Primary Supervisor: Dr Damon Huber, School of Biosciences

Secondary supervisor: Dr Manuel Banzhaf

PhD project title: Identification of novel accessory Sec components in bacteria using high-throughput methods

University of Registration: University of Birmingham

Project outline:

Every compartment of a cell contains proteins, and yet all of these proteins are initially synthesised inside the cell in the cytoplasm. Proteins that do not normally reside inside the cytoplasmic compartment must be transported across one or several membrane in order to be localised to the correct compartment. In most cases, the first step in their correct localisation is transport across the cytoplasmic membrane by evolutionarily conserved Sec machinery. The core Sec machinery has been extensively investigated in the model organism Escherichia coli. Proteins are transported through a channel in the cytoplasmic membrane (SecYEG). Transport through SecYEG is powered by an ATPase (SecA), and a number of additional components, including SecDF, YidC, YajC and SecB, assist protein transport. However, recent work by our group suggests that there is a much larger network of proteins that assists the Sec machinery, which we have termed Accessory Sec Components (or ASCs). ASCs are less well conserved than the core machinery, suggesting that they may be required for adaptation to specific ecological niches. However, understanding how ASCs function would provide critical insight in the mechanism of the Sec machinery. The goal of this project is to identify potential ASCs in E. coli and investigate their function. To this end, the student will use high-throughput genetic screening methods and cutting-edge methodologies in molecular genetics and biochemistry.

References:

1. Cranford Smith T, Wynne M, Carter C, Jiang C, Jamshad M, Milner MT, Djouider Y, Hutchinson E, Lund PA, Henderson I, Huber D. (2020) AscA (YecA) is a molecular chaperone involved in Sec-dependent protein translocation in Escherichia coli. BioRxiv 215244.
2. Cranford-Smith T, Jamshad M, Jeeves M, Chandler RA, Yule J, Robinson A, Alam F, Dunne KA, Aponte Angarita EH, Alanazi M, Carter C, Henderson IR, Lovett JE, Winn P, Knowles T, Huber D. (2020) Iron is a ligand of SecA-like metal-binding domains in vivo. J Biol Chem. 295:7516-7528.
3. Cranford Smith T and Huber D. (2018) The way is the goal: how SecA transports proteins across the cytoplasmic membrane in bacteria. FEMS Microbiol Lett. 365, doi: 10.1093/femsle/fny093

BBSRC Strategic Research Priority: Understanding the Rules of Life: Microbiology

Techniques that will be undertaken during the project:

• Molecular biology
• Molecular genetics
• High-throughput sequencing
• High-throughput screening
• Bioinformatics

Contact: Dr Damon Huber, University of Birmingham