Optimization of DTD-tRNA code and mito-tRNA(Gly) discriminator base is important for emergence of mitochondria.

D-aminoacyl-tRNA deacylase (DTD) acts on achiral glycine, in addition to D-amino acids, attached to tRNA. We have recently shown that this activity enables DTD to clear non-cognate Gly-tRNAAla with 1000-fold higher efficiency than its activity on Gly-tRNAGly, indicating tRNA-based modulation of DTD (Pawar et al., 2017). Here, we show that tRNA’s discriminator base predominantly accounts for this activity difference and is the key to selection by DTD. Accordingly, the uracil discriminator base, serving as a negative determinant, prevents Gly-tRNAGly misediting by DTD and this protection is augmented by EF-Tu. Intriguingly, eukaryotic DTD has inverted discriminator base specificity and uses only G3•U70 for tRNAGly/Ala discrimination. Moreover, DTD prevents alanine-to-glycine misincorporation in proteins rather than only recycling mischarged tRNAAla. Overall, the study reveals the unique co-evolution of DTD and discriminator base, and suggests DTD’s strong selection pressure on bacterial tRNAGlys to retain a pyrimidine discriminator code.

Homochirality of the cellular proteome is attributed to the L-chiral bias of the translation apparatus. The chiral specificity of enzymes was elegantly explained using the ‘four-location’ model by Koshland two decades ago. In accordance with the model, it was envisaged and noted that some aminoacyl-tRNA synthetases (aaRS) that charge larger amino acids are porous to D-amino acids. However, a recent study showed that alanyl-tRNA synthetase (AlaRS) can mischarge D-alanine and that its editing domain, but not the universally present D-aminoacyl-tRNA deacylase (DTD), is responsible for correcting the chirality-based error. Here, using in vitro and in vivo data coupled with structural analysis, we show that AlaRS catalytic site is a strict D-chiral rejection system and therefore does not activate D-alanine. It obviates the need for AlaRS editing domain to be active against D-Ala-tRNAAla and we show that it is indeed the case as it only corrects L-serine and glycine mischarging. We further provide direct biochemical evidence showing activity of DTD on smaller D-aa-tRNAs that corroborates with the L-chiral rejection mode of action proposed earlier. Overall, while removing anomalies in the fundamental recognition mechanisms, the current study further substantiates how chiral fidelity is perpetuated during protein biosynthesis.

In this paper, we construct a model with the help of modular symmetry in the framework of minimal inverse seesaw [ISS(2,3)]. We have used Γ(3) modular group which is isomorphic to non-Abelian discrete symmetry group A 4 . In this group there are three Yukawa modular forms of weight 2. Through this model, we study neutrino masses and mixing for both normal and inverted hierarchy. Use of modular symmetry reduces the need for extra flavons and their specific VEV alignments, as such, minimality of the model is maintained to a great extent. Along with A 4 symmetry group, we have used Z 3 to restrict certain interaction terms in the Lagrangian. Further we calculate the effective mass to address the phenomena of neutrinoless double-beta decay (0νββ).The values of effective mass is found to lie within the bound (m ef f < 0.165 eV) as predicted by different 0νββ experiments.

10D-aminoacyl-tRNA deacylase (DTD) acts on achiral glycine, in addition to D-amino acids, 11 attached to tRNA. We have recently shown that this activity enables DTD to clear non-cognate 12 Gly-tRNA Ala with 1000-fold higher efficiency than its activity on Gly-tRNA Gly , indicating 13 tRNA-based modulation of DTD (Pawar et al., 2017). Here, we show that tRNA's 14 discriminator base predominantly accounts for this activity difference and is the key to 15 selection by DTD. Accordingly, the uracil discriminator base, serving as a negative 16 determinant, prevents Gly-tRNA Gly misediting by DTD and this protection is augmented by 17 EF-Tu. Intriguingly, eukaryotic DTD has inverted discriminator base specificity and uses only 18 G3•U70 for tRNA Gly/Ala discrimination. Moreover, DTD prevents alanine-to-glycine 19 misincorporation in proteins rather than only recycling mischarged tRNA Ala . Overall, the study 20 reveals the unique co-evolution of DTD and discriminator base, "reciprocally" in Bacteria and 21 Eukarya, and suggests DTD's strong selection pressure on bacterial tRNA Gly s to retain a 22 pyrimidine discriminator code. 23 24 Quality control during translation of the genetic code involves multiple stages and a multitude 25 of proofreading factors (Guo and Schimmel, 2012; Ibba and Söll, 2000; Ogle and 26 Ramakrishnan, 2005). A compromise in editing leads to serious pathologies including 27 neurodegeneration in mouse, and even cell death (Bacher et al., 2005; Bullwinkle et al., 2014; 28 Karkhanis et al., 2007; Korencic et al., 2004; Lee et al., 2006; Liu et al., 2014; Lu et al., 29 2014; Moghal et al., 2016; Nangle et al., 2002; Roy et al., 2004). Among these proofreading 30 factors, D-aminoacyl-tRNA deacylase (DTD) is the one that specifically decouples wrongly 31 acylated D-amino acids from tRNAs (Calendar and Berg, 1967; Soutourina et al., 1999, 32 2000). Our studies have shown that DTD is an RNA-based catalyst that uses an invariant Gly-33 cisPro motif as a "chiral selectivity filter" to achieve substrate chiral specificity only through 34 rejection of L-amino acid from the active site, thereby leading to Gly-tRNA Gly misediting 35 (Ahmad et al., 2013; Routh et al., 2016; Routh and Sankaranarayanan, 2017). Recently, 36we have also shown that DTD's activity on achiral glycine helps in clearing Gly-tRNA Ala , a 37 misaminoacylation product of alanyl-tRNA synthetase (AlaRS), thus resolving a long-standing 38 question in translational quality control (Pawar et al., 2017). 39 As DTD acts on multiple tRNAs charged with D-amino acids or glycine, tRNA's role 40 in modulating DTD's activity was previously thought to be inconsequential (Calendar and 41 Berg, 1967). However, our recent work has shown that DTD's activity on Gly-tRNA Ala is about 42 1000-fold higher than on Gly-tRNA Gly , clearly demonstrating the profound effect of tRNA 43 elements on DTD and suggesting an underlying tRNA code for DTD's action. G3•U70, the 44 universal tRNA Ala -specific determinant for AlaRS, is also a determinant for DTD. Ho...