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Rick Lewis' Research Interests

I am Professor of Structural Biology at the Institute for Cell and Molecular Biosciences, Newcastle University, where I have been based since 2003. In previous positions I worked in equivalent groups in York and in Oxford. I run an active research group, teach to all years in our undergraduate degree programs and to our postgraduate MRes students, and participate in various administrative duties across the Institute and the wider University.

The primary goal of the lab is to solve structures of proteins and protein complexes from the Gram+ model bacterium, Bacillus subtilis, using X-ray crystallography. I have studied this organism, and its response to environmental challenge, for nearly 20 years. More recently, we have concentrated on defining key protein complexes in central carbon catabolism, in RNA degradation and in osmoprotection. A major focus of the lab's current activities is in the co-ordination of events on either side of the membrane during cell division and cell growth, and how these impact on the biosynthesis of the bacterial cell wall. Other than crystallography, we have used electron microscopy to study large macromolecules that have not yielded well-diffracting crystals. Of course, solving the structure of interesting proteins does not always answer all the questions one might ask, and so we try to back up our crystallographic data with biochemistry, biophysics, cell biology and genetics. Some of these disciplines require us to collaborate, and we have an active network of friends across Europe that extends as far as Australia.

In regard to current projects, the lab enjoys BBSRC funds in these areas:

Bacterial cell wall

The cell wall is a fundamental defining structure in a wide range of Gram positive bacteria. It acts as a protective layer and defines the shape of the cell. It interacts with host defense systems during infection; many fragments of cell wall are recognised by different elements of the innate and adaptive arms of the immune system. The cell wall is also the target for our best antibiotics; beta-lactams like penicillins and cephalosporins, and glycopeptides such as vancomycin, which sequesters a key precursor for wall synthesis. The major component of the wall of most eubacteria is peptidoglycan, the glycan building block of which is a disaccharide. Short peptides are attached to one of the sugars, and these cross-link to form a mesh-like molecule covering the whole surface of the cell. Peptidoglycan is chemically modified in the formation of the mature cell wall by the covalent attachment of wall teichoic acids and by the presence of lipoteichoic acids, which are not covalently attached to peptidoglycan, but instead are associated with the lipid membrane. Steps for the biosynthesis of peptidoglycan and the teichoic acids take place both inside and outside the cell, raising the question of how these processes are co-ordinated. Furthermore, as the cell divides, new cell wall must be deposited at the division septum, and therefore the cell wall synthetic machinery must co-ordinate with the activity of the divisome. Finally, the wall must be a robust, yet dynamic structure, increasing in size as the bacterium grows to avoid placing restrictions on cellular growth. Our goal is to understand the synthesis and the assembly of the cell wall in Bacillus subtilis and how it is used to adapt the organism to the challenges of a variable and potentially hostile environment.

We have recently solved the structure of LtaS, a key enzyme in lipoteichoic acid synthesis. LtaS makes long chains of poly-glycerolphosphate from single glycerolphosphate molecules. In its active site we found a phosphorylated threonine, the expected nucleophile in the polymerisation reaction. The phosphate can be seen in the cleft on the enzyme's surface in the figure below.

We published this work with our colleagues in the Centre for Bacterial Cell Biology in 2009:

    Schirner, K., Marles-Wright, J., Lewis, R.J. & Errington, J. (2009) Distinct and essential morphogenic functions for wall- and lipo-teichoic acids in Bacillus subtilis. EMBO J 28, 830-842.[Pubmed]

We have also been investigating the modification of peptidoglycan by wall teichoic acids. These polymers are present in large quantities, often equal or exceeding that of peptidoglycan itself. The last step in cell wall assembly is the formation of a phosphodiester bond between the teichoic acid and one of the sugars of peptidoglycan, thus connecting the two major polymers in building the mature, functional cell wall. We have solved several structures of the defining members of the enzyme class that ligates wall teichoic acid and peptidoglycan. The structures unexpectedly contained mimics of the reaction substrates and products, enabling us to visualise better the reaction pathway for these enzymes.

This part of the cell wall project study was yet again a collaborative effort with colleagues in CBCB:

    Kawai Y., Marles-Wright J., Cleverley R.M., Emmins R., Ishikawa S., Kuwano M., Heinz N., Bui N.K., Hoyland C.N., Ogasawara N., Lewis R.J., Vollmer W., Daniel R.A., Errington J. (2011) A widespread family of bacterial cell wall assembly proteins. EMBOJ 30, 4931-41[Pubmed]
    Eberhardt A, Hoyland CN, Vollmer D, Bisle S, Cleverley RM, Johnsborg O, Håvarstein LS, Lewis RJ, Vollmer W (2012) Attachment of capsular polysaccharide to the cell wall in Streptococcus pneumoniae. Microb Drug Resist. 18, 240-55. [Pubmed]

Current co-workers: Robert Cleverley, Christopher Hoyland, Vincent Rao and Arnaud Basle.

Collaborators: Waldemar Vollmer, Jeff Errington, Richard Daniel (all CBCB, Newcastle University); Eefjan Breukink (Utrecht); Tanja Schneider (Bonn); Chandra Verma (Singapore).


Systems biology

In recent years it has become clear that many key aspects of physiology are regulated not by discrete enzymes, but by multi-component complexes. Consequently, we have been engaged in a pan-European consortium to identify and to validate the role of protein complexes in central carbon metabolism, in RNA degradation and in adaptive responses. In metabolism, macromolecular complexes are likely to confer special properties to the reactions catalysed by metabolic enzymes. For instance, maintaining two enzymes that catalyse consecutive steps in a biochemical pathway in close proximity will increase the rate at which substrate A is converted to product C via intermediate B, through the process of substrate chanelling. Moreover, some of the enzymes in central carbon catabolism associate with ribonucleases to form a large protein complex called the RNA degradosome, which links metabolism to RNA processing. We have studied the interactions between proteins at the heart of the degradosome and solve structures of individual metabolic enzymes and RNases. The characterisation of the binding affinities and rates provide vital information in the mathematical modelling (the systems biology approach) of the relevant pathway. Whilst we are characterising the protein complexes, we also try to study their structures and analyse them in the context of protein:protein contacts.

    Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J. (2012) RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Mol Microbiol. 84, 1005-17. [Pubmed]
    Newman, J.A., Hewitt, L., Rodrigues, C., Solovyova, A.S., Harwood, C.R., Lewis RJ. (2012) Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. J. Mol. Biol. 416, 121-36. [Pubmed]
    Newman, J.A., Hewitt, L., Rodrigues, C., Solovyova, A., Harwood, C.R. & Lewis, R.J. (2011) Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNase J1. Structure 19, 1241-51. [Pubmed]

The timely and appropriate response to fluctuating environments is fundamental to the survival of all living organisms. Bacteria survive changes to their environments by adopting a number of survival strategies. For instance, the bacterium may develop motility and swim along a nutrient gradient; take up genetic material in the hope that the foreign DNA provides a competitive advantage; differentiate into a spore, a hardy, dormant cell that awaits more favourable growth conditions, when it will germinate; communicate and collaborate with neighbouring cells to form a biofilm or up-regulate the transcription of stress-responsive genes. We are studying the developmental choices made by this bacterium, including biofilm development and the general stress response, which is controlled by the stressosome, a >1.5 MDa protein complex that co-ordinates the response to environmental stress. We solved the structure of this by EM methods in 2008 and are collaborating with others to understand the activation process at a structural, temporal and systems-level.

    Marles-Wright, J., Grant, T., Delumeau, O., van Duinen, G., Firbank, S.J., Lewis, P.J., Murray, J.W., Newman, J.A., Quin, M.B., Rohou, A., Tichelaar, W., van Heel, M. & Lewis, R.J. (2008) Molecular architecture of the "stressosome," a signal integration and transduction hub. Science 322, 92-96.[Pubmed]

Current co-workers: Joseph Newman, Cecilia Rodrigues, Lorraine Hewitt.

Collaborators: Jörg Stülke (Göttingen); Jan Pané-Farré (Greifswald); Ulf Liebal (Rostock); Gerald Seidel (Ehrlangen); Oscar Kuipers (Groningen); Malkhey Verma (Manchester); Christine Ziegler (Frankfurt); Gottfried Otting (Canberra); the BaCell SysMO2 network.


Archaeal DNA polymerases

Replication of the genome is a fundamental requirement for any living organism. Replication of the genome must be carried out in a timely but accurate manner to ensure that as cells divide, each cell contains a faithful copy of the genome. Central to this process is the replicative DNA polymerase that carries out the copying process. Replicative polymerases contain two active sites, one for primer extension and a second to remove incorrectly incorporated nucleotides from the newly formed primer strand. This second enzymatic activity is referred to as proof reading; the replicative polymerases can correct their own mistakes. The balance between these two activities helps govern the speed and accuracy of the DNA replication process. The polymerase is assisted by the sliding clamp, which travels with the polymerase, tethering the polymerase to the DNA. Whilst the polymerase remains associated with the sliding clamp as it switches between these two activities, it is not known how the association between the two proteins changes. Moreover, the archaeal replicative DNA polymerases uniquely exhibit a method for trapping deaminated bases prior to their reaching the polymerising site, thus preventing mutations from entering the genome. The polymerase has >100 fold higher affinity for DNA containing a deaminated base than standard DNA. This property has been exploited in a recent structural publication from this lab and is also exploited in current experiments testing the balance between the two polymerase activities and in other properties of the archaeal enzymes, with a view to improving their performance in the polymerase chain reaction.

    Firbank, S.J., Wardle, J., Heslop, P, Lewis, R.J. & Connolly, B.A. (2008) Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. J. Mol. Biol. 381, 529-539.[Pubmed]

Current co-workers: Thomas Kinsman.

Collaborators: Bernard Connolly (Newcastle).


Collaborative research

We also collaborate with others in ICaMB, such as Harry Gilbert in studying the molecular basis of protein:carbohydrate interactions, Jeremy Lakey in outer membrane proteins and Robin Harris on collagen and cholesterol. We also work with others further afield, such as Peter Lewis in Newcastle, New South Wales, Australia, on RNA polymerase. A selection of collaborative papers can be found here:

    McKee LS, Peña MJ, Rogowski A, Jackson A, Lewis RJ, York WS, Krogh KB, Viksø-Nielsen A, Skjøt M, Gilbert HJ, Marles-Wright J. (2012) Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains. Proc Natl Acad Sci U S A. 109, 6537-42. [Pubmed]
    Harris, J.R., Soliakov, A., Lewis, R.J., Depoix, F., Watkinson, A. & Lakey, J.H. (2011) Alhydrogel® adjuvant, ultrasonic dispersion and protein binding: a TEM and analytical study. Micron 43, 192-200[Pubmed]
    Yang, X., Molimau, S., Doherty, G.P., Marles-Wright, J., Rathnagel, R., Hankamer, B., Lewis, R.J., & Lewis, P.J. (2009) The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA. EMBO Rep. 10, 997-1002.[Pubmed]
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Highlights

February 2014
JBC Best paper of the year 2013 awarded to Pr. Rick Lewis
Read more...

January 2014
2014 is the year of Crystallography
Read more...

January 2014
CCP4 Study Weekend
3-5th of January, Nottingham University Read more...

Contact Info

Newcastle Structural Biology Laboratory
ICAMB, Medical School University of Newcastle Framlington place NE2 4HH, Newcastle upon Tyne, UK

Phone: (191) 222-7436
Fax: (191) 222-7424