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Dr Mark Shepherd

Senior Lecturer in Microbial Biochemistry

School of Biosciences


Dr. Mark Shepherd joined the School of Biosciences in 2011. He was born in England, was brought up in North Wales, and subsequently studied Biochemistry at the University of Sheffield (1996-1999). He stayed in the Department of Molecular Biology & Biotechnology to undertake a PhD with Professor Neil Hunter FRS (1999-2003), where he developed his interest in the enzymology and spectroscopy of chlorophyll and haem biosynthesis. After completing his PhD studies, he conducted postdoctoral research with Prof. Harry Dailey at the University of Georgia (2003-2005), where his research focussed on the terminal enzymes of haem biosynthesis. This was followed by a move back to the University of Sheffield in 2005 to take up a postdoctoral position with Prof. Robert Poole, where he developed interests in E. coli respiration, globin proteins, and the response of bacteria to nitric oxide. A subsequent position at the University of Queensland (2010-2011) with Prof. Mark Schembri focussed on nitric oxide stress in Uropathogenic E. coli. In 2011 he moved to the University of Kent, where he is a Lecturer in Microbial Biochemistry, a member of the Microbial Pathogenesis Group, and Programme Director for the MSc Infectious Diseases course.

Location: Stacey G18

Twitter: @ShepherdLabKent

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Also view these in the Kent Academic Repository

Skotnicová, P. et al. (2018). The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase. Journal of Biological Chemistry [Online]. Available at:
Hobbs, C., Reid, J. and Shepherd, M. (2017). The coproporphyrin ferrochelatase of Staphylococcus aureus: mechanistic insights into a regulatory iron binding site. Biochemical Journal [Online] 474:3513-3522. Available at:
Shepherd, M. et al. (2016). The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection. Scientific reports [Online] 6:35285. Available at:
Hobbs, C., Dailey, H. and Shepherd, M. (2016). The HemQ coprohaem decarboxylase generates reactive oxygen species: implications for the evolution of classical haem biosynthesis. Biochemical Journal [Online] 473:3997-4009. Available at:
Holyoake, L. et al. (2016). CydDC-mediated reductant export in Escherichia coli controls the transcriptional wiring of energy metabolism and combats nitrosative stress. Biochemical Journal [Online] 473:693-701. Available at:
Holyoake, L., Poole, R. and Shepherd, M. (2015). The CydDC Family of Transporters and Their Roles in Oxidase Assembly and Homeostasis. Advances in Microbial Physiology [Online] 66:1-53. Available at:
Shepherd, M. (2015). The CydDC ABC transporter of Escherichia coli: new roles for a reductant efflux pump. Biochemical Society Transactions [Online] 43:908-912. Available at:
Yamashita, M. et al. (2014). Structure and Function of the Bacterial Heterodimeric ABC Transporter CydDC: Stimulation of the ATPase Activity by Thiol and Heme Compounds. The Journal of biological chemistry [Online] 289:23177-23188. Available at:
Tinajero-Trejo, M. and Shepherd, M. (2013). The globins of Campylobacter jejuni. Advances in microbial physiology [Online] 63:97-145. Available at:
Shepherd, M. et al. (2013). Structural and functional characterisation of ScsC, a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium. Antioxidants and Redox Signaling [Online] 19:1494-1506. Available at:
Taylor, S. et al. (2013). Measuring protein reduction potentials using 15N HSQC NMR spectroscopy. Chemical Communications [Online] 49:1847-1849. Available at:
King, N. et al. (2012). Characterisation of a cell wall-anchored protein of Staphylococcus saprophyticus associated with linoleic acid resistance. BMC Microbiology [Online] 12. Available at:
Burda, W. et al. (2011). Neutral metallated and meso-substituted porphyrins as antimicrobial agents against Gram-positive pathogens. European Journal of Clinical Microbiology & Infectious Diseases [Online] 31:327-335. Available at:
Arroyo Mañez, P. et al. (2011). Role of the distal hydrogen-bonding network in regulating oxygen affinity in the truncated hemoglobin III from Campylobacter jejuni. Biochemistry [Online] 50:3946-56. Available at:
Frey, A. et al. (2011). The single-domain globin of Vitreoscilla: augmentation of aerobic metabolism for biotechnological applications. Advances in Microbial Physiology [Online] 58:81-139. Available at:
Thomas, M. et al. (2011). Two respiratory enzyme systems in Campylobacter jejuni NCTC 11168 contribute to growth on L-lactate. Environmental Microbiology [Online] 13:48-61. Available at:
Smith, H. et al. (2011). The NO-responsive hemoglobins of Campylobacter jejuni: Concerted responses of two globins to NO and evidence in vitro for globin regulation by the transcription factor NssR. Nitric Oxide: Biology and Chemistry [Online] 25:234-41. Available at:
Shepherd, M., Bernhardt, P. and Poole, R. (2011). Globin-mediated nitric oxide detoxification in the foodborne pathogenic bacterium Campylobacter jejuni proceeds via a dioxygenase or denitrosylase mechanism. Nitric Oxide: Biology and Chemistry [Online] 25:229-33. Available at:
Shepherd, M. et al. (2010). The single-domain globin from the pathogenic bacterium Campylobacter jejuni: novel D-helix conformation, proximal hydrogen bonding that influences ligand binding, and peroxidase-like redox properties. Journal of Biological Chemistry [Online] 285:12747-54. Available at:
Shepherd, M. et al. (2010). Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. Journal of Biological Chemistry [Online] 285:18464-72. Available at:
Shepherd, M. and Dailey, H. (2009). Peroxidase activity of cytochrome c facilitates the protoporphyrinogen oxidase reaction. Cellular and Molecular Biology [Online] 55:6-14. Available at:
Mason, M. et al. (2009). Cytochrome bd confers nitric oxide resistance to Escherichia coli. Nature Chemical Biology [Online] 5:94-6. Available at:
Book section
Shepherd, M. and Poole, R. (2012). Bacterial Respiratory Chains. in: Roberts, G. C. K. ed. Encyclopedia of Biophysics. EBSA Publishers, pp. 172-177.
Burda, W., Shaw, L. and Shepherd, M. (2012). Porphyrins: Properties and Applications. in: Kaibara, A. and Matsumara, G. eds. Handbook of Chemistry, Biochemistry and Biology: New Frontiers. Nova Publishers, pp. 429-438.
Poole, R. and Shepherd, M. (2012). Bacterial Globins. in: Roberts, G. C. K. ed. Encyclopedia of Biophysics. EBSA Publishers, pp. 156-160.
Showing 25 of 33 total publications in KAR. [See all in KAR]


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Topics of interest include antibiotic resistance, stress tolerance, respiratory metabolism, haem biosynthesis, disulphide folding, and biofuel production. A collaborative approach is adopted using a wide variety of techniques including chromosomal engineering, transcriptomics, proteomics, metabolomics, microscopy, protein biochemistry, enzyme kinetics, and structural biology.


Antimicrobial resistance in E. coli clinical isolates

E. coli causes serious conditions including sepsis, bladder infections, kidney failure, and dysentery. The emergence of drug resistance in pathogenic strains is an increasing problem on a global scale. We liaise with collaborators in the NHS to collect E. coli clinical isolates for antibiotic screening and for other phenotypic characterisation. Collaborative studies are underway to sequence the genomes of a large number of isolates that will provide insights into the prevalence, evolution, and spread of antibiotic resistance in this deadly human pathogen.

See the following link on ‘Antimicrobial resistance in E. coli clinical isolates’ project:


Adaptations to nitric oxide (NO) in uropathogenic E. coli

Uropathogenic E. coli (UPEC) strains are a major cause of urinary tract infections (UTIs), and emergence of antibiotic resistance in UPEC is becoming an increasingly serious problem. Of special interest is the response of E. coli to nitric oxide (NO), a remarkable regulatory molecule and a powerful tool used by mammalian cells to combat microbial infection. Bacteria encounter nitric oxide from host NO synthases in the gut, and NO is also encountered by UPEC in the human urinary tract during UTI. The toxic effects of NO to bacterial cells are diverse: NO can readily diffuse across cell membranes to react with various targets, including haems, iron-sulphur clusters, and protein thiols. Invading E. coli respond in a variety of ways that confer tolerance to NO exposure and enable persistence in the host. The overarching goal is to advance the understanding of NO tolerance mechanisms in drug-resistant UPEC strains.


Bacterial disulphide bond formation

Proteins must be assembled and correctly folded to function, and a key step in the protein-folding pathway is the introduction of disulphide bonds between cysteine residues. Many bacterial virulence factors, such as fimbriae, flagella, and toxins either contain disulphide bonds or require them in some component of their assembly pathway. In addition, the yield and quality of disulphide-containing protein therapeutics produced in E. coli, such as antibodies and hormones, is influenced by the expression of recombinant folding chaperones. Our current focus is to elucidate the biochemical properties and physiological roles of disulphide chaperones in virulence and survival and to determine their suitability to improve disulphide folding of proteins of biotechnological importance.


Biofuel production in Clostridium

Solventogenic strains of Clostridium are used to produce acetone, butanol and ethanol via the process of ABE fermentation. Besides their use as biofuels, derivatives of ABE fermentation are used to manufacture latex paints, lacquers, enamels, automotive coatings and industrial coatings, and are used are used as solvents in vinyl, cellulosic, acrylics, urethanes and epoxy coatings. We combine strain engineering approaches with metabolomics and genomics to gain a fundamental understanding of Clostridium metabolism, and apply this knowledge to optimise solvent yields.


Bacterial haem synthesis

Bacteria require the cofactor haem for a number of essential cellular processes. Haem biosynthetic enzymes remain a long-term interest in the Shepherd lab, and we have a particular focus on enzymatic metal chelation and porphyrinogen oxidation reactions. We employ a combination of bacterial genetics, bioinformatics, protein biochemistry, enzymology and a variety of spectroscopic approaches to study interests ranging from pathway evolution to mechanistic enzymology.



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Ph.D Students:

Applications will be considered from self-funded students (for MSc & PhD) and from postdoctoral researchers intent on securing their own fellowship.


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Enquiries: Phone: +44 (0)1227 823743

School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ

Last Updated: 27/09/2017