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Randau, L. and Söll, D. (2008) tRNA genes in pieces. EMBO Rep. 9, 623-628. Abstract Yuan, J., Sheppard, K. and Söll, D.L (2008) Amino acid modifications on tRNA. Acta Biochim. Biophys. Sin. 40, 539-553. Abstract RajBhandary, U.L. and Söll, D. (2008) Aminoacyl-tRNAs, the bacterial cell envelope, and antibiotics. Proc. Natl. Acad. Sci. USA 105, 5285-5286. Abstract Randau, L., Schröder, I. and Söll, D. (2008) Life without RNase P. Nature 453, 120-123. Abstract Sheppard, K., Yuan, J., Hohn, M., Jester, B., Devine, K.M. and Söll, D. (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucl. Acids Res. 36, 1813-1825. Abstract Sherrer, R.L., Ho, J. and Söll, D. (2008) Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase. Nucl. Acids Res. 36, 1871-1880. Abstract 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. Abstract Sheppard, K. and Söll, D. (2008) On the evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE. J. Mol. Biol. 377, 831-844. Abstract Hendrickson, E.L., Liu, Y., Rosas-Sandoval, G., Porat, I., Söll, D., Whitman, W.B. and Leigh, J.A. (2008) Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J. Bacteriol. 190, 2198-2205. Abstract Sherrer, R.L., O'Donoghue, P. and Söll, D. (2008) Characterization and evolutionary history of an archaeal kinase involved in Sec-tRNASec formation. Nucl. Acids Res. 36, 1247-1259. Abstract Araiso, Y., Palioura, S., Ishitani, R., Sherrer, R. L., Yuan, J., Oshikane, H., Domae, N., DeFranco, J., Söll, D. and Nureki, O. (2008) Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. Nucl. Acids Res. 36, 1187-1199. Abstract Sheppard, K., Akochy, P-M. and Söll, D. (2008) Assays for transfer RNA-dependent amino acid biosynthesis. Methods 44, 139-145. Abstract
Herring, S., Ambrogelly, A., Gundllapalli, S., O'Donoghue, P., Polycarpo, C.R. and Söll, D. (2007) The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity. FEBS Lett. 581, 3197-3203. Abstract Kavran, J.M., Gundllapalli, S., O'Donoghue, P., Englert, M., Söll, D. and Steitz, T.A. (2007) The structure of pyrrolysyl-tRNA synthetase: an archaeal enzyme for genetic code innovation. Proc. Natl. Acad. Sci. USA 104, 11268-11273. Abstract Herring, S., Ambrogelly, A., Gundllapalli, S., O'Donoghue, P., Polycarpo, C.R., Söll, D. (2007). The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity. FEBS Lett. 581, 3197-3203. Abstract 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-tRNAGln. J. Biol. Chem. 282, 11866-11873. Abstract Helgadóttir, S., Rosas-Sandoval, G., Söll, D. and Graham, D.E. (2007) Biosynthesis of phosphoserine in the Methanococcales. J. Bacteriol. 189, 575-582. Abstract Namgoong, S., Sheppard, K., Sherrer, R.L. and Söll, D. (2007) Co-evolution of the archaeal tRNA-dependent amidotransferase GatCAB with tRNAAsn. FEBS Lett. 581, 309-314. Abstract Herring, S., Ambrogelly, A., Polycarpo, C. R. and Söll, D. (2007) Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase. Nucl. Acids Res. 35, 1270-1278. Abstract Kamtekar, S., Hohn, M.J., Park, H-S., Schnitzbauer, M., Sauerwald, A., Söll, D. and Steitz, T.A. (2007) Toward understanding phosphoseryl-tRNACys formation: The crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 104, 2620-2625. Abstract Ambrogelly, A., Gundllapalli, S., Herring, S., Polycarpo, C., Frauer, C. and Söll, D. (2007) Pyrrolysine is not hardwired for cotranslational insertion at UAG codons. Proc. Natl. Acad. Sci. USA 104, 3141-3146. Abstract Ambrogelly, A., Palioura, S. and Söll, D. (2007) Natural expansion of the genetic code. Nat. Chem. Biol. 3, 29-35. Abstract
Yuan, J., Palioura, S., Salazar, J. C., Su, D., O'Donoghue, P., Hohn, M. J., Cardoso, A. M., Whitman, W. B. and Söll, D. (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. USA 103, 18923-18927. Abstract Hohn, M.J., Park, H-S., O'Donoghue, P., Schnitzbauer, M. and Söll, D. (2006) Emergence of the universal genetic code imprinted in an RNA record. Proc. Natl. Acad. Sci. USA 103, 18095-18100. Abstract Cardoso, A.M., Polycarpo, C., Martins, O.B. and Söll, D. (2006) A non-discriminating aspartyl-tRNA synthetase from Halobacterium salinarum. RNAbiology 3, 110-114. Abstract 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. Abstract Bilokapic, S., Maier, T., Ahel, D., Gruic-Sovulj, I., Söll, D., Weygand-Durasevic, I. and Ban, H. (2006) Structure of the unusual methanogen seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J. 25, 2498-2509. Abstract Charrière, F., Helgadóttir, S., Horn, E.K., Söll, D. and Schneider, A. (2006) Dual targeting of a single tRNATrp requires two different tryptophanyl-tRNA synthetases in Trypanosma brucei. Proc. Natl. Acad. Sci. USA 103, 6847-6852. Abstract Sabina, J. and Söll, D. (2006) The RNA-binding PUA domain of archaeal tRNA-guanine transglycosylase is not required for archaeosine formation. J. Biol. Chem. 281, 6993-7001. Abstract
Ruan, B. and Söll, D. (2005) The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNACys deacylase. J. Biol. Chem. 280, 25887-25891. Abstract Sauerwald, A., Zhu, W., Major, T.A., Roy, H., Palioura, S., Jahn, D., Whitman, W., Yates, J.R., 3rd, Ibba, M. and Söll, D. (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307, 1969-1972. Abstract Feng, L., Yuan, J., Toogood, H., Tumbula-Hansen, D. and Söll, D. (2005) Aspartyl-tRNA synthetase requires a conserved proline in the anticodon-binding loop for tRNAAsn recognition in vivo. J. Biol. Chem. 280, 20638-20641. Abstract Rinehart, J., Krett, B., Rubio, M.A., Alfonzo, J.D. and Söll, D. (2005) Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev. 19, 583-592. Abstract Randau, L., Münch, R., Hohn, M.J., Jahn, D. and Söll, D. (2005) Nanoarchaeum equitans creates functional tRNA from separate genes for their 5'- and 3'-halves. Nature 433, 537-541. Abstract 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. Abstract Ruan, B., Bovee, M.L., Sacher, M., Stathopoulos, C., Poralla, K., Francklyn, C.S. and Söll, D. (2005) A unique hydrophobic cluster near the active site contributes to differences of borrelidin inhibition among threonyl-tRNA synthetases. J. Biol. Chem. 280, 571-577. Abstract
Ambrogelly, A., Kamtekar, S., Sauerwald, A., Ruan, B., Tumbula-Hansen, D., Kennedy, D., Ahel, I. and Söll, D. (2004) Cys-tRNACys formation and cysteine biosynthesis in Methanocaldococcus jannaschii: two faces of the same problem? Cell. Mol. Life Sci. 61, 2437-2445. Abstract Korencic, D., Polycarpo, C., Weygand-Durasevic, I. and Söll (2004) Differential modes of tRNASer recognition in Methanosarcina barkeri. J. Biol. Chem. 279, 48780-48786. Abstract Polycarpo, C., Ambrogelly, A., Bérubé, A., Winbush, S.M., McCloskey, J.A., Crain, P.F., Wood, J.L. and Söll, D. (2004) An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl. Acad. Sci. USA 101, 12450-12454. Abstract Korencic, D., Ahel, I., Schelert, J., Sacher, M., Ruan, B., Stathopoulos, C., Blum, P., Ibba, M. and Söll (2004) A freestanding proofreading domain is required for protein synthesis quality control in archaea. Proc. Natl. Acad. Sci. USA 101, 10260-10265. Abstract Randau, L., Schauer, S., Ambrogelly, A., Salazar, J. C., Moser, J., Sekine, S.-I., Yokoyama, S., Söll, D. and Jahn, D. (2004) Glutamyl-tRNA identity determinants for glutamyl-tRNA reductase. J. Biol. Chem. 279, 34931-34937. Abstract Salazar, J. C., Ambrogelly, A., Crain. P. F., McCloskey, J. A. and Söll, D. (2004). A truncated aminoacyl-tRNA synthetase modifies RNA. Proc. Natl. Acad. Sci. USA. 101, 7536–7541. Abstract Ibba, M. and Söll, D. (2004) Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev. 18, 731-738. Abstract Rinehart, J., Horn, E. K., Wei, D., Söll, D. and Schneider, A. (2004) Non-canonical eukaryotic glutaminyl- and glutamyl-tRNA synthetases form mitochondrial aminoacyl-tRNA in Trypanosoma brucei. J. Biol. Chem. 279, 1161-1166. Abstract Ruan, B., Nakano, H., Tanaka, M., Mills, J.A., DeVito, J.A., Low, K.B., Battista, J.R. and Söll, D. (2004) Cysteinyl-tRNACys formation in Methanocaldococcus jannaschii: the mechanism is still unkown. J. Bacteriol. 186, 8-14. Abstract
Ahel, I., Korencic, D., Ibba, M. and Söll (2003) Trans-editing of mischarged tRNAs. Proc. Natl. Acad. Sci. USA 100, 15422-15427. Abstract Sabina, J., Dover, N., Templeton, L. J., Smulski, D. R., Söll, D. and LaRossa, A. R. (2003) Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K12. J. Bacteriol. 185, 6158-6170. Abstract Salazar, J.C., Ahel, I., Orellana, O., Tumbula-Hansen, D., Krieger, R., Daniels, L. and Söll, D. (2003) Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates. Proc. Natl. Acad. Sci. USA 100, 13863-13868. Abstract Polycarpo, C., Ambrogelly, A. Ruan, B., Tumbula-Hansen, D., Ataide, S. F., Ishitani, R., Yokoyama, S., Nureki, O., Ibba, M. and Söll, D. (2003) Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Mol. Cell 12, 287-294. Abstract Min, B., Kitabatake, M., Polycarpo, C., Pelaschier, J., Raczniak, G., Ruan, B., Kobayashi, H., Namgoong, S. and Söll, D. (2003) Protein synthesis in Escherichia coli with mischarged tRNA. J. Bacteriol. 185, 3524-3526. Abstract Feng, L., Tumbula-Hansen, D., Toogood, H. and Söll, D. (2003) Expanding tRNA recognition of a tRNA synthetase by a single amino acid change. Proc. Natl. Acad. Sci. USA 100, 5676-5681. Abstract Kamtekar, S., Kennedy, W. D., Wang, J., Stathopoulos, C., Söll, D. and Steitz. T. A. (2003) The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases. Proc. Natl. Acad. Sci. USA 100, 1673-1678. Abstract
Rosas-Sandoval, G., Ambrogelly, A., Rinehart, J., Wei, D., Cruz-Vera, L.R., Graham, D.E., Stetter, K.O., Guarneros, G. and Söll, D. (2002) Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. Proc. Natl. Acad. Sci. USA 99, 16707-16712. Abstract Gruic-Sovulj, I., Landeka, I., Söll, D. and Weygand-Durasevic, I. (2002) tRNA-dependent amino acid discrimination by yeast seryl-tRNA synthetase. Eur. J. Biochem. 269, 5271-5279. Abstract Tumbula-Hansen, D., Feng, L., Toogood, H., Stetter, K.O. and Söll, D. (2002) Evolutionary divergence of the archaeal aspartyl-RNA synthetases into discriminating and non-discriminating forms. J. Biol. Chem. 277, 37184-37190. Abstract Korencic, D., Söll, D. and Ambrogelly, A. (2002) A one-step method for in vitro production of tRNA transcripts. Nucleic Acids Res. 30, E105-5. Abstract Ahel, I., Stathopoulos, C., Ambrogelly, A., Sauerwald, A., Toogood, H., Hartsch, T. and Söll, D. (2002) Cysteine activation is an inherent property of prolyl-tRNA synthetases. J. Biol. Chem. 277, 34743-34748. Abstract Ambrogelly, A., Ahel, I., Polycarpo, C., Bunjun-Srihari, S., Krett, B., Jacquin-Becker, C., Köhrer, C., Stathopoulos, C., RajBhandary, U.L. and Söll, D. (2002) Methanocaldococcus jannaschii prolyl-tRNA synthetase charges tRNAPro with cysteine. J. Biol. Chem. 277, 34749-34754. Abstract Kitabatake, M., Ali, K., Demain, A., Sakamoto, K., Yokoyama, S. and Söll, D. (2002) Indolmycin resistance of Streptomyces coelicolor A3(2) by induced expression of one of its two tryptophanyl-tRNA synthetases. J. Biol. Chem. 277, 23882-23887. Abstract Terada, T., Nureki, O., Ishitani, R., Ambrogelly, A., Ibba, M., Söll, D. and Yokoyama, S. (2002) Functional convergence of two lysyl-tRNA synthetases with unrelated topologies. Nat. Struct. Biol. 9, 257-262. Abstract Min, B., Pelaschier, J.T., Graham, D., Tumbula-Hansen, D. and Söll, D. (2002) Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. USA 99, 2678-2683. Abstract Feng, L., Stathopoulos, C., Ahel, I., Mitra, A., Tumbula-Hansen, D., Hartsch, T. and Söll, D. (2002) Aminoacyl-tRNA formation in the hyperthermophile Thermus thermophilus. Extremophiles 6, 167-174. Abstract
Raczniak, G. Becker, H.D., Min, B. and Söll, D. (2001) A single amidotransferase forms asparaginyl-tRNA and glutaminyl-tRNA in Chlamydia trachomatis. J. Biol. Chem. 276, 45862-45867. Abstract Ibba, M., Stathopoulos, C. and Söll, D. (2001) Protein synthesis: Twenty three amino acids and counting. Current Biology 11, R563-R565. Abstract Ibba, M. and Söll, D. (2001) The renaissance of aminoacyl-tRNA synthesis. EMBO Reports 2, 382-387. Abstract McCormac, A.C., Fischer, A., Kumar, A.M., Söll, D. and Terry, M.J. (2001) Regulation of HEMA1 expression by phytochrome and a plastid signal during de-etiolation in Arabidopsis thaliana. Plant J. 25, 549-562. Abstract Raczniak, G., Ibba, M. and Söll, D. (2001) Genomics-based identification of targets in pathogenic bacteria for potential therapeutic and diagnostic use. Toxicology 160, 181-189. Abstract Stathopoulos, C., Jacquin-Becker, C., Becker, H.D., Li, T., Ambrogelly, A. Longman, R. and Söll, D. (2001) Methanococcus jannaschii prolyl-cysteinyl-tRNA synthetase possesses overlapping amino acid binding sites. Biochemistry 40, 46-52. Abstract Yu, S.L., Lei, H.Y., Chang, W.Z., Söll, D. and Hong, G.F. (2001) Protein phosphatase 2A: Identification in Oryza sativa of the gene encoding the regulatory A subunit. Plant Mol. Biol. 45, 107-112. Abstract Salazar, J.C., Zuñiga, R., Lefimil, C., Söll, D. and Orellana, O. (2001) Conserved amino acids near the carboxy terminus of bacterial tyrosyl-tRNA synthetase are involved in tRNA and Tyr-AMP binding. FEBS Lett. 491, 257-260. Abstract
Hamano-Takaku, F., Iwama, T., Saito-Yano, S., Takaku, K., Monden, Y., Kitabatake, M., Söll, D. and Nishimura, S. (2000) A mutant Escherichia coli tyrosyl-tRNA synthetase utilizes the unnatural amino acid azatyrosine more efficiently than tyrosine. J. Biol. Chem. 275, 40324-40328. Abstract Bunjun, S., Stathopoulos, C., Graham, D., Min, B., Kitabatake, M., Wang, A.L., Wang, C.C., Vivarès, C.P., Weiss, L.M. and Söll, D. (2000) A dual-specificity aminoacyl-tRNA synthetase in the deep-rooted eukaryote Giardia lamblia. Proc. Natl. Acad. Sci. USA 97, 12997-13002. Abstract Prætorius-Ibba, M., Stange-Thomann, N., Kitabatake, M., Ali, K., Söll, I., Carter, C., Ibba, M. and Söll, D. (2000) Ancient adaptation of the active site of tryptophanyl-tRNA synthetase for tryptophan binding. Biochemistry 39, 13136-13143. Abstract Ibba, M. and Söll, D. (2000) Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69, 617-650. Abstract Tumbula, D.L., Becker, H.D., Chang, W-Z. and Söll, D. (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature 407, 106-110. Abstract Ibba, M., Becker, H.D., Stathopoulos, C. Tumbula, D.L. and Söll, D. (2000) The Adaptor Hypothesis revisited. Trends Biochem. Sci. 25, 311-316. Abstract Becker, H.D., Min, B., Jacobi, C., Raczniak, G., Pelaschier, J., Roy, H., Klein, S., Kern, D. and Söll, D . (2000) The heterotrimeric Thermus thermophilus Asp-tRNAAsn amidotransferase can also generate Gln-tRNAGln FEBS Lett. 476, 140-144. Abstract Woese, C.R., Olsen, G., Ibba, M. and Söll, D. (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64, 202-236. Abstract Stathopoulos, C., Li, T., Longman, R., Vothknecht, U.C., Becker, H., Ibba, M. and Söll, D. (2000) One polypeptide with two aminoacyl-tRNA synthetase activities. Science 287, 479-482. Abstract Kitabatake, M., So, M.W., Tumbula, D.L. and Söll, D. (2000) Cysteine biosynthesis in the archaeon Methanosarcina barkeri encoded by acquired bacterial genes? J. Bacteriol. 182, 143-145. Abstract Kumar, A.M. and Söll, D. (2000) Antisense HEMA1 RNA expression inhibits heme and chlorophyll biosynthesis in Arabidopsis. Plant Physiol. 122, 49-56. Abstract |
