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

Li, Yicong; Wang, Rui; Pu, Feiyang; Feng, Xili; Jin, Li; Ma, Zhiyong; Ma, Xiaoxia

doi:10.3389/fcimb.2021.771010

Cited by 5 publications

(9 citation statements)

References 73 publications

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“…In general, synonymous codon usage bias is able to participate in most aspects of viral life cycle. This biased synonymous codon usage is not neutral but involved in nucleotide usage bias ( 28 , 29 , 43 ), mRNA stability ( 44 , 45 ), translation accuracy and efficiency ( 46 , 47 ), and protein folding formation ( 48 ). Of note, BVDV did not follow nucleotide usage pattern of its susceptible host (i.e., newborn calf) in which the genome of cells contains high GC content to perform viral life cycle, but it accumulated adenine content in its ORF ( Supplementary Table 4 ) and suppressed the selection of synonymous codons with CG dinucleotides ( Supplementary Table 5 ).…”

Section: Discussionmentioning

confidence: 99%

“…In general, when the RSCU value is higher than 1.0, the corresponding synonymous codon displays a positive codon usage trend. In contrast, when the RSCU value is <1.0, the corresponding synonymous codon reflects a negative codon usage trend (28,29). To identify the extent of 59 synonymous codon usage bias, RSCU values of higher than 1.6 and <0.6 were defined as "overrepresented" and "underrepresented" codons, respectively (30).…”

Section: Analyzing Synonymous Codon Usage Patterns For the Bvdv Isolatesmentioning

confidence: 99%

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Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages

Wang

Feng

et al. 2022

Front. Vet. Sci.

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Bovine viral diarrhea virus (BVDV), serving as an important pathogen for newborn calves, poses threat to reproductive and economic losses in the cattle industry. To survey the infection rate and genetic diversity of BVDV in newborn calves in northern China, a total of 676 sera samples of newborn calves were collected from four provinces between 2021 and 2022. All sera samples were individually detected for BVDV infection by RT-PCR and ELISA. Our results showed that the overall serological rate was 9.76% (66/676) and the average positive rate of BVDV RNA was 8.14% (55/676) in the newborn calves. Eight BVDV strains were successfully isolated from RT-PCR positive sera samples, and four isolates displayed the cytopathic effect (CPE). Based on phylogenetic tree at the genome level, the eight strains were classified into subgenotype 1c. Moreover, the BVDV isolates had a close genetic relationship with the GSTZ strain at either nucleotide or codon usage level. Interestingly, in comparison of synonymous codon usage patterns between the BVDV isolates with CPE and ones without CPE, there were four synonymous codons (UCG, CCC, GCA, and AAC) which displayed the significant differences (p < 0.05) at codon usage pattern, suggesting that synonymous codon usage bias might play a role in BVDV-1c biotypes. In addition, the usage of synonymous codons containing CpG dinucleotides was suppressed by the BVDV-1c isolates, reflecting one of strategies of immune evasion of BVDV to its host. Taken together, our study provided data for monitoring and vaccination strategies of BVDV for newborn calves in northern China.

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Section: Discussionmentioning

confidence: 99%

Section: Analyzing Synonymous Codon Usage Patterns For the Bvdv Isolatesmentioning

confidence: 99%

Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages

Wang

Feng

et al. 2022

Front. Vet. Sci.

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“…By using a different analysis workflow, we revealed that the host factor, serving as one of the evolutionary dynamics, plays an important role in the genetic divergence of HEV derived from different hosts at synonymous codon usages. Synonymous codon usage bias, which can reflect the equilibrium between mutation pressure and natural selection, is a widespread genetic feature throughout the genomic evolution [33][34][35]. Although the HEV genome has a high mutation rate in its nucleotide sequence like other RNA viruses, the dispersion of the overall codon usage pattern of HEV displays the speciesspecific genetic feature.…”

Section: Discussionmentioning

confidence: 99%

“…Synonymous codon usage bias, which can reflect the equilibrium between mutation pressure and natural selection, is a widespread genetic feature throughout the genomic evolution [33–35]. Although the HEV genome has a high mutation rate in its nucleotide sequence like other RNA viruses, the dispersion of the overall codon usage pattern of HEV displays the species‐specific genetic feature.…”

Section: Discussionmentioning

confidence: 99%

Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts

et al. 2022

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Hepatitis E virus (HEV) is an important zoonotic pathogen infecting a wide range of host species. It has a positive-sense, single-stranded RNA genome encoding three open reading frames (ORFs). Synonymous codon usages of viruses essentially determine their survival and adaptation to susceptible hosts. To better understand the interplay between the ever-expanding host range and synonymous codon usages of HEV, we quantified the dispersion of synonymous codon usages of HEV genomes isolated from different hosts via V s calculation and information entropy. HEV ORFs show species-specific synonymous codon usage patterns. Ruminant-derived HEV ORFs own the most synonymous codons with stable usage patterns (V s value <0.1) which leads to the stable overall codon usage patterns (R value being close to zero). Swine-derived HEV ORFs own more concentrated synonymous codons than those from wild boar. Compared with HEV strains isolated from other hosts, the human-derived HEV exhibits a distinct pattern at the overall codon usage (R < 0). Generally, ORF1 contains more synonymous codons with stable usage patterns (V s < 0.1) than those of ORFs 2 and 3. Moreover, ORF3 contains more synonymous codons with varied patterns (V s > 1.0) than ORFs 1 and 2. The host factor serving as one of the evolutionary dynamics probably influences synonymous codon usage patterns of the HEV genome. Taken together, synonymous codons with stable usage patterns in ORF1 might help to sustain the infection, while that with varied usage patterns in ORF3 may facilitate cross-species infection and expand the host range.

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“…In a recent study, the CUB of the ATG13 gene across eukaryotes has been reported [ 24 ]. However, the genetic pattern of the codon usage bias involved in human autophagy is not yet known.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

Jamil

Uddin²,

Alam

et al. 2022

Cells

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Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.

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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

Cited by 5 publications

References 73 publications

Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages

Genetic features of bovine viral diarrhea virus subgenotype 1c in newborn calves at nucleotide and synonymous codon usages

Dispersion of synonymous codon usage patterns in hepatitis E virus genomes derived from various hosts

Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy

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