A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

Kuncha, Santosh Kumar; Mazeed, Mohd; Singh, Raghvendra; Kattula, Bhavita; Routh, Satya Brata; Sankaranarayanan, Rajan

doi:10.1038/s41467-017-02204-w

Cited by 33 publications

(32 citation statements)

References 67 publications

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“…Calculations show that primitive tRNAs formed from several ribonucleotides and capable of specific binding to an L-amino acid by hydrogen bonds are in most cases unable to recognize D-amino acids with the same specificity, because their lateral substituent groups are sterically difficult to fit into the amino acid binding site of tRNA (Balasubramanian 1983). In addition, this process is complicated by a special enzyme D-aminoacyl-tRNA deacylase (DTD) that possesses a proofreading activity and removes D-isomers of amino acids accidentally binding with tRNA (Kuncha et al 2018). Thus, the coexistence of D-ribonucleotides and L-amino acids is necessary for certain types of biological interactions.…”

Section: Evolutionary Aspects Of the Origin Of D-amino Acidsmentioning

confidence: 99%

D-amino acids in nature, agriculture and biomedicine

et al. 2019

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Information accumulated over the past decades on the physiological functions and metabolic pathways of biosynthesis and degradation of D-amino acids has led to a renewed interest in their study. These isomers are known to form both in nature and during the chemical synthesis of L-amino acids for feeding and pharmacological purposes, as well as in the industrial processing of some raw materials. This article discusses the positive and negative effects of D-amino acids on the human body, animals and the environment. In addition, the scientific data concerning the mechanisms of cytotoxic action of D-amino acids and their industrial and biomedical potential are summarized. ARTICLE HISTORY

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Section: Evolutionary Aspects Of the Origin Of D-amino Acidsmentioning

confidence: 99%

D-amino acids in nature, agriculture and biomedicine

et al. 2019

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“…The rather efficient deacylation of cognate Pro-tRNA Pro observed for the Hs trans-editing enzyme in vitro is surprising and suggests that other factors in the cell likely prevent this undesired reaction. Based on the ability of bacterial elongation factor Tu (EF-Tu) to protect correctly charged tRNAs from free-standing editing domains, including bacterial ProXp-ala (22,37), we propose that Hs EF-1A may outcompete Hs ProXpala for binding to Pro-tRNA Pro , allowing only deacylation of the mischarged Ala-tRNA Pro species in cells. If editing occurred in cis (i.e., by a ProRS editing domain prior to substrate dissociation) rather than in trans, this competition would be less likely to be successful and may explain why eukaryotic ProRSs rely on a free-standing transediting enzyme for proofreading.…”

Section: Discussionmentioning

confidence: 99%

Human trans-editing enzyme displays tRNA acceptor stem specificity and relaxed amino acid selectivity

Vargas-Rodriguez

Bakhtina

McGowan

et al. 2020

Preprint

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Accurate translation of genetic information into proteins is vital for cell sustainability. ProXp-ala prevents proteome-wide Pro-to-Ala mutations by hydrolyzing misacylated Ala-tRNAPro, which is synthesized by prolyl-tRNA synthetase (ProRS). Bacterial ProXp-ala was previously shown to combine a size-based exclusion mechanism with conformational and chemical selection for the recognition of the alanyl moiety, while tRNAPro is selected via recognition of tRNA acceptor stem elements G72 and A73. The identity of these critical bases changed during evolution with eukaryotic cytosolic tRNAPro possessing a cytosine at the corresponding positions. The mechanism by which eukaryotic ProXp-ala adapted to these changes remains unknown. In this work, recognition of the aminoacyl moiety and tRNA acceptor stem by human (Hs) ProXp-ala was examined. Enzymatic assays revealed that Hs ProXp-ala requires C72 and C73 in the context of Hs cytosolic tRNAPro for efficient deacylation of mischarged Ala-tRNAPro. The strong dependence on these bases prevents cross-species deacylation of bacterial Ala-tRNAPro or of Hs mitochondrial Ala-tRNAPro by the human enzyme. Similar to the bacterial enzyme, Hs ProXp-ala showed strong tRNA acceptor-stem recognition but differed in its amino acid specificity profile relative to bacterial ProXp-ala. Changes at conserved residues in both the Hs and bacterial ProXp-ala substrate binding pockets modulated this specificity. These results illustrate how the mechanism of substrate selection diverged during the evolution of the ProXp-ala family and provides the first example of a trans-editing domain whose specificity evolved to adapt to changes in its tRNA substrate.

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“…The genes encoding E. coli DTD and Thermus thermophilus EF-Tu, and cDNA encoding M. musculus (residues 1-147) were cloned (with C-terminal 6X His-tag), expressed and purified as mentioned in Ahmad et al, 2013 and Kuncha et al, 2018. Briefly the proteins were overexpressed in E. coli BL21(DE3) by growing the culture to 0.6 OD (600 nM) at 37°C, followed by induction using 0.5 mM IPTG for 12 hours at 18°C.…”

Section: Methodsmentioning

confidence: 99%

A discriminator code-based DTD surveillance ensures faithful glycine delivery for protein biosynthesis in bacteria

Sankaranarayanan

Kuncha

Suma

et al. 2018

Preprint

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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...

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A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

Cited by 33 publications

References 67 publications

D-amino acids in nature, agriculture and biomedicine

D-amino acids in nature, agriculture and biomedicine

Human trans-editing enzyme displays tRNA acceptor stem specificity and relaxed amino acid selectivity

A discriminator code-based DTD surveillance ensures faithful glycine delivery for protein biosynthesis in bacteria

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