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(*contributed equally, #corresponding author)
138. Warring, S.L.,# Sisson, H.M., Fineran, P.C. and Rabiey, M.# (2024) Strategies for the biocontrol Pseudomonas infections pre-fruit harvest. Microbial Biotechnology. doi.org/10.1111/1751-7915.70017
137. Kamata, K., Birkholz, N., Ceelen, M., Fagerlund, R.D., Jackson, S.A. and Fineran, P.C.# (2024) Repurposing an Endogenous CRISPR-Cas System to Generate and Study Subtle Mutations in Bacteriophages. The CRISPR Journal. doi.org/10.1089/crispr.2024.0047
136. Birkholz, N.,# and Fineran, P.C.# (2024) Anti-CRISPRs deconstruct bacterial defence. Molecular Cell. 84. 3172-3174
135. Birkholz, N., Kamata, K., Feussner, M., Wilkinson, M.E., Samaniego, C.C., Migur, A., Kimanius, D., Ceelen, M., Went, S.C., Usher, B., Blower, T.R., Brown, C.M., Beisel, C.L., Weinberg, Z., Fagerlund, R.D., Jackson, S.A. and Fineran, P.C.# (2024) Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein. Nature. 631. 670-677
134. Payne, L.J., Hughes, T.C.D., Fineran, P.C. and Jackson, S.A.# (2024). New antiviral defences are genetically embedded within prokaryotic immune systems. bioRxiv. doi.org/10.1101/2024.01.29.577857
133. Schwartz, E.A.,* Bravo, J.K.P.,* Ahsan, M.,* Macias, L.A., McCafferty, C.L., Dangerfield, T.L., Walker, J.N., Brodbelt, J.S., Palermo, G.,# Fineran, P.C., Fagerlund, R.D.# and Taylor, D.W.# (2024). RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nature Communications. 15. 3324. doi.org/10.1038/s41467-024-47506-y
132. Sisson, H.M., Jackson, S.A., Fagerlund, R.D., Warring, S.L. and Fineran, P.C.# (2024).Gram-negative endolysins: overcoming the outer membrane obstacle. Current Opinion in Microbiology. 78:102433. doi: 10.1016/j.mib.2024.102433.
131. Sisson, H.M., Fagerlund, R.D., Jackson, S.A., Briers, Y., Warring, S.L. and Fineran, P.C.# (2024). Antibacterial synergy between a phage endolysin and citric acid against the Gram-negative kiwifruit pathogen Pseudomonas syringae pv. actinidiae. Applied and Environmental Microbiology. doi.org/10.1128/aem.01846-23
130. Mayo-Muñoz, D.,* Pinilla-Redondo, R.,*# Camara-Wilpert, S., Birkholz, N. and Fineran, P.C.# (2024). Inhibitors of bacterial immune systems: discovery, mechanisms and applications. Nature Reviews Genetics. doi.org/10.1038/s41576-023-00676-9
129. Adler, B.A., Trinidad, M. I., …41 authors…, Fineran., P.C., ...7 authors..., Banfield, J.F., Savage, D.F., and Doudna, J.A. (2024). CasPEDIA Database: A function classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Research. 52. D590–D596
128. Sitter, T.L., Schoof, M., Glare, T.R., Cox, M.P., Fineran, P.C., Gardner, P.P. and Hurst, M.R.H. (2024). Serratia based Toxin cluster elements are associated with a Type I fimbria. MicrobiologyOpen. doi.org/10.1002/mbo3.1395
127. Smith, L.M., Hampton, H.G., Yevstigneyeva, M.S., Mahler, M., Paquet, Z.S.M. and Fineran, P.C.# (2024). CRISPR-Cas immunity is repressed by the LysR-type transcriptional regulator PigU. Nucleic Acids Research. 52. 755–768
126. Wang, X., Jowsey, W.J., Cheung, C-Y, Seeto, N.E., Waller, N.J., Chrisp, M.T., Peterson, A.L., Nijagal, B., Fineran, P.C., Cook, G.M., Jackson, S.A. and McNeil, M.B. (2023). KatG inactivation generates vulnerabilities in isoniazid resistant strains of Mycobacterium tuberculosis. bioRxiv. doi.org/10.1101/2023.12.07.570702
125. Camara-Wilpert, S., * Mayo-Muñoz, D.,* Russel, J., Fagerlund, R.D., Madsen, J.S., Fineran, P.C.#, Sørensen, S.J. and Pinilla-Redondo, R.# (2023). Bacteriophages suppress CRISPR-Cas immunity using RNA-based anti-CRISPRs. Nature. 623. 601–607
124. López-Rojo, A., Jackson, S.A., Bernal-Bernal, D., Galbis-Martínez, M., Fineran, P.C. and Elías-Arnanz, M. (2023). Genome sequences of Mx1, the first Myxococcus phage isolated, and Mx4, a generalized transducing myxophage. Microbial Resource Announcements. doi: 10.1128/MRA.00904-23.
123. Shearer, H.L., Pace, P.E., Smith, L.M., Fineran, P.C., Matthews, A.J., Camilli, A., Dickerhof, N. and Hampton, M.B. (2023). Identification of Streptococcus pneumoniae genes associated with hypothiocyanous acid tolerance through genome-wide screening. Journal of Bacteriology. 4:e0020823.
122. Harding, K.R, Kyte, N. and Fineran, P.C.# (2023). Jumbo Phages. Current Biology. 33. R743–R759
121. Mayo-Muñoz, D., Pinilla-Redondo, R.,* Birkholz, N.* and Fineran, P.C.# (2023). A host of armour: prokaryotic immune strategies against mobile genetic elements. Cell Reports. 42. 112672
120. McBride, T.M., Cameron, S.C., Fineran, P.C.# and Fagerlund, R.D.# (2023). The biology and type I/III hybrid nature of type I-D CRISPR-Cas systems. Biochemical Journal. 470. 471-488
119. Mahler, M.,* Malone, L.M.,* van den Berg, D.F., Smith, L.M., Brouns, S.J.J. and Fineran, P.C.# (2023). An OmpW-dependent T4-like phage infects Serratia sp. ATCC39006. Microbial Genomics. 9. doi.org/10.1099/mgen.0.000968
118. Smith, L.M. and Fineran, P.C.# (2023). Phage capsid recognition triggers activation of a bacterial toxin-antitoxin defense system. Molecular Cell. 83. 165-166
117. Mahler, M., Costa, A.R., van Beljouw, S.P.B., Fineran, P.C. and Brouns, S.J.J. (2023). Approaches for bacteriophage genome engineering. Trends in Biotechnology. 41. 669-685
116. Mayo-Muñoz, D., Smith, L.M., García-Doval, C., Malone, L.M., Harding, K.R., Jackson, S.A., Hampton, H.G., Fagerlund, R.D., Gumy, L.F. and Fineran, P.C.# (2022). Type III CRISPR–Cas provides resistance against nucleus-forming jumbo phages via abortive infection. Molecular Cell. 82. 4471-4486
115. Kim, G.E., Lee, S.Y., Birkholz, N., Kamata, K., Jeong, J.-H., Kim, Y.-G., Fineran, P.C. and Park, H.H. (2022) Molecular basis of dual anti-CRISPR and auto-regulatory functions of AcrIF24. Nucleic Acids Research. 50. 11344-11358
114. Shehreen, S., Birkholz, N., Fineran, P.C. and Brown C.M. (2022). Widespread repression of anti-CRISPR production by anti-CRISPR-associated proteins. Nucleic Acids Research.50. 8615-8625
113. 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. 8919-8928
112. Warring, S.L.,* Malone, L.M.,* Jayaraman, J., Easingwood, R.A., Rigano, L., Frampton, R.A., Visnovsky, S.B., Addison, S.M., Hernandez, L., Pitman, A.R., Lopez Acedo, E., Kleffmann, T., Templeton, M.D., Bostina, M. and Fineran, P.C.# (2022). A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance. Environmental Microbiology. 24. 4834-4852
111. Smith, L.M., Rey Campa, A. and Fineran, P.C.# (2022). Regulation of CRISPR-Cas expression and function. Chapter 10 In CRISPR: Biology and Applications. ASM Press. Editors: Marraffini, Barrangou and Sontheimer. 1st ed.
110. Birkholz, N. and Fineran, P.C.# (2022). Turning down the (C)BASS: Phage-encoded inhibitors jam bacterial immune signaling. Molecular Cell. 82. 2185-2187
109. Payne, L.J., Meaden, S., Mestre, M.R., Palmer, C., Toro, N., Fineran, P.C. and Jackson, S.A.# (2022). PADLOC: a web server for the identification of antiviral defence systems in microbial genomes. Nucleic Acids Research. 50. W541-50
108. Schwartz, E.A.,* McBride, T.M.,* Bravo, J.K.P.,* Wrapp, D., Fineran, P.C., Fagerlund, R.D. and Taylor, D.W.# (2022). Structural rearrangements allow nucleic acid discrimination by typeI-D Cascade. Nature Communications. 13. 2829
107. Pinilla-Redondo, R.,* Russel, J.,* Mayo-Muńoz, D.,* Shah, S.A., Garrett, R.A., Nesme, J., Madsen, J.S., Fineran, P.C. and Sørensen, S.J.# (2022). CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Research. 50. 4315–4328 (Cover)
106. Birkholz, N., Jackson, S.A., Fagerlund, R.D. and 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. 3348-3361
105. Malone, L.M., Hampton, H.G., Morgan, X.C. and Fineran, P.C.# (2022). Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress. Nucleic Acids Research. 50. 160-174
104. Meaden, S.,# Biswas, A., Arkipova, K., Morales, S.E., Dutilh, B.E., Westra, E.R. and 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
103. Meaden, S.# and Fineran, P.C.# (2021). Bacterial defense islands limit viral attack. Science. 374. 399-400
102. Payne, L.J., Todeschini, T.C., Wu, T., Perry, B.J., Ronson, C.W., Fineran, P.C., Nobrega, F.L. and 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. 10868–10878
101. Rey Campa, A., Smith, L.M.,* Hampton, H.G.,* Sharma, S., Jackson, S.A., Bischler, T., Sharma, C.M. and Fineran, P.C.# (2021). The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. Nucleic Acids Research. 49. 9508–9525
100. Smith, L.M., Jackson, S.A., Gardner, P.P. and Fineran, P.C.# (2021). SorTn-seq: a high-throughput functional genomics approach to discovering regulators of bacterial gene expression. Nature Protocols. 16. 4382-4418
99. Usher, B., Birkholz, N., Beck, I.N., Fagerlund, R.D., Jackson, S.A., Fineran, P.C. and Blower, T.R.# (2021). Crystal structure of the anti-CRISPR repressor Aca2. Journal of Structural Biology. 213. 107752
98. Malone, L.M.,* Birkholz, N.* and Fineran, P.C.# (2021). Conquering CRISPR: How phages overcome bacterial adaptive immunity. Current Opinion in Biotechnology. 68. 30-36
97. Sitter, T.L.,# Vaughan, A.L., Schoof, M., Jackson, S.A., Glare, T.R., Cox, M.P., Fineran, P.C., Gardner, P.P. and Hurst, M.R.H. (2021). Adaptive evolution of virulence in a novel family of transmissible mega-plasmids. Environmental Microbiology. 23. 5289-5304
96. Smith, L.M., Jackson, S.A., Malone, L.M., Ussher, J.E., Gardner, P.P. and 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
95. Pinilla-Redondo, R.,* Shehreen, S.,* Marino, N.D., Fagerlund, R.D., Brown, C.M., Sørensen, S.J., Fineran, P.C.# and Bondy-Denomy, J.# (2020). Discovery of multiple anti-CRISPRs uncovers anti-defense gene clustering in mobile genetic elements. Nature Communications. 11. 5652
94. McBride, T.M.,* Schwartz, E.A.,* Kumar, A., Taylor, D.W., Fineran, P.C. and 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.e7
93. Jackson, S.A.,# Fellows, B.J. and Fineran, P.C. (2020). Complete genomes of the Escherichia coli donor strains ST18 and MFDpir. Microbiology Resource Announcements. 9. e01014-20
92. Hampton, H.G., Smith, L.M., Ferguson, S., Meaden, S., Jackson, S.A. and Fineran, P.C.# (2020). Functional genomics reveals the toxin-antitoxin repertoire and AbiE activity in Serratia. Microbial Genomics. 6. mgen000458
91. Jayaraman, J., Jones, W.T., Harvey, D., Yoon, M., McCann, H.C., Hemara, L., Warring, S.L., Fineran, P.C., Mesarich, C.H. and Templeton, M.D.# (2020). Variation at the common polysaccharide antigen locus drives lipopolysaccharide diversity within the P. syringae species complex. Environmental Microbiology. 22. 5356-5372
90. Cai, Y., Usher, B., Gutierrez, C., Tolcan, A., Mansour, M., Fineran, P.C., Condon, C., Neyrolles, O., Genevaux, P.# and Blower, T.R.# (2020). A nucleotidyltransferase toxin inhibits growth of Mycobacterium tuberculosis through inactivation of tRNA acceptor stems. Science Advances. 6. eabb6651
89. Beck, I.N., Usher, B., Hampton, H.G., Fineran, P.C. and 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
88. Rollie, C.,# Chevallereau, A., Watson, B.N.J., Chyou, T-y., Fradet, O., McLeod, I., Fineran, P.C., Brown, C.M, Gandon, S. and Westra, E.R.# (2020). Imperfect targeting of temperate phages drives loss of type I CRISPR-Cas immune systems. Nature. 578. 149-153
87. Hampton, H.G.,* Watson, B.N.J.* and Fineran, P.C.# (2020) The arms race between bacteria and their phage foes. Nature. 577. 327–336
86. Malone, L.M., Warring, S.L., Jackson, S.A., Warnecke, C., Gardner, P.P., Gumy, L.F. and 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
85. Watson, B.N.J., Vercoe, R.B., Salmond, G.P.C., Westra, E.R., Staals, R.H.J. and 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
84. 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
83.Bergman, J.M., Fineran, P.C., Petty, N.K. and Salmond, G.P.C.# (2019). Transduction: The Transfer of Host by Bacteriophages. In The Encyclopedia of Microbiology (4th edition). Edited by Moselio Schaechter. pp 458-473
82. Edwards, R.A.,# Vega, 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
81. Greisch, J-F, Tamara, S., Scheltema, R.A., Maxwell, H.W.R., Fagerlund, R.D., Fineran, P.C., Tetter, S., Hilvert, D and Heck, A.J.R.# (2019). Expanding the Mass Range for UVPD Based Native Top-Down Mass Spectrometry. RSC Chemical Science. 10. 7163-7171
80. Hampton, H.G.,* Patterson, A.G.,* Chang, J.T., Taylor, C. and Fineran, P.C.# (2019). GalK limits type I-F CRISPR-Cas expression in a CRP-dependent manner. FEMS Microbiology Letters. 366. fnz137
79. Wotjus, J.K.,* Frampton, R.A.,* Warring, S., Hendrickson, H. and Fineran, P.C.# (2019). Genome sequence of a jumbo bacteriophage that is a potential biocontrol against the kiwifruit phytopathogen Pseudomonas syringae pv. actinidiae. Microbial Resource Announcements. 8. e00224-19
78. Jackson, S.A. and Fineran, P.C.# (2019). Bacterial dormancy curbs phage epidemics. Nature. 570. 173-174
77. Fineran, P.C.# (2019). Resistance is not futile: bacterial ‘innate’ and ‘adaptive’ immune systems. Fleming Prize Award Article. Microbiology. 165. 834-841
76. 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 & Microbe. 25. 250-260
75. Fagerlund, R.D.,# Ferguson, T.J., Maxwell, H.W.R. Opel-Reading, H.K., Krause, K.L. and Fineran, P.C.# (2019). Reconstitution of CRISPR adaptation in vitro and its detection by PCR. Volume 617: CRISPR-Cas Enzymes. Methods in Enzymology. 616. 411-433
74. Fineran, P.C.# (2019) CRISPR-Cas impedes archaeal mating. Nature Microbiology. 4:2-3
73. Shehreen, S., Chyou, T-y., Fineran, P.C. and 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. 20180384
72. Watson, B.N.J., Easingwood, R.A., Tong, B., Wolf, M., Salmond, G.P.C., Staals, R.H.J., Bostina, M.# and 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. 20180090
71. 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
70. Dy, R.L.,# Rigano, L. and Fineran, P.C.# (2018). Phage-based biocontrol strategies and their application in agriculture and aquaculture. Biochemical Society Transactions. 46. 1605-1613
69. Bondy-Denomy, J.,# Davidson, A.R., Doudna, J.A., Fineran, P.C., Maxwell, K.L., Moineau, S., Peng, X., Sontheimer, E.J. and Wiedenheft, B. (2018). A Unified Resource for Tracking Anti-CRISPR Names. The CRISPR Journal. 1. 304-305.
68. 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
67. Watson, B.N.J., Staals, R.H.J. and Fineran, P.C.# (2018). CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction. mBio 9:e02406-17.
Highlight: Du Toit A. (2018). Viral infection: CRISPR-Cas enhances HGT by transduction. Nature Reviews Microbiology. 16:186.
66. Silas, S., Lucas-Elío, P., Jackson, S.A., Aroca-Crevillén, A., Hansen, L.L., Fineran, P.C., Fire, A.Z., 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
65. Fagerlund, R.D.,* Wilkinson, M.E.,* Klykov, O.,* Barendregt, A., Pearce, F.G., Kieper, S.N., Maxwell, H.W.R., Capolupo, A., Heck, A.J.R., Krause, K.L., Bostina, M., Scheltema, R.A., Staals, R.H.J. and Fineran, P.C.# (2017). Spacer capture and integration by a type I-F Cas1:Cas2-3 CRISPR adaptation complex. Proc. Natl. Acad. Sci. (USA). 114. E5122-E5128.
64. 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
63. Patterson, A.G., Yevstigneyeva, M. and Fineran, P.C.# (2017). Regulation of CRISPR-Cas adaptive immune systems. Current Opinion in Microbiology. 37. 1-7. (invited)
62. Mesarich, C.H., Rees-George, J., Gardner, P.P., Ghomi, F.A., Gerth, M.L., Andersen, M.T., Rikkerink, E.H.A., Fineran,P.C. and Templeton, M.D.# (2017). Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS ONE. 12. e0172790
61. Blower, T.R., Chai, R., Przybilski, R., Chindhy, S., Fang, X., Kidman, S., Tan, H., Luisi, B.F., Fineran, P.C. and Salmond, G.P.C.# (2017). Bacteriophage phiM1 of Pectobacterium atrosepticum evolves to escape two bifunctional Type III toxin-antitoxin and abortive infection systems through mutations in a single viral gene. Applied and Environmental Microbiology.
60. Patterson, A.G., Jackson, S.A., Taylor, C., Evans, G.B., Salmond, G.P.C., Przybilski, R., Staals, R.H.J. and Fineran, P.C.# (2016). Quorum sensing controls adaptive immunity through the regulation of multiple CRISPR-Cas systems. Molecular Cell. 64. 1102–1108
59. 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
58. Pawluk, A., Staals, R.H.J., Taylor, C., Watson, B.N.J., Saha, S., Fineran, P.C., Maxwell, K.L.# and Davidson, A.R.# (2016). Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nature Microbiology. 1. 16805
57. Biswas, A., Staals, R.H.J., Morales, S.E., Fineran, P.C. and Brown, C.M.# (2016). CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics. 17.356
56. Hampton, H.G., McNeil, M.B., Paterson, T.J., Ney, B., Williamson, N.R., Easingwood, R.A., Bostina, M., Salmond, G.P.C. and 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.
55. Panda, P., Vanga, B.R., Lu, A., Fiers, M., Fineran, P.C., Butler, R., Armstrong, K., Ronson, C.W. and 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
54. Wilkinson, M.E., Nakatani, Y., Staals, R.H.J., Kieper, S.N., Opel-Reading, H.K., McKenzie, R.E., Fineran, P.C.# and 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
53. Fagerlund, R.D., Staals, R.H. and Fineran, P.C.# (2015). The CRISPR-Cas protein Cpf1 expands genome-editing tools. Genome Biology. 16. 251
52. Salmond, G.P.C.# and Fineran, P.C.# (2015). A century of the phage: past, present and future. Nature Reviews Microbiology. 13. 777-786
51. Templeton, M.D.,# Warren, B.A., Andersen, M.T., Rikkerink, E.H.A. and Fineran,P.C. (2015). The Complete DNA Sequence of Pseudomonas syringae pv. actinidiae the Causal Agent of Kiwifruit Canker Disease. Genome Announcements. 3. e01054-15
50. Holguín, A.V., Rangel, G., Clavijo, V., Prada, C., Mantilla, M., Gomez, M.C., Kutter, E., Taylor, C., Fineran, P.C. González Barrios, A.F. and Vives, M.J.# (2015). Phage ΦPan70, a putative temperate phage, controls Pseudomonas aeruginosa in planktonic, biofilm and burn mouse model assays. Viruses. 7. 4602-4623
49. Frampton, R.A.,* Lopez-Acedo, E.,* Young, V.L., Chen, D., Tong, B., Taylor, C., Easingwood, R.A., Pitman, A.R., Kleffmann, T., Bostina, M.# and Fineran, P.C.# (2015). Genome, proteome and structure of a T7-like bacteriophage of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Viruses. 7. 3361-3379
48. Patterson, A.G., Chang, J.T., Taylor, C. and 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. 6038-6048
47. Lundgren, M., Charpentier, E. and Fineran, P.C. (Eds) (2015). CRISPR: Methods and Protocols. Methods in Molecular Biology. Volume 1311. Humana Press, 366 pages.
46. Biswas, A., Fineran, P.C. and Brown, C.M.# (2015). Computational detection of CRISPR/crRNA targets. Methods in Molecular Biology. 1311:77-89
45. Richter, C.,* Dy, R.L.,* McKenzie, R.E.,* Watson, B.N.J., Taylor, C., Chang, J.T., McNeil, M.B., Staals, R.H.J. and 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. 8516-8526
44. Dy, R.L., Richter, C., Salmond, G.P.C. and Fineran, P.C.# (2014). Remarkable Mechanisms in Microbes to Resist Viral Infections. Annual Reviews of Virology. 1. 307-331
43. Fineran, P.C.#, Gerritzen, M.J.H., Suárez-Diez, M., Künne, T., Boekhorst, J., van Hijum, S.A.F.T., Staals, R.H.J. and Brouns, S.J.J.# (2014). Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl. Acad. Sci. (USA). 111. E1629–E1638
42. Westra, E.R.,# Buckling, A. and Fineran, P.C. (2014). CRISPR-Cas: More than Adaptive Immunity. Nature Reviews Microbiology. 12. 317-326
41. Fineran, P.C.# and Dy, R.L. (2014). Gene regulation by engineered CRISPR-Cas systems. Current Opinion in Microbiology. 18. 83-89
40. Biswas, A., Fineran, P.C. and Brown, C.M.# (2014). Accurate computational prediction of the transcribed strand of CRISPR noncoding RNAs. Bioinformatics. 30. 1805-1813
39. Frampton, R.A., Taylor, C., Holguin Moreno, A.V., Visnovsky, S.B., Petty, N.K., Pitman, A.R. and Fineran, P.C.# (2014). Identification of bacteriophages for the biocontrol of the kiwifrut canker phytopathogen Pseudomonas syringae pv. actinidiae. Applied and Environmental Microbiology. 80. 2216-2228
38. Dy, R.L., Przybilski, R., Semeijn, K., Salmond, G.P.C. and Fineran, P.C.# (2014). A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Research. 42. 4590-4605
37. McNeil, M.B., Hampton, H.G., Hards, K.J., Watson, B.N.J., Cook, G.M. and 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. 514-521
36. Fineran, P.C.,# Iglesias Cans, M.C., Ramsay, J.P., Wilf, N., Cossyleon, D., McNeil, M.B., Williamson, N.R., Monson, R.E., Becher, S.A., Stanton, J.S., Brügger, K, Brown, S.D. and Salmond, G.P.C.# (2013). Draft genome sequence of Serratia sp. strain ATCC 39006, a model bacterium for the analysis of the biosynthesis and regulation of prodigiosin, a carbapenem and gas vesicles. Genome Announcements. 1. e01039-13
35. Dy, R.L., Pitman, A.R. and Fineran, P.C.# (2013). Chromosomal targeting by CRISPR-Cas can contribute to genome plasticity in bacteria. Mobile Genetic Elements. 3. e26831
34. Richter, C. and Fineran, P.C.# (2013). The type I-F CRISPR-Cas system influences pathogenicity island retention in Pectobacterium atrosepticum via crRNA generation and Csy complex formation. Biochemical Society Transactions. 41. 1468-74
33. McNeil, M.B. and 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. 7628–40
32. Sangal, V., Fineran, P.C. and Hoskisson, P.A.# (2013). Novel configurations of Type I and II CRISPR/Cas systems in Corynebacterium diphtheriae. Microbiology. 159. 2118-2126
31. McNeil, M.B., Iglesias Cans, M., Clulow, J.S. and 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
30. Vercoe, R.B., Chang, J.T., Dy, R.L., Taylor, C., Gristwood, T., Clulow, J.S., Richter, C., Przybilski, R., Pitman, A.R. and 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.
29. Westra, E.R., Staals, R.H.J., Gort, G., Hoegh, S., Neumann, S., de la Cruz, F., Fineran, P.C. and Brouns, S.J.J.# (2013). CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biology. 10. 22-34.
28. Biswas, A., Gagnon, J.N., Brouns, S.J.J., Fineran, P.C.# and Brown, C.M.# (2013). CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biology. 10. 82-92.
27. Cook, G.M.,# Robson, J.R., Frampton, R.A., McKenzie, J., Przybilski, R., Fineran, P.C#. and Arcus, V.L.# (2013) Ribonucleases in Bacterial Toxin-Antitoxin Systems. BBA - Gene Regulatory Mechanisms. 1829. 523-531. (invited review)
26. Short, F.L., Pei, X.Y., Blower, T.R., Ong, S.L., Fineran, P.C., Luisi, B.F. and Salmond, G.P.C.# (2013). Self-assembly and selective bacterial toxin inhibition by an antitoxic non-coding RNA pseudoknot. Proc. Natl. Acad. Sci. (USA). 110. E241-9.
25. McNeil, M.B. and Fineran, P.C.# (2013). Prokaryotic assembly factors for the attachment of flavin to complex II. BBA Bioenergetics. 1827. 637-647. (invited review)
24. Richter, C., Gristwood, T., Clulow, J.S. and Fineran, P.C.# (2012). In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas system. PLoS ONE.7. e49549.
23. Blower, T.R., Short, F.L., Fineran, P.C. and Salmond, G.P.C.# (2012). Viral molecular mimicry circumvents abortive infection and suppresses bacterial suicide to make hosts permissive for replication. Bacteriophage. 2. 234-238.
22. Fineran, P.C.# and Charpentier, E.# (2012). Memory of viral infection by CRISPR-Cas immune systems: acquisition of new information. Virology. 434. 202-209.
21. Richter, C., Chang, J.T. and Fineran, P.C.# (2012). The function and regulation of CRISPR/Cas systems. Viruses. 4. 2291-2311. (invited review)
20. Blower, T.R., Evans, T.J., Przybilski, R., Fineran, P.C. and Salmond, G.P.C.# (2012). A bacteriophage-derived non-coding RNA mimics antitoxic activity to inhibit abortive infection by a Type III toxin-antitoxin system. PLoS Genetics. 8. e1003023.
19. Frampton, R.A. Pitman, A.R. and Fineran, P.C.# (2012). Advances in Bacteriophage-Mediated Control of Plant Pathogens. International Journal of Microbiology. 2012. 326452.
18. McNeil, M.B., Clulow, J.S., Wilf, N., Salmond, G.P.C. and Fineran, P.C.# (2012). SdhE is a conserved protein required for the flavinylation of succinate dehydrogenase in bacteria. Journal of Biological Chemistry. 287. 18418–18428.
17. Blower, T.R., Short, F.L., Rao, F. Mizoguchi, K., Pei, X.Y., Fineran, P.C., Luisi, B.F. and Salmond, G.P.C.# (2012). Identification and classification of bacterial Type III toxin-antitoxin systems and antiviral abortive infection systems encoded in chromosomal and plasmid genomes. Nucleic Acids Research.40. 6158-6173.
16. Przybilski, R., Richter, C., Gristwood, T., Clulow, J.S., Vercoe, R.B. and Fineran, P.C.# (2011). Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum. RNA Biology. 8. 517-528.
15. Gristwood, T., McNeil, M.B., Clulow, J.S., Salmond, G.P.C.# and 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. 1076-1085.
14. Blower, T.R., Pei, X.Y., Short, F.L., Fineran, P.C., Humpreys, D.P., Luisi, B.F. and Salmond, G.P.C.# (2011). A processed non-coding RNA regulates a bacterial antiviral system. Nature Structural and Molecular Biology. 18. 185-190.
13. Blower, T.R., Evans, T.J., Fineran, P.C., Toth, I.K., Foulds, I.J. and Salmond, G.P.C.# (2010) Chapter 53. Phage-receptor interactions and phage abortive infection: potential biocontrol factors in a bacterial plant pathogen. In Biology of Molecular Plant-Microbe Interactions. Antoun, H., Avis T., Brisson L., Prévost D. and Trepanier M., eds. International Society for Molecular Plant-Microbe Interactions, St. Paul, MN. Volume 7: 1-7.
12. Fineran, P.C., Petty, N.K. and Salmond, G.P.C.# (2009). Transduction: Host DNA Transfer by Bacteriophages. In The Encyclopedia of Microbiology (3rd edition). Edited by Moselio Schaechter. 666-679.
11. Blower, T.R., Fineran, P.C., Johnson, M.J., Toth, I.K., Humpreys, D.P and Salmond, G.P.C.# (2009). Mutagenesis and functional characterisation of the RNA and protein components of the toxINabortive infection / toxin-antitoxin locus of Erwinia. Journal of Bacteriology. 191. 6029-6039.
10. Gristwood, T., Fineran, P.C., Everson, L., Williamson, N.R. and Salmond, G.P.C.# (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.
9. Fineran, P.C., Blower, T.R., Foulds, I.J., Humpreys, D.P., Lilley, K.S. and Salmond, G.P.C.# (2009).The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. (USA). 106. 894-899.
8. Gristwood, T., Fineran, P.C., Everson, L. and Salmond, G.P.C.# (2008). PigZ, a TetR/AcrR family transcriptional repressor, regulates secondary metabolism via the expression of a putative resistance-nodulation-cell-division efflux pump, ZrpADBC, in Serratia. Molecular Microbiology. 69. 418-435.
7. Williamson, N.R.,* Fineran, P.C.,* Ogawa, W., Woodley, LR. and 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 RhlA-dependent surfactant biosynthesis in Serratia. Environmental Microbiology. 10. 1202-1217.
6. Williamson, N.R., Fineran, P.C., Gristwood, T., Chawrai, S.R., Leeper, F.J. and Salmond, G.P.C.# (2007). Anticancer and Immunosuppressant Properties of Bacterial Prodiginines. Future Microbiology.2. 605-618.
5. Fineran, P.C.,* Williamson, N.R.,* Lilley, K.S. and 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. 7653-7662.
4. Petty, N.K.*, Evans, T.J.,* Fineran, P.C.* and Salmond, G.P.C.# (2007). Biotechnological Exploitation of Bacteriophage Research. Trends in Biotechnology. 25: 7-15. (Cover)
3. Williamson, N.R.,* Fineran, P.C.,* Leeper, F.J. and Salmond, G.P.C.# (2006). The Regulation and Biosynthesis of Bacterial Prodiginines. Nature Reviews Microbiology. 4. 887-899. (Cover)
2. Fineran, P.C., Everson, L., Slater, H., and Salmond, G.P.C.# (2005). A GntR family transcriptional regulator (PigT) controls gluconate-mediated repression and defines a new, independent pathway for regulation of the tripyrrole antibiotic, prodigiosin, in Serratia. Microbiology 151. 3833-3845.
1. Fineran, P.C., Slater, H., Everson, L., Hughes, K., and Salmond, G.P.C.# (2005). Biosynthesis of tripyrrole and β-lactam secondary metabolites in Serratia: integration of quorum sensing with multiple new regulatory components in the control of prodigiosin and carbapenem antibiotic production. Molecular Microbiology 56: 1495-1517. (Cover)
