Synonymous Codon Substitution Matrices

Abstract Abstract 2197 Hemophilia B is characterized by structural and functional defects in coagulation factor IX (FIX) caused by mutations in the F9 gene. Various mutations (nonsense, missense, etc.) are known to be associated with the disease, including a synonymous V107V mutation reported recently by Knobe and colleagues (Knobe et al., Hemophilia, 2008). However the mechanism by which this synonymous mutation contributes to the disease has not yet been elucidated. Earlier we have shown that synonymous codon substitutions in the mRNA of the multidrug resistance protein (MDR1) may change the conformation of the protein and result in altered functionality (Kimchi-Sarfaty et al., Science, 2008). Here we have performed in silico analyses of the synonymous codon substitution (GTGàGTA) leading to the V107V polymorphism and found that it may change the mRNA structure, stability, codon usage, and 3D structure of the encoded protein. We hypothesize that changes in codon usage might affect the rhythm of protein translation and thus result in slightly altered FIX conformation. In vitro analyses of FIX mRNA and protein expression supported our in silico analyses. The GTGàGTA (V107V) synonymous mutation results in reduced expression levels as well as an encoded protein with a slightly different conformation compared to wild-type FIX. These results show that the V107V polymorphism is not silent and might cause mild hemophilia B. This work sheds further light on ways in which synonymous mutations impact disease. The findings and conclusions in this article have not been formally disseminated by the Food and Drug Administration and should not be construed to represent any Agency determination policy Disclosures: No relevant conflicts of interest to declare.

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A codon model of nucleotide substitution with selection on synonymous codon usage

10.1101/007849 ◽

2014 ◽

Author(s):

Laura Kubatko ◽

Premal Shah ◽

Radu Herbei ◽

Michael Gilchrist

Keyword(s):

Protein Production ◽

Synonymous Codon ◽

Error Rates ◽

Selection Model ◽

Substitution Model ◽

Protein Coding ◽

New Model ◽

Protein Coding Genes ◽

Codon Substitution ◽

Yeast Genes

The quality of phylogenetic inference made from protein-coding genes depends, in part, on the realism with which the codon substitution process is modeled. Here we propose a new mechanistic model that combines the standard M0 substitution model of Yang (1997) with a simplified model from Gilchrist (2007) that includes selection on synonymous substitutions as a function of codon-specific nonsense error rates. We tested the newly proposed model by applying it to 104 protein-coding genes in brewer's yeast, and compared the fit of the new model to the standard M0 model and to the mutation-selection model of Yang and Nielsen (2008) using the AIC. Our new model provided significantly better fit in approximately 85% of the cases considered for the basic M0 model and in approximately 25% of the cases for the M0 model with estimated codon frequencies, but only in a few cases when the mutation-selection model was considered. However, our model includes a parameter that can be interpreted as a measure of the rate of protein production, and the estimates of this parameter were highly correlated with an independent measure of protein production for the yeast genes considered here. Finally, we found that in some cases the new model led to the preference of a different phylogeny for a subset of the genes considered, indicating that substitution model choice may have an impact on the estimated phylogeny.

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Single synonymous codon substitution eliminates pausing during chloramphenicol acetyl transferase synthesis onEscherichia coliribosomes in vitro

FEBS Letters ◽

10.1016/s0014-5793(02)02261-5 ◽

2002 ◽

Vol 512 (1-3) ◽

pp. 209-212 ◽

Cited By ~ 13

Author(s):

Vasanthi Ramachandiran ◽

Gisela Kramer ◽

Paul M Horowitz ◽

Boyd Hardesty

Keyword(s):

Synonymous Codon ◽

Chloramphenicol Acetyl Transferase ◽

Codon Substitution

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Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes

10.1101/2020.05.13.091652 ◽

2020 ◽

Author(s):

Alexander G Lucaci ◽

Sadie R Wisotsky ◽

Stephen D. Shank ◽

Steven Weaver ◽

Sergei L. Kosakovsky Pond

Keyword(s):

Evolutionary Dynamics ◽

Synonymous Codon ◽

Model Misspecification ◽

Empirical Support ◽

Simulated Data ◽

Small Subset ◽

Evolutionary Models ◽

Single Nucleotide Change ◽

Codon Substitution ◽

Alignment Errors

AbstractDespite many attempts to introduce evolutionary models that permit substitutions that instantly alter more than one nucleotide in a codon, the prevailing wisdom remains that such changes are rare and generally negligible (or are reflective of non-biological artifacts, such as alignment errors), and codon models continue to posit that only single nucleotide change have non-zero rates. We develop and test a simple hierarchy of codon-substitution models with non-zero evolutionary rates for only one-nucleotide (1H), one- and two-nucleotide (2H), or any (3H) codon substitutions. Using 35,000 empirical alignments, we find widespread statistical support for multiple hits: 58% of alignments prefer models with 2H allowed, and 22% – with 3H allowed. Analyses of simulated data suggest that these results are not likely to be due to simple artifacts such as model misclassification or alignment errors. Further modeling revealed that synonymous codon island jumping among codons encoding serine, especially along short branches, contributes significantly to this 3H signal. While serine codons were prominently involved in multiple-hit substitutions, there were other common exchanges contributing to better model fit. It appears that a small subset of sites in most alignments have unusual evolutionary dynamics not well explained by existing model formalisms, and that commonly estimated quantities, such as dN/dS ratios may be biased by model misspecification. Our findings highlight the need for continued evaluation of assumptions underlying workhorse evolutionary models and subsequent evolutionary inference techniques. We provide a software implementation for evolutionary biologists to assess the potential impact of extra base hits in their data in the HyPhy package.

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Soluble Expression of hFGF19 without Fusion Protein through Synonymous Codon Substitutions and DsbC Co-Expression in E. coli

Microorganisms ◽

10.3390/microorganisms8121942 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1942

Author(s):

Hye-Ji Choi ◽

Dae-Eun Cheong ◽

Su-Kyoung Yoo ◽

Jaehong Park ◽

Dong-Hyun Lee ◽

...

Keyword(s):

Fusion Protein ◽

Synonymous Codon ◽

Biological Activities ◽

Thioredoxin Reductase ◽

Soluble Expression ◽

High Cell Density Culture ◽

E Coli ◽

Codon Substitution ◽

Efficient Alternative ◽

Disulfide Bond Isomerase

Human fibroblast growth factor 19 (hFGF19) is a difficult-to-express protein that is frequently fused with another protein for soluble expression. However, residual amino acids after cleavage with protease represent one of the major problems in therapeutic protein development. Here, we introduced synonymous codon substitutions in the N-terminal region encoding sequence of hFGF19 and co-expressed disulfide bond isomerase (ΔssDsbC) to functionally express hFGF19 without any fusion protein. Synonymous codon substitution significantly increased hFGF19 expression. Subsequent co-expression of ΔssDsbC with a selected variant of hFGF19 (scvhFGF19) further increased the proportion of soluble hFGF19 expression in Escherichia coli XL1-Blue. Both total and soluble scvhFGF19 expression increased remarkably in the alternative host, E. coli Origami 2 with mutated thioredoxin reductase and glutathione reductase. scvhFGF19 purification by anion exchange and heparin affinity chromatography resulted in a yield of 6.5 mg/L under normal induction conditions in flask culture. As such, a high cell density culture is expected to achieve an even higher yield. The biological activities of purified scvhFGF19 were assessed based on its ability to activate ERK1/2 signaling pathway in HepG2 hepatocarcinoma cells. In conclusion, the strategy described here may represent an efficient alternative process for the production of hFGF19 and/or related proteins.

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Synonymous and nonsynonymous distances help untangle convergent evolution and recombination

Statistical Applications in Genetics and Molecular Biology ◽

10.1515/sagmb-2014-0078 ◽

2015 ◽

Vol 14 (4) ◽

Cited By ~ 2

Author(s):

Peter B. Chi ◽

Sujay Chattopadhyay ◽

Philippe Lemey ◽

Evgeni V. Sokurenko ◽

Vladimir N. Minin

Keyword(s):

Sequence Alignment ◽

Convergent Evolution ◽

Detection Method ◽

Synonymous Codon ◽

Multiple Sequence ◽

Phylogenetic Incongruence ◽

Recombination Detection ◽

Codon Substitution ◽

Tree Estimation ◽

Recombination Detection Method

AbstractWhen estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because different segments of the sequence alignment support different phylogenies. Similarly, convergent selective pressures at the molecular level can also lead to phylogenetic tree incongruence across the sequence alignment. Current methods for detection of phylogenetic incongruence are not equipped to distinguish between these two different mechanisms and assume that the incongruence is a result of recombination or other horizontal transfer of genetic information. We propose a new recombination detection method that can make this distinction, based on synonymous codon substitution distances. Although some power is lost by discarding the information contained in the nonsynonymous substitutions, our new method has lower false positive probabilities than the comparable recombination detection method when the phylogenetic incongruence signal is due to convergent evolution. We apply our method to three empirical examples, where we analyze: (1) sequences from a transmission network of the human immunodeficiency virus, (2)

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A mutation-selection model of protein evolution under persistent positive selection

10.1101/2021.05.18.444611 ◽

2021 ◽

Author(s):

Asif U Tamuri ◽

Mario dos Reis

Keyword(s):

Positive Selection ◽

Protein Evolution ◽

First Principles ◽

Synonymous Codon ◽

Selection Model ◽

Inference Procedure ◽

Codon Substitution ◽

Adaptive Radiations ◽

Surrogate Measure ◽

Evolution Of Proteins

We use first principles of population genetics to model the evolution of proteins under persistent positive selection (PPS). PPS may occur when organisms are subjected to persistent environmental change, during adaptive radiations, or in host-pathogen interactions. Our mutation-selection model indicates protein evolution under PPS is an irreversible Markov process, and thus proteins under PPS show a strongly asymmetrical distribution of selection coefficients among amino acid substitutions. Our model shows the criteria ω > 1 (where ω is the ratio of non-synonymous over synonymous codon substitution rates) to detect positive selection is conservative and indeed arbitrary, because in real proteins many mutations are highly deleterious and are removed by selection even at positively-selected sites. We use a penalized-likelihood implementation of our model to successfully detect PPS in plant RuBisCO and influenza HA proteins. By directly estimating selection coefficients at protein sites, our inference procedure bypasses the need for using ω as a surrogate measure of selection and improves our ability to detect molecular adaptation in proteins.

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Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes

PLoS ONE ◽

10.1371/journal.pone.0248337 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248337

Author(s):

Alexander G. Lucaci ◽

Sadie R. Wisotsky ◽

Stephen D. Shank ◽

Steven Weaver ◽

Sergei L. Kosakovsky Pond

Keyword(s):

Evolutionary Dynamics ◽

Synonymous Codon ◽

Model Misspecification ◽

Empirical Support ◽

Simulated Data ◽

Small Subset ◽

Evolutionary Models ◽

Single Nucleotide Change ◽

Codon Substitution ◽

Alignment Errors

Despite many attempts to introduce evolutionary models that permit substitutions to instantly alter more than one nucleotide in a codon, the prevailing wisdom remains that such changes are rare and generally negligible or are reflective of non-biological artifacts, such as alignment errors. Codon models continue to posit that only single nucleotide change have non-zero rates. Here, we develop and test a simple hierarchy of codon-substitution models with non-zero evolutionary rates for only one-nucleotide (1H), one- and two-nucleotide (2H), or any (3H) codon substitutions. Using over 42, 000 empirical alignments, we find widespread statistical support for multiple hits: 61% of alignments prefer models with 2H allowed, and 23%—with 3H allowed. Analyses of simulated data suggest that these results are not likely to be due to simple artifacts such as model misspecification or alignment errors. Further modeling reveals that synonymous codon island jumping among codons encoding serine, especially along short branches, contributes significantly to this 3H signal. While serine codons were prominently involved in multiple-hit substitutions, there were other common exchanges contributing to better model fit. It appears that a small subset of sites in most alignments have unusual evolutionary dynamics not well explained by existing model formalisms, and that commonly estimated quantities, such as dN/dS ratios may be biased by model misspecification. Our findings highlight the need for continued evaluation of assumptions underlying workhorse evolutionary models and subsequent evolutionary inference techniques. We provide a software implementation for evolutionary biologists to assess the potential impact of extra base hits in their data in the HyPhy package and in the Datamonkey.org server.

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The A756T Mutation of the ERG11 Gene Associated With Resistance to Itraconazole in Candida Krusei Isolated From Mycotic Mastitis of Cows

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.634286 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jun Du ◽

Wenshuang Ma ◽

Jiaqi Fan ◽

Xiaoming Liu ◽

Yujiong Wang ◽

...

Keyword(s):

Synonymous Codon ◽

Clinical Mastitis ◽

Candida Krusei ◽

Clinical Isolates ◽

Molecular Characteristics ◽

Sequencing Analysis ◽

Pcr Assay ◽

Qrt Pcr ◽

Flight Mass Spectrometry ◽

Codon Substitution

Candida krusei (C. krusei) has been recently recognized as an important pathogen involved in mycotic mastitis of cows. The phenotypic and molecular characteristics of 15 C. krusei clinical isolates collected from cows with clinical mastitis in three herds of Yinchuan, Ningxia, were identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry. In addition to sequencing analysis, the ERG11 gene that encodes 14α-demethylases, the expression of the ERG11 gene, and efflux transporters ABC1 and ABC2 in itraconazole-susceptible (S), itraconazole-susceptible dose dependent (SDD), and itraconazole-resistant (R) C. krusei isolates was also quantified by a quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) assay. Sequencing analysis revealed three synonymous codon substitutions of the ERG11 gene including T939C, A756T, and T642C in these C. krusei clinical isolates. Among them, T642C and T939C mutations were detected in itraconazole-resistant and -susceptible C. krusei isolates, but the A756T substitution was found only in itraconazole-resistant isolates. Importantly, the expression of the ERG11 gene in itraconazole-resistant isolates was significantly higher compared with itraconazole-SDD and itraconazole-susceptible isolates (p = 0.052 and p = 0.012, respectively), as determined by the qRT-PCR assay. Interestingly, the expression of the ABC2 gene was also significantly higher in itraconazole-resistant isolates relative to the itraconazole-SDD and itraconazole-susceptible strains. Notably, the expression of ERG11 was positively associated with resistance to itraconazole (p = 0.4177 in SDD compared with S, p = 0.0107 in SDD with R, and p = 0.0035 in S with R, respectively). These data demonstrated that mutations of the ERG11 gene were involved in drug resistance in C. krusei. The A756T synonymous codon substitution of the ERG11 gene was correlated with an increased expression of drug-resistant genes including ERG11 and ABC2 in itraconazole-resistant C. krusei isolates examined in this study.

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