Synthetic Biology

The Vickers Group, led by Group Leader Associate Professor Claudia Vickers, applies synthetic biology approaches to answer key fundamental biological questions and to develop/improve industrial bio-processes. In particular, they are interested in using biology to replace current industrial practices (largely based on finite petrochemical resources) with sustainable, environmentally friendly processes. To this end, they use the tools of systems and synthetic biology for metabolic engineering of organisms. Metabolic engineering is the rational redesign of organisms for production of specific industrially-useful compounds.

The Group is particularly interested in a large group of natural products called isoprenoids. Isoprenoids have many different biological functions, and they also have a multitude of biotechnological applications (e.g. biofuels, agricultural chemicals, flavours, fragrances, pharmaceuticals, and food additives).

Research Highlights

The Vickers group currently works in yeast (Saccharomyces cerevisiae), Escherichia coli, cyanobacteria (Synechocystis and Synechococcus spp.), Pseudomonas putida, and plants (various species).  These diverse areas are linked though application of synthetic biology to understand fundamental biology, and applying this understanding to industrial bioprocesses.

The group is experienced in working closely with colleagues in other disciplines and with a wide range companies interested in pursuing emerging opportunities in these fields.

Researchers


Students


2015-2016

Vickers, C.E. (2016) Bespoke design of whole-cell microbial machinesMicrobial Biotechnology  (invited)

Vickers, C.E.* (2016) The minimal genome comes of ageNature Biotechnology 34(5):623-624

Williams, T. C.; Peng, B.-Y.; Vickers, C.E.*; Nielsen, L.K. (2016) The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-productionMetabolic Engineering Communications 3:142-152

Shi, Z.* & Vickers, C.E. (2016) Molecular Cloning Designer Simulator (MCDS): All-in-one Molecular Cloning and Genetic Engineering Design, Simulation & Management Software for Complex Synthetic Biology and Metabolic Engineering ProjectsMetabolic Engineering Communications 3:173-186

Peng, B.; Williams, T.C.; Henry, M.; Nielsen, L.K.; Vickers, C.E.* (2015) Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activitiesMicrobial Cell Factories 14:91.

Williams, T.C.; Esponisa, M.I.; Nielsen, L.K.; Vickers, C.E.* (2015) Dynamic regulation of gene expression using sucrose responsive promoters and RNA interference in Saccharomyces cerevisiaeMicrobial Cell Factories 14:43

Williams, T.C.; Averesch, N.J.H.; Winter G.; Plan, M.R.; Vickers, C.E.; Nielsen, L.K.; Krömer, J.O.* (2015) Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiaeMetabolic Engineering 29:124-34

Bongers, M.; Chrysanthopoulos, P. K.; Behrendorff, J.B. Y. H.; Hodson, M.P.; Vickers, C. E.*; Nielsen, L. K. (2015) Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metaboliteMicrobial Cell Factories 14:193

Book Chapters

Vickers, C.E.*; Sabri, S. (2015) IsopreneIn: Kamm B. (ed.) Biotechnology of Isoprenoids. Advances in Biochemical Engineering/Biotechnology, vol. 148. Springer: Berlin, Heidelberg; pp. 289-317.

Vickers, C.E.*; Behrendorff, J.B.Y.H.; Bongers, M.; Brennan, T.C. R.; Bruschi, M., Nielsen, L.K. (2015) Production of industrially-relevant isoprenoid compounds in engineered microbesIn: Kamm B. (ed.) Microorganisms in Biorefineries. Microbiology Monographs, vol. 26. Springer: Berlin, Heidelberg; pp. 303-334.

Vickers, C.E.*; Bongers, M.; Bydder, S.F.; Chrysanthopoulos, P.; Hodson, M.P. (2015) Protocols for the Production and Analysis of Isoprenoids in Bacteria and YeastIn: McGenity, T.J.; Timmis, K.N.; Nogales, B. (ed.) Hydrocarbon and Lipid Microbiology Protocols, vol. 26. Springer: Berlin, Heidelberg; Ch. 11 pp. 23-52.

*Asterisks show corresponding author

2013-2014

Jardine, K.; Chambers, J.; Nielsen, L.K.; Alves, E.G.; Teixeira, A.; Garcia, S.; Holm, J.; Higuchi, N.; Manzi, A.; Abrell, L.; Fuentas, J.; Nielsen, L.K.; Torn, M; Vickers, C.E. (2014) Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress. Plant Physiology 166(4): 2051-2064

Arifin, Y.; Archer, C.; Lim, S.; Quek, L.-E.; Sugiarto, H.; Marcellin, E.; Vickers, C.; Krömer, J.; Nielsen, L.K. (2014) Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formationApplied Microbiology and Biotechnology 98(21): 9033-44

Bell, K.L; Rangan, H., Fowler, R.; Kull, C.A.; Pettigrew, J.D.; Vickers, C.E.; Murphy, D.J. (2014) Genetic diversity and biogeography of the Australian boab, Adansonia gregorii (Malvaceae: Bombacoideae)Australian Journal of Botany 62(2):164-174

Ryan, A. C.; Hewitt, C. N.; Possell, M.; Vickers, C.E.; Purnell, A.; Mullineaux, P. M., Davies, W. J.; Dodd, I.C. (2014) Isoprene emission protects photosynthesis but reduces plant productivity during drought in transgenic tobacco plantsNew Phytologist 201(1):205-16

Tattini, M.; Velikova, V. Vickers, C.E.; Brunetti, C.; Di Ferdinando, M.; Trivellini, A.; Fineschi, S.; Agati, G.; Ferrini, F.; Loreto, F. (2014) Isoprene production in transgenic tobacco alters isoprenoids, non-structural carbohydrates and phenylpropanoids metabolism, and protects photosynthesis from drought stressPlant, Cell & Environment 37(8):1950-64

Vickers, C.E.*; Bongers, M.; Qing, L.; Delatte, T.; Bouwmeester, H. (2014) Metabolic engineering of volatile isoprenoids in plants and microbesPlant, Cell & Environment 37(8):1753-1775 (invited)

Steen, J.A.; Bohlke, N.; Vickers, C.E.*; Nielsen, L.K. (2014) The trehalose phosphotransferase system (PTS) in coli W can transport low levels of sucrose that are sufficient to facilitate induction of the csc sucrose catabolism operonPLoS One 9(2): e88688

Behrendorff, J.B.Y.H.; Vickers, C.E.*; Chrysanthopoulos, P; Nielsen, L.K. (2013) 2,2-Diphenyl-1-picrylhydrazyl as a screening tool for recombinant monoterpene biosynthesisMicrobial Cell Factories 12:76. Open Access; as of 14/08/16, accessed 6046 times since publication (23/08/2013).

Vickers, C.E.*; Bydder, S.F.; Zhou, Y.; Nielsen, L.K. (2013) Dual gene expression cassette vectors with antibiotic selection markers for engineering in Saccharomyces cerevisiaeMicrobial Cell Factories 12:96. Open Access; as of 14/08/16, accessed 8425 times since publication on 25/10/2013. Open Access; as of 14/08/16, accessed 8425 times since publication on 25/10/2013. Multiple plasmid requests from researchers across the world

Jardine, K.J.*; Meyers, K.; Abrell, L.; Alves, E.G.; Serrano, A.M.Y; Manzi, A; Kesselmeier, J.; Karl, T.; Guenther, A; Chambers, J.; Vickers, C.E. (2013) Emissions of putative isoprene oxidation products from mango branches under abiotic stressJournal of Experimental Botany, 64: 3697-3709

Williams, T.C.; Nielsen, L.K.; Vickers, C.E.* (2013) Engineered quorum-sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiaeACS Synthetic Biology 2(3):136-149. One of the 10 most-read articles in ACS Synthetic Biology for Q1, 2013.

Sabri, S.; Steen, J.A.; Bongers, M.; Nielsen, L.K.; Vickers, C.E.*; (2013) Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised lociMicrobial Cell Factories, 12:60. Open Access; listed as “Highly Accessed”. As of 14/08/15, accessed 12,318 times since publication (24/06/2013). Multiple plasmid requests from researchers across the world.

Sabri, S.; Nielsen, L.K.; Vickers, C.E.* (2013) Molecular control of sucrose utilization in Escherichia coli W, an efficient sucrose-utilizing strainApplied and Environmental Microbiology 79(2):478-487.

2010-2012

Bruschi, M.; Boyes, S.; Sugiarto, H.; Nielsen, L.K.; Vickers, C.E.* (2012) A transferable sucrose utilization approach for non-sucrose-utilizing E. coli strainsBiotechnology Advances 30(5):1001-1010

Vickers, C.E.*; Klein-Marcuschamer, D.; Krömer, J.O. (2012) Examining the feasibility of bulk commodity production in Escherichia coliBiotechnology Letters 34(4): 585-596

Pettigrew, J.D.*; Bell, K.L.; Bhagwandin, A.;  Grinan, E.; Jillani, N.; Meyer, J.; Wabuyele, E.; Vickers, C.E. (2012) Morphology, ploidy and molecular phylogenetics reveal a new diploid species from Africa in the baobab genus Adansonia (Bombacoideae; Malvaceae)Taxon 61(6):1240

Arifin, Y.; Sabri, S.; Sugiarto, H.; Kroemer, J.0.; Vickers, C.E.*, Nielsen, L.K. (2011) Deletion of cscR in Escherichia coli W improves growth and poly-3-hydroxyburyrate (PHB) production from sucrose in fed batch cultureJournal of Biotechnology, 156(4):275-278

Wicks, J.R.*; Oldridge, N.O.; Nielsen, L.K.; Vickers, C.E. (2011) Heart Rate Index – a simple method for prediction of oxygen uptake. Medicine & Science in Sports & Exercise 43(10):2005-2012

Vickers, C.E.*; Possell, M.; Laothawornkitkul, J.; Ryan, A.C.; Hewitt, C.N.; Mullineaux, P. (2011) Isoprene synthesis in plants: lessons from a transgenic tobacco modelPlant, Cell & Environment 34(6):1043–1053

Archer, C.T.; Kim,J.F.;Jeong, H.; Park,J.H.; Vickers, C.E.*; Lee, S.Y.; Nielsen, L. (2011) The genome sequence of coli W ATCC 9637: comparative genome analysis and an improved genome-scale reconstruction of E. coliBMC Genomics 12:9 Online First DOI:10.1186/1471-2164-12-9. Open Access; as of 14/08/16, accessed 19,451 times since publication; listed as “highly accessed”.

Vickers, C.E.*; Blank, L.M.; Kroemer, J.O. (2010) Chassis cells for industrial biochemical productionNature Chemical Biology 6(12):875–877

Lee, J.W.; Choi, S.;Park, J.H.; Vickers, C.E.; Nielsen, L.; Lee, S.Y.* (2010) Development of sucrose-utilizing Escherichia coli K-12 strain by cloning β-fructofuranosidases and its application for L-threonine productionApplied Microbiology and Biotechnology 88(4):905-913

Possell, M.; Ryan, A.;Vickers, C.E.; Mullineaux, P.; Hewitt, C.N.* (2010) Effects of fosmidomycin on plant photosynthesis as measured by gas exchange and chlorophyll fluorescencePhotosynthesis Research 104 (1):49-59

Vickers, C.E.*; Possell, M.; Hewitt, C. N.; Mullineaux, P. M. (2010) Genetic structure and regulation of isoprene synthase in Poplar (Populus )Plant Molecular Biology, 73(4-5):547-558

Jaochimsthal, E. L.; Reeves, R.; Hung, J.; Klieve, A.; Ouwerkerk, D.; Nielsen, L.K.; Vickers, C.E.* (2010) Production of bacteriocins in Australian farm ruminant species. Journal of Applied Microbiology 108(2):428-436

2003-2009

Vickers, C.E.*; Gershenzon, J.; Lerdau, M.; Loreto, F. (2009) A unified mechanism of action for volatile isoprenoids in plant abiotic stress. Nature Chemical Biology 5:283-291 (invited; Highly Cited in WoS Essential Science Indicators)

Vickers, C.E.*, Possell, M.; Cojocariu, C.; Velikova, V.; Laothawornkitcul, J.; Ryan, A.; Mullineaux, P.M.; Hewitt, C.N. (2009) Isoprene synthesis protects transgenic plants from oxidative stress. Plant, Cell & Environment 32:520-531

Laothawornkitkul, J.; Paul, N.D.; Vickers, C.E.; Possell, M.; Taylor, J.; Mullineaux, P.; Hewitt, C.N.* (2008) Isoprene emissions influence herbivore feeding decisions. Plant, Cell & Environment 31:1410-1405

Laothawornkitkul J., Paul N.D., Vickers C.E., Possell M., Taylor J.E., Mullineaux PM, Hewitt C.N.* (2008). The role of isoprene in insect herbivory. 3(12):1141-1142

Vickers, C.E.*, Schenk, P.M.; Mullineaux, P.M. Gresshoff, P.M. (2007) pGFPGUSPlus, a new binary vector for gene expression studies and optimising transformation systems in plants. Biotechnology Letters 29(11):1793-1796

Vickers, C.E.*; Xue, G-P.; Gresshoff, P.M. (2006) A novel cis-acting element, ESP, contributes to high level endosperm-specific expression in an oat globulin promoter. Plant Molecular Biology, 62(1-2):195-214

Wilkinson, M.J.; Owen, S.M.; Possell, M.; Hartwell, J.; Gould, P.; Hall, A.; Vickers, C.; Hewitt, C.N.* (2006) Circadian control of isoprene emissions from oil palm (Elaeis guineensis). Plant Journal, 47(6):960-968

Buzas, D.M., Lohar, D., Sato, S., Nakamura, Y., Tabata, S., Vickers, C.E., Stiller, J., Gresshoff, P.M.* (2005) Promoter trapping in Lotus japonicus reveals novel root and nodule GUS expression domains. Plant and Cell Physiology 46(8):1202-12

Schünmann, P.H.D.; Richardson, A.E.; Vickers, C.E.; Delhaize, E.* (2004) Promoter analysis of the barley Pht1;1 phosphate transporter gene identifies regions controlling root expression and responsiveness to phosphate deprivation. Plant Physiology 136(4):4205-4214

Schenk, P.M.*; Vickers, C.E., Manners, J.M. (2003) Rapid cloning of novel genes and promoters for functional analyses. Transgenics 4:151-156.

Vickers, C. E.*; Gresshoff, P.M.; Xue, G.P. (2003) A synthetic xylanase as a novel reporter in plants. Plant Cell Reports 22(2): 135-140

Xue, G-P.*, Patel, M., Johnson, J.S., Smyth, D.J. and Vickers, C.E. (2003) Selectable marker-free transgenic barley producing a high level of cellulase (1,4-β-glucanase) in developing grains. Plant Cell Reports 21(11): 1088-1094

We have developed a variety of synthetic biology tools to facilitate engineering and more general investigation in many different species. All plasmids are available from Addgene here. Software and other tools available at the links in the sections below.

Yeast Tools

Dual gene expression cassette vectors with antibiotic selection markerDual gene expression cassette vectors with antibiotic selection marker

The pCEV vectors allow over-expression of 2-3 genes from one plasmid in yeast using antibiotic resistance for selection. This is particularly useful for industrial strains that do not have engineered auxotrophies, or for heavily engineered strains that have no auxotrophic markers remaining for selection. Genomic integration is also possible. Read the paper and view Figure here, and get the plasmids here.


Novel yeast promoters for dynamic gene regulationNovel yeast promoters for dynamic gene regulation

Promoters characterised for different carbon substrates and for exponential and ethanol phase growth – read about them here

Figure: Sucrose responsive promoters: grow on glucose to increase the biomass then switch to sucrose to initiate gene expression (or repression) – read about the approach and view Figure here, and get the Suc promoter plasmids here.


Quorum sensing modules for cell-density-dependent gene controlQuorum sensing modules for cell-density-dependent gene control

Engineered quorum-sensing using pheromone-mediated cell-to-cell communication in Saccharomyces cerevisiae. Used to trigger gene expression (or repression using RNAi) according to cell density. Read more and view Figure here. Get the plasmids here.

Figure: (i) When S. cerevisiae population density is low, there is insufficient pheromone (red dots) present to induce GFP expression (blue S. cerevisiae). (ii) Pheromone becomes more concentrated as the population grows; at sufficient pheromone concentration, GFP expression is triggered (green S. cerevisiae). (iii) at sufficient pheromone concentration, GFP is induced across the whole population.


Engineered RNAi for Saccharomyces cerevisiaeEngineered RNAi for Saccharomyces cerevisiae

The RNAi system from S. castelli was imported into S. cerevisiae for gene knock-down. We tested it for shikimate pathway engineering linked to a quorum sensing module and in a sucrose-response-repression system.

Circuit topology of engineered S. cerevisiae. Tryptophan-initiated pheromone quorum sensing, the shikimate pathway, the pheromone responsive FUS1J2promoter and RNAi gene knockout were used to produce high levels of PHBA. See Fig.1b, Williams et al, Metabolic Engineering 29 (2015): 124-134, linked above. Click to enlarge.

Dynamic repression of GFP expression using sucrose mediated RNAi. Expression of a hairpin GFP construct is triggered using SUC2 promoter during growth on sucrose, causing GFP expression to be repressed via RNA interference. See Fig.4b, Williams et al, Microbial Cell Factories (2015) 14:43, linked above. Click to enlarge.

E. coli Tools

 Large DNA insertion onto the E. coli genomeKIKO Vectors: Large DNA insertion onto the E. coli genome

The KIKO vector series is used for rapid, efficient integration of very large DNA sequences onto the E. coli genome at well-characterised non-essential insertion loci. These plasmids are particularly useful for introduction of multiple genes and pathways, for example when reconstructing long metabolic pathways for metabolic engineering applications. Read more here and get the plasmids here.

Knock-in/Knock-out (KIKO) vector. Three operons (OP1a, OP1, OP2-H) carrying genes of the MEP pathway, and a single MEP pathway gene (HDR), have been cloned into the multiple cloning site (MCS) for integration into the E. coli genome by homologous recombination. Click to enlarge images.

Genome of E. coli MG1655Shows locations of KIKO non-essential target lociarsBrbsAR and lacZ. Inset shows bright green fluorescence produced by engineered strain carrying green fluorescent protein (gfp), xylanase (xyn) and sucrose utilization (csc) genes. See Figures 1, 2 and 5 (Sabri et al., 2013) here.


Sucrose Utilisation ModuleSucrose Utilisation Module

Sucrose is a cheap, abundant carbon source – but most lab and industrial strains of E. coli cannot utilise it. We developed a transferable sucrose utilization approach for non-sucrose-utilizing E. coli strains. Read about it here and get the plasmid here.

pCSCx plasmid. FRT-CmR-FRT (flippase recognition target, chloramphenical resistance gene) cassette and cscAKB genes were cloned into lacZ gene. TheHomologous Recombination Cassette for transferable sucrose utilization was amplified from this plasmid. HA = homologous arm.


Genome Sequence and Genome Scale Reconstruction of E.ColiGenome Sequence and Genome Scale Reconstruction of E. coli W

We sequenced the genome of a sucrose-utilising E. coli strain and developed an improved genome-scale reconstruction of E. coli. Read more and download tools here.

Circular map of E. coli W chromosome. Circles from outside to inside: Outer, position in bp; 2nd, 3rd and 4th (blue), forward ORFs, reverse ORFs and pseudogenes, respectively; 5th (green), pseudoknot; 7th, large mobile elements – phage-like elements (PLEs, green), prophages (red); inner, G+C (purple) and A+T (tan) content. See Fig 1, Archer et al (2011), linked above.

Plant Tools

Binary Vectors for Plant TransformationBinary Vectors for Plant Transformation

pGFPGUSPlus: a dual reporter gene binary vector for plant transformation. Contains cassettes for both GUSPlus and GFP. Useful for developing and improving transformation systems; you can also replace one reporter gene with your gene of interest and use the other reporter to track transformation, do linked segregation studies in progeny, etc. Read more here and get the plasmid here.


Endosperm-specific cereal promotersEndosperm-specific cereal promoters

Strong, endosperm-specific promoters for cereal crops. Can be used for cereal seed improvement and plant bio-factory applications. Read more here and get the plasmids here.


GUSPlus PlasmidUbi:GUSPlus Plasmid

The GUSPlus reporter gene driven by the constitutive, ubiquitous ubi promoter. Useful as a reporter gene control for plasmid work in plants. Publication here and get the plasmid here.

General Tools

Molecular Cloning Designer Simulator (MCDS)Molecular Cloning Designer Simulator (MCDS)

All-in-one Molecular Cloning and Genetic Engineering Design, Simulation & Management Software for Complex Synthetic Biology and Metabolic Engineering Projects. A fantastic resource for complex synthetic biology and metabolic engineering projects; does all your in-silico design, handles project workflows including experimental notes and flow-on updating, and acts as a project database. And it’s free! Read the paper here and download the software here.


​Xylanase Reporter GeneXylanase Reporter Gene

sXynA: A synthetic xylanase reporter gene for functional analysis. We tested it in plants but it also works fine in E. coli and probably other organisms – the gene is a fungal gene. Can be used in conjunction with the GUSPlus reporter gene for promoter analysis here and get the plasmids here.


​GFP RNAiGFP RNAi

Green fluorescent protein RNAi construct – can be used to knock down GFP conditionally. Currently under the control of a sucrose-responsive promoter in a yeast expression vector (see here for details), but can be sub-cloned into other constructs for your bespoke applications. Get the plasmid here.


Rapid, High-Throughput Cloning MethodRapid, High-Throughput Cloning Method

A rapid cloning technique for functional analysis of genes and promoters. A bit old-tech but it works. Download it here


High-Throughput Screening for Monoterpene ProductionHigh-Throughput Screening for Monoterpene Production

A 2,2-diphenyl-1-pycrylhydrazyl (DPPH) based method for high-throughput screening and selection of monoterpene production strains. Read about it here