Publications

Higgins, M. A. ; Shi, X. ; Soler, J. ; Harland, J. B. ; Parkkila, T. ; Lehnert, N. ; Garcia-Borràs, M. ; Du, Y. – L. ; Ryan, K. S. Structural And Mechanistic Views Of Enzymatic, Heme-Dependent Nitrogen-Nitrogen Bond Formation. bioRxiv 2023, https://doi.org/10.1101/2023.12.15.571702.
He, H. – Y. ; Niikura, H. ; Du, Y. – L. ; Ryan, K. S. Synthetic And Biosynthetic Routes To Nitrogen–Nitrogen Bonds. Chem. Soc. Rev. 2022, 51, 2991-3046.
Morgan, K. D. ; Williams, D. E. ; Ryan, K. S. ; Andersen, R. J. Dentigerumycin F And G: Dynamic Structures Retrieved Through A Genome-Mining/nitrogen-Nmr Methodology. Tetrahedron Letters 2022, 94, 153688.
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. Natural Products Produced In Culture By Biosynthetically Talented Salinispora Arenicola Strains Isolated From Northeastern And South Pacific Marine Sediments. Molecules 2022, 27, 3569.
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. Biocatalysis. Nature Reviews Methods Primers 2021, 1, 46.

He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nature Chemistry. DOI: 10.1038/s41557-021-00656-8.

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. DOI: 10.1021/acschembio.0c00995

Higgins MA, Ryan KS. Generating a fucose permease deletion mutant in Bifidobacterium longum subspecies infantis ATCC 15697. Anaerobe. DOI: 10.1016/j.anaerobe.2021.102320.

Kuzuyama T, Ryan KS. Mechanistic biology in the biosynthesis of specialized metabolites. Curr. Opin. Chem. Biol. 59: A1-A3 (2020). 

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. ACS Chem. Biol. 15(12):3253-3261 (2020).

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 spp. That Is Necessary for Induced Systemic Susceptibility. mBio. 11(3):e00575-20 (2020).

Morgan KD, Williams DE, Patrick BO, Remigy M, Banuelos CA, Sadar MD, Ryan KS, Andersen RJ. Org. Lett.22(11):4053-4057 (2020)

 

Hoffarth ER, Rothchild KW, Ryan KS. Emergence of oxygen- and pyridoxal phosphate-dependent reractions. The FEBS Journal. 287(7):1403-1428 (2020).

Wang, M., Niikura, H., He, H.-Y., Daniel-Ivad, P., Ryan K.S. Biosynthesis of the nitrogen-nitrogen bond containing L-alanosine. Angew. Chem. Int. Ed. 59(10):3881-3885 (2020).

Hedges, J.B., Ryan K.S. Biosynthetic pathways to non-proteinogenic α-amino acids. Chem. Rev. 120(6):3161-3209 (2020)

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).

Du, Y.-L., Higgins, M.A., Zhao, G., Ryan K.S. Convergent biosynthetic transformations to a bacterial specialized metabolite. Nat. Chem. Biol. 15, 1043-1048 (2019).

Guo, J., Higgins, M.A., Daniel-Ivad, P., Ryan K.S. An Asymmetric Reductase that Intercepts Acyclic Imino Acids Produced In Situ by a Partner Oxidase. J. Am. Chem. Soc. 141(31):12258-12267 (2019).

Hedges, J.B, Ryan K.S. In vitro reconstitution of the biosynthetic pathway to the nitroimidazole azomycin. Angew. Chem. Int. Ed. 58(34):11647-11651 (2019).

Morgan, K.D., Andersen, R.J., Ryan, K.S. Piperazic acid-containing natural products: structures and biosynthesis. Nat. Prod. Rep. 36(12):1628-1653 (2019).

He, H.-Y., Henderson, A.C., Du, Y.-L., Ryan, K.S. A Two-Enzyme Pathway Links L-Arginine to Nitric Oxide in N-Nitroso Biosynthesis. J. Am. Chem. Soc. 141, 4026-4033 (2019). 

Du, Y.-L., Ryan K.S. Pyridoxal phosphate-dependent reactions in the biosynthesis of natural products. Nat. Prod. Rep. 36, 1628-1653 (2018).

Ryan, K.S., Drennan C.L. Editorial: Metalloenzymes in natural product biosynthetic pathways. Nat. Prod. Rep. 35, 612-613 (2018).

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. ACS Chem. Biol. 13, 965-974 (2018).    

Du, Y.-L., He, H.Y., Higgins M.A. & Ryan, K.S. A heme-dependent enzyme forms the nitrogen-nitrogen bond in piperazate. Nat. Chem. Biol. 13, 836-838 (2017).   

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. Nat. Chem. Biol. 12, 194-199 (2016).   

Du, Y.-L. & Ryan, K.S. Catalytic repertoire of bacterial bisindole formation. Curr. Opin. Chem. Biol. 31, 74-81 (2016).

Alkhalaf, L.M., Du, Y.-L. & Ryan, K.S. Synthetic biology approaches to new bisindoles. Methods Enzymol. 575, 21-37 (2016).

Du, Y.-L., Alkhalaf, L.M. & Ryan, K.S. In vitro reconstitution of indolmycin biosynthesis reveals the molecular basis of oxazolinone assembly. Proc. Natl. Acad. Sci. U. S. A. 112, 2717–2722 (2015).

Alkhalaf, L.M. & Ryan, K.S. Biosynthetic manipulation of tryptophan in bacteria: pathways and mechanisms. Chem. Biol. 22, 317-328 (2015).

Du, Y.-L. & Ryan, K.S. Expansion of bisindole biosynthetic pathways by combinatorial construction. ACS Synth. Biol. 4, 682–688 (2015). Cover article.

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. Malar. J. 14, 428 (2015).

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. ACS Chem. Biol. 9, 2748–2754 (2014).

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. Proc. Natl. Acad. Sci. U. S. A. 111, 1957-1962 (2014).

Du, Y.-L., Ding, T., Patrick, B.O. & Ryan, K.S. Xenocladoniamide F, minimal indolotryptoline from the cladoniamide pathway. Tetrahedron Lett. 54, 5635–5638 (2013).

Du, Y.-L., Dalisay, D.S., Andersen, R.J. & Ryan, K.S. N-carbamoylation of 2,4-diaminobutyrate reroutes the outcome in padanamide biosynthesis. Chem. Biol. 20, 1002–1011 (2013).

Du, Y.-L., Ding, T. & Ryan, K.S. Biosynthetic O-methylation protects cladoniamides from self-destruction. Org. Lett. 15, 2538–2541 (2013).

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. Biochemistry, 52, 1788-1801 (2013).

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. Chem. Biol. 19, 855-865 (2012).

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. J. Am. Chem. Soc. 134, 12434–12437 (2012).

Davies, J. & Ryan, K.S. Introducing the parvome: bioactive compounds in the microbial world. ACS Chem. Biol. 7, 252-259 (2012)

Ryan, K.S. Biosynthetic gene cluster for the cladoniamides, bis-indoles with a rearranged scaffold. PLoS One, 6, e23694 (2011).

Roberts, A.A., Ryan, K.S., Moore, B.S. & Gulder, T.A.M. Total (bio)synthesis: strategies of nature and of chemists. Top. Curr. Chem. 297, 149–203 (2010).

Ryan KS, Moore BS. Alkaloid biosynthesis takes root. Nat. Chem. Biol. 5, 140-141 (2009).

Ryan, K.S. & Drennan, C.L. Divergent pathways in the biosynthesis of bisindole natural products. Chem. Biol. 16, 351–364 (2009).

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. Biochemistry 47, 13506-13513 (2008).

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. J. Biol. Chem. 283, 6467–6475 (2008).

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. Proc. Natl. Acad. Sci. U. S. A. 104, 15311-15316 (2007).

Reiss, B.D., Mao, C., Solis, D.J., Ryan, K.S., Thomson, T. & Belcher, A.M. Biological routes to metal alloy ferromagnetic nanostructures. Nano Lett. 4, 1127-1132 (2004).

Malamy, J.E. & Ryan, K.S. Environmental regulation of lateral root initiation in Arabidopsis. Plant Physiol. 127, 899–909 (2001).