Research Theme within School of Biosciences: Molecular Microbiology
X-Ray crystallography and structure: function relationships of bacterial proteins
My laboratory uses X-ray crystallography to study the molecular basis of protein function. We are interested in a variety of bacterial systems - especially those with the potential for antibiotic development. One of these systems involves analysis of the remarkable predatory bacterium Bdellovibrio bacteriovorus (in collaboration with Professor Liz Sockett at Nottingham). Predatory bacteria feed off and eventually kill other bacteria, and thus research into this process has potential therapeutic possibilities. Bdellovibrio is the model predatory organism, and possesses an unusual lifestyle where it enters its prey through the outer membrane and resides in the periplasm. The host cell changes shape (forming a structure termed the "bdelloplast") and the Bdellovibrio cell grows and replicates using material obtained from prey breakdown. Progeny then exit the dead host to start the cycle anew. Host-independent forms of Bdellovibrio may be grown separate from prey in rich media.
We are using X-ray crystallography to study Bdellovibrio proteins with the aim of understanding:
the precise function of proteins involved in predation events
how Bdellovibrio responds to the challenges of intraperiplasmic growth
what specifically regulates the alteration to a host-independent (non-predatory) lifestyle
Many of these proteins are unique to Bdellovibrio, and are thus termed part of the "predatosome". Of course, there is much more to study, not forgetting prey recognition events, membrane entry, bdelloplast formation, host material hydrolysis, predation on biofilms, and signalling/regulation of all of the above!
Reviews on this topic are included in the references below and short summaries can be found at http://en.wikipedia.org/wiki/Bdellovibrio and by downloading the PDF www.sgm.ac.uk/pubs/micro_today/pdf/110805.pdf .
The laboratory has a number of other collaborations and projects ongoing, both within and external to Birmingham.
Figure 1: Bdellovibrio predation lifecycle
Lovering AL, Gretes MC, Safadi SS, Danel F, De Castro L, Page MG, Strynadka NC. Structural Insights into the Anti- Methicillin-Resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole. J Biol Chem. 2012 (Epub)
Anwari K, Webb CT, Poggio S, Perry AJ, Belousoff M, Celik N, Ramm G, Lovering A, Sockett RE, Smit J, Jacobs-Wagner C, Lithgow T. The Evolution of New Protein Subunits of the Bacterial Outer Membrane BAM Complex. Mol Microbiol. 2012 84(5) 832-44
Usha V, Lloyd AJ, Lovering AL, Besra GS. Structure and function of Mycobacterium tuberculosis meso-di aminopimelic acid (DAP) biosynthetic enzymes. FEMS Microbiol Lett. 2012 Feb 16. doi: 10.1111
Pubmed link: http://www.ncbi.nlm.nih.gov/pubmed/22339732
Lerner TR, Lovering AL, Bui NK, Uchida K, Aizawa S, Vollmer W, Sockett RE. Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory Bdellovibrio and Increase Population Fitness. PLoS Pathog. 2012 Feb;8(2):e1002524.
PubMed link: http://www.ncbi.nlm.nih.gov/pubmed/22346754
Lovering AL, Capeness MJ, Lambert C, Hobley L, Sockett RE. The Structure of an unconventional HD-GYP Protein from Bdellovibrio Reveals the Roles of Conserved Residues in This Class of Cyclic-di-GMP Phosphodiesterases. mBio. 2011 Oct 11;2(5).
Lovering AL, Safadi SS, Strynadka NCJ. Structural Perspective of Peptidoglycan Biosynthesis and Assembly. Ann Rev Biochem. 2012 81. Accepted Sept 2011.
Usha V, Gurcha SS, Lovering AL, Lloyd AJ, Papaemmanouil A, Reynolds RC, Besra GS. Identification of novel diphenyl urea inhibitors of Mt-GuaB2 active against Mycobacterium tuberculosis. Microbiology. 2011 157(1) 290-9.
Alderwick LJ, Lloyd GS, Lloyd AJ, Lovering AL, Eggeling L, Besra GS. Biochemical characterization of the Mycobacterium tuberculosis phosphoribosyl-1-pyrophosphate synthetase. Glycobiology. 2011 21(4) 410-25.
Cosgriff S, Chintakayala K, Chim YT, Chen X, Allen S, Lovering AL, Grainger DC. Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA. Mol Microbiol . 2010 77(5) 1289-300.
Lovering AL, Lin LC, Sewell EW, Brown ED, Strynadka NC. Structure of the cell wall teichoic acid polymerase TagF: details of membrane-binding and catalysis. Nature Struct Mol Biol. 2010 17(5) 582-9.
Lovering AL, De Castro L, Strynadka NC. Identification of dynamic structural motifs involved in peptidoglycan glycosyltransfer. J Mol Biol. 2008 Oct 31;383(1):167-77.
Lovering AL, Gretes M, Strynadka NC. Structural details of the glycosyltransferase step of peptidoglycan assembly. Curr Opin Struct Biol. 2008 : 18(5) 534-43.
Lovering AL, Strynadka NC. High-resolution structure of the major periplasmic domain from the cell shape-determining filament MreC. J Mol Biol. 2007 Sep 28;372(4):1034-44.
Ugochukwu E, Lovering AL, Mather OC, Young TW, White SA. The crystal structure of the cytosolic exopolyphosphatase from Saccharomyces cerevisiae reveals the basis for substrate specificity. J Mol Biol. 2007 Aug 24;371(4):1007-21.
Race PR, Lovering AL, White SA, Grove JI, Searle PF, Wrighton CW, Hyde EI. Kinetic and structural characterisation of Escherichia coli nitroreductase mutants showing improved efficacy for the prodrug substrate CB1954. J Mol Biol. 2007 Apr 27;368(2):481-92.
Lovering AL, de Castro LH, Lim D, Strynadka NC. Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis. Science. 2007 Mar 9;315(5817):1402-5.
Lovering AL, De Castro L, Lim D, Strynadka NC. Structural analysis of an "open" form of PBP1B from Streptococcus pneumoniae. Protein Sci. 2006 Jul;15(7):1701-9.
Kim YW, Lovering AL, Chen H, Kantner T, McIntosh LP, Strynadka NC, Withers SG. Expanding the thioglycoligase strategy to the synthesis of alpha-linked thioglycosides allows structural investigation of the parent enzyme/substrate complex. J Am Chem Soc. 2006 Feb 22;128(7):2202-3.
Wilke MS*, Lovering AL*, Strynadka NC. Beta-lactam antibiotic resistance: a current structural perspective. Curr Opin Microbiol. 2005 Oct;8(5):525-33. (*equal authorship)
Ravelli RB, Nanao MH, Lovering A, White S, McSweeney S. Phasing in the presence of radiation damage. J Synchrotron Radiat.2005 May;12(Pt 3):276-84.
Race PR, Lovering AL, Green RM, Ossor A, White SA, Searle PF, Wrighton CJ, Hyde EI. Structural and mechanistic studies of Escherichia coli nitroreductase with the antibiotic nitrofurazone. Reversed binding orientations in different redox states of the enzyme. J Biol Chem. 2005 Apr 8;280(14):13256-64.
Gunawan J, Simard D, Gilbert M, Lovering AL, Wakarchuk WW, Tanner ME, Strynadka NC.Â Structural and mechanistic analysis of sialic acid synthase NeuB from Neisseria meningitidis in complex with Mn2+, phosphoenolpyruvate, and N-acetylmannosaminitol. J Biol Chem. 2005 Feb 4;280(5):3555-63.
Lovering AL, Lee SS, Kim YW, Withers SG, Strynadka NC. Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate. J Biol Chem. 2005 Jan 21;280(3):2105-15.
Searle PF, Chen MJ, Hu L, Race PR, Lovering AL, Grove JI, Guise C, Jaberipour M, James ND, Mautner V, Young LS, Kerr DJ, Mountain A, White SA, Hyde EI. Nitroreductase: a prodrug-activating enzyme for cancer gene therapy. Clin Exp Pharmacol Physiol. 2004 Nov;31(11):811-6
Loschi L, Brokx SJ, Hills TL, Zhang G, Bertero MG, Lovering AL, Weiner JH, Strynadka NC.Â Structural and biochemical identification of a novel bacterial oxidoreductase. J Biol Chem.2004 Nov 26;279(48):50391-400.
Lovering AL, Ride JP, Bunce CM, Desmond JC, Cummings SM, White SA. Crystal structures of prostaglandin D(2) 11-ketoreductase (AKR1C3) in complex with the nonsteroidal anti-inflammatory drugs flufenamic acid and indomethacin. Cancer Res. 2004 Mar 1;64(5):1802-10.
Grove JI, Lovering AL, Guise C, Race PR, Wrighton CJ, White SA, Hyde EI, Searle PF. Generation of Escherichia coli nitroreductase mutants conferring improved cell sensitization to the prodrug CB1954. Cancer Res.2003 Sep 1;63(17):5532-7.
Lovering AL, Hyde EI, Searle PF, White SA. The structure of Escherichia coli nitroreductase complexed withnicotinic acid: three crystal forms at 1.7 A, 1.8 A and 2.4 A resolution. J Mol Biol. 2001 May 25;309(1):203-13.