Analysis of synonymous codon usage of transcriptome database in<i>Rheum palmatum</i>

Huo, Xiaowei; Liu, Sisi; Li, Yimin; Wu, Hao; Gao, Jing; Yan, Yi‐Lin; Zhang, Gang; Liu, Mengmeng

doi:10.7717/peerj.10450

Cited by 17 publications

(13 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this research, it was discovered that the average GC content was close to GC3s content (both moderately less than 50%), indicating that the overall AU content in the C. panzhihuaensis genome was slightly higher than GC, and the codon tended to end in A/U slightly. Interestingly, this result is similar to GC3s content in gymnosperms such as Ginkgo biloba [31], Gnetifer Hypothesis [32], and most dicotyledons [32][33][34][35]. However, monocotyledons such as Triticum Aestivum [36],Zea Mays [37], Hordeum Vulgare [38], and Oryza Sativa [39] all showed high GC content and tended to end in G/C.…”

Section: Discussionsupporting

confidence: 61%

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Jian¹,

Wang²,

Li³

et al. 2022

Preprint

View full text Add to dashboard Cite

Codon use bias is an important characteristic in the process of genetic information transmission of species. With the publication of the genome of C. panzhihuaensis, it is of great significance to investigate the codon use bias for understanding the genetic evolution of this species and for molecular breeding. In this study, Perl language and CodonW 1.4.2 software was used to systematically analyze the coding gene sequences of the C. panzhihuaensis genome, obtain the characteristics of codon use, and identify the sources of variation affecting codon use. The results showed that GC3s content, GCall content, and ENC value were 46.75%, 47.67%, and 52.8 respectively. As the first seed plant, the GC3 content of Cycas is similar to that of most gymnosperms and most dicotyledons, but considerably different from that of monocotyledons.RSCU value was greater than 1, among which 21 codons ended in U or A. Enc-plot analysis, PR2-plot neutral plot analysis, and correlation coefficient analysis of Axis1 with GC3s and CAI revealed that the codon bias was mainly affected by natural selection, but also by mutation pressure and other factors. Thirty-one optimal codons of Cycas genes were screened. This research can provide a reference for the phylogeny and genome codon evolution of Cycas.

show abstract

Section: Discussionsupporting

confidence: 61%

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Jian¹,

Wang²,

Li³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…The crucial codon bias is evident in specific cells, such as monocytes, B and T lymphocytes. Previously the mutational bias influenced the codon bias in monocytes, while the translational selection could affect codon usage in B and T cells [ 18 ]. Thus, optimization for T cell codon usage should benefit the expression of the Rep4E3mCherry in Jurkat cells.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, suboptimal codon usage affected the translation process and mRNA stability [ 14 ]. Interestingly, specific cell types, such as immune cells, have distinct codon usage patterns among other immune cell types [ 18 ]. Therefore, in the genetic engineering approach, the codon usage of the target gene is usually optimized to increase the protein expression level.…”

Section: Introductionmentioning

confidence: 99%

Validation of Promoters and Codon Optimization on CRISPR/Cas9-Engineered Jurkat Cells Stably Expressing αRep4E3 for Interfering with HIV-1 Replication

Chupradit

Sornsuwan

Saiprayong

et al. 2022

IJMS

View full text Add to dashboard Cite

Persistent and efficient therapeutic protein expression in the specific target cell is a significant concern in gene therapy. The controllable integration site, suitable promoter, and proper codon usage influence the effectiveness of the therapeutic outcome. Previously, we developed a non-immunoglobulin scaffold, alpha repeat protein (αRep4E3), as an HIV-1 RNA packaging interference system in SupT1 cells using the lentiviral gene transfer. Although the success of anti-HIV-1 activity was evidenced, the integration site is uncontrollable and may not be practical for clinical translation. In this study, we use the CRISPR/Cas9 gene editing technology to precisely knock-in αRep4E3 genes into the adeno-associated virus integration site 1 (AAVS1) safe harbor locus of the target cells. We compare the αRep4E3 expression under the regulation of three different promoters, including cytomegalovirus (CMV), human elongation factor-1 alpha (EF1α), and ubiquitin C (UbC) promoters with and without codon optimization in HEK293T cells. The results demonstrated that the EF1α promoter with codon-optimized αRep4E3mCherry showed higher protein expression than other promoters with non-optimized codons. We then performed a proof-of-concept study by knocking in the αRep4E3mCherry gene at the AAVS1 locus of the Jurkat cells. The results showed that the αRep4E3mCherry-expressing Jurkat cells exhibited anti-HIV-1 activities against HIV-1NL4-3 strain as evidenced by decreased capsid (p24) protein levels and viral genome copies as compared to the untransfected Jurkat control cells. Altogether, our study demonstrates that the αRep4E3 could interfere with the viral RNA packaging and suggests that the αRep4E3 scaffold protein could be a promising anti-viral molecule that offers a functional cure for people living with HIV-1.

show abstract

“…Based on these two factors, the origin of codon usage can be clarified. But it seems that these two factors aren't sufficient enough to confirm attributes of codon usage [22]. The disease-related wet-lab experiments are needed for confirmation about the codon usage pattern but with time constraints the codon usage bias analytical technique has been a boon approach to predict and analyze the CUB computationally.…”

Section: Discussionmentioning

confidence: 99%

Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

et al. 2021

View full text Add to dashboard Cite

Crimean-congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.

show abstract

Analysis of synonymous codon usage of transcriptome database inRheum palmatum

Cited by 17 publications

References 40 publications

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Genome-Wide Analysis of Synonymous Codon Usage Bias in Cycas panzhihuaensis

Validation of Promoters and Codon Optimization on CRISPR/Cas9-Engineered Jurkat Cells Stably Expressing αRep4E3 for Interfering with HIV-1 Replication

Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

Contact Info

Product

Resources

About