Publications

Publications

53. Lawrence, S.L., Burgess, E.J., Pairama, C., Black, A., Patrick, W.M., Mitchell, I., Perry, N.B. and Gerth, M.L. (2019) Mātauranga-guided screening of New Zealand native plants reveals flavonoids from kānuka (Kunzea robusta) with anti-Phytophthora activity. Journal of the Royal Society of New Zealand. DOI: https://doi.org/10.1080/03036758.2019.1648303

52. Murugayah, S.A. and Gerth, M.L. (2019). Engineering quorum quenching enzymes: progress and perspectives. Biochemical Society Transactions, DOI: 10.1042/BST20180165.

51. Murugayah, S.A., Warring, S.L. and Gerth, M.L. (2019). Optimisation of a high-throughput fluorescamine assay for detection of N-acyl-l-homoserine lactone acylase activity. Analytical Biochemistry, 566, 10-12.

50. Rehman, A., Patrick, W.M. and Lamont, I.L. (2019). Mechanisms of ciprofloxacin resistance in Pseudomonas aeruginosa: new approaches to an old problem. Journal of Medical Microbiology, 68, 1-10.

49. Mutreja, I., Warring, S.L, Lim, K.S., Swadi, T., Clinch, K., Mason, J.M., Sheen, C.R., Thompson, D.R., Ducati, R.G., Chambers, S.T, Evans, G.B., Gerth, M.L., Miller, A.G., and Woodfield, T.B.F (2019). Biofilm inhibition via delivery of novel methylthioadenosine nucleosidase inhibitors from PVA-tyramine hydrogels while supporting mesenchymal stromal cell viability. ACS Biomaterials Science & Engineering, DOI: 10.1021/acsbiomaterials.8b0114

48. Clifton, B.E., Kaczmarski, J.A., Carr, P.D., Gerth, M.L., Tokuriki, N. and Jackson, C.J. (2018). Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nature Chemical Biology 14, 542-547.

47. Newton, M.S., Arcus, V.L., Gerth, M.L. and Patrick, W.M. (2018). Enzyme evolution: innovation is easy, optimization is complicated. Current Opinion in Structural Biology, 48, 110-116. 

46. Ehrhardt, M.K.G., Warring, S.L. and Gerth, M.L. (2018). A thermal shift assay for screening chemoreceptor ligand interactions. In Chemosensing: Methods in Molecular Biology, 281-290.

45. Wai, D.C.C., Szyszka, T.N., Campbell, A.E., Kwong, C., Wilkinson-White, L.E., Silva, A.P.G., Low, J.K.K., Kwan, A.H., Gamsjaeger, R., Chalmers, J.D., Patrick, W.M., Lu, B., Vakoc, C.R., Blobel, G.A. and Mackay, J.P. (2018). The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. Journal of Biological Chemistry, 293, 7160-7175.

44. Maddock, D.J., Gerth, M.L. and Patrick, W.M. (2017). An engineered glycerol dehydratase with improved activity for the conversion of meso-2,3-butanediol to butanone. Biotechnology Journal, 12, 1700480.

43. Oulavallickal, T., Brewster, J.L., McKellar, J.L.O., Fairhurst, M.J., Tenci, N.A. and Gerth, M.L. (2017). The Pseudomonas syringaepv. actinidiae chemoreceptor protein F (PscF) periplasmic sensor domain: cloning, purification and X-ray crystallographic analysis. Acta Crystallographica Section F, 73, 701-705.

42. Ferla, M.P., Brewster, J.L., Hall, K.R., Evans, G.B. and Patrick, W.M. (2017). Primordial-like enzymes from bacteria with reduced genomes. Molecular Microbiology, 105, 508-524. [And see the associated MicroCommentary by Burckhard Seelig here]

41. Gerth, M.L., Liu, Y., Jiao, W., Zhang, X.-X., Baker, E.N., Lott, J.S., Rainey, P.B. and Johnston, J.M. (2017). Crystal structure of a bicupin protein HutD involved in histidine utilization in PseudomonasProteins: Structure, Function, and Bioinformatics, 85, 1580-1588.

40. Patrick, W.M. (2017). Biochemical evolution: the pursuit of perfection (second edition). Quarterly Review of Biology, 92, 332-333.

39. Lawrence, S.A., Armstrong, C.B., Patrick, W.M. and Gerth, M.L. (2017). High-throughput chemical screening identifies compounds that inhibit different stages of the Phytophthora agathidicida and Phytophthora cinnamomi life cycles. Frontiers in Microbiology, 8, 1340.

38. Newton, M.S., Guo, X., Söderholm, A., Näsvall, J., Lundström, P., Andersson, D.I., Selmer, M. and Patrick, W.M. (2017). Structural and functional innovations in the real-time evolution of new (βα)8 barrel enzymes. Proceedings of the National Academy of Sciences USA, 114, 4727-4732.

37. 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.

36. Brewster, J.L., McKellar, J.L.O., Finn, T.J., Newman, J., Peat, T.S. and Gerth, M.L. (2016). Structural basis for ligand recognition by a Cache chemosensory domain that mediates carboxylate sensing in Pseudomonas syringaeScientific Reports, 6, 35198.

35. Soo, V.W.C., Yosaatmadja, Y., Squire, C.J. and Patrick, W.M. (2016). Mechanistic and evolutionary insights from the reciprocal promiscuity of two pyridoxal phosphate-dependent enzymes. Journal of Biological Chemistry, 291, 19873-19887.

34. Brewster, J.L., Finn, T.J., Ramirez, M.A. and Patrick, W.M. (2016). Whither life? Conjectures on the future evolution of biochemistry. Biology Letters, 12, 20160269.

33. Read, H.M., Mills, G., Johnson, S., Tsai, P., Dalton, J., Barquist, L., Print, C.G., Patrick, W.M. and Wiles, S. (2016). The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentiumPeerJ, 4, e2130.

32. Söderholm, A., Guo, X., Newton, M.S., Evans, G.B., Näsvall, J., Patrick, W.M. and Selmer, M. (2015). Two-step ligand binding in a (βα)8 barrel enzyme – substrate-bound structures shed new light on the catalytic cycle of HisA. Journal of Biological Chemistry, 290, 24657-24668.

31. Maddock, D.J., Patrick, W.M. and Gerth, M.L. (2015). Substitutions at the cofactor phosphate-binding site of a clostridial alcohol dehydrogenase lead to unexpected changes in substrate specificity. Protein Engineering, Design and Selection, 28, 251-258.

30. Chambers, C.R. and Patrick, W.M. (2015). Archaeal nucleic acid ligases and their potential in biotechnology. Archaea, 2015, 170571.

29. McKellar, J.L.O., Minnell, J.J. and Gerth, M.L. (2015). A high-throughput screen for ligand binding reveals the specificities of three amino acid chemoreceptors from Pseudomonas syringae pv. actinidiaeMolecular Microbiology, 96, 694-707. [And see the associated MicroCommentary by Tino Krell here]

28. Newton, M.S., Arcus, V.L. and Patrick, W.M. (2015). Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes. Journal of the Royal Society Interface, 12, 20150036.

27. Patrick, W.M. and Gerth, M.L. (2014). ITCHY: Incremental truncation for the creation of hybrid enzymes. Methods in Molecular Biology, 1179, 225-244.

26. Copp, J.N., Hanson-Manful, P., Ackerley, D.F. and Patrick, W.M. (2014). Error-prone PCR and effective generation of gene variant libraries for directed evolution. Methods in Molecular Biology, 1179, 3-22.

25. Ferla, M.P. and Patrick, W.M. (2014). Bacterial methionine biosynthesis. Microbiology, 160, 1571-1584.

24. Bernhardt, H.S. and Patrick, W.M. (2014). Genetic code evolution started with the incorporation of glycine, followed by other small hydrophilic amino acids. Journal of Molecular Evolution, 78, 307-309.

23. Köpke, M., Gerth, M.L., Maddock, D.J., Mueller, A.P., Liew, F., Simpson, S.D. and Patrick, W.M. (2014). Reconstruction of an acetogenic 2,3-butanediol pathway involving a novel NADPH-dependent primary-secondary alcohol dehydrogenase. Applied and Environmental Microbiology, 80, 3394-3403. [And check out the Spotlight from the Editors here]

22. Ferla, M.P., Thrash, J.C., Giovannoni, S.J. and Patrick, W.M. (2013). New rRNA gene-based phylogenies of the Alphaproteobacteriaprovide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS ONE, 8, e83383.

21. Wilson, R.H., Morton, S.K., Deiderick, H., Gerth, M.L., Paul, H.A., Gerber, I., Patel, A., Ellington, A.D., Hunicke-Smith, S.P. and Patrick, W.M. (2013). Engineered DNA ligases with improved activities in vitroProtein Engineering, Design and Selection, 26, 471-478.

20. Saraswat, M., Grand, R.S. and Patrick, W.M. (2013). Desalting DNA by drop dialysis increases library size upon transformation. Bioscience, Biotechnology and Biochemistry, 77, 402-404.

19. Hanson-Manful, P. and Patrick, W.M. (2013). Construction and analysis of randomized protein-encoding libraries using error-prone PCR. Methods in Molecular Biology, 996, 251-267.

18. Gerth, M.L., Ferla, M.P. and Rainey, P.B. (2012). The origin and ecological significance of multiple branches for histidine utilization in Pseudomonas aeruginosa PAO1. Environmental Microbiology, 14, 1929-1940.

17. Gerth, M.L., Nigon, L.V. and Patrick, W.M. (2012). Characterization of the indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa PAO1. The Protein Journal, 31, 359-365.

16. Setiyaputra, S., Mackay, J.P. and Patrick, W.M. (2011). The structure of a truncated phosphoribosylanthranilate isomerase suggests a unified model for evolution of the (βα)8 barrel fold. Journal of Molecular Biology, 408, 291-303.

15. Soo, V.W.C., Hanson-Manful, P. and Patrick, W.M. (2011). Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coliProceedings of the National Academy of Sciences USA, 108, 1484-1489.

14. Patrick, W.M., Nakatani, Y., Cutfield, S.M., Sharpe, M.L., Ramsay, R.J. and Cutfield, J.F. (2010). Carbohydrate binding sites in Candida albicans exo-β-1,3-glucanase and the role of the Phe-Phe ‘clamp’ at the active site entrance. FEBS Journal, 277, 4549-4561.

13. Firth, A.E. and Patrick, W.M. (2008). GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries. Nucleic Acids Research, 36, W281-W285.

12. Patrick, W.M. and Matsumura, I. (2008). A study in molecular contingency: glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase. Journal of Molecular Biology, 377, 323-336.

11. Gerth, M.L. and Lutz, S. (2007). Non-homologous recombination of deoxyribonucleoside kinases from human and Drosophila melanogaster yields human-like enzymes with novel activities. Journal of Molecular Biology, 370, 742-751.

10. Patrick, W.M., Quandt, E.M, Swartzlander, D.B. and Matsumura, I. (2007). Multicopy suppression underpins metabolic evolvability. Molecular Biology and Evolution, 24, 2716-2722.

9. Gerth, M.L. and Lutz, S. (2007). Mutagenesis of non-conserved active site residues improves the activity and narrows the specificity of human thymidine kinase 2. Biochemical and Biophysical Research Communications, 354, 802-807.

8. O’Loughlin, T.L., Patrick, W.M. and Matsumura, I. (2006). Natural history as a predictor of protein evolvability. Protein Engineering, Design and Selection, 19, 439-442.

7. Firth, A.E. and Patrick, W.M. (2005). Statistics of protein library construction. Bioinformatics, 21, 3314-3315.

6. Patrick, W.M. and Blackburn, J.M. (2005). In vitro selection and characterization of a stable subdomain of phosphoribosylanthranilate isomerase. FEBS Journal, 272, 3684-3697.

5. Patrick, W.M. and Firth, A.E. (2005). Strategies and computational tools for improving randomized protein libraries. Biomolecular Engineering, 22, 105-112.

4. Gerth, M.L., Patrick, W.M. and Lutz, S. (2004). A second-generation system for unbiased reading frame selection. Protein Engineering, Design and Selection, 17, 595-602.

3. Lutz, S. and Patrick, W.M. (2004). Novel methods for directed evolution of enzymes: quality, not quantity. Current Opinion in Biotechnology, 15, 291-297.

2. Patrick, W.M., Firth, A.E. and Blackburn, J.M. (2003). User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Engineering, 16, 451-457.

1. Patrick, W.M., Weisner, J. and Blackburn, J.M. (2002). Site-directed mutagenesis of Tyr354 of Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance. ChemBioChem, 3, 789-792.