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Staff Profile

Dr Kevin Whitley

Lecturer in Microbiology

Background

I’m a biophysicist working at the intersection of single-molecule biophysics, nanotechnology, and bacterial cell biology. I try to understand how the proteins inside bacteria function together as natural 'nanomachines' to complete complex tasks like dividing the cell and building their cell walls. Both of these complex tasks - cell division and cell wall biosynthesis - are major targets for antibiotics.

Background:

Postdoctoral Research Associate  2017 - 2022

Delft University of Technology, Bionanoscience Department

Newcastle University, Centre for Bacterial Cell Biology

Supervisors: Cees Dekker (Delft), Séamus Holden (Newcastle)

My postdoc was an exciting and unique opportunity in that it was not only shared between two labs with complementary expertise in two different countries. At TU Delft, I used nanofabrication and soft lithography to design and construct microfluidic devices for immobilizing bacterial cells vertically, then used bespoke microscopes at Newcastle University to investigate the dynamics of the essential bacterial 'cytoskeleton' protein FtsZ and how this is coordinated with biosynthesis of the bacterial cell wall in live cells.

PhD (Biophysics and Computational Biology) 2010 - 2017

University of Illinois at Urbana-Champaign, Department of Physics

Supervisor: Yann R. Chemla

During my PhD, I had two broad research directions, both involving use of an instrument combining fluorescence with high-resolution optical tweezers (a.k.a. “fleezers“). One research direction was investigating the elasticity and hybridization kinetics of ultrashort nucleic acids (DNA and RNA), while the other was investigating the detailed mechanisms of the bacterial helicases UvrD and Rep (helicases are a type of 'motor protein' that unwinds the DNA double helix).

BSc (Biochemistry and Molecular Biophysics) 2006 - 2010

University of Arizona, Department of Chemistry and Biochemistry

Supervisor: Michael A. Cusanovich

I worked in the lab of Michael Cusanovich for ~2.5 years as an undergraduate. My main project was to investigate the electron transport chain of the photosynthetic bacterium Rhodobacter capsulatus by characterizing point mutants of the cytochrome bc1 complex in vitro.

Research

Overall, my group is interested in how biomolecules inside bacteria work together as natural ‘nanomachines’ to perform the impressive engineering tasks of expanding and dividing cells.


Biosynthesis of the bacterial cell wall:

The emergence and spread of antibiotic-resistant bacteria is a major global health problem. New antibiotics—and other strategies of prevention and treatment—are urgently needed to combat this growing threat. Most successful antibiotics in clinical use (e.g. penicillin) target some aspect of bacterial cell wall biosynthesis, both because bacteria generally need their walls to survive and because the bacterial proteins involved are shared across many species.

The bacterial cell wall is a mesh-like structure that protects them from their environments and prevents them from exploding due to high internal pressure. For a bacterial cell to grow, it needs to expand this wall. This involves many biomolecules working together to build and remodel the wall carefully without the cell bursting. In some ways this is like expanding the hull of a submarine while it's under pressure deep underwater.

Over the past 15 years or so, research has shown that the proteins involved in building the cell wall are highly dynamic inside the cell, and that these dynamics are an inseparable part of how they work. The enzymes building the wall move along with the bacterial 'cytoskeleton' and numerous regulatory factors to synthesize the wall across the whole cell with complicated coordination.

In my group, we are expanding our knowledge of how bacteria have evolved different strategies to build their cell walls using the bacterium Corynebacterium glutamicum. This bacterium is used widely in biotechnology for the mass production of amino acids and is a close relative of the major human pathogens Corynebacterium diphtheriae and Mycobacterium tuberculosis. We use C. glutamicum as a model for studying this entire clade of bacteria, which have evolved a radically different mode of growth from the most commonly studied model species. We look at how they build their cell walls using single-molecule fluorescence microscopy and our newly-developed vertical cell imaging setup.


Mechanism of bacterial cell division:

Cell division is a fundamental requirement for bacteria and therefore also a key antibiotic target. It is also a remarkable feat of engineering by the cell: a collection of nano-scale proteins must coordinate their activities over a micrometer scale (1000x larger) to build a cross-wall (septum) down the middle of the cell against heavy outward pressure.

During my postdoc, I and colleagues showed how the filaments of the bacterial cytoskeleton protein FtsZ dynamically assemble into a division ring through 'treadmilling' dynamics, and how the enzymes synthesizing the cell wall coordinate their catalytic activity with these dynamics using new microscopy methods to image the bacterial division ring with unprecedented sensitivity.

As with our understanding of bacterial cell wall biosynthesis, in my group we are expanding our knowledge of how bacteria divide to the understudied phylum Actinobacteria using Corynebacterium glutamicum as a model system. Actinobacteria lack many of the division factors that are essential in nearly all other bacteria, and have several new factors whose functions remain unknown. We look at how these bacteria have evolved new mechanisms for division, with implications for advances in both biotechnology and medicine.


Method development in bacterial microscopy:

The field of microbiology owes its existence to the development of the microscope by Antoni van Leeuwenhoek in the 17th century. Since then, microscope technology has improved substantially, especially recently with advances in microscope engineering, chemistry of fluorescent dyes, and image processing / analysis methods.

I and colleagues contributed to this during my postdoc through the development of a new method called VerCINI (Vertical Cell Imaging by Nanostructured Immobilization) and its sister method μVerCINI (microfluidic VerCINI), where we confine bacteria vertically in bacteria-shaped 'micro-holes' (made from nanofabricated silicon wafers). This method enables us to image any process along the short axes of bacteria (e.g. division) more easily and with higher resolution than with conventional approaches.

An often overlooked and underappreciated aspect of modern microscopy is image analysis - that is, the ability to take microscopy images or videos and somehow extract useful, quantitative information from them (actually, this is the majority of the work I do!). I have written a few software packages for quantitative analysis of bacterial cell division dynamics (among other things), and in my current group we continue to push for greater precision and throughput in image analysis of our microscopy data.

Teaching

Fellow of the Higher Education Academy (FHEA)

BGM3057 - Integrated Biochemistry (Module Leader)

MMB8016 - Molecular Microbiology

CMB3000 - Stage 3 Research Projects

Publications
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