Gene Expression Levels Are Correlated with Synonymous Codon Usage, Amino Acid Composition, and Gene Architecture in the Red Flour Beetle, Tribolium castaneum

Wigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossina brevipalpis, is characterized by extreme genome reduction and AT nucleotide composition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high and low expression levels, thus indicating a lack of translational selection. Extreme AT composition bias across the genome also drives relative amino acid usage, but predicted high-expression genes (ribosomal proteins and chaperonins) use GC-rich amino acids more frequently than do low-expression genes. The levels and configuration of amino acid differences between Wigglesworthia and Escherichia coli were compared to test the hypothesis that the relatively GC-rich amino acid profiles of high-expression genes reflect greater amino acid conservation at these loci. This hypothesis is supported by reduced levels of protein divergence at predicted high-expression Wigglesworthia genes and similar configurations of amino acid changes across expression categories. Combined, the results suggest that codon and amino acid usage in the Wigglesworthia genome reflect a strong AT mutational bias and elevated levels of genetic drift, consistent with expected effects of an endosymbiotic lifestyle and repeated population bottlenecks. However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes.

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Compelling Evidence Suggesting the Codon Usage of SARS-CoV-2 Adapts to Human After the Split From RaTG13

Evolutionary Bioinformatics ◽

10.1177/11769343211052013 ◽

2021 ◽

Vol 17 ◽

pp. 117693432110520

Author(s):

Yanping Zhang ◽

Xiaojie Jin ◽

Haiyan Wang ◽

Yaoyao Miao ◽

Xiaoping Yang ◽

...

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Synonymous Codon ◽

Mrna Translation ◽

Synonymous Codon Usage ◽

Fast Decoding ◽

Rate Limiting Step ◽

Human Lungs ◽

Human Sample ◽

Rate Limiting

SARS-CoV-2 needs to efficiently make use of the resources from hosts in order to survive and propagate. Among the multiple layers of regulatory network, mRNA translation is the rate-limiting step in gene expression. Synonymous codon usage usually conforms with tRNA concentration to allow fast decoding during translation. It is acknowledged that SARS-CoV-2 has adapted to the codon usage of human lungs so that the virus could rapidly proliferate in the lung environment. While this notion seems to nicely explain the adaptation of SARS-CoV-2 to lungs, it is unable to tell why other viruses do not have this advantage. In this study, we retrieve the GTEx RNA-seq data for 30 tissues (belonging to over 17 000 individuals). We calculate the RSCU (relative synonymous codon usage) weighted by gene expression in each human sample, and investigate the correlation of RSCU between the human tissues and SARS-CoV-2 or RaTG13 (the closest coronavirus to SARS-CoV-2). Lung has the highest correlation of RSCU to SARS-CoV-2 among all tissues, suggesting that the lung environment is generally suitable for SARS-CoV-2. Interestingly, for most tissues, SARS-CoV-2 has higher correlations with the human samples compared with the RaTG13-human correlation. This difference is most significant for lungs. In conclusion, the codon usage of SARS-CoV-2 has adapted to human lungs to allow fast decoding and translation. This adaptation probably took place after SARS-CoV-2 split from RaTG13 because RaTG13 is less perfectly correlated with human. This finding depicts the trajectory of adaptive evolution from ancestral sequence to SARS-CoV-2, and also well explains why SARS-CoV-2 rather than other viruses could perfectly adapt to human lung environment.

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Construction of anti-codon table of the plant kingdom and evolution of tRNA selenocysteine (tRNASec)

BMC Genomics ◽

10.1186/s12864-020-07216-3 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Tapan Kumar Mohanta ◽

Awdhesh Kumar Mishra ◽

Abeer Hashem ◽

Elsayed Fathi Abd_Allah ◽

Abdul Latif Khan ◽

...

Keyword(s):

Amino Acids ◽

Zea Mays ◽

Amino Acid ◽

Codon Usage ◽

Synonymous Codon ◽

Protein Translation ◽

Synonymous Codon Usage ◽

Papaver Somniferum ◽

Plant Kingdom ◽

Ostreococcus Tauri

Abstract Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not. Results Therefore, we analysed the tRNAnome of 128 plant species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNAMet has highest (5.039%) whereas GCG anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons (isoacceptor) at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and we found that tRNASec showed anti-codon switch during the course of evolution. Conclusion The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation.

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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae

International Journal of Molecular Sciences ◽

10.3390/ijms19124010 ◽

2018 ◽

Vol 19 (12) ◽

pp. 4010

Author(s):

Zhaocai Li ◽

Wen Hu ◽

Xiaoan Cao ◽

Ping Liu ◽

Youjun Shang ◽

...

Keyword(s):

Amino Acid ◽

Codon Usage ◽

Synonymous Codon ◽

Family Members ◽

Synonymous Codon Usage ◽

Amino Acid Usage ◽

Codon Usage Pattern ◽

Evolutionary Trend ◽

Mutation Pressure ◽

Wide Range

The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

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Construction of Anti-codon Table of the Plant Kingdom and Evolution of tRNA Selenocysteine (tRNAsec)

10.21203/rs.3.rs-43566/v1 ◽

2020 ◽

Author(s):

Tapan Kumar Kumar Mohanta ◽

Awdhesh Kumar Mishra ◽

Abeer Hashem ◽

Elsayed Fathi Abd_Allah ◽

Ahmed Al-Harrasi

Keyword(s):

Amino Acids ◽

Zea Mays ◽

Amino Acid ◽

Codon Usage ◽

Synonymous Codon ◽

Protein Translation ◽

Synonymous Codon Usage ◽

Papaver Somniferum ◽

Plant Kingdom ◽

Ostreococcus Tauri

Abstract Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not. Results Therefore, we analysed the tRNAnome of 128 species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNAMet has highest (5.039%) whereas CGC anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and it has undergone anti-codon switch during the course of evolution. Conclusion The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation.

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Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

Genetics ◽

10.1093/genetics/136.3.927 ◽

1994 ◽

Vol 136 (3) ◽

pp. 927-935 ◽

Cited By ~ 29

Author(s):

H Akashi

Keyword(s):

Drosophila Melanogaster ◽

Natural Selection ◽

Amino Acid ◽

Codon Usage ◽

Protein Function ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Drosophila Virilis ◽

Codon Preference ◽

Translational Accuracy

Abstract I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the protein level. The frequency of preferred codons is significantly higher at codons conserved for amino acids than at nonconserved codons in 38 genes compared between D. melanogaster and Drosophila virilis or Drosophila pseudoobscura (Z = 5.93, P < 10(-6)). Preferred codon usage is also significantly higher in putative zinc-finger and homeodomain regions than in the rest of 28 D. melanogaster transcription factor encoding genes (Z = 8.38, P < 10(-6)). Mutational alternatives (within-gene differences in mutation rates, amino acid changes altering codon preference states, and doublet mutations at adjacent bases) do not appear to explain this association between synonymous codon usage and amino acid constraint.

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Construction of Anti-codon Table of the Plant Kingdom and Evolution of tRNA Selenocysteine (tRNASec)

10.21203/rs.3.rs-43566/v3 ◽

2020 ◽

Author(s):

Tapan Kumar Kumar Mohanta ◽

Awdhesh Kumar Mishra ◽

Abeer Hashem ◽

Elsayed Fathi Abd_Allah ◽

Abdul Latif Khan ◽

...

Keyword(s):

Amino Acids ◽

Zea Mays ◽

Amino Acid ◽

Codon Usage ◽

Synonymous Codon ◽

Protein Translation ◽

Synonymous Codon Usage ◽

Papaver Somniferum ◽

Plant Kingdom ◽

Ostreococcus Tauri

Abstract Background The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein translation chain. However, we did not know about the exact abundance of anti-codons in the genome and whether the frequency of abundance remains same across the plant lineage or not. Results Therefore, we analysed the tRNAnome of 128 species and reported an anti-codon table of the plant kingdom. We found that CAU anti-codon of tRNAMet has highest (5.039%) whereas GCG anti-codon of tRNAArg has lowest (0.004%) abundance. However, when we compared the anti-codon frequencies according to the tRNA isotypes, we found tRNALeu (7.808%) has highest abundance followed by tRNASer (7.668%) and tRNAGly (7.523%). Similarly, suppressor tRNA (0.036%) has lowest abundance followed by tRNASec (0.066%) and tRNAHis (2.109). The genome of Ipomoea nil, Papaver somniferum, and Zea mays encoded the highest number of anti-codons at 59 each whereas the genome of Ostreococcus tauri was found to encode only 18 isoacceptors. The tRNASec genes undergone losses more frequently than duplication and we found that tRNASec showed anti-codon switch during the course of evolution.Conclusion The anti-codon table of the plant tRNA will enable us to understand the synonymous codon usage of the plant kingdom and can be very helpful to understand which codon is preferred over other during the translation.

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Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.771010 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yicong Li ◽

Rui Wang ◽

Huihui Wang ◽

Feiyang Pu ◽

Xili Feng ◽

...

Keyword(s):

Amino Acid ◽

Codon Usage ◽

Codon Usage Bias ◽

Essential Gene ◽

Synonymous Codon ◽

Phylogenetic Analyses ◽

Nucleotide Composition ◽

Synonymous Codon Usage ◽

Related Gene ◽

Codon Positions

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.

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Codon clusters with biased synonymous codon usage represent hidden functional domains in protein-coding DNA sequences

10.1101/530345 ◽

2019 ◽

Author(s):

Zhen Peng ◽

Yehuda Ben-Shahar

Keyword(s):

Amino Acid ◽

Nucleic Acid ◽

Codon Usage ◽

Dna Sequences ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Functional Domains ◽

Protein Coding ◽

Protein Coding Genes ◽

Usage Patterns

1.AbstractProtein-coding DNA sequences are thought to primarily affect phenotypes via the peptides they encode. Yet, emerging data suggest that, although they do not affect protein sequences, synonymous mutations can cause phenotypic changes. Previously, we have shown that signatures of selection on gene-specific codons usage bias are common in genomes of diverse eukaryotic species. Thus, synonymous codon usage, just as amino acid usage pattern, is likely a regular target of natural selection. Consequently, here we propose the hypothesis that at least for some protein-coding genes, codon clusters with biased synonymous codon usage patterns might represent “hidden” nucleic-acid-level functional domains that affect the action of the corresponding proteins via diverse hypothetical mechanisms. To test our hypothesis, we used computational approaches to identify over 3,000 putatively functional codon clusters (PFCCs) with biased usage patterns in about 1,500 protein-coding genes in the Drosophila melanogaster genome. Specifically, our data suggest that these PFCCs are likely associated with specific categories of gene function, including enrichment in genes that encode membrane-bound and secreted proteins. Yet, the majority of the PFCCs that we have identified are not associated with previously annotated functional protein domains. Although the specific functional significance of the majority of the PFCCs we have identified remains unknown, we show that in the highly conserved family of voltage-gated sodium channels, the existence of rare-codon cluster(s) in the nucleic-acid region that encodes the cytoplasmic loop that constitutes inactivation gate is conserved across paralogs as well as orthologs across distant animal species. Together, our findings suggest that codon clusters with biased usage patterns likely represent “hidden” nucleic-acid-level functional domains that cannot be simply predicted from the amino acid sequences they encode. Therefore, it is likely that on the evolutionary timescale, protein-coding DNA sequences are shaped by both amino-acid-dependent and codon-usage-dependent selective forces.

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