Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

Xiang, Heng; Zhang, Ruizhi; Butler, Robert R.; Liu, Tie; Zhang, Li; Pombert, Jean‐François; Zhou, Zeyang

doi:10.1371/journal.pone.0129223

Cited by 36 publications

(25 citation statements)

References 32 publications

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“…43 This report suggests a strong relationship between the host and the virus. The RSCUmax value was 2.35 for CUG codon coding for leucine and 1.87 for GUG codon coding valine in HCV clearance candidate genes, displaying the maximum frequency of G-ending codons.…”

Section: Relative Synonymous Codon Usage Bias In Hcv Clearance Candmentioning

confidence: 78%

Codon usage of human hepatitis C virus clearance genes in relation to its expression

Singh

Venkatesan

Gulyás

et al. 2019

J of Cellular Biochemistry

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Hepatitis C virus (HCV) infection is among the leading causes of hepatocellular carcinoma and liver cirrhosis globally, with a high economic burden. The disease progression is well established, but less is known about the spontaneous HCV infection clearance. This study tries to establish the relationship between codon biasness and expression of HCV clearance candidate genes in normal and HCV infected liver tissues. A total of 112 coding sequences comprising 151 679 codons were subjected to the computation of codon indices, namely relative synonymous codon usage, an effective number of codon (Nc), frequency of optimal codon, codon adaptation index, codon bias index, and base compositions. Codon indices report of GC3s, GC12, hydropathicity, and aromaticity implicates both mutational and translational selection in the candidate gene set. This was further correlated with the differentially expressed genes among the selected genes using BioGPS. A significant correlation is observed between the gene expression of normal liver and cancerous liver tissues with codon bias (Nc). Gene expression is also correlated with relative codon bias values, indicating that CCL5, APOA2, CD28, IFITM1, and TNFSF4 genes have higher expression. These results are quite encouraging in selecting the high responsive genes in HCV clearance. However, there could be additional genes which could also orchestrate the clearance role with the above mentioned first line of defensive genes.

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Section: Relative Synonymous Codon Usage Bias In Hcv Clearance Candmentioning

confidence: 78%

Codon usage of human hepatitis C virus clearance genes in relation to its expression

Singh

Venkatesan

Gulyás

et al. 2019

J of Cellular Biochemistry

View full text Add to dashboard Cite

show abstract

“…In genetics, the GC content is the percentage of the nitrogenous bases on a DNA molecule that are either guanine or cytosine. The overall GC content was computed using a Perl script from the inspiring study on microsporidia by Xiang et al [40] (https://github.com/hxiang1019/calcGCcontent.git). We divided the prokaryotes into groups according to their environmental characteristics and pathogenicity and then we compared the distributions of the GC content values belonging to these groups.…”

Section: Gc Contentmentioning

confidence: 99%

Codon usage bias in prokaryotic genomes and environmental adaptation

Arella

Dilucca

Giansanti

2020

Preprint

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In each genome, some codons are favored over others by selection likely because they are translated more efficiently and accurately. The selectively favored codons tend to correspond to the most highly expressed tRNAs. It has been recognized that this codon usage bias can influence the cellular fitness and that might be associated with the lifestyle of the organism. To test the impact of environments on genome evolution we studied the codon usage bias of 615 prokaryotes. We found that the extent of codon usage corresponds to the environment in witch the prokaryotes live. In particular, measuring the degree of codon usage bias by the tRNA adaptation index (tAI), we obtained that organisms living in a specialized habitat have high extents of codon usage bias, consistent with their need to adapt efficiently to specific environmental constraints. Differently, organisms able to live in multiple habitats exhibit low codon usage bias as they need to adapt to various physical and chemical conditions. Our results suggest the importance of co-evolution between tRNA availability and codon usage of an organism, in relation with the environmental adaptation.

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“…However, for organisms where data about tRNA populations and other parameters is not available-and this is the case for the vast majority of genome sequences-applying the established approaches can be problematic. For example, current methods cannot be applied to many interesting organisms, such as organisms with extreme lifestyles like parasites [21][22][23] or thermophiles.…”

Section: Introductionmentioning

confidence: 99%

Hidden patterns of codon usage bias across kingdoms

Deng

Hedayioglu

Kalfon

et al. 2020

J. R. Soc. Interface.

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The genetic code is necessarily degenerate with 64 possible nucleotide triplets being translated into 20 amino acids. Eighteen out of the 20 amino acids are encoded by multiple synonymous codons. While synonymous codons are clearly equivalent in terms of the information they carry, it is now well established that they are used in a biased fashion. There is currently no consensus as to the origin of this bias. Drawing on ideas from stochastic thermodynamics we derive from first principles a mathematical model describing the statistics of codon usage bias. We show that the model accurately describes the distribution of codon usage bias of genomes in the fungal and bacterial kingdoms. Based on it, we derive a new computational measure of codon usage bias—the distance D capturing two aspects of codon usage bias: (i) differences in the genome-wide frequency of codons and (ii) apparent non-random distributions of codons across mRNAs. By means of large scale computational analysis of over 900 species across two kingdoms of life, we demonstrate that our measure provides novel biological insights. Specifically, we show that while codon usage bias is clearly based on heritable traits and closely related species show similar degrees of bias, there is considerable variation in the magnitude of D within taxonomic classes suggesting that the contribution of sequence-level selection to codon bias varies substantially within relatively confined taxonomic groups. Interestingly, commonly used model organisms are near the median for values of D for their taxonomic class, suggesting that they may not be good representative models for species with more extreme D , which comprise organisms of medical and agricultural interest. We also demonstrate that amino acid specific patterns of codon usage are themselves quite variable between branches of the tree of life, and that some of this variability correlates with organismal tRNA content.

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Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

Cited by 36 publications

References 32 publications

Codon usage of human hepatitis C virus clearance genes in relation to its expression

Codon usage of human hepatitis C virus clearance genes in relation to its expression

Codon usage bias in prokaryotic genomes and environmental adaptation

Hidden patterns of codon usage bias across kingdoms

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