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Microbiology Logo Microbiology & Immunology
Te Tari Moromoroiti me te Ārai Mate

Dr Simon Jackson


Current research:

The overall aim of my research group is to understand the interactions between bacterial viruses (phages) and their hosts. Currently, we are funded to study bacterial phage defence systems, such as CRISPR-Cas adaptive immune systems. With the rise of antimicrobial resistance (AMR) in bacterial pathogens, we urgently need to find new ways to treat bacterial infections. Exploiting phages as natural antimicrobials to kill bacterial pathogens, termed phage therapy, is a promising approach to address the AMR crisis. However, the success of phage therapy is dependent on understanding the complex interaction between phages and bacteria. To address these challenges, we use a combination of bioinformatic, comparative genomics and molecular biology approaches. In 2017, I was awarded the IlluminaTM Emerging Researcher Award, as the top New Zealand Molecular Biologist within 5 years of PhD completion.

Areas of Current Research Focus:

  • Understanding how bacteria update their CRISPR-Cas adaptive immune systems, termed CRISPR adaptation.
  • Exploring cooperation between diverse CRISPR-Cas systems to prevent viral escape from immunity.
  • Discovery and characterisation of new types of phage defense system encoded by bacteria.
  • The relationships between phage defense and symbiosis in Rhizobia.

Applications:

  • Exploiting phages to enhance legume productivity.
  • Developing new types of molecular diagnostics to detect bacterial and viral infections.
  • Exploiting phage-encoded enzymes as new antimicrobials.
  • Developing technologies to unlock the potential of antimicrobial biosynthesis pathways encoded in metagenome libraries.

Links:

Google Scholar: https://scholar.google.co.nz/citations?user=RMiXfysAAAAJ&hl=en

Scopus: https://www.scopus.com/authid/detail.uri?authorId=55419787700

GitHub: https://github.com/JacksonLab

Maurice Wilkins Center for Molecular Biodiscovery

Postgraduate Student (co)-supervision:

PhD:

Nils Birkholz, current
Leah Smith, current
Hannah Hampton, 2015-2018

MSc:

Bridget Fellows, current
Stephanie Trickey, current
Nils Birkholz, 2016
Julian Taffner, 2014

BSc(Hons):

Leighton Payne, 2019
Maureen Yin, 2019
Nick Donaldson, 2018
Matthew Prouse, 2014
Lauren Nichol, 2014
Jack Hervey, 2013

Summer studentships:

Leighton Payne, 2019-2020
Maureen Yin, 2018-2019
Nick Donaldson, 2017-2018
Jack Hervey, 2012-2013  

Research Funding and Fellowships:

2019   University of Otago Research Grant ($37,471) as PI. ‘A new approach to discover phage defence systems in bacteria.’

2019   MBIE SmartIdeas ($1,000,000) as a Key Researcher (PI: Prof. Peter Fineran). ‘Phage-inspired custom antimicrobials to target bacterial pathogens.’

2019   Deans Bequest (University of Otago, $21,000) as PI. ‘New types of phage defences encoded in bacterial genomes.’

2019   Maurice Wilkins Centre Flexible Research Grant ($26,000) as an AI (PI: Dr Jeremy Owen, Victoria University of Wellington). ‘Development of new synthetic biological tools for cloning and expression of antibiotic biosynthetic gene clusters from microbial genomes.’

2018   Marsden Fast Start Grant (RSNZ), as PI ($300,000) (AI: Prof. Antonio Sánchez-Amat, University of Murcia, Spain). ‘Mobile CRISPR-Cas systems and the genesis of hybrid adaptive immunity in bacteria.’

2018   EMBO Workshop ‘Viruses of Microbes 2018’ travel grant (€500).

2017   Deans Bequest (University of Otago, $16,000) as an AI (PI: Prof. Peter Fineran). ‘Chimeric CRISPR-Cas systems – the evolution of new bacterial immunity?’

2016   Deans Bequest (University of Otago, $21,648) as an AI (PI: Prof. Peter Fineran). ‘You’re 1 in a million: a novel high-throughput methodology for finding key regulators of gene expression in bacteria.’

2013   Division of Health Sciences Career Development Postdoctoral Fellowship (~$150,000, University of Otago). ‘Assembly and photoprotection of Photosystem II in Synechocystis sp. PCC 6803.’

Publications:

* Equal contribution authors; # Corresponding author

2020:

Malone, L.M., Warring, S.L., Jackson, S.A., Warnecke, C., Gardner, P.P., Gumy, L.F. and Fineran, P.C.# (2020) A jumbophage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nature Microbiology, 5: 48-55

2019:

Jackson, S.A. and Fineran, P.C. (2019) Bacterial dormancy curbs phage epidemics. Nature, 570: 173-174.

Birkholz, N., Fagerlund, R.D.*, Smith, L.M., Jackson, S.A.* and Fineran, P.C.# (2019) The autoregulator Aca2 mediates anti-CRISPR repression. Nucleic Acids Research, 47: 9658-9665

Jackson, S.A.#, Birkholz, N., Malone, L.M. and Fineran, P.C.# (2019) Imprecise spacer acquisition generates CRISPR-Cas immune diversity through primed adaptation. Cell Host and Microbe, 25: 250-260

Nicholson, T.J.*, Jackson, S.A.*, Croft, B.I., Staals, R.H.J., Fineran, P.C.# and Brown, C.M. # (2019) Bioinformatic evidence of widespread priming in Type I and II CRISPR-Cas systems. RNA Biology, 16: 566-576

2018:

Hampton, H.G., Jackson, S.A., Fagerlund, R.D., Vogel, A.I.M., Dy, R.L., Blower, T.R. and Fineran, P.C. # (2018) AbiEi Binds Cooperatively to the Type IV abiE Toxin-Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation. Journal of Molecular Biology, 430: 1141-1156

2017:

Silas, S., Lucas-Elío, P., Jackson, S.A., Aroca-Crevillén, A., Hansen, L.L., Fineran, P.C., Fire, A.Z. and Sánchez-Amat, A.# (2017) Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. eLife, 6. e27601

Jackson, S.A.*, McKenzie, R.E.*, Fagerlund, R.D., Kieper, S.N., Fineran, P.C.# and Brouns, S.J.J.# (2017) CRISPR-Cas: adapting to change. Science, 356: eaal5056. doi: 10.1126/science.aal5056

2016:

Patterson, A.G., Jackson, S.A., Taylor, C., Evans, G.B., Salmond, G.P., Przybilski, R., Staals, R.H.J. and Fineran, P.C.# (2016) Quorum sensing controls adaptive immunity through multiple CRISPR-Cas systems. Molecular Cell, 64: 1102-1108

Staals, R.H.J., Jackson, S.A., Biswas, A., Brouns, S.J.J., Brown, C.M. and Fineran, P.C.# (2016) Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nature Communications, 7: 12853

Jackson, S.A. and Eaton-Rye, J.J.# (2016) Modular growth vessels for the cultivation of the cyanobacterium Synechococcus sp. PCC 7002. New Zealand Journal of Botany, DOI: 10.1080/0028825X.2016.1231123

2015:

Jackson, S.A.*, Eaton-Rye, J.J., Bryant, D.A. Posewitz, M.C. and Davies, F.K.*,# (2015) Dynamics of photosynthesis in a glycogen-deficient glgC mutant of Synechococcus sp. PCC 7002. Applied and Environmental Microbiology, 81: 6210-6222

Jackson, S.A. and Eaton-Rye, J.J.# (2015) Characterization of a Synechocystis sp. PCC 6803 double mutant lacking the CyanoP and Ycf48 proteins of Photosystem II. Photosynthesis Research, 124: 217-229

2014:

Jackson, S.A., Hervey, J.R.D., Dale, A.J. and Eaton-Rye, J.J.# (2014) Removal of both Ycf48 and Psb27 in Synechocystis sp. PCC 6803 disrupts Photosystem II assembly and alters QA- oxidation in the mature complex. FEBS Letters, 588: 3751-3760

Luo, H., Jackson, S.A., Fagerlund, R.D., Summerfield, T.C. and Eaton-Rye, J.J.# (2014) The importance of the hydrophilic region of PsbL for the plastoquinone electron acceptor complex of Photosystem II. Biochim Biophys Acta Bioenergetics, 1837: 1435-1446

2013:

Jackson, S.A., Fagerlund, R.D., Hinds, M.G., Wilbanks, S.M. and Eaton-Rye, J.J. (2013) Structure-function studies of the Photosystem II extrinsic subunits PsbQ and PsbP from the cyanobacterium Synechocystis sp. PCC 6803. Photosynthesis for Food, Fuel and the Future. Springer, 86-90.

2012:

Jackson, S.A., Hinds, M.G. and Eaton-Rye, J.J.# (2012) Solution structure of CyanoP from Synechocystis sp. PCC 6803: New insights on the structural basis for functional specialization amongst PsbP family proteins. Biochim Biophys Acta Bioenergetics, 1817: 1331-1338

2010:

Jackson S.A.*, Fagerlund R.D.*, Wilbanks S.M. and Eaton-Rye J.J.# (2010) Crystal structure of PsbQ from Synechocystis sp. PCC 6803 at 1.8 Å: implications for binding and function in cyanobacterial Photosystem II. Biochemistry, 49: 2765-2767