Center for RNA Biology Publications

Publications by Michael Ibba since 2000

• Yu Zeng, Hervé Roy, Preeti B Patil, Michael Ibba, and Shawn Chen
  "Characterization of two seryl-tRNA synthetases in albomycin-producing Streptomyces sp. strain ATCC 700974."
  Antimicrob. Agents Chemother. 53, 4619-27 (2009).

• Hervé Roy and Michael Ibba
  "Broad range amino acid specificity of RNA-dependent lipid remodeling by multiple peptide resistance factors."
  J. Biol. Chem. 284, 29677-83 (2009).

• Srujana S Yadavalli, Liron Klipcan, Alexey Zozulya, Rajat Banerjee, Dmitri Svergun, Mark Safro, and Michael Ibba
  "Large-scale movement of functional domains facilitates aminoacylation by human mitochondrial phenylalanyl-tRNA synthetase."
  FEBS Lett. 583, 3204-8 (2009).

• Jiqiang Ling, Byung Ran So, Srujana S Yadavalli, Hervé Roy, Shinichiro Shoji, Kurt Fredrick, Karin Musier-Forsyth, and Michael Ibba
  "Resampling and editing of mischarged tRNA prior to translation elongation."
  Mol. Cell 33, 654-60 (2009).

• Hervé Roy, Kiley Dare, and Michael Ibba
  "Adaptation of the bacterial membrane to changing environments using aminoacylated phospholipids."
  Mol. Microbiol. 71, 547-550 (2009).

• Kurt Fredrick and Michael Ibba
  "Protein synthesis Errors rectified in retrospect."
  Nature 457, 157-8 (2009).

• Sandro F Ataide, Theresa E Rogers, and Michael Ibba
  "The CCA anticodon specifies separate functions inside and outside translation in Bacillus cereus."
  RNA Biol 6, 479-87 (2009).

• Jiqiang Ling, Noah Reynolds, and Michael Ibba
  "Aminoacyl-tRNA synthesis and translational quality control."
  Annu. Rev. Microbiol. 63, 61-78 (2009).

• Srujana S Yadavalli, Karin Musier-Forsyth, and Michael Ibba
  "The return of pretransfer editing in protein synthesis."
  Proc. Natl. Acad. Sci. U.S.A. 105, 19031-2 (2008).

• Corinne D Hausmann and Michael Ibba
  "Aminoacyl-tRNA synthetase complexes molecular multitasking revealed."
  FEMS Microbiol. Rev. 32, 705-21 (2008).

• Corinne D Hausmann and Michael Ibba
  "Structural and functional mapping of the archaeal multi-aminoacyl-tRNA synthetase complex."
  FEBS Lett. 582, 2178-82 (2008).

• Hervé Roy and Michael Ibba
  "RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors."
  Proc. Natl. Acad. Sci. U.S.A. 105, 4667-72 (2008).

• Hervé Roy and Michael Ibba
  "Monitoring Lys-tRNALys phosphatidylglycerol transferase activity."
  Methods 44, 164-9 (2008).

• Michael Ibba
  "Methods for studying aminoacyl-tRNA."
  Methods 44, 73 (2008).

• Sandro F Ataide, Sharnise N Wilson, Sandy Dang, Theresa E Rogers, Bappaditya Roy, Rajat Banerjee, Tina M Henkin, and Michael Ibba
  "Mechanisms of resistance to an amino acid antibiotic that targets translation."
  ACS Chem. Biol. 2, 819-27 (2007).

• Jiqiang Ling, Srujana S Yadavalli, and Michael Ibba
  "Phenylalanyl-tRNA synthetase editing defects result in efficient mistranslation of phenylalanine codons as tyrosine."
  RNA 13, 1881-6 (2007).

• Jeffrey D Levengood, Hervé Roy, Ryuichiro Ishitani, Dieter Söll, Osamu Nureki, and Michael Ibba
  "Anticodon recognition and discrimination by the alpha-helix cage domain of class I lysyl-tRNA synthetase."
  Biochemistry 46, 11033-8 (2007).

• Jiqiang Ling, Hervé Roy, Daoming Qin, Mary Anne T Rubio, Juan D Alfonzo, Kurt Fredrick, and Michael Ibba
  "Pathogenic mechanism of a human mitochondrial tRNAPhe mutation associated with myoclonic epilepsy with ragged red fibers syndrome."
  Proc. Natl. Acad. Sci. U.S.A. 104, 15299-304 (2007).

• Vlatka Godinic, Marko Mocibob, Sanda Rocak, Michael Ibba, and Ivana Weygand-Durasevic
  "Peroxin Pex21p interacts with the C-terminal noncatalytic domain of yeast seryl-tRNA synthetase and forms a specific ternary complex with tRNASer."
  FEBS J. 274, 2788-99 (2007).

• Corinne D Hausmann, Jiqiang Ling, and Michael Ibba
  "The unnatural culture of amino acids."
  Nat. Methods 4, 205-6 (2007).

• Mette Praetorius-Ibba, Corinne D Hausmann, Molly Paras, Theresa E Rogers, and Michael Ibba
  "Functional association between three archaeal aminoacyl-tRNA synthetases."
  J. Biol. Chem. 282, 3680-7 (2007).

• Jiqiang Ling, Hervé Roy, and Michael Ibba
  "Mechanism of tRNA-dependent editing in translational quality control."
  Proc. Natl. Acad. Sci. U.S.A. 104, 72-7 (2007).

• Corinne D Hausmann, Mette Praetorius-Ibba, and Michael Ibba
  "An aminoacyl-tRNA synthetaseelongation factor complex for substrate channeling in archaeal translation."
  Nucleic Acids Res. 35, 6094-102 (2007).

• Hervé Roy and Michael Ibba
  "Molecular biology sticky end in protein synthesis."
  Nature 443, 41-2 (2006).

• Hervé Roy and Michael Ibba
  "Phenylalanyl-tRNA synthetase contains a dispensable RNA-binding domain that contributes to the editing of noncognate aminoacyl-tRNA."
  Biochemistry 45, 9156-62 (2006).

• Anastasia Metlitskaya, Teymur Kazakov, Aigar Kommer, Olga Pavlova, Mette Praetorius-Ibba, Michael Ibba, Igor Krasheninnikov, Vyacheslav Kolb, Inessa Khmel, and Konstantin Severinov
  "Aspartyl-tRNA synthetase is the target of peptide nucleotide antibiotic Microcin C."
  J. Biol. Chem. 281, 18033-42 (2006).

• Sandro F Ataide and Michael Ibba
  "Small molecules big players in the evolution of protein synthesis."
  ACS Chem. Biol. 1, 285-97 (2006).

• Shiming Wang, Mette Praetorius-Ibba, Sandro F Ataide, Hervé Roy, and Michael Ibba
  "Discrimination of cognate and noncognate substrates at the active site of class I lysyl-tRNA synthetase."
  Biochemistry 45, 3646-52 (2006).

• Mary Anne T Rubio, Frank L Ragone, Kirk W Gaston, Michael Ibba, and Juan D Alfonzo
  "C to U editing stimulates A to I editing in the anticodon loop of a cytoplasmic threonyl tRNA in Trypanosoma brucei."
  J. Biol. Chem. 281, 115-20 (2006).

• Hervé Roy, Jiqiang Ling, Juan Alfonzo, and Michael Ibba
  "Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase."
  J. Biol. Chem. 280, 38186-92 (2005).

• Sandro F Ataide, Brian C Jester, Kevin M Devine, and Michael Ibba
  "Stationary-phase expression and aminoacylation of a transfer-RNA-like small RNA."
  EMBO Rep. 6, 742-7 (2005).

• Mette Praetorius-Ibba, Theresa E Rogers, Rachel Samson, Zvi Kelman, and Michael Ibba
  "Association between Archaeal prolyl- and leucyl-tRNA synthetases enhances tRNAPro aminoacylation."
  J. Biol. Chem. 280, 26099-104 (2005).

• Alexandre Ambrogelly, Magali Frugier, Michael Ibba, Dieter Söll, and Richard Giegé
  "Transfer RNA recognition by class I lysyl-tRNA synthetase from the Lyme disease pathogen Borrelia burgdorferi."
  FEBS Lett. 579, 2629-34 (2005).

• Anselm Sauerwald, Wenhong Zhu, Tiffany A Major, Hervé Roy, Sotiria Palioura, Dieter Jahn, William B Whitman, John R Yates, Michael Ibba, and Dieter Söll
  "RNA-dependent cysteine biosynthesis in archaea."
  Science 307, 1969-72 (2005).

• Hervé Roy, Jiqiang Ling, Michael Irnov, and Michael Ibba
  "Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase."
  EMBO J. 23, 4639-48 (2004).

• Sandro F Ataide and Michael Ibba
  "Discrimination of cognate and noncognate substrates at the active site of class II lysyl-tRNA synthetase."
  Biochemistry 43, 11836-41 (2004).

• Dragana Korencic, Ivan Ahel, James Schelert, Meik Sacher, Benfang Ruan, Constantinos Stathopoulos, Paul Blum, Michael Ibba, and Dieter Söll
  "A freestanding proofreading domain is required for protein synthesis quality control in Archaea."
  Proc. Natl. Acad. Sci. U.S.A. 101, 10260-5 (2004).

• Michael Ibba and Christopher Francklyn
  "Turning tRNA upside down When aminoacylation is not a prerequisite to protein synthesis."
  Proc. Natl. Acad. Sci. U.S.A. 101, 7493-4 (2004).

• Thomas Bentin, Ramin Hamzavi, Johan Salomonsson, Hervé Roy, Michael Ibba, and Peter E Nielsen
  "Photoreactive bicyclic amino acids as substrates for mutant Escherichia coli phenylalanyl-tRNA synthetases."
  J. Biol. Chem. 279, 19839-45 (2004).

• Jeffrey Levengood, Sandro F Ataide, Hervé Roy, and Michael Ibba
  "Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases."
  J. Biol. Chem. 279, 17707-14 (2004).

• Michael Ibba and Dieter Söll
  "Aminoacyl-tRNAs setting the limits of the genetic code."
  Genes Dev. 18, 731-8 (2004).

• Ivan Ahel, Dragana Korencic, Michael Ibba, and Dieter Söll
  "Trans-editing of mischarged tRNAs."
  Proc. Natl. Acad. Sci. U.S.A. 100, 15422-7 (2003).

• Brian C Jester, Jeffrey D Levengood, Hervé Roy, Michael Ibba, and Kevin M Devine
  "Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code."
  Proc. Natl. Acad. Sci. U.S.A. 100, 14351-6 (2003).

• Carla Polycarpo, Alexandre Ambrogelly, Benfang Ruan, Debra Tumbula-Hansen, Sandro F Ataide, Ryuichiro Ishitani, Shigeyuki Yokoyama, Osamu Nureki, Michael Ibba, and Dieter Söll
  "Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases."
  Mol. Cell 12, 287-94 (2003).

• Mette Praetorius-Ibba and Michael Ibba
  "Aminoacyl-tRNA synthesis in archaea different but not unique."
  Mol. Microbiol. 48, 631-7 (2003).

• Alexandre Ambrogelly, Dragana Korencic, and Michael Ibba
  "Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer."
  J. Bacteriol. 184, 4594-600 (2002).

• Michael Ibba and Dieter Söll
  "Genetic code introducing pyrrolysine."
  Curr. Biol. 12, R464-6 (2002).

• Takaho Terada, Osamu Nureki, Ryuichiro Ishitani, Alexandre Ambrogelly, Michael Ibba, Dieter Söll, and Shigeyuki Yokoyama
  "Functional convergence of two lysyl-tRNA synthetases with unrelated topologies."
  Nat. Struct. Biol. 9, 257-62 (2002).

• J A McCloskey, D E Graham, S Zhou, P F Crain, M Ibba, J Konisky, D Söll, and G J Olsen
  "Post-transcriptional modification in archaeal tRNAs identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales."
  Nucleic Acids Res. 29, 4699-706 (2001).

• M Ibba
  "Protein synthesis. Discriminating right from wrong."
  Science 294, 70-1 (2001).

• M Ibba, C Stathopoulos, and D Söll
  "Protein synthesis twenty three amino acids and counting."
  Curr. Biol. 11, R563-5 (2001).

• N Mejlhede, P E Nielsen, and M Ibba
  "Adding new meanings to the genetic code."
  Nat. Biotechnol. 19, 532-3 (2001).

• M Ibba and D Söll
  "The renaissance of aminoacyl-tRNA synthesis."
  EMBO Rep. 2, 382-7 (2001).

• D Söll, H D Becker, P Plateau, S Blanquet, and M Ibba
  "Context-dependent anticodon recognition by class I lysyl-tRNA synthetases."
  Proc. Natl. Acad. Sci. U.S.A. 97, 14224-8 (2000).

• M Praetorius-Ibba, N Stange-Thomann, M Kitabatake, K Ali, I Söll, C W Carter, M Ibba, and D Söll
  "Ancient adaptation of the active site of tryptophanyl-tRNA synthetase for tryptophan binding."
  Biochemistry 39, 13136-43 (2000).

• M Ibba, H D Becker, C Stathopoulos, D L Tumbula, and D Söll
  "The adaptor hypothesis revisited."
  Trends Biochem. Sci. 25, 311-6 (2000).

• C R Woese, G J Olsen, M Ibba, and D Söll
  "Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process."
  Microbiol. Mol. Biol. Rev. 64, 202-36 (2000).

• C Stathopoulos, T Li, R Longman, U C Vothknecht, H D Becker, M Ibba, and D Söll
  "One polypeptide with two aminoacyl-tRNA synthetase activities."
  Science 287, 479-82 (2000).

• M Ibba and D Soll
  "Aminoacyl-tRNA synthesis."
  Annu. Rev. Biochem. 69, 617-50 (2000).