Publications

Publications Citing NIH T32 Training Grant Support:

2019

Pardo, J., C. M. Wai, H. Chay, C. F. Madden, H. W. M. Hilhorst, J. M. Farrant and R. VanBuren (2019). Intertwined signatures of desiccation and drought tolerance in grasses. bioRxiv: 662379. doi: https://doi.org/10.1101/662379

Preiser, A.L., Fisher, N., Banerjee, A. and Sharkey, T.D., 2019. Plastidic glucose-6-phosphate dehydrogenases are regulated to maintain activity in the light. Biochemical Journal476(10), pp.1539-1551. doi: https://doi.org/10.1042/BCJ20190234

McClain, A.M. and Sharkey, T.D., 2019. Triose phosphate utilization and beyond: from photosynthesis to end product synthesis. Journal of experimental botany70(6), pp.1755-1766.  https://doi.org/10.1093/jxb/erz058

Li, L., Lavell, A., Meng, X., Berkowitz, O., Selinski, J., van de Meene, A., Carrie, C., Benning, C., Whelan, J., De Clercq, I. and Wang, Y., 2019. Arabidopsis DGD1 SUPPRESSOR 1 is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis. The Plant Cell, pp.tpc-00885. doi: https://doi.org/10.1105/tpc.18.00885

Lavell, A., Froehlich, J.E., Baylis, O., Rotondo, A. and Benning, C., 2019. A Predicted Plastid Rhomboid Protease Affects Phosphatidic Acid Metabolism in Arabidopsis thaliana. The Plant Journal. doi: https://onlinelibrary.wiley.com/doi/epdf/10.1111/tpj.14377

Fan, P., B.J. Leong, R.L. Last. 2019. Tip of the trichome: evolution of acylsugar metabolic diversity in Solanaceae. Curr. Opin. Plant Biol. 49:8-16. doi: https://www.sciencedirect.com/science/article/pii/S1369526618300906?via%3Dihub

Leong, B.J., Lybrand, D.B., Lou, Y.R., Fan, P., Schilmiller, A.L. and Last, R.L., 2019. Evolution of metabolic novelty: a trichome-expressed invertase creates specialized metabolic diversity in wild tomato. Science Advances5(4), p.eaaw3754. doi: https://advances.sciencemag.org/content/5/4/eaaw3754.abstract

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

Medina-Cucurella A^, Steiner PJ^, Faber MS^, Beltran J, Borelli A^, Kirby M^, Cutler S, Whitehead TA*, (2019) User-defined single pot mutagenesis using unamplified oligo pools. Protein Engineering Design & Selection, accepted

2018

Agostoni, M., Logan-Jackson, A.R., Heinz, E.R., Severin, G.B., Bruger, E.L., Waters, C.M. and Montgomery, B.L., 2018. Homeostasis of second messenger cyclic-di-AMP is critical for cyanobacterial fitness and acclimation to abiotic stress. Frontiers in microbiology9. doi: https://doi.org/10.3389/fmicb.2018.01121

Angelos, E. and Brandizzi, F., 2018. NADPH oxidase activity is required for ER stress survival in plants. The Plant Journal96(6), pp.1106-1120. doi: https://doi.org/10.1111/tpj.14091

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:

Weise, S.E., Liu, T., Childs, K.L., Preiser, A.L., Katulski, H.M., Perrin-Porzondek, C., and Sharkey, T.D., 2019. Transcriptional regulation of the glucose-6-phosphate/Phosphate translocator 2 is related to carbon exchange across the chloroplast envelope. accepted to Frontiers in Plant Science.

Panchy, N.L., Azodi, C.B., Winship, E.F., O’Malley, R.C. and Shiu, S.H., 2019. Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC evolutionary biology, 19(1), p.77. doi: https://doi.org/10.1186/s12862-019-1398-z

Li, J., Weraduwage, S.M., Peiser, A.L., Tietz, S., Weise, S.E., Strand, D.D., Froehlich, J.E., Kramer, D.M., Hu, J. and Sharkey, T.D., 2019. A Cytosolic Bypass and G6P Shunt in Plants Lacking Peroxisomal Hydroxypyruvate Reductase. Plant physiology, pp.pp-00256. doi: https://doi.org/10.1104/pp.19.00256

Johnson, S.R., Bhat, W.W., Sadre, R., Miller, G.P., Garcia, A.S. and Hamberger, B., 2019. Promiscuous terpene synthases from Prunella vulgaris highlight the importance of substrate and compartment switching in terpene synthase evolution. New Phytologist. doi: https://doi.org/10.1111/nph.15778

Lantz, A.T., Solomon, C., Gog, L., McClain, A.M., Weraduwage, S.M. and Sharkey, T.D., 2019. Isoprene suppression by CO2 is not due to triose phosphate utilization (TPU) limitation. Frontiers in Forests and Global Change2, p.8. doi:  https://doi.org/10.3389/ffgc.2019.00008

Zuo, Z., Weraduwage, S.M., Lantz, A.T., Sanchez, L.M., Weise, S.E., Wang, J., Childs, K.L., and Sharkey, T.D., 2019. Expression of isoprene synthase in Arabidopsis alters plant growth and expression of key abiotic and biotic stress-related genes under unstressed conditions. Plant Physiology in press. doi:  https://doi.org/10.1104/pp.18.01391

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

Dums, J.T., Murphree, C.A., Vasani, N., Young, D. and Sederoff, H., 2018. Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented with Ammonium Derived from Glutamine. Frontiers in Marine Science5, p.311. doi: https://doi.org/10.3389/fmars.2018.00311

Johnson, S.R., Bhat, W.W., Bibik, J., Turmo, A., Hamberger, B., Hamberger, B., Boachon, B., Buell, C.R., Crisovan, E., Dudareva, N. and Garcia, N., 2019. A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae). Journal of Biological Chemistry294(4), pp.1349-1362. doi: https://doi.org/10.1074/jbc.RA118.006025

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

Murphree, C.A., Dums, J.T., Jain, S.K., Zhao, C., Young, D.Y., Khoshnoodi, N., Tikunov, A., Macdonald, J., Pilot, G. and Sederoff, H., 2017. Amino acids are an ineffective fertilizer for Dunaliella spp. growth. Frontiers in Plant Science8, p.847. doi: https://doi.org/10.3389/fpls.2017.00847.

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.