scholarly journals Study of Codon Usage Bias Between Genes of SARS-CoV-2 and Human Tissue-specific Genes

2021 ◽  
Vol 3 (3) ◽  
pp. 35-40
Author(s):  
Liheng Lai ◽  
Junqi Zhang ◽  
Zeyu Chen ◽  
Chonghe Sun ◽  
Yipeng Zhang
Keyword(s):  
Codon Usage ◽  
Human Tissue ◽  
Codon Usage Bias ◽  
Tissue Specific

scholarly journals Study of Codon Usage Bias Between Genes of SARS-CoV-2 and Human Tissue-specific Genes

2021 ◽  
Vol 3 (3) ◽  
pp. 35-40
Author(s):  
Liheng Lai ◽  
Junqi Zhang ◽  
Zeyu Chen ◽  
Chonghe Sun ◽  
Yipeng Zhang
Keyword(s):  
Codon Usage ◽  
Human Tissue ◽  
Codon Usage Bias ◽  
Tissue Specific

scholarly journals Distinct responses to rare codons in select Drosophila tissues

2022 ◽  
Author(s):  
Scott R. Allen ◽  
Rebeccah K Stewart ◽  
Michael Rogers ◽  
Ivan Jimenez Ruiz ◽  
Erez Cohen ◽  
...  
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Critical Role ◽  
Specific Protein ◽  
Human Testis ◽  
Rare Codon ◽  
Tissue Specific ◽  
Rare Codons ◽  
Drosophila Testis

Codon usage bias has long been appreciated to influence protein production. Yet, relatively few studies have analyzed the impacts of codon usage on tissue-specific mRNA and protein expression. Here, we use codon-modified reporters to perform an organism-wide screen in Drosophila melanogaster for distinct tissue responses to codon usage bias. These reporters reveal a cliff-like decline of protein expression near the limit of rare codon usage in endogenously expressed Drosophila genes. Near the edge of this limit, however, we find the testis and brain are uniquely capable of expressing rare codon-enriched reporters. We define a new metric of tissue-specific codon usage, the tissue-apparent Codon Adaptation Index, to reveal a conserved enrichment for rare codon usage in the endogenously expressed genes of both Drosophila and human testis. We further demonstrate a role for rare codons in restricting protein expression of an evolutionarily young gene, RpL10Aa, to the Drosophila testis. Rare codon-mediated restriction of this testis-specific protein is critical for female fertility. Our work highlights distinct responses to rarely used codons in select tissues, revealing a critical role for codon bias in tissue biology.

scholarly journals ExtRamp Online: Enabling ramp sequence calculations via an intuitive web interface.

2021 ◽  
Author(s):  
Justin B. Miller ◽  
Matthew W. Hodgman ◽  
Kyle N. Miller ◽  
Taylor E. Meurs ◽  
Mark T. W. Ebbert ◽  
...  
Keyword(s):  
Codon Usage ◽  
Human Tissue ◽  
Translational Efficiency ◽  
Web Interface ◽  
Cell Type ◽  
Web Browser ◽  
Tissue Specific ◽  
Genome Wide ◽  
Evolutionarily Conserved ◽  
Cell Type Specific

Abstract Motivation: Ramp sequences are an understudied evolutionarily-conserved mechanism for regulating protein translational efficiency. Slowly-translated codons concentrated at the 5' end of genes form ramp sequences that counterintuitively increase overall translational efficiency by evenly spacing ribosomes at initiation, which limits downstream ribosomal collisions. We previously developed ExtRamp, which is the only algorithm to identify translational ramp sequences in single genes. ExtRamp currently lacks a web interface to facilitate wider adoption and application for non-programmers. Additionally, ExtRamp currently identifies ramp sequences using only species-wide codon efficiencies that may lack the specificity of tissue and cell type-specific codon usage biases.Results: We present an online interface for ExtRamp to facilitate wider adoption and application for non-programmers, along with a significant improvement to the underlying algorithm to calculate tissue and cell type-specific ramp sequences (https://ramps.byu.edu/ExtRampOnline). ExtRamp Online contains all options available in the original ExtRamp algorithm with additional pre-set default values to enable researchers to calculate human tissue-specific or genome-wide ramp sequences on any web browser. Human tissue and cell type-specific codon usage biases have been precomputed and can be applied with a simple drop-down menu. Hover-over hints provide users with detailed information on all available options, which will help facilitate future creative analyses using ramp sequences. Availability: ExtRamp Online is publicly available at https://ramps.byu.edu/ExtRampOnline. All associated scripts are publicly available at https://github.com/ridgelab/ExtRampOnline.

scholarly journals Patterns of genome-wide codon usage bias in tobacco, tomato and potato

2021 ◽  
Vol 35 (1) ◽  
pp. 657-664
Author(s):  
Ali Mostafa Anwar ◽  
Maha Aljabri ◽  
Mohamed El-Soda
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Genome Wide

scholarly journals Codon usage bias and environmental adaptation in microbial organisms

2021 ◽  
Author(s):  
Davide Arella ◽  
Maddalena Dilucca ◽  
Andrea Giansanti
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Synonymous Codon ◽  
Principal Component ◽  
Gene Copy ◽  
Phenotypic Traits ◽  
Translational Efficiency ◽  
Microbial Organisms

AbstractIn each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.

scholarly journals Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 912
Author(s):  
Saadullah Khattak ◽  
Mohd Ahmar Rauf ◽  
Qamar Zaman ◽  
Yasir Ali ◽  
Shabeen Fatima ◽  
...  
Keyword(s):  
Standard Deviation ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Geographic Location ◽  
Mutation Pressure ◽  
Genome Wide ◽  
Margin Of Error ◽  
Usage Patterns ◽  
Causative Agents ◽  
Virus Genomes

The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons’ A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% ± 5.84%) and the GC3 value (30.14% ± 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome’s level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.

Analysis of codon usage bias in mitochondrial CO gene among Platyhelminthes

2021 ◽  
pp. 111410
Author(s):  
Gulshana A. Mazumder ◽  
Arif Uddin ◽  
Supriyo Chakraborty
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias

scholarly journals Understanding multicellular function and disease with human tissue-specific networks

2015 ◽  
Vol 47 (6) ◽  
pp. 569-576 ◽  
Author(s):  
Casey S Greene ◽  
Arjun Krishnan ◽  
Aaron K Wong ◽  
Emanuela Ricciotti ◽  
Rene A Zelaya ◽  
...  
Keyword(s):  
Human Tissue ◽  
Tissue Specific
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