Publications

Publications Citing NIH T32 Training Grant Support:

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.

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. 2018. Robust predictions of specialized metabolism genes through machine learning. Robust predictions of specialized metabolism genes through machine learning. bioRxivhttps://doi.org/10.1101/304873.

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

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

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

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

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.

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

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:

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.