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.

Plants provide us with food, textiles, building materials and numerous metabolic compounds used in health and industry. They also provide the potential for rapid production of complex molecules from water and light. Until recently, we lacked the tools and data necessary for complex engineering of plant systems. The application of engineering principles to plant biology has enabled us to establish platforms for high-throughput, automated, experimentation at nanoscales. In our lab, we develop and apply engineering approaches to understand biological complexity and advance plant biotechnology.

Our research is focused on:

Understanding the intrinsic and emergent properties of gene regulatory elements, the role of network motifs and, ultimately, how phenotypes emerge from network functions. We apply computational tools and use rewiring and reconstruction to investigate the relationship between sequence and function. Our long-term goals are to develop the knowledge and technologies required to manipulate plant responses through the rational engineering of gene regulatory networks.
Exploring and utilising metabolic diversity. Plants synthesise a multitude of specialised metabolites, many of which have potential in human health and industry. We integrate genomics, metabolomics and transcriptomics to investigate the genetic basis of these molecules, enabling us to understand mechanisms of metabolic diversification and explore methods for biomanufacturing. We also develop plants as photosynthetic biomanufacturing platforms, applying engineering approaches to improve purity and yield.

Projects.

Earth Biogenome Project

Exploring the metabolic diversity of UK plants

Recoding Regulation

Improving Plants for Biomanufacturing

Sustainable bioproduction of insect pheromones for pest control in agriculture

Plant Genome Engineering

Automated Nanoscale DNA Assembly

Team members.

Yaomin Cai,

Postdoctoral Scientist

Daria Golubova,

PhD Student

Carolina Grandellis,

Earlham Biofoundry Manager

Lesley Ives,

Automation Senior Research Assistant, Earlham Biofoundry

Nicola Patron,

Synthetic Biology Group Leader

Melissa Salmon,

Postdoctoral Scientist

Honghao Su,

PhD Student

Connor Tansley,

Postdoctoral Research Scientist

Mehmet Tufan Oz,

Postdoctoral Scientist

Samuel Witham,

PhD Student

Visiting and affiliated colleagues.

Quentin Dudley,

Visiting Scientist

Alumni.

Adam Elliston,

Research Assistant

Tools.

You can find all of our published plasmids at

https://www.addgene.org/Nicola_Patron/

Synthetic promoters from Cai et al (2020) Rational design of minimal synthetic promoters for plants. Nucleic Acids Res. 2020 Aug 28. pii: 5897334. doi: 10.1093/nar/gkaa682

#154477 – #154753 Level 0 promoter parts and Level 1reporter constructs

LOOP assembly plasmids from Sauret-Gueto et al (2020) Systematic tools for reprogramming plant gene expression in a simple model, Marchantia polymorpha. ACS Synth Biol. 2020 Mar 12. doi: 10.1021/acssynbio.9b00511.

#136695 Loop acceptor plasmid (odd level position 1)

#136696 Loop acceptor plasmid (odd level position 2)

#136697 Loop acceptor plasmid (odd level position 3)

#136698 Loop acceptor plasmid (odd level position 4)

Plasmids from Raitskin et al (2019) Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants. An expanded toolkit for plant genome engineering:

#49770 pICSL90004 Level 0 SpCas9-h (with stop codon)

#117520 pICSL90005 Level 0 SpCas9-h (no stop codon)

#117521 pEPOR0SP0013 Level 0 SpCas9-p (with stop codon)

#117522 pEPOR0SP0009 Level 0 SpCas9-p (no stop codon)

#117523 pEPOR0SP0001 Level 0 SpCas9-DE (no stop codon)

#117524 pEPOR0SP0014 Level 0 SpCas9-KA (with stop codon)

#117525 pEPOR0SP0015 Level 0 SpCas9-KA (no stop codon)

#117526 pEPOR0SP0016 Level 0 Sp-eCas9 1.0 (with stop codon)

#117527 pEPOR0SP0017 Level 0 Sp-eCas9 1.0 (no stop codon)

#117528 pEPOR0SP0018 Level 0 Sp-eCas9 1.1 (with stop codon)

#117529 pEPOR0SP0019 Level 0 Sp-eCas9 1.1 (no stop codon)

#117530 pEPOR0SP0011 Level 0 Sp-xCas9 3.7 (no stop codon)

#117531 pEPOR0SP0020 Level 0 SaCas9 (with stop codon)

#117532 pEPOR0SP0021 Level 0 SaCas9 (no stop codon)

#117533 pEPOR0SP0012 Level 0 eSaCas9 (no stop codon)

#117534 pEPOR0SP0007 Level 0 LbCas12a (with stop codon)

#117535 pEPOR0SP0008 Level 0 AsCas12a (with stop codon)

#117536 pICSL50005 Level 0 c-term tag YFP

#50269 pICH51288 Level 0 2x35S_(promoter + 5UTR)

#68261 pICSL90002 Level 0 At U6-26 (promoter)

#50339 pICH41421 Level 0 Nos (3UTR + terminator)

#117542 pICSL11023 Level 1 2x35S_+ SpCas9-h:YFP + Nos

#117543 pEPOR1CB0002 Level 1 2x35S_+ SpCas9-p:YFP + Nos

#117544 pEPOR1CB0008 Level 1 2x35S_+ SpCas9-DE:YFP + Nos

#117545 pEPOR1CB0009 Level 1 2x35S_+ SpCas9-K855A:YFP + Nos

#117546 pEPOR1CB0010 Level 1 2x35S_+ Sp-eCas91.0:YFP + Nos

#117547 pEPOR1CB0011 Level 1 2x35S_+ Sp-eCas91.1:YFP + Nos

#117548 pEPOR1CB0112 Level 1 2x35S_+ Sp-xCas9 3.7.1:YFP + Nos

#117549 pEPOR1CB0013 Level 1 2x35S_+ LbCas12a + Nos

#117550 pEPOR1CB0014 Level 1 2x35S_+ AsCas12a + Nos

#117551 pEPOR1CB0015 Level 1 2x35S_+ SaCas9:YFP + Nos

#117552 pEPOR1CB0113 Level 1 2x35S_+ eSaCas9:YFP + Nos

The Universal Acceptor Plasmid from Patron et al (2015) Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts:

#63674 pUAP1 (Universal Acceptor Plasmid 1)

Plasmids from Lawrenson et al (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease:

#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)

#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.

A biofoundry workflow for the identification of genetic determinants of microbial growth inhibition.

Moffat AD, Elliston A, Patron NJ, Truman AW, Carrasco Lopez JA. Synth Biol (Oxf). 2021 Jan 28;6(1):ysab004. doi: 10.1093/synbio/ysab004.

80 questions for UK biological security

Kemp L, Aldridge DC, Booy O, Bower H, Browne D, Burgmann M, Burt A, Cunningham AA, Dando M, Dick JTA, Dye C, Weiss Evans S, Gallardo B, Godfray HCJ, Goodfellow I, Gubbins S, Holt LA, Jones KE, Kandil H, Martin P, McCaughan M, McLeish C, Meany T, Millett K, ÓhÉigeartaigh SS, Patron NJ, Rhodes C, Roy HE, Shackelford G, Smith D, Spence N, Steiner H, Sundaram LS, Voeneky S, Walker JR, Watkins H, Whitby S, Wood J, Sutherland WJ (2021). PLoS One. 2021 Jan 6;16(1):e0241190.

doi: 10.1371/journal.pone.0241190.

Rational design of minimal synthetic promoters for plants.

Cai YM, Kallam K, Tidd H, Gendarini G, Salzman A, Patron NJ. Nucleic Acids Res. 2020 Dec 2;48(21):11845-11856.

doi: 10.1093/nar/gkaa682.

Phytobricks: Manual and Automated Assembly of Constructs for Engineering Plants.

Cai YM, Carrasco Lopez JA, Patron NJ. Methods Mol Biol. 2020;2205:179-199.

doi: 10.1007/978-1-0716-0908-8_11.

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

Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, Wulff BBH. Plant Biotechnol J. 2020 Aug 3.

doi: 10.1111/pbi.13460.

Generating and characterizing single- and multigene mutants of the Rubisco small subunit family in Arabidopsis.

Khumsupan P, Kozlowska MA, Orr DJ, Andreou AI, Nakayama N, Patron N, Carmo-Silva E, McCormick AJ. J Exp Bot. 2020 Oct 7;71(19):5963-5975.

doi: 10.1093/jxb/eraa316.

Bioengineering horizon scan 2020

Kemp L*, Adam L, Boehm CR, Breitling R, Casagrande R, Dando M, Djikeng A, Evans NG, Hammond R, Hills K, Holt LA, Kuiken T, Markotić A, Millett P, Napier JA, Nelson C, ÓhÉigeartaigh SS, Osbourn A, Palmer M, Patron NJ, Perello E, Piyawattanametha W, Restrepo-Schild V, Rios-Rojas C, Rhodes C, Roessing A, Scott D, Shapira P, Simuntala C, Smith RD, Sundaram LS, Takano E, Uttmark G, Wintle B, Zahra NB, Sutherland WJ. Elife. 2020 May 29;9:e54489.

doi: 10.7554/eLife.54489.

Beyond natural: synthetic expansions of botanical form and function

Patron NJ. New Phytol. 2020 Jul;227(2):295-310.

doi: 10.1111/nph.16562. Epub 2020 Apr 23.

Systematic Tools for Reprogramming Plant Gene Expression in a Simple Model, Marchantia polymorpha.

Sauret-Güeto S, Frangedakis E, Silvestri L, Rebmann M, Tomaselli M, Markel K, Delmans M, West A, Patron NJ, Haseloff J. ACS Synth Biol. 2020 Apr 17;9(4):864-882.

doi: 10.1021/acssynbio.9b00511. Epub 2020 Apr 2.

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