Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia

Alqahtani, Taha; Khandia, Rekha; Puranik, Nidhi; Alqahtani, Ali; Alghazwani, Yahia; Alshehri, Saad Ali; Chidambaram, Kumarappan; Kamal, Mohammad Amjad

doi:10.3389/fgene.2022.884348

Cited by 8 publications

(2 citation statements)

References 81 publications

(100 reference statements)

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“…In the present study, the mean AT and GC skew values were −0.028 and −0.033, respectively and it suggested that T and C are preferred over A and G. The average values of other skews were also negative (−0.170, −0.175, −0.202 and −0.143 for purine, pyrimidine, amino and keto skews, respectively). An index related to gene expression CAI is shown to be influenced by nucleotide skew [ 53 ]. Except for AT skew, all the skews were significantly negatively correlated with gene expression ( p < 0.001).…”

Section: Resultsmentioning

confidence: 99%

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

et al. 2023

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Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.

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Section: Resultsmentioning

confidence: 99%

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

et al. 2023

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“…In many cases, some codons are favored over others for amino acid encoding purposes [7][8][9]. Codon Usage Bias (CUB) is a prevalent occurrence wherein synonymous codons manifest with distinct frequencies [10][11][12][13]. Throughout the course of evolution, synonymous mutations, also known as "silent mutations", are not anticipated to modify the original sequence or primary structure of proteins.…”

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Analysis of Codon Usage Bias of Thioredoxin in Apicomplexan Protozoa

Yang

2023

Preprint

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Background Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs. Methods Codon Usage Bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa. Results The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codons (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym) and length of amino acids (L_aa) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias. Conclusions In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for protein function research.

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Analysis of codon usage bias of thioredoxin in apicomplexan protozoa

Wang,

Yang

2023

Parasites Vectors

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Background Apicomplexan protozoa are a diverse group of obligate intracellular parasites causing many diseases that affect humans and animals, such as malaria, toxoplasmosis, and cryptosporidiosis. Apicomplexan protozoa possess unique thioredoxins (Trxs) that have been shown to regulate various cellular processes including metabolic redox regulation, parasite survival, and host immune evasion. However, it is still unknown how synonymous codons are used by apicomplexan protozoa Trxs. Methods Codon usage bias (CUB) is the unequal usage of synonymous codons during translation which leads to the over- or underrepresentation of certain nucleotide patterns. This imbalance in CUB can impact a variety of cellular processes including protein expression levels and genetic variation. This study analyzed the CUB of 32 Trx coding sequences (CDS) from 11 apicomplexan protozoa. Results The results showed that both codon base composition and relative synonymous codon usage (RSCU) analysis revealed that AT-ended codons were more frequently used in Cryptosporidium spp. and Plasmodium spp., while the Eimeria spp., Babesia spp., Hammondia hammondi, Neospora caninum, and Toxoplasma gondii tended to end in G/C. The average effective number of codon (ENC) value of these apicomplexan protozoa is 46.59, which is > 35, indicating a weak codon preference among apicomplexan protozoa Trxs. Furthermore, the correlation analysis among codon base composition (GC1, GC2, GC3, GCs), codon adaptation index (CAI), codon bias index (CBI), frequency of optimal codons (FOP), ENC, general average hydropathicity (GRAVY), aromaticity (AROMO), length of synonymous codons (L_sym), and length of amino acids (L_aa) indicated the influence of base composition and codon usage indices on CUB. Additionally, the neutrality plot analysis, PR2-bias plot analysis, and ENC-GC3 plot analysis further demonstrated that natural selection plays an important role in apicomplexan protozoa Trxs codon bias. Conclusions In conclusion, this study increased the understanding of codon usage characteristics and genetic evolution of apicomplexan protozoa Trxs, which expanded new ideas for vaccine and drug research. Graphical Abstract

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Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia

Cited by 8 publications

References 81 publications

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts

Analysis of Codon Usage Bias of Thioredoxin in Apicomplexan Protozoa

Analysis of codon usage bias of thioredoxin in apicomplexan protozoa

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