Mechanistic Insights Into Catalytic RNA–Protein Complexes Involved in Translation of the Genetic Code

Routh, Satya Brata; Sankaranarayanan, Rajan

doi:10.1016/bs.apcsb.2017.04.002

Cited by 5 publications

(3 citation statements)

References 253 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…On the contrary, in the signal recognition particle, the RNA bears the burden of scaffolding and promotes the interaction with the SRP receptor, while a protein subunit works as the enzymatic moiety performing GTP hydrolysis (Peluso et al, 2000). In the ribosome, rRNA usually excels in both duties, serving as the skeleton and the catalytic heart of this giant complex, whereas proteins are relegated to secondary roles (Ban et al, 2000;Muth et al, 2000;Nissen et al, 2000;Routh and Sankaranarayanan, 2017). However, mitochondrial ribosomes often deviate from this rule: in the extreme case of trypanosomatids, the mitochondrial rRNA has suffered such profound structural erosion that the scaffolding task almost entirely falls to the hypertrophied protein shell (Ramrath et al, 2018;Soufari et al, 2020).…”

Section: Class I: Constitutive Rnpsmentioning

confidence: 99%

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Gerovac

Vogel

Smirnov

2021

Front. Mol. Biosci.

View full text Add to dashboard Cite

Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.

show abstract

Section: Class I: Constitutive Rnpsmentioning

confidence: 99%

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Gerovac

Vogel

Smirnov

2021

Front. Mol. Biosci.

View full text Add to dashboard Cite

show abstract

“…As a result, a peptide bond is formed between the A-site amino acid (of aa-tRNA) and the P-site peptidyl moiety (of the pt-tRNA), with a concomitant deacylation of tRNA and the translocation of the mRNA by a codon, thereby preparing the ribosome for the next round of polypeptide elongation (85,86). The newly formed peptidyl moiety of pt-tRNA will now have one amino acid more than the earlier pt-tRNA (87,88). In this plethora of events of peptide synthesis, how D-aa-tRNAs are treated by the ribosome is of specific interest and is essential for tweaking the ribosome for making noncanonical peptides.…”

Section: Ribosomementioning

confidence: 99%

Chiral checkpoints during protein biosynthesis

Kuncha

Kruparani

Sankaranarayanan

2019

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Edited by Karin Musier-Forsyth Protein chains contain only L-amino acids, with the exception of the achiral glycine, making the chains homochiral. This homochirality is a prerequisite for proper protein folding and, hence, normal cellular function. The importance of D-amino acids as a component of the bacterial cell wall and their roles in neurotransmission in higher eukaryotes are well-established. However, the wider presence and the corresponding physiological roles of these specific amino acid stereoisomers have been appreciated only recently. Therefore, it is expected that enantiomeric fidelity has to be a key component of all of the steps in translation. Cells employ various molecular mechanisms for keeping D-amino acids away from the synthesis of nascent polypeptide chains. The major factors involved in this exclusion are aminoacyl-tRNA synthetases (aaRSs), elongation factor thermo-unstable (EF-Tu), the ribosome, and D-aminoacyl-tRNA deacylase (DTD). aaRS, EF-Tu, and the ribosome act as "chiral checkpoints" by preferentially binding to L-amino acids or L-aminoacyl-tRNAs, thereby excluding D-amino acids. Interestingly, DTD, which is conserved across all life forms, performs "chiral proofreading," as it removes D-amino acids erroneously added to tRNA. Here, we comprehensively review D-amino acids with respect to their occurrence and physiological roles, implications for chiral checkpoints required for translation fidelity, and potential use in synthetic biology. The authors declare that they have no conflicts of interest with the contents of this article.

show abstract

“…Among these proofreading factors, D-aminoacyl-tRNA deacylase (DTD) is the one that specifically decouples wrongly acylated D-amino acids from tRNAs ( Calendar and Berg, 1967 ; Soutourina et al, 1999 ; 2000 ). Our studies have shown that DTD is an RNA-based catalyst that uses an invariant Gly- cis Pro motif as a ‘chiral selectivity filter’ to achieve substrate chiral specificity only through rejection of L-amino acid from the active site, thereby leading to Gly-tRNA Gly misediting ( Ahmad et al, 2013 ; Routh et al, 2016 ; Routh and Sankaranarayanan, 2017 ). Recently, we have also shown that DTD’s activity on achiral glycine helps in clearing Gly-tRNA Ala , a misaminoacylation product of alanyl-tRNA synthetase (AlaRS), thus resolving a long-standing question in translational quality control ( Pawar et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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

Kuncha

Suma

Pawar

et al. 2018

eLife

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Mechanistic Insights Into Catalytic RNA–Protein Complexes Involved in Translation of the Genetic Code

Cited by 5 publications

References 253 publications

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Chiral checkpoints during protein biosynthesis

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

Contact Info

Product

Resources

About