Dr Richard Daniel
- Email: firstname.lastname@example.org
- Telephone: +44 (0) 191 208 3239
- Fax: +44 (0) 191 208 7424
- Address: The Centre for Bacterial Cell Biology
Baddily Clark Building
Newcastle upon Tyne
Education and qualifications:
10/1996 – 11/2000 D.Phil. (Physiological Sciences) at Sir William Dunn School of Pathology, University of Oxford, Supervisor: Prof. J. Errington
10/1986 – 07/1989 BSc with Hons. (Bacteriology and Molecular Genetics) University of Bristol,
Part II Supervisor: Dr. J Grinsted
2010 - Senior Lecturer, Centre for Bacterial Cell Biology Newcastle University
2006 - 2009 Lecturer, ICaMB, University of Newcastle
2004 – 2006 University Research Lecturer, Sir William Dunn School of Pathology, Oxford University
2000 – 2006 Consultant, Prolysis Ltd, Oxford
2000 – 2004 Senior Research
assistant (RS II), Sir William Dunn School of Pathology, Oxford
1990 - 1999 Research Assistant, Sir William Dunn School of Pathology, Oxford University
1989 – 1990 Medical Laboratory
Scientific Officer, Dept. of Paediatrics, John Radcliffe Hospital,
BBSRC Peer review panel BBSRC Committee B: Plants, Microbes, Food and Sustainability panel since 2012
Management of the CBCB Microscopy facility.
Member of the Bio Imaging committee for the Medical Faculty
Member of the Robotics committee for the Medical Faculty
Current lab members:
Post Graduate Students:
Karzan Sidiq - (international funding)
Jad Sassine - (MC studentship - AMBER project)
Man Chow - (Self funded)
Postdoctoral Research Fellows:
Aurelie Guyet (BBSRC)
Gabriella Henriques (MC visiting fellowship)
VACANCIES - I am always open to informal enquiries for PhD or Post-doctoral positions in this lab, and often find a way to fund good candidates. Please feel free to email me if you are interested (Richard.Daniel@ncl.ac.uk ).
A bacterial cell as a gross simplification is sometimes described as a collection of enzymes and nucleic acid enclosed in a lipid bag. In reality this is far from the truth, the bacterial cell has levels of organisation and complexity comparable to higher organisms, but due the difference in scale these properties were invisible. Recent advances in imaging techniques are just beginning to reveal these complexities that at almost at the limit of resolution for light microscopy and invisible to electron microscopy. Characterising and understanding the processes that generate and maintain this organisation represents the next challenge.
Research in this lab predominantly utilises the Gram-positive bacterium Bacillus subtilis as a model system, but may also use Listeria spp. Corynebacterium glutamicum, Staph. aureus and Strep. pneumonia for comparison due to their interesting morphological diversity. To support this work we are able to utilise a wide range of techniques most of which are available in the Centre.
Currently the main areas of research are focused on:-
The physical properties of the cell envelope of Bacillus subtilis:
The interface the bacterial cell and its environment has an intricate role in biology. It must permit the selective passage of material too and from the cell membrane, but be structurally robust enough to prevent osmotic lysis of the cell, the entry of large toxic molecules and repel the attacks of enzymes and bacteriophages. However it must also be capable for dynamic remodelling to allow the enlargement and division of the cell. Thus an understanding of the composition of the cell wall and the roles of the individual components is critical.
Determination of the composition of the cell wall and how it changes according to the phase of growth or environmental conditions. (K. Sidiq)
Design and characterisation of probes to investigate the bacterial cell wall and its basic physical properties as extracted sacculi as well as in vivo. (Man Chow)
Bacterial cell wall biosynthesis:
Bacterial cell wall helps to maintain cell shape but most importantly it provides protection to the cells, and has been one of the targets for antibiotics. However, the mechanisms involved in cell wall biosynthesis are still poorly understood. Most of the analysis has been restricted to either the biosynthetic pathway required for synthesis of the major cell wall precursors (e.g. mur or mra genes) or the final steps of peptidoglycan synthesis (carried out by penicillin-binding proteins). Very little is known about the intermediate steps whereby the precursors are exported from the cytoplasm to the outside of the cell and incorporated into the existing structure to allow cell enlargement or division. Recent studies have provided evidence for specific complexes, (cytoskeletal structures) central to these events. However, the mechanism and the functional components of these complexes have yet to be clearly defined. Thus, there are many areas to explore, including peptidoglycan precursor export and incorporation, cell wall maturation and degradation, secondary polymer biosynthesis, export and incorporation (e.g. teichoic acids).
Defining the roles of specific PBPs in peptidoglycan synthesis and maturation (A. Guyet)
Constructing strains with the minimum complement of enzymes necessary for normal growth and division (A. Bone and G. Henriques)
Understanding the mechanisms that coordinate peptidoglycan synthesis and degradation, to allow controlled growth and division (A. Guyet)
Determination of antibiotic resistance determinants and their mode of action - primarily focusing on wall active compounds (K. Sidiq)
Biological role of membrane proteins
Following on form the "omic" revolutions, we now have a vast data base of genes that are present in bacteria, but a limited understanding of their biological function. One sub class of proteins that are generally very variable are the membrane spanning proteins, many of which are annotated with potential functions, but not definitive experimental data supports these predictions. To correct this gap in our understanding we are looking at systematic methods to identify the functions of this sub set of proteins using classical genetic techniques combined with robotics. This work is designed to aid the development of the minimal genome by defining genes that are either redundant in function or are unnecessary except under specific condition.
The ultimate objective being the construction of strains with the minimal gene content for viable replication that can be customised with a specific gene complement (set of bio-bricks) to fulfil a specific function.
High throughput genetic manipulation of strains using various selection systems and screening methods for phenotypic characterisation (G. Henriques)
Current teaching at undergraduate and masters level:
MIC2026 Microbial Cell Biology Module Leader
MIC2028 Practical Skills in Medical Microbiology Practical Supervisor
MIC3044 Integrated Microbiology and Immunology Lecturer
MMB8008 Cell Cycle Control and Cell Signalling in Health and Disease Lecturer
Pastoral Tutor for undergraduates in years 1, 2 and 3.
Research project supervision:
Undergraduate project supervisor
MRes and MSci project supervisor
M. Phil supervisor for M. Chow (2014).
PhD supervisor for M. Xu ( D.Phil in Oxford 2008), P. Gamba (2011), A. Doble (2012), S. Moore (2013), K Sidiq (2012-2015), and Jad Sassine (2013-2016).
- Sassine J, Xu M, Sidiq KR, Emmins R, Errington J, Daniel RA. Functional redundancy of division specific penicillin-binding proteins in Bacillus subtilis. Molecular Microbiology 2017, 106(2), 304-318.
- Emami K, Guyet A, Kawai Y, Devi J, Wu LJ, Allenby N, Daniel RA, Errington J. RodA as the missing glycosyltransferase in Bacillus subtilis and antibiotic discovery for the peptidoglycan polymerase pathway. Nature Microbiology 2017, 2, 16253.
- Gamba P, Hamoen LW, Daniel RA. Cooperative Recruitment of FtsW to the Division Site of Bacillus subtilis. Frontiers in Microbiology 2016, 7, 1808.
- Gamba P, Rietkötter E, Daniel RA, Hamoen LW. Tetracycline hypersensitivity of an ezrA mutant links GalE and TseB (YpmB) to cell division. Frontiers in Microbiology 2015, 6, 346.
- 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.
- Domínguez-Cuevas P, Porcelli I, Daniel RA, Errington J. Differentiated roles for MreB-actin isologues and autolytic enzymes in Bacillus subtilis morphogenesis. Molecular Microbiology 2013, 89(6), 1084-1098.
- Wolf D, Dominguez-Cuevas P, Daniel RA, Mascher T. Cell Envelope Stress Response in Cell Wall-Deficient L-Forms of Bacillus subtilis. Antimicrobial Agents and Chemotherapy 2012, 56(11), 5907-5915.
- Halbedel S, Hahn B, Daniel RA, Flieger A. DivIVA affects secretion of virulence-related autolysins in Listeria monocytogenes. Molecular Microbiology 2012, 83(4), 821-839.
- Bulmer DM, Kharraz L, Grant AJ, Dean P, Morgan FJ, Karavolos MH, Doble AC, McGhie EJ, Koronakis V, Daniel RA, Mastroeni P, Khan CMA. The bacterial cytoskeleton modulates motility, type 3 secretion, and colonization in Salmonella. PLoS Pathogens 2012, 8(1), e1002500.
- Fukushima T, Furihata I, Emmins R, Daniel RA, Hoch JA, Szurmant H. A role for the essential YycG sensor histidine kinase in sensing cell division. Molecular Microbiology 2011, 79(2), 503-522.
- 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.
- Leaver M, Dominguez-Cuevas P, Coxhead JM, Daniel RA, Errington J. Life without a wall or division machine in Bacillus subtilis. Nature 2009, 457(7231), 849-853.
- Kawai Y, Daniel RA, Errington J. Regulation of cell wall morphogenesis in Bacillus subtilis by recruitment of PBP1 to the MreB helix. Molecular Microbiology 2009, 71(5), 1131-1144.
- Muñoz-Espín D, Daniel R, Kawai Y, Carballido-López R, Castilla-Llorente V, Errington J, Meijer WJJ, Salas M. The actin-like MreB cytoskeleton organizes viral DNA replication in bacteria. Proceedings of the National Academy of Sciences 2009, 106(32), 13347-13352.
- Gamba P, Veening JW, Saunders NJ, Hamoen LW, Daniel RA. Two-Step Assembly Dynamics of the Bacillus subtilis Divisome. Journal of Bacteriology 2009, 191(13), 4186-4194.
- Bramkamp M, Emmins R, Weston L, Donovan C, Daniel RA, Errington J. A novel component of the division site selection system of Bacillus subtilis and a new mode of action for the division inhibitor MinCD. Molecular Microbiology 2008, 70(6), 1556-1569.
- Valbuena N, Letek M, Ordonez E, Ayala J, Daniel RA, Gil JA, Mateos LM. Characterization of HMW-PBPs from the rod-shaped actinomycete Corynebacterium glutamicum: Peptidoglycan synthesis in cells lacking actin-like cytoskeletal structures. Molecular Microbiology 2007, 66(3), 643-657.
- Deghorain M, Goffin P, Fontaine L, Mainardi J-L, Daniel R, Errington J, Hallet B, Hols P. Selectivity for D-lactate incorporation into the peptidoglycan precursors of Lactobacillus plantarum: Role of Aad, a VanX-like D-alanyl-D-alanine dipeptidase. Journal of Bacteriology 2007, 189(11), 4332-4337.
- Daniel RA, Noirot-Gros M-F, Noirot P, Errington J. Multiple interactions between the transmembrane division proteins of Bacillus subtilis and the role of FtsL instability in divisome assembly. Journal of Bacteriology 2006, 188(21), 7396-7404.
- Bramkamp M, Weston L, Daniel RA, Errington J. Regulated intramembrane proteolysis of FtsL protein and the control of cell division in Bacillus subtilis. Molecular Microbiology 2006, 62(2), 580-591.
- Daniel RA, Errington J. Control of Cell Morphogenesis in Bacteria: Two Distinct Ways to Make a Rod-Shaped Cell. Cell 2003, 113(6), 767-776.
- Errington J, Daniel RA, Scheffers DJ. Cytokinesis in bacteria. Microbiology and Molecular Biology Reviews 2003, 67(1), 52-65.
- Errington J, Daniel RA. Cell division during growth and sporulation. In: Sonenshein, L; Losick, R; Hoch, JA, ed. Bacillus Subtilis and Its Closest Relatives: From Genes to Cells. Washington, D.C: American Society for Microbiology, 2002, pp.97-109.
- Thomas JD, Daniel RA, Errington J, Robinson C. Export of active green fluorescent protein to the periplasm by the twin-arginine translocase (Tat) pathway in scherichia coli. Molecular Microbiology 2001, 39(1), 47-53.
- Dervyn E, Suski C, Daniel RA, Bruand C, Chapuis J, Errington J, Jannière L, Ehrlich SD. Two Essential DNA Polymerases at the Bacterial Replication Fork. Science 2001, 294(5547), 1716-1719.
- Daniel RA, Errington J. Intrinsic instability of the essential cell division protein FtsL of Bacillus subtilis and a role for DivIB protein in FtsL turnover. Molecular Microbiology 2000, 36(2), 278-289.
- Daniel RA, Harry EJ, Errington J. Role of penicillin-binding protein PBP 2B in assembly and functioning of the division machinery of Bacillus subtilis. Molecular Microbiology 2000, 35(2), 299-311.
- Feucht A, Daniel RA, Errington J. Characterization of a morphological checkpoint coupling cell-specific transcription to septation in Bacillus subtilis. Molecular Microbiology 1999, 33(5), 1015-1026.
- Daniel RA, Harry EJ, Katis VL, Wake RG, Errington J. Characterization of the essential cell division gene ftsL (yllD) of Bacillus subtilis and its role in the assembly of the division apparatus. Molecular Microbiology 1998, 29(2), 593-604.
- Errington J, Daniel RA, Feucht A, Lewis PJ, Wu LJ. Regulation of prespore-specific transcription during sporulation in Bacillus subtilis. In: Molecular Microbiology. 1998, Birmingham, UK: Berlin Heidelberg: Springer-Verlag.
- Zhang B, Daniel RA, Errington J, Kroos L. Bacillus subtilis SpoIIID protein binds to two sites in the spoVD promoter and represses transcription by sE RNA polymerase. Journal of Bacteriology 1997, 179(3), 972-975.
- Daniel RA, Haiech J, Denizot F, Errington J. Isolation and characterization of the lacA gene encoding b-galactosidase in Bacillus subtilis and a regulator gene, lacR. Journal of Bacteriology 1997, 179(17), 5636-5638.
- Daniel RA, Williams AM, Errington J. A complex four-gene operon containing essential cell division gene pbpB in Bacillus subtilis. Journal of Bacteriology 1996, 178(8), 2343-2350.
- Parker GF, Daniel RA, Errington J. Timing and genetic regulation of commitment to sporulation in Bacillus subtilis. Microbiology 1996, 142(12), 3445-3452.
- Daniel RA, Drake S, Buchanan CE, Scholle R, Errington J. The Bacillus subtilis spoVD gene encodes a mother-cell-specific penicillin-binding protein required for spore morphogenesis. Journal of Molecular Biology 1994, 235(1), 209-220.
- Yanouri A, Daniel RA, Errington J, Buchanan CE. Cloning and sequencing of the cell division gene pbpB, which encodes penicillin-binding protein 2B in Bacillus subtilis. Journal of Bacteriology 1993, 175(23), 7604-7616.
- Daniel RA, Errington J. Cloning, DNA sequence, functional analysis and transcriptional regulation of the genes encoding dipicolinic acid synthesis required for sporulation in Bacillus subtilis. Journal of Molecular Biology 1993, 232(2), 468-483.
- Daniel RA, Errington J. DNA sequence of the murE-murD region of Bacillus subtilis 168. Journal of General Microbiology 1993, 139(2), 361-370.
- Stevens CM, Daniel R, Illing N, Errington J. Characterization of a sporulation gene, spoIVA, involved in spore coat morphogenesis in Bacillus subtilis. Journal of Bacteriology 1992, 174(2), 586-594.
- Errington J, Appleby L, Daniel RA, Goodfellow H, Partridge SR, Yudkin MD. Structure and function of the spoIIIJ gene of Bacillus subtilis: a vegetatively expressed gene that is essential for σG activity at an intermediate stage of sporulation. Journal of General Microbiology 1992, 138(12), 2609-2618.