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Obtaining molecular insights of effector competition of oncogenic RAS signalling


   Molecular and Cell Biology

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  Dr K Tanaka, Dr Andrey Revyakin  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

The RAS family of small GTPases act as signalling hubs regulating cell proliferation and differentiation. Notably, about 20% of all human cancers harbour mutations in RAS genes (COSMIC). Ras acts as a signalling hub to trigger the activation of multiple effectors by directly interacting with them. It is generally assumed that oncogenic RAS molecules over-activate all the downstream pathways. However, we recently showed that a constitutive RAS signalling results in over-activation of one of the downstream pathways, but not all (Kelsall, Vertesy et al., bioRxiv, 2018). In this work, we exploited a relatively simple yet physiological setting of the fission yeast mating process, where Ras1, the unique fission yeast RAS homologue, activates two pathways, MAPKSpk1 and Cdc42 (a prototype small G-protein in yeast). We demonstrated that a constitutively active Ras1 mutant causes prolonged activation of Cdc42, whilst MAPK Spk1 activation is only transient. The result indicates that the activated RAS may develop a preference towards specific downstream pathways, or some pathways may be more rigorously downregulated than others.

Compared to the well-characterised process of RAS-mediated MAPK activation, the molecular mechanism of RAS-mediated activation of small G-proteins (small-Gs) is largely unknown. We hypothesised that in yeast, Ras1 induces Cdc42 activation by directly interacting with Scd1, a GDP-GTP exchanging factor (GEF) for Cdc42; in other words, by interacting with Ras1, Scd1 is activated and then activates Cdc42. We confirmed the direct interaction between Ras1 and Scd1 for the first time by analysing bacterially expressed recombinant Ras1 and Scd1 complex using NMR and pull-down assays (Tariq et al., manuscript in preparation).

Having established the importance and molecular mechanism of the RAS-mediated small-G activation pathway, we now wish to address the next question; How does RAS manage to activate multiple downstream targets in a coordinated manner? Does RAS simultaneously interact with multiple targets? Or does RAS jump between different targets?

In the PhD project, we will address the question by combining structural biology, cell biology and single-molecule analysis. One of the unique features of the single-molecule analysis is that it allows us to obtain kon and koff rate of interacting molecules through live observation of these molecules. This allows us to study how multiple RAS effectors are competing with each other for the active RAS at a molecular level.

We will exploit both fission yeast and human tissue culture systems, where chromosomal endogenous RAS gene loci bear oncogenic constitutively active mutations. Studying two divergent systems allows us to establish common core features of RAS signalling. We firstly focus on the simple yeast model, which helps us to recognise essential key properties of RAS signalling. The outcome will be applied to the human cell culture system to examine whether such properties are conserved or not.

Competition of multiple Ras effectors for the active Ras has been proposed in the past. However, the kinetics under the physiological setting is still elusive. In fission yeast, we confirmed that both in vivo and in vitro, RAS binding domains (RBDs) of Scd1 and Byr2 (yeast MAPKKK) compete for Ras1 (Kelsall, Vertesy et al., bioRxiv, 2018). In the PhD project, we will further develop this observation. For in vitro studies, single-molecule analyses, as well as competition NMR analysis, will be conducted. For in vivo studies, co-localisation of Ras1, RBD-Scd1, and RBD-Byr2 will be examined through live cell imaging through super-resolution microscopy, split-GFP assays and fluorescence resonance energy transfer (FRET). In parallel, we will conduct human counterpart experiments using human KRAS and its representative effectors, BRAF, Rgl2 and RALGDS. Collectively, the successful delivery of the project will bring a novel conserved concept of RAS signalling.

Entry requirements:

  • Those who have a 1st or a 2.1 undergraduate degree in a relevant field are eligible.
  • Evidence of quantitative training is required. For example, AS or A level Maths, IB Standard or Higher Maths, or university level maths/statistics course.
  • Those who have a 2.2 and an additional Masters degree in a relevant field may be eligible.
  • Those who have a 2.2 and at least three years post-graduate experience in a relevant field may be eligible.
  • Those with degrees abroad (perhaps as well as postgraduate experience) may be eligible if their qualifications are deemed equivalent to any of the above.

For further information please contact [Email Address Removed]

Application advice:

To apply please refer the application instructions at

https://le.ac.uk/study/research-degrees/funded-opportunities/bbsrc-mibtp

You will need to apply for the PhD place at University of Leicester and also submit your online application notification to MIBTP.  Links for both are on the above web page.

Project / Funding Enquiries: For further information please contact [Email Address Removed]

Application enquiries to [Email Address Removed]


Funding Notes

All MIBTP students will be provided with a 4 years studentship.
Studentships include:
Tuition fees at UK rate*
• a tax free stipend of at least £15,609* p.a (to rise in line with UKRI recommendation)
• a travel allowance in year 1
• a travel / conference budget
• a generous consumables budget
• use of a laptop for the duration of the programme.
* International students are welcome to apply but must be able to fund the difference between UK
and International fees for the duration of their studies.
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