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Using ribosomes as molecular thermometers to predict optimal growth conditions and peer into the ancient history of life on Earth


Biosciences Institute

Dr S Melnikov , Dr P.T. Chivers , Dr P Etchells Friday, January 22, 2021 Competition Funded PhD Project (Students Worldwide)
Newcastle United Kingdom Biochemistry Bioinformatics Evolution Molecular Biology Palaeontology Structural Biology

About the Project

Introduction:

We invite you to work with us to establish a new revolutionary method to peer into the ancient history of life on our planet. We will make this possible by studying ribosomes – the most ancient molecular machines in a living cell, the origin of which dates back to the beginning of life 4 billion years ago.

Aims:

We will use:

1. cryo-electron microscopy to determine structures of ribosomes from

bacteria that are adapted to extreme environments, such as boiling water or extreme cold;

2. big data analysis to reveal hidden rules of ribosome adaptations to extreme environments;

3a. protein biophysics to assess how sequence variations in ribosomal proteins affect their melting temperatures;

3b. using plant genetics, assess how ribosomal mutations affect plant temperature tolerance;

4. using advanced 3D printing, create a museum exhibit to illustrate how biological molecules adapt to extreme environments.

Outcomes:

This study will reveal how ribosomes adapt to extreme temperatures and how ribosomes can be used as ‘molecular thermometers’: instead of running laboratory experiments, we will be able to accurately predict the optimal growth environment for a given organism by sequencing its ribosomal genes. This may forever change our approach to studying unculturable and extinct species and the history of climate change on our planet.

 Training:

You will receive advanced training in structural biology and bioinformatics (at Newcastle University) and basic training in protein biophysics and plant genetics (at Durham University). You will also cooperate with a private company to master 3D printing of biological molecules and prepare part of our museum exhibit: ‘Evolution in the world that Darwin never saw’.

We encourage and train our students to master the arts of academic writing, oral communication and project/time management. We will help the student to publish at least two first-author papers and will do our best to support their transition to the next stage of their career in academia or industry.

Requirements:

We value most your intellectual curiosity, motivation, friendliness and a strong work ethic. A basic understanding of molecular biology or physics is desired.

Our mentorship philosophy:

We believe that effective mentors help mentees succeed by adjusting the learning challenges to be ‘just right’ for them. We consider your PhD training as your professional life from the stage of “birth” to “maturity”: we will help you make your first baby steps and gradually become an independent, world-class expert leading your own research project.

More:

http://www.melnikovlab.com/phd-projects

Informal enquiries may be made to

HOW TO APPLY 

Applications should be made by emailing with a CV and a covering letter, including whatever additional information you feel is pertinent to your application; you may wish to indicate, for example, why you are particularly interested in the selected project/s and at the selected University. Applications not meeting these criteria will be rejected. We will also require electronic copies of your degree certificates and transcripts.

In addition to the CV and covering letter, please email a completed copy of the Newcastle-Liverpool-Durham (NLD) BBSRC DTP Studentship Application Details Form (Word document) to , noting the additional details that are required for your application which are listed in this form. A blank copy of this form can be found at: https://www.nld-dtp.org.uk/how-apply.


Funding Notes

Studentships are funded by the Biotechnology and Biological Sciences Research Council (BBSRC) for 4 years. Funding will cover tuition fees at the UK rate only, a Research Training and Support Grant (RTSG) and stipend. We aim to support the most outstanding applicants from outside the UK and are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme.

References

1. Archaeal ribosomal proteins possess NLS-type motifs: implications for the origin of the cell nucleus. (2020) Molecular Biology and Evolution, 37(1), 124.
2. Insights into the role of diphthamide in elongation factor 2 in mRNA reading-frame maintenance. (2018) Journal of Molecular Biology 430 (17), 2677.
3. Mechanistic insights into the slow peptide bond formation with D-amino acids. (2018) Nucleic Acids Research 47 (4), 2089.
4. Loss of protein synthesis quality control in host-restricted organisms. (2018) PNAS 115, E11505.
5. Error-prone protein synthesis in parasites with the smallest eukaryotic genome. (2018) PNAS 115, E6245.
6. Revising the structural diversity of ribosomal proteins across the three domains of life. (2018) Molecular Biology and Evolution 35 (7), 1588.
7. Bacterial sensors define intracellular free energies for correct enzyme metalation. (2019) Nature Chemical Biology 15, 241.
8. Elucidation of the biosynthesis of the methane catalyst coenzyme F430. (2017) Nature 543, 78.
9. A PXY-Mediated transcriptional network Integrates signaling mechanisms to control vascular development in Arabidopsis. (2020) The Plant Cell 32 (2), 319.
10. Three PIGGYBACK genes that specifically influence leaf patterning encode ribosomal proteins. (2008) Development 135 (7), 1315.
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