Dr Alex Johnson

Supervisor Details

Contact Details

School of Life Sciences, University of Warwick

Scientific Background

Research Interests

My research investigates the cell biology underlying how organisms sense and respond to their environment, focusing on the molecular mechanisms of clathrin-mediated endocytosis. Endocytosis is physiologically significant because it represents a major route of entry into the cell, and by internalising receptors and transporters from the cell surface it directly controls how sensitively a cell perceives and responds to environmental stimuli.

I work primarily in the model plant Arabidopsis thaliana, and increasingly in diatoms, photosynthetic algae separated from plants by around a billion years of evolution. Comparing these systems with each other and with animal and yeasts cells lets me ask which features of endocytosis are universal and which are lineage-specific solutions to the same cellular problem.

The key questions I investigate are:

How do single events of endocytosis work?
How does endocytosis mediate organism-environment interactions?
How does endocytosis in photosynthetic organisms compare with other eukaryotic models?

Scientific Inspiration

Christien Merrifield. He was a true pioneer of imaging endocytosis and showed the power and beauty of combining advanced microscopy with ingenious analysis. The pulse-pH assay is a perfect example of combining different skills to create something greater than the sum of its parts.

Research Groups

Cells & Development

Plant & Agricultural Biosciences

Quantitative, Systems and Engineering Biology (QSEB)

Supervision Style

In three words or phrases: Supportive, structured, development-focused.

Provision of Training

I take responsibility for your technical training at the start of your PhD, working alongside you at the microscope and bench, with the aim of building towards genuine independence as the project develops. You will also learn from other members of the group, and I will actively seek out training opportunities elsewhere where specialist expertise would benefit your project.

Progression Monitoring and Management

We will meet one-to-one every week at the start of your PhD, moving to fortnightly as you take fuller ownership of the project, and we will set and review goals together rather than my imposing them. I have high expectations, but if progress stalls I would always rather we discuss it early and agree a plan together than have you work around a problem alone.

Communication

I am in the lab regularly and my door is open, so most things can be dealt with as they arise. I am very happy to discuss anything affecting your ability to work or your wellbeing, whether or not it relates directly to the project, and will help you find further support where that is more appropriate.

Meetings

PhD Students can expect scheduled meetings with me at least once per month. These meetings will be a mixture of face-to-face and via video chat or telephone. I am usually contactable for an instant response on every working day.

Work Patterns

Certain tasks in my lab need to occur at set times, and students need to be able to commit to a rota/timetable shared with other members of the team.

Notice Period for Feedback

I need at least 2 weeks' notice to provide feedback on written work of up to 5,000 words.

MIBTP Project Details

Primary supervisor for:

Charting the unknown: Endocytosis in diatoms

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Charting the unknown: Endocytosis in diatoms

Secondary Supervisor(s): Dr Richard Puxty

University of Registration: University of Warwick

BBSRC Research Themes:

Understanding the Rules of Life (Microbiology, Plant Science)

Project Outline

Clathrin-mediated endocytosis (CME) is essential across eukaryotic life, setting how sensitively a cell responds to its environment by controlling the receptors and transporters at its surface. Its mechanisms are well defined in animals and yeast, but we have shown that plants break those rules, bending membranes without actin and using machinery with no animal equivalent (Narasimhan et al., eLife 2020; Johnson et al., PNAS 2021). This raises the question of how well conserved CME is across the tree of life. Diatoms offer the vital missing comparison: an independent branch that diverged from both animals and plants, produces around a fifth of the oxygen on Earth, and whose endocytic machinery has never been characterised.

We have generated Phaeodactylum tricornutum lines expressing fluorescently tagged clathrin and captured the first images of single endocytic events in a living diatom. This project will build on that foundation to characterise diatom CME and compare it directly with plants and animals.

Objectives

Quantify the dynamics, density and spatial organisation of single endocytic events in living P. tricornutum, using live super-resolution microscopy and automated image analysis.
Identify which core endocytic components are conserved in diatoms, using comparative genomics, fluorescence and electron microscopy to determine their physiological roles.
Determine how endocytic dynamics respond to environmental stresses relevant to ocean change, including salinity, temperature and nutrient limitation.

This project will give you training across quantitative imaging and analysis, molecular biology and comparative cell biology, while delivering the first mechanistic account of endocytosis in diatoms and revealing which principles of this fundamental eukaryotic process are truly universal.

Bending the rules: How plants bend endocytic membranes without actin

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Bending the rules: How plants bend endocytic membranes without actin

Secondary Supervisor(s): Professor Séamus Holden

University of Registration: University of Warwick

BBSRC Research Themes:

Sustainable Agriculture and Food (Plant and Crop Science)
Understanding the Rules of Life (Plant Science)

Project Outline

Plants control their sensitivity to the environment by regulating how many receptors and transporters sit on the cell surface, a process mediated by clathrin-mediated endocytosis. This removes the receptor by bending the plasma membrane inwards, against extreme opposing turgor pressure, to create a spherical vesicle. We have shown that plants do this without actin, overturning a cell biology dogma established in animals and yeast (Narasimhan and Johnson et al., eLife 2020), and that they depend instead on the TPLATE complex (Johnson et al., PNAS 2021). However, the membrane bending machinery remains unknown.

This project will test a family of candidate membrane-remodelling proteins, asking how they deform the membrane, and how they perform when environmental stress alters the mechanics of the cell. Using quantitative imaging, molecular biology and in vitro reconstitution assays you will achieve the following objectives:

Objectives

Define the recruitment of the candidate proteins at single endocytic events relative to TPLATE and clathrin, using live super-resolution microscopy in intact Arabidopsis.
Determine whether disrupting candidate function alters endocytic structure morphology, using inducible dominant-negative mutants with electron microscopy.
Test the membrane-bending capacity of the recombinant proteins directly, using liposome tubulation assays and transmission electron microscopy.
Establish how salt, osmotic and temperature stress affect candidate recruitment and endocytic efficiency, and whether specific family members confer robustness.

Together, this project will give you training across cell biology and biophysics using state-of-the-art methodologies, while revealing the cell biology underlying plant-environmental interactions and how a universal eukaryotic process has been solved differently across evolution.