scholarly journals Network analysis of synonymous codon usage

2020 ◽  
Vol 36 (19) ◽  
pp. 4876-4884
Author(s):  
Khalique Newaz ◽  
Gabriel Wright ◽  
Jacob Piland ◽  
Jun Li ◽  
Patricia L Clark ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Protein Structures ◽  
Synonymous Codon Usage ◽  
Supplementary Information ◽  
Rare Codons ◽  
Model Protein ◽  
Structural Positions

Abstract Motivation Most amino acids are encoded by multiple synonymous codons, some of which are used more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionarily conserved. Analyses of their positions in protein 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. Results We model protein structures as networks and use network centrality to measure the structural position of an amino acid. We first validate that amino acids buried within the structural core are network-central, and those on the surface are not. Then, we study potential differences between network centralities and thus structural positions of amino acids encoded by conserved rare, non-conserved rare and commonly used codons. We find that in 84% of proteins, the three codon categories occupy significantly different structural positions. We examine protein groups showing different codon centrality trends, i.e. different relationships between structural positions of the three codon categories. We see several cases of all proteins from our data with some structural or functional property being in the same group. Also, we see a case of all proteins in some group having the same property. Our work shows that codon usage is linked to the final protein structure and thus possibly to co-translational protein folding. Availability and implementation https://nd.edu/∼cone/CodonUsage/. Supplementary information Supplementary data are available at Bioinformatics online.

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

BMC Genomics ◽  
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.

scholarly journals A code within the genetic code: codon usage regulates co-translational protein folding

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Yi Liu
Keyword(s):  
Protein Folding ◽  
Codon Usage ◽  
Genetic Code ◽  
Synonymous Codon ◽  
Protein Structures ◽  
Translation Efficiency ◽  
Intrinsically Disordered ◽  
Synonymous Codons ◽  
Eukaryotic Organisms ◽  
And Function

Abstract The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding.

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

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.

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

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.

scholarly journals Synonymous codon substitutions perturb co-translational protein foldingin vivoand impair cell fitness

2019 ◽  
Author(s):  
Ian M. Walsh ◽  
Micayla A. Bowman ◽  
Iker F. Soto ◽  
Anabel Rodriguez ◽  
Patricia L. Clark
Keyword(s):  
Protein Folding ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Cellular Protein ◽  
Synonymous Codon Usage ◽  
Folding Mechanism ◽  
C Terminus ◽  
Essential Enzyme

AbstractIn the cell, proteins are synthesized from N- to C-terminus and begin to fold during translation. Co-translational folding mechanisms are therefore linked to elongation rate, which varies as a function of synonymous codon usage. However, synonymous codon substitutions can affect many distinct cellular processes, which has complicated attempts to deconvolve the extent to which synonymous codon usage can promote or frustrate proper protein foldingin vivo. Although previous studies have shown that some synonymous changes can lead to different final structures, other substitutions will likely be more subtle, perturbing predominantly the protein folding pathway without radically altering the final structure. Here we show that synonymous codon substitutions encoding a single essential enzyme lead to dramatically slower cell growth. These mutations do not prevent active enzyme formation; instead, they predominantly alter the protein folding mechanism, leading to enhanced degradationin vivo. These results support a model where synonymous codon substitutions can impair cell fitness by significantly perturbing co-translational protein folding mechanisms, despite the chaperoning provided by the cellular protein homeostasis network.SignificanceMany proteins that are incapable of refoldingin vitronevertheless fold efficiently to their native state in the cell. This suggests that more information than the amino acid sequence is required to properly fold these proteins. Here we show that synonymous mRNA mutations can alter a protein folding mechanismin vivo, leading to changes in cellular fitness. This work demonstrates that synonymous codon selection can play an important role in supporting efficient protein productionin vivo.

scholarly journals Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell fitness

2020 ◽  
Vol 117 (7) ◽  
pp. 3528-3534 ◽  
Author(s):  
Ian M. Walsh ◽  
Micayla A. Bowman ◽  
Iker F. Soto Santarriaga ◽  
Anabel Rodriguez ◽  
Patricia L. Clark
Keyword(s):  
Protein Folding ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Cellular Protein ◽  
Synonymous Codon Usage ◽  
Cellular Processes ◽  
C Terminus ◽  
Enzyme Formation ◽  
Essential Enzyme

In the cell, proteins are synthesized from N to C terminus and begin to fold during translation. Cotranslational folding mechanisms are therefore linked to elongation rate, which varies as a function of synonymous codon usage. However, synonymous codon substitutions can affect many distinct cellular processes, which has complicated attempts to deconvolve the extent to which synonymous codon usage can promote or frustrate proper protein folding in vivo. Although previous studies have shown that some synonymous changes can lead to different final structures, other substitutions will likely be more subtle, perturbing predominantly the protein folding pathway without radically altering the final structure. Here we show that synonymous codon substitutions encoding a single essential enzyme lead to dramatically slower cell growth. These mutations do not prevent active enzyme formation; instead, they predominantly alter the protein folding mechanism, leading to enhanced degradation in vivo. These results support a model in which synonymous codon substitutions can impair cell fitness by significantly perturbing cotranslational protein folding mechanisms, despite the chaperoning provided by the cellular protein homeostasis network.

scholarly journals Quantifying shifts in natural selection on codon usage between protein regions: A population genetics approach

2020 ◽  
Author(s):  
Alexander L. Cope ◽  
Michael A. Gilchrist
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Protein Structure ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Empirical Studies ◽  
Protein Structures ◽  
Synonymous Codon Usage ◽  
Genome Wide ◽  
Computational Analyses

AbstractEmpirical studies indicate changes to synonymous codon usage can impact protein folding. However, genome-wide computational analyses attempting to establish a more general relationship between codon usage and protein structure have often led to contradictory results. Using a population genetics model, we quantified codon-specific shifts in natural selection across and within protein structures, revealing a complex relationship between codon usage and protein structure. However, these shifts are small, suggesting differences in selection related to protein structure are either very weak or apply to relatively few codons. Using a previously published result, we demonstrate how tests for selection on codon usage can be confounded when failing to account for amino acid biases and gene expression. This work demonstrates the value of using population genetics-based models to quantify and tests for shifts in selection on codon usage. Extensions to this approach are discussed.

scholarly journals %MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

2017 ◽  
Vol 27 (1) ◽  
pp. 356-362 ◽  
Author(s):  
Anabel Rodriguez ◽  
Gabriel Wright ◽  
Scott Emrich ◽  
Patricia L. Clark
Keyword(s):  
Protein Folding ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Versatile Tool
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