Project publications

Koper K.#, Han S-W.#, Kothadia R., Salamon H., Yoshikuni Y., Maeda H.A. (2024) Multi-substrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. bioRvix doi: 10.1101/2024.03.19.585368 #These authors contributed equally.

Maeda H.A., de Oliveira M.V.V. (2024) VAS1-mediated nitrogen shufffling for aromatic amino acid homeostasis. Trends Plant Sci. online

De Raad M., Koper K., Deng K., Bowen B.P., Maeda H.A., Northen T.R. (2023) Mass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme J. Biol. Chem. 299, 102939

Huß S. and Nikoloski Z. (2023) Systematic comparison of local approaches for isotopically nonstationary metabolic flux analysis. Front. Plant Sci. DOI: 10.3389/fpls.2023.1178239

Koper K., Hataya S., Hall A.G., Takasuka T.E., Maeda H.A. (2023) Biochemical characterization of plant aromatic aminotransferases Methods Enzymol. 680, 35-83

Han S-W., Yoshikuni Y (2022) Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes. Curr. Opin. in Microbiol. 68, 102172

Huß S., Judd R.S., Koper K., Maeda H.A., Nikoloski Z.(2022) An automated workflow that generates atom mappings for large scale metabolic models and its application to Arabidopsis thaliana Plant J 111, 1486-1500

Koper K., Han S-W., Pastor D.C., Yoshikuni Y., Maeda H.A. (2022) Evolutionary Origin and Functional Diversification of Aminotransferases J. Biol. Chem. 298: 102122

Relevant prior publications by PIs

Arnold, A. & Nikoloski, Z. Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. Plant Physiol. 165, 1380–1391 (2014).

Arnold, A., Sajitz-Hermstein, M. & Nikoloski, Z. Effects of varying nitrogen sources on amino acid synthesis costs in Arabidopsis thaliana under different light and carbon-source conditions. PLoS ONE 10, e0116536 (2015).

Bianchetti, C. M., Takasuka, T. E., Deutsch, S., Udell, H. S., Yik, E. J., Bergeman, L. F. & Fox, B. G. Active site and laminarin binding in glycoside hydrolase family 55. J. Biol. Chem. 290, 11819–11832 (2015).

Deng, K., Takasuka, T. E., Heins, R., Cheng, X., Bergeman, L. F., Shi, J., Aschenbrener, R., Deutsch, S., Singh, S., Sale, K. L., Simmons, B. A., Adams, P. D., Singh, A. K., Fox, B. G. & Northen, T. R. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem. Biol. 9, 1470–1479 (2014).

Dornfeld, C., Weisberg, A. J., K C, R., Dudareva, N., Jelesko, J. G. & Maeda, H. A. Phylobiochemical characterization of class-Ib aspartate/prephenate aminotransferases reveals evolution of the plant arogenate phenylalanine pathway. Plant Cell 26, 3101–3114 (2014).

Eloundou-Mbebi, J. M. O., Küken, A., Omranian, N., Kleessen, S., Neigenfind, J., Basler, G. & Nikoloski, Z. A network property necessary for concentration robustness. Nat Commun. 7, (2016).

Gao, J., Louie, K. B., Steinke, P., Bowen, B. P., Raad, M. de, Zuckermann, R. N., Siuzdak, G. & Northen, T. R. Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry. Anal. Chem. 89, 6521–6526 (2017).

Greving, M., Cheng, X., Reindl, W., Bowen, B., Deng, K., Louie, K., Nyman, M., Cohen, J., Singh, A., Simmons, B., Adams, P., Siuzdak, G. & Northen, T. Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Anal Bioanal Chem 403, 707–711 (2012).

Heise, R., Arrivault, S., Szecowka, M., Tohge, T., Nunes-Nesi, A., Stitt, M., Nikoloski, Z. & Fernie, A. R. Flux profiling of photosynthetic carbon metabolism in intact plants. Nat. Protoc. 9, 1803–1824 (2014).

Holland, C. K., Berkovich, D. A., Kohn, M. L., Maeda, H. & Jez, J. M. Structural basis for substrate recognition and inhibition of prephenate aminotransferase from Arabidopsis. Plant J. 94, 304–314 (2018)

Küken, A. & Nikoloski, Z. Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. Plant Physiol. 179, 894–906 (2019)

Maeda, H., Yoo, H. & Dudareva, N. Prephenate aminotransferase directs plant phenylalanine biosynthesis via arogenate. Nat. Chem. Biol. 7, 19–21 (2011).

Northen, T. R., Yanes, O., Northen, M. T., Marrinucci, D., Uritboonthai, W., Apon, J., Golledge, S. L., Nordström, A. & Siuzdak, G. Clathrate nanostructures for mass spectrometry. Nature 449, 1033–1036 (2007).

Northen, T. R., Lee, J.-C., Hoang, L., Raymond, J., Hwang, D.-R., Yannone, S. M., Wong, C.-H. & Siuzdak, G. A nanostructure-initiator mass spectrometry-based enzyme activity assay. Proc. Natl. Acad. Sci. U.S.A. 105, 3678–3683 (2008).

de Raad, M., de Rond, T., Rübel, O., Keasling, J. D., Northen, T. R. & Bowen, B. P. OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging. Anal. Chem. 89, 5818–5823 (2017).

Rübel, O., Greiner, A., Cholia, S., Louie, K., Bethel, E. W., Northen, T. R. & Bowen, B. P. OpenMSI: a high-performance web-based platform for mass spectrometry imaging. Anal. Chem. 85, 10354–10361 (2013).

Szecowka, M., Heise, R., Tohge, T., Nunes-Nesi, A., Vosloh, D., Huege, J., Feil, R., Lunn, J., Nikoloski, Z., Stitt, M., Fernie, A. R. & Arrivault, S. Metabolic fluxes in an illuminated Arabidopsis rosette. Plant Cell 25, 694–714 (2013).

Takasuka, T. E., Walker, J. A., Bergeman, L. F., Vander Meulen, K. A., Makino, S., Elsen, N. L. & Fox, B. G. Cell-free translation of biofuel enzymes. Methods Mol. Biol. 1118, 71–95 (2014).

Töpfer, N., Caldana, C., Grimbs, S., Willmitzer, L., Fernie, A. R. & Nikoloski, Z. Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis. Plant Cell 25, 1197–1211 (2013).

Wang, M. & Maeda, H. A. Aromatic amino acid aminotransferases in plants. Phytochem Rev 1–29 (2017).

Wang, M., Toda, K. & Maeda, H. A. Biochemical properties and subcellular localization of tyrosine aminotransferases in Arabidopsis thaliana. Phytochemistry 132, 16–25 (2016).

Wang, M., Toda, K., Block, A. & Maeda, H. A. TAT1 and TAT2 tyrosine aminotransferases have both distinct and shared functions in tyrosine metabolism and degradation in Arabidopsis thaliana. J. Biol. Chem. 294, 3563–3576 (2019).

Yoshikuni, Y. & Keasling, J. D. Pathway engineering by designed divergent evolution. Curr Opin Chem Biol 11, 233–239 (2007).

Yoshikuni, Y., Martin, V. J. J., Ferrin, T. E. & Keasling, J. D. Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chem. Biol. 13, 91–98 (2006).

Yoshikuni, Y., Ferrin, T. E. & Keasling, J. D. Designed divergent evolution of enzyme function. Nature 440, 1078–1082 (2006).