The University of Sheffield
Department of Molecular Biology and Biotechnology

Molecular Microbiology


Prof D J Kelly
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1. Molecular microbiology and physiology of Campylobacter and Helicobacter

Research in my laboratory is mainly focussed on understanding the physiology of two important and related human pathogens - Campylobacter jejuni and Helicobacter pylori. The aim is to elucidate fundamental aspects of the metabolism of these bacteria that relate to stress responses and survival in the environment and to growth in the host.

Campylobacter jejuni

Campylobacters are common animal pathogens and C. jejuni is now the most frequent cause of human food-borne gastroenterits in the western world. C. jejuni is a commensal of many species of birds, and colonisation of poultry is a particular problem. Our work is centered on understanding the following aspects of physiology of this bacterium (i) How does C. jejuni adapt to the low oxygen conditions found in the gut? We are investigating the nature and functions of the various respiratory chains, the response of C. jejuni to varying oxygen concentrations and its ability to resist oxidative stress. (ii) What are the metabolic pathways used by C. jejuni   in vivo? We have found that amino-acid transport and catabolism is of major importance and we have several projects to characterise the various pathways involved.

Helicobacter pylori

Since its discovery in 1982, H. pylori has come to be recognised as perhaps the commonest bacterial infection in Man and is the causative agent of certain types of gastritis and virtually all duodenal and most gastric ulcers. Long-term infection with H. pylori is also a risk factor for gastric cancer. Despite its obvious importance as a pathogen, we still know surprisingly little about the fundamental biology of this fascinating bacterium which occupies a unique ecological niche. We are currently investigating two major areas; (i) the respiratory chain and the molecular basis for microaerophilic growth (ii), central metabolic pathways and the identification of novel enzymes as potential new targets for anti-microbial chemotherapy.

 

2. The ‘TRAP’ transporter family - A New Type of Bacterial Solute Transporter

A second area of interest has arisen out of our discovery of a completely new family of Tripartite, ATP-independent Periplasmic (‘TRAP’) bacterial solute transport systems, which rely on a periplasmic-binding protein for their operation but which appear to be energised by the proton-motive force rather than by ATP hydrolysis as in "conventional" periplasmic tranporters. We are investigating the structure, function and mechanism of these novel systems, which appear to be widespread in many types of bacteria and archea, including pathogens, photosynthetic and denitrifying bacteria. This work is being carried out in collaboration with Dr Gavin H. Thomas, Department of Biology, University of York, UK.

 

Campylobacter jejuni Figure 1 - Campylobacter jejuni, causative agent of human food-borne gastroenteritis.

 

Helicobacter pylori Figure 2 - Helicobacter pylori, the causative agent of gastric and duodenal ulcers, and a risk factor for gastric cancer.

 

3. Exploiting phototrophic bacteria and their enzymes to produce energy, biomass and useful products from lignocellulosic wastes

The phototrophic purple bacterium Rhodopseudomonas palustris is one of the most versatile bacteria known, with the ability to grow in a wide range of environments by respiration, photosynthesis and fermentation, under aerobic and anaerobic conditions with a large range of carbon sources from carbon dioxide to complex organic compounds, including lignin breakdown products. It also expresses three distinct nitrogenases, which catalyse the photoproduction of hydrogen. In this project we are investigating the potential of this bacterium to contribute to renewable energy production from lignin, by dissecting the transport and metabolic pathways for lignin monomer breakdown, using a combination of biochemical and genetic approaches. We are also interested in exploiting the wide range of enzymes for aromatic compound metabolism encoded in the genome for useful biotransformations.

 

Rhodopseudomonas palustris Figure 3 - Cells of Rhodopseudomonas palustris. Credit: F. Harrison. genome.jgi-psf.org/ rhop8/rhop8.home.htm

 

Selected Publications

MÜLLER, A., SEVERI, E., MULLIGAN, C., WATTS, A.G., KELLY, D.J., WILSON, K., WILKINSON, A.J. AND THOMAS, G.H. (2006) Conservation of Structure and Mechanism in Primary and Secondary Transporters Exemplified by SiaP, a Sialic Acid Binding Virulence Factor from Haemophilus influenzae. Journal of Biological Chemistry, 281, 22212 – 22222.
MÜller, A., Leon-Kempis., M. Dodson, E., Wilson, K., Wilkinson, A.R. and Kelly, D.J. (2007) A bacterial virulence factor with a dual role as an adhesin and a solute binding-protein: The crystal structure at 1.5A resolution of the PEB1a protein from the human food-borne pathogen Campylobacter jejuni. Journal of Molecular Biology 372, 160-171.
Crossley, R.A., D J. H. Gaskin, K Holmes, F Mulholland, J M. Wells, D J. Kelly, A H.M. van Vliet and N J. Walton (2007) Riboflavin biosynthesis is associated with ferric reduction and iron acquisition of Campylobacter jejuni. Applied and Environmental Microbiology. 73, 7819-7825.
Pajaniappan, M., J. E. Hall, S. Cawthraw, D. G. Newell, E. C. Gaynor, J. A. Fields, K. M. Rathbun, W. A. Agee, C. M. Burns, S. J. Hall, D. J. Kelly and S. A. Thompson (2008) A temperature-regulated Campylobacter jejuni gluconate dehydrogenase is involved in respiration-dependent energy conservation and chicken colonization. Molecular Microbiology. 68, 474-491.
Wright, J.A., A. J. Grant, D. Hurd, M. Harrison, E. J. Guccione, D. J. Kelly and D. J. Maskell (2009). Metabolite and transcriptome analysis of Campylobacter jejuni  in vitro growth reveals a stationary-phase physiological switch. Microbiology 155, 80-94.
Mulligan, c., GEERTSMA, E.R., SEVERI, E., KELLY, D.J., POOLMAN, B. AND THOMAS, G.H. (2009) The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter. Proc. Natl. Acad. Sci. USA 106, 1778-1783.
Reduction of fumarate, mesaconate and crotonate by Mfr, a novel oxygen-regulated periplasmic reductase in Campylobacter jejuni. Guccione E, Hitchcock A, Hall SJ, Mulholland F, Shearer N, van Vliet AH, Kelly DJ. Environ Microbiol. 2009 Nov 17. In press
A role for tungsten in the biology of Campylobacter jejuni: tungstate stimulates formate dehydrogenase activity and is transported via an ultra-high affinity ABC system distinct from the molybdate transporter. Smart JP, Cliff MJ, Kelly DJ. Mol Microbiol. 2009 Nov;74(3):742-57.
Oxidative stress in Campylobacter jejuni: responses, resistance and regulation. Atack JM, Kelly DJ. Future Microbiol. 2009 Aug;4:677-90.
A Multicopper oxidase (Cj1516) and a CopA homologue (Cj1161) are major components of the copper homeostasis system of Campylobacter jejuni. Hall SJ, Hitchcock A, Butler CS, Kelly DJ. J Bacteriol. 2008 Dec;190(24):8075-85.
Contribution of the stereospecific methionine sulphoxide reductases MsrA and MsrB to oxidative and nitrosative stress resistance in the food-borne pathogen Campylobacter jejuni. Atack JM, Kelly DJ. Microbiology. 2008 Aug;154(Pt 8):2219-30.
The Campylobacter jejuni thiol peroxidases Tpx and Bcp both contribute to aerotolerance and peroxide-mediated stress resistance but have distinct substrate specificities. Atack JM, Harvey P, Jones MA, Kelly DJ. J Bacteriol. 2008 Aug;190(15):5279-90.
Amino acid-dependent growth of Campylobacter jejuni: key roles for aspartase (AspA) under microaerobic and oxygen-limited conditions and identification of AspB (Cj0762), essential for growth on glutamate. Guccione E, Leon-Kempis Mdel R, Pearson BM, Hitchin E, Mulholland F, van Diemen PM, Stevens MP, Kelly DJ. Mol Microbiol. 2008 Jul;69(1):77-93.
Growth of Campylobacter jejuni on nitrate and nitrite: electron transport to NapA and NrfA via NrfH and distinct roles for NrfA and the globin Cgb in protection against nitrosative stress. Pittman MS, Elvers KT, Lee L, Jones MA, Poole RK, Park SF, Kelly DJ. Mol Microbiol. 2007 Jan;63(2):575-90.
Structure, mechanism and physiological roles of bacterial cytochrome c peroxidases. Atack JM, Kelly DJ. Adv Microb Physiol. 2007;52:73-106.
The Campylobacter jejuni PEB1a adhesin is an aspartate/glutamate-binding protein of an ABC transporter essential for microaerobic growth on dicarboxylic amino acids. Leon-Kempis Mdel R, Guccione E, Mulholland F, Williamson MP, Kelly DJ. Mol Microbiol. 2006 Jun;60(5):1262-75.
Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters. Thomas GH, Southworth T, León-Kempis MR, Leech A, Kelly DJ. Microbiology. 2006 Jan;152(Pt 1):187-98.
Myers, J.D. and Kelly, D.J. (2005) A sulphite respiration system in the chemoheterotrophic human pathogen Campylobacter jejuni Microbiology 151, 233-242
Velayudhan, J., Jones, M., Barrow, P.A. and Kelly, D.J. (2004) L-serine catabolism via an oxygen labile L-serine dehydratase (SdaA) is essential for colonisation of the avian gut by Campylobacter jejuni. Infection and Immunity, 72, 260-268.
Comtois, S., Gidley, M. and Kelly, D.J. (2003) The role of the thioredoxin system and the thiol-peroxidases Tpx and Bcp in mediating resistance to oxidative and nitrosative stress in Helicobacter pylori. Microbiology. 149, 121-129.
Sellars, M.J., Hall, S.J. and Kelly, D.J. (2002) Growth of Campylobacter jejuni supported by respiration of fumarate, nitrate, nitrite, trimethylamine-N-oxide or dimethylsulfoxide requires oxygen. Journal of Bacteriology, 184, 4187-4196.
Waidner, B., Greiner, S., Odenbreit, S., Kavermann, H., Velayudhan, J., Stahler, F., Guhl, J., Bisse, E., van Vliet, A.H.M, Andrews, S., Kusters, J.G., Kelly, D.J., Haas, R., Kist, M. and Bereswill, S. (2002). Essential role of ferritin Pfr in Helicobacter pylori iron metabolism and gastric colonisation. Infection and Immunity 70, 3923-3929.
Velayudhan, J., and Kelly, D.J. (2002) Analysis of gluconeogenic and anaplerotic enzymes in Campylobacter jejuni: An essential role for phosphoenolpyruvate carboxykinase. Microbiology 148, 685-694.
Kelly, D.J. (2001). The physiology and metabolism of Campylobacter jejuni and Helicobacter pylori. Journal of Applied Microbiology 90, 16S-24S.
Kelly, D.J. and Thomas, G.H. (2001) The tripartite ATP-independent periplasmic (TRAP) transporters of bacteria and archaea. FEMS Microbiology Reviews 25, 405-424.
Velayudhan, J., Hughes, N. J., McColm, A.A., Bagshaw, J., Clayton, C.L., Andrews, S.A. and Kelly, D.J. (2000) Iron acquisition and virulence in Helicobacter pylori: a major role for FeoB, a high-affinity ferrous iron transporter.. Molecular Microbiology 37, 274-286.