UU/UA Dinucleotide Frequency Reduction in Coding Regions Results in Increased mRNA Stability and Protein Expression

BackgroundCodon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species.ResultRNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, especially in 'Molecular function’ category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences.ConclusionA comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species.

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“…This phenomenon can be explained by the hypothesis that reducing UA may increase protein production via inhibition of mRNA degradation [36]. …”

Section: Resultsmentioning

confidence: 99%

“…On the other hand, 37 pairs (26.2%) had UA at the junction (Additional file 3), which may also increase the rate of protein production [36]. These two types were also underrepresented compared to others in overall neighboring codon pairs (Figure 2J), as were mononucleotide repeats, GGGGGG, CCCCCC, UUUUUU.…”

Section: Resultsmentioning

confidence: 99%

Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data

Feng

Wang

et al. 2013

BMC Genomics

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“…All transfection experiments were carried out in triplicate. A red fluorescent protein expression vector (LentiORF™ pLEX‐JRed‐TurboGFP*, ∆GFP Vector), harboring the Puromycin gene was used at ¼ ratio of the test plasmid concentration for normalization of the transfection efficiencies . Transfected cells were maintained at 37 °C in a humidified incubator supplemented with 5% CO 2 .…”

Section: Methodsmentioning

confidence: 99%

Application of the 3′‐noncoding region of poliovirus RNA for cell‐based regulation of mRNA stability: Implication for biotechnological applications

Rasekhian

Roohvand

Teimoori‐Toolabi

et al. 2014

Biotech and App Biochem

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Enrichment of production yield of therapeutic proteins in mammalian cell cultures by modulation of the mRNA stability of the target protein to increase its in vivo half-life is a new strategy in biotechnological applications. The present article describes one of the most novel approaches to modulate mRNA stability by application of 3'-noncoding region (3'NCR) from RNA viral genome in the expression constructs. Our data indicated that although utilizing the 3'NCR sequence form poliovirus (PV-3'NCR) downstream of the target gene might generally stabilize the secondary structure of RNA, it influenced the mRNA stability (and thereby the amount of protein production) in a cell type and time-dependent manner, thus indicating a central role of mRNA-stabilizing binding sites/cellular factors in this process. Our data might be of interest to the biotechnology community to improve recombinant protein production in mammalian cell cultures and RNA-based therapy/vaccination approaches.

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“…The base composition may have an impact on translational activity and stability of mRNA [56, 57]. For example, reduction of the frequency of UU and UA dinucleotides results in increased mRNA stability and protein expression [58]. Besides this, replacing rare codons with frequently used synonymous codons is a common strategy to improve protein expression [59, 60].…”

Section: Chemical Modification Of Mrnamentioning

confidence: 99%

Biomedical applications of mRNA nanomedicine

et al. 2018

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As an attractive alternative to plasmid DNA, messenger RNA (mRNA) has recently emerged as a promising class of nucleic acid therapeutics for biomedical applications. Advances in addressing the inherent shortcomings of mRNA and in the development of nanoparticle-based delivery systems have prompted the development and clinical translation of mRNA-based medicines. In this review, we discuss the chemical modification strategies of mRNA to improve its stability, minimize immune responses, and enhance translational efficacy. We also highlight recent progress in nanoparticle-based mRNA delivery. Considerable attention is given to the increasingly widespread applications of mRNA nanomedicine in the biomedical fields of vaccination, protein-replacement therapy, gene editing, and cellular reprogramming and engineering.

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UU/UA Dinucleotide Frequency Reduction in Coding Regions Results in Increased mRNA Stability and Protein Expression

Cited by 53 publications

References 29 publications

Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data

Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data

Application of the 3′‐noncoding region of poliovirus RNA for cell‐based regulation of mRNA stability: Implication for biotechnological applications

Biomedical applications of mRNA nanomedicine

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