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Synthetic Biology From Molecular Biology to Synthetic Biology, what’s new? Sandra Taylor, Senior Research Technician, BSc (Hons), Mphil, Rsci, MIScT [email protected] (0161) 306 5131 Small beginnings in Norwich, after my first degree • 1987 - First lab job veterinary tests: Bacteriology, post mortems, blood, urine, faeces tests etc. Plant Molecular Genetics 1988 to 1998 – the lab grew from 6 to 16 people and several papers were published on the way that flowering is controlled. 1998 to 2001: Biochemistry Division, School of Biological Sciences, Manchester University – I supported 6 research groups, sharing expertise. Topics from cell division (in toads) to asthma (in horses and people), and cultured human cells. Career Break from 2001 to 2007 • Starting again after 6 years was a challenge but I soon got back up to speed. Technical roles are very varied, never boring, a bit like being a Mum! 2007 to present • I spent 7 years in the Michael Smith Building (Life Sciences) – various roles (cell culture, cloning, yeast two-hybrid) • In 2014 I moved to the MIB – more Chemistry/Biochemistry focussed Nano-scale 3D printing?! Micro-titre plates with 96, 384 or even 1536 sample wells – technology is being developed to “write” strings of DNA into these tiny wells using 3D nano-printing technology. Present Challenges Supporting SYNBIOCHEM • New subject(s) and equipment to learn about • The new SYMBIOCHEM team is 10 people and 4 robots! • IT technology means writing electronic lab notebooks instead of paper ones! • The new team is multidisciplinary so lots to learn but good fun! • This is now the age of writing DNA, as opposed to just reading it Publications (please note publications I contributed prior to 2006 were under my maiden name of Doyle) Structural Basis for Specific Interaction of TGFβ Signaling Regulators SARA/Endofin with HD-PTP. (2017) Deepankar Gahloth , Colin Levy, Louise Walker, Lydia Wunderley, A. Paul Mould, Sandra Taylor, Philip Woodman, and Lydia Tabernero. Strucutre 25(7):p1011–1024 Functional Exchangeability of Oxidase and Dehydrogenase Reactions in the Biosynthesis of Hydroxyphenylglycine, a Nonribosomal Peptide Building Block (2015) Veronica Diez, Mark Loznik, Sandra Taylor, Michael Winn, Nicholas J. W. Rattray, Helen Podmore, Jason Micklefield, Royston Goodacre, Marnix H. Medema, Ulrike Müller, Roel Bovenberg, Dick B. Janssen, and Eriko Takano. ACS Synthetic Biology. - Ali N, Zhang L, Taylor S, Mironov A, Urbé S, Woodman P. (2013) Recruitment of UBPY and ESCRT Exchange Drive HD-PTP- Dependent Sorting of EGFR to the MVB. Curr Biol. 23(6):453-61. UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting - Flavia Stefani, Ling Zhang, Sandra Taylor, Johanna Donovan, Sara Rollinson, Aurelie Doyotte, Kim Brownhill, Janis Bennion, Stuart Pickering-Brown, Philip Woodman. (2011) UBAP1 Is a Component of an Endosome-Specific ESCRT-I Complex that Is Essential for MVB Sorting. Curr Biol 21(14):1245-50. - Addinall, SG., Mayr, P.S., Doyle, S., Sheehan, J.K., Woodman, P.W., and Allan, V.J. (2001). Phosphorylation by cdc2-CyclinB1 kinase releases cytoplasmic dynein from membranes. J. Biol. Chem. 276, 15939-15944. - Schultz, E., Carpenter, R, Doyle, S. and Coen, E. (2001). The gene finbriata interacts non-cell autonomously with floral regulatory genes. The Plant Journal 25(5), 499-507. - McSteen, P.C.M., Vincent, C.A., Doyle, S., Carpenter, R. and Coen, E.S. (1999) Control of floral homeotic gene expression and organ morphogenesis in Antirhinum. Development 125, 2359-2369. - Ingram, G.C., Doyle, S., Carpenter, R., Schultz, E.A., Simon, R and Coen, E.S. (1997). Dual role for fimbriata in regulating floral homeotic genes and cell division in Antirhinum. EMBO J., 16, 6521-6534. - Carpenter, R., Copsey, L., Vincent, C., Doyle, S., Magrath, R. and Coen, E. (1995) Control of flower development and phyllotaxy by meristem identity genes in Antirhinum. The Plant Cell 7, 2001-2011. - Simon, R., Carpenter, R., Doyle, S. and Coen, E.S. (1994) Fimbriata controls flower development by mediating between mertistem and organ identity genes. Cell 78, 99-107. - Hudson, A., Carpenter, R., Doyle, S., and Coen, E.S. (1993) Olive: a key gene required for chlorophyll biosynthesis in Antirhinum majus. EMBO J. 12, 3711-3719. - Luo, D., Coen, E.S., Doyle, S. and Carpenter, R. (1991). Pigmentation mutants produced by transposon mutagenesis in Antirhinum majus. Plant J. 1, 59-69. - Coen, E.S., Romero, J.M., Doyle, S. Elliott, R., Murphy, G. and Carpenter, R. (1990). Floricaula: a homoetic gene required for flower development in Antirhinum majus. Cell 63, 1311-1322. Published Abstract Davies, L., Gkourtza, A., Symeou, C., Lynch, J., Taylor, S., Demonacos C. and M Krstic-Demonacos (2009). Endocrine Abstracts 19 Society for Endocrinology BES 2009. - Six Synthetic Biology Centres across the UK • Centre for Synthetic Biology and Innovation in London • Synthetic Biology Research Centre in Nottingham • BrisSynBio in Bristol • The UK Centre for Mammalian Synthetic Biology in Edinburgh • Warwick Integrative Synthetic Biology Centre • SYNBIOCHEM in Manchester (speciality and fine chemicals) DESIGN-BUILD-TEST (What is SYNBIOCHEM?) Current research themes • Terpenoids • Alkaloids • Flavanoids • Technology/platform development Our semi-automated laboratory SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals Pablo Carbonell, Andrew Currin, Mark Dunstan, Donal Fellows, Ad rian Jervis, Nicholas J.W. Rattray, Christopher J. Robinson, Neil Sw ainston, Maria Vinaixa, Alan Williams, Cunyu Yan, Perdita Barran, Rainer Breitling, George Guo-Qiang Chen, Jean- Loup Faulon, Carole Goble, Royston Goodacre, Douglas B. Kell, Ro salind Le Feuvre, Jason Micklefield, Nigel S. Scrutton, Philip Shapir a, Eriko Takano, Nicholas J. Turner Biochemical Society Transactions Jun 09, 2016,44(3)675- 677;DOI: 10.1042/BST20160009 “The Manchester Synthetic Biology Research Centre (SYNBIOCHEM) is a foundry for the biosynthesis and sustainable production of fine and speciality chemicals. The Centre's integrated technology platforms provide a unique capability to facilitate predictable engineering of microbial bio-factories for chemicals production.” Scientometrics September 2017, Volume 112, Issue 3, pp 1439–1469 “Tracking the emergence of synthetic biology” Philip Shapira, Seokbeom Kwon, Jan Youtie “Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years.” Fragrances and flavours Natural fragrances and flavours are used in many forms and are found in many types of foods and beverages. These can be produced naturally, but sometimes there is more demand than can be supplied. We will look at a range of natural “smells” and ask how these can be used and whether there are any substitutes? Part of our research is to look at novel ways to make in- demand fragrances. The search for novel materials • Materials (Basel). 2016 Jul 11;9(7). pii: E560. doi: 10.3390/ma9070560. • Biomineralization of Engineered Spider Silk Protein-Based Composite Materials for Bone Tissue Engineering. • Hardy JG1, Torres-Rendon JG2, Leal-Egaña A3, Walther A4, Schlaad H5, Cölfen H6, Scheibel TR7. • Author information • Abstract • Materials based on biodegradable polyesters, such as poly(butylene terephthalate) (PBT) or poly(butylene terephthalate-co-poly(alkylene glycol) terephthalate) (PBTAT), have potential application as pro-regenerative scaffolds for bone tissue engineering. Herein, the preparation of films composed of PBT or PBTAT and an engineered spider silk protein, (eADF4(C16)), that displays multiple carboxylic acid moieties capable of binding calcium ions and facilitating their biomineralization with calcium carbonate or calcium phosphate is reported. Human mesenchymal stem cells cultured on films mineralized with calcium phosphate show enhanced levels of alkaline phosphatase activity suggesting that such composites have potential use for bone tissue engineering. • KEYWORDS: • biodegradable polymers; biomaterials; biomineralization; bone tissue engineering; recombinant protein; spider silk • PMID: 28773681 PMCID: PMC5456849 DOI: 10.3390/ma9070560 Menthol Minty flavour, cool sensation Mentha avensis and mentha piperita Used for over 2000 years in some parts of the world. Earliest reference in the West in 1771. Novel ways to produce rare or novel compounds • Select a host organism to express the chosen enzyme pathway – Escherichia coli, yeast, etc • Design team use Big Data and algorithms to select good candidate pathways – varying elements like varying strength promoters, ribosomal binding sites, heterologous enzymes with useful function, etc • Build team use automation to assemble and then express as many permutations as possible. • Test team analyse the expressed compounds to identify what amount of target chemical was synthesised • Design team analyse results and re-run algorithms to come up with better designs which are then made and tested • Finally strain and media optimisation to maximise yields Advantages • Relatively cheap feed stocks (e.g glucose and glycerol) • Using relatively simple host organisms, well characterised, defined media and growth conditions • Able to test many permutations of pathways quickly to optimise production • Some chemical processes are expensive or difficult but biological enzymes could do the same job • Agriculture is crop dependent (time of year) and weather dependent and
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