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(BBSRC DTP CASE) Engineering new biosurfactants by harnessing the power of CRISPR and AlphaFold


   Department of Chemical Engineering

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  Dr J Winterburn, Prof Robert Field, Prof D Delneri  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

This CASE PhD project in collaboration with Holiferm Limited will investigate the enzyme(s) that catalyse sophorolipid production in Starmerella bombicola. This information can aid in the selection of novel substrates for the production of novel sophorolipid products with interesting and useful properties.

Sophorolipid biosurfactants are naturally occurring amphiphiles with a range of unique properties including biodegradability and tolerance over a wide range of temperatures and pH. These properties have facilitated the commercialisation of these biosurfactants by a number of companies in recent years, in a range of personal care, home care and laundry care applications. There is further significant interest in molecules produced from industrial biotechnology routes and the use of biosurfactants such as sophorolipids as bulk chemicals, in particular for bioremediation and enhanced oil recovery, though the cost of production is currently prohibitive.

This PhD project will investigate enzymes in the native biosynthetic route in Starmerella bombicola for the production of sophorolipids. The pathway is known (Van Bogaert et al., 2007) and in combination with the available genome sequence (Matsuzawa et al., 2015) now allows for the construction of an enzyme structure via AlphaFold (Jumper et al., 2021). The binding of the substrates can be estimated by docking and molecular modelling. Together with sequence alignment to find conserved residues allows us to estimate how the substrates sit in the active site. This information will then function as a guide for selecting other substrates that can be catalysed and form novel biosurfactant products. Characterisation of these new to nature substrates can be tested with varied biochemical techniques and might result in a range of novel properties, opening up a range of potential applications in formulated products. The proposed project will deliver new production routes for modified sophorolipids, from a non-GMO origin, giving potential new functionality and hence additional market applications. Having access to structural information of the enzyme can then also be used to design mutants that potentially create new products from a GMO origin. Mutants can target binding of the sugar and/or fatty alcohol resulting in an even larger assortment of new products. Upon successful identification of desirable products, the genome of Starmerella bombicola will be edited with state-of-the-art molecular cloning methods like CRISPR-Cas12 (Zhang et al., 2022). The final stage of the research will involve optimisation of fermentation conditions for these novel sophorolipids at 2L bioreactors scale, as larger quantities of surfactants is required for detailed characterisation of their unique properties. Having access to a fully characterised library of alternative and novel sophorolipid molecules and their functionality, will be followed by formulation testing and evaluation of the techno-economic and environmental sustainability performance of the modified sophorolipids.

https://www.research.manchester.ac.uk/portal/james.winterburn.html

https://www.research.manchester.ac.uk/portal/robert.field.html

https://www.research.manchester.ac.uk/portal/d.delneri.html

https://holiferm.com/

Eligibility

Applicants must have obtained or be about to obtain a First or Upper Second class UK honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science, engineering or technology. 

Before you Apply

Applicants must make direct contact with preferred supervisors before applying. It is your responsibility to make arrangements to meet with potential supervisors, prior to submitting a formal online application.

How To Apply

To be considered for this project you MUST submit a formal online application form - full details on eligibility how to apply can be found on the BBSRC DTP website https://www.bmh.manchester.ac.uk/study/research/bbsrc-dtp/

Your application form must be accompanied by a number of supporting documents by the advertised deadlines. Without all the required documents submitted at the time of application, your application will not be processed and we cannot accept responsibility for late or missed deadlines. Incomplete applications will not be considered. If you have any queries regarding making an application please contact our admissions team [Email Address Removed]

Equality, Diversity and Inclusion

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. The full Equality, diversity and inclusion statement can be found on the website https://www.bmh.manchester.ac.uk/study/research/apply/equality-diversity-inclusion/


Funding Notes

This is a 4 year CASE studentship in partnership with Holiferm Limited. This scheme is open to both the UK and international applicants. We are only able to offer a limited number of studentships to applicants outside the UK. Therefore, full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.

References

[1] Van Bogaert, I. N. A. et al.(2007) ‘Microbial production and application of sophorolipids’, Applied Microbiology and Biotechnology, 76(1), pp. 23–34. doi: 10.1007/s00253-007-0988-7.[2] Jumper, J. et al.(2021) ‘Highly accurate protein structure prediction with AlphaFold’, Nature, 596(7873), pp. 583–589. doi: 10.1038/s41586-021-03819-2.[3] Matsuzawa, T. et al.(2015) ‘Draft Genome Sequence of the Yeast Starmerella bombicolaNBRC10243, a Producer of Sophorolipids, Glycolipid Biosurfactants’, Genome Announcements, 3(2), pp. e00176-15. doi: 10.1128/genomeA.00176-15.[4] Zhang, M. et al.(2022) ‘A CRISPR–Cas12a system for multi-gene editing (CCMGE) and metabolic pathway assembly in Starmerella bombicola’, Systems Microbiology and Biomanufacturing. doi: 10.1007/s43393-022-00093-9.
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