Contact Details
- Phone
- +64 3 479 7735
- peter.fineran@otago.ac.nz
- Position
- Professor
- Department
- Department of Microbiology and Immunology
- Qualifications
- BSc (Hons) PhD
- Research summary
- Molecular microbiology and bacteriophages, Genetics, Biochemistry, Molecular biology
Research
Our research goal is to understand the interactions between mobile genetic elements, such as bacteriophages and plasmids, and their bacterial hosts. Our main interest is in phage resistance mechanisms.
The page-bacterium ‘arms race’
Accumulating evidence demonstrates that viruses are the most abundant biological entities on the planet. They outnumber bacteria by approximately 10 to 1 and there are an estimated >1030 tailed bacteriophages globally! The result is an obvious selective pressure for bacteria to acquire resistance to phage attack and for phages to acquire counter defence mechanisms. Indeed, many mechanisms of phage resistance are known, ranging from bacterial cell surface alterations, through restriction and modification, to abortive infection. Our research focuses on:
- Abortive infection and toxin-antitoxin 'innate immune systems'
- CRISPR-Cas 'adaptive immune systems'
- Phages as antimicrobial agents
Publications
Meulenberg, A., Pavez, M., Gowing, E. K., Mayo-Muñoz, D., Birkholz, N., Suhono, G., Fineran, P. C., Fagerlund, R. D., & Gumy, L. F. (2026). Comparison of CRISPR-Cas-based knockdown of endogenous mRNA in sensory neurons. CRISPR Journal. Advance online publication. doi: 10.1177/25731599261489437 Journal - Research Article
Kyte, N., Fuchs, M., Smith, L. M., & Fineran, P. C. (2026). Defining the essential genome of diverse phages with phage Tn-seq. Nature Microbiology. Advance online publication. doi: 10.1038/s41564-026-02486-1 Journal - Research Article
Feussner, M., Birkholz, N., Lee, S. Y., Beisel, C. L., Park, H. H., Brown, C. M., Fineran, P. C., & Weinberg, Z. (2026). An expanded realm of anti-CRISPR-associated proteins and regulatory mechanisms. Nucleic Acids Research, 54(17), gkag862. doi: 10.1093/nar/gkag862 Journal - Research Article
Wang, X., Jowsey, W. J., Cheung, C.-Y., Dickerhof, N., Chapman, C. L., Taka, J. R. H., Hampton, M. B., … Gardner, P., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2026). Genome scale CRISPRi reveals both shared and strain-specific vulnerabilities in genetically diverse drug-resistant strains of Mycobacterium tuberculosis. Nature Communications. Advance online publication. doi: 10.1038/s41467-026-73952-x Journal - Research Article
Wang, X., Jowsey, W. J., Cheung, C.-Y., Dickerhof, N., Taka, J. R. H., Hampton, M. B., … Gardner, P., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2026, February). Genetic vulnerabilities in rifampicin resistant strains of Mycobacterium tuberculosis [Invited]. Verbal presentation at the Genetics Otago (GO) Annual Symposium, Dunedin, New Zealand. Conference Contribution - Verbal presentation and other Conference outputs
2026
Journal - Research Article
Meulenberg, A., Pavez, M., Gowing, E. K., Mayo-Muñoz, D., Birkholz, N., Suhono, G., Fineran, P. C., Fagerlund, R. D., & Gumy, L. F. (2026). Comparison of CRISPR-Cas-based knockdown of endogenous mRNA in sensory neurons. CRISPR Journal. Advance online publication. doi: 10.1177/25731599261489437
Kyte, N., Fuchs, M., Smith, L. M., & Fineran, P. C. (2026). Defining the essential genome of diverse phages with phage Tn-seq. Nature Microbiology. Advance online publication. doi: 10.1038/s41564-026-02486-1
Feussner, M., Birkholz, N., Lee, S. Y., Beisel, C. L., Park, H. H., Brown, C. M., Fineran, P. C., & Weinberg, Z. (2026). An expanded realm of anti-CRISPR-associated proteins and regulatory mechanisms. Nucleic Acids Research, 54(17), gkag862. doi: 10.1093/nar/gkag862
Wang, X., Jowsey, W. J., Cheung, C.-Y., Dickerhof, N., Chapman, C. L., Taka, J. R. H., Hampton, M. B., … Gardner, P., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2026). Genome scale CRISPRi reveals both shared and strain-specific vulnerabilities in genetically diverse drug-resistant strains of Mycobacterium tuberculosis. Nature Communications. Advance online publication. doi: 10.1038/s41467-026-73952-x
Conference Contribution - Verbal presentation and other Conference outputs
Wang, X., Jowsey, W. J., Cheung, C.-Y., Dickerhof, N., Taka, J. R. H., Hampton, M. B., … Gardner, P., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2026, February). Genetic vulnerabilities in rifampicin resistant strains of Mycobacterium tuberculosis [Invited]. Verbal presentation at the Genetics Otago (GO) Annual Symposium, Dunedin, New Zealand.
2025
Journal - Research Article
Lee, S. Y., Birkholz, N., Lee, J. H., Fineran, P. C., & Park, H. H. (2025). Regulation of anti-CRISPR operons by structurally distinct families of Aca proteins. Communications Biology, 8, 1698. doi: 10.1038/s42003-025-09101-9
Martinez-Cazorla, A., Martinez-Jimenez, C., Lucas-Elio, P., Fineran, P. C., Jackson, S., & Sanchez-Amat, A. (2025). The early injected genomic region determines sensitivity to Type I restriction-modification defence against Autographiviridae phages. Nucleic Acids Research, 53(18), gkaf926. doi: 10.1093/nar/gkaf926
Silk, E., Harding, K., Mahler, M., Fineran, P. C., & Meaden, S. (2025). Abiotic environmental conditions determine phage resistance outcomes in a salt-marsh bacterium. Philosophical Transactions of the Royal Society B, 380(1934), 20240071. doi: 10.1098/rstb.2024.0071
Meaden, S., Westra, E. R., & Fineran, P. C. (2025). Phage defence-system abundances vary across environments and increase with viral density. Philosophical Transactions of the Royal Society B, 380(1934), 380, 20240069. doi: 10.1098/rstb.2024.0069
Smith, L. M., & Fineran, P. C. (2025). Type I CRISPR-Cas immunity primes type III spacer acquisition. Cell Host & Microbe. Advance online publication. doi: 10.1016/j.chom.2025.07.021
Mahler, M., Cui, L., Smith, L. M., Wandera, K. G., Dietrich, O., Mayo-Muñoz, D., … Dubrulle, J., Malone, L. M., Jackson, S. A., … Fineran, P. C. (2025). Phage arabinosyl-hydroxy-cytosine DNA modifications result in distinct evasion and sensitivity responses to phage defense systems. Cell Host & Microbe, 33, 1173-1190. doi: 10.1016/j.chom.2025.06.005
Warring, S., Sisson, H. M., Randall, G., Grimon, D., Dams, D., Gutiérrez, D., Fellner, M., Fagerlund, R. D., … Jackson, S. A., & Fineran, P. C. (2025). Engineering an antimicrobial chimeric endolysin that targets the phytopathogen Pseudomonas syringae pv. actinidiae. Journal of Biological Chemistry. Advance online publication. doi: 10.1016/j.jbc.2025.110224
Hodgkinson-Bean, J., Ayala, R., Jayawardena, N., Rutter, G. L., Watson, B. N. J., Mayo-Muñoz, D., … Fineran, P. C., … Bostina, M. (2025). Global structural survey of the flagellotropic myophage φTE infecting agricultural pathogen Pectobacterium atrosepticum. Nature Communications, 16, 3257. doi: 10.1038/s41467-025-58514-x
Harding, K. R., Malone, L. M., Kyte, N. A. P., Jackson, S. A., Smith, L. M., & Fineran, P. C. (2025). Genome-wide identification of bacterial genes contributing to nucleus-forming jumbo phage infection. Nucleic Acids Research, 53, gkae1194. doi: 10.1093/nar/gkae1194
Journal - Research Other
Lim, C. S., Mace, P., Fineran, P. C., & Gardner, P. P. (2025). Towards a phylogenetically informed approach to solving protein-protein interactions [Perspective]. Biochemical Society Transactions, 53, 1457-1467. doi: 10.1042/bst20253031
Conference Contribution - Published proceedings: Abstract
Wang, X., Jowsey, W. J., Cheung, C.-Y., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2025). Defining therapeutic vulnerabilities in drug-resistant strains of Mycobacterium tuberculosis. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
2024
Journal - Research Article
Wang, X., Jowsey, W. J., Cheung, C.-Y., Smart, C. J., Klaus, H. R., Seeto, N. E. J., Waller, N. J. E., … Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2024). Whole genome CRISPRi screening identifies druggable vulnerabilities in an isoniazid resistant strain of Mycobacterium tuberculosis. Nature Communications, 15, 9791. doi: 10.1038/s41467-024-54072-w
Warring, S. L., Sisson, H. M., Fineran, P. C., & Rabiey, M. (2024). Strategies for the biocontrol Pseudomonas infections pre-fruit harvest. Microbial Biotechnology, 17, e70017. doi: 10.1111/1751-7915.70017
Kamata, K., Birkholz, N., Ceelen, M., Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2024). Repurposing an endogenous CRISPR-Cas system to generate and study subtle mutations in bacteriophages. CRISPR Journal, 7(6), 343-354. doi: 10.1089/crispr.2024.0047
Birkholz, N., Kamata, K., Feussner, M., Wilkinson, M. E., Samaniego, C. C., Migur, A., … Ceelen, M., … Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2024). Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Nature, 631, 670-677. doi: 10.1038/s41586-024-07644-1
Schwartz, E. A., Bravo, J. P. K., Ahsan, M., Macias, L. A., McCafferty, C. L., Dangerfield, T. L., … Fineran, P. C., Fagerlund, R. D., & Taylor, D. W. (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications, 15, 3324. doi: 10.1038/s41467-024-47506-y
Sisson, H. M., Jackson, S. A., Fagerlund, R. D., Warring, S. L., & Fineran, P. C. (2024). Gram-negative endolysins: Overcoming the outer membrane obstacle [Review]. Current Opinion in Microbiology, 78, 102433. doi: 10.1016/j.mib.2024.102433
Sisson, H. M., Fagerlund, R. D., Jackson, S. A., Briers, Y., Warring, S. L., & Fineran, P. C. (2024). Antibacterial synergy between a phage endolysin and citric acid against the Gram-negative kiwifruit pathogen Pseudomonas syringae pv. actinidiae. Applied & Environmental Microbiology, 90(3), aem.01846-23. doi: 10.1128/aem.01846-23
Mayo-Muñoz, D., Pinilla-Redondo, R., Camara-Wilpert, S., Birkholz, N., & Fineran, P. C. (2024). Inhibitors of bacterial immune systems: Discovery, mechanisms and applications. Nature Reviews Genetics, 25, 237-254. doi: 10.1038/s41576-023-00676-9
Sitter, L., Schoof, M., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2024). Serratia-based toxin cluster elements are associated with a type I fimbria. MicrobiologyOpen, 13, e1395. doi: 10.1002/mbo3.1395
Smith, L. M., Hampton, H. G., Yevstigneyeva, M. S., Mahler, M., Paquet, Z. S. M., & Fineran, P. C. (2024). CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU. Nucleic Acids Research, 52, 755-768. doi: 10.1093/nar/gkad1165
Journal - Research Other
Birkholz, N., & Fineran, P. C. (2024). Anti-CRISPRs deconstruct bacterial defense [Spotlight]. Molecular Cell, 84, 3172-3174. doi: 10.1016/j.molcel.2024.08.008
Conference Contribution - Published proceedings: Abstract
Sisson, H. M., Fagerlund, R. D., Jackson, S. A., Briers, Y., Warring, S. L., & Fineran, P. C. (2024). Antibacterial synergy between a phage endolysin and citric acid against the gram-negative kiwifruit pathogen pseudomonas syringae pv. actinidiae. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/
Mayo-Muñoz, D., Hampton, H. G., Sharma, S., Wakelin, H., Vallabhjee, D., Yevstigneyeva, M. S., … Gardner, P. P., & Fineran, P. C. (2024). Hfq and small RNA regulation of anti-phage systems in Serratia. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/
Cameron, S. C., Warring, S. L., Fineran, P. C., & Fagerlund, R. D. (2024). Repurposing the type 1-D CRISPR-Cas system into a programmable gene silencing tool. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/
Smith, L. M., Hampton, H. G., Yevstigneyeva, M. S., Mahler, M. S., Paquet, Z. S. M., & Fineran, P. C. (2024). The LysR-type regulator PigU controls CRISPR-based defense against phages and plasmids. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/
Birkholz, N., Kamata, K., Feußner, M., Wilkinson, M. E., Samaniego, C. C., Migur, A., … Ceelen, M., … Brown, C. M., … Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2024). Phage helix-turn-helix proteins bind RNA and DNA to control anti-CRISPR dynamics. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/
Harding, K. R., Malone, L. M., Kyte, N. A. P., Jackson, S. A., Smith, L. M., & Fineran, P. C. (2024). Genome-wide identification of bacterial genes used in nucleus-forming jumbo phage infection. Viruses of Microbes (VoM) Scientific Conference. Retrieved from https://www.vom2024.org/
Kamata, K., Celeen, M., Birkholz, N., Fagerlund, R., Jackson, S., & Fineran, P. (2024). CRISPR-based bacteriophage engineering reveals essentiality of anti-CRISPR-associated gene. Journal of Biological Chemistry, 300(3, Suppl.), 1335. doi: 10.1016/j.jbc.2024.105832
Conference Contribution - Verbal presentation and other Conference outputs
Fineran, P. (2024, September). Defence and counter-defence strategies in the phage-bacterium arms race [FAOBMB Lecture]. Verbal presentation at the Biomolecular Horizons Congress: Discover Create Innovate, Melbourne, Australia.
McLeod, M., Morgaine, K., Fineran, P., Priest, P., & Jackson, S. (2024, August). Developing phage therapies for carbapenem-resistant acinetobacter baumannii and exploring public acceptance. Verbal presentation at the BMS Postgraduate Symposium, Dunedin, New Zealand.
Wang, X., Jowsey, W. J., Cheung, C.-Y., Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2024, September). Exploring collateral vulnerabilities in drug-resistant Mycobacterium tuberculosis: A path to novel anti-TB therapies. Verbal presentation at the Queenstown Research Week (QRW) Pathogen Genomics Meeting, Queenstown, New Zealand.
Wang, X., Jowsey, W. J., Cheung, C.-Y., Smart, C., Klaus, H., Seeto, N. E., Waller, N. J. E., Chrisp, M. T., … Fineran, P. C., Cook, G. M., Jackson, S. A., & McNeil, M. B. (2024, September). Genome wide essentiality screens to define therapeutic vulnerabilities in an isoniazid-resistant catalase mutant of Mycobacterium tuberculosis. Verbal presentation at the 34th Queenstown Molecular Biology Meeting (QMB), Queenstown, New Zealand.
Fineran, P., & Birkholz, N. (2024, July). Phage counter-defence strategies and their regulation. Invited presentation at the Viruses of Microbes (VoM) Scientific Conference, Cairns, Australia.
2023
Journal - Research Article
Camara-Wilpert, S., Mayo-Muñoz, D., Russel, J., Fagerlund, R. D., Madsen, J. S., Fineran, P. C., … Pinilla-Redondo, R. (2023). Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs. Nature, 623, 601-607. doi: 10.1038/s41586-023-06612-5
Shearer, H. L., Pace, P. E., Smith, L. M., Fineran, P. C., Matthews, A. J., Camilli, A., Dickerhof, N., & Hampton, M. B. (2023). Identification of Streptococcus pneumoniae genes associated with hypothiocyanous acid tolerance through genome-wide screening. Journal of Bacteriology, 205(10). doi: 10.1128/jb.00208-23
Mahler, M., Malone, L. M., van den Berg, D. F., Smith, L. M., Brouns, S. J. J., & Fineran, P. C. (2023). An OmpW-dependent T4-like phage infects Serratia sp. ATCC 39006. Microbial Genomics, 9(3), 000968. doi: 10.1099/mgen.0.000968
Mahler, M., Costa, A. R., van Beljouw, S. P. B., Fineran, P. C., & Brouns, S. J. J. (2023). Approaches for bacteriophage genome engineering [Review]. Trends in Biotechnology, 41(5), 669-685. doi: 10.1016/j.tibtech.2022.08.008
Journal - Research Other
López-Rojo, A., Jackson, S. A., Bernal-Bernal, D., Galbis-Martínez, M., Fineran, P. C., & Elías-Arnanz, M. (2023). Genome sequences of Mx1, the first Myxococcus phage isolated, and Mx4, a generalized transducing myxophage. Microbiology Resource Announcements, 12(12), e00904-23. doi: 10.1128/MRA.00904-23
Harding, K. R., Kyte, N., & Fineran, P. C. (2023). Jumbo phages [Quick guide]. Current Biology, 33, R750-R751. doi: 10.1016/j.cub.2023.05.056
Mayo-Muñoz, D., Pinilla-Redondo, R., Birkholz, N., & Fineran, P. C. (2023). A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Reports, 42(7), 112672. doi: 10.1016/j.celrep.2023.112672
McBride, T. M., Cameron, S. C., Fineran, P. C., & Fagerlund, R. D. (2023). The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochemical Journal, 480(7), 471-488. doi: 10.1042/bcj20220073
Smith, L. M., & Fineran, P. C. (2023). Phage capsid recognition triggers activation of a bacterial toxin-antitoxin defense system [Spotlight]. Molecular Cell, 83, 165-166. doi: 10.1016/j.molcel.2022.12.020
Conference Contribution - Published proceedings: Abstract
Gardner, P., Coray, D. S., Sibaeva, N., McGimpsey, S., Smith, L., Chen, A., & Fineran, P. (2023). The mutational robustness of RNA and protein. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference
Kyte, N., Harding, K., Malone, L., Jackson, S., Smith, L., & Fineran, P. (2023). Unlocking the secrets of jumbo phages: Harnessing Tn-Seq and CRISPRi to reveal bacterial genes involved in phage infection. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference
Sisson, H., Warring, S. L., Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2023). Antibacterial synergy between a phage endolysin and an organic acid against the gram-negative kiwifruit pathogen Pseudomonas syringae pv. actinidiae. Proceedings of the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) 50th Anniversary Conference. Retrieved from https://www.nzsbmb.org/conference
Camara-Wilpert, S., Mayo-Muñoz, D., Russel, J., Fagerlund, R. D., Madsen, J. S., Fineran, P. C., … Pinilla-Redondo, R. (2023). Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs. Proceedings of the Genetics Otago (GO) Annual Symposium & Workshops. Retrieved from https://blogs.otago.ac.nz/go
Conference Contribution - Verbal presentation and other Conference outputs
Birkholz, N., de Roode, S., Kamata, K., Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2023, August-September). Bacteria and their enemies: An armoury for Aotearoa's bioprotection battle? Verbal presentation at the He taonga tuku iho: Queenstown Molecular Biology (QMB) Bioprotection Aotearoa Satellite, Queenstown, New Zealand.
2022
Journal - Research Article
Mayo-Muñoz, D., Smith, L. M., Garcia-Doval, C., Malone, L. M., Harding, K. R., Jackson, S. A., Hampton, H. G., Fagerlund, R. D., Gumy, L. F., & Fineran, P. C. (2022). Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Molecular Cell, 82, 4471-4486.e9. doi: 10.1016/j.molcel.2022.10.028
Kim, G. E., Lee, S. Y., Birkholz, N., Kamata, K., Jeong, J.-H., Kim, Y.-G., Fineran, P. C., & Park, H. H. (2022). Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24. Nucleic Acids Research, 50(19), 11344-11358. doi: 10.1093/nar/gkac880
Shehreen, S., Birkholz, N., Fineran, P. C., & Brown, C. M. (2022). Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Research, 50(15), 8615-8625. doi: 10.1093/nar/gkac674
Warring, S. L., Malone, L. M., Jayaraman, J., Easingwood, R. A., Rigano, L. A., Frampton, R. A., … Kleffmann, T., … Bostina, M., & Fineran, P. C. (2022). A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance. Environmental Microbiology, 24(10), 4834-4852. doi: 10.1111/1462-2920.16106
Lee, S. Y., Birkholz, N., Fineran, P. C., & Park, H. H. (2022). Molecular basis of anti-CRISPR operon repression by Aca10. Nucleic Acids Research, 50(15), 8919-8928. doi: 10.1093/nar/gkac656
Payne, L. J., Meaden, S., Mestre, M. R., Palmer, C., Toro, N., Fineran, P. C., & Jackson, S. A. (2022). PADLOC: A web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Research, 50, W541-W550. doi: 10.1093/nar/gkac400
Schwartz, E. A., McBride, T. M., Bravo, J. P. K., Wrapp, D., Fineran, P. C., Fagerlund, R. D., & Taylor, D. W. (2022). Structural rearrangements allow nucleic acid discrimination by type I-D Cascade. Nature Communications, 13, 2829. doi: 10.1038/s41467-022-30402-8
Birkholz, N., Jackson, S. A., Fagerlund, R. D., & Fineran, P. C. (2022). A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease. Nucleic Acids Research, 50(6), 3348-3361. doi: 10.1093/nar/gkac147
Malone, L. M., Hampton, H. G., Morgan, X. C., & Fineran, P. C. (2022). Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress. Nucleic Acids Research, 50(1), 160-174. doi: 10.1093/nar/gkab1210
Pinilla-Redondo, R., Russell, J., Mayo-Muñoz, D., Shah, S. A., Garrett, R. A., Nesme, J., … Fineran, P. C., & Sørensen, S. J. (2022). CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Research, 50(8), 4315-4328. doi: 10.1093/nar/gkab859
Journal - Research Other
Birkholz, N., & Fineran, P. C. (2022). Turning down the (C)BASS: Phage-encoded inhibitors jam bacterial immune signaling. Molecular Cell, 82(12), 2185-2187. doi: 10.1016/j.molcel.2022.05.030
Meaden, S., Biswas, A., Arkhipova, K., Morales, S. E., Dutilh, B. E., . . ., & Fineran, P. C. (2022). High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. Current Biology, 32, 220-227. doi: 10.1016/j.cub.2021.10.038
Conference Contribution - Published proceedings: Abstract
Mayo-Muñoz, D., Smith, L. M., Garcia-Doval, C., Malone, L. M., Harding, K. R., Jackson, S. A., Hampton, H. G., Fagerlund, R. D., Gumy, L. F., & Fineran, P. C. (2022). Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Sisson, H. M. J., Warring, S. L., Adams, D., Grimon, D., Fagerlund, R. D., Gutiérrez, D., Jackson, S. A., … Fineran, P. C. (2022). Phage-derived antimicrobials against kiwifruit pathogen Pseudomonas syringae pv. actinidiae. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Cameron, S., McBride, T., Fineran, P. C., & Fagerlund, R. D. (2022). Development of a gene silencing platform using the type 1-D CRISPR-Cas system. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Birkholz, N., Jackson, S. A., Fagerlund, R. D., & Fineran, P. C. (2022). A mobile restriction-modification phage defence system resolves an epigenetic conflict with an antagonistic endonuclease. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Smith, L. M., Mayo-Muñoz, D., García-Doval, C., Malone, L. M., Harding, K., Jackson, S. A., Hampton, H. G., Gumy, L. F., & Fineran, P. C. (2022). CRISPR-Cas targeting of a nucleus-forming jumbo phage induces abortive infection. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
Harding, K. R., Malone, L. M., Kyte, N., & Fineran, P. C. (2022). Characterising the molecular interactions between jumbo phages and serratia. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
White, L., Halpin, J., Leith, C., Poudel, A., Saunderson, S., Jackson, S., Fagerlund, R., Fineran, P., & McLellan, A. (2022). Exploiting the intrinsic insolubility of T cell and NK cell-activating cytokines and chemokines for Escherichia coli expression. Proceedings of the New Zealand Branch of the Australian and New Zealand Society for Immunology (NZASI) Conference. (pp. 45). Retrieved from https://nzasi2022.com/programme
Conference Contribution - Poster Presentation (not in published proceedings)
Sisson, H. M. J., Warring, S. L., Dams, D., Grimon, D., Fagerlund, R. D., Gutiérrez, D., Jackson, S. A., … Fineran, P. C. (2022, August). Phage-derived antimicrobials against kiwifruit pathogen Pseudomonas syringae pv. actinidiae. Poster session presented at the Webster Centre for Infectious Diseases Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Payne, L. J., Todeschini, T. C., Wu, Y., Meaden, S., Mestre, M. R., Palmer, C., … Hughes, T., Perry, B. J., Ronson, C. W., Fineran, P. C., … Jackson, S. A. (2022, August). Identification of CRISPR-Cas and novel phage defense systems to expand our molecular toolkit. Poster session presented at the CRISPR Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Hodgkinson-Bean, J., Jayawardena, N., Fineran, P., Wolf, M., & Bostina, M. (2022, August). Cryo-EM structure of the oversized bacteriophage ΦTE capsid. Verbal presentation at the Advances in Microscopy Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Birkholz, N., Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2022, August). Insights into anti-CRISPR control by the autoregulator Aca2. Verbal presentation at the CRISPR Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Mayo-Muñoz, D., García-Doval, C., Malone, L. M., Smith, L. M., Hampton, H. G., Gumy, L. F., … Fineran, P. C. (2022, August). Type III CRISPR-Cas enables resistance against nucleus-forming jumbo phages. Verbal presentation at the CRISPR Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
Smith, L. M., Jackson, S. A., Malone, L. M., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2022, August). Inverse regulation of CRISPR-Cas and surface-based immunity discriminates plasmids versus phages. Verbal presentation at the CRISPR Technologies Satellite Meeting: Queenstown Research Week, Queenstown, New Zealand.
2021
Journal - Research Article
Payne, L. J., Todeschini, T. C., Wu, Y., Perry, B. J., Ronson, C. W., Fineran, P. C., … Jackson, S. A. (2021). Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Nucleic Acids Research, 49(19), 10868-10878. doi: 10.1093/nar/gkab883
Rey Campa, A., Smith, L. M., Hampton, H. G., Sharma, S., Jackson, S. A., Bischler, T., … Fineran, P. C. (2021). The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. Nucleic Acids Research, 49(16), 9508-9525. doi: 10.1093/nar/gkab704
Usher, B., Birkholz, N., Beck, I. N., Fagerlund, R. D., Jackson, S. A., Fineran, P. C., & Blower, T. R. (2021). Crystal structure of the anti-CRISPR repressor Aca2. Journal of Structural Biology, 213, 107752. doi: 10.1016/j.jsb.2021.107752
Sitter, T. L., Vaughan, A. L., Schoof, M., Jackson, S. A., Glare, T. R., Cox, M. P., Fineran, P. C., Gardner, P. P., & Hurst, M. R. H. (2021). Evolution of virulence in a novel family of transmissible mega-plasmids. Environmental Microbiology, 23(9), 5289-5304. doi: 10.1111/1462-2920.15595
Smith, L. M., Jackson, S. A., Malone, L. M., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2021). The Rcs stress response inversely controls surface and CRISPR–Cas adaptive immunity to discriminate plasmids and phages. Nature Microbiology, 6, 162-172. doi: 10.1038/s41564-020-00822-7
Journal - Research Other
Meaden, S., & Fineran, P. C. (2021). Bacterial defense islands limit viral attack. Science, 374(6566), 399-400. doi: 10.1126/science.abm2444
Smith, L. M., Jackson, S. A., Gardner, P. P., & Fineran, P. C. (2021). SorTn-seq: A high-throughput functional genomics approach to discovering regulators of bacterial gene expression. Nature Protocols, 16, 4382-4418. doi: 10.1038/s41596-021-00582-6
Malone, L. M., Birkholz, N., & Fineran, P. C. (2021). Conquering CRISPR: How phages overcome bacterial adaptive immunity. Current Opinion in Biotechnology, 68, 30-36. doi: 10.1016/j.copbio.2020.09.008
Conference Contribution - Published proceedings: Abstract
Kamata, K., Celeen, M., Birkholz, N., Fagerlund, R. D., Jackson, S. A., & Fineran, P. C. (2021). Studying biological roles of anti-CRISPR control through phage engineering. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 263). Retrieved from https://www.faobmb2021.org
Mayo-Muñoz, D., García-Doval, C., Malone, L. M., Smith, L. M., Harding, K., Hampton, H. G., Gumy, L. F., … Fineran, P. C. (2021). Type III CRISPR-Cas enables resistance against nucleus-forming jumbo phages. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 229). Retrieved from https://www.faobmb2021.org
Payne, L. J., Todeschini, T. C., Wu, Y., Perry, B. J., Ronson, C. W., Fineran, P. C., … Jackson, S. A. (2021). Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 20). Retrieved from https://www.faobmb2021.org
Fineran, P. (2021). Phage strategies to overcome bacterial defence systems. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 272). Retrieved from https://www.faobmb2021.org
Meaden, S., Biswas, A., Arkhipova, K., Morales, S. E., Dutilh, B. E., Westra, E. R., & Fineran, P. C. (2021). High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 217). Retrieved from https://www.faobmb2021.org
Chyou, T.-y., Biswas, A., Fineran, P., & Brown, C. (2021). Predicting hosts of nucleic acid sequences using CRISPR spacers. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 121). Retrieved from https://www.faobmb2021.org
Smith, L. M., Jackson, S. A., Malone, L., Ussher, J. E., Gardner, P. P., & Fineran, P. C. (2021). Inverse control of surface and CRISPR-Cas adaptive immunity discriminates plasmids and phages. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 120). Retrieved from https://www.faobmb2021.org
Birkholz, N., Jackson, S. A., Fagerlund, R. D., & Fineran, P. C. (2021). A methyltransferase involved in bacterial defence and intracellular conflict between restriction endonucleases. Proceedings of the 16th Congress of the Federation of Asian & Oceanic Biochemists & Molecular Biologists (FAOBMB). (pp. 119). Retrieved from https://www.faobmb2021.org
Harding, K., Malone, L., & Fineran, P. (2021). Characterising host factors involved in jumbo phage infection in Serratia [Invited]. Proceedings of the Genetics Otago (GO) Annual Symposium. Retrieved from https://blogs.otago.ac.nz/go
2020
Journal - Research Article
McBride, T. M., Schwartz, E. A., Kumar, A., Taylor, D. W., Fineran, P. C., & Fagerlund, R. D. (2020). Diverse CRISPR-Cas complexes require independent translation of small and large subunits from a single gene. Molecular Cell, 80, 971-979. doi: 10.1016/j.molcel.2020.11.003
Pinilla-Redondo, R., Shehreen, S., Marino, N. D., Fagerlund, R. D., Brown, C. M., Sørensen, S. J., Fineran, P. C., & Bondy-Denomy, J. (2020). Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nature Communications, 11(1), 5652. doi: 10.1038/s41467-020-19415-3
Hampton, H. G., Smith, L. M., Ferguson, S., Meaden, S., Jackson, S. A., & Fineran, P. C. (2020). Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia. Microbial Genomics, 6, 1-15. doi: 10.1099/mgen.0.000458
Jayaraman, J., Jones, W. T., Harvey, D., Hemara, L. M., McCann, H. C., Yoon, M., Warring, S. L., Fineran, P. C., … Templeton, M. D. (2020). Variation at the common polysaccharide antigen locus drives lipopolysaccharide diversity within the Pseudomonas syringae species complex. Environmental Microbiology, 22(12), 5356-5372. doi: 10.1111/1462-2920.15250
Cai, Y., Usher, B., Gutierrez, C., Tolcan, A., Mansour, M., Fineran, P. C., … Blower, T. R. (2020). A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems. Science Advances, 6(31), eabb6651. doi: 10.1126/sciadv.abb6651
Beck, I. N., Usher, B., Hampton, H. G., Fineran, P. C., & Blower, T. R. (2020). Antitoxin autoregulation of M. tuberculosis toxin-antitoxin expression through negative cooperativity arising from multiple inverted repeat sequences. Biochemical Journal, 477, 2401-2419. doi: 10.1042/bcj20200368
Rollie, C., Chevallereau, A., Watson, B. N. J., Chyou, T.-y., Fradet, O., McLeod, I., Fineran, P. C., Brown, C. M., … Westra, E. R. (2020). Targeting of temperate phages drives loss of type I CRISPR-Cas systems. Nature, 578, 149-153. doi: 10.1038/s41586-020-1936-2
Malone, L. M., Warring, S. L., Jackson, S. A., Warnecke, C., Gardner, P. P., Gumy, L. F., & Fineran, P. C. (2020). A jumbo phage 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. doi: 10.1038/s41564-019-0612-5
Journal - Research Other
Jackson, S. A., Fellows, B. J., & Fineran, P. C. (2020). Complete genome sequences of the Escherichia coli donor strains ST18 and MFDpir. Microbiology Resource Announcements, 9(45), e1014-20. doi: 10.1128/mra.01014-20
Hampton, H. G., Watson, B. N. J., & Fineran, P. C. (2020). The arms race between bacteria and their phage foes. Nature, 577(7790), 327-336. doi: 10.1038/s41586-019-1894-8
2019
Chapter in Book - Research
Bergmann, J. M., Fineran, P. C., Petty, N. K., & Salmond, G. P. C. (2019). Transduction: The transfer of host DNA by bacteriophages. In T. M. Schmidt (Ed.), Encyclopedia of microbiology. (pp. 458-473). Academic Press. doi: 10.1016/B978-0-12-801238-3.11350-9
Fagerlund, R. D., Ferguson, T. J., Maxwell, H. W. R., Opel-Reading, H. K., Krause, K. L., & Fineran, P. C. (2019). Reconstitution of CRISPR adaptation in vitro and its detection by PCR. In S. Bailey (Ed.), Methods in enzymology (Vol. 616: CRISPR-Cas enzymes). (pp. 411-433). Cambridge, MA: Academic Press. doi: 10.1016/bs.mie.2018.10.024
Journal - Research Article
Watson, B. N. J., Vercoe, R. B., Salmond, G. P. C., Westra, E. R., Staals, R. H. J., & Fineran, P. C. (2019). Type I–F CRISPR-Cas resistance against virulent phages results in abortive infection and provides population-level immunity. Nature Communications, 10, 5526. doi: 10.1038/s41467-019-13445-2
Birkholz, N., Fagerlund, R. D., Smith, L. M., Jackson, S. A., & Fineran, P. C. (2019). The autoregulator Aca2 mediates anti-CRISPR repression. Nucleic Acids Research, 47(18), 9658-9665. doi: 10.1093/nar/gkz721
Greisch, J.-F., Tamara, S., Scheltema, R. A., Maxwell, H. W. R., Fagerlund, R. D., Fineran, P. C., … Heck, A. J. R. (2019). Expanding the mass range for UVPD-based native top-down mass spectrometry. Chemical Science, 10, 7163-7171. doi: 10.1039/c9sc01857c
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., … Fineran, P. C., … Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nature Microbiology, 4, 1727-1736. doi: 10.1038/s41564-019-0494-6
Hampton, H. G., Patterson, A. G., Chang, J. T., Taylor, C., & Fineran, P. C. (2019). GalK limits type I-F CRISPR-Cas expression in a CRP-dependent manner. FEMS Microbiology Letters, 366, fnz137. doi: 10.1093/femsle/fnz137
Shehreen, S., Chyou, T.-y., Fineran, P. C., & Brown, C. M. (2019). Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. Philosophical Transactions of the Royal Society B, 374(1772), 20180384. doi: 10.1098/rstb.2018.0384
Watson, B. N. J., Easingwood, R. A., Tong, B., Wolf, M., Salmond, G. P. C., Staals, R. H. J., Bostina, M., & Fineran, P. C. (2019). Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spacers. Philosophical Transactions of the Royal Society B, 374(1772), 20180090. doi: 10.1098/rstb.2018.0090
Jackson, S. A., Birkholz, N., Malone, L. M., & Fineran, P. C. (2019). Imprecise spacer acquisition generates CRISPR-Cas immune diversity through primed adaptation. Cell Host & Microbe, 25, 250-260. doi: 10.1016/j.chom.2018.12.014
Fineran, P. C. (2019). CRISPR-Cas impedes archaeal mating. Nature Microbiology, 4(1), 2-3. doi: 10.1038/s41564-018-0326-0
Nicholson, T. J., Jackson, S. A., Croft, B. I., Staals, R. H. J., Fineran, P. C., & Brown, C. M. (2019). Bioinformatic evidence of widespread priming in type I and II CRISPR-Cas systems. RNA Biology, 16(4), 566-576. doi: 10.1080/15476286.2018.1509662
Journal - Research Other
Jackson, S. A., & Fineran, P. C. (2019). Bacterial dormancy curbs phage epidemics. Nature, 570, 173-174. doi: 10.1038/d41586-019-01595-8
Wojtus, J. K., Frampton, R. A., Warring, S., Hendrickson, H., & Fineran, P. C. (2019). Genome sequence of a jumbo bacteriophage that infects the kiwifruit phytopathogen Pseudomonas syringae pv. actinidiae. Microbiology Resource Announcements, 8(22), e00224-19. doi: 10.1128/mra.00224-19
Fineran, P. C. (2019). Resistance is not futile: Bacterial 'innate' and CRISPR-Cas 'adaptive' immune systems. Microbiology, 165(8), 834-841. doi: 10.1099/mic.0.000802
Conference Contribution - Verbal presentation and other Conference outputs
Hampton, H., & Fineran, P. (2019, August-September). Function and regulation of Class 1 CRISPR-Cas systems. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Working Paper; Discussion Paper; Technical Report
Penman, D., Scott, B., Allison, J., Buckley, T., Dearden, P., Drummond, A., … Henaghan, M., … Matisoo-Smith, L., … Robertson, S., Wilcox, P., Everett-Hincks, J., King, M., … Fineran, P., Gemmell, N., … Scott, M. (2019). Gene editing: Scenarios in pest control. Wellington, New Zealand: Royal Society Te Apārangi. [Technical/Scientific Report].
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., … Fineran, P. C., … Dutilh, B. E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. bioRxiv. doi: 10.1101/527796
Other Research Output
Fineran, P. (2019, May). Resistance is (not) futile: Bacterial innate and adaptive immune system. University of Otago, Dunedin, New Zealand. [Inaugural Professorial Lecture].
2018
Journal - Research Article
Dy, R. L., Rigano, L. A., & Fineran, P. C. (2018). Phage-based biocontrol strategies and their application in agriculture and aquaculture. Biochemical Society Transactions, 46(4), BST20180178, 1605-1613. doi: 10.1042/bst20180178
Hampton, H. G., Jackson, S. A., Fagerlund, R. D., Vogel, A. I. M., Dy, R. L., Blower, T. R., & 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(8), 1141-1156. doi: 10.1016/j.jmb.2018.02.022
Watson, B. N. J., Staals, R. H. J., & Fineran, P. C. (2018). CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction. mBio, 9(1), e02406-17. doi: 10.1128/mBio.02406-17
Conference Contribution - Published proceedings: Abstract
Ferguson, T. J., Fagerlund, R. D., & Fineran, P. C. (2018). Integration host factor is required for primed adaptation by type I CRISPR-Cas systems. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 120). Retrieved from https://www.nzmsconference.org.nz
Warring, S., Frampton, R., Herandez, L., Visnovsky, S., Addison, S., Templeton, M., Pitman, A., & Fineran, P. (2018). Bacteriophages for the biocontrol of Pseudomonas syringae pv. actinidiae infection in kiwifruit plants. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 117-118). Retrieved from https://www.nzmsconference.org.nz
Smith, L. M., Gardner, P. P., Jackson, S. A., Ussher, J. E., & Fineran, P. C. (2018). Developing SorTn-Seq: A state-of-the-art method to study CRISPR-Cas regulation. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 109). Retrieved from https://www.nzmsconference.org.nz
McBride, T., Fineran, P. C., & Fagerlund, R. D. (2018). Composition and nucleic acid binding of the type I-D CRISPR-Cas interference complex. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 107-108). Retrieved from https://www.nzmsconference.org.nz
Malone, L. M., Warnecke, C., Kleffmann, T., Morgan, X. C., & Fineran, P. C. (2018). The activity of type I-E, I-F and III-A CRIPR-CAS systems during phage infection. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 106). Retrieved from https://www.nzmsconference.org.nz
Rey Campa, A., Fineran, P. C., & Pitman, A. R. (2018). Regulation of CRISPR-Cas systems in Serratia through the Rsm pathway. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 83). Retrieved from https://www.nzmsconference.org.nz
Shehreen, S., Chyou, D., Fineran, P., & Brown, C. (2018). Horizontal transfer of antibiotic resistance genes: A CRISPR connection? Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 81-82). Retrieved from https://www.nzmsconference.org.nz
Hampton, H., Maxwell, H., Jackson, S., & Fineran, P. (2018). Quorum sensing regulates both innate and adaptive bacterial defence systems. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 76). Retrieved from https://www.nzmsconference.org.nz
Watson, B. N. J., Easingwood, R. A., Tong, B., Wolf, M., Salmond, G. P. C., Staals, R. H. J., Bostina, M., & Fineran, P. C. (2018). Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spacers. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 73). Retrieved from https://www.nzmsconference.org.nz
Maxwell, H., Hampton, H., & Fineran, P. (2018). Does inhibition of quorum sensing increase the spread of antibiotic resistance? Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 68). Retrieved from https://www.nzmsconference.org.nz
Fagerlund, R. D., Ferguson, T. J., Watson, B. N. J., & Fineran, P. C. (2018). Integration host factor influences CRISPR-Cas immunity. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 58-59). Retrieved from https://www.nzmsconference.org.nz
Jackson, S. A., Birkholz, N., Malone, L. M., & Fineran, P. C. (2018). Imprecise spacer acquisition generates CRISPR-Cas immune diversity through primed adaptation. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 56). Retrieved from https://www.nzmsconference.org.nz
Birkholz, N., Jackson, S. A., Fagerlund, R. D., Smith, L. M., & Fineran, P. C. (2018). Transcriptional regulation by the anti-CRISPR-associated protein Aca2. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 45-46). Retrieved from https://www.nzmsconference.org.nz
Watson, B. N. J., Easingwood, R. A., Tong, B., Wolf, M., Salmond, G. P. C., Staals, R. H. J., Bostina, M., & Fineran, P. C. (2018). Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spaces. Proceedings of the New Zealand Microbiological Society (NZMS) New Zealand Society for Biochemistry and Molecular Biology (NZSBMB) Joint Annual Conference: Microbes & Molecules. (pp. 40). Retrieved from https://www.nzmsconference.org.nz
Shehreen, S., Chyou, T.-y., Fineran, P. C., & Brown, C. M. (2018). Horizontal transfer of antibiotic resistance genes: A CRISPR connection? Proceedings of the Otago Global Health Institute (OGHI) 11th Annual Conference. (pp. 23-24). Retrieved from https://www.otago.ac.nz/global-health/annual-conference
2017
Journal - Research Article
Silas, S., Lucas-Elio, P., Jackson, S. A., Aroca-Crevillén, A., Hansen, L. L., Fineran, P. C., … Sánchez-Amat, A. (2017). Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. eLIFE, 6, e27601. doi: 10.7554/eLife.27601
Fagerlund, R. D., Wilkinson, M. E., Klykov, O., Barendregt, A., Pearce, F. G., Kieper, S. N., Maxwell, H. W. R., … Krause, K. L., Bostina, M., … Staals, R. H. J., & Fineran, P. C. (2017). Spacer capture and integration by a type I-F Cas1–Cas2-3 CRISPR adaptation complex. PNAS, 114(26), E5122-E5128. doi: 10.1073/pnas.1618421114
Jackson, S. A., McKenzie, R. E., Fagerlund, R. D., Kieper, S. N., Fineran, P. C., & Brouns, S. J. J. (2017). CRISPR-Cas: Adapting to change. Science, 356(6333), eaal5056. doi: 10.1126/science.aal5056
Patterson, A. G., Yevstigneyeva, M. S., & Fineran, P. C. (2017). Regulation of CRISPR-Cas adaptive immune systems [Review]. Current Opinion in Microbiology, 37(1), 1-7. doi: 10.1016/j.mib.2017.02.004
Mesarich, C. H., Rees-George, J., Gardner, P. P., Ghomi, F. A., Gerth, M. L., Andersen, M. T., … Fineran, P. C., & Templeton, M. D. (2017). Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS ONE, 12(3), e0172790. doi: 10.1371/journal.pone.0172790
Blower, T. R., Chai, R., Przybilski, R., Chindhy, S., Fang, X., Kidman, S. E., … Fineran, P. C., & Salmond, G. P. C. (2017). Evolution of Pectobacterium bacteriophage ΦM1 to escape two bifunctional type III toxin-antitoxin and abortive infection systems through mutations in a single viral gene. Applied & Environmental Microbiology, 83(8), e03229-16. doi: 10.1128/aem.03229-16
Conference Contribution - Published proceedings: Abstract
Patterson, A. G., Jackson, S. A., Taylor, C., Evans, G. B., Salmond, G. P. C., Przybilski, R., … Fineran, P. C. (2017). Quorum sensing controls adaptive immunity through multiple CRISPR-Cas systems. Proceedings of the 22nd Biennial Evergreen Bacteriophage Conference. (pp. 141). Retrieved from http://blogs.evergreen.edu/phage/about/meetings/2017-evergreen-meeting
Jackson, S. A., Birkholz, N., Taylor, C., & Fineran, P. C. (2017). Imprecision during spacer acquisition by type I CRISPR-Cas systems increases CRISPR diversity in bacterial populations. Proceedings of the 22nd Biennial Evergreen Bacteriophage Conference. (pp. 140). Retrieved from http://blogs.evergreen.edu/phage/about/meetings/2017-evergreen-meeting
Fagerlund, R. D., Wilkinson, M. E., Klykov, O., Barendregt, A., Pearce, F. G., Kieper, S. N., … Krause, K. L., … Fineran, P. C. (2017). Spacer capture and integration by a type I-F Cas1: Cas2-3 CRISPR adaptation complex. Proceedings of the 22nd Biennial Evergreen Bacteriophage Conference. (pp. 139). Retrieved from http://blogs.evergreen.edu/phage/about/meetings/2017-evergreen-meeting
Watson, B. N. J., Staals, R. H. J., & Fineran, P. C. (2017). CRISPR-Cas affects horizontal gene transfer by transduction. Proceedings of the 22nd Biennial Evergreen Bacteriophage Conference. (pp. 21). Retrieved from http://blogs.evergreen.edu/phage/about/meetings/2017-evergreen-meeting
Addison, S., Frampton, R., Hernandez, L., Visnovsky, S., Taylor, C., Pitman, A., … Fineran, P. C. (2017). Bacteriophage-mediated control of Pseudomonas syringae pv. actinidae on kiwifruit plants. Proceedings of the New Zealand Microbiological Society (NZMS) Annual Conference. 130. Retrieved from http://www.nzmsconference.org.nz/
Fineran, P. C. (2017). Adapt or perish: The function of CRISPR-Cas adaptive immune systems [Invited]. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 792. Retrieved from http://gen2017.w.events4you.currinda.com
Brown, C., Chyou, D., Biswas, A., Baltazar, P., Nicholson, T., Croft, B., & Fineran, P. (2017). Bioinformatic discovery of noncoding RNA genes. Proceedings of the Annual Conference of the Genetics Society of Australasia (GSA) with the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB). 655. Retrieved from http://gen2017.w.events4you.currinda.com
Conference Contribution - Poster Presentation (not in published proceedings)
Smith, L. M., Gardner, P. P., Jackson, S. A., Ussher, J. E., & Fineran, P. C. (2017, September). Developing SorTn-Seq: A state-of-the-art method to study CRISPR-Cas regulation. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Fagerlund, R. D., Wilkinson, M. E., Klykov, O., Barendregt, A., Pearce, F. G., Maxwell, H. W. R., … Krause, K. L., Bostina, M., … Staals, R. H. J., & Fineran, P. C. (2017, September). DNA capture and integration by the type I-F CRISPR-Cas adaptation complex from Pectobacterium atrosepticum. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Ferguson, T. J., Fagerlund, R. D., & Fineran, P. C. (2017, September). Investigating the role of integration host factor in the function of multiple CRISPR-Cas systems. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Rey-Campa, A., Pitman, A. R., & Fineran, P. C. (2017, September). Loss and gain of CRISPR-Cas systems and genomic islands: A delicate balancing act? Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Yevstigneyeva, M. S., Patterson, A. G., Taylor, C., & Fineran, P. C. (2017, September). Discovery of regulators of CRISPR-Cas adaptive immunity in Serratia. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Birkholz, N., Jackson, S. A., Taylor, C., & Fineran, P. C. (2017, September). Imprecision during spacer acquisition by type I CRISPR-Cas systems increases CRISPR diversity in bacterial populations. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Maxwell, H. W. R., Fagerlund, R. D., & Fineran, P. C. (2017, September). Analysis of the type I-F CRISPR Cas complexes from Pectobacterium atrosepticum in vitro. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Malone, L. M., & Fineran, P. C. (2017, September). Effectiveness of CRISPR-Cas systems in response to diverse phage infections. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Jackson, S. A., Birkholz, N., Taylor, C., & Fineran, P. C. (2017, September). The arms race between bacterial CRISPR-Cas adaptive immune systems, phages and mobile genetic elements. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Hampton, H. G., Jackson, S. A., Fagerlund, R. D., Vogel, A. I. M., Dy, R. L., Blower, T. R., & Fineran, P. C. (2017, September). Cooperative autoregulation of the Type IV abiE toxin-antitoxin operon involves a charged surface on AbiEi. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Brown, C. M., Chyou, D., Biswas, A., Baltazar, P., Nicholson, T., Croft, B., & Fineran, P. (2017, September). Bioinformatic discovery of noncoding RNA genes. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Other Research Output
Johnston, J., Fineran, P., Gavaghan, C.and Harre Hindmarsh, J. (2017, September). Perfectly healthy: Disease-free by technology?. Editing our genes: Promises and pitfalls, Royal Society of New Zealand Prestigious speakers series, Dunedin, New Zealand. [Public Seminar].
2016
Journal - Research Article
Patterson, A. G., Jackson, S. A., Taylor, C., Evans, G. B., Salmond, G. P. C., Przybilski, R., Staals, R. H. J., & Fineran, P. C. (2016). Quorum sensing controls adaptive immunity through the regulation of multiple CRISPR-Cas systems. Molecular Cell, 64(6), 1102-1108. doi: 10.1016/j.molcel.2016.11.012
Staals, R. H. J., Jackson, S. A., Biswas, A., Brouns, S. J. J., Brown, C. M., & 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. doi: 10.1038/ncomms12853
Pawluk, A., Staals, R. H. J., Taylor, C., Watson, B. N. J., Saha, S., Fineran, P. C., … Davidson, A. R. (2016). Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nature Microbiology, 1, 16085. doi: 10.1038/nmicrobiol.2016.85
Biswas, A., Staals, R. H. J., Morales, S. E., Fineran, P. C., & Brown, C. M. (2016). CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics, 17, 356. doi: 10.1186/s12864-016-2627-0
Panda, P., Vanga, B. R., Lu, A., Fiers, M., Fineran, P. C., Butler, R., … Ronson, C. W., & Pitman, A. R. (2016). Pectobacterium atrosepticum and Pectobacterium carotovorum harbor distinct, independently acquired integrative and conjugative elements encoding coronafacic acid that enhance virulence on potato stems. Frontiers in Microbiology, 7, 397. doi: 10.3389/fmicb.2016.00397
Hampton, H. G., McNeil, M. B., Paterson, T. J., Ney, B., Williamson, N. R., Easingwood, R. A., Bostina, M., … Fineran, P. C. (2016). CRISPR-Cas gene-editing reveals RsmA and RsmC act through FlhDC to repress the SdhE flavinylation factor and control motility and prodigiosin production in Serratia. Microbiology, 162(6), 1047-1058. doi: 10.1099/mic.0.000283
Wilkinson, M. E., Nakatani, Y., Staals, R. H. J., Kieper, S. N., Opel-Reading, H. K., McKenzie, R. E., Fineran, P. C., & Krause, K. L. (2016). Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system. Biochemical Journal, 473, 1063-1072. doi: 10.1042/bcj20160078
Conference Contribution - Verbal presentation and other Conference outputs
Yevstigneyeva, M., Patterson, A. G., Taylor, C., & Fineran, P. C. (2016, November). A transposon mutagenesis pipeline to identify regulators of CRISPR-Cas in Serratia. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Malone, L. M., Easingwood, R. A., Bostina, M., & Fineran, P. C. (2016, November). Isolation and characterization of novel Serratia phages. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Staals, R. H. J., Jackson, S. A., Biswas, A., Brouns, S. J. J., Brown, C. M., & Fineran, P. C. (2016, November). Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Tong, B., Watson, B. N. J., Frampton, R. A., Young, V. L., Taylor, C., Easingwood, R. A., Pitman, A. R., Kleffmann, T., … Fineran, P. C., & Bostina, M. (2016, November). Cryo-electron microscopy structure and proteome of phages infecting plant pathogenic bacteria. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Hampton, H. G., Jackson, S. A., Vogel, A. I. M., Dy, R. L., Blower, T. R., & Fineran, P. C. (2016, November). Mode of action of a widespread Type IV toxin-antitoxin phage abortive infection resistance system. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Patterson, A. G., Jackson, S. A., Taylor, C., Evans, G. B., Salmond, G. P. C., Przybilski, R., Staals, R. H. J., & Fineran, P. C. (2016, November). Quorum sensing controls adaptive immunity through multiple CRISPR-Cas systems. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Watson, B. N. J., Staals, R. H. J., Taylor, C., & Fineran, P. C. (2016, November). CRISPR-Cas interference limits horizontal gene transfer by inhibiting transduction. Verbal presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
Fineran, P. (2016, November). The function and regulation of Class 1 CRISPR-Cas systems. Plenary presentation at the Joint Meeting of the New Zealand Microbiological Society (NZMS) and the New Zealand Society for Biochemistry and Molecular Biology (NZSBMB), Christchurch, New Zealand.
2015
Edited Book - Research
Lundgren, M., Charpentier, E., & Fineran, P. C. (Eds.). (2015). CRISPR: Methods and protocols: Methods in molecular biology (Vol. 1311). Humana Press, 366p. doi: 10.1007/978-1-4939-2687-9
Chapter in Book - Research
Biswas, A., Fineran, P. C., & Brown, C. M. (2015). Computational detection of CRISPR/crRNA targets. In M. Lundgren, E. Charpentier & P. C. Fineran (Eds.), CRISPR: Methods in molecular biology (Vol. 1311). (pp. 77-89). New York, NY: Humana Press. doi: 10.1007/978-1-4939-2687-9_5
Journal - Research Article
Fagerlund, R. D., Staals, R. H. J., & Fineran, P. C. (2015). The Cpf1 CRISPR-Cas protein expands genome-editing tools. Genome Biology, 16, 251. doi: 10.1186/s13059-015-0824-9
Salmond, G. P. C., & Fineran, P. C. (2015). A century of the phage: Past, present and future. Nature Reviews Microbiology, 777-786. doi: 10.1038/nrmicro3564
Templeton, M. D., Warren, B. A., Anderson, M. T., Rikkerink, E. H. A., & Fineran, P. C. (2015). Complete DNA sequence of Pseudomonas syringae pv. actinidiae, the causal agent of kiwifruit canker disease. Genome Announcements, 3(5), e01054 -e01055 . doi: 10.1128/genomeA.01054-15
Holguín Moreno, A. V., Rangel, G., Clavijo, V., Prada, C., Mantilla, M., Gomez, M. C., … Fineran, P. C., … Vives, M. J. (2015). Phage ΦPan70, a putative temperate phage, controls Pseudomonas aeruginosa in planktonic, biofilm and burn mouse model assays. Viruses, 7(8), 4602-4623. doi: 10.3390/v7082835
Frampton, R. A., Lopez Acedo, E., Young, V. L., Chen, D., Tong, B., Taylor, C., Easingwood, R. A., … Kleffmann, T., Bostina, M., & Fineran, P. C. (2015). Genome, proteome and structure of a T7-like bacteriophage of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Viruses, 7(7), 3361-3379. doi: 10.3390/v7072776
Patterson, A. G., Chang, J. T., Taylor, C., & Fineran, P. C. (2015). Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference. Nucleic Acids Research, 43(12), 6038-6048. doi: 10.1093/nar/gkv517
Conference Contribution - Published proceedings: Abstract
Chen, D., Bostina, M., & Fineran, P. (2015). Structural characterisation of the novel bateriophage Φ-Psa17 for the biocontrol of the kiwifruit canker phytopathogen Pseudomonas syringae pv. Actinidiae. Proceedings of the 27th National Conference on Microscopy. Retrieved from http://microscopy2015.otago.ac.nz/index.html
Conference Contribution - Poster Presentation (not in published proceedings)
Hampton, H. G., Jackson, S. A., Vogel, A. I. M., Dy, R. L., & Fineran, P. C. (2015, August-September). Investigating the mode of action of the type IV AbiE toxin-º©-antitoxin phage resistance system. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Patterson, A. G., Chang, J. T., Taylor, C., & Fineran, P. C. (2015, August-September). Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Wilkinson, M. E., Staals, R. H. J., Nakatani, Y., Fagerlund, R. D., Kieper, S., Opel-Reading, H. K., Krause, K. L., & Fineran, P. C. (2015, August-September). The structure of Cas1 and its role in adaptation in Type I-F CRISPR-Cas systems. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Conference Contribution - Verbal presentation and other Conference outputs
Fineran, P. C. (2015, August-September). Refuse/Resist: Bacterial innate and adaptive immune systems. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Croft, B., Biswas, A., Fineran, P. C., & Brown, C. M. (2015, August). Analysis of rumen methanogens CRISPR-Cas systems. Verbal presentation at the 7th Annual New Zealand Next Generation Sequencing (NGS) Conference, Palmerston North, New Zealand.
2014
Journal - Research Article
Dy, R. L., Richter, C., Salmond, G. P. C., & Fineran, P. C. (2014). Remarkable mechanisms in microbes to resist phage infections. Annual Review of Virology, 1, 307-331. doi: 10.1146/annurev-virology-031413-085500
Richter, C., Dy, R. L., McKenzie, R. E., Watson, B. N. J., Taylor, C., Chang, J. T., McNeil, M. B., Staals, R. H. J., & Fineran, P. C. (2014). Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Research, 42(13), 8516-8526. doi: 10.1093/nar/gku527
Fineran, P. C., Gerritzen, M. J. H., Suárez-Diez, M., Künne, T., Boekhorst, J., van Hijum, S. A. F. T., Staals, R. H. J., & Brouns, S. J. J. (2014). Degenerate target sites mediate rapid primed CRISPR adaptation. PNAS, 111(16), E1629-E1638. doi: 10.1073/pnas.1400071111
Fineran, P. C., & Dy, R. L. (2014). Gene regulation by engineered CRISPR-Cas systems. Current Opinion in Microbiology, 18, 83-89. doi: 10.1016/j.mib.2014.02.007
Biswas, A., Fineran, P. C., & Brown, C. M. (2014). Accurate computational prediction of the transcribed strand of CRISPR noncoding RNAs. Bioinformatics, 30(13), 1805-1813. doi: 10.1093/bioinformatics/btu114
Frampton, R. A., Taylor, C., Holguín Moreno, A. V., Visnovsky, S. B., Petty, N. K., Pitman, A. R., & Fineran, P. C. (2014). Identification of bacteriophages for the biocontrol of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Applied & Environmental Microbiology, 80(7), 2216-2228. doi: 10.1128/aem.00062-14
McNeil, M. B., Hampton, H. G., Hards, K. J., Watson, B. N. J., Cook, G. M., & Fineran, P. C. (2014). The succinate dehydrogenase assembly factor, SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria. FEBS Letters, 588(3), 414-421. doi: 10.1016/j.febslet.2013.12.019
Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C., & Fineran, P. C. (2014). A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Research, 42(7), 4590-4605. doi: 10.1093/nar/gkt1419
Journal - Research Other
Westra, E. R., Buckling, A., & Fineran, P. C. (2014). CRISPR-Cas systems: Beyond adaptive immunity. Nature Reviews Microbiology, 12, 317-326. doi: 10.1038/nrmicro3241
Conference Contribution - Verbal presentation and other Conference outputs
Fineran, P. C. (2014, August). Priming acquisition by the CRISPR-Cas 'adaptive immune' systems. Verbal presentation at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Fineran, P. (2014, September). Immune systems of bacteria: Adapting to competition. Verbal presentation at the Division of Health Sciences Research Forum: Learning Different Research Languages, Dunedin, New Zealand.
2013
Journal - Research Article
Dy, R. L., Pitman, A. R., & Fineran, P. C. (2013). Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria. Mobile Genetic Elements, 3(5), e26831. doi: 10.4161/mge.26831
Fineran, P. C., Iglesias Cans, M. C., Ramsay, J. P., Wilf, N. M., Cossyleon, D., McNeil, M. B., … Stanton, J.-A. L., … Salmond, G. P. C. (2013). Draft genome sequence of Serratia sp. strain ATCC 39006, a model bacterium for analysis of the biosynthesis and regulation of prodigiosin, a carbapenem, and gas vesicles. Genome Announcements, 1(6), e01039-13. doi: 10.1128/genomeA.01039-13
Richter, C., & Fineran, P. C. (2013). The subtype I-F CRISPR-Cas system influences pathogenicity island retention in Pectobacterium atrosepticum via crRNA generation and Csy complex formation. Biochemical Society Transactions, 41(6), 1468-1474. doi: 10.1042/bst20130151
Sangal, V., Fineran, P. C., & Hoskisson, P. A. (2013). Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphtheriae. Microbiology, 159(Pt 10), 2118-2126. doi: 10.1099/mic.0.070235-0
McNeil, M. B., & Fineran, P. C. (2013). The conserved RGxxE motif of the bacterial FAD assembly factor SdhE is required for succinate dehydrogenase flavinylation and activity. Biochemistry, 52, 7628-7640. doi: 10.1021/bi401006a
Biswas, A., Gagnon, J. N., Brouns, S. J. J., Fineran, P. C., & Brown, C. M. (2013). CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biology, 10(5), 817-827. doi: 10.4161/rna.24046
Westra, E. R., Staals, R. H. J., Gort, G., Høgh, S., Neumann, S., de la Cruz, F., Fineran, P. C., & Brouns, S. J. J. (2013). CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biology, 10(5), 749-761. doi: 10.4161/rna.24202
McNeil, M. B., Iglesias Cans, M. C., Clulow, J. S., & Fineran, P. C. (2013). YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY). Microbiology, 159, 1352-1365. doi: 10.1099/mic.0.068510-0
Vercoe, R. B., Chang, J. T., Dy, R. L., Taylor, C., Gristwood, T., Clulow, J. S., Richter, C., Przybilski, R., … Fineran, P. C. (2013). Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genetics, 9(4), e1003454. doi: 10.1371/journal.pgen.1003454
Cook, G. M., Robson, J. R., Frampton, R. A., McKenzie, J., Przybilski, R., Fineran, P. C., & Arcus, V. L. (2013). Ribonucleases in bacterial toxin–antitoxin systems. Biochimica et Biophysica Acta: Gene Regulatory Mechanisms, 1829, 523-531. doi: 10.1016/j.bbagrm.2013.02.007
Short, F. L., Pei, X. Y., Blower, T. R., Ong, S.-L., Fineran, P. C., Luisi, B. F., & Salmond, G. P. C. (2013). Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot. PNAS, 110(3), 820-821. doi: 10.1073/pnas.1216039110
McNeil, M. B., & Fineran, P. C. (2013). Prokaryotic assembly factors for the attachment of flavin to complex II. Biochimica et Biophysica Acta: Bioenergetics, 1827, 637-647. doi: 10.1016/j.bbabio.2012.09.003
2012
Journal - Research Article
Blower, T. R., Short, F. L., Fineran, P. C., & Salmond, G. P. C. (2012). Viral molecular mimicry circumvents abortive infection and suppresses bacterial suicide to make hosts permissive for replication. Bacteriophage, 2(4), 234-238. doi: 10.4161/bact.23830
Richter, C., Gristwood, T., Clulow, J. S., & Fineran, P. C. (2012). In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas system. PLoS ONE, 7(12), e49549. doi: 10.1371/journal.pone.0049549
Fineran, P. C., & Charpentier, E. (2012). Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information. Virology, 434, 202-209. doi: 10.1016/j.virol.2012.10.003
Blower, T. R., Evans, T. J., Przybilski, R., Fineran, P. C., & Salmond, G. P. C. (2012). Viral evasion of a bacterial suicide system by RNA–based molecular mimicry enables infectious altruism. PLoS Genetics, 8(10), e1003023. doi: 10.1371/journal.pgen.1003023
Richter, C., Chang, J. T., & Fineran, P. C. (2012). Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR associated (Cas) systems. Viruses, 4(10), 2291-2311. doi: 10.3390/v4102291
Frampton, R. A., Pitman, A. R., & Fineran, P. C. (2012). Advances in bacteriophage-mediated control of plant pathogens. International Journal of Microbiology, 2012, 326452. doi: 10.1155/2012/326452
Blower, T. R., Short, F. L., Rao, F., Mizuguchi, K., Pei, X. Y., Fineran, P. C., … Salmond, G. P. C. (2012). Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes. Nucleic Acids Research, 40(13), 6158-6173. doi: 10.1093/nar/gks231
McNeil, M. B., Clulow, J. S., Wilf, N. M., Salmond, G. P. C., & Fineran, P. C. (2012). SdhE is a conserved protein required for the flavinylation of succinate dehydrogenase in bacteria. Journal of Biological Chemistry, 287(22), 18418-18428. doi: 10.1074/jbc.M111.293803
Conference Contribution - Verbal presentation and other Conference outputs
McNeil, M., & Fineran, P. (2012, November). Functional characterisation of the FAD cofactor chaperone SdhE. Verbal presentation at the 57th New Zealand Microbiological Society (NZMS) Annual Scientific Meeting, Dunedin, New Zealand.
Richter, C., Gristwood, T., Clulow, J., Luckner, S., Opel-Reading, H.-K., Chang, J., Krause, K., & Fineran, P. (2012, November). Protein complexes related to CRISPR/Cas resistance in Pectobacterium atrosepticum. Verbal presentation at the 57th New Zealand Microbiological Society (NZMS) Annual Scientific Meeting, Dunedin, New Zealand.
2011
Journal - Research Article
Przybilski, R., Richter, C., Gristwood, T., Clulow, J. S., Vercoe, R. B., & Fineran, P. C. (2011). Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum. RNA Biology, 8(3), 517-528. doi: 10.4161/rna.8.3.15190
Blower, T. R., Pei, X. Y., Short, F. L., Fineran, P. C., Humphreys, D. P., Luisi, B. F., & Salmond, G. P. C. (2011). A processed noncoding RNA regulates an altruistic bacterial antiviral system. Nature Structural & Molecular Biology, 18(2), 185-191. doi: 10.1038/nsmb.1981
Gristwood, T., McNeil, M. B., Clulow, J. S., Salmond, G. P. C., & Fineran, P. C. (2011). PigS and PigP regulate prodigiosin biosynthesis in Serratia via differential control of divergent operons, which include predicted transporters of sulfur-containing molecules. Journal of Bacteriology, 193(5), 1076-1085. doi: 10.1128/JB.00352-10
Conference Contribution - Poster Presentation (not in published proceedings)
Richter, C., Gristwood, T., Clulow, J., & Fineran, P. (2011, September). Protein-protein interactions and complex formation for CRISPR-mediated defence against foreign genetic elements in Pectobacterium atrosepticum. Poster session presented at the Queenstown Molecular Biology (QMB) Meetings, Queenstown, New Zealand.
Other Research Output
Fineran, P. C. (2011, March). Molecular characterisation of the small RNA-mediated phage resistance CRISPR system in Pectobacterium atrosepticum. University of Otago Department of Microbiology & Immunology Seminar, Dunedin, New Zealand. [Department Seminar].
2009
Chapter in Book - Research
Fineran, P. C., Petty, N. K., & Salmond, G. P. C. (2009). Transduction: Host DNA transfer by bacteriophages. In M. Schaechter (Ed.), Encyclopedia of microbiology (Vol. 3). (3rd ed.) (pp. 666-679). Oxford, UK: Elsevier.
Journal - Research Article
Blower, T. R., Fineran, P. C., Johnson, M. J., Toth, I. K., Humphreys, D. P., & Salmond, G. P. C. (2009). Mutagenesis and functional characterization of the RNA and protein components of the toxIN abortive infection and toxin-antitoxin locus of Erwinia. Journal of Bacteriology, 191(19), 6029-6039. doi: 10.1128/JB.00720-09
Gristwood, T., Fineran, P. C., Everson, L., Williamson, N. R., & Salmond, G. P. (2009). The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate. BMC Microbiology, 9, 112. doi: 10.1186/1471-2180-9-112
Fineran, P. C., Blower, T. R., Foulds, I. J., Humphreys, D. P., Lilley, K. S., & Salmond, G. P. C. (2009). The phage abortive infection system, toxIN, functions as a protein-RNA toxin-antitoxin pair. PNAS, 106(3), 894-899. doi: 10.1073/pnas.0808832106
Conference Contribution - Published proceedings: Abstract
McNeil, M. B., Iglesias Cans, M., Richter, C., Gristwood, T., Salmond, G. P. C., & Fineran, P. C. (2009). A putative signal transduction system that is widely conserved in enteric bacteria. Proceedings of the ComBio2009 Conference. [CD-ROM] [Abstract]
2008
Journal - Research Article
Williamson, N. R., Fineran, P. C., Ogawa, W., Woodley, L. R., & Salmond, G. P. C. (2008). Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhIA-dependent surfactant biosynthesis in Serratia. Environmental Microbiology, 10(5), 1202-1217. doi: 10.1111/j.1462-2920.2007.01536.x
Gristwood, T., Fineran, P. C., Everson, L., & Salmond, G. P. C. (2008). PigZ, a TetR/AcrR family repressor, modulates secondary metabolism via the expression of a putative four-component resistance-nodulation-cell-division efflux pump, ZrpADBC, in Serratia sp. ATCC 39006. Molecular Microbiology, 69(2), 418-435. doi: 10.1111/j.1365-2958.2008.06291.x
Conference Contribution - Published proceedings: Abstract
Fineran, P. C., Blower, T. R., Foulds, I. J., & Salmond, G. P. C. (2008). The phage abortive infection system, ToxIN, functions as a toxin-antitoxin pair. Proceedings of the New Zealand Microbiological Society Microbiology Conference. (pp. 28). NZMS. Retrieved from http://www.nzmsconference08.org.nz/files/Oral-Abstracts-NZMS-2008.pdf
2007
Journal - Research Article
Williamson, N. R., Fineran, P. C., Gristwood, T., Chawrai, S. R., Leeper, F. J., & Salmond, G. P. C. (2007). Anticancer and immunosuppressive properties of bacterial prodiginines. Future Microbiology, 2(6), 605-618.
Fineran, P. C., Williamson, N. R., Lilley, K. S., & Salmond, G. P. C. (2007). Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. Journal of Bacteriology, 189(21), 7653-7662.
Petty, N. K., Evans, T. J., Fineran, P. C., & Salmond, G. P. C. (2007). Biotechnological exploitation of bacteriophage research. Trends in Biotechnology, 25(1), 7-15.
2006
Journal - Research Other
Williamson, N. R., Fineran, P. C., Leeper, F. J., & Salmond, G. P. C. (2006). The biosynthesis and regulation of bacterial prodiginines. Nature Reviews Microbiology, 4, 887-899. doi: 10.1038/nrmicro1531
Awarded Doctoral Degree
Fineran, P. C. (2006). Investigation of a regulatory network controlling secondary metabolism in Serratia (PhD). University of Cambridge, UK. 256p.