Current Research
The molecular mechanisms and biological consequences of DNA transposition Transposons are mobile genetic elements that can excise from their original locus and re-insert at a new target site elsewhere in the genome. They were first recognized because they promoted chromosomal rearrangements and failed to obey the usual laws of inheritance. In bacteria, this can result in the dissemination of antibiotic resistance, while in higher organisms transposons have expanded up to 50% of the genome. Transposons have also been domesticated. In humans, 47 genes are derived from transposons, including the V(D)J recombinase on which the immune system is based. Although transposons are highly evolved and widely distributed in nature, they are connected by common themes and mechanisms. The laboratory is therefore interested in a number of different elements from bacteria, insects and humans. Tn10 transposition is responsible for genetic rearrangements and the spread of tetracycline resistance in bacteria. Transposition requires the cleavage of four strands of DNA, followed by integration of the broken ends at a new target site. We have defined sequential conformational changes in the nucleoprotein complex, or "transpososome", that take place during the reaction and provide insight into the relationship between structure and function. In many eukaryotic transposons the polarity of the reaction chemistry is reversed. We have extended our work to the V(D)J recombination system to ask how this reversal is accommodated in the nucleoprotein complex. The mariner element is the most widespread transposon in nature. We are addressing the structure of the transpososome, one of the great mysteries remaining in transposon biology. To do this we are using the human SETMAR protein which we have found to be a relatively tractable system. Neisseria meningitidis has hundreds of elements derived from a mariner family transposon. We are investigating their role in the genome-wide control of transcription and the population biology of this important human pathogen. Group members: Dr Danxu Liu Dr Azeem Siddique Mr Corentin Claeys Bouuaert Mr Neil Walker PUBLICATIONS
41, Liu, D., Haniford, D., and Chalmers, R. (2011). H-NS mediates the dissociation of a refractory protein-DNA complex during Tn10/IS10 transposition. Nucleic Acids Res., In the press.
40, Siddique, A., Buisine, N., and Chalmers, R. (2011). The transposon-like correia elements encode numerous strong promoters and provide a potential new mechanism for phase variation in the meningococcus. PLoS Genet 7, e1001277.
39, Claeys Bouuaert, C., and Chalmers, R. (2011). A simple topological-filter in a eukaryotic transposon as a mechanism to suppress genome instability. Mol. Cell Biol., 31, 317-327. doi:10.1128/MCB.01066-10
38, Claeys Bouuaert, C. & Chalmers, R. (2010). Transposition of the human Hsmar1 transposon: rate limiting steps and the importance of the flanking TA dinucleotide. Nucleic Acids Res., 38, 190-202.
37, Atkinson, H. & Chalmers, R. (2010). Delivering the goods: viral and non-viral gene therapy vectors and the inherent limits on cargo DNA and internal sequences. Genetica 135, 485-489.
36, Claeys Bouuaert, C. & Chalmers, R. (2010). Gene therapy vectors: the prospects and potentials of the cut-and-paste transposons. Genetica, 138, 473-484.
35, Bischerour, J., Lu, C., Roth, DB & Chalmers, R. (2009). Base flipping in V(D)J recombination: insights into the mechanism of hairpin formation and the 12/23 rule. Mol. Cell Biol., 29, 5889-5899.
34, Bischerour, J. & Chalmers, R. (2009). Base flipping in Tn10 transposition: an active flip and capture mechanism. PLoS ONE 4(7): e6201.
33, Lopez, M., Siddique, A., Bischerour, J., Lorite, P., *Chalmers, R. *Palomeque, T. (2008). Transposition of Mboumar-9: Identificaton of a new naturally active mariner-family transposon. J. Mol. Biol., 382, 567-572
*Corresponding authors
32, Bischerour, J. & Chalmers, R. (2007). Base flipping dynamics in a DNA hairpin processing reaction. Nucleic Acids Res., 35, 2584-2595.
31, Liu, D., Bischerour, J., Siddique, A., Buisine, N., Bigot, Y. & Chalmers, R. (2007). The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase. Mol. Cell Biol., 27, 1125-1132.
30, Liu, D., Sewitz, S., Crellin, P. & Chalmers, R. (2006). Functional coupling between the two active sites during Tn10 transposition buffers the mutation of sequences critical for DNA hairpin processing. Mol. Microbiol. 62, 1522-1533.
29, Liu, D., Crellin, P. & Chalmers, R. (2005). Cyclic changes in the affinity of protein-DNA interactions drive the progression and regulate the outcome of the Tn10 transposition reaction. Nucleic Acids Res., 33, 1982-1992.
28, Wright, J.C., Hood, D.W., Randle, G.A., Makepeace, K., Cox, A.D., Chalmers, R., Richards, J.C. & Moxon, E.R. (2004). lpt6, a gene required for addition of phosphoethanolamine to inner core lipopolysaccharide of Neisseria meningitidis and Haemophilus influenzae. J. Bacteriol., 186, 6970-6982.
27, Buisine, N. & Chalmers, R. (2004). yBLAST, a graphical front end for the stand alone BLAST suit. Biotechniques, 37, 987-989.
26, Lipkow, K., Buisine, N. & Chalmers, R. (2004). Promiscuous target interactions in the mariner transposon Himar1. J. Biol. Chem., 279, 48569-48575.
25, Lipkow, K., Buisine, N., Lampe, D.J. & Chalmers, R. (2004). Early intermediates of mariner transposition: catalysis without synapsis of the transposon ends suggests a novel architecture of the synaptic complex. Mol. Cell Biol., 24, 8301-8311.
24, Crellin, P., Sewitz, S. & Chalmers, R. (2004). DNA looping and catalysis: the IHF-folded arm of Tn10 promotes conformational changes and hairpin resolution. Mol. Cell, 13, 537-547. (Also chosen for the Front Cover Illustration).
23, Sewitz, S., Crellin, P. & Chalmers, R. (2003). The positive and negative regulation of Tn10 transposition by IHF is mediated by structurally asymmetric transposon arms. Nucleic Acids Res., 31, 5865-5876
22, Buisine, N., Tang, C.M. & Chalmers, R. (2002). Transposon-like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp. FEBS Letters, 522, 52-58
21, Mackinnon, F.G., Cox, A.D., Plested, J.S., Tang, C.M., Makepeace, K., Coull, P.A., Wright, J.C., Chalmers, R., Hood, D.W., Richards, J.C. and Moxon, E.R. (2002). Identification of a gene (lpt-3) required for the addition of phosphoethanolamine to the lipopolysaccharide inner core of Neisseria meningitidis and its role in mediating susceptibility to bactericidal killing and opsonophagocytosis. Mol. Microbiol., 43, 931-943
20, Tang, C.M., Stroud, D., Mackinnon, F., Makepeace, K., Plested, J., Moxon, E.R. and Chalmers, R. (2002). Genetic linkage analysis to identify a gene required for the addition of phosphoethanolamine to meningococcal lipopolysaccharide. Gene, 284, 133-140
19, Crellin, P. and Chalmers, R. (2001). Protein-DNA contacts and conformational changes in the Tn10 transpososome during assembly and activation for cleavage. EMBO J. 20, 3882-3891
18, Bakshi, S., Sun Y-H., Chalmers, R. and Tang C. M. (2001). Signature tagged mutagenesis. In Meningococcal Disease (Pollard, A.J. & Maiden, M.C.J. eds.), Humana Press, New Jersey, pp. 679 - 692
17, Sun Y-H., Bakshi, S., Chalmers, R.† and Tang C. M.† (2000). Functional genomics of Neisseria meningitidis pathogenesis. Nature Medicine, 6, 1269-1273
† Joint corresponding authors. See also News & Views, Nature Medicine, 6, 1215-1216.
16, Chalmers, R., Sewitz, S., Lipkow, K. and Crellin, P. (2000). The complete nucleotide sequence of Tn10. J. Bacteriol., 182, 2970-2972
15, Chalmers, R. and Blot, M. (1999). IS sequences and transposons. In Organization of the Prokaryotic Genome (Charlebois, R.L. ed.), American Society for Microbiology, Washington D.C., pp. 151-169
14, Chalmers, R., Guhathakurta, A., Benjamin, H. & Kleckner, N. (1998). IHF Modulation of Tn10 Transposition: Sensory Transduction of Supercoiling Status via a Proposed Protein/DNA Molecular Spring. Cell, 93, 897-908
13, Chalmers, R. M. & Kleckner, N. (1996). IS10/Tn10 Transposition efficiently accommodates diverse transposon end configurations. EMBO J. 15, 5112-5122
12, Kleckner, N., Chalmers, R. M., Kwon, D., Sakai, J. & Bolland, S. (1996). Tn10 and IS10 transposition and chromosome rearrangements: mechanism and regulation in vivo and in vitro. In Transposable Elements. Current Topic in Microbiology and Immunology (Saedler, H. & Gierl, A., eds.), Springer-Verlag, Berlin, pp. 49-82
11, Sakai, J., Chalmers, R. M. & Kleckner, N (1995). Identification and characterization of a precleavage synaptic complex that is an early intermediate in Tn10 transposition. EMBO J. 14, 4374-4383
10, Kwon, D., Chalmers, R. M. & Kleckner, N, (1995). Structural domains of IS10 transposase and reconstitution of transposition activity from proteolytic fragments lacking an inter-domainal linker. Proc. Natl. Acad. Sci. USA. 92, 8234-8238
9, Chalmers, R. M. & Kleckner, N. (1994). Tn10/IS10 transposase purification, activation and in vitro reaction. J. Biol. Chem. 269, 8029-8035
8, Fewson, C. A., Baker, D. P., Chalmers, R. M., Keen, J. N., Hamilton, I. D., Scott, A. J. & Yasin, M. (1993). Relationships amongst some bacterial and yeast lactate and mandelate dehydrogenases. J. Gen. Microbiol. 139, 1345-1352
7, Chalmers, R. M., Keen, J. N. & Fewson, C. A. (1991). Comparison of benzyl alcohol dehydrogenases and benzaldehyde dehydrogenases from the benzyl alcohol and mandelate pathways in Acinetobacter calcoaceticus and from the toluene pathway in Pseudomonas putida: N-terminal amino acid sequences, amino acid compositions and immunological cross-reactions. Biochem J. 273, 99-107
6, Chalmers, R. M., Scott, A. J. & Fewson, C. A. (1990). Purification of the benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase encoded by the TOL plasmid pWW53 of Pseudomonas putida MT53 and their preliminary comparison with benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase I & II from Acinetobacter calcoaceticus. J. Gen. Microbiol. 136, 637-643
5, Chalmers, R. M. (1990). Purification and characterisation of benzaldehyde dehydrogenase I from Acinetobacter calcoaceticus and the TOL plasmid encoded benzaldehyde dehydrogenase and benzyl alcohol dehydrogenase from Pseudomonas putida. Ph.D. thesis, University of Glasgow, Glasgow, UK.
4, Chalmers, R. M. & Fewson, C. A. (1989). Purification and characterisation of benzaldehyde dehydrogenase I from Acinetobacter calcoaceticus. Biochem. J. 263, 913-919
3, Chalmers, R. M. & Fewson, C. A. (1988). The evolution of metabolic pathways: an immunological approach to the evolution of aromatic alcohol and aldehyde dehydrogenases. In Enzymology & Molecular Biology of Carbonyl Metabolism 2 (Weiner, H. & Flynn, T. G., eds.), pp. 193-207, Alan R. Liss, New York
2, Chalmers, R. M. & Fewson, C. A., (1988). Quantitative immunoblotting in the study of bacterial evolution. Biochem. Soc. Trans. 16, 153-154.
1, Suckling C. J., Chalmers R. and Suckling K. E., (1986). The effect of some tentacle molecules upon model lipid membranes. Biochem. Soc. Trans. 14, 749-750