Exploiting a novel peptide cyclase to make new antibiotics


   Faculty of Biological Sciences

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Dr Ryan Seipke Dr Glyn Hemsworth Prof Michael Webb  No more applications being accepted  Competition Funded PhD Project (European/UK Students Only)

About the Project

Without new antibiotics the global healthcare system will collapse. Many antibiotics originate from a class of microbial natural products called non-ribosomal peptides, the vast majority of which are cyclic. Cyclisation of these peptides is often inefficient so new approaches are sought after in this area. We recently identified a novel non-ribosomal peptide cyclase with considerable substrate promiscuity. If this promiscuity can be understood, then it can be harnessed for biotechnology to improve chemical synthesis of antibiotics and other high-value cyclic peptides.

In this project you will purify the peptide cyclase and interrogate its substrate specificity in vitro. You will also pursue structural studies with the cyclase using X-ray crystallography and use the resulting structure to rationally re-engineer its substrate specificity. The activities pursued during the project are supported by World-class infrastructure and support within the Astbury Centre for Structural Molecular Biology. You will have an opportunity to learn a wide range of techniques including: protein purification, peptide synthesis, LC-MS, NMR, X-ray crystallography and many others. The outcomes of this project will have a direct impact on the AMR crisis by developing methodology for enhancing the synthesis of novel peptide antibiotics.

Funding Notes

White Rose BBSRC Doctoral Training Partnership in Mechanistic Biology
4 year fully-funded programme of integrated research and skills training, starting Oct 2020:
• Research Council Stipend
• UK/EU Tuition Fees
• Conference and research funding

Requirements:
At least a 2:1 honours degree or equivalent. We welcome students with backgrounds in biological, chemical or physical sciences, or mathematical backgrounds with an interest in biological questions.

EU candidates require 3 years of UK residency to receive full studentship

Not all projects will be funded; the DTP will appoint a limited number of candidates via a competitive process.

https://phd.leeds.ac.uk/funding/81-white-rose-bbsrc-doctoral-training-partnership-in-mechanistic-biology

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Project supervisors

Career overview

Dr. Ryan F. Seipke was awarded a BA in Biology from Adrian College in 2003 and subsequently obtained a PhD in Microbiology from Cornell University in 2008. Following this, Dr. Seipke undertook a USDA-funded postdoctoral position with Prof. Rosemary Loria in the Department of Plant-Microbe Biology at Cornell University from 2008 to 2009. Dr. Seipke then moved to the University of East Anglia, where he worked as an MRC-funded postdoc with Prof. Matt Hutchings from 2009 to 2012, followed by a NERC-funded postdoc from 2012 to 2013. In 2013, Dr. Seipke was appointed to a Lectureship in the Faculty of Biological Sciences at the University of Leeds and was promoted to Associate Professor in 2020.


Research interests

Dr. Ryan F. Seipke''s research focuses on the regulation, biosynthesis, and genomics of microbial secondary metabolism, primarily in *Streptomyces* species. His lab is currently composed of three postdoctoral research associates and three PhD students, and has received support from BBSRC, InnovateUK, The Royal Society, and the Wellcome Trust. Current research projects include a standalone cyclase of non-ribosomal peptides and genome-scale functional genomics in *Streptomyces* species using CRISPR interference.

View Dr. Ryan F. Seipke's profile 

Career overview

Dr Glyn Hemsworth studied at the University of Sheffield, where he obtained a BSc in Biochemistry followed by a PhD in Structural Biology. He then moved to the University of York, where he spent six and a half years as a postdoctoral researcher. In 2016, Dr Hemsworth joined the University of Leeds as a University Academic Fellow and a BBSRC David Phillips Fellow. His research primarily utilises X-ray crystallography and biochemical techniques to gain molecular insights into protein function. Dr Hemsworth''s focus has largely been on enzymes, which are proteins that catalyse many reactions essential for life. He has studied enzymes involved in DNA replication, nucleotide homeostasis, and nutrient acquisition from food. Currently, he is investigating proteins that may play a role in biomass degradation, aiming to utilise them for generating more sustainable biofuels in the future.


Research interests

Dr Hemsworth''s research focuses on the discovery and characterisation of new proteins with potential biotechnological applications. He primarily uses X-ray crystallography and biochemical techniques to gain molecular insight into how proteins function, with a particular emphasis on enzymes that catalyse reactions essential for life. His work includes studying enzymes involved in DNA replication, nucleotide homeostasis, and nutrient acquisition from food. Currently, he is investigating proteins that may contribute to the degradation of biomass, aiming to utilise them for generating more sustainable biofuels in the future. Dr Hemsworth combines structural, biochemical, and biophysical methods to achieve a molecular-level understanding of enzymatic function.

View Dr. Glyn Hemsworth's profile 

Career overview

Professor Michael Webb is a biological chemist with a particular interest in the emerging field of engineering biology. He obtained his PhD from the University of Cambridge, where he worked with the late Professor Chris Abell. Following this, he undertook postdoctoral research with Professor Stephen Benkovic at Penn State University and Professor Alison Smith in Plant Sciences at Cambridge. Professor Webb joined the School of Chemistry at the University of Leeds as a Lecturer in Chemical Biology in 2007, was promoted to Associate Professor in 2014, and became a Professor of Biological Chemistry in 2023. His research interests lie at the interface of biochemistry and chemistry, and he is a member of the Astbury Centre for Structural Molecular Biology.


Research interests

Professor Webb''s research interests lie at the interface of biochemistry and chemistry, with a particular focus on biosynthesis and mechanistic aspects of protein chemistry. His work has included investigations into the pathways for essential metabolites such as pantothenate (vitamin B5), thiamine (vitamin B1), purines (the building blocks of DNA), and sirohaem, with current studies concentrating on the regulation within these pathways. Recently, he has developed interests in the controlled modification of proteins, the chemical biology of phosphorylation, and the biosynthesis of natural products. Notable highlights from his research include the characterisation of a fifth protein essential for pantothenate biosynthesis in bacteria, the development of methods for quantitative N-terminal labelling of proteins, and the synthesis of stable analogues of phosphorylated histidine. His research group employs a variety of biophysical approaches, including calorimetry, macromolecular crystallography, and organic synthesis. More detailed information about recent research and current projects can be found on the group website.

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