Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions

The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5’-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5’-UTR and the downstream 3’-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine () complicates some of these optimization processes because is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly.

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Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

Frontiers in Marine Science ◽

10.3389/fmars.2020.602323 ◽

2020 ◽

Vol 7 ◽

Author(s):

Xiao Chen ◽

Chundi Wang ◽

Bo Pan ◽

Borong Lu ◽

Chao Li ◽

...

Keyword(s):

Codon Usage ◽

Single Cell ◽

Stop Codon ◽

Genomic Data ◽

Evolutionary Strategy ◽

Genomic Sequencing ◽

Ribosomal Frameshifting ◽

Genomic Features ◽

First Time ◽

Stop Codon Reassignment

Peritrichs are one of the largest groups of ciliates with over 1,000 species described so far. However, their genomic features are largely unknown. By single-cell genomic sequencing, we acquired the genomic data of three sessilid peritrichs (Cothurnia ceramicola, Vaginicola sp., and Zoothamnium sp. 2). Using genomic data from another 53 ciliates including 14 peritrichs, we reconstructed their evolutionary relationships and confirmed genome skimming as an efficient approach for expanding sampling. In addition, we profiled the stop codon usage and programmed ribosomal frameshifting (PRF) events in peritrichs for the first time. Our analysis reveals no evidence of stop codon reassignment for peritrichs, but they have prevalent +1 or -1 PRF events. These genomic features are distinguishable from other ciliates, and our observations suggest a unique evolutionary strategy for peritrichs.

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Comparative Analysis of Eight Mitogenomes of Bark Beetles and Their Phylogenetic Implications

Insects ◽

10.3390/insects12100949 ◽

2021 ◽

Vol 12 (10) ◽

pp. 949

Author(s):

Huicong Du ◽

Jiaxing Fang ◽

Xia Shi ◽

Sufang Zhang ◽

Fu Liu ◽

...

Keyword(s):

Codon Usage ◽

Bark Beetle ◽

Phylogenetic Relationships ◽

Bark Beetles ◽

Sequence Data ◽

Stop Codon ◽

Structural Characteristics ◽

Gene Arrangement ◽

Beetle Species ◽

Phylogenetic Implications

Many bark beetles of the subfamily Scolytinae are the most economically important insect pests of coniferous forests worldwide. In this study, we sequenced the mitochondrial genomes of eight bark beetle species, including Dendroctonus micans, Orthotomicus erosus, Polygraphus poligraphus, Dryocoetes hectographus, Ips nitidus, Ips typographus, Ips subelongatus, and Ips hauseri, to examine their structural characteristics and determine their phylogenetic relationships. We also used previously published mitochondrial genome sequence data from other Scolytinae species to identify and localize the eight species studied within the bark beetle phylogeny. Their gene arrangement matched the presumed ancestral pattern of these bark beetles. Start and stop codon usage, amino acid abundance, and the relative codon usage frequencies were conserved among bark beetles. Genetic distances between species ranged from 0.037 to 0.418, and evolutionary rates of protein-coding genes ranged from 0.07 for COI to 0.69 for ND2. Our results shed light on the phylogenetic relationships and taxonomic status of several bark beetles in the subfamily Scolytinae and highlight the need for further sequencing analyses and taxonomic revisions in additional bark beetle species.

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Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Journal of Biological Chemistry ◽

10.1074/jbc.m114.606632 ◽

2014 ◽

Vol 289 (44) ◽

pp. 30334-30342 ◽

Cited By ~ 34

Author(s):

Gürkan Korkmaz ◽

Mikael Holm ◽

Tobias Wiens ◽

Suparna Sanyal

Keyword(s):

Codon Usage ◽

Stop Codon ◽

Gc Content ◽

Comprehensive Analysis ◽

Expression Level ◽

Release Factor ◽

Relative Level ◽

Stop Codons ◽

Release Factors ◽

Highly Expressed Genes

We present a comprehensive analysis of stop codon usage in bacteria by analyzing over eight million coding sequences of 4684 bacterial sequences. Using a newly developed program called “stop codon counter,” the frequencies of the three classical stop codons TAA, TAG, and TGA were analyzed, and a publicly available stop codon database was built. Our analysis shows that with increasing genomic GC content the frequency of the TAA codon decreases and that of the TGA codon increases in a reciprocal manner. Interestingly, the release factor 1-specific codon TAG maintains a more or less uniform frequency (∼20%) irrespective of the GC content. The low abundance of TAG is also valid with respect to expression level of the genes ending with different stop codons. In contrast, the highly expressed genes predominantly end with TAA, ensuring termination with either of the two release factors. Using three model bacteria with different stop codon usage (Escherichia coli, Mycobacterium smegmatis, and Bacillus subtilis), we show that the frequency of TAG and TGA codons correlates well with the relative steady state amount of mRNA and protein for release factors RF1 and RF2 during exponential growth. Furthermore, using available microarray data for gene expression, we show that in both fast growing and contrasting biofilm formation conditions, the relative level of RF1 is nicely correlated with the expression level of the genes ending with TAG.

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Different stop codon usage in two pseudohypotrich ciliates

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2001.tb10958.x ◽

2001 ◽

Vol 205 (2) ◽

pp. 259-263 ◽

Cited By ~ 1

Author(s):

Pilar Perez-Romero ◽

Eduardo Villalobo ◽

Antonio Torres

Keyword(s):

Codon Usage ◽

Stop Codon

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Universal Features for the Classification of Coding and Non-coding DNA Sequences

Bioinformatics and Biology Insights ◽

10.4137/bbi.s2236 ◽

2009 ◽

Vol 3 ◽

pp. BBI.S2236 ◽

Cited By ~ 5

Author(s):

Nicolas Carels ◽

Ramon Vidal ◽

Diego Frías

Keyword(s):

Codon Usage ◽

Success Rate ◽

Dna Sequences ◽

Stop Codon ◽

Chemical Properties ◽

Natural Consequence ◽

Coding Sequences ◽

Physico Chemical ◽

Simple Features

In this report, we revisited simple features that allow the classification of coding sequences (CDS) from non-coding DNA. The spectrum of codon usage of our sequence sample is large and suggests that these features are universal. The features that we investigated combine (i) the stop codon distribution, (ii) the product of purine probabilities in the three positions of nucleotide triplets, (iii) the product of Cytosine, Guanine, Adenine probabilities in 1st, 2nd, 3rd position of triplets, respectively, (iv) the product of G and C probabilities in 1st and 2nd position of triplets. These features are a natural consequence of the physico-chemical properties of proteins and their combination is successful in classifying CDS and non-coding DNA (introns) with a success rate >95% above 350 bp. The coding strand and coding frame are implicitly deduced when the sequences are classified as coding.

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