scholarly journals The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity

2020 ◽  
Vol 48 (11) ◽  
pp. 6170-6183 ◽  
Author(s):  
Ketty Pernod ◽  
Laure Schaeffer ◽  
Johana Chicher ◽  
Eveline Hok ◽  
Christian Rick ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Bacterial Genomes ◽  
Eukaryotic Translation ◽  
Eukaryotic Ribosome ◽  
Translation Fidelity ◽  
Translation Systems ◽  
Eukaryotic Genomes ◽  
Paralysis Virus ◽  
Decoding Fidelity

Abstract Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.

scholarly journals Context-specific action of macrolide antibiotics on the eukaryotic ribosome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Maxim S. Svetlov ◽  
Timm O. Koller ◽  
Sezen Meydan ◽  
Vaishnavi Shankar ◽  
Dorota Klepacki ◽  
...  
Keyword(s):  
Amino Acid Sequences ◽  
Macrolide Antibiotics ◽  
Single Mutation ◽  
Sequence Motifs ◽  
Eukaryotic Translation ◽  
Eukaryotic Ribosome ◽  
Cellular Translation ◽  
Distinct Sequence ◽  
Exit Tunnel ◽  
Context Specific

AbstractMacrolide antibiotics bind in the nascent peptide exit tunnel of the bacterial ribosome and prevent polymerization of specific amino acid sequences, selectively inhibiting translation of a subset of proteins. Because preventing translation of individual proteins could be beneficial for the treatment of human diseases, we asked whether macrolides, if bound to the eukaryotic ribosome, would retain their context- and protein-specific action. By introducing a single mutation in rRNA, we rendered yeast Saccharomyces cerevisiae cells sensitive to macrolides. Cryo-EM structural analysis showed that the macrolide telithromycin binds in the tunnel of the engineered eukaryotic ribosome. Genome-wide analysis of cellular translation and biochemical studies demonstrated that the drug inhibits eukaryotic translation by preferentially stalling ribosomes at distinct sequence motifs. Context-specific action markedly depends on the macrolide structure. Eliminating macrolide-arrest motifs from a protein renders its translation macrolide-tolerant. Our data illuminate the prospects of adapting macrolides for protein-selective translation inhibition in eukaryotic cells.

scholarly journals The Nematode Eukaryotic Translation Initiation Factor 4E/G Complex Works with a trans-Spliced Leader Stem-Loop To Enable Efficient Translation of Trimethylguanosine-Capped RNAs

2010 ◽  
Vol 30 (8) ◽  
pp. 1958-1970 ◽  
Author(s):  
Adam Wallace ◽  
Megan E. Filbin ◽  
Bethany Veo ◽  
Craig McFarland ◽  
Janusz Stepinski ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Mrna Translation ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Eukaryotic Translation Initiation Factor ◽  
Stem Loop ◽  
Eukaryotic Translation ◽  
Spliced Leader ◽  
Eukaryotic Translation Initiation ◽  
Translation Systems

ABSTRACT Eukaryotic mRNA translation begins with recruitment of the 40S ribosome complex to the mRNA 5′ end through the eIF4F initiation complex binding to the 5′ m7G-mRNA cap. Spliced leader (SL) RNA trans splicing adds a trimethylguanosine (TMG) cap and a sequence, the SL, to the 5′ end of mRNAs. Efficient translation of TMG-capped mRNAs in nematodes requires the SL sequence. Here we define a core set of nucleotides and a stem-loop within the 22-nucleotide nematode SL that stimulate translation of mRNAs with a TMG cap. The structure and core nucleotides are conserved in other nematode SLs and correspond to regions of SL1 required for early Caenorhabditis elegans development. These SL elements do not facilitate translation of m7G-capped RNAs in nematodes or TMG-capped mRNAs in mammalian or plant translation systems. Similar stem-loop structures in phylogenetically diverse SLs are predicted. We show that the nematode eukaryotic translation initiation factor 4E/G (eIF4E/G) complex enables efficient translation of the TMG-SL RNAs in diverse in vitro translation systems. TMG-capped mRNA translation is determined by eIF4E/G interaction with the cap and the SL RNA, although the SL does not increase the affinity of eIF4E/G for capped RNA. These results suggest that the mRNA 5′ untranslated region (UTR) can play a positive and novel role in translation initiation through interaction with the eIF4E/G complex in nematodes and raise the issue of whether eIF4E/G-RNA interactions play a role in the translation of other eukaryotic mRNAs.

scholarly journals mosaicFlye: Resolving long mosaic repeats using long error-prone reads

2020 ◽  
Author(s):  
Anton Bankevich ◽  
Pavel Pevzner
Keyword(s):  
Human Chromosome ◽  
Human Genome ◽  
Genome Assembly ◽  
Chromosome 6 ◽  
Segmental Duplications ◽  
Bacterial Genomes ◽  
Long Read ◽  
Human Chromosome 6 ◽  
Genome Assemblies ◽  
Eukaryotic Genomes

AbstractLong-read technologies revolutionized genome assembly and enabled resolution of bridged repeats (i.e., repeats that are spanned by some reads) in various genomes. However, the problem of resolving unbridged repeats (such as long segmental duplications in the human genome) remains largely unsolved, making it a major obstacle towards achieving the goal of complete genome assemblies. Moreover, the challenge of resolving unbridged repeats is not limited to eukaryotic genomes but also impairs assemblies of bacterial genomes and metagenomes. We describe the mosaicFlye algorithm for resolving complex unbridged repeats based on differences between various repeat copies and show how it improves assemblies of the human genome as well as bacterial genomes and metagenomes. In particular, we show that mosaicFlye results in a complete assembly of both arms of the human chromosome 6.

Codon Signature Extremes In Eukaryote genomes

2006 ◽  
Vol 52 (3-4) ◽  
pp. 281-297 ◽  
Author(s):  
Samuel Karlin ◽  
Dorit Carmelli
Keyword(s):  
Amino Acids ◽  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Mammalian Species ◽  
Life Domains ◽  
Codon Site ◽  
Bacterial Genomes ◽  
Noncoding Regions ◽  
Genome Wide ◽  
Eukaryotic Genomes

Twenty-one complete eukaryotic genomes are compared for codon signature biases. The codon signature refers to the dinucleotide relative abundance values at codon sites {1, 2}, {2, 3}, and {3, 4} (4 = 1 of the next codon site). The genomes under study include human, mouse, chicken, three invertebrates, one plant species, eight fungi, and six protists. The dinucleotide CpG is significantly underrepresented at all contiguous codon sites and drastically suppressed in noncoding regions in mammalian species, in yeast-like genomes, in the dicot Arabidopsis thaliana, but not in the filamentous fungi Neurospora crassa and Asperigillus fumigatus, and in the protist Entamoeba histolytica. The dinucleotide TpA, probably due to DNA structural weaknesses, is underrepresented genome-wide and significantly underrepresented in the codon signature for all contiguous codon sites in mammals, inverterbrates, plants, and fungi, but somewhat restricted to codon sites {1, 2} among protists helping in avoidance of stop codons. The amino acid Ser, not of abundance in bacterial genomes, generally ranks among the two most used amino acids among eukaryotes ostensibly resulting from greater activity in the nucleus. The observed differences are linked to specifics of methylation, context-dependent mutation, DNA repair, and replication. For example, the amino acid Leu is broadly abundant in all life domains generally resulting from extra occurrences of the codon TTR, R purine. The malarial protist Plasmodium falciparum shows many codon signature extremes.

scholarly journals Aminoglycoside interactions and impacts on the eukaryotic ribosome

2017 ◽  
Vol 114 (51) ◽  
pp. E10899-E10908 ◽  
Author(s):  
Irina Prokhorova ◽  
Roger B. Altman ◽  
Muminjon Djumagulov ◽  
Jaya P. Shrestha ◽  
Alexandre Urzhumtsev ◽  
...  
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Conformational Dynamics ◽  
Therapeutic Interventions ◽  
80S Ribosome ◽  
Eukaryotic Translation ◽  
Eukaryotic Ribosome ◽  
X Ray Crystallography ◽  
Single Molecule Fret ◽  
Translation Mechanism

Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored. Here, we use the combination of X-ray crystallography and single-molecule FRET analysis to reveal the interactions of distinct classes of aminoglycosides with the 80S eukaryotic ribosome. Crystal structures of the 80S ribosome in complex with paromomycin, geneticin (G418), gentamicin, and TC007, solved at 3.3- to 3.7-Å resolution, reveal multiple aminoglycoside-binding sites within the large and small subunits, wherein the 6′-hydroxyl substituent in ring I serves as a key determinant of binding to the canonical eukaryotic ribosomal decoding center. Multivalent binding interactions with the human ribosome are also evidenced through their capacity to affect large-scale conformational dynamics within the pretranslocation complex that contribute to multiple aspects of the translation mechanism. The distinct impacts of the aminoglycosides examined suggest that their chemical composition and distinct modes of interaction with the ribosome influence PTC read-through efficiency. These findings provide structural and functional insights into aminoglycoside-induced impacts on the eukaryotic ribosome and implicate pleiotropic mechanisms of action beyond decoding.

scholarly journals Genomic GC content drifts slowly downward in most bacterial genomes

2020 ◽  
Author(s):  
Bert Ely
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Bacterial Genomes ◽  
Base Pairs ◽  
Wide Range ◽  
Biased Gene Conversion ◽  
Prokaryotic Genomes ◽  
Genome Content ◽  
Genomic Gc Content ◽  
Eukaryotic Genomes

AbstractIn every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is slowly declining in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing at a slow rate. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genome content as well.

scholarly journals A distinct pathway for tetrahymanol synthesis in bacteria

2015 ◽  
Vol 112 (44) ◽  
pp. 13478-13483 ◽  
Author(s):  
Amy B. Banta ◽  
Jeremy H. Wei ◽  
Paula V. Welander
Keyword(s):  
Tetrahymena Pyriformis ◽  
Ring Expansion ◽  
Bacterial Genomes ◽  
Water Column Stratification ◽  
Expression Studies ◽  
Aerobic Methanotrophs ◽  
Biochemical Mechanisms ◽  
Ancient Ecosystems ◽  
Eukaryotic Genomes ◽  
Bacterial Domain

Tetrahymanol is a polycyclic triterpenoid lipid first discovered in the ciliate Tetrahymena pyriformis whose potential diagenetic product, gammacerane, is often used as a biomarker for water column stratification in ancient ecosystems. Bacteria are also a potential source of tetrahymanol, but neither the distribution of this lipid in extant bacteria nor the significance of bacterial tetrahymanol synthesis for interpreting gammacerane biosignatures is known. Here we couple comparative genomics with genetic and lipid analyses to link a protein of unknown function to tetrahymanol synthesis in bacteria. This tetrahymanol synthase (Ths) is found in a variety of bacterial genomes, including aerobic methanotrophs, nitrite-oxidizers, and sulfate-reducers, and in a subset of aquatic and terrestrial metagenomes. Thus, the potential to produce tetrahymanol is more widespread in the bacterial domain than previously thought. However, Ths is not encoded in any eukaryotic genomes, nor is it homologous to eukaryotic squalene-tetrahymanol cyclase, which catalyzes the cyclization of squalene directly to tetrahymanol. Rather, heterologous expression studies suggest that bacteria couple the cyclization of squalene to a hopene molecule by squalene-hopene cyclase with a subsequent Ths-dependent ring expansion to form tetrahymanol. Thus, bacteria and eukaryotes have evolved distinct biochemical mechanisms for producing tetrahymanol.

scholarly journals Genomic GC content drifts downward in most bacterial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0244163
Author(s):  
Bert Ely
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Bacterial Genomes ◽  
Evolutionary Time ◽  
Base Pairs ◽  
Wide Range ◽  
Biased Gene Conversion ◽  
Prokaryotic Genomes ◽  
Genomic Gc Content ◽  
Eukaryotic Genomes

In every kingdom of life, GC->AT transitions occur more frequently than any other type of mutation due to the spontaneous deamination of cytidine. In eukaryotic genomes, this slow loss of GC base pairs is counteracted by biased gene conversion which increases genomic GC content as part of the recombination process. However, this type of biased gene conversion has not been observed in bacterial genomes, so we hypothesized that GC->AT transitions cause a reduction of genomic GC content in prokaryotic genomes on an evolutionary time scale. To test this hypothesis, we used a phylogenetic approach to analyze triplets of closely related genomes representing a wide range of the bacterial kingdom. The resulting data indicate that genomic GC content is drifting downward in bacterial genomes where GC base pairs comprise 40% or more of the total genome. In contrast, genomes containing less than 40% GC base pairs have fewer opportunities for GC->AT transitions to occur so genomic GC content is relatively stable or actually increasing. It should be noted that this observed change in genomic GC content is the net change in shared parts of the genome and does not apply to parts of the genome that have been lost or acquired since the genomes being compared shared common ancestor. However, a more detailed analysis of two Caulobacter genomes revealed that the acquisition of mobile elements by the two genomes actually reduced the total genomic GC content as well.

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