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Publications

Below is a list of publications co-authored by participants (shown in bold) in the Plant Genomics@MSU REU program. Congratulations to all!!!  

  1. Lavell A, Smith M, Xu Y, Froehlich JE, De La Mora C, Benning C (2021) Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10. Plant Journal 108: 1332 1345 https://doi.org/10.1111/tpj.15514
  2. Rohnke BA, Rodriguez-Pérez KJ, Montgomery BM (2020) Linking the dynamic response of the carbon dioxide-concentrating mechanism to carbon assimilation behavior in Fremyella diplosiphon. Molecular Biology and Physiology 11: e01052-2020 https://doi.org/10.1128/mBio.01052-20  
  3. Moore BM, Wang P, Fan P, Lee A, Leong BJ, Lou Y-R, Schenck CA, Sugimoto K, Last RL, Lehti-Shiu MD, Barry CS, Shiu S-H (2020) Within and cross species predictions of plant specialized metabolism genes using transfer learning. in silico Plants 2: https://doi.org/10.1093/insilicoplants/diaa005
  4. Fan P, Wang P, Lou Y-R, Leong BJ, Moore BJ, Schenck CA, Combs R, Cao P, Brandizzi F, Shiu S-H, Last RL (2020) Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity.  eLife 9:e56717 https://dx.doi.org/10.7554%2FeLife.56717
  5. Takeuchi T, Sears BB, Lindeboom CD, Lin Y-T, Fekaris N, Zienkiewicz K, Zienkiewicz A, Poliner E, Benning C (2020) Chlamydomonas CHT7 is required for an effective quiescent state by regulating nutrient-responsive cell cycle gene expression. Plant Cell DOI: https://doi.org/10.1105/tpc.19.00628
  6. Shee PK, Ratnayake ND, Walter T, Goethe O, Onyeozili EN, Walker KD (2019) Exploring the scope of an α/β-aminomutase for the amination of cinnamate epoxides to arylserines and arylisoserines. ACS Catalysis 9: 7418-7430 https://doi.org/10.1021/acscatal.9b01557
  7. Lantz AT, Solomon C, Gog L, McClain AM, Weraduwage SM, Cruz JA, Sharkey TD (2019) Isoprene suppression by CO2 is not due to triose phosphate utilization (TPU) limitation. Frontiers in Forests and Global Change 2: article 8 https://doi.org/10.3389/ffgc.2019.00008
  8. Edger PP, Poorten TJ, VanBuren R, Hardigan MA, Colle M, McKain MR, Smith RD, Teresi SJ, Nelson ADL, Wai CM, Alger EI, Bird KA, Yocca AE, Pumplin N, Ou S, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Acharya CB, Cole GS, Mower JP, Childs KL, Jiang N, Lyons E, Freeling M, Puzey JR, Knapp SJ (2019) Origin and evolution of the octoploid strawberry genome. Nature Genetics 51: 541-547  https://doi.org/10.1038/s41588-019-0356-4
  9. Zuo Z, Weraduwage SM, Lantz AT, Sanchez LM, Weise SE, Wang J, Childs K, Sharkey TD (2019) Isoprene acts as a signaling molecule in gene networks important for stress responses and plant growth. Plant Physiology https://doi.org/10.1104/pp.18.01391
  10. VanBuren R, Pardo J, Wai CM, Evans S, Bartels D (2019) Massive tandem proliferation of ELIPs supports convergent evolution of desiccation tolerance across land plants. Plant Physiology 179: 1040-1049 https://doi.org/10.1104/pp.18.01420 
  11. Du Z-Y, Alvaro J, Hyden B, Zienkiewicz K, Benning N, Zienkiewicz A, Bonito G, Benning C (2018) Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata. Biotechnology for Biofuels 11: article 174. https://doi.org/10.1186/s13068-018-1172-2
  12. Lloyd, JP, Tsai, ZT, Sowers, RP, Panchy, NL and Shiu, SH (2018) A Model-Based Approach for Identifying Functional Intergenic Transcribed Regions and Noncoding RNAs. Molec. Biol. Evol. 35: 1422-1436. https://doi.org/10.1093/molbev/msy035
  13. Fan P, Miller AM, Liu X, Jones AD, Last RL (2017) Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity. Nature Communications 8: article number 2080 http://dx.doi.org/10.1038/s41467-017-02045-7
  14. Liu X, Enright M, Barry CS, Jones AD (2017) Profiling, isolation and structure elucidation of specialized acylsucrose metabolites accumulating in tichomes of Petunia species. Metabolomics 13: http://dx.doi.org/10.1007/s11306-017-1224-9
  15. Busch AWU, WareJoncas Z, Montgomery BL (2017) Tryptophan-rich sensory protein / translocator protein (TSPO) from cyanobacterium Fremyella diplosiphon binds a broad range of functionally relevant tetrapyrroles. Biochemistry 56: 73-84 http://dx.doi.org/10.1021/acs.biochem.6b01019
  16. Ratnayake ND, Theisen C, Walter T, Walker KD (2016) Whole-cell biocatalytic production of variously substituted β-aryl- and β-heteroaryl-β-amino acids, J. Biotechnol. 217, 12-21 http://dx.doi.org/10.1016/j.jbiotec.2015.10.012
  17. Yang JT, Preiser AL, Li Z, Weise SE, Sharkey TD (2016) Triose phosphate use limitation of photosynthesis short-term and long-term effects. Planta 243: 687-698 http://dx.doi.org/10.1007/s00425-015-2436-8 
  18. Fan P, Miller AM, Schilmiller AL, Liu X, Ofner I, Jones AD, Zamir D, Last RL (2016) In vitro reconstruction and analysis of evolutionary variation of the tomato acylsucrose metabolic network. Proceedings of the National Academy of Sciences of the United States of America 113: E239-248 http://dx.doi.org/10.1073/pnas.1517930113 
  19. Lloyd JP, Seddon AE, Moghe GD, Simenc MC, Shiu S-H (2015) Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes. The Plant Cell 27: 2133-2147 http://dx.doi.org/10.1105/tpc.15.00051
  20. Poliner E, Panchy N, Newton L, Wu G, Lapinsky A, Bullard B, Zienkiewicz A, Benning C, Shiu S-H, Farré EM (2015) Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles. The Plant Journal 83: 1097-1113 http://dx.doi.org/10.1111/tpj.12944
  21. Ning J, Moghe G, Leong B, Kim J, Ofner I, Wang Z, Adams C, Jones AD, Zamir D, Last RL (2015) A feedback insensitive isopropylmalate synthase affects acylsugar composition in cultivated and wild tomato. Plant Physiology 169: 1821-1835 http://dx.doi.org/10.1104/pp.15.00474 
  22. Ghosh B, Westbrook TC, Jones AD (2014) Comparative structural profiling of trichome specialized metabolites in tomato (Solanum lycopersicum) and S. habrochaites: acylsugar profiles revealed by UHPLC/MS and NMR. Metabolomics 10: 496-507 http://dx.doi.org/10.1007/s11306-013-0585-y 
  23. Sharkey TD, Gray DW, Pell HK, Breneman SR, Topper L (2013) Isoprene synthase genes for a monophyletic clade of acyclic terpene synthases in the TPS-B terpene synthase family. Evolution 67: 1026-1040 http://dx.doi.org/10.1111/evo.12013 
  24. Nadakuduti SS, Pollard M, Kosma DK, Allen C, Ohlrogge JB, Barry CS (2012) Pleiotropic phenotypes of the sticky peel mutant provide new insight into the role of CUTIN DEFICIENT2 in epidermal cell function in tomato. Plant Physiology 159: 945-960 http://dx.doi.org/10.1104/pp.112.198374  
  25. Gonzales-Vigil E, Hufnagel DE, Kim J, Last RL, Barry CS (2012) Evolution of TPS20-related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites. Plant Journal 71: 921-935 http://dx.doi.org/10.1111/j.1365-313x.2012.05040.x 
  26. Costigan SE, Warnasooriya SN, Humphries BA, Montgomery BL (2011) Root-localized phytpchrome chromophore synthesis is required for photoregulation of root elongation and impacts root sensitivity to jasmonic acid in Arabidopsis. Plant Physiology 157: 1138 -1150 http://dx.doi.org/10.1104/pp.111.184689
  27. Yang Y, Sage TL, Liu Y, Ahmad TR, Marshall WF, Shiu SH, Froehlich JE, Imre KM, Osteryoung KW (2011) CLUMPED CHLOROPLASTS 1 is required for plastid separation in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 108: 18530-18535 http://dx.doi.org/10.1073/pnas.1106706108 
  28. Wanninayake U, DePorre Y, Ondari M, Walker KD (2011) (S)-Styryl-alpha-alanine used to probe the intermolecular mechanism of an intramolecular MIO-aminomutase. Biochemistry 50: 10082-10090 http://dx.doi.org/10.1021/bi2012299 
  29. Ajjawi I, Coku A, Froehlich JE, Yang Y, Osteryoung KW, Benning C, Last RL (2011) A J-like protein influences fatty acid composition of chloroplast lipids in Arabidopsis. Plos One 6: e25368 http://dx.doi.org/10.1371/journal.pone.0025368  
  30. Gao JP, Ajjawi I, Manoli A, Sawin A, Xu CC, Froehlich JE, Last RL, Benning C (2009) FATTY ACID DESATURASE4 of Arabidopsis encodes a protein distinct from characterized fatty acid desaturases. Plant Journal 60: 832-839 http://dx.doi.org/10.1111/j.1365-313x.2009.04001.x