Strong negative correlation between codon usage bias and protein structural disorder impedes protein expression after codon optimization

2021 ◽  
Author(s):  
Kunshan Liu ◽  
Yaqi Ouyang ◽  
Ru Lin ◽  
Chenyu Ge ◽  
Mian Zhou
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Negative Correlation ◽  
Codon Usage Bias ◽  
Codon Optimization ◽  
Structural Disorder ◽  
Strong Negative Correlation

scholarly journals Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Zhipeng Zhou ◽  
Yunkun Dang ◽  
Mian Zhou ◽  
Haiyan Yuan ◽  
Yi Liu
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Transcription Termination ◽  
Model Organism ◽  
Open Reading Frames ◽  
Strong Negative Correlation ◽  
Rare Codons ◽  
Cleavage And Polyadenylation ◽  
Mouse Cells

Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here, we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and abolishment of full-length mRNA. PTT is a wide-spread phenomenon in Neurospora, and there is a strong negative correlation between codon usage bias and PTT events. Rare codons lead to the formation of putative poly(A) signals and PTT. A similar role for codon usage bias was also observed in mouse cells. Together, these results suggest that codon usage biases co-evolve with the transcription termination machinery to suppress premature termination of transcription and thus allow for optimal gene expression.

scholarly journals Human Codon Usage: The Genetic Basis of Pathogen Latency

2021 ◽  
Author(s):  
Darja Kanduc
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Genetic Basis ◽  
Codon Optimization ◽  
Quantitative Relationship ◽  
Infectious Agents ◽  
Front Line ◽  
Chronic Infections ◽  
Synonymous Codons ◽  
Definition Of

AbstractInfectious diseases pose two main compelling issues. First, the identification of the molecular factors that allow chronic infections, that is, the often completely asymptomatic coexistence of infectious agents with the human host. Second, the definition of the mechanisms that allow the switch from pathogen dormancy to pathologic (re)activation. Furthering previous studies, the present work (1) analyzes the frequency of occurrence of synonymous codons in coding DNA, that is, codon usage, as a genetic tool that rules protein expression; (2) describes how human codon usage can inhibit protein expression of infectious agents during latency, so that pathogen genes the codon usage of which does not conform to the human codon usage cannot be translated; and (3) frames human codon usage among the front-line instruments of the innate immunity against infections. In parallel, it is shown that, while genetics can account for the molecular basis of pathogen latency, the changes of the quantitative relationship between codon frequencies and isoaccepting tRNAs during cell proliferation offer a biochemical mechanism that explains the pathogen switching to (re)activation. Immunologically, this study warns that using codon optimization methodologies can (re)activate, potentiate, and immortalize otherwise quiescent, asymptomatic pathogens, thus leading to uncontrollable pandemics.

scholarly journals A New Look at Codon Usage and Protein Expression

10.29007/d4tz ◽  
2019 ◽  
Author(s):  
Gabriel Wright ◽  
Anabel Rodriguez ◽  
Patricia Clark ◽  
Scott Emrich
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Empirical Data ◽  
Codon Usage Bias ◽  
Elongation Rate ◽  
Translation Rate ◽  
Translation Elongation ◽  
Promising Alternative ◽  
Highly Expressed Genes ◽  
Adaptation Index

%MinMax, a model of intra-gene translational elongation rate, relies on codon usage frequencies. Historically, %MinMax has used tables that measure codon usage bias for all genes in an organism, such as those found at HIVE-CUT. In this paper, we provide evidence that codon usage bias based on all genes is insufficient to accurately measure absolute translation rate. We show that alternative ”High-φ” codon usage tables, generated by another model (ROC-SEMPPR), are a promising alternative. By creating a hybrid model, future codon usage analyses and their applications (e.g., codon harmonization) are likely to more accurately measure the ”tempo” of translation elongation. We also suggest a High- φ alternative to the Codon Adaptation Index (CAI), a classic metric of codon usage bias based on highly expressed genes. Significantly, our new alternative is equally well correlated with empirical data as traditional CAI without using experimentally determined expression counts as input.

scholarly journals Overcoming codon-usage bias in heterologous protein expression in Streptococcus gordonii

Microbiology ◽  
2009 ◽  
Vol 155 (11) ◽  
pp. 3581-3588 ◽  
Author(s):  
Song F. Lee ◽  
Yi-Jing Li ◽  
Scott A. Halperin
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Heterologous Protein ◽  
Trna Gene ◽  
Heterologous Protein Expression ◽  
Streptococcus Gordonii ◽  
Heterologous Proteins ◽  
Single Chain ◽  
Rare Codons

One of the limitations facing the development of Streptococcus gordonii into a successful vaccine vector is the inability of this bacterium to express high levels of heterologous proteins. In the present study, we have identified 12 codons deemed as rare codons in S. gordonii and seven other streptococcal species. tRNA genes encoding 10 of the 12 rare codons were cloned into a plasmid. The plasmid was transformed into strains of S. gordonii expressing the fusion protein SpaP/S1, the anti-complement receptor 1 (CR1) single-chain variable fragment (scFv) antibody, or the Toxoplasma gondii cyclophilin C18 protein. These three heterologous proteins contained high percentages of amino acids encoded by rare codons. The results showed that the production of SpaP/S1, anti-CR1 scFv and C18 increased by 2.7-, 120- and 10-fold, respectively, over the control strains. In contrast, the production of the streptococcal SpaP protein without the pertussis toxin S1 fragment was not affected by tRNA gene supplementation, indicating that the increased production of SpaP/S1 protein was due to the ability to overcome the limitation caused by rare codons required for the S1 fragment. The increase in anti-CR1 scFv production was also observed in Streptococcus mutans following tRNA gene supplementation. Collectively, the findings in the present study demonstrate for the first time, to the best of our knowledge, that codon-usage bias exists in Streptococcus spp. and the limitation of heterologous protein expression caused by codon-usage bias can be overcome by tRNA supplementation.

scholarly journals Optimization of Codon Usage Enhances the Immunogenicity of a DNA Vaccine Encoding Mycobacterial Antigen Ag85B

2005 ◽  
Vol 73 (9) ◽  
pp. 5666-5674 ◽  
Author(s):  
Hyun-Jeong Ko ◽  
Sung-Youl Ko ◽  
Yeon-Jeong Kim ◽  
Eun-Gae Lee ◽  
Sang-Nae Cho ◽  
...  
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Dna Vaccine ◽  
Codon Optimization ◽  
Cytotoxic T Cell ◽  
Mycobacterial Antigen ◽  
T Cell Immune Responses ◽  
Aerosol Infection

ABSTRACT In spite of its many other benefits, DNA vaccine is limited in its application by its insufficient immunogenicity. One promising approach for enhancing its immunogenicity is to maximize its expression in the immunized host. In the current study, we investigated whether codon optimization of the mycobacterial antigen Ag85B gene could enhance the expression and immunogenicity of the Ag85B DNA vaccine. We generated a synthetic humanized Ag85B (hAg85B) gene in which codon usage was optimized for expression in human cells. DNA plasmids with codon-optimized hAg85B increased the level of protein expression in vitro and in vivo. DNA vaccine with hAg85B induced stronger Th1-like and cytotoxic T-cell immune responses in BALB/c mice and generated higher protective immunity in a BALB/c mouse model of Mycobacterium tuberculosis aerosol infection than did the DNA vaccine with wild-type Ag85B. Therefore, our results suggest that codon optimization of mycobacterial antigens (e.g., Ag85B) could improve protein expression and thereby enhance the immunogenicity of DNA vaccines against M. tuberculosis.

Codon usage bias affects α-amylase mRNA level by altering RNA stability and cytosine methylation patterns in Escherichia coli

2020 ◽  
Vol 66 (9) ◽  
pp. 521-528
Author(s):  
Yanzi Xing ◽  
Ruiqing Gong ◽  
Yichun Xu ◽  
Kunshan Liu ◽  
Mian Zhou
Keyword(s):  
Escherichia Coli ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Cytosine Methylation ◽  
Codon Optimization ◽  
Mrna Level ◽  
Protein Translation ◽  
Transcriptional Level ◽  
Translation Efficiency

Codon usage bias exists in almost every organism and is reported to regulate protein translation efficiency and folding. Besides translation, the preliminary role of codon usage bias on gene transcription has also been revealed in some eukaryotes such as Neurospora crassa. In this study, we took as an example the α-amylase-coding gene (amyA) and examined the role of codon usage bias in regulating gene expression in the typical prokaryote Escherichia coli. We confirmed the higher translation efficiency on codon-optimized amyA RNAs and found that the RNA level itself was also affected by codon optimization. The decreased RNA level was caused at least in part by altered mRNA stability at the post-transcriptional level. Codon optimization also altered the number of cytosine methylation sites. Examination on dcm knockouts suggested that cytosine methylation may be a minor mechanism adopted by codon bias to regulate gene RNA levels. More studies are required to verify the global effect of codon usage and to reveal its detailed mechanism on transcription.

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

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Li Gun ◽  
Ren Yumiao ◽  
Pan Haixian ◽  
Zhang Liang
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Strong Negative Correlation ◽  
Synonymous Codons ◽  
The Relationship ◽  
Adaptation Index

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.

scholarly journals Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Yide Huang ◽  
Ting Lin ◽  
Lingfang Lu ◽  
Fan Cai ◽  
Jie Lin ◽  
...  
Keyword(s):  
Pichia Pastoris ◽  
Protein Expression ◽  
Codon Usage ◽  
Codon Optimization ◽  
Software Tool ◽  
Expression Levels ◽  
Gene Design ◽  
Codon Pair Bias ◽  
Codon Pair ◽  
Synthetic Gene Design

Abstract Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris.

Sign in / Sign up

Export Citation Format

Share Document