Dr Abhinav Koyamangalath Vadakkepat

Supervisor Details

Contact Details

Dr Abhinav Koyamangalath Vadakkepat

Department of Molecular and Cell Biology, University of Leicester

Scientific Background

Research Interests

Our research is centered around two broad themes:

Conjugative systems in bacteria: Our lab is interested in understanding how bacteria use secretion systems for exchanging genetic material through conjugation to maintain genomic diversity and achieve saltational evolution into pathogenic species causing widespread infectious diseases related mortality. This exchange of genetic material between bacteria, also referred to as horizontal gene transfer (HGT) is fundamental to the dissemination of antimicrobial resistance (AMR) within bacteria, a formidable biomedical challenge, and an area of active research. After working extensively with gram- bacteria and studying Type-4 secretion systems (T4SS) involved in classical conjugation, our current focus is to understand how gram+ mycobacteria, a family of considerable importance in infectious diseases and AMR undertakes a distinctive form of HGT (called distributive conjugal transfer (DCT)) to facilitate its evolution into pathogenic mycobacteria and develop antimicrobial resistance. The overarching aim of this research program is to establish a structural basis for DCT by characterizing the multimegadalton membrane-integrated Type-7 secretion systems (T7SS) and associated complexes involved in substrate processing and translocation using a combination of biophysical chemistry and structural methods with a long-term vision of developing targeted antibiotics against these systems.
Bacteriophage defense mechanisms in bacteria: Research interest in bacterial-bacteriophage interactions has come to the centerstage due to its importance in bacterial evolution, as gene editing tools (CRISPR-Cas) and most importantly in the development of phage therapies to treat or prevent hard-to-treat bacterial infections and combat antibiotic resistance. Although this strategy has many advantages, the main drawback is the risk of encountering or favouring the emergence of phage resistant/insensitive bacterial pathogens, molecular mechanisms of which remain completely unexplored. In this arms-race between microorganisms, bacteria have evolved numerous defence strategies to combat phage infections like the Restriction-Modification Systems (RM), DNA degradation systems and CRISPR-Cas Systems. Our lab is particularly interested in characterizing the Abortive infection (Abi) system which is usually a measure of last resort as it involves the bacterial cell committing suicide after sensing infection before the phage can complete its replication cycle. Although a plethora of Abi systems are now known, we are particularly interested in dissecting how λ-lysogenic prophage encoded RexA/RexB Abi system prevents infection of other bacteriophages like the T4, T5 and T7 phages in E. coli. Research on Abi systems in bacteria is expected to accelerate the design of better bacteriophage-based therapies against persistent pathogens like M. tuberculosis, M. ulcerans, M. abscessus, C. difficile, P. aeruginosa, S. aureus, A. baumannii and K. pneumoniae.

Our goal is to understand how these biological processes work and to achieve this, we use a multi-disciplinary approach combining structural (X-ray crystallography and electron microscopy (cryo-EM)), molecular (cloning, tagging), membrane-protein biochemistry, biophysical (mass spectrometry, EPR, FRET, etc.), in-sillico (AL/ML-led molecular modelling and molecular dynamics) and cell biological (live-cell imaging and fluorescence microscopy) techniques.

Scientific Inspiration

Late Dorothy Mary Crowfoot Hodgkin, University of Oxford is my scientific inspiration as she exemplified academic excellence and human pursuit of knowledge while ensuring her colleagues and lab members are mentored well so that they each of them become an original thinker and a future leader in science. I have personally benefited from her working style as my PhD supervisor received his scientific training in her lab and he inculcated many of these traits in his students.

Research Groups

Abhinav Lab

Supervision Style

In a few words or phrases: Detail-oriented, mentoring-teaching, understanding, collaborative, and inclusive.

Provision of Training

I prefer to take responsibility for your technical training at first, leading to more independence later.

Progression Monitoring and Management

I like to be kept up to date, and will expect to see evidence of method development/data generation results on a daily/weekly basis. Although I will set out my expectations of your progression on a weekly/monthly basis, if these progression criteria are not met, we will always discuss a plan of action together.

Communication

In addition to email, the team has a WhatsApp group chat with which we regularly communicate during the week and weekends. Whilst I expect you to keep up with my/ team communications I will expect you to manage your work/life balance.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per week

In year 1 of PhD Study

At least once per week

In year 2 of PhD Study

At least once per week

In year 3 of PhD Study

At least once per fortnight

These one on one meetings will be face to face, and I am usually contactable for an instant response on every working day.

Working Pattern

Work in my lab requires being present on site (be it in a laboratory or at a field site) during core hours.

Notice Period for Feedback

I need at least 1 week’s notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Structural and Functional Analysis of Copper-Transporting ATPases in MRSA: Targets for Antimicrobial Intervention

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Structural and Functional Analysis of Copper-Transporting ATPases in MRSA: Targets for Antimicrobial Intervention

Secondary Supervisor(s): Dr Julie Morrissey, Professor Joan Geoghegan

University of Registration: University of Leicester

BBSRC Research Themes:

Understanding the Rules of Life (Immunology, Microbiology, Structural Biology)
Integrated Understanding of Health (Pharmaceuticals)

Project Outline

Importance

Copper is an essential trace element, crucial for various biological processes, but in high concentrations, it is toxic to cells¹. Host organisms, including humans, exploit this toxicity by using copper as an antibacterial weapon during infections^2,3,4. During infection, host cells actively transport copper into the phagosomes containing bacteria, where elevated copper levels help neutralize the invading pathogens. Pathogenic bacteria such as Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA), have developed defence mechanisms, including copper-transporting ATPases like CopA, CopB and CopX, to manage copper toxicity and survive within the host (Figure 1a and 1b)^5,6 and evade the host's defences^6,7,8. Despite their importance as promising targets for novel antibacterial therapies, little is known about the detailed structure and function of these ATPases in MRSA. This PhD project aims to investigate the structural and functional mechanisms of CopA, CopX and CopB from S. aureus strains JE2 and MRSA252 respectively, using a combination of cloning, expression, purification, and structural analysis techniques. Understanding these copper pumps will provide insights into their role in copper homeostasis and their potential as therapeutic targets for combating multidrug-resistant bacterial infections like MRSA⁹.

Aims

This project aims to answer the following questions about the structure and function of the copper ATPases in S. aureus:

What are the structural features of the ATPases that facilitate copper transport and detoxification in S. aureus and how do these structural differences compare in different clinical isolates?

How do ATP and copper binding influence the structural and functional dynamics of these proteins?

How do these ATPases respond to different copper concentrations, and what role do they play in copper homeostasis in MRSA?

The longer-term aim is to investigate if inhibiting the function of the ATPases can provide a viable therapeutic strategy for combating MRSA infections.

Research Plan

The project will be divided into several phases. Initially, the genes encoding CopA and CopB/CopX from S. aureus strains JE2 and MRSA252 will be cloned and expressed in E. coli and solubilised from membranes using detergents. The proteins will then be purified using His-tag affinity chromatography and size exclusion chromatography. We will also try and stabilise these proteins by optimizing the buffer conditions as well as reconstituting them into SMALPs and amphipols. The next phase will involve the biochemical characterization of the purified proteins through ATPase and copper transport assays to confirm their activity. Once functional, the structural characterization will be conducted using single-particle cryo-electron microscopy (cryo-EM) to determine the high-resolution structures of CopA and CopB in both their Apo and ATP-analog bound states. Structural analysis of the Apo-, the non-hydrolysable ATP analog (AMPPNP) and product bound (ADP-bound) states will allow the identification of key regions involved in copper binding and dynamics during transport. Hypotheses generated from the structural data will be tested using site-directed mutagenesis, targeting specific residues that are predicted to play important roles in ATPase activity or copper transport. The functional impact of these mutations will be evaluated through ATPase and transport assays. Finally, in vivo studies will be conducted in collaboration with Prof. Julie Morissey’s group to assess the physiological relevance of these findings in S. aureus mutants.

Expected Outcomes and Impact

By integrating structural data with functional assays, this project on copper-transporting ATPases will elucidate the mechanisms by which they manage copper toxicity in S. aureus. These findings could pave the way for the development of new antimicrobial strategies that target copper detoxification systems in bacteria, offering a novel approach to combating antibiotic-resistant infections like MRSA.

Techniques

Techniques that will be undertaken during the project:

Cloning, over-expression and purification of recombinant protein-complexes.

Membrane-protein biochemistry, Biophysical and Activity assays.

Cryo-electron microscopy (cryo-EM) and integrative structural biology.

References

Halliwell B, Gutteridge JM. Oxygen toxicity, oxygen radicals, transition metals and disease. Biochem J. 1984; 219:1-14.

Achard ME, Stafford SL, Bokil NJ, Chartres J, Bernhardt PV, Schembri MA, Sweet MJ, McEwan AG. Copper redistribution in murine macrophages in response to Salmonella infection. Biochem J. 2012; 444:51-7.

White C, Lee J, Kambe T, Fritsche K, Petris MJ. A role for the ATP7A copper-transporting ATPase in macrophage bactericidal activity. J Biol Chem. 2009; 284:33949-56.

Johnson MD, Kehl-Fie TE, Klein R, Kelly J, Burnham C, Mann B, Rosch JW. Role of copper efflux in pneumococcal pathogenesis and resistance to macrophage-mediated immune clearance. Infect Immun. 2015; 83:1684-94.

Sitthisak S, Knutsson L, Webb JW, Jayaswal RK. Molecular characterization of the copper transport system in Staphylococcus aureus. Microbiology (Reading). 2007; 153:4274-4283.

Kaur I, Purves J, Harwood M, Ketley JM, Andrew PW, Waldron KJ, Morrissey JA. Role of horizontally transferred copper resistance genes inStaphylococcus aureusandListeria monocytogenes. Microbiology (Reading). 2022; 168:001162.

Zapotoczna M, Riboldi GP, Moustafa AM, Dickson E, Narechania A, Morrissey JA, Planet PJ, Holden MTG, Waldron KJ, Geoghegan JA. Mobile-Genetic-Element-Encoded Hypertolerance to Copper Protects S. aureus from Killing by Host Phagocytes. mBio. 2018; 9:e00550-18.

Purves J, Thomas J, Riboldi GP, Zapotoczna M, Tarrant E, Andrew PW, Londoño A, Planet PJ, Geoghegan JA, Waldron KJ, Morrissey JA. A horizontally gene transferred copper resistance locus confers hyper-resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages. Environ Microbiol. 2018; 20:1576-1589.
Saenkham-Huntsinger P, Hyre AN, Hanson BS, Donati GL, Adams LG, Ryan C, Londoño A, Moustafa AM, Planet PJ, Subashchandrabose S. Copper Resistance Promotes Fitness of Methicillin-Resistant Staphylococcus aureus during Urinary Tract Infection. mBio. 2021; 12:e0203821.

Co-supervisor on a project with Dr Helen O'Hare.

Previous Projects (2024-25)

Primary supervisor for:

Molecular characterization of suicidal phage-resistance mechanisms in bacteria