• Research group

Patron Group

Taking a synthetic biology approach to study the function of DNA sequences and developing bioengineering and genome engineering technologies for photosynthetic organisms.

Group leader
Nicola Patron

Group activities.

Photosynthetic organisms like plants and algae utilise CO2 and sunlight to produce a diverse range of organic compounds. Agriculture is the ultimate large-scale, decentralised production systems, using 40% of earth’s landmass and providing us with food, medicines, fibres, fuels, adhesives, dyes and resins.

In our lab we are taking a synthetic biology approach to study the function of DNA sequences and to develop molecular tools and genome engineering technologies for photosynthetic organisms. We aim to engineer photosynthetic organisms for the biosynthesis of materials and therapeutics and to improve plants for increased production and nutritive value.

We are also interested the societal impacts of synthetic biology, particularly in the complex intellectual property and licensing issues that surround genetic sequences and natural products. We believe in open and responsible innovation and are engaged with efforts to extend this ethos to bioresources and bioengineering.

Tools.

We have published a number of tools for Type-IIs mediated DNA assembly and genome engineering: Please note that we are unable to handle the number of requests that we receive for plasmids and therefore cannot send plasmids directly from our lab. All of our published plasmids (see below) are available from the non-profit organisation, AddGene (https://www.addgene.org/). If you deposit your own plasmids with AddGene you will accrue points that allow you to request plasmids free-of-charge. Otherwise, there is an administrative fee to pay for shipping, handling, maintenance and quality assurance.

The Golden Gate Modular Cloning Toolbox for Plants:

This toolkit was described in Engler, C., et al. A Golden Gate Modular Cloning Toolbox for Plants ACS Synthetic Biology 11, 839–843 (2014) DOI: 10.1021/sb4001504

The toolkit consists of two plates:

The Golden Gate MoClo Plant Toolkit (http://www.addgene.org/cloning/MoClo/Marillonnet/)
The Golden Gate MoClo Plant Parts Kit (http://www.addgene.org/cloning/MoClo/Patron/)
We have also produced a set of training videos for this toolkit, these are available on YouTube (https://www.youtube.com/watch?v=xusiavAC_Xk)

The Universal Acceptor for cloning new parts in the Plant Common Syntax:

This is described in Patron, N.J. et al. Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts New Phytologist 208,13-9 (2015) DOI: 10.1111/nph.13532
pUAP1 - #63674.  A sheet describing how to use this tool to make new standard parts.

Molecular tools for RNA-guided Cas9-mediated genome engineering in plants: We have described and demonstrated the use of parts for RNA-guided Cas9-mediated genome engineering compatible with parts and tools from Golden Gate MoClo Plant Toolbox in:

Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease.

Lawrenson, T., Shorinola, O., Stacey, N., Liu, C., Østergaard, L., Patron, N.J., Uauy, C. & Harwood, W.  Genome Biology 16, 258 (2015)

and

Multigene Engineering with RNA-guided Cas9 nuclease.

Raitskin, O. & Patron, N.J.  Current Opinion in Biotechnology 37, 69-75 (2016) DOI: 10.1016/j.copbio.2015.11.008

The following parts were used to construct circuits for Cas9-induced targeted mutagenesis in barley (Hordeum vulgare) and/or Brassica oleracea:

#68262 pICSL90003  Level 0: PROM U6 (Triticum aestivum)
#68261 pICSL90002  Level 0: PROM U6-26 (Arabidopsis thaliana)
#68257 pICSL12009  Level 0: PROM Ubi (Zea mays)
#50270 pICSL12006  Level 0: PROM CsVMV (Cassava Vein Mosaic Virus)
#68260 pICSL80037  Level 0: CDS neomycin phosphotransferase II (Escherichia coli)
#68259 pICSL80036  Level 0: CDS hygromycin phosphotransferase II (Escherichia coli)
#50339 (from the Kamoun lab) Level 0: CDS Cas9 (Streptococcus pyogenes)
#46966 (from the Kamoun lab) Level 0: sgRNA scaffold
#68263 pICSL11059  Level 1, Position 1: CaMV35s:TMV-Omega_hptII with intron_CaMV35s
#68252 pICSL11055  Level 1: CaMV 35S_nptII_nos
#68264 pICSL11060  Level 1, Position 2: CsVMV_Cas9_CaMV35s
#68258 pICSL11056  Level 1, Position 2: ZmUbi_Cas9_CaMV35s

Publications.

Blueprints for green biotech: development and application of standards for plant synthetic biology.

Patron, N.J.  Biochemical Society Transactions 44, 702-708 (2016) DOI: 10.1042/BST20160044

Multigene Engineering with RNA-guided Cas9 nuclease.

Raitskin, O. & Patron, N.J.  Current Opinion in Biotechnology 37, 69-75 (2016) DOI: 10.1016/j.copbio.2015.11.008

GARNet/OpenPlant CRISPR-Cas Workshop.

Parry, G., Patron, N.J., Bastow, R. & Matthewman, C. Methods in Plant Biology 12,16 (2016) DOI: 10.1186/s13007-016-0104-z

Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease.

Lawrenson, T., Shorinola, O., Stacey, N., Liu, C., Østergaard, L., Patron, N.J., Uauy, C. & Harwood, W. Genome Biology 16, 258 (2015) DOI: 10.1186/s13059-015-0826-7

Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts

Patron, N.J. et al.  New Phytologist 208,13-9 (2015) DOI: 10.1111/nph.13532

An Introduction to Synthetic Biology in Plant Systems.

Carmichael, R.E., Boyce, A., Matthewman, C. & Patron, N.J.  New Phytologist 208, 20-2 (2015) DOI: 10.1111/nph.13433

A Standard Type IIS Syntax for Plants (2015)

Rutten, V. et al. BBF RFC 106:

Editing plant genomes with CRISPR/Cas9.

Belhaj, K., Chaparro-Garcia, A., Kamoun, S., Patron, N.J. & Nekrasov, V.  Current Opinion in Biotechnology 32, 76–84 (2015)  DOI: 10.1016/j.copbio.2014.11.007

DNA assembly for plant biology: techniques and tools.

Patron, N.J. Current Opinion in Plant Biology 19, 14–19 (2014) DOI:10.1016/j.pbi.2014.02.004

A Golden Gate Modular Cloning Toolbox for Plants.

Engler, C., et al. ACS Synthetic Biology 11, 839–843 (2014) DOI: 10.1021/sb4001504

Reduced lignin content and altered lignin composition in the warm season forage grass Paspalum dilatatum by down-regulation of a Cinnamoyl CoA Reductase Gene.

Giordano, A. et al. Transgenic Research 23, 503-17 (2014) DOI: 10.1007/s11248-014-9784-1

Related reading.