Search Google Appliance


Browse more profiles
Dr. John J. Perona
Dr. John J. Perona

Professor of Biochemistry and Biophysics

Ph.D. | Yale University, 1990

Post-Doctoral Research Fellow 1990-1994 | University of California, San Francisco


Research Interests

Our laboratory studies protein synthesis in all three domains of life. Studies encompass detailed mechanistic investigations by enzymology and Xray crystallography, bioinformatics-aided gene discovery, and molecular genetics approaches in methanogenic Archaea. Our laboratory includes equilibrium and stopped-flow fluorescence instruments, a rapid chemical quench kinetics apparatus, and automated robotics for high-throughput crystallization. An OHSU affiliation enables access to Xray diffraction equipment and to a high-energy synchrotron beamline.

Mechanisms by which glutamine and glutamate are incorporated into protein are addressed by intensive protein engineering studies of the model enzyme Escherichia coli glutaminyl-tRNA synthetase (GlnRS). We study a novel role for tRNA in assisting the protein active site to select against noncognate amino acids. This project includes detailed mapping of the intramolecular communication pathways connecting the amino acid and tRNA binding sites. Other enzymes studied include yeast cytoplasmic and mitochondrial GluRS/GlnRS, and the human GlnRS and GluRS. In eukaryotic organelles and all Archaea, glutamine is incorporated by a two-step pathway involving a nondiscriminating GluRS that misacylates tRNA(Gln) with Glu. We seek to uncover the molecular determinants that functionally differentiate GluRS enzymes into those that are highly specific for one class of tRNA isoacceptors and those that are not.

Modification of tRNA is essential to its folding, stability and function. We have recently developed a new approach to monitoring tRNA folding via aminoacylation kinetics, and have used it to demonstrate that the set of modifications in a bacterial tRNA function to speed folding but do not affect the folding equilibrium. Use of this assay to monitor modification-dependent folding of unusual organellar tRNAs is now possible.

The specificity of protein synthesis is also maintained by hydrolytic editing mechanisms: some tRNA synthetases misacylate closely related amino acids to their cognate tRNAs, but are capable of hydrolyzing the misacylated tRNA in either the synthetic active site or in a separate, spatially distinct post-transfer editing active site. Structure-function relationships in these more complex enzymes, including those specific for isoleucine, valine, and leucine, are under investigation in collaboration with the laboratory of Ita Gruic-Sovulj in Zagreb, Croatia. Particular emphasis is placed on understanding the key conformational changes involved in transitioning the RNP complex from synthetic to editing modes.

Methanogenic archaea and the closely related Archaeoglobi are unique in possessing the enzyme phosphoseryl-tRNA synthetase (SepRS), which aminoacylates tRNA(Cys) with phosphoserine (Sep). Sep-tRNA(Cys) is then converted to Cys-tRNA(Cys) by the sulfur-transfer enzyme SepCysS. Using bioinformatics and molecular genetics approaches, we are addressing the general question of why this ancient two-step pathway has been retained only in methanogens. Another question relates to why some methanogens also possess the much more common CysRS enzyme, so that cysteine incorporation in these organism proceeds by redundant pathways. tRNAs specific for cysteine have also proliferated in some methanogens, and their aminoacylation, by SepRS or CysRS, depends on anticodon-specific tRNA methylation. This project encompasses characterization of novel tRNA modifying enzymes and of companion enzymes to SepCysS, which likely requires persulfidation at a conserved cysteine residue for optimal function. The role of methanogens in processing most methane in the biosphere suggests some significance to the phenomena of greenhouse warming.

Representative Publications

  • Hancock S, Hiller DA, Perona JJ & Jen-Jacobson L. The energetic contribution of induced electrostatic asymmetry to DNA bending by a site-specific protein. J. Mol. Biol., 406, 285-312 (2011).
  • Rodríguez-Hernández A & Perona JJ. Heat maps for intramolecular communication in an RNP enzyme encoding glutamine. Structure, 19, 386-396 (2011).
  • Menezes S, Kirk G, Krivos KL, Apolinario EE, Reich NO, Sowers K, Limbach P & Perona JJ. Enzymatic synthesis of tRNA m2G6 in thermophilic methanogens by the novel tRNA methyltransferase Trm14. Nucleic Acids Research, Jun 21. PMID:21693558 (2011).
  • Bhaskaran H & Perona JJ. Two-step aminoacylation of tRNA without channeling Archaea. J. Mol. Biol., 411, 854-869 (2011).
  • Dulic M, Cvetesic N, Perona JJ & Gruic-Sovulj I. Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J. Biol.Chem., 285, 23799-23809 (2010).
  • Rodríguez-Hernández A, Bhaskaran H, Hadd A & Perona JJ. Synthesis of Glu-tRNAGln by natural and engineered aminoacyl-tRNA synthetases. Biochemistry, 49, 6727-6736 (2010).
  • Christian T, Lahoud G, Liu C, Hoffmann K, Perona JJ & Hou YM. Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. RNA, 16, 2484-2492 (2010).
  • Hauenstein S, Hou Y-M & Perona JJ. The homotetrameric phosphoseryl-tRNA synthetase from Methanosarcina mazei exhibits half-of-the-sites activity. J. Biol. Chem., 283, 21997-22006 (2008).
  • Hauenstein S & Perona JJ. Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei. J. Biol. Chem., 283, 22007-22017 (2008).