scholarly journals Disruption of evolutionarily correlated tRNA elements impairs accurate decoding

2020 ◽  
Vol 117 (28) ◽  
pp. 16333-16338
Author(s):  
Ha An Nguyen ◽  
S. Sunita ◽  
Christine M. Dunham
Keyword(s):  
Ribosomal Rna ◽  
Molecular Basis ◽  
Anticodon Loop ◽  
Wild Type ◽  
Stem Loop ◽  
Transfer Rnas ◽  
Translational Accuracy ◽  
Bacterial Ribosome ◽  
Evolutionarily Conserved ◽  
23S Ribosomal Rna

Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem−loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how these two tRNA features combine to ensure accurate decoding is unclear. Here, we solved structures of the bacterial ribosome containing either wild-typetRNAGGCAlaortRNAGGCAlacontaining a reversed 32–38 pair on cognate and near-cognate codons. Structures of wild-typetRNAGGCAlabound to the ribosome reveal 23S ribosomal RNA (rRNA) nucleotide A1913 positional changes that are dependent on whether the codon−anticodon interaction is cognate or near cognate. Further, the 32–38 pair is destabilized in the context of a near-cognate codon−anticodon pair. Reversal of the pairing intRNAGGCAlaablates A1913 movement regardless of whether the interaction is cognate or near cognate. These results demonstrate that disrupting 32–38 and anticodon sequences alters interactions with the ribosome that directly contribute to misreading.

scholarly journals Molecular basis for t6A modification in human mitochondria

2020 ◽  
Vol 48 (6) ◽  
pp. 3181-3194 ◽  
Author(s):  
Jing-Bo Zhou ◽  
Yong Wang ◽  
Qi-Yu Zeng ◽  
Shi-Xin Meng ◽  
En-Duo Wang ◽  
...  
Keyword(s):  
Base Pair ◽  
Molecular Basis ◽  
Protein Modification ◽  
Trna Modification ◽  
Anticodon Loop ◽  
Recognition Mechanism ◽  
Trna Recognition ◽  
Translational Accuracy

Abstract N 6-Threonylcarbamoyladenosine (t6A) is a universal tRNA modification essential for translational accuracy and fidelity. In human mitochondria, YrdC synthesises an l-threonylcarbamoyl adenylate (TC-AMP) intermediate, and OSGEPL1 transfers the TC-moiety to five tRNAs, including human mitochondrial tRNAThr (hmtRNAThr). Mutation of hmtRNAs, YrdC and OSGEPL1, affecting efficient t6A modification, has been implicated in various human diseases. However, little is known about the tRNA recognition mechanism in t6A formation in human mitochondria. Herein, we showed that OSGEPL1 is a monomer and is unique in utilising C34 as an anti-determinant by studying the contributions of individual bases in the anticodon loop of hmtRNAThr to t6A modification. OSGEPL1 activity was greatly enhanced by introducing G38A in hmtRNAIle or the A28:U42 base pair in a chimeric tRNA containing the anticodon stem of hmtRNASer(AGY), suggesting that sequences of specific hmtRNAs are fine-tuned for different modification levels. Moreover, using purified OSGEPL1, we identified multiple acetylation sites, and OSGEPL1 activity was readily affected by acetylation via multiple mechanisms in vitro and in vivo. Collectively, we systematically elucidated the nucleotide requirement in the anticodon loop of hmtRNAs, and revealed mechanisms involving tRNA sequence optimisation and post-translational protein modification that determine t6A modification levels.

THE MOLECULAR THROUGH ECOLOGICAL GENETICS OF ABNORMAL ABDOMEN. III. TISSUE-SPECIFIC DIFFERENTIAL REPLICATION OF RIBOSOMAL GENES MODULATES THE ABNORMAL ABDOMEN PHENOTYPE IN DROSOPHILA MERCATORUM

Genetics ◽  
1986 ◽  
Vol 112 (4) ◽  
pp. 877-886
Author(s):  
Rob DeSalle ◽  
Alan R Templeton
Keyword(s):  
Ribosomal Rna ◽  
Molecular Basis ◽  
Ribosomal Genes ◽  
Ecological Genetics ◽  
Wild Type ◽  
Rdna Genes ◽  
Tissue Specific ◽  
Type D ◽  
Drosophila Mercatorum ◽  
Specific Control

ABSTRACT The abnormal abdomen (aa) syndrome in Drosophila mercatorum is controlled by two major X-linked genetic elements. We have previously shown that the major X-linked element of aa is associated with the presence of large inserts in the 28S gene of the ribosomal RNA (rDNA) genes. We show that, in polytene tissue of wild-type D. mercatorum, the uninterrupted rDNA repeats are overreplicated relative to interrupted repeats. Uninterrupted rDNA repeats are also overreplicated in polytene tissue of hybrid larval offspring from wild-type and aa parents. This overreplication of uninterrupted repeats is not observed in diploid tissues of wild-type hybrids (of wild-type and aa parents) and homozygous aa larvae or in polytene tissue of aa larvae. Furthermore, molecular analysis of an aa line that has reverted to the wild type indicates that the reversion phenomenon is associated with the ability to overreplicate uninterrupted rDNA repeats in polytene tissues. The patterns of differential replication of rDNA genes in wild-type hybrids and aa larvae of D. mercatorum offer a possible mechanism for the tissue-specific control of the aa phenotype and suggest that the molecular basis for the second X-linked genetic element of aa is involved in the control of differential replication in polytene tissues.

Pleiotropic effects of mutations at positions 13 and 914 in Escherichia coli 16S ribosomal RNA

1995 ◽  
Vol 73 (11-12) ◽  
pp. 907-913 ◽  
Author(s):  
Léa Brakier-Gingras ◽  
Robert Pinard ◽  
François Dragon
Keyword(s):  
Escherichia Coli ◽  
Ribosomal Rna ◽  
Pleiotropic Effects ◽  
16S Ribosomal Rna ◽  
Order Structure ◽  
Initiation Complex ◽  
Stem Loop ◽  
Translational Initiation ◽  
Slowing Down ◽  
Translational Accuracy

Mutations at position 13 or 914 of Escherichia coli 16S ribosomal RNA exert pleiotropic effects on protein synthesis. They interfere with the binding of streptomycin, a translational miscoding drug, to the ribosomes. They increase translational fidelity, and this effect can be related to a perturbation of the higher order structure of the 530 stem–loop, a key region for tRNA selection. In contrast, the structure of the decoding center is not perturbed. The mutations also affect translational initiation, slowing down the formation of the 30S initiation complex. This effect can be related to a destabilization of the pseudoknot helix (17–19/916–918), at the convergence of the three major domains of 16S ribosomal RNA.Key words: ribosomal RNA, translational accuracy, translational initiation.

scholarly journals Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

2021 ◽  
Author(s):  
Kaitlyn Tsai ◽  
Vanja Stojkovic ◽  
Lianet Noda-Garcia ◽  
Iris D. Young ◽  
Alexander G. Myasnikov ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Binding Sites ◽  
Molecular Basis ◽  
Direct Evidence ◽  
Resistance Mechanisms ◽  
Cross Resistance ◽  
Peptidyl Transferase ◽  
Peptidyl Transferase Center ◽  
Bacterial Ribosome ◽  
Mechanisms Of Adaptation

Many clinically useful antibiotics inhibit the bacterial ribosome. The ribosomal RNA-modifying enzyme Cfr methylates an adenosine (m8A2503) in the peptidyl transferase center and causes cross-resistance to several classes of antibiotics. Despite the prevalence of this mode of resistance, mechanisms of adaptation to antibiotic pressure that exploit ribosome modification by Cfr are poorly understood. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. To address these questions, we evolved Cfr under antibiotic selection to generate variants that confer increased resistance and methylation of rRNA, provided by enhanced Cfr expression and stability. Using a variant which achieves near-stoichiometric methylation, we determined a 2.2Å cryo-EM structure of the Cfr-modified ribosome, revealing the molecular basis for resistance and informing design of antibiotics that overcome Cfr resistance.

scholarly journals Differences in 23S ribosomal RNA mutations between wild-type and mutant macrolide-resistant Chlamydia trachomatis isolates

2015 ◽  
Vol 10 (3) ◽  
pp. 1189-1193 ◽  
Author(s):  
YONG JIANG ◽  
HUI ZHU ◽  
LI-NA YANG ◽  
YUAN-JUN LIU ◽  
SHU-PING HOU ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Ribosomal Rna ◽  
Wild Type ◽  
23S Ribosomal Rna

scholarly journals DIFFERENTIATION OF DROSOPHILA CELLS LACKING RIBOSOMAL DNA, IN VITRO

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 429-434
Author(s):  
J James Donady ◽  
R L Seecof ◽  
M A Fox
Keyword(s):  
Drosophila Melanogaster ◽  
Ribosomal Rna ◽  
Ribosomal Dna ◽  
Rna Synthesis ◽  
Wild Type ◽  
Drosophila Cells

ABSTRACT Drosophila melanogaster embryos that lacked ribosomal DNA were obtained from appropriate crosses. Cells were taken from such embryos before overt differentiation took place and were cultured in vitro. These cells differentiated into neurons and myocytes with the same success as did wild-type controls. Therefore, ribosomal RNA synthesis is not necessary for the differentiation of neurons and myocytes in vitro.

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