{"id":10,"date":"2016-11-22T12:02:29","date_gmt":"2016-11-22T19:02:29","guid":{"rendered":"https:\/\/blogs.ubc.ca\/ksryan\/?page_id=10"},"modified":"2025-05-07T22:44:19","modified_gmt":"2025-05-08T05:44:19","slug":"publications","status":"publish","type":"page","link":"https:\/\/blogs.ubc.ca\/ksryan\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
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Wang, M., Wei, Z.-W., Ryan, K.S. (2025) A heme-dependent enzyme forms the hydrazine in the antibiotic negamycin.\u00a0Nature Chemical Biology,\u00a0<\/em>https:\/\/doi.org\/10.1038\/s41589-025-01898-0.<\/a><\/p>\n

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Hagar, M., Kang, S. Andersen, R.J., Oh, D.-C. Ryan, K.S. (2025) Targeted Isolation of Piperazate-Containing Molecules: Bioinformatics and Spectroscopy, Current Opinion in Microbiology<\/em>, In press.<\/a><\/p>\n

Higgins, M.A., Shi, X., Soler, J., Harland, J.B., Parkkila, T., Lehnert, N., Garcia-Borr\u00e0s, M., Du, Y.-L., Ryan, K.S. (2025) Structure and mechanism of haem-dependent nitrogen-nitrogen bond formation in piperazate synthase Nature Catalysis<\/em>, https:\/\/doi.org\/10.1038\/s41929-024-01280-8.<\/a><\/p>\n<\/div>\n<\/div>\n<\/div>\n

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Hagar, M., Andersen, R.J., Ryan, K.S. (2024) Prephenate Decarboxylase: An Unexplored Branchpoint to Unusual Natural Products. Cell Chem. Biol. <\/em>31(9):1610-1626<\/a><\/p>\n

Daniel-Ivad, P., Ryan, K.S. (2024) New Reactions by Pyridoxal Phosphate-Dependent Enzymes. Curr. Opin. Chem. Biol.<\/em> 81, 102472. DOI: 10.1016\/j.cbpa.2024.102472.<\/a><\/p>\n

Hagar, M., Morgan, K., Stumpf, S., Tsingos, M., Banuelos, C., Sadar, M.D., Blodgett, J., Andersen, R.J.,^ Ryan, K.S. (2024) Piperazate-Guided Isolation of Caveamides A and B, Non-ribosomal Peptides from a Cave Actinomycete Containing Cyclohexenylalanine. Org. Lett<\/em>. 26(19), 4127-31.<\/a><\/p>\n

Rothchild, K.W., Hagar, M.,Berry, D., Ryan, K.S. (2024) Two iron(II), \u03b1-ketoglutarate-dependent enzymes encoded by the PPZ<\/em>gene cluster of\u00a0Metarhizium majus<\/em>enable production of 8-hydroxyperamine. J. Am. Chem. Soc.<\/em>, 146(15), 10263-7.<\/a><\/p>\n

Daniel-Ivad, P., Ryan, K.S. (2024) An imine reductase that captures reactive intermediates in the biosynthesis of the indolocarbazole reductasporine. J. Biol. Chem. <\/em>300(2), 105642.<\/a><\/p>\n

Daniel-Ivad, P., Ryan, K.S. (2024) Structure of methyltransferase RedM that forms the dimethylpyrrolinium of the bisindole reductasporine. J. Biol. Chem. <\/em>300(1): 105520.<\/a><\/p>\n

Daniel-Ivad, P., Van Lanen, S., Ryan K.S. (2023) Structure of the oxygen, pyridoxal phosphate-dependant capuramycin biosynthetic protein Cap15. Biochemistry<\/em> 62(17), 2611-2621.<\/a><\/p>\n<\/div>\n<\/div>\n<\/div>\n

Wang, M., Ryan K.S.^ (2023) Reductases Produce Nitric Oxide in an Alternative Pathway to Form the Diazeniumdiolate Group of L-Alanosine. J. Am. Chem. Soc. 145(30), 16718\u201316725<\/a><\/div>\n
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Wei, Z., Niikura, H., Wang, M., Ryan, K.S.^ (2023) Identification of the azaserine biosynthetic gene cluster implicates hydrazine as an intermediate to the diazo moiety. Org. Lett. 25(22), 4061\u20134065<\/a><\/div>\n
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Daniel-Ivad, P., Ryan, K.S. (2023) Structure of methyltransferase RedM that forms the dimethylpyrrolinium of the bisindole reductasporine. Journal of Biological Chemistry. DOI: https:\/\/doi.org\/10.1016\/j.jbc.2023.105520<\/a><\/div>\n<\/div>\n
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Daniel-Ivad, P., Van Lanen, S., Ryan K.S. (2023) Structure of the oxygen, pyridoxal phosphate-dependant capuramycin biosynthetic protein Cap15. Biochemistry 62(17), 2611-2621.<\/a><\/div>\n
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Wei, Z. – W. ; Niikura, H. ; Morgan, K. D. ; Vacariu, C. M. ; Andersen, R. J. ; Ryan, K. S.\u00a0<\/span>Free Piperazic Acid As A Precursor To Nonribosomal Peptides<\/span>. J. Am. Chem. Soc. 2022, 144, 30, 13556-12564<\/a>.\"\"<\/span><\/div>\n<\/div>\n
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He, H. – Y. ; Niikura, H. ; Du, Y. – L. ; Ryan, K. S.\u00a0<\/span>Synthetic And Biosynthetic Routes To Nitrogen\u2013Nitrogen Bonds<\/span>. Chem. Soc. Rev. 2022, 51, 2991-3046<\/a>.<\/span><\/div>\n
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Morgan, K. D. ; Williams, D. E. ; Ryan, K. S. ; Andersen, R. J.\u00a0<\/span>Dentigerumycin F And G: Dynamic Structures Retrieved Through A Genome-Mining\/nitrogen-Nmr Methodology<\/span>. Tetrahedron Letters 2022, 94, 153688.<\/span><\/a><\/div>\n
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Williams, D. E. ; Morgan, K. D. ; Dalisay, D. S. ; Matainaho, T. ; Perrachon, E. ; Viller, N. ; Delcroix, M. ; Gauchot, J. ; Niikura, H. ; Patrick, B. O. ; Ryan, K. S. ; Andersen, R. J.\u00a0<\/span>Natural Products Produced In Culture By Biosynthetically Talented Salinispora Arenicola Strains Isolated From Northeastern And South Pacific Marine Sediments<\/span>. Molecules 2022, 27, 3569.<\/span><\/a><\/div>\n<\/div>\n<\/div>\n
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Hoffarth, E. R. ; K. Haatveit, C. ; Kuatsjah, E. ; MacNeil, G. A. ; Saryoa, S. ; Walsby, C. J. ; Eltis, L. D. ; Houk, K. N. ; Garcia-Borr\u00e0s, M. ; Ryan, K. S.\u00a0<\/span>A Shared Mechanistic Pathway For Pyridoxal Phosphate-Dependent Arginine Oxidases<\/span>. PNAS 2021, 118, e2012591118.<\/span><\/a><\/div>\n
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Hoffarth, E. R. ; Kong, S. ; He, H. – Y. ; Ryan, K. S.\u00a0<\/span>An Engineered Biosynthetic-Synthetic Platform For Production Of Halogenated Indolmycin Antibiotics<\/span>.\u00a0Chemical Science\u00a02021,\u00a012.<\/a><\/div>\n
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Bell, E. L. ; Finnigan, W. ; France, S. P. ; Green, A. P. ; Hayes, M. A. ; Hepworth, L. J. ; Lovelock, S. L. ; Niikura, H. ; Osuna, S. ; Romero, E. ; Ryan, K. S. ; Turner, Nj.; Flitsch, S. L.\u00a0<\/span>Biocatalysis<\/span>. Nature Reviews Methods Primers 2021, 1, 46.<\/span><\/a><\/div>\n
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He HY, Ryan KS. Glycine-derived nitronates bifurcate to\u00a0O-<\/em>methylation or denitrification in bacteria.\u00a0Nature Chemistry<\/em>. DOI: 10.1038\/s41557-021-00656-8.<\/a><\/p>\n

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Higgins MA, Tegl G, MacDonald SA, Arnal G, Brumer H, Withers SG, Ryan KS. N-Glycan Degradation Pathways in Gut- and Soil-Dwelling Actinobacteria Share Common Core Genes. ACS Chem. Biol. <\/em>DOI: 10.1021\/acschembio.0c00995<\/a><\/p>\n

Higgins MA, Ryan KS.\u00a0Generating a fucose permease deletion mutant in Bifidobacterium longum<\/em> subspecies infantis<\/em> ATCC 15697.\u00a0Anaerobe<\/em>. DOI: 10.1016\/j.anaerobe.2021.102320.<\/a><\/p>\n

Kuzuyama T, Ryan KS. Mechanistic biology in the biosynthesis of specialized metabolites.\u00a0Curr. Opin. Chem. Biol.\u00a0<\/em>59: A1-A3 (2020).\u00a0<\/a><\/p>\n

Kudo Y, Awakawa T, Du Y-L, Jordan PA, Creamer KE, Jensen PR, Linington RC, Ryan KS, Moore BS. Expansion of Gamma-Butyrolactone Signaling Molecule Biosynthesis to Phosphotriester Natural Products.\u00a0ACS Chem. Biol.\u00a0<\/em>15(12):3253-3261 (2020).<\/a><\/p>\n

Beskrovnaya P, Melnyk RA, Liu Z, Liu Y, Higgins MA, Song Y, Ryan KS, Haney CH. Comparative Genomics Identified a Genetic Locus in Plant-Associated Pseudomonas<\/em> spp. That Is Necessary for Induced Systemic Susceptibility.\u00a0mBio<\/em>. 11(3):e00575-20 (2020).<\/a><\/p>\n

Morgan KD, Williams DE, Patrick BO, Remigy M, Banuelos CA, Sadar MD, Ryan KS, Andersen RJ.\u00a0Org. Lett.<\/em>22(11):4053-4057 (2020)<\/a><\/p>\n

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Hoffarth ER, Rothchild KW, Ryan KS. Emergence of oxygen- and pyridoxal phosphate-dependent reractions.\u00a0The FEBS Journal<\/em>. 287(7):1403-1428 (2020).<\/a><\/p>\n

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Wang, M., Niikura, H., He, H.-Y., Daniel-Ivad, P., Ryan K.S. Biosynthesis of the nitrogen-nitrogen bond containing L-alanosine.\u00a0Angew. Chem. Int. Ed. <\/em>59(10):3881-3885 (2020).<\/a><\/p>\n

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Hedges, J.B., Ryan K.S. Biosynthetic pathways to non-proteinogenic \u03b1-amino acids.\u00a0Chem. Rev. <\/em>120(6):3161-3209 (2020)<\/a><\/p>\n

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Zhao, G. Yao, S., Rothchild, K.W., Liu, T., Liu, Y., Lian, J., He, H.-Y., Ryan, K.S., Du, Y.-L. The biosynthetic gene cluster of pyrazomycin-A C-nucleoside antibiotic with a rare pyrazole moiety. 21(5):644-649 (2020).<\/a><\/p>\n

Du, Y.-L., Higgins, M.A., Zhao, G., Ryan K.S. Convergent biosynthetic transformations to <\/span>a bacterial specialized metabolite.\u00a0Nat. Chem.<\/em> Biol. 15<\/strong>, 1043-1048 (2019).<\/span><\/a><\/p>\n

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Guo, J., Higgins, M.A., Daniel-Ivad, P., Ryan K.S. An Asymmetric Reductase that Intercepts Acyclic Imino Acids Produced\u00a0In Situ\u00a0<\/em>by a Partner Oxidase.\u00a0J. Am. Chem.<\/em> Soc. 141(31):12258-12267 (2019).<\/a><\/p>\n

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Hedges, J.B, Ryan K.S. In vitro reconstitution of the biosynthetic pathway to the nitroimidazole azomycin.\u00a0Angew. Chem. Int. Ed.<\/em> 58(34):11647-11651 (2019).<\/a><\/p>\n

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Morgan, K.D., Andersen, R.J., Ryan, K.S. Piperazic acid-containing natural products: structures and biosynthesis.\u00a0Nat. Prod. Rep. <\/em>36(12):1628-1653 (2019).<\/a><\/p>\n

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He, H.-Y., Henderson, A.C., Du, Y.-L., Ryan, K.S.\u00a0A Two-Enzyme Pathway Links L-Arginine to Nitric Oxide in\u00a0N<\/i>-Nitroso Biosynthesis. J. Am. Chem. Soc. <\/em>141<\/strong>, 4026-4033 (2019).\u00a0<\/a>
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Du, Y.-L., Ryan K.S. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products.\u00a0Nat. Prod. Rep. <\/em>36<\/strong>, 1628-1653\u00a0(2018).<\/a><\/p>\n

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Ryan, K.S., Drennan C.L. Editorial: Metalloenzymes in natural product biosynthetic pathways.\u00a0Nat. Prod. Rep.\u00a0<\/em>35<\/strong>, 612-613 (2018).<\/a><\/p>\n

Hedges, J.B., Kuatsjah, E., Du, Y.-L., Eltis, L.D. & Ryan K.S. Snapshots of the catalytic cycle of an O2, pyridoxal phosphate-dependent hydroxylase.\u00a0ACS Chem. Biol. <\/em>13<\/strong>, 965-974 (2018).<\/a>\u00a0 \u00a0\u00a0\"\"<\/a><\/p>\n

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Du, Y.-L., He, H.Y., Higgins M.A. & Ryan, K.S. A heme-dependent enzyme forms the nitrogen-nitrogen bond in piperazate.\u00a0Nat. Chem. Biol.\u00a0<\/em>13<\/strong>, 836-838\u00a0(2017).<\/a>\u00a0 \u00a0\"\"<\/a><\/p>\n

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Du, Y.-L., Singh, R., Alkhalaf, L.M., Kuatsjah, E., He, H.-Y., Eltis, L.D. & Ryan, K.S. A pyridoxal phosphate-dependent enzyme that oxidizes an unactivated carbon-carbon bond.\u00a0Nat. Chem. Biol.<\/em>\u00a012,<\/strong>\u00a0194-199 (2016).<\/a>\u00a0 \u00a0\"\"<\/a><\/p>\n

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Du, Y.-L. & Ryan, K.S. Catalytic repertoire of bacterial bisindole formation.\u00a0Curr. Opin. Chem. Biol.<\/em>\u00a031<\/strong>, 74-81 (2016).<\/a><\/p>\n

Alkhalaf, L.M., Du, Y.-L. & Ryan, K.S. Synthetic biology approaches to new bisindoles.\u00a0Methods Enzymol.<\/em>\u00a0575,<\/strong>\u00a021-37 (2016).<\/a><\/p>\n

Du, Y.-L., Alkhalaf, L.M. & Ryan, K.S. In vitro reconstitution of indolmycin biosynthesis reveals the molecular basis of oxazolinone assembly.\u00a0Proc. Natl. Acad. Sci. U. S. A.<\/em>\u00a0112,<\/strong>\u00a02717\u20132722 (2015).<\/a><\/p>\n

Alkhalaf, L.M. & Ryan, K.S. Biosynthetic manipulation of tryptophan in bacteria: pathways and mechanisms.\u00a0Chem. Biol.<\/em>\u00a022,<\/strong>\u00a0317-328 (2015).<\/a><\/p>\n

Du, Y.-L. & Ryan, K.S. Expansion of bisindole biosynthetic pathways by combinatorial construction.\u00a0ACS Synth. Biol.<\/em>\u00a04,<\/strong>\u00a0682\u2013688 (2015). Cover article.<\/a><\/p>\n

Deng, X.-Y., Duffy, S.P., Myrand-Lapierre, M.-E., Matthews, K., Santoso, A.T., Du, Y.-L., Ryan, K.S. & Ma, H. Reduced deformability of parasitized red blood cells as a biomarker for anti-malarial drug efficacy.\u00a0Malar. J.<\/em>\u00a014,<\/strong>\u00a0428 (2015).<\/a><\/p>\n

Du, Y.-L., Williams, D.E., Patrick, B.O., Andersen, R.J. & Ryan, K.S. Reconstruction of cladoniamide biosynthesis reveals nonenzymatic routes to bisindole diversity.\u00a0ACS Chem. Biol.<\/em>\u00a09,<\/strong>\u00a02748\u20132754 (2014).<\/a><\/p>\n

Yamanaka, K., Reynolds, K.A., Kersten, R.D., Ryan, K.S., Gonzalez, D.J., Nizet, V., Dorrestein, P.C. & Moore, B.S. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A.\u00a0Proc. Natl. Acad. Sci. U. S. A.<\/em>\u00a0111,<\/strong>\u00a01957-1962 (2014).<\/a><\/p>\n

Du, Y.-L., Ding, T., Patrick, B.O. & Ryan, K.S. Xenocladoniamide F, minimal indolotryptoline from the cladoniamide pathway.\u00a0Tetrahedron Lett.<\/em>\u00a054,<\/strong>\u00a05635\u20135638 (2013).<\/a><\/p>\n

Du, Y.-L., Dalisay, D.S., Andersen, R.J. & Ryan, K.S. N-carbamoylation of 2,4-diaminobutyrate reroutes the outcome in padanamide biosynthesis.\u00a0Chem. Biol.<\/em>\u00a020,<\/strong>\u00a01002\u20131011 (2013).<\/a><\/p>\n

Du, Y.-L., Ding, T. & Ryan, K.S. Biosynthetic O-methylation protects cladoniamides from self-destruction.\u00a0Org. Lett.<\/em>\u00a015,<\/strong>\u00a02538\u20132541 (2013).<\/a><\/p>\n

Sydor, A.M., Jost, M., Ryan, K.S., Turo, K.E., Douglas, C.D., Drennan, C.L. & Zamble, D.B. Metal-binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases.\u00a0Biochemistry,<\/em>\u00a052,<\/strong>\u00a01788-1801 (2013).<\/a><\/p>\n

Goldman, P., Ryan, K.S., Hamill, M.J., Howard-Jones, A.R., Walsh, C.T., Elliott, S.J. & Drennan, C.L. An unusual role for a mobile flavin in StaC-like indolocarbazole biosynthetic enzymes.\u00a0Chem. Biol.<\/em>\u00a019,<\/strong>\u00a0855-865 (2012).<\/a><\/p>\n

Yamanaka, K., Ryan, K.S., Gulder, T.A.M., Hughes, C.C. & Moore, B.S. Flavoenzyme-catalyzed atropo-selective N,C-bipyrrole homocoupling in marinopyrrole biosynthesis.\u00a0J. Am. Chem. Soc<\/em>.\u00a0134,<\/strong>\u00a012434\u201312437 (2012).<\/a><\/p>\n

Davies, J. & Ryan, K.S. Introducing the parvome: bioactive compounds in the microbial world.\u00a0ACS Chem. Biol.<\/em>\u00a07,<\/strong>\u00a0252-259 (2012)<\/a><\/p>\n

Ryan, K.S. Biosynthetic gene cluster for the cladoniamides, bis-indoles with a rearranged scaffold.\u00a0PLoS One,<\/em>\u00a06,<\/strong>\u00a0e23694 (2011).<\/a><\/p>\n

Roberts, A.A., Ryan, K.S., Moore, B.S. & Gulder, T.A.M. Total (bio)synthesis: strategies of nature and of chemists.\u00a0Top. Curr. Chem<\/em>.\u00a0297,<\/strong>\u00a0149\u2013203 (2010).<\/a><\/p>\n

Ryan KS, Moore BS. Alkaloid biosynthesis takes root.\u00a0Nat. Chem. Biol.<\/em>\u00a05,<\/strong>\u00a0140-141 (2009).<\/a><\/p>\n

Ryan, K.S. & Drennan, C.L. Divergent pathways in the biosynthesis of bisindole natural products.\u00a0Chem. Biol.<\/em>\u00a016,<\/em>\u00a0351\u2013364 (2009).<\/a><\/p>\n

Ryan, K.S., Chakraborty, S., Howard-Jones, A.R., Walsh, C.T., Ballou, D.P. & Drennan, C.L. The FAD cofactor of RebC shifts to an IN conformation upon flavin reduction.\u00a0Biochemistry<\/em>\u00a047,<\/strong>\u00a013506-13513 (2008).<\/a><\/p>\n

Ryan, K.S., Balibar, C.J., Turo, K.E., Walsh, C.T. & Drennan, C.L. The violacein biosynthetic enzyme VioE shares a fold with lipoprotein transporter proteins.\u00a0J. Biol. Chem.<\/em>\u00a0283,<\/strong>\u00a06467\u20136475 (2008).<\/a><\/p>\n

Ryan, K.S., Howard-Jones, A.R., Hamill, M.J., Elliott, S.J., Walsh, C.T. & Drennan, C.L. Crystallographic trapping in the rebeccamycin biosynthetic enzyme RebC.\u00a0Proc. Natl. Acad. Sci. U. S. A.<\/em>\u00a0104,<\/strong>\u00a015311-15316 (2007).<\/a><\/p>\n

Reiss, B.D., Mao, C., Solis, D.J., Ryan, K.S., Thomson, T. & Belcher, A.M. Biological routes to metal alloy ferromagnetic nanostructures.\u00a0Nano Lett.<\/em>\u00a04,<\/strong>\u00a01127-1132 (2004).<\/a><\/p>\n

Malamy, J.E. & Ryan, K.S. Environmental regulation of lateral root initiation in Arabidopsis.\u00a0Plant Physiol.<\/em>\u00a0127,<\/strong>\u00a0899\u2013909 (2001).<\/a><\/p>\n

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Wang, M., Wei, Z.-W., Ryan, K.S. (2025) A heme-dependent enzyme forms the hydrazine in the antibiotic negamycin.\u00a0Nature Chemical Biology,\u00a0https:\/\/doi.org\/10.1038\/s41589-025-01898-0. Hagar, M., Kang, S. Andersen, R.J., Oh, D.-C. Ryan, K.S. (2025) Targeted Isolation of Piperazate-Containing Molecules: Bioinformatics and Spectroscopy, Current Opinion in Microbiology, In press. Higgins, M.A., Shi, X., Soler, J., Harland, J.B., Parkkila, T., Lehnert, […]<\/p>\n","protected":false},"author":46186,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"template-full-width.php","meta":{"footnotes":""},"class_list":["post-10","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/pages\/10","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/users\/46186"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/comments?post=10"}],"version-history":[{"count":55,"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/pages\/10\/revisions"}],"predecessor-version":[{"id":784,"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/pages\/10\/revisions\/784"}],"wp:attachment":[{"href":"https:\/\/blogs.ubc.ca\/ksryan\/wp-json\/wp\/v2\/media?parent=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}