Laboratory of Microbial Biochemistry

Skidmore College


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Research Articles

Skidmore Undergraduate Co-authors Underlined. For link, click on publication number. Select articles, click on title for a PDF version.

23) Nair, N., Raff, H., Islam, M.T., Feen, M., Garofalo, D.M., and Sheppard, K. (2016) The Bacillus subtilis and Bacillus halodurans aspartyl-tRNA synthetases retain recognition of tRNAAsn. J. Mol. Biol., 428, 618-630.

22) Suzuki, T., Nakamura, A., Kato, K., Söll, D., Tanaka, I., Sheppard, K., and Yao, M. (2015) Structure of the Pseudomonas aeruginosa transamidosome reveals unique aspects of bacterial tRNA-dependent asparagine biosynthesis. Proceedings of the National Academy of Sciences 112, 382-387.

21) Alperstein, A., Ulrich, B., Garofalo, D.M., Dreisbach, R., Raff, H., and Sheppard, K. (2014) The predatory bacterium Bdellovibrio bacteriovorus aspartyl-tRNA synthetase recognizes tRNAAsn as a substrate. PLoS ONE 9(10): e110842.

20) Mladenova, S.R., Stein, K.R., Bartlett, L., and Sheppard, K. (2014) Relaxed tRNA specificity of the Staphylococcus aureus aspartyl-tRNA synthetase enables RNA-dependent asparagine biosynthesis. FEBS Lett. 588, 1808-1812.

19) O’Donoghue, P., Sheppard, K., Nureki, O., and Söll, D. (2011) Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase.  Proc. Natl. Acad. Sci. U.S.A. 108, 20485-20490.

18) Englert, M., Sheppard, K., Aslanian, A., Yates III, J., and Söll, D. (2011) Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. Proc. Natl. Acad. Sci. U.S.A. 108, 1290-1295. 

17) Englert, M., Sheppard, K., Gundllapalli, S., Beier, H., and Söll, D. (2010) Branchiostoma floridae has separate healing and sealing enzymes for 5′-phosphate RNA ligation. Proc. Natl. Acad. Sci. U.S.A. 107, 16834-16839. 

16) Nureki, O., O’Donoghue, P., Watanabe, N., Ohmori, A., Oshikane, H., Araiso, Y., Sheppard, K., Söll, D., and Ishitani, R. (2010) Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. Nucleic Acids Res. 38, 7286-7297. 

15) Rampias, T.*, Sheppard K.*, and Söll, D. (2010) The archaeal transamidosome for RNA-dependent glutamine biosynthesis.  Nucleic Acids Res. 38, 5774-5783.
* denotes authors contributed equally to this work. 
Selected as a Featured Article by the journal.

14) Nakamura, A., Sheppard, K., Yamane, J., Yao, M., Söll, D., and Tanaka, I. (2010) Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition. Nucleic Acids Res. 38, 672-682.
Selected as a Featured Article by the journal.

13) Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Kwon, S-T., Söll, D., and Smith, J.L. (2009) Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme. J. Mol. Biol. 391, 703-711.

12) Yuan, J.*, Sheppard, K.*, and Söll, D. (2008) Amino acid modifications on tRNA.  Acta Biochim. Biophys. Sin. (Shanghai) 40, 539-553.
* denotes authors contributed equally to this work.

11) Sheppard, K., Sherrer, R.L., and Söll, D. (2008) Methanothermobacter thermautotrophicus tRNAGln confines the amidotransferase GatCAB to asparaginyl-tRNAAsn formation.  J. Mol. Biol. 377, 845-853.

10) Sheppard, K., and Söll, D. (2008) On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE.  J. Mol. Biol. 377, 831-844. 

9)   Sheppard, K.*, Yuan, J.*, Hohn, M.J., Jester, B., Devine, K., and Söll, D. (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis.  Nucleic Acids Res. 36, 1813-1825. 
* denotes authors contributed equally to this work.

8)   Sheppard, K., Akochy, P.M., and Söll, D. (2008) Assays for transfer RNA-dependent amino acid biosynthesis.  Methods 44, 139-145.

7)   Sheppard, K.*, Akochy, P.M.*, Salazar, J.C., and Söll, D. (2007) The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGlnJ. Biol. Chem. 282, 11866-11873. 
* denotes authors contributed equally to this work.

6)   Namgoong, S., Sheppard, K., Sherrer, R.L., and Söll, D. (2007) Co-evolution of the archaeal tRNA-dependent amidotransferase GatCAB with tRNAAsnFEBS Lett. 581, 309-314. 

5)   Oshikane, H.*, Sheppard, K.*, Fukai, S., Nakamura, Y., Ishitani, R., Numata, T., Sherrer, R.L., Feng, L., Schmitt, E., Panvert, M., Blanquet, S., Mechulam, Y., Söll, D., and Nureki, O. (2006) Structural basis of RNA-dependent recruitment of glutamine to the genetic code.  Science 312, 1950-1954. 
* denotes authors contributed equally to this work.
Faculty of 1000 Biology Must Read, F1000 Factor 6.4.

4)   Feng, L., Sheppard, K., Tumbula-Hansen, D., and Söll, D. (2005) Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.  J. Biol. Chem. 280, 8150-8155. 

3)   Feng, L., Sheppard, K., Namgoong, S., Ambrogelly, A., Polycarpo, C., Randau, L., Tumbula-Hansen, D., and Söll, D. (2004) Aminoacyl-tRNA synthesis by pre-translational amino acid modification.  RNA Biol. 1, 16-20. 

2)   Olivier, M., Bustos, V.I., Levy, M.R., Smick, G.A., Moreno, I., Bushard, J.M., Almendras, A.A., Sheppard, K., Zierten, D.L., Aggarwal, A., Carlson, C.S., Foster, B.D,. Vo, N., Kelly, L., Liu, X., and Cox, D.R. (2001) Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21.  Genomics 78, 64-72. 

1)   Olivier, M., Aggarwal, A., Allen, J., Almendras, A.A., Bajorek, E.S., Beasley, E.M., Brady, S.D., Bushard, J.M., Bustos, V.I., Chu, A., Chung, T.R., De Witte, A., Denys, M.E., Dominguez, R., Fang, N.Y., Foster, B.D., Freudenberg, R.W., Hadley, D., Hamilton, L.R., Jeffrey, T.J., Kelly, L., Lazzeroni, L., Levy, M.R., Lewis, S.C., Liu, X., Lopez, F.J., Louie, B., Marquis, J.P., Martinez, R.A., Matsuura, M.K., Misherghi, N.S., Norton, J.A., Olshen, A., Perkins, S.M., Perou, A.J., Piercy, C., Piercy, M., Qin, F., Reif, T., Sheppard, K., Shokoohi, V., Smick, G.A., Sun, W.L., Stewart, E.A., Fernando, J.T., Tran, N.M., Trejo, T., Vo, N.T., Yan, S.C., Zierten, D.L., Zhao, S., Sachidanandam, R., Trask, B.J., Myers, R.M., and Cox, D.R. (2001) A high-resolution radiation hybrid map of the human genome draft sequence.  Science 291, 1298-1302.