Professor David Grainger

Understanding multiple antibiotic resistance in pathogenic bacteria

Secondary Supervisor(s): Professor Jessica Blair

University of Registration: University of Birmingham

BBSRC Research Themes:

• Sustainable Agriculture and Food (Microbial Food Safety)
• Understanding the Rules of Life (Microbiology)

Project Outline

Antibiotics have transformed medical practice, increased life expectancy and, together with vaccination, led to near eradication of many bacterial diseases (1). However, overuse has driven emergence of drug-resistant bacteria. Such microbes cause millions of infections annually, with thousands of lives lost, at a societal cost of $ billions. In enteric pathogens, a small group of AraC-XylS family transcription factors is often implicated. The prototypical example is the multiple antibiotic resistance activator, MarA, protein of Escherichia coli (1,2). Encoded by the mar operon, expression of marA can be induced by antimicrobial compounds (1). Alternatively, antibiotic resistant E. coli may carry genetic changes and constitutively produce MarA (1). Upon expression, MarA alters gene expression globally, by binding DNA sites called marboxes, and this drives antibiotic resistance (1,2). Hence, the complete system comprises both the mar operon and genes subject to regulation by MarA. Whilst some aspects of the response are understood, such as up-regulation of efflux pump expression, most MarA regulated genes are unknown or have no obvious connection to drug resistance (2).

We have developed an approach to accurately identify MarA regulated genes (3). Furthermore, by mutating marboxes at different chromosomal sites, we have discovered strong synergistic interactions, between regulated genes, that individually appear inconsequential (3). This project will build on these findings to answer two major questions: which genes are controlled by MarA and how do synergistic interactions between them drive antibiotic resistance? You can expect to learn a wide range of techniques, both laboratory based and computational. The lab approaches will include whole genome and focused molecular microbiological tools.

1 Blair, J. M. A. et al. Nature Reviews Microbiology 13, 42–51 (2015)

2 Sharma, P. et al. Nat. Commun. 8, 1444 (2017)

3 Trigg, A. et al. PLoS Genet. 21: e1011639 (2025)

Understanding the pandemic microbe Vibrio cholerae

Secondary Supervisor(s): Professor Andy Lovering

University of Registration: University of Birmingham

BBSRC Research Themes:

• Sustainable Agriculture and Food (Microbial Food Safety)
• Understanding the Rules of Life (Microbiology)

Project Outline

Understanding the rules of species evolution is a fundamental question in biology. The emergence, spread and demise of harmful organisms, which can cause pandemics, is particularly important. You will focus on the bacterial species Vibrio cholerae. Currently, we cannot explain how the strain causing the current cholera pandemic arose, let alone predict why, where or when the next one might arise. The “success” of V. cholerae depends on its ability to adapt to different surroundings. Normally, the bacterium resides in aquatic environments and persists by forming biofilms on the chitinous surfaces of plankton and shellfish. These biofilms are rapidly disassembled on ingestion by a human or aquatic host. Following host colonisation, disease is caused by the extrusion of toxins. Hence, to understand what is special about the “pandemic” strain, it is essential to understand how the bacterium is able to switch between lifestyles. Recent work has generated a wealth of V. cholerae genome sequences (>10,000) from decades of outbreaks associated with the current worldwide pandemic. You will use these data to try and understand key genetic changes that influence lifestyle choice and pandemic potential. You will apply bacterial genomics, molecular biology, and host organism colonisation models, to study lifestyle changes.

Haycocks, JRJ, Warren, GZL, Walker, LM, Chlebek, JL, Dalia, TN, Dalia, AB, Grainger, D (2019) The quorum sensing transcription factor AphA directly regulates natural competence in Vibrio cholerae. PLoS Genetics. 15:e1008362.

Walker, LM, Haycocks, JRJ, van Kessel, JC, Dalia, TN, Dalia, AB, Grainger, D (2023) A simple mechanism for integration of quorum sensing and cAMP signalling in V. cholerae. eLife 12:RP86699

Understanding the rules of life: mechanisms of gene regulation in bacteria

Secondary Supervisor(s): Professor Steve Busby

University of Registration: University of Birmingham

BBSRC Research Themes:

• Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

In all lifeforms DNA is transcribed to create RNA templates for protein synthesis. This is known as the central dogma of molecular biology. Transcription is stimulated by regions of DNA called promoters. Transcription stops at DNA sequences called terminators. We have discovered that the processes of transcription initiation and termination can be coupled to each other at special DNA sequences that we refer to as coupled promoter-terminators. We believe that this process, never described previously, is common to all bacteria but its function is unknown. You will determine the function of coupled promoter-terminators in controlling gene expression. You will use a combination of genomic and molecular tools.

Warman EA, Forrest D, Guest T, Haycocks JJRJ, Wade JT, Grainger DC (2021) Widespread divergent transcription from bacterial and archaeal promoters is a consequence of DNA-sequence symmetry. Nat Microbiol. 6(6):746-756.