Professor Marshall Stark

  • Professor of Molecular Genetics (Molecular Biosciences)

telephone: 01413305116
email: Marshall.Stark@glasgow.ac.uk

R504c Level 5, Institute of MC&SB, Bower Building, Glasgow G12 8QQ

Import to contacts

ORCID iDhttps://orcid.org/0000-0001-8086-2572

Biography

My first degree was in Chemistry (Glasgow University, 1980). For my Ph.D I studied the biosynthetic pathway to a group of fungal antibiotics (also in the Chemistry Department in Glasgow). Following a post-doc in Cambridge (studying the biosynthesis of porphyrins) and a spell in industry (ICI/Zeneca, Manchester, working on synthesis of specialized organic light-absorbing compounds), I returned to Glasgow and a post-doc in the Genetics Department with Prof. David Sherratt. My project aimed to understand the mechanism of the site-specific recombination system of the bacterial penicillin resistance transposon Tn3. In 1999 I was fortunate to be awarded a Royal Society University Research Fellowship, which funded me for the next 10 years and gave me the freedom and resources to continue my site-specific recombination research independently. When my Fellowship ended I was appointed as a Reader here and was subsequently made Professor of Molecular Genetics. My research group and I continue to study DNA site-specific recombination. We are interested in the structures and molecular mechanisms of the recombinases (the enzymes that catalyse recombination), and how these remarkable enzymes can be used as tools for editing DNA sequences for biotechnology, synthetic biology and gene therapy.

Research interests

Mechanisms, structures and applications of site-specific recombination

We study enzymes that can rearrange the structure of DNA molecules. Site-specific recombinases break both strands of a DNA molecule at two defined points, and rejoin the four ends of the double helix in a new arrangement. For example, Tn3 resolvase is a small protein (20 kDa), yet it can promote complete site-specific recombination (recognizing the two sites, bringing them together, breaking the four DNA strands, rearranging the ends, and rejoining them to new partners).

We are studying the reactions of resolvase and other recombinases in vitro, using innovative techniques, and interpreting our results in the context of crystal structures of complexes of the recombinases with DNA. We aim to develop a detailed picture of the structures and mechanisms involved in the site-specific recombination process and its regulation.



Site-specific recombination reactions are excellent model systems for studying the properties and functions of proteins that bind to and act on DNA. In the course of our work, we are gaining insight into the behaviour of the DNA molecule itself, and how proteins deal with it. We are also working on ways of developing these biological systems as potentially very useful tools for Synthetic Biology, Biotechnology and gene therapy.

Current PhD students

Rich Clubbe - Serine Integrase-based "landing pad" systems for chromosomal Integrations of heterologous genes.
Jumai Abioye - Designer recombinases targeting the HIV provirus.

Research groups

Publications

List by: Type | Date

Jump to: 2024 | 2023 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2012 | 2011 | 2010 | 2009 | 2008 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001
Number of items: 53.

2024

MacDonald, A. I., Baksh, A., Holland, A., Shin, H., Rice, P. A., Stark, W. M. and Olorunniji, F. J. (2024) Variable orthogonality of serine integrase interactions within the ϕC31 family. Scientific Reports, 14(1), 26280. (doi: 10.1038/s41598-024-77570-9) (PMID:39487291)

2023

Abioye, J., Lawson‐Williams, M., Lecanda, A., Calhoon, B., McQue, A. L., Colloms, S. D. , Stark, W. M. and Olorunniji, F. J. (2023) High fidelity one‐pot DNA assembly using orthogonal serine integrases. Biotechnology Journal, 18(3), 2200411. (doi: 10.1002/biot.202200411) (PMID:36504358)

Montaño, S. P., Rowland, S.-J., Fuller, J. R., Burke, M. E., MacDonald, A. I., Boocock, M. R., Stark, W. M. and Rice, P. A. (2023) Structural basis for topological regulation of Tn3 resolvase. Nucleic Acids Research, 51(3), pp. 1001-1018. (doi: 10.1093/nar/gkac733) (PMID:36100255) (PMCID:PMC9943657)

2020

Rowland, S.-J., Boocock, M. R., Burke, M. E., Rice, P. A. and Stark, W. M. (2020) The protein-protein interactions required for assembly of the Tn3 resolution synapse. Molecular Microbiology, 114(6), pp. 952-965. (doi: 10.1111/mmi.14579) (PMID:33405333)

Waraich, N. F., Jain, S., Colloms, S. D. , Stark, W. M. , Burton, N. P. and Maxwell, A. (2020) A novel decatenation assay for DNA topoisomerases using a singly-linked catenated substrate. BioTechniques, 69(5), pp. 356-362. (doi: 10.2144/btn-2020-0059) (PMID:33000631)

2019

Olorunniji, F. J., Lawson-Williams, M., McPherson, A. L., Paget, J. E., Stark, W. M. and Rosser, S. J. (2019) Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing. Nucleic Acids Research, 47(21), pp. 11452-11460. (doi: 10.1093/nar/gkz936) (PMID:31667500) (PMCID:PMC6868429)

Gao, H., Murugesan, B., Hoßbach, J., Evans, S. K., Stark, W. M. and Smith, M. C.M. (2019) Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina. BMC Biotechnology, 19, 32. (doi: 10.1186/s12896-019-0521-y) (PMID:31164159) (PMCID:PMC6549336)

2018

Trejo, C. S., Rock, R. S., Stark, W. M. , Boocock, M. R. and Rice, P. A. (2018) Snapshots of a molecular swivel in action. Nucleic Acids Research, 46(10), pp. 5286-5296. (doi: 10.1093/nar/gkx1309) (PMID:29315406) (PMCID:PMC6007550)

Pokhilko, A., Ebenhöh, O., Stark, W. M. and Colloms, S. D. (2018) Mathematical model of a serine integrase-controlled toggle switch with a single input. Journal of the Royal Society: Interface, 15(143), 20180160. (doi: 10.1098/rsif.2018.0160) (PMID:29875284) (PMCID:PMC6030632)

Fogg, P. C.M., Younger, E., Fernando, B. D., Khaleel, T., Stark, W. M. and Smith, M. C.M. (2018) Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif. Nucleic Acids Research, 46(3), pp. 1308-1320. (doi: 10.1093/nar/gkx1233) (PMID:29228292) (PMCID:PMC5814800)

2017

Olorunniji, F. J., McPherson, A. L., Rosser, S. J., Smith, M. C.M., Colloms, S. D. and Stark, W. M. (2017) Control of serine integrase recombination directionality by fusion with the directionality factor. Nucleic Acids Research, 45(14), pp. 8635-8645. (doi: 10.1093/nar/gkx567) (PMID:28666339) (PMCID:PMC5737554)

Stark, W. M. (2017) Making serine integrases work for us. Current Opinion in Microbiology, 38, pp. 130-136. (doi: 10.1016/j.mib.2017.04.006) (PMID:28599144)

Fogg, P. C.M., Haley, J. A., Stark, W. M. and Smith, M. C.M. (2017) Genome integration and excision by a new Streptomyces Bacteriophage ϕJoe. Applied and Environmental Microbiology, 83(5), e02767-16. (doi: 10.1128/AEM.02767-16) (PMID:28003200) (PMCID:PMC5311408)

Olorunniji, F. J., Merrick, C., Rosser, S. J., Smith, M. C.M., Stark, W. M. and Colloms, S. D. (2017) Multipart DNA assembly using site-specific recombinases from the large serine integrase family. In: Eroshenko, N. (ed.) Site-Specific Recombinases: Methods and Protocols. Series: Methods in molecular biology (1642). Springer New York, pp. 303-323. ISBN 9781493971671 (doi: 10.1007/978-1-4939-7169-5_19)

Olorunniji, F. J., Rosser, S. J. and Stark, W. M. (2017) Purification and in vitro characterization of zinc finger recombinases. In: Eroshenko, N. (ed.) Site-Specific Recombinases: Methods and Protocols. Series: Methods in molecular biology (1642). Humana Press, pp. 229-245. ISBN 9781493971671 (doi: 10.1007/978-1-4939-7169-5_15)

2016

Bebel, A., Karaca, E., Kumar, B., Stark, W. M. and Barabas, O. (2016) Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending. eLife, 5, e19706. (doi: 10.7554/eLife.19706) (PMID:28009253) (PMCID:PMC5241119)

Pokhilko, A., Zhao, J., Ebenhöh, O., Smith, M. C.M., Stark, W. M. and Colloms, S. D. (2016) The mechanism of φC31 integrase directionality: experimental analysis and computational modelling. Nucleic Acids Research, 44(15), pp. 7360-7372. (doi: 10.1093/nar/gkw616) (PMID:27387286) (PMCID:PMC5009753)

Olorunniji, F. J., Rosser, S. J. and Stark, W. M. (2016) Site-specific recombinases: molecular machines for the genetic revolution. Biochemical Journal, 473(6), pp. 673-684. (doi: 10.1042/bj20151112) (PMID:26965385)

Barrett, M. , Sloan, W. , Stark, W. and Watson, I. (2016) New Developments in Synthetic Biology at the University of Glasgow. Industrial Biotechnology Innovation Centre Annual Conference, Glasgow, UK, 28-29 Jan 2016.

Pokhilko, A., Zhao, J., Stark, W. M. , Colloms, S. D. and Ebenhöh, O. (2016) A simplified mathematical model of directional DNA site-specific recombination by serine integrases. Journal of the Royal Society: Interface, 14, 20160618. (doi: 10.1098/rsif.2016.0618) (PMID:28077763) (PMCID:PMC5310728)

2015

Olorunniji, F. J., McPherson, A. L., Pavlou, H. J., McIlwraith, M. J., Brazier, J. A., Cosstick, R. and Stark, W. M. (2015) Nicked-site substrates for a serine recombinase reveal enzyme–DNA communications and an essential tethering role of covalent enzyme–DNA linkages. Nucleic Acids Research, (doi: 10.1093/nar/gkv521) (PMID:25990737) (PMCID:PMC4499144))

Stark, W. M. (2015) The serine recombinases. In: Craig, N., Chandler, M., Gellert, M., Lambowitz, A., Rice, P. and Sandmeyer, S. (eds.) Mobile DNA III. ASM Press: Washington, DC, pp. 73-89. (doi: 10.1128/9781555819217)

2014

Fogg, P. C.M., Colloms, S. , Rosser, S., Stark, M. and Smith, M. C.M. (2014) New applications for phage integrases. Journal of Molecular Biology, 426(15), pp. 2703-2716. (doi: 10.1016/j.jmb.2014.05.014) (PMID:24857859) (PMCID:PMC4111918)

Colloms, S.D. , Merrick, C.A., Olorunniji, F.J., Stark, W.M. , Smith, M.C.M., Osbourn, A., Keasling, J.D. and Rosser, S.J. (2014) Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Research, 42(4), e23. (doi: 10.1093/nar/gkt1101) (PMID:24225316) (PMCID:PMC3936721)

2012

Olorunniji, F. J., Buck, D. E., Colloms, S. D. , McEwan, A. R., Smith, M. C. M., Stark, W. M. and Rosser, S. J. (2012) Gated rotation mechanism of site-specific recombination by ϕC31 integrase. Proceedings of the National Academy of Sciences of the United States of America, 109(48), pp. 19661-19666. (doi: 10.1073/pnas.1210964109)

Prorocic, M.M., Wenlong, D., Olorunniji, F.J., Akopian, A., Schloetel, J.-G., Hannigan, A., McPherson, A.L. and Stark, W.M. (2012) Zinc-finger recombinase activities in vitro. Nucleic Acids Research, 39(21), pp. 9316-9328. (doi: 10.1093/nar/gkr652) (PMID:21849325) (PMCID:PMC3241657)

2011

Keenholtz, R.A., Rowland, S.-J., Boocock, M.R., Stark, W.M. and Rice, P.A. (2011) Structural Basis for Catalytic Activation of a Serine Recombinase. Structure, 19(6), pp. 799-809. (doi: 10.1016/j.str.2011.03.017)

Proudfoot, C., McPherson, A.L., Kolb, A.F. and Stark, W.M. (2011) Zinc finger recombinases with adaptable DNA sequence specificity. PLoS ONE, 6(4), e19537. (doi: 10.1371/journal.pone.0019537) (PMID:21559340) (PMCID:PMC3084882)

Stark, W.M. (2011) Cutting out the φC31 prophage. Molecular Microbiology, 80(6), pp. 1417-1419. (doi: 10.1111/j.1365-2958.2011.07699.x) (PMID:21564340) (PMCID:PMC3132441)

Stark, W.M. , Boocock, M.R., Olorunniji, F.J. and Rowland, S.-J. (2011) Intermediates in serine recombinase-mediated site-specific recombination. Biochemical Society Transactions, 39(2), pp. 617-622. (doi: 10.1042/BST0390617)

2010

Mouw, K.W., Steiner, A.M., Ghirlando, R., Li, N.-S., Rowland, S.-J., Boocock, M.R., Stark, W.M. , Piccirilli, J.A. and Rice, P.A. (2010) Sin resolvase catalytic activity and oligomerization state are tightly coupled. Journal of Molecular Biology, 404(1), pp. 16-33. (doi: 10.1016/j.jmb.2010.08.057)

Olorunniji, F.J. and Stark, W.M. (2010) Catalysis of site-specific recombination by Tn3 resolvase. Biochemical Society Transactions, 38(2), pp. 417-421. (doi: 10.1042/BST0380417) (PMID:20298194)

Rice, P.A., Mouw, K.W., Montaño, S.P., Boocock, M.R., Rowland, S.-J. and Stark, W.M. (2010) Orchestrating serine resolvases. Biochemical Society Transactions, 38(2), pp. 384-387. (doi: 10.1042/BST0380384)

Stark, W.M. , Luisi, B.F. and Bowater, R.P. (2010) Machines on genes: enzymes that make, break and move DNA and RNA. Biochemical Society Transactions, 38(2), pp. 381-383. (doi: 10.1042/BST0380381)

2009

Olorunniji, F.J. and Stark, W.M. (2009) The catalytic residues of Tn3 resolvase. Nucleic Acids Research, 37(22), pp. 7590-7602. (doi: 10.1093/nar/gkp797) (PMID:19789272) (PMCID:PMC2794168)

Rowland, S.J., Boocock, M.R., MacPherson, A.L., Mouw, K.W., Rice, P.A. and Stark, M.S. (2009) Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome. Molecular Microbiology, 74(2), pp. 282-298. (doi: 10.1111/j.1365-2958.2009.06756.x)

2008

Olorunniji, F.J., He, J., Wenwieser, S.V.C.T., Boocock, M.R. and Stark, W.M. (2008) Synapsis and catalysis by activated Tn3 resolvase mutants. Nucleic Acids Research, 36(22), pp. 7181-7191. (doi: 10.1093/nar/gkn885)

Mouw, K.W., Rowland, S.-J., Gajjar, M.M., Boocock, M.R., Stark, W.M. and Rice, P.A. (2008) Architecture of a serine recombinase-DNA regulatory complex. Molecular Cell, 30(2), pp. 145-155. (doi: 10.1016/j.molcel.2008.02.023)

2006

Kilbride, E., Burke, M., Boocock, M. and Stark, W. (2006) Determinants of product topology in a hybrid Cre-Tn3 resolvase site-specific recombination system. Journal of Molecular Biology, 355, pp. 185-195. (doi: 10.1016/j.jmb.2005.10.046)

Rowland, S., Boocock, M. and Stark, W. (2006) DNA bending in the Sin recombination synapse: functional replacement of HU by IHF. Molecular Microbiology, 59, pp. 1730-1743. (doi: 10.1111/j.1365-2958.2006.05064.x)

2005

Nollmann, M., Byron, O. and Stark, W. (2005) Behavior of Tn3 resolvase in solution and its interaction with res. Biophysical Journal, 89, pp. 1920-1931. (doi: 10.1529/biophysj.104.058164)

Nollmann, M., Stark, W. and Byron, O. (2005) A global multi-technique approach to study low-resolution solution structures. Journal of Applied Crystallography, 38, pp. 874-887. (doi: 10.1107/S0021889805026191)

Rowland, S., Boocock, M. and Stark, W. (2005) Regulation of Sin recombinase by accessory proteins. Molecular Microbiology, 56, pp. 371-382. (doi: 10.1111/j.1365-2958.2005.04550.x)

Stark, W. (2005) Site-specific DNA recombinases as instruments for genomic surgery. Advances in Genetics, 55, pp. 1-23. (doi: 10.1016/S0065-2660(05)55001-6)

2004

Nöllmann, M., He, J., Byron, O. and Stark, W. M. (2004) Solution structure of the Tn3 resolvase-crossover site synaptic complex. Molecular Cell, 16(1), pp. 127-137. (doi: 10.1016/j.molcel.2004.09.027) (PMID:15469828)

Nöllmann, M., Stark, W. M. and Byron, O. (2004) Low-resolution reconstruction of a synthetic DNA Holliday junction. Biophysical Journal, 86(5), pp. 3060-3069. (doi: 10.1016/S0006-3495(04)74355-6) (PMID:15111420) (PMCID:PMC1304172)

Burke, M., Arnold, P., He, J., Wenwieser, S., Rowland, S., Boocock, M. and Stark, W. (2004) Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation. Molecular Microbiology, 51, pp. 837-948. (doi: 10.1046/j.1365-2958.2003.03831.x)

2003

Akopian, A., He, J., Boocock, M. and Stark, W. (2003) Chimeric recombinases with designed DNA sequence recognition. Proceedings of the National Academy of Sciences of the United States of America, 100(15), pp. 8688-8691. (doi: 10.1073/pnas.1533177100)

Stark, W. (2003) Designer recombinases: tools to cut and paste genomic DNA sequences. Discovery Medicine, 3(18), pp. 34-35.

2002

Brown, J., He, J., Sherratt, D., Stark, W. and Boocock, M. (2002) Interactions of protein complexes on supercoiled DNA: The mechanism of selective synapsis by Tn3 resolvase. Journal of Molecular Biology, 319, pp. 371-383. (doi: 10.1016/S0022-2836(02)00309-1)

He, J., McIlwraith, M., Burke, M., Boocock, M. and Stark, W. (2002) Synapsis of Tn3 recombination sites: Unpaired sites destabilize synapses by a partner exchange mechanism. Journal of Molecular Biology, 319, pp. 385-393. (doi: 10.1016/S0022-2836(02)00310-8)

Rowland, S., Stark, W. and Boocock, M. (2002) Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting. Molecular Microbiology, 44, pp. 607-619.

2001

Sarkis, G., Murley, L., Leschziner, A., Boocock, M., Stark, W. and Grindley, N. (2001) A model for the gamma delta resolvase synaptic complex. Molecular Cell, 8, pp. 623-631.

This list was generated on Fri Nov 22 04:10:11 2024 GMT.
Jump to: Articles | Book Sections | Conference or Workshop Item
Number of items: 53.

Articles

MacDonald, A. I., Baksh, A., Holland, A., Shin, H., Rice, P. A., Stark, W. M. and Olorunniji, F. J. (2024) Variable orthogonality of serine integrase interactions within the ϕC31 family. Scientific Reports, 14(1), 26280. (doi: 10.1038/s41598-024-77570-9) (PMID:39487291)

Abioye, J., Lawson‐Williams, M., Lecanda, A., Calhoon, B., McQue, A. L., Colloms, S. D. , Stark, W. M. and Olorunniji, F. J. (2023) High fidelity one‐pot DNA assembly using orthogonal serine integrases. Biotechnology Journal, 18(3), 2200411. (doi: 10.1002/biot.202200411) (PMID:36504358)

Montaño, S. P., Rowland, S.-J., Fuller, J. R., Burke, M. E., MacDonald, A. I., Boocock, M. R., Stark, W. M. and Rice, P. A. (2023) Structural basis for topological regulation of Tn3 resolvase. Nucleic Acids Research, 51(3), pp. 1001-1018. (doi: 10.1093/nar/gkac733) (PMID:36100255) (PMCID:PMC9943657)

Rowland, S.-J., Boocock, M. R., Burke, M. E., Rice, P. A. and Stark, W. M. (2020) The protein-protein interactions required for assembly of the Tn3 resolution synapse. Molecular Microbiology, 114(6), pp. 952-965. (doi: 10.1111/mmi.14579) (PMID:33405333)

Waraich, N. F., Jain, S., Colloms, S. D. , Stark, W. M. , Burton, N. P. and Maxwell, A. (2020) A novel decatenation assay for DNA topoisomerases using a singly-linked catenated substrate. BioTechniques, 69(5), pp. 356-362. (doi: 10.2144/btn-2020-0059) (PMID:33000631)

Olorunniji, F. J., Lawson-Williams, M., McPherson, A. L., Paget, J. E., Stark, W. M. and Rosser, S. J. (2019) Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing. Nucleic Acids Research, 47(21), pp. 11452-11460. (doi: 10.1093/nar/gkz936) (PMID:31667500) (PMCID:PMC6868429)

Gao, H., Murugesan, B., Hoßbach, J., Evans, S. K., Stark, W. M. and Smith, M. C.M. (2019) Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina. BMC Biotechnology, 19, 32. (doi: 10.1186/s12896-019-0521-y) (PMID:31164159) (PMCID:PMC6549336)

Trejo, C. S., Rock, R. S., Stark, W. M. , Boocock, M. R. and Rice, P. A. (2018) Snapshots of a molecular swivel in action. Nucleic Acids Research, 46(10), pp. 5286-5296. (doi: 10.1093/nar/gkx1309) (PMID:29315406) (PMCID:PMC6007550)

Pokhilko, A., Ebenhöh, O., Stark, W. M. and Colloms, S. D. (2018) Mathematical model of a serine integrase-controlled toggle switch with a single input. Journal of the Royal Society: Interface, 15(143), 20180160. (doi: 10.1098/rsif.2018.0160) (PMID:29875284) (PMCID:PMC6030632)

Fogg, P. C.M., Younger, E., Fernando, B. D., Khaleel, T., Stark, W. M. and Smith, M. C.M. (2018) Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif. Nucleic Acids Research, 46(3), pp. 1308-1320. (doi: 10.1093/nar/gkx1233) (PMID:29228292) (PMCID:PMC5814800)

Olorunniji, F. J., McPherson, A. L., Rosser, S. J., Smith, M. C.M., Colloms, S. D. and Stark, W. M. (2017) Control of serine integrase recombination directionality by fusion with the directionality factor. Nucleic Acids Research, 45(14), pp. 8635-8645. (doi: 10.1093/nar/gkx567) (PMID:28666339) (PMCID:PMC5737554)

Stark, W. M. (2017) Making serine integrases work for us. Current Opinion in Microbiology, 38, pp. 130-136. (doi: 10.1016/j.mib.2017.04.006) (PMID:28599144)

Fogg, P. C.M., Haley, J. A., Stark, W. M. and Smith, M. C.M. (2017) Genome integration and excision by a new Streptomyces Bacteriophage ϕJoe. Applied and Environmental Microbiology, 83(5), e02767-16. (doi: 10.1128/AEM.02767-16) (PMID:28003200) (PMCID:PMC5311408)

Bebel, A., Karaca, E., Kumar, B., Stark, W. M. and Barabas, O. (2016) Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending. eLife, 5, e19706. (doi: 10.7554/eLife.19706) (PMID:28009253) (PMCID:PMC5241119)

Pokhilko, A., Zhao, J., Ebenhöh, O., Smith, M. C.M., Stark, W. M. and Colloms, S. D. (2016) The mechanism of φC31 integrase directionality: experimental analysis and computational modelling. Nucleic Acids Research, 44(15), pp. 7360-7372. (doi: 10.1093/nar/gkw616) (PMID:27387286) (PMCID:PMC5009753)

Olorunniji, F. J., Rosser, S. J. and Stark, W. M. (2016) Site-specific recombinases: molecular machines for the genetic revolution. Biochemical Journal, 473(6), pp. 673-684. (doi: 10.1042/bj20151112) (PMID:26965385)

Pokhilko, A., Zhao, J., Stark, W. M. , Colloms, S. D. and Ebenhöh, O. (2016) A simplified mathematical model of directional DNA site-specific recombination by serine integrases. Journal of the Royal Society: Interface, 14, 20160618. (doi: 10.1098/rsif.2016.0618) (PMID:28077763) (PMCID:PMC5310728)

Olorunniji, F. J., McPherson, A. L., Pavlou, H. J., McIlwraith, M. J., Brazier, J. A., Cosstick, R. and Stark, W. M. (2015) Nicked-site substrates for a serine recombinase reveal enzyme–DNA communications and an essential tethering role of covalent enzyme–DNA linkages. Nucleic Acids Research, (doi: 10.1093/nar/gkv521) (PMID:25990737) (PMCID:PMC4499144))

Fogg, P. C.M., Colloms, S. , Rosser, S., Stark, M. and Smith, M. C.M. (2014) New applications for phage integrases. Journal of Molecular Biology, 426(15), pp. 2703-2716. (doi: 10.1016/j.jmb.2014.05.014) (PMID:24857859) (PMCID:PMC4111918)

Colloms, S.D. , Merrick, C.A., Olorunniji, F.J., Stark, W.M. , Smith, M.C.M., Osbourn, A., Keasling, J.D. and Rosser, S.J. (2014) Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Research, 42(4), e23. (doi: 10.1093/nar/gkt1101) (PMID:24225316) (PMCID:PMC3936721)

Olorunniji, F. J., Buck, D. E., Colloms, S. D. , McEwan, A. R., Smith, M. C. M., Stark, W. M. and Rosser, S. J. (2012) Gated rotation mechanism of site-specific recombination by ϕC31 integrase. Proceedings of the National Academy of Sciences of the United States of America, 109(48), pp. 19661-19666. (doi: 10.1073/pnas.1210964109)

Prorocic, M.M., Wenlong, D., Olorunniji, F.J., Akopian, A., Schloetel, J.-G., Hannigan, A., McPherson, A.L. and Stark, W.M. (2012) Zinc-finger recombinase activities in vitro. Nucleic Acids Research, 39(21), pp. 9316-9328. (doi: 10.1093/nar/gkr652) (PMID:21849325) (PMCID:PMC3241657)

Keenholtz, R.A., Rowland, S.-J., Boocock, M.R., Stark, W.M. and Rice, P.A. (2011) Structural Basis for Catalytic Activation of a Serine Recombinase. Structure, 19(6), pp. 799-809. (doi: 10.1016/j.str.2011.03.017)

Proudfoot, C., McPherson, A.L., Kolb, A.F. and Stark, W.M. (2011) Zinc finger recombinases with adaptable DNA sequence specificity. PLoS ONE, 6(4), e19537. (doi: 10.1371/journal.pone.0019537) (PMID:21559340) (PMCID:PMC3084882)

Stark, W.M. (2011) Cutting out the φC31 prophage. Molecular Microbiology, 80(6), pp. 1417-1419. (doi: 10.1111/j.1365-2958.2011.07699.x) (PMID:21564340) (PMCID:PMC3132441)

Stark, W.M. , Boocock, M.R., Olorunniji, F.J. and Rowland, S.-J. (2011) Intermediates in serine recombinase-mediated site-specific recombination. Biochemical Society Transactions, 39(2), pp. 617-622. (doi: 10.1042/BST0390617)

Mouw, K.W., Steiner, A.M., Ghirlando, R., Li, N.-S., Rowland, S.-J., Boocock, M.R., Stark, W.M. , Piccirilli, J.A. and Rice, P.A. (2010) Sin resolvase catalytic activity and oligomerization state are tightly coupled. Journal of Molecular Biology, 404(1), pp. 16-33. (doi: 10.1016/j.jmb.2010.08.057)

Olorunniji, F.J. and Stark, W.M. (2010) Catalysis of site-specific recombination by Tn3 resolvase. Biochemical Society Transactions, 38(2), pp. 417-421. (doi: 10.1042/BST0380417) (PMID:20298194)

Rice, P.A., Mouw, K.W., Montaño, S.P., Boocock, M.R., Rowland, S.-J. and Stark, W.M. (2010) Orchestrating serine resolvases. Biochemical Society Transactions, 38(2), pp. 384-387. (doi: 10.1042/BST0380384)

Stark, W.M. , Luisi, B.F. and Bowater, R.P. (2010) Machines on genes: enzymes that make, break and move DNA and RNA. Biochemical Society Transactions, 38(2), pp. 381-383. (doi: 10.1042/BST0380381)

Olorunniji, F.J. and Stark, W.M. (2009) The catalytic residues of Tn3 resolvase. Nucleic Acids Research, 37(22), pp. 7590-7602. (doi: 10.1093/nar/gkp797) (PMID:19789272) (PMCID:PMC2794168)

Rowland, S.J., Boocock, M.R., MacPherson, A.L., Mouw, K.W., Rice, P.A. and Stark, M.S. (2009) Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome. Molecular Microbiology, 74(2), pp. 282-298. (doi: 10.1111/j.1365-2958.2009.06756.x)

Olorunniji, F.J., He, J., Wenwieser, S.V.C.T., Boocock, M.R. and Stark, W.M. (2008) Synapsis and catalysis by activated Tn3 resolvase mutants. Nucleic Acids Research, 36(22), pp. 7181-7191. (doi: 10.1093/nar/gkn885)

Mouw, K.W., Rowland, S.-J., Gajjar, M.M., Boocock, M.R., Stark, W.M. and Rice, P.A. (2008) Architecture of a serine recombinase-DNA regulatory complex. Molecular Cell, 30(2), pp. 145-155. (doi: 10.1016/j.molcel.2008.02.023)

Kilbride, E., Burke, M., Boocock, M. and Stark, W. (2006) Determinants of product topology in a hybrid Cre-Tn3 resolvase site-specific recombination system. Journal of Molecular Biology, 355, pp. 185-195. (doi: 10.1016/j.jmb.2005.10.046)

Rowland, S., Boocock, M. and Stark, W. (2006) DNA bending in the Sin recombination synapse: functional replacement of HU by IHF. Molecular Microbiology, 59, pp. 1730-1743. (doi: 10.1111/j.1365-2958.2006.05064.x)

Nollmann, M., Byron, O. and Stark, W. (2005) Behavior of Tn3 resolvase in solution and its interaction with res. Biophysical Journal, 89, pp. 1920-1931. (doi: 10.1529/biophysj.104.058164)

Nollmann, M., Stark, W. and Byron, O. (2005) A global multi-technique approach to study low-resolution solution structures. Journal of Applied Crystallography, 38, pp. 874-887. (doi: 10.1107/S0021889805026191)

Rowland, S., Boocock, M. and Stark, W. (2005) Regulation of Sin recombinase by accessory proteins. Molecular Microbiology, 56, pp. 371-382. (doi: 10.1111/j.1365-2958.2005.04550.x)

Stark, W. (2005) Site-specific DNA recombinases as instruments for genomic surgery. Advances in Genetics, 55, pp. 1-23. (doi: 10.1016/S0065-2660(05)55001-6)

Nöllmann, M., He, J., Byron, O. and Stark, W. M. (2004) Solution structure of the Tn3 resolvase-crossover site synaptic complex. Molecular Cell, 16(1), pp. 127-137. (doi: 10.1016/j.molcel.2004.09.027) (PMID:15469828)

Nöllmann, M., Stark, W. M. and Byron, O. (2004) Low-resolution reconstruction of a synthetic DNA Holliday junction. Biophysical Journal, 86(5), pp. 3060-3069. (doi: 10.1016/S0006-3495(04)74355-6) (PMID:15111420) (PMCID:PMC1304172)

Burke, M., Arnold, P., He, J., Wenwieser, S., Rowland, S., Boocock, M. and Stark, W. (2004) Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation. Molecular Microbiology, 51, pp. 837-948. (doi: 10.1046/j.1365-2958.2003.03831.x)

Akopian, A., He, J., Boocock, M. and Stark, W. (2003) Chimeric recombinases with designed DNA sequence recognition. Proceedings of the National Academy of Sciences of the United States of America, 100(15), pp. 8688-8691. (doi: 10.1073/pnas.1533177100)

Stark, W. (2003) Designer recombinases: tools to cut and paste genomic DNA sequences. Discovery Medicine, 3(18), pp. 34-35.

Brown, J., He, J., Sherratt, D., Stark, W. and Boocock, M. (2002) Interactions of protein complexes on supercoiled DNA: The mechanism of selective synapsis by Tn3 resolvase. Journal of Molecular Biology, 319, pp. 371-383. (doi: 10.1016/S0022-2836(02)00309-1)

He, J., McIlwraith, M., Burke, M., Boocock, M. and Stark, W. (2002) Synapsis of Tn3 recombination sites: Unpaired sites destabilize synapses by a partner exchange mechanism. Journal of Molecular Biology, 319, pp. 385-393. (doi: 10.1016/S0022-2836(02)00310-8)

Rowland, S., Stark, W. and Boocock, M. (2002) Sin recombinase from Staphylococcus aureus: synaptic complex architecture and transposon targeting. Molecular Microbiology, 44, pp. 607-619.

Sarkis, G., Murley, L., Leschziner, A., Boocock, M., Stark, W. and Grindley, N. (2001) A model for the gamma delta resolvase synaptic complex. Molecular Cell, 8, pp. 623-631.

Book Sections

Olorunniji, F. J., Merrick, C., Rosser, S. J., Smith, M. C.M., Stark, W. M. and Colloms, S. D. (2017) Multipart DNA assembly using site-specific recombinases from the large serine integrase family. In: Eroshenko, N. (ed.) Site-Specific Recombinases: Methods and Protocols. Series: Methods in molecular biology (1642). Springer New York, pp. 303-323. ISBN 9781493971671 (doi: 10.1007/978-1-4939-7169-5_19)

Olorunniji, F. J., Rosser, S. J. and Stark, W. M. (2017) Purification and in vitro characterization of zinc finger recombinases. In: Eroshenko, N. (ed.) Site-Specific Recombinases: Methods and Protocols. Series: Methods in molecular biology (1642). Humana Press, pp. 229-245. ISBN 9781493971671 (doi: 10.1007/978-1-4939-7169-5_15)

Stark, W. M. (2015) The serine recombinases. In: Craig, N., Chandler, M., Gellert, M., Lambowitz, A., Rice, P. and Sandmeyer, S. (eds.) Mobile DNA III. ASM Press: Washington, DC, pp. 73-89. (doi: 10.1128/9781555819217)

Conference or Workshop Item

Barrett, M. , Sloan, W. , Stark, W. and Watson, I. (2016) New Developments in Synthetic Biology at the University of Glasgow. Industrial Biotechnology Innovation Centre Annual Conference, Glasgow, UK, 28-29 Jan 2016.

This list was generated on Fri Nov 22 04:10:11 2024 GMT.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • The directionality mechanism of DNA site-specific recombination by serine integrases
    Biotechnology and Biological Sciences Research Council
    2022 - 2025
     
  • Elucidation of the rotary mechanism of serine recombinases
    Biotechnology and Biological Sciences Research Council
    2018 - 2021
     
  • A platform for rapid and precise DNA module rearrangements in Synthetic Biology
    Biotechnology and Biological Sciences Research Council
    2012 - 2018
     
  • Chimaeric site-specific recombinases for 'genomic surgery'
    Biotechnology and Biological Sciences Research Council
    2008 - 2011
     
  • Regulation of catalysis in the resolvase synaptosome
    Wellcome Trust
    2008 - 2010
     
  • The mechanism of DNA strand exchange by serine recombinases
    Biotechnology and Biological Sciences Research Council
    2007 - 2010
     
  • Recombinase-mediated site-specific gene integration in mammalian somatic cells
    Biotechnology and Biological Sciences Research Council
    2005 - 2008
     
  • Site-specific recombination by resolvase - assembly and activation of the catalytic tetramer
    Wellcome Trust
    2003 - 2006
     

Supervision

Projects for postgraduate students are available in any of the following areas:

  1. We are investigating the very unusual “subunit rotation” mechanism of the serine recombinases, which is not yet properly understood. We are using state-of-the-art single-molecule fluorescence methods to observe individual DNA-recombinase complexes in real time as they undergo recombination, aiming to understand the mechanism in detail.
  2. We are studying one group of recombinases called the serine integrases, whose properties make them especially suitable as tools for Synthetic Biology. We wish to understand how they catalyse recombination and how they can be engineered to optimize their performance as gene-editing enzymes.
  3. By splicing together parts of serine recombinases with zinc finger or TALE DNA-binding domains we have created “zinc finger recombinases” (ZFRs) and “TALE recombinases” (TALERs) that can be targeted to specific chosen sequences (for example, target sequences in cellular genomic DNA). Using these enzymes we can integrate transgenic DNA sequences at a specific genetic locus, or delete specific sequences from the genome. We aim to optimize the efficiency and specificity of these ZFRs and TALERs so as to make them useful gene editing tools.

Recently completed PhD students/projects in my lab:
Hayley Macfarlane (2017) - Engineering site-specific recombinases for use in Synthetic Biology.
Jeffrey Kentner (2015) - Engineering zinc finger recombinases for use in targeted genomic editing.
Stephanie Holt (2014) - Target site recognition by Tn3 and Sin resolvases.
Jan-Gero Schloetel (2011) - Single-molecule FRET studies of the mechanism of strand exchange in site-specific recombination by Tn3 resolvase.

Teaching

  • Postgraduate Research Convenor for IMCSB
  • L4 DNA Option: Course coordinator
  • L4 Tutorials: for Genetics, MCB, and Biochemistry students
  • L3 Genetics: lectures on recombination
  • L3 Genetics/MCB/Biotechnology: lectures on Mobile DNA

Research datasets

Jump to: 2024
Number of items: 1.

2024

Cadden, G., Schloetel, J.-G., McKenzie, G., Boocock, M., Magennis, S. and Stark, M. (2024) Direct observation of subunit rotation during DNA strand exchange by serine recombinases. [Data Collection]

This list was generated on Thu Nov 21 17:34:43 2024 GMT.

Additional information

Editorial Board

  • 2007 - present: Biochemical Journal - Editor

Grant Advisory Board

  • 2011 - present: BBSRC - Pool of Experts Panel D

Invited International Presentations

  • 2010: Montreal, Canada - ASM conference: Mobile DNA
  • 2010: Oleron, France - Site-specific recombination conference
  • 2010: Sheffield, UK - NACON VIII conference
  • 2009: Cambridge, UK - Meeting organizer and Session Chair: International meeting "Machines on Genes" (sponsored by Biochemical Society)
  • 2008: Chicago, USA - University of Chicago - Z-resolvases: Tools for genomic surgery"
  • 2008: Sussex, UK - University of Sussex - "Resolvase: How to switch it on?"
  • 2008: Cambridge, UK - University of Cambridge - "Resolvase: How to switch it on?"
  • 2008: Wood's Hole, USA - International meeting
  • 2006: Warwick University, Warwick, UK - Co-organizer and session Chair of international conference: “Meiosis and the causes and consequences of recombination” (sponsored by Genetics Society/Biochemical Society)
  • 2004: Wood's Hole, USA - Site-specific recombination meeting
  • 2004: Roscoff, France - EMBO Transposition meeting
  • 2003: Glasgow, UK - Tenovus Symposium, 'Eukaryotic Gene Expression' Session Chair
  • 2003: University College London, UK
  • 2002: Oxford, UK. - 2002 Workshop on site-specific recombination and transposition.

Professional Learned Society

  • 2007 - present: Genetics Society - Member
  • 2004 - 2009: Biochemical Society - Member of 'Genes' Theme Panel from 2005

Research Fellowship

  • 1989 - 1999: Royal Society University Research Fellowship

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