of the HD-GYP domain have thus far focused on the regulatory protein RpfG from the plant pathogen Xanthomonas campestris. However, our understanding of the role(s) that HD-GYP domains play in cyclic-di-GMP signalling is still rudimentary when compared to the knowledge acquired from investigations into the roles played by GGDEF and EAL domain proteins. This work is attempting to broaden our understanding of the cellular function of HD-GYP domain proteins by determining the crystal structures of the HD-GYP domain proteins from Pseudomonas aeruginosa.

 

Figure 2. Effects of mutation of genes encoding HD-GYP domain proteins on biofilm architecture in P. aeruginosa.

Teaching

BI40051 - Bacterial Signalling

Publications

Caly, D. L., D. Bellini, M. A. Walsh, J. M. Dow and R. P. Ryan (2015). "Targeting cyclic di-GMP signalling: a strategy to control biofilm formation?" Curr Pharm Des 21(1): 12-24.
25189859

Earl, C. S., T. W. Keong, S. Q. An, S. Murdoch, Y. McCarthy, J. Garmendia, J. Ward, J. M. Dow, L. Yang, G. A. O'Toole and R. P. Ryan (2015). "Haemophilus influenzae responds to glucocorticoids used in asthma therapy by modulation of biofilm formation and antibiotic resistance." EMBO Mol Med.
10.15252/emmm.201505088
25995336

Earl, C. S., S. Q. An and R. P. Ryan (2015). "The changing face of asthma and its relation with microbes." Trends Microbiol.
10.1016/j.tim.2015.03.005
25840766

An, S. Q., J. H. Allan, Y. McCarthy, M. Febrer, J. M. Dow and R. P. Ryan (2014). "The PAS domain-containing histidine kinase RpfS is a second sensor for the diffusible signal factor of Xanthomonas campestris." Mol Microbiol 92(3): 586-597.
10.1111/mmi.12577
24617591

An, S. Q., D. L. Caly, Y. McCarthy, S. L. Murdoch, J. Ward, M. Febrer, J. M. Dow and R. P. Ryan (2014). "Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence." PLoS Pathog 10(10): e1004429.
10.1371/journal.ppat.1004429
25329577

Bellini, D., D. L. Caly, Y. McCarthy, M. Bumann, S. Q. An, J. M. Dow, R. P. Ryan and M. A. Walsh (2014). "Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre." Mol Microbiol 91(1): 26-38.
10.1111/mmi.12447
24176013

Short, F. L., S. L. Murdoch and R. P. Ryan (2014). "Polybacterial human disease: the ills of social networking." Trends Microbiol 22(9): 508-516.
10.1016/j.tim.2014.05.007
24938173

An, S. Q., K. H. Chin, M. Febrer, Y. McCarthy, J. G. Yang, C. L. Liu, D. Swarbreck, J. Rogers, J. Maxwell Dow, S. H. Chou and R. P. Ryan (2013). "A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis." EMBO J 32(18): 2430-2438.
10.1038/emboj.2013.165
23881098

An, S. Q., M. Febrer, Y. McCarthy, D. J. Tang, L. Clissold, G. Kaithakottil, D. Swarbreck, J. L. Tang, J. Rogers, J. M. Dow and R. P. Ryan (2013). "High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis." Mol Microbiol 88(6): 1058-1069.
10.1111/mmi.12229
23617851

Twomey, K. B., M. Alston, S. Q. An, O. J. O'Connell, Y. McCarthy, D. Swarbreck, M. Febrer, J. M. Dow, B. J. Plant and R. P. Ryan (2013). "Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation." PLoS One 8(12): e82432.
10.1371/journal.pone.0082432
24358183