Publications

Publications Citing NIH T32 Training Grant Support:

2019

Lavell, A.A. and Benning, C. 2019. Cellular organization and regulation of plant glycerolipid metabolism. Plant and Cell Physiol. doi: https://doi.org/10.1093/pcp/pcz016

Jack, C.N., Rowe, S.L., Porter, S.S. and Friesen, M.L., 2019. A high‐throughput method of analyzing multiple plant defensive compounds in minimized sample mass. Applications in Plant Sciences, p.e01210.

Moore, B.M., Wang, P., Fan, P., Leong, B., Schenck, C.A., Lloyd, J.P., Lehti-Shiu, M., Last, R.L., Pichersky, E., Shiu, S.-H. 2019. Robust predictions of specialized metabolism genes through machine learning. Proc. Nat. Acad Sci. USA. doi: https://doi.org/10.1073/pnas.1817074116.

Wrenbeck, E.E., Bedewitz, M.A., Klesmith, J.R., Noshin, S.R., Barry, C. and Whitehead, T.A., 2019. An automated data-driven pipeline for improving heterologous enzyme expression. ACS Synthetic Biology. doi: https://pubs.acs.org/doi/full/10.1021/acssynbio.8b00486

Clark, T.J., Friel, C.A., Grman, E., Friesen, M.L. and Shachar‐Hill, Y., 2019. Unfair trade underground revealed by integrating data with Nash bargaining models. New Phytologist. doi: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.15703

2018

Leong, B.J., Lybrand, D., Lou, Y.R., Fan, P., Schilmiller, A.L., Last, R.L. 2018. Evolution of metabolic novelty: a trichome-expressed invertase creates specialized metabolic diversity in wild tomato. In press at Sci. Adv. and available at bioRxiv, https://doi.org/10.1101/502971

Xu, H., D. Lybrand, S. Bennewitz, A. Tissier, R.L. Last and E. Pichersky. 2018. Production of trans-chrysanthemic acid, the monoterpene acid moiety of natural pyrethrin insecticides, in tomato fruit. Metab. Eng. 47:271-278 https://doi.org/10.1016/j.ymben.2018.04.004.

Rowe, S.R., Norman, J.S., Friesen, M.L. 2018. Coercion in the evolution of plant-microbe communication: a perspective. Molec. Plant Microbe Interact. https://doi.org/10.1094/MPMI-11-17-0276-CR

Duhl, K.L., Tefft, N.M., TerAvest, M.A. 2018. Shewanella oneidensis MR-1 utilizes both sodium- and proton-pumping NADH dehydrogenases during aerobic growth. Appl. Environ. Microbiol. 84:e00415-1810. doi: 1128/AEM.00415-18.

Medina-Cucurella, A., Zhu, Y., Bowen, S.J., Bergeron, L.M. and Whitehead, T.A. 2018. Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti-NGF monoclonal antibodies, Biotech. and Bioeng. doi: 10.1002/bit.26606.

Poliner E., Takeuchi T., Du, Z.Y., Benning, C., Farré, E.M. 2018.“Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, Nannochloropsis oceanica CCMP1779.” ACS Synth. Biol.  Mar 14. doi: 10.1021/acssynbio.7b00362

Medina-Cucurella A. and Whitehead, T.A. 2018. Characterizing Protein-Protein Interactions Using Deep Sequencing Coupled to Yeast Surface Display, Methods Mol. Biol.,1764:101-121, doi: 10.1007/978-1-4939-7759-8_7

2017

Leong, B.J. and Last, R.L. Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism. 2017. Curr. Opin. Struct. Biol., 47:105–112 https://doi.org/10.1016/j.sbi.2017.07.005.

Wrenbeck E.E., Azouz L.R., Whitehead T.A. 2017. Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded, Nature Comm. 8, Article number: 15695. doi:10.1038/ncomms15695

Moghe, G.D., Leong, B.J., Hurney, S. Jones, A.D. and Last, R.L. 2017. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant defense related specialized metabolic pathway. eLife 2017;6:e28468 DOI: 10.7554/eLife.28468.

Clark, T.J., Friel, C.A., Grman, E., Shachar-Hill, Y. and Friesen, M.L. 2017. Modelling nutritional mutualisms: challenges and opportunities for data integration. Ecol. Letts. doi: 10.1111/ele.12810

Angelos, E., Ruberti, C., Kim, S.J., and Brandizzi, F. 2017. Maintaining the factory: the roles of the unfolded protein response in cellular homeostasis in plants. Plant J. 90:671-682. doi:10.1111.tpj.13449

Wrenbeck E. E., Faber, M. S., Whitehead, T. A. 2017. Deep sequencing methods for protein engineering and design. Curr. Opin. Struct. Biol., 45:36-44, doi: 10.1016/j.sbi.2016.11.001

Klesmith, J.R., Bacik, J.P., Wrenbeck, E.E., Michalczyk, R., Whitehead, T.A. 2017. Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning. Proc. Natl. Acad. Sci. U.S.A., 114:2265-2270, doi: 10.1073/pnas.1614437114

Panchy NL, Azodi C.B., Winship EF, O'Malley RC, Shiu SH. 2017. Asymmetric evolution of the transcription profiles and cis-regulatory sites contributes to the retention of transcription factor duplicates. bioRxiv DOI:10.1101/115857

Yang, Y., Zienkiewicz, A., Lavell, A. and Benning, C. 2017. Coevolution of Domain Interactions in the Chloroplast TGD1, 2, 3 Lipid Transfer Complex Specific to Brassicaceae and Poaceae Plants. Plant Cell, 29:1500–1515. DOI: https://doi.org/10.1105/tpc.17.00182

2014-16

Wrenbeck, E.E., Klesmith, J.R., Stapleton, J.A., Adeniran, A., Tyo, K.E.J. and Whitehead T.A. 2016. Plasmid-based one-pot saturation mutagenesis. Nature Methods, 13:928–930. doi:10.1038/nmeth.4029.

Ning, J., Moghe, G., Leong, B.J., Kim, J., Ofner, I., Wang, Z., Adams, C., Jones, A., Zamir, D., Last, RL. 2015.  A feedback insensitive isopropylmalate synthase affects acylsugar composition in cultivated and wild tomato. Plant Physiol. 169:1821-1835. doi:10.1104/pp.15.00474

Tsai, C.H., Warakanont, J., Takeuchi, T., Sears, B.B., Moellering, E.R., Benning, C. 2014. The protein Compromised Hydrolysis of Triacylglycerols 7 (CHT7) acts as a repressor of cellular quiescence in Chlamydomonas. Proc. Natl. Acad. Sci. U.S.A. 111:15833–15838. doi:/10.1073/pnas.1414567111.

Other Publications from our Trainees:

Medina-Cucurella, A.V., Mizrahi, R.A., Asensio, M.A., Edgar, R.C., Leong, J., Leong, R., Lim, Y.W., Nelson, A., Niedecken, A.R., Simons, J.F., Spindler, M.J., Stadtmiller, K., Wayham, N., Adler, A.S., Johnson, D.S. 2019. Preferential Identification of Agonistic OX40 Antibodies by Using Cell Lysate to Pan Natively Paired, Humanized Mouse-Derived Yeast Surface Display libraries. Antibodies.  doi: https://www.mdpi.com/2073-4468/8/1/17/htm

Hoopes, G.M., Hamilton, J.P., Wood, J.C., Esteban, E., Pasha, A., Vaillancourt, B., Provart, N.J. and Buell, C.R., 2018. An updated gene atlas for maize reveals organ‐specific and stress‐induced genes. The Plant Journal. doi: https://onlinelibrary.wiley.com/doi/10.1111/tpj.14184

Li, J., Weraduwage, S.M., Preiser, A.L., Weise, S.E., Strand, D.D., Froehlich, J.E., Kramer D.M., Hu, J., Sharkey, T.D. 2018. Loss of hydroxypruvate reductase inhibits triose phosphate isomerase but stimulates cyclic photosynthetic electron flow and the Glc-6P-phosphate shunt. Biorxiv doi: 10.1101/278580

Uygun S., Seddon, A.E., Azodi, C.B. and Shiu, S.  2017. Predictive models of spatial transcriptional response to high salinity. Plant Physiol. 174: 450-464. doi: 10. 1104/ pp. 16. 01828

Dowdell, A.S., Murphy, M.D., Azodi, C.B., Swanson, S.K., Florens, L.F., Chen, S. and Zückert, W.R. 2017. Comprehensive spatial analysis of the Borrelia burgdorferi lipoproteome reveals a compartmentalization bias toward the bacterial surface. J. Bacteriol. vol. 199 no. 6 e00658-16. doi: 10.1128/JB.00658-16

Murphree, C.A., Dums, J.T., Jain, S.K., Zhao,C., Young, D.Y., Khoshnoodi, N., Tikunov, A., Macdonald, J., Pilot, G., & Sederoff, H. 2017. Amino acids are an ineffective fertilizer for Dunaliella spp. growth. Front. Plant Sci., 8:847, doi: 10.3389/fpls.2017.00847

Hoopes, G.M., Hamilton, J.P., Kim, J., Zhao, D., Wiegert-Rininger, K., Crisovan, E., and Buell, C.R. 2018. Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anti-Cancer and Anti-Malarial Cardenolides. G3. Feb 2;8(2):385-391. doi: 10.1534/g3.117.300331

Malmstrom, C.M., Bigelow, P., Trebicki, P., Busch, A.K., Friel, C., Cole, E., Abdel-Azim, H., Phillippo, C. and Alexander, H.M. 2017. Virus Res. doi.org/10.1016/j.virusres.2017.07.006

Banerjee A., Preiser A.L., Sharkey, T.D. Engineering of Recombinant Poplar Deoxy-D-xylulose-5-phosphate Synthase (PtDXS) by Site-directed Mutagenesis Improves Its Activity. 2016. PLoSOne. 11(8). https://doi.org/10.1371/journal.pone.0165028 

Yang J., Preiser A.L., Li Z, Weise S.E., Sharkey T.D. 2016. Triose phosphate use limitation of photosynthesis short-term and long-term effects. Planta. 243(3): 687-98. doi:10.1007/s00425-015-2436-8

Clark. T. J., & Lu. Y. 2015. Analysis of loss-of-function mutants in aspartate kinase and homoserine dehydrogenase genes points to complexity in the regulation of aspartate-derived amino acid contents. Plant Physiol. 168:15121526.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528744/.

Lantz. A.T., Cardiello. J., Gee. T., Richards. M.,Rosenstiel. T., Fisher. A. 2015. Biochemical characterization of an isoprene synthase from Campylopus introflexus (heath star moss).  Plant Physiol. and Biochem. 94:209-215. doi: 10.1016/j.plaphy.2015.06.008

Brasher, M., Surmacz, L., Leong, B., Pitcher, J., Swiezewska, E., Pichersky, E., Akhtar, T.A. 2015.  A two-component enzyme complex is required for doichol biosynthesis in tomato.  Plant J. 82:903-14. doi: 10.1111/tpj.12859

Thireault, C., Shyu, C., Yoshida, Y., St Aubin, B., Campos, M.L. and Howe, G.A. 2015. Repression of jasmonate signaling by a non-TIFY JAZ protein in Arabidopsis. Plant J., 82:669-79 doi: 10.1111/tpj.12841, 25846245

Takeuchi T, Newton L, Burkhardt A, Mason S, Farré, E (2014). Light and circadian clock mediate time-specific changes in sensitivity to UV-B stress under light/dark cycles. J. Exp. Bot. 65: 6003-6012.

Bienick, M., Young, K., Klesmith, J., Detwiler, E.E., Tomek K., Whitehead T. (2014). The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate. PLOSOne 9(10): e109105. DOI: 10.1371/journal.pone.0109105.