• 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.

Synthetic Biology 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.

Building a global alliance of biofoundries

Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Le Feuvre R, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, Keasling JD, Kitney RI, Kondo A, Liu C, Martin VJJ, Menolascina F, Ogino C, Patron NJ et al. (2019) Nature communications 10, 2040. DOI: https://dx.doi.org/doi:10.1038/s41467-019-10079-2

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

Tuncel A, Corbin KR, Ahn-Jarvis J, Harris S, Hawkins E, Smedley MA, Harwood W, Warren FJ, Patron NJ, Smith AM. (2019) Plant Biotechnology Journal DOI: https://doi.org/10.1111/pbi.13137

Unraveling the subtleties of glucan phosphorylase specificity in the GH94, GH149 and GH161 glycoside hydrolase families

Kuhaudomlarp S, Pergolizzi G, Patron NJ, Henrissat B, Field RA. (2019) Journal of Biological Chemistry 294, 6483-6493 DOI: https://doi.org/10.1074/jbc.RA119.007712

An edit for good?

Bickerton P, Patron NJ (2019) Laboratory News

Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants. An expanded toolkit for plant genome engineering.

Raitskin O, Schudoma C, West A, Patron NJ (2019) PLoS ONE 14(2):e0211598

Loop Assembly: a simple and open system for recursive fabrication of DNA circuits

Pollack B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F*, Haseloff J* (2019) New Phytologist 222(1):689-640

Opening options for material transfer

Kahl L*, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, Johnson R and Endy D* (2018) Nature Biotechnology 36:923-927

Plant metabolic engineering in the synthetic biology era: plant chassis selection

Stewart CN*, Patron NJ, Hanson AD and Jez JM (2018) Plant Cell Reports 37(10):1357-1358

Zinc-Finger Nuclease (ZFN)-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template

Ran Y, Patron N, Kay P, Wong D, Buchanan M, Cao Y, Sawbridge T, Davies J, Mason J, Webb S, Spangenberg G, Ainley W, Walsh T, Hayden M* (2018) Plant Biotechnology Journal 16(12):2088-2101

Plant genetic resources for Food and Agriculture: opportunities and challenges emerging from the science and information technology revolution.

Halewood M, Chiurugwi T, Sackville-Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron NJ, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, and Powell W* (2018) New Phytologist 217(4):1407-1419

DNA assembly standards: Setting the low-level programming code for plant biotechnology

Vazquez-Vilar M, Orzaez D, Patron N* (2018) Plant Science 273:33-41

Identification of Euglena gracilis β-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149

Kuhaudomlarp S, Patron NJ, Henrissat B, Rejzeka M, Saalbacha G, Field RA* (2018) Journal of Biological Chemistry 23 (293:8):2865-2876

The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley

Hatta MA, Johnson R, Matny O, Smedley MA, Yu G. Chakraborty S, Bhatt D, Xia X, Arora S, Steuernagel B, Richardson T, Mago R, Lagudah E, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan SK, Steffenson BJ, Wulff BH* (2018) bioRxiv Preprint (in review)

CRISPR-based tools for plant genome engineering

Volpi e, Silva N and Patron NJ* (2017) Emerging Topics in Life Sciences 1(2):135-149

Harnessing Plant Metabolic Diversity

Owen C, Patron NJ, Huang A, Osbourn A (2017) Current Opinion in Chemical Biology 40:24-30

Feeding the Future: The Case for Open Source Technology and an Inclusive Plant Bioengineering Community

Patron NJ* (2017) SynBioLEAP

Point of View: A transatlantic perspective on 20 emerging issues in biological engineering

Wintle BC, Boehm CR, Rhodes C, Molloy J, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Linda Kahl L, Kuiken T, Lichman BR, Matthewman CA, Johnathan Napier J, Ó hÉigeartaigh S, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJ (2017) eLife 6:e30247

SMRT Gate: A method for validation of synthetic constructs on Pacific Biosciences sequencing platforms

D’Amore R, Johnson J, Haldenby S, Hall N, Hughes M, Joynson R, Kenny JG Patron NJ, Hertz-Fowler C and Hall A* (2017) BioTechniques 63(1):13-20

Synthetic Botany

Boehm CR, Pollak B, Purswani N, Patron NJ and Haseloff J* (2017) Cold Spring Harbor Perspectives in Biology 9:a023887

Synthia: Playing God in a sandbox

Richardson S and Patron NJ* (2016) Microbiology Today What is life? (May 2016 Issue): 66-69

Synthetic Biology Handbook

Patron NJ* (2016) Synthetic Plants in Synthetic Biology Handbook Ed: Darren Nesbeth. CRC Press. ISBN 978146656847

Encyclopedia of Applied Plant Sciences 2nd Edition

Patron NJ* (2016) Synthetic Biology and Gene Cloning in Encyclopedia of Applied Plant Sciences 2nd Edition Editor-in-Chiefs: Brian Thomas Denis J Murphy Brian G Murray. Academic Press. eBook ISBN: 9780123948083 Hardcover ISBN: 9780123948076

Meeting report: GARNet/OpenPlant CRISPR-Cas workshop

Parry G*, Patron NJ, Bastow R, Matthewman C (2016) GARNet/OpenPlant CRISPR-Cas workshop in Plant Methods 12(6)

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.