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BBMB Undergraduate Publications

Undergraduate Researchers in Bold



Palhano Zanela TM, Woudenberg A, Romero Bello KG, Underbakke ES. Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation. Structure 2023 31(4), 447.

Watanabe M, Khu T.M, Warren G, Shin J, Stewart C, Roche J (2023) Evidence of DISC1 as an arsenic binding protein and implications regarding its role as a translational activator. Front. Mol. Biosci.10:1308693.
doi: 10.3389

Zhang N., Julian JD., Yap CE., Swaminathan S., Zabotina OA. (2023) The Arabidopsis xylosyltransferases, XXT3, XXT4, and XXT5, are essential to complete the fully xylosylated glucan backbone XXXG‐type structure of xyloglucans, New Phytologist, 238, 6, 1986-1999 (doi: 10.1111/nph.18851).



Chaudhry, N., Sica, M., Surabhi, S., Hernandez, D.S., Mesquita, A., Selimovic, A., Riaz, A., Lescat, L., Bai, H., MacIntosh, G.C. and Jenny, A., 2022. Lamp1 mediates lipid transport, but is dispensable for autophagy in Drosophila. Autophagy, 18(10), pp.2443-2458


Dershwitz, P., N.L. Bandow, J. Yang, J.D. Semrau, M.T. McEllistrem, R.A. Heinze, M. Fonseca, J.C. Ledesma, J.R. Jennett, A.M. DiSpirito, N.S. Athwal, M.S. Hargrove, T.A. Bobik, H. Zischka, and A.A. DiSpirito. 2021. Oxygen generation via water splitting by a novel biogenic metal ion binding compound. Applied and Environmental Microbiology. 87: issue 14.

Ehrlich JJ, Weerts RM., Shome S., Culbertson AT., Honzatko RB., Jernigan RL., Zabotina OA. Xyloglucan Xylosyltransferase 1 displays promiscuity toward donor substrates during in vitro reactions. 2021, Plant Cell Physiology, doi: 10.1093/pcp/pcab114.

Kang, C.S., X. Liang, P. Dershwitz, W. Gu, A. Schepers, A. Flatley, J. Lichtmanneger, H. Zischka, L. Zhang, X. Lu, B. Gu, J.C. Ledesma, D.J. Pelger, A.A. DiSpirito, and J.D. Semrau. 2021. Evidence for methanobactin “theft” and novel chalkophore production in Methanotrophs: impact on methanotrophic-mediated methylmercury degradation. International Society for Microbial Ecology (ISME) Journal. 

Zabotina OA, Zang N, Weerts R. Polysaccharide Biosynthesis: Glycosyltransferases and their complexes (review) 2021, Front Plant Science, 12:625307, doi: 10.3389/fpls.2021.625307

Zhang, J., Li, R., Xu, M., Hoffmann, R.I., Zhang, Y., Liu, B., Zhang, M., Yang, B., Li, Z., Peters, R.J. (2021) “A (Conditional) Role for Labdane-Related Diterpenoid Natural Products in Rice Stomatal Closure”, New Phytol., 230:698-709. 


Lemke, C., Whitham, O., Peters, R.J. (2020) “Magnesium-specific ring expansion/ contraction catalysed by the class II diterpene cyclase from pleuromutilin biosynthesis”, Org. Biomol. Chem., 18(29):5586-5588. 

Reem NT, Chambers L, Zhang N, Abdullah SF, Chen Y, Feng G, Gao S, Soto-Burgos J, Pogorelko G, Bassham DC, Anderson CT, Walley JW, Zabotina OA. Post-Synthetic reduction of pectin methylesterification causes morphological abnormalities and alterations to stress response in Arabidopsis thaliana. 2020, Plants (Basel), 9:1558 (doi: 10.3390/plants9111558).



Hohenstein JD, Studham ME, Kovinich N, Klein AT, Barry K, Lee YJ, MacIntosh GC (2019) Transcriptional and chemical changes in soybean leaves in response to long-term aphid colonization. Frontiers in Plant Science, 10: 310. doi: 10.3389/fpls.2019.00310

Ilgu, M., S. Yan, R.M. Khounlo, M.H. Lamm, and M. Nilsen-Hamilton. 2019. Common Secondary and Tertiary Structural Features of Aptamer–Ligand Interaction Shared by RNA Aptamers with Different Primary Sequences. Molecules. 24:4535-4546. DOI: 10.3390/molecules24244535

Jia, M., Mishra, S.K., Tufts, S., Jernigan, R.L., Peters, R.J. (2019) “Combinatorial biosynthesis and the basis for substrate promiscuity in class I diterpene synthases”,Met. Eng., 55:44-58.

Lemke, C., Potter, K.C., Schulte, S., Peters, R.J. (2019) “Conserved bases for the initial cyclase in gibberellin phytohormone biosynthesis: from bacteria to plants”, Biochem. J., 476(18):2607-2621.


Auwardt, S. L.; Seo, Y.-J.; Ilgu, M.; Ray, J.; Feldges, R. R.; Shubham, S.; Bendickson, L.; Levine, H. A.; Nilsen-Hamilton, M. Scientific Reports 2018, 8, 15712-15712.

Culbertson AT, Ehrlich JJ, Choe JY, Honzatko RB, Zabotina OA. (2018) Structure of xyloglucan xylosyltransferase 1 reveals simple steric rules that define biological patterns of xyloglucan polymers. PNAS, 115: 6064-6069 (doi: 10.1073/pnas.1801105115).

Hanson QM, Carley JR, Gilbreath TJ, Smith BC, Underbakke ES. Calmodulin-induced conformational control and allostery underlying neuronal nitric oxide synthase activation. J. Mol. Biol. 2018 430(7) 935- 947

Herring TI, Harris TN, Chowdhury C, Mohanty SK, Bobik TA. (2018) a bacterial microcompartment is used for choline fermentation by Escherichia coli 536. J. Bacteriol. 200, 1-13.

Nagel, R., Bieber, J., Schmidt-Dannert, M.G., Nett, R.S., Peters, R.J. (2018) “A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria”,Front. Microbiol., 9:2916.

Schulte, S., Potter, K.P., Lemke, C., Peters, R.J. (2018) “Catalytic bases and stereo-control in Lamiaceae class II diterpene cyclases”, Biochemistry, 57(25):3473-3479.

Teklemariam T.A., Rivera O.D., and Nelson S.W. (2018) Kinetic Analysis of the Exonuclease Activity of the Bacteriophage T4 Mre11-Rad50 Complex. Methods Enzymol. 600:135-156.

Wang, X., Tamiev, D., Alagurajan, J., DiSpirito, AA., Phillips, GJ., Hargrove, MS. The role of the NADH- dependent nitrite reductase, Nir, from Escherichia coli in fermentative ammonification. Archives of Microbiology, doi: 10.1007/s00203-018-1590-3. (2018)


Blacketer, M. J., Gannon, M. K., Young, I. A., Shogren-Knaak. M. A. “Solid-phase synthesis of highly repetitive chromatin assembly templates.” Anal Biochem, 2017, 531:12-15.

Jia, M., Zhou, K., Tufts, S., Schulte, S., Peters, R.J. (2017) “A pair of residues that interactively affect diterpene synthase product outcome”, ACS Chem. Biol., 12(3):862-867.

Xu, M., Hillwig, M.L., Tiernan, M.S., Peters, R.J. (2017) “Probing labdane-related diterpenoid biosynthesis in the fungal genus Aspergillus”, J. Nat. Prod., 80(2):328-333.


Culbertson A, Chou YH, Smith AL, Young ZT, Tietze AA, Cottaz S, Fauré R, Zabotina OA. (2016) Enzymatic Activity of Xyloglucan Xylosyltransferase 5. Plant Physiology, 171(3):1893-1904. (pii: pp.00361.2016).

Culbertson AT, Smith AL, Cook MD, Zabotina OA. (2016) Truncations of xyloglucan xylosyltransferase 2 provide insights into the roles of the N- and C-terminus. Phytochemistry, 128:12-19, (doi: 10.1016/j.phytochem.2016.03.016).

Culbertson AT, Tietze AA, Tietze D, Chou YH, Smith AL, Young ZT, Zabotina OA. (2016) A Homology Model of Xyloglucan Xylosyltransferase 2 Reveals Critical Amino Acids Involved in Substrate Binding. Glycobiology, 26:961:972. (doi: 10.1093/glycob/cww050).

Gao Y., Meyer J.R., and Nelson S.W. (2016) A network of allosterically coupled residues in the bacteriophage T4 Mre11-Rad50 complex. Protein Sci. 25(11):2054-2065.

Gu, W., UI-H M. Farhan, B.S. Baral, E.A. Turpin, N.L. Bandow, A.A. DiSpirito, J. Lichtmannegger, E. Kremmer, H. Zischka and J.D. Semrau. 2016. A TonB dependent transporter is responsible for methanobactin uptake by Methylosinus trichosporium OB3b. Applied and Environmental Microbiology. 82: 1917-1923.

Hillwig MS, Chiozza M, Casteel CL, Lau ST, Hohenstein J, Hernández E, Jander G, MacIntosh GC (2016) Abscisic acid deficiency increases defense responses against Myzus persicae in Arabidopsis. Molecular Plant Pathology 17: 225-235. doi: 10.1111/mpp.12274

Pogorelko GV, Reem NT, Young ZT, *Chambers L, Zabotina OA. (2016) Post-synthetic defucosylation of AGP by Aspergillus nidulans α-1,2-fucosidase expressed in Arabidopsis apoplast induces compensatory upregulation of α-1,2-fucosyltransferases. PLoS ONE, 11(4): e0150983. (doi:10.1371/journal.pone.0150983).

Potter, K.C., Zi, J., Young, Y.J., Schulte, S., Malchow, B.K., Tantillo, D.J., Peters, R.J. (2016) “Blocking deprotonation with retention of aromaticity in a plant ent-copalyl diphosphate synthase leads to product rearrangement”, Angew. Chem. Int. Ed., 55(2):634-638.

Reem NT, Pogorelko G, Lionetti V, Chambers L, Held MA, Bellincampi D, Zabotina OA. (2016) Decreased Polysaccharide Feruloylation Compromises Plant Cell Wall Integrity and Increases Susceptibility to Necrotrophic Fungal Pathogens. Front Plant Sci., 7:630,(doi: 10.3389/fpls.2016.00630).

Shah,M. Teixeira, F.M. Soares, E.L., Soares, A.A., Carvalho, P.C. Domont, G.B., Thornburg, R.W., Nogueira, F.C.S., and Campos, F.A.P. (2016) Time-course proteome analysis of developing extrafloral nectaries of Ricinus communis. Proteomics 16:629-633. DOI 10.1002/pmic.201500292

Xue, C., Whitis, N.R. and D.G. Sashital. (2016) Conformational control of Cascade interference and priming activities in CRISPR immunity. Mol Cell. 64, 826-834.


Barfoot T., Herdendorf T.J., Behning B.R., Stohr B.A., Gao Y., Kreuzer K.N., and Nelson S.W. (2015) Functional Analysis of the Bacteriophage T4 Rad50 Homolog (gp46) Coiled-coil Domain. J. Biol Chem. 290, 23905-23915.

Chou Y, Pogorelko G, Young ZT, Zabotina OA. (2015) Protein-Protein Interactions Among Xyloglucan- Synthesizing Enzymes and Formation of Golgi-Localized Multiprotein Complexes. Plant Cell Physiol. 56:255-267.

Farhan, UI-H M., B. Kalidass, N.L. Bandow, E. Turpin, A.A. DiSpirito and J.D. Semrau. 2015. Cerium regulates expression of alternative methanol dehydrogenases in Methylosinus trichosporium OB3b. Applied and Environmental Microbiology. 81: 7546 – 7554.

Lu, X., Hershey, D.M., Wang, L., Bogdanove, A.J., Peters, R.J. (2015) “An ent-kaurene derived diterpenoid virulence factor from Xanthomonas oryzae pv. oryzicola”, New Phytol., 206(1):295-302.

Mafu, S., Potter, K.C., Hillwig, M.L., Schulte, S., Criswell, J., Peters, R.J. (2015) “Efficient heterocyclisation by (di)terpene synthases”, Chem. Commun., 51(70):13485-13487.

Sturms R, Streauslin NA, Cheng S, Bobik TA. (2015). In Salmonella enterica, ethanolamine utilization is repressed by 1,2-Propanediol to prevent detrimental mixing of components of two different bacterial microcompartments. J. Bacteriol. 197, 2412-2421

von Aderkas, P., Prior, N., Jesse, S., Little, S., Cross T., Hardie, D., Borchers, C., Thornburg, R.W., Hou, C., Lunny, A. (2015) Degradome and Secretome of Pollination Drops of Ephedra. Botanical Review DOI: 10.1007/s12229-014-9147-x


Ambrosio L, Morriss S, Riaz A, Bailey R, Ding J, MacIntosh GC (2014) Phylogenetic analyses and characterization of RNase X25 from Drosophila melanogaster suggest a conserved housekeeping role and additional functions for RNase T2 enzymes in protostomes. PLoS ONE 9(8): e105444. doi:10.1371/journal.pone.0105444

Baral, B.S., N.L. Bandow, A. Vorobev, B.C. Freemeier, B.H. Bergman, T. Herdendorf, N. Fuentes, L. Ellias, E. Turpin, J.D. Semrau, and A.A. DiSpirito. 2014. Mercury binding by methanobactin from Methylocystis strain SB2. Journal of Inorganic Biochemistry 141: 161 – 169.

Brown CS, Lee MS, Leung DW, Wang T, Xu W, Luthra P, Anantpadma M, Shabman RS, Melito LM, Macmillan KS, Borek DM, Otwinowski Z, Ramanan P, Stubbs AJPeterson DS, Binning JM, Tonelli M, Olson MA, Davey RA, Ready JM, Basler CF, Amarasinghe GK. In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity. J Mol Biol. 2014 Feb 1. [Epub ahead of print]

Cai, W., C. Wang, Y. Li, L. Shen, S. Liu, C. Yao, X. Bao, P. Schnable, J. Girton, J. Johansen and K.M. Johansen (2014) Genome-wide analysis of regulation of gene expression and H3K9me2  distribution by JIL-1 mediated histone H3S10 phosphorylation in DrosophilaNucleic Acids Res. 42: 5456-67.

Jackson, A.J., Hershey, D.M., Chesnut, T., Xu, M., Peters, R.J. (2014) “Biochemical characterization of the castor bean ent-kaurene synthase(-like) family supports quantum chemical view of diterpene cyclization”, Phytochemistry, 103(1):13-21.

Miller M.E., Parrott E.E., Singh R., Nelson S.W. (2014) A High-Throughput Assay to Identify Inhibitors of the Apicoplast DNA Polymerase from Plasmodium falciparum. Journal of Biomolecular Screening. 19(6):967-73.

McNamara, DE, Cascio, D, Jorda, J, Bustos, C., Wang, TC, Rasche, M. E., Yeates, T. O. and Bobik, TA (2014). Structure of Dihydromethanopterin Reductase: A Cubic Protein Cage for Redox Transfer. J Biol Chem. [Epub ahead of print]

Gao, W., Sun, H-X, Xiao, H, Cui, G., Hillwig, ML, Jackson, A., Wang, X., Shen, Y., Zhao, N., Zhang, L., Wang, X.-J, Peters, RJ, Huang, L. (2014) “Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza”, BMC Genomics, 15:73.

Hershey, DM, Lu, X, Zi, J, Peters, RJ (2014) “Functional conservation of the capacity for ent-kaurene biosynthesis and an associated operon in certain rhizobia”, J. Bact., 196(1):100-106.

Xu, M., Hillwig, M.L., Lane, A., Tiernan, M.S., Moore, B.S., Peters, R.J. (2014) “Characterization of an orphan diterpenoid biosynthetic operon from Salinapora arenicola”, J. Nat. Prod., 77(9):2144-2147.

Zi, J., Matsuba, Y., Hong, Y.J., Jackson, A.J., Tantillo, D.J., Pichersky, E., Peters, R.J. (2014) “Biosynthesis of lycosantalonol, a cis-prenyl derived diterpenoid”, J. Am. Chem. Soc., 136(49):16951-16953.


Wingert BM, Parrott EE, Nelson SW. Fidelity, mismatch extension, and proofreading activity of the Plasmodium falciparum apicoplast DNA polymerase. Biochemistry. 2013 Nov 5;52(44):7723-30.

McIntyre AP, Mukerjea R, Robyt JF. Reducing values: dinitrosalicylate gives over-oxidation and invalid results whereas copper bicinchoninate gives no over-oxidation and valid results. Carbohydr Res. 2013 Oct 18;380:118-23.

Mukerjea R, Gray AN, Robyt JF. Significant increases in potato Starch-Synthase and Starch-Branching-Enzyme activities by dilution with buffer containing dithiothreitol and polyvinyl alcohol 50 K. Carbohydr Res. 2013 Feb 15;367:25-8.


Zhou, K., Xu, M., Tiernan, MS., Xie, Q., Toyomasu, T., Sugawara, C., Oku, M., Usui, M., Mitsuhashi, W., Chono, M., Chandler, PM, Peters, RJ (2012) “Functional characterization of wheat ent-kaurene(-like) synthases indicates continuing evolution of labdane-related diterpenoid metabolism in the cereals”, Phytochemistry, 84:47-55.

Mann, FM, Xu, M., Davenport, EK, Peters, RJ (2012) “Functional characterization and evolution of the isotuberculosinol operon in Mycobacterium tuberculosis and related mycobacteria”, Front. Microbiol., 3:368. Xu, M., Galhano, R., Weimann, P., Bueno, E., Tiernan, M., Wu, W., Gershenzon, J., Tudzynski, B., Sesma, A., Peters, R.J. (2012) “Genetic evidence for natural product mediated plant-plant allelopathy in rice”, New Phytol., 193(3):570-575.

Bandow N, Gilles VS, Freesmeier B, Semrau JD, Krentz B, Gallagher W, McEllistrem MT, Hartsel SC, Choi DW, Hargrove MS, Heard TM, Chesner LN, Braunreiter KM, Cao BV, Gavitt MM, Hoopes JZ, Johnson JM, Polster EM, Schoenick BD, Umlauf AM, DiSpirito AA. Spectral and copper binding properties of methanobactin from the facultative methanotroph Methylocystis strain SB2. J Inorg Biochem. 2012 May;110:72-82.

Vorobev A, Jagadevan S, Baral BS, Dispirito AA, Freemeier BC, Bergman BH, Bandow NL, Semrau JD. Detoxification of mercury by methanobactin from Methylosinus trichosporium OB3b. Appl Environ Microbiol. 2013 Oct;79(19):5918-26.

Mukerjea R, McIntyre AP, Robyt JF. Potent inhibition of starch-synthase by Tris-type buffers is responsible for the perpetuation of the primer myth for starch biosynthesis. Carbohydr Res. 2012 Jul 1;355:28-34.


Hillwig MS, Contento AL, Meyer A, Ebany D, Bassham DC, Macintosh GC (2011) RNS2, a conserved member of the RNase T2 family, is necessary for ribosomal RNA decay in plants. Proc Natl Acad Sci USA 108: 1093-1098.

Ramanan P, Shabman RS, Brown CS, Amarasinghe GK, Basler CF, Leung DW. (2011) Filoviral immune evasion mechanisms. Viruses. 2011 Sep;3(9):1634-49.

Falconer DJ, Mukerjea R, Robyt JF. Biosynthesis of dextrans with different molecular weights by selecting the concentration of Leuconostoc mesenteroides B-512FMC dextransucrase, the sucrose concentration, and the temperature. Carbohydr Res. 2011 Feb 1;346(2):280-4.

Jing F, Cantu DC, Tvaruzkova J, Chipman JP, Nikolau BJ, Yandeau-Nelson MD, Reilly PJ.  2011.  Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity. BMC Biochemistry. 12:44.

Johnston DA, Mukerjea R, Robyt JF. Preparation and characterization of new and improved soluble-starches, -amylose, and -amylopectin by reaction with benzaldehyde/zinc chloride. Carbohydr Res. 2011 Dec 13;346(17):2777-84.

De la Rosa MB, Nelson SW. An interaction between the Walker A and D-loop motifs is critical to ATP hydrolysis and cooperativity in bacteriophage T4 Rad50. J Biol Chem. 2011 Jul 22; 286(29):26258-66.

Zischka, H,  J. Lichtmannegger, S Schulz, S Schmitt, N. Jägemann, D. Hamöller, L. Jennen, C. Rust, N. Larochette, L. Galluzzi, V. Chajes, N. Bandow, VS Gilles, AA DiSpirito, I. Esposito, M Goettlicher, KH Summer and G Kroemer. 2011. Mitochondria membrane crosslinking and fragmentation in Wilson disease. J. Clin. Investigation. 121: 1508 – 1518.

Pogorelko G, Fursova O, Lin M, Pyle E, Jass J, Zabotina OA*. (2011) Post-synthetic modification of plant cell walls by expression of microbial hydrolases in the apoplast. Plant Mol. Biol. 77:433-445.

Bandow NL, Gallagher WH, Behling L, Choi DW, Semrau JD, Hartsel SC, Gilles VS, Dispirito AA. Isolation of methanobactin from the spent media of methane-oxidizing bacteria. Methods Enzymol. 2011;495:259-69.

Hillwig, ML, Xu, M, Toyomasu, T, Tiernan, MS, Gao, W., Cui, G., Huang, L., Peters, R.J. (2011) “Domain loss has independently occurred multiple times in plant terpene synthase evolution”, Plant J., 68(6):1051-1060.

Morrone, D, Hillwig, ML, Mead, MELowry, L, Fulton, DB, Peters, RJ (2011) “Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals”, Biochem. J., 435(3):589-595.