New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species

Gajbhiye, Shivani; Patra, P.K.; Yadav, Manoj Kumar

doi:10.1016/j.actatropica.2017.07.025

Cited by 17 publications

(12 citation statements)

References 47 publications

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“…Highly expressed genes exhibit a high tendency to use certain codons and tend to use them frequently [68,69]. In the present study, the low CAI of G. duodenalis indicated that highly expressed genes faced greater translation selection pressure in shaping CUB, which is similar to the codon usage in T. saginata [20] and P. falciparum [70].…”

Section: Discussionsupporting

confidence: 47%

Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Wang

Gong

et al. 2021

Genes

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Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

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Section: Discussionsupporting

confidence: 47%

Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Wang

Gong

et al. 2021

Genes

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“…Here, f k is estimated using the formula: f k = ( nS − 1)/( n − 1), where n is the total number of occurrences of the codons for that amino acid and S = ∑( n i / n ) 2 ( i = 1 ⋯ k ), and n i here is the total number of occurrences of the i th codon for that amino acid. Genes for which the codon choice is only constrained by a mutation bias will lie on or just below the curve of the expected ENC values [ 20 ]. Therefore, to elucidate the relationship between GC 3 and ENC values, the expected ENC values for different GC 3 were calculated as follows [ 21 ]:

where s represents the given GC 3 %.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

Ren

Haixian

et al. 2018

BioMed Research International

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Phenomenon of unequal use of synonymous codons in Mycobacterium tuberculosis is common. Codon usage bias not only plays an important regulatory role at the level of gene expression, but also helps in improving the accuracy and efficiency of translation. Meanwhile, codon usage pattern of Mycobacterium tuberculosis genome is important for interpreting evolutionary characteristics in species. In order to investigate the codon usage pattern of the Mycobacterium tuberculosis genome, 12 Mycobacterium tuberculosis genomes from different area are downloaded from the GeneBank. The correlations between G3, GC12, whole GC content, codon adaptation index, codon bias index, and so on of Mycobacterium tuberculosis genomes are calculated. The ENC-plot, relationship between A3/(A3 + T3) and G3/(G3 + C3), GC12 versus GC3 plot, and the RSCU of overall/separated genomes all show that the codon usage bias exists in all 12 Mycobacterium tuberculosis genomes. Lastly, relationship between CBI and the equalization of ENC shows a strong negative correlation between them. The relationship between protein length and GC content (GC3 and GC12) shows that more obvious differences in the GC content may be in shorter protein. These results show that codon usage bias existing in the Mycobacterium tuberculosis genomes could be used for further study on their evolutionary phenomenon.

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“…We implemented a set of correlation analysis ( Pearson ) between ENC and GC 3 values for the AT biased plasmodia. A correlation between ENC and GC 3 in P. falciparum was first spotted in other works (Gajbhiye et al 2017). Results are collected in Tab.2.…”

Section: Resultsmentioning

confidence: 65%

Evolutionary Pressures and Codon Bias in Low Complexity Regions of Plasmodia Parasites

Cappannini

Forcelloni

Giansanti

2020

Preprint

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In this work, we perform a systematic analysis of evolutionary forces (i.e. mutational bias and natural selection) acting in plasmode proteomes. The main focus is to clarify the origin of low complexity strands in plasmodium proteins. For this purpose, we consider P.falciparum as the principal case of study and we take into account the other parasites as a suitable benchmark with which compare the low complexity enrichment, GC content and evolutionary pressures acting on codon bias. Using different bioinformatic tools and a new index that we call here selective pressure index, we find evidences that low complexity insertions are inserted in proteins where mutational bias acts as the primarily evolutionary force. Protein length has revealed to be an important evolutionary and fitness characteristic for proteins (Wang et al.we lead a further study on protein length finding a preferential LC insertion in longer proteins, which are , in turn, less subject to natural selection. Additionally, dividing the proteins between LCPs (Low complexity containing proteins) and nLCPs (the counterpart), we observe that LCPs are significantly longer than nLCP. Overall, we find evidence that this class of proteins containing long low-complexity segments could be a signal of evolutionary and adapting path for these parasites.

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New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species

Cited by 17 publications

References 47 publications

Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

Evolutionary Pressures and Codon Bias in Low Complexity Regions of Plasmodia Parasites

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