INTRODUCTION TOPICS LIST:

INTRODUCTION

Author: Loredano Pollegioni
(Universitą degli Studi dell'Insubria)


CHIRAL PROOFREADING DURING TRANSLATION OF THE GENETIC CODE

Author: Rajan Sankaranarayanan
(CSIR-CCMB - Hyderabad)

Chirality from the greek word for "hand" was introduced by Lord Kelvin (1904). Chirality and stereoisomerism configuration are distinct and should not be combined. The two forms are non-superimposable mirror images of each other (definition from Kurt Mislow, 1999).

The two forms are called enantiomers or optical isomers because they rotate plane-polarized light either to the right or to the left. The enantiomers show different adsorbtion of circularly polarized UV light. Nearby all biological polymers are homochiral to function.

The L and D convention refers to the optical activity of the isomer of glyceraldehyde (D-glyceraldehyde is dextrorotatory and L-glyceraldehyde is levorotatory) from which the amino acid can be synthesized.
The left and right handed forms have identical free energy: for the reaction of changing left-handed to right-handed amino acid (L to R), or the reverse, ΔG = 0, so K = 1 (or close).

The absolute stereochemistry is indicated by the (S) and (R) designators (IUPAC nomenclature). A mixture containing 50:50 of L- and R-enantiomers is called a racemate or a racemic mixture.
All amino acids (except glycine) are asymmetric and dissymetric.


The long story of this terminology:

Jons Jakob Berzelius (1779-1884) «isomer» and «isomerism»
Aleksandr Butlerov (1828-1886) «chemical structure»
Louis Pasteur (1848) «dissymetric and dissymetry»
(even if he was not the first to use these terms!)
Jacobus Henricus van’t Hoff (1874) «asymmetric carbon atom»
Viktor Meyer (1884-1894) «stereochemistry»
Aemilius Wunderlich (1886) «configuration»
William Thompson (1894) «chiral» and «chirality»
Kurt Mislow (1962)
publicly introduced «chirality» term
into a chemistry paper (JACS)

At the early of 1800, the phenomenon of natural optical activity was first observed by the French scientists Arago and Biot.
Shortly after, Fresnel developed a theory of optical rotation based on the differential refraction of right- and left-circularized polarized light; the entantiomers show different adsorbtion of circulary polarized UV light.
Louis Pasteur in 1848 was the first person on history to resolve a racemate: he used tweezers to separate the left and right-handed crystals of sodium  ammonium tartrate (PTA). The sodium ammonium salt of PTA cristallyzed as a molecular mixture of two distinct crystal types: they showed optical activity equal in magnitude but opposite in direction.
Pasteur was fortunate: only two of the 19 chiral amino acids self-resolve in crystalline form and only below 23 °C (in the 19st century laboratories were not well heated!)
He continued his studies on molecular and crystal chirality for another 10 years.

CHIRAL PROOFREADING DURING TRANSLATION OF THE GENETIC CODE Go to the TOPICS LIST

Proteins are essentially homochiral in nature since they are composed of only L-amino acids (besides glycine which is achiral). However, the cellular pool consists of significant amounts of various free D-amino acids which do have important physiological roles; for instance, D-serine and D-aspartate act as neurotransmitters in neurons (Dunlop et al., 1986; Hashimoto et al., 1992). It is necessary to exclude D-amino acids from the translational machinery because heterochiral polypeptides cannot take proper 3D form due to geometric constraints and will therefore undergo spontaneous misfolding and degradation. Multiple steps during translation act as cellular checkpoints to prevent infiltration of D-amino acids in proteins. Nevertheless, some of the aminoacyl-tRNA synthetases (aaRSs)—which carry out the first step of translation by coupling amino acids to their cognate tRNAs—are not adequately enantioselective and thus sometimes mischarge D-amino acids on tRNAs. An enzyme, named D-tyrosyl RNA deacylase (DTD), was discovered in 1967 by Calendar and Berg which could remove D-tyrosine and D-phenylalanine mischarged on tRNATyr and tRNAPhe, respectively (Calendar and Berg, 1967). Later biochemical characterization showed that DTD can act on multiple D-aminoacyl-tRNAs (Soutourina et al., 1999), and the enzyme was rechristened D-aminoacyl-tRNA deacylase (the abbreviation DTD was, however, retained). Hence, DTD was implicated in perpetuating homochirality in proteins, and its activity on D-aminoacyl-tRNAs was referred to as “chiral proofreading” (Ahmad et al., 2013). Structural studies deciphered the underlying mechanistic basis of DTD’s enantioselectivity, wherein an invariant cross-subunit Gly-cisPro motif was found to be responsible for the same (Fig. 1) (Ahmad et al., 2013). Further investigations demonstrated that DTD’s chiral proofreading site uses only L-chiral rejection and not D-chiral selection as the design principle to ensure substrate specificity (Fig. 1).



Figure 1. Mechanistic basis of DTD’s enantioselectivity. DTD uses an invariant cross-subunit Gly-cisPro motif to ensure substrate specificity through L-chiral rejection.

This naturally led to the finding that DTD has significant activity on the achiral cognate substrate Gly-tRNAGly, thereby engendering “glycine misediting” paradox. It was found that elongation factor thermo unstable (EF-Tu), which delivers aminoacyl-tRNAs to ribosome, confers protection on the achiral substrate against DTD and therefore resolves the paradox (Fig. 2). However, DTD’s concentration in the cell must be tightly regulated because higher DTD levels can overcome the protection given to Gly-tRNAGly by EF-Tu, thereby causing cellular toxicity (Fig. 2) (Routh et al., 2016). Another interesting aspect about DTD is that the side chains in the active site are dispensable; DTD uses main chain atoms for substrate selectivity and the 2′-OH of 3′-terminal A76 of tRNA for catalysis (Routh et al., 2016). DTD is thus a primordial RNA-based catalyst in which the protein acts as a scaffold to provide an environment conducive for the aminoacyl-tRNA to perform (substrate-assisted) catalysis.


Figure 2. Model for “glycine misediting” paradox and its resolution. DTD efficiently decouples D-aminoacyl-tRNAs, but does not act on the L-counterparts. In the absence of EF-Tu, DTD deacylates (hydrolyzes) Gly-tRNAGly, thereby creating “glycine misediting” paradox. EF-Tu is able to resolve this problem by conferring protection on the achiral substrate. However, if DTD levels become high, it is able to relieve this protection, thus causing cellular toxicity.

References for "Introduction":

  • Barron L.D. "Chirality of Life" (2008) Space Sci. Rev. 135: 187 - 201
  • Cronin J., Reisse J. "Chirality and the Origin of Homochirality" (2005) in Lectures in Astrobiology. Pages 73 - 114
  • Gal J. "Louis Pasteur, Language, and MolecularChirality. I. Background and Dissymetry" (2011). Chirality 23: 1 - 16
  • Gal J. "Carl Friedrich Naumann and the Introduction of Enantio Terminology: A Review and Analysis on the 150th Anniversary" (2007). Chirality 19: 89 - 98
  • Kadyshevich E.A., Ostrovskii V.E. "Natural Mechanism of Origination and Conservation of Monochirality of Amino Acids" - Chirality (2015)

 

References for "Chiral proofreading during translation of the genetic code":

  • Ahmad S, Routh SB, Kamarthapu V, Chalissery J, Muthukumar S, Hussain T, Kruparani SP, Deshmukh MV, Sankaranarayanan R. Mechanism of chiral proofreading during translation of the genetic code. eLife. 2013 Dec 3;2:01519. doi: 10.7554/eLife.01519.
  • Calendar R, Berg P. D-Tyrosyl RNA: formation, hydrolysis and utilization for protein synthesis. J Mol Biol. 1967 May 28;26(1):39–54. doi: 10.1016/0022-2836(67)90259-8.
  • Dunlop DS, Neidle A, McHale D, Dunlop DM, Lajtha A. The presence of free D-aspartic acid in rodents and man. Biochem Biophys Res Commun. 1986 Nov 26;141(1):27–32. doi: 10.1016/S0006-291X(86)80329-1.
  • Hashimoto A, Nishikawa T, Hayashi T, Fujii N, Harada K, Oka T, Takahashi K. The presence of D-serine in rat brain. FEBS Lett. 1992 Jan 13;296(1):33–6. doi: 10.1016/0014-5793(92)80397-Y.
  • Routh SB, Pawar KI, Ahmad S, Singh S, Suma K, Kumar M, Kuncha SK, Yadav K, Kruparani SP, Sankaranarayanan R. Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase. PLoS Biol. 2016 May 25;14(5):e1002465. doi: 10.1371/journal.pbio.1002465.
  • Soutourina J, Plateau P, Delort F, Peirotes A, Blanquet S. Functional characterization of the D-Tyr-tRNATyr deacylase from Escherichia coli. J Biol Chem. 1999 Jul 2;274(27):19109–14. doi: 10.1074/jbc.274.27.19109.