Professor Rick Lewis
Prof of Structural Biology
- Email: email@example.com
- Telephone: +44 (0) 191 208 5482
- Fax: +44 (0) 191 208 7424
- Personal Website: http://sbl.ncl.ac.uk
- Address: Institute for Cell and Molecular Biosciences
The Medical School
University of Newcastle
3rd Floor Catherine Cookson Building
BA (Hons) Biochemistry, University of Oxford, 1991
D. Phil. Biochemistry, University of Oxford, 1994
The main component of research in this group is in the determination of macromolecular structures by X-ray crystallography. However, since not all proteins crystallize, every effort is made to complete our understanding of how proteins function by utilizing other methods, such as microbial genetics, monitoring protein:ligand interactions by biochemical and biophysical methods, electron microscopy and bioinformatics.
Variations in environmental factors, such as reduced aeration, extremes of temperature and the availability of essential nutrients, restrict microbial growth. As a result, bacteria spend much of their life cycle in stationary phase. The requirement for acclimatisation to the environment has forced bacteria to develop a series of complex adaptive responses to stress. One of the initial responses to stress of some Gram+ bacteria, including Bacillus subtilis, is to synthesise a large and diverse family of ?B-dependent general stress proteins. ?B is an alternative RNA polymerase subunit conferring promoter specificity thus directing gene expression in a defined manner.
?B is kept under strict control by the gene products found in the sigB operon, which may be functionally divided into "upstream" and "downstream" modules. Each module comprises an ATP-dependent serine/threonine protein kinase (RsbW, RsbT), a phospho-serine/phospho-threonine protein phosphatase (RsbU, RsbX), and a "switch" protein substrate for the kinase and phosphatase (RsbV, RsbS). In both modules, the kinases also participate in alternative protein:protein recognition events. Together, the binding partner for the kinase and the phosphorylation state of the switch molecules control the activity of ?B.
We utilize a multi-disciplinary approach to studying the proteins and their interactions with small and large ligands, with the focus on determining the X-ray crystal structures of the proteins and larger assemblies. For instance, with collaborators in the Microbiology Unit, University of Oxford, we have established the KM for ATP and KI for ADP of RsbW, the stoichiometry of the RsbW:?B and RsbW:RsbV complexes, the affinity of RsbW for its two alternative partners and the concentration of these three proteins in the cell, before and during stress. We have crystallized fragments of rsbU that encode the N-terminal or C-terminal domains, with crystals of N-RsbU diffracting X-rays to at least 1.6 Å. This structure has recently been solved by selenomethionyl MAD, revealing a dimeric structure comprised of two 4-helical bundles. We are replacing the functional copy of rsbU in the chromosome with a truncated form, encoding solely the catalytic domain, and monitoring ?B activity in the cell by fusing a reporter gene, lacZ, to a ?B-dependent gene. It is our belief that the function of N-RsbU is in molecular recognition and recruitment of the stimulatory factor, the kinase RsbT, and in the (de)regulation of the phosphatase activity of RsbU. We are determining the kinetic and equilibrium constants for RsbT and RsbU in order to map the RsbT-binding surface in RsbU. Intriguingly, the human pathogen Staphylococcus aureus encodes a ?B regulon that is similar to that of B. subtilis, but does not encode an RsbT orthologue, and thus the regulation of RsbU must differ in this organism. This is an interesting difference in physiology between phylogenetically closely-related members of the same bacterial group, which we will investigate biochemically as well as structurally.
In contrast, the alternative binding partner for RsbT is a large, approximately megadalton-sized complex formed between RsbR and RsbS, evidence for the existence of which in vivo is accumulating. We are examining this structure by cryo electron microscopy and single particle analysis. The differences between the structures of the RsbR:RsbS complex and the kinase-recruitment domain of RsbU in the context of molecular recognition by RsbT are the focus of current thinking. They contrast dramatically in terms of size. The likely functions of the RsbR paralogs in B. subtilis are the subject of further thought, and perhaps here bioinformatics will be a useful tool to study these proteins.
The structural biology group in the School of Cell and Molecular Biosciences is being established in the summer of 2003. We will have state-of-the art X-ray and computing facilities in a newly refurbished lab. The group will be small initially, and tightly focused, with expertise present in many aspects of structural biology. From October, it is expected to number 8 in total, comprising a mixture of PIs, postdocs, postgrads and a research technician. More details will be posted here when appropriate, including details of on-going collaborative research with colleagues within the school. There are no posts available at the moment, but informal enquiries to R.J.L. (firstname.lastname@example.org) are always welcome.
Wellcome Trust, BBSRC, Royal Society
- Cleverley RM, Rismondo J, Lockhart-Cairns MP, vanBentum P, Egan AJF, Vollmer W, Halbedel S, Baldock C, Breukimk E, Lewis RJ. Subunit arrangement in GpsB a regulator of cell wall biosynthesis. Microbial Drug Resistance 2016, 22(6), 1-15.
- Harris JR, Lewis RJ. The collagen type I segment long spacing (SLS) and fibrillar forms: Formation by ATP and sulphonated diazo dyes. Micron 2016, 86, 36-47.
- Peters K, Kannan S, Rao VA, Biboy J, Vollmer D, Erickson SW, Lewis RJ, Young KD, Vollmer W. The redundancy of peptidoglycan carboxypeptidases ensures robust cell shape maintenance in Escherichia coli. mBio 2016, 7(3), e00819-16.
- Wilson WC, Hornig-Do HT, Bruni F, Chang JC, Jourdain AA, Martinou JC, Falkenberg M, Spåhr H, Larsson NG, Lewis RJ, Hewitt L, Baslé A, Cross HE, Tong L, Lebel RR, Crosby AH, Chrzanowska-Lightowlers ZMA, Lightowlers RN. A human mitochondrial poly(A) polymerase mutation reveals the complexities of post-transcriptional mitochondrial gene expression. Human Molecular Genetics 2014, 23(23), 6345-6355.
- Mehne FM, Schroder-Tittmann K, Eijlander RT, Herzberg C, Hewitt L, Kaever V, Lewis RJ, Kuipers OP, Tittmann K, Stulke J. Control of the Diadenylate Cyclase CdaS in Bacillus subtilis: An Autoinhibitory Domain Limits c-di-AMP Production. Journal of Biological Chemistry 2014, 289, 21098-21107.
- Muller M, Reiss S, Schluter R, Mader U, Beyer A, Reiss W, Marles-Wright J, Lewis RJ, Pfortner H, Volker U, Riedel K, Hecker M, Engelmann S, Pane-Farre J. Deletion of membrane-associated Asp23 leads to upregulation of cell wall stress genes in Staphylococcus aureus. Molecular Microbiology 2014, 93(6), 1259-1268.
- Jean NL, Bougault CM, Lodge A, Derouaux A, Callens G, Egan AJF, Ayala I, Lewis RJ, Vollmer W, Simorre J-P. Elongated structure of the outer-membrane activator of peptidoglycan synthesis LpoA: Implication for PBP1A stimulation. Structure 2014, 22(7), 1047-1054.
- Mickiewicz KM, Gays F, Lewis RJ, Brooks CG. Mutagenesis of Ly49B Reveals Key Structural Elements Required for Promiscuous Binding to MHC Class I Molecules and New Insights into the Molecular Evolution of Ly49s. Journal of Immunology 2014, 192(4), 1558-1569.
- Cleverley RM, Barrett JR, Baslé A, Bui NK, Hewitt L, Solovyova A, Xu Z-Q, Daniel RA, Dixon NE, Harry EJ, Oakley AJ, Vollmer W, Lewis RJ. Structure and function of a spectrin-like regulator of bacterial cytokinesis. Nature Communications 2014, 5, 5421.
- Hoyland CN, Aldridge C, Cleverley RM, Duchêne MC, Minasov G, Onopriyenko O, Sidiq K, Stogios PJ, Anderson WF, Daniel RA, Savchenko A, Vollmer W, Lewis RJ. Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure 2014, 22(7), 949-960.
- Diethmaier C, Newman JA, Kovacs AT, Kaever V, Herzberg C, Rodrigues C, Boonstra M, Kuipers OP, Lewis RJ, Stulke J. The YmdB Phosphodiesterase Is a Global Regulator of Late Adaptive Responses in Bacillus subtilis. Journal of Bacteriology 2014, 196(2), 265-275.
- Harris JR, Soliakov A, Lewis RJ. In vitro fibrillogenesis of collagen type I in varying ionic and pH conditions. Micron 2013, 49, 60-68.
- Newman JA, Lewis RJ. Exploring the role of SlrR and SlrA in the SinR epigenetic switch. Communicative & Integrative Biology 2013, 6(6), e25658-1-e25658-3.
- Newman JA, Rodrigues CA, Lewis RJ. Molecular Basis of the Activity of SinR Protein, the Master Regulator of Biofilm Formation in Bacillus subtilis. Journal of Biological Chemistry 2013, 288(15), 10766-10778.
- Liebal UW, Millat T, Marles-Wright J, Lewis RJ, Wolkenhauer O. Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. BMC Systems Biology 2013, 7(1), 3.
- Harris JR, Soliakov A, Lewis RJ, Depoix F, Watkinson A, Lakey JH. Alhydrogel® adjuvant, ultrasonic dispersion and protein binding: A TEM and analytical study. Micron 2012, 43(2-3), 192-200.
- Eberhardt A, Hoyland CN, Vollmer D, Bisle S, Cleverley RM, Johnsborg O, Havarstein LS, Lewis RJ, Vollmer W. Attachment of capsular polysaccharide to the cell wall in Streptococcus pneumoniae. Microbial Drug Resistance 2012, 18(3), 240-255.
- Newman JA, Hewitt L, Rodrigues C, Solovyova AS, Harwood CR, Lewis RJ. Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. Journal of Molecular Biology 2012, 416(1), 121-136.
- Mckee LS, Pena MJ, Rogowski A, Jackson A, Lewis RJ, York WS, Krogh KBRM, Vikso-Nielsen A, Skjot M, Gilbert HJ, Marles-Wright J. Introducing endo-xylanase activity into an exo-acting arabinofuranosidase that targets side chains. Proceedings of the National Academy of Sciences 2012, 109(17), 6537-6542.
- Tan HL, Glen E, Topf A, Hall D, O'Sulliyan JJ, Sneddon L, Wren C, Avery P, Lewis RJ, ten Dijke P, Arthur HM, Goodship JA, Keavney BD. Nonsynonymous variants in the SMAD6 gene predispose to congenital cardiovascular malformation. Human Mutation 2012, 33(4), 720-727.
- Lehnik-Habrink M, Lewis RJ, Mader U, Stulke J. RNA degradation in Bacillus subtilis: an interplay of essential endo- and exoribonucleases. Molecular Microbiology 2012, 84(6), 1005-1017.
- Pagett HE, Abrahams JL, Bones J, O'Donoghue N, Marles-Wright J, Lewis RJ, Harris JR, Caldwell GS, Rudd PM, Clare AS. Structural characterisation of the N-glycan moiety of the barnacle settlement-inducing protein complex (SIPC). Journal of Experimental Biology 2012, 215(7), 1192-1198.
- Pitts AC, Tuck LR, Faulds-Pain A, Lewis RJ, Marles-Wright J. Structural insight into the Clostridium difficile ethanolamine utilisation microcompartment. PLoS ONE 2012, 7(10), e48360.
- Quin MB, Berrisford JM, Newman JA, Baslé A, Lewis RJ, Marles-Wright J. The Bacterial Stressosome: A Modular System that Has Been Adapted to Control Secondary Messenger Signaling. Structure 2012, 20(2), 350-363.
- Debieux CM, Dridge EJ, Mueller CM, Splatta P, Paszkiewicza K, Knight I, Florance H, Love J, Titball RW, Lewis RJ, Richardson DJ, Butler CS. A bacterial process for selenium nanosphere assembly. Proceedings of the National Academy of Sciences of the United Status of America 2011, 108(33), 13480-13485.
- Montanier CY, Correia MA, Flint JE, Zhu Y, Baslé A, McKee LS, Prates JA, Polizzi SJ, Coutinho PM, Lewis RJ, Henrissat B, Fontes CM, Gilbert HJ. A novel, noncatalytic carbohydrate-binding module displays specificity for galactose-containing polysaccharides through calcium-mediated oligomerization. Journal of Biological Chemistry 2011, 286(25), 22499-22509.
- Kawai Y, Marles-Wright J, Cleverley RM, Emmins R, Ishikawa S, Kuwano M, Heinz N, Bui NK, Hoyland CN, Ogasawara N, Lewis RJ, Vollmer W, Daniel RA, Errington J. A widespread family of bacterial cell wall assembly proteins. EMBO Journal 2011, 30(24), 4931-4941.
- Cuskin F, Solovyova AS, Lewis RJ, Race PR. Crystallization and preliminary X-ray analysis of the bacillaene synthase trans-acting acyltransferase PksC. Acta Crystallographica. Section F: Structural Biology and Crystallization Communications Online 2011, 67(4), 464-466.
- Tan HL, Glen EA, Topf AL, Hall DH, O'Sullivan JJ, Sneddon L, Wren C, Avery P, Lewis RJ, ten Dijke P, Arthur HM, Goodship JA, Keavney BD. Non-synonymous SMAD6 mutations impaired inhibition of BMP signalling in patients with congenital cardiovascular malformation. In: Heart: Annual Conference of the British Cardiovascular Society (BCS). 2011, Manchester, UK: BMJ Group.
- Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, Herzberg C, Commichau FM, Lewis RJ, Stulke J. RNase Y in Bacillus subtilis: a Natively Disordered Protein That Is the Functional Equivalent of RNase E from Escherichia coli. Journal of Bacteriology 2011, 193(19), 5431-5441.
- Correia MA, Mazumder K, Bras JL, Firbank SJ, Zhu Y, Lewis RJ, York WS, Fontes CM, Gilbert HJ. Structure and Function of an Arabinoxylan-specific Xylanase. Journal of Biological Chemistry 2011, 286(25), 22510-22520.
- Cartmell A, McKee LS, Pena MJ, Larsbrink J, Brumer H, Kaneko S, Ichinose H, Lewis RJ, Vikso-Nielsen A, Gilbert HJ, Marles-Wright J. The Structure and Function of an Arabinan-specific α-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases. Journal of Biological Chemistry 2011, 286(17), 15483-15495.
- Marles-Wright J, Lewis RJ. The structure of a D-lyxose isomerase from the sigma(B) regulon of Bacillus subtilis. Proteins 2011, 79(6), 2015-2019.
- Newman JA, Hewitt L, Rodrigues C, Solovyova A, Harwood CR, Lewis RJ. Unusual, dual endo- and exonuclease activity in the degradosome explained by crystal structure analysis of RNaseJ1. Structure 2011, 19(9), 1241-1251.
- Schirner K, Marles-Wright J, Lewis RJ, Errington J. Distinct and essential morphogenic functions for wall- and lipo-teichoic acids in Bacillus subtilis. EMBO Journal 2009, 28(7), 830-842.
- Montanier C, van Bueren AL, Dumon C, Flint JE, Correia MA, Prates JA, Firbank SJ, Lewis RJ, Grondin GG, Ghinet MG, Gloster TM, Herve C, Knox JP, Talbot BG, Turkenburg JP, Kerovuo J, Brzezinski R, Fontes CMGA, Davies GJ, Boraston AB, Gilbert HJ. Evidence that family 35 carbohydrate binding modules display conserved specificity but divergent function. Proceedings of the National Academy of Sciences 2009, 106(9), 3065-3070.
- Emami K, Topakas E, Nagy T, Henshaw J, Jackson KA, Nelson KE, Mongodin EF, Murray JW, Lewis RJ, Gilbert HJ. Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system. Journal of Biological Chemistry 2009, 284(2), 1086-1096.
- Pane-Farre J, Jonas B, Hardwick SW, Gronau K, Lewis RJ, Hecker M, Engelmann S. Role of RsbU in controlling SigB activity in Staphylococcus aureus following alkaline stress. Journal of Bacteriology 2009, 191(8), 2561-2573.
- Dumon C, Varvak A, Wall MA, Flint JE, Lewis RJ, Lakey JH, Morland C, Luginbuhl P, Healey S, Todaro T, DeSantis G, Sun M, Parra-Gessert L, Tan XQ, Weiner DP, Gilbert HJ. Engineering hyperthermostability into a GH11 xylanase is mediated by subtle changes to protein structure. Journal of Biological Chemistry 2008, 283(33), 22557-22564.
- Marles-Wright J, Grant T, Delumeau O, van Duinen G, Firbank S, Lewis P, Murray J, Newman J, Quin M, Race P, Rohou A, Tichelaar W, van Heel M, Lewis RJ. Molecular architecture of the "stressosome," a signal integration and transduction hub. Science 2008, 322(5898), 92-96.
- Firbank S, Wardle J, Heslop P, Lewis RJ, Connolly BR. Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. Journal of Molecular Biology 2008, 381(3), 529-539.
- Gill S, O'Neill R, Lewis RJ, Connolly BA. Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. Journal of Molecular Biology 2007, 372(4), 855-863.
- Marles-Wright J, Lewis RJ. Stress responses of bacteria. Current Opinion in Structural Biology 2007, 17(6), 755-760.
- Hardwick SW, Pané-Farré J, Delumeau O, Marles-Wright J, Hecker M, Lewis RJ. Structural and Functional Characterization of Partner Switching Regulating the Environmental Stress Response in Bacillus subtilis. Journal of Biological Chemistry 2007, 282(15), 11562-11572.
- Dridge EJ, Richardson DJ, Lewis RJ, Butler CS. Developing structure-based models to predict substrate specificity of D-group (Type II) molybdenum enzymes: application to a molybdo-enzyme of unknown function from Archaeglobus fulgidus. Biochemical Society Transactions 2006, 34(1), 118-121.
- Delumeau O, Chen C, Murray J, Yudkin M, Lewis RJ. High-molecular-weight complexes of RsbR and paralogues in the environmental signaling pathway of Bacillus subtilis. Journal of Bacteriology 2006, 188(22), 7885-7892.
- Xie HF, Flint JE, Vardakou M, Lakey JH, Lewis RJ, Gilbert HJ, Dumon C. Probing the Structural Basis for the Difference in Thermostability Displayed by Family 10 Xylanases. Journal of Molecular Biology 2006, 360(1), 157-167.
- Vardakou M, Flint JE, Christakopoulos P, Lewis RJ, Gilbert HJ, Murray JW. A family 10 Thermoascus aurantiacus xylanase utilizes arabinose decorations of xylan as significant substrate specificity determinants. Journal of Molecular Biology 2005, 352(5), 1060-1067.
- Stephenson K, Lewis RJ. Molecular insights into the initiation of sporulation in Gram-positive bacteria: new technologies for an old phenomenon. FEMS Microbiology Reviews 2005, 29(2), 281-301.
- Murray JW, Delumeau O, Lewis RJ. Structure of a nonheme globin in environmental stress signaling. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(48), 17320-17325.
- Pané-Farré J, Lewis RJ, Stülke J. The RsbRST stress module in bacteria: a signalling system that may interact with different output modules. Journal of Molecular Microbiology and Biotechnology 2005, 9(2), 65-76.
- Muchová K, Lewis RJ, Perečko D, Brannigan JA, Ladds JC, Leech A, Wilkinson AJ, Barák I. Dimer-induced signal progation in Spo0A. Molecular Microbiology 2004, 53(3), 829-842.
- Dong TC, Cutting SM, Lewis RJ. DNA-binding studies on the Bacillus subtilis transcriptional regulator and AbrB homologue, SpoVT. FEMS Microbiology Letters 2004, 233(2), 247-256.
- Delumeau O, Dutta S, Brigulla M, Kuhnke G, Hardwick SW, Völker U, Yudkin MD, Lewis RJ. Functional and Structural Characterization of RsbU, a Stress Signaling Phosphatase 2C. Journal of Biological Chemistry 2004, 279(39), 40927-40937.
- Chen C-C, Lewis RJ, Harris R, Yudkin MD, Delumeau O. A supramolecular complex in the environmental stress signaling pathway of Bacillus subtilis. Molecular Microbiology 2003, 49(6), 1657-1669.
- Dutta S, Lewis RJ. Crystallisation and preliminary crystallographic analysis of the kinase-recruitment domain of the PP2C-type phosphatase, RsbU. Acta Crystallographica. Section D: Biological Crystallography 2003, 59(1), 191-193.
- Ladds JC, Muchová K, Blaškovič B, Lewis RJ, Brannigan JA, Wilkinson AJ, Barák I. Response regulator Spo0A from Bacillus subtilis is heterologously phosphorylated in Escherichia coli. FEMS Microbiology Letters 2003, 223(2), 153-157.
- Lewis RJ, Scott DJ, Brannigan JA, Ladds JC, Cervin MA, Spiegelman GB, Hoggett JA, Barák I, Wilkinson AJ. Dimer formation and transcription activation in the sporulation response regulator Spo0A. Journal of Molecular Biology 2002, 316(2), 253-245.
- Muchová K, Kutejová E, Scott DJ, Brannigan JA, Lewis RJ, Wilkinson AJ, Barák I. Oligomerization of the Bacillus subtilis division protein DivIVA. Microbiology 2002, 148(3), 807-813.
- Delumeau O, Lewis RJ, Yudkin MD. Protein-protein interactions that regulate the energy stress activation of σB in Bacillus subtilis. Journal of Bacteriology 2002, 184(20), 5583-5589.
- Ducros VM-A, Lewis RJ, Verma CS, Dodson EJ, Leonard G, Turkenburg JP, Murshudov GN, Wilkinson AJ, Brannigan JA. Crystal structure of GerE, the ultimate transcriptional regulator of spore formation in Bacillus subtilis. Journal of Molecular Biology 2001, 306(4), 759-771.
- Seavers PR, Lewis RJ, Brannigan JA, Wilkinson AJ. Crystallisation and preliminary X-ray analysis of the sporulation factor SpoIIAA in both its native and phosphorylated forms. Acta Crystallographica 2001, D57(2), 292-295.
- Lewis RJ, Brannigan JA, Barák I, Wilkinson AJ. Lessons and questions from the structure of the Spo0A activation domain: Response. Trends in Microbiology 2001, 9(4), 150-151.
- Seavers PR, Lewis RJ, Brannigan JA, Verschueren KHG, Murshudov GN, Wilkinson AJ. Structure of the Bacillus cell fate determinant SpoIIAA in phosphorylated and unphosphorylated forms. Structure 2001, 9(7), 605-614.
- Johnson LN, Lewis RJ. The structural basis for control by phosphorylation. Chemical Reviews 2001, 101(8), 2209-2242.