Building a fluorescent toolbox for exploring translation in Vibrio natriegens

One fully-funded PhD project is available in the School of Molecular & Cellular Biology. We invite applications from prospective postgraduate researchers who wish to commence study for a PhD in the academic year 2025/26. The successful candidate will use genome engineering and super-resolution microscopy to investigate protein synthesis in order to better understand, and better engineer, microbial cells as factories for therapeutics. A background in either molecular biology, microbiology, synthetic biology or biophysics, and interests in synthetic and quantitative biology, would be strengths for this project.

<h5>Background:</h5> <p>Central to the effectiveness of a given microbial strain for synthetic biology is the capacity of their ribosomes to support efficient translation of synthetic gene circuits while maintaining fast cellular growth. As a result, there has been much interest in the field dedicated to optimising the use of ribosomes by synthetic gene circuits (classic examples being ribosome binding site and codon optimisation), as well as to engineering cells to balance the ribosomal ‘resources’ used by the synthetic pathways with the requirements of the host cell.</p> <p><em>Vibrio natriegens</em> has recently emerged as a promising synthetic biology chassis organism with properties superior to <em>E. coli</em>. Besides an ability to grow on a wide range of media, it is particularly notable for its ultrafast growth kinetics (doubling times down to ~10 minutes) and high ribosome concentration (over 100,000 per cell from 11 rRNA operons). While much progress has been made recently in characterising part libraries and developing tools for <em>V. natriegens</em> engineering, relatively little is known about the ribosome biology that may underlie its promise as a ‘microbial cell factory’.</p> <h5>Objectives:</h5> <p>Building on our published work on the fluorescent tracking of engineered ribosomes in E. coli (Csibra et al., 2023), this project will aim to expand the fluorescent toolbox for tagging and tracking ribosomes in living cells in V. natriegens. You will create and optimise the production of fluorescent ribosomes with RNA aptamers and protein labels, and use super-resolution microscopy to follow the dynamics of translation in living cells to quantitatively study their biogenesis and regulation. You will use genome engineering, high throughput reporter assays, sequencing and microscopy to understand how ribosome biogenesis and activity is controlled in this uniquely fast-paced species. Finally, you will use these insights to design and engineer cells with optimised synthetic translation machinery as next-generation microbial cell factories.</p> <h5>Training:</h5> <p>You will join a laboratory focused on the intersection of fundamental and engineering biology of microbial protein synthesis (Eszter Csibra, School of Molecular and Cellular Biology), and be supported by experts in bacterial genome engineering (Ryan Seipke, School of Molecular and Cellular Biology) and super-resolution microscopy (Aleks Ponjavic, School of Physics and Astronomy). You will receive training in a wide range of cutting-edge techniques including RNA and protein engineering, CRISPR, sequencing, super-resolution microscopy and programmatic data analysis.</p> <h5>References</h5> <ul> <li><strong>Csibra E</strong>*, Klopprogge B, Sorensen GH and Gorochowski T*. 2023. (*co-corresponding author) Engineering orthogonal ribosomes for real-time monitoring using fluorescence. <em>bioRxiv</em>. doi: 10.1101/2023.11.19.567736 link: <a href="https://www.biorxiv.org/content/10.1101/2023.11.19.567736v1">https://www.biorxiv.org/content/10.1101/2023.11.19.567736v1</a></li> <li><strong>Csibra E</strong>, Stan GB. 2022. Absolute protein quantification using fluorescence measurements with FPCountR. <em>Nat Commun</em> <strong>13</strong>, 6600. doi: 10.1038/s41467-022-34232-6 link: <a href="https://www.nature.com/articles/s41467-022-34232-6">https://www.nature.com/articles/s41467-022-34232-6</a></li> <li>Boo A, Ellis T and Stan GB. 2021. Host-aware synthetic biology. doi: 10.1016/j.coisb.2019.03.001 link: <a href="https://www.sciencedirect.com/science/article/pii/S245231001930006X">https://www.sciencedirect.com/science/article/pii/S245231001930006X</a></li> <li>Hoff J et al. 2020. Vibrio natriegens: an ultrafast-growing marine bacterium as emerging synthetic biology chassis. Environmental Microbiology <strong>22 </strong>(10) 4394-4408. doi: 10.1111/1462-2920.15128 link: <a href="https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15128">https://onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15128</a></li> </ul> <h5>Links</h5> <ul> <li><a href="https://biologicalsciences.leeds.ac.uk/biological-sciences/staff/3562/dr-eszter-csibra">https://biologicalsciences.leeds.ac.uk/biological-sciences/staff/3562/dr-eszter-csibra</a></li> <li><a href="https://www.csibra-lab.com">https://www.csibra-lab.com</a></li> <li><a href="https://biologicalsciences.leeds.ac.uk/molecular-and-cellular-biology/staff/134/dr-ryan-f-seipke">https://biologicalsciences.leeds.ac.uk/molecular-and-cellular-biology/staff/134/dr-ryan-f-seipke</a></li> <li><a href="https://eps.leeds.ac.uk/physics/staff/8090/dr-aleks-ponjavic">https://eps.leeds.ac.uk/physics/staff/8090/dr-aleks-ponjavic</a></li> <li><a href="https://biologicalsciences.leeds.ac.uk/research-innovation">https://biologicalsciences.leeds.ac.uk/research-innovation</a></li> <li><a href="https://astbury.leeds.ac.uk">https://astbury.leeds.ac.uk</a></li> </ul>

<p>To apply for this scholarship opportunity applicants should complete an<a href="https://biologicalsciences.leeds.ac.uk/research-degrees/doc/how-to-apply"> online application form</a> and attach the following documentation to support their application. </p> <ul> <li>a full academic CV</li> <li>degree certificate and transcripts of marks</li> <li>Evidence that you meet the University's minimum English language requirements (if applicable)</li> </ul> <p>To help us identify that you are applying for this project please ensure you provide the following information on your application form;</p> <ul> <li>Select PhD in Biological Sciences as your programme of study</li> <li>Give the full project title and name the supervisors listed in this advert</li> <li>Please state "Faculty Funded Scholarship" when asked for source of funding</li> </ul> <p>If English is not your first language, you must provide evidence that you meet the University’s minimum English language requirements (below)</p> <p><em>As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people</em></p>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline. The criteria for entry for some research degrees may be higher, for example, several faculties, also require a Masters degree.

The minimum English language entry requirement for research postgraduate research study is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid.

<p>This scholarship is funded by the Faculty of Biological Sciences. The scholarship will provide academic fees at the UK rate, as well as a stipend matching the UKRI rate (£19,237 for 2024/25) for a maximum of 3.5 years. Due to limited funding we can only consider applicants eligible to pay academic fees at the UK fee rate.</p>

<p>Interested applicants are encouraged to contact the lead investigator Dr. Eszter Csibra to learn more about this opportunity</p> <p>e: <a href="mailto:e.csibra@leeds.ac.uk">e.csibra@leeds.ac.uk</a></p> <p>For further information about the admissions process please contact the FBS PGR Admissions Team<br /> e: <a href="mailto:fbsgrad@leeds.ac.uk">fbsgrad@leeds.ac.uk</a></p>