An Evaluation of Measures of Synonymous Codon Usage Bias

Comeron, Josep M.; Aguadé, Montserrat

doi:10.1007/pl00006384

Cited by 302 publications

(222 citation statements)

References 20 publications

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“…The minimal number of differences found between males and females coupled with the individual variation already observed suggests that the differences are unlikely to represent expression of alternative genes. Furthermore, sequence polymorphism is a well described phenomenon in Drosophila XDH (32)(33)(34). Multiplicity of AOX genes has been established for some organisms (19 -24), and in plants these data are supported by multiple cDNA sequences of approximately 80% identity (19,20).…”

Section: Table III Quantitation Of Rna Hybridizationmentioning

confidence: 99%

cDNA Cloning, Sequencing, and Characterization of Male and Female Rat Liver Aldehyde Oxidase (rAOX1)

Wright

Clayton

Riley

et al. 1999

Journal of Biological Chemistry

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Molecular characterization of male and female rat liver aldehyde oxidase is reported. As described for the mouse liver, male and female rat liver expressed kinetically distinct forms of aldehyde oxidase. Our data suggest that the two forms arise as a result of differences in redox state and are most simply explained by expression of a single gene encoding aldehyde oxidase in rats. In support of this argument we have sequenced cDNAs from male and female rat liver. We examined mRNA expression by Northern blot analysis with RNA from males and females, from several tissues, and following androgen induction. Purified rat liver enzyme from males or females revealed a single 150-kDa species consistent with cDNA sequence analysis. Both male and female forms were reactive to the same carboxyl-terminal directed antisera. K m(app) values obtained in crude extracts of male or female rat liver and post-benzamidine-purified aldehyde oxidase differed substantially from each other but could be interconverted by chemical reduction with dithiothreitol or oxidation with 4,4-dithiodipyridine. Our data indicate that a single gene is most likely expressed in male or female rat liver and that the kinetic differences between male and female rat liver aldehyde oxidases are sensitive to redox manipulation. Aldehyde oxidase (AOX)1 is a member of the molybdenum cofactor containing enzymes. Native AOX is routinely prepared as a homodimer of 300 kDa. Each 150-kDa subunit contains two iron-sulfur centers, an FAD, and the molybdenum-pterin cofactor (MoCo) (1-3). AOX (EC 1.2.3.1) catalyzes the oxidation of a wide range of aldehydic compounds, purines, quinoliniums, and numerous pharmacologic agents. While substrate specificity for AOX is very broad, and wide species variation in substrate specificity exists, the general catalytic reaction takes the form of hydroxyl transfer from water to an aldehyde creating the cognate acid. For example, conversion of benzaldehyde to benzoic acid is a very efficient reaction for AOX from most species. Conversion of N-1-methyl nicotinamide (NMN) to the 2-or -4-pyridone has been used as a standard definition of AOXs, although it is usually a kinetically less efficient reaction than benzaldehyde oxidation.AOX is of interest both for its role in drug metabolism and as a source of the reactive oxygen species (ROS), hydrogen peroxide, and the superoxide anion, that have been related to numerous human pathologies. The human gene encoding AOX has been linked to a rare form of amyotrophic lateral sclerosis, although it is unknown if AOX encodes the amyotrophic lateral sclerosis locus itself (4 -6). ROS are generated from AOX in an oxidative half-reaction following reduction of the enzyme by substrate. The FeS, FAD, and MoCo cofactors comprise an internal electron transfer chain in which electrons are passed from the active site molybdenum center to the FeS centers and finally to FAD. Partial reduction of oxygen at the the reduced FAD site produces ROS. Unlike the related enzyme xanthine dehydrogenase (XDH), AOX does no...

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Section: Table III Quantitation Of Rna Hybridizationmentioning

confidence: 99%

cDNA Cloning, Sequencing, and Characterization of Male and Female Rat Liver Aldehyde Oxidase (rAOX1)

Wright

Clayton

Riley

et al. 1999

Journal of Biological Chemistry

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“…This relative difference in the frequency of event for each codon is called codon bias. The codon usage table for a species Homo sapiens and E. coli gives the codon bias information for that species (27). To date, the heterologous gene expression is applied as a fundamental methodology in biological process with some restrictions in implementation (33).…”

Section: Discussionmentioning

confidence: 99%

“…MN002309.3) which was optimized for fully expression in E. coli. Genetic codons of amino acids coded by more than one codon were changed to synonymous codons commonly used by E. coli (27). The optimized sequence was chemically synthesized and inserted in to the expression vector pET-28a (+) with BamHI and XbaI restriction sites (Generay Biotech Co., Ltd).…”

Section: Constructing Expression Vector Of Pet-28a (+)-Hlifmentioning

confidence: 99%

Codon Optimization, Cloning and Expression of the Human Leukemia Inhibitory Factor (hLIF) in E. coli

et al. 2012

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“…A phenomenon designated codon usage bias (1)(2)(3). Codon usage bias among synonymous codons has been documented for numerous genes in variant species (3)(4)(5)(6)(7)(8)(9). It is reported that synonymous codon usage bias may be connected with different biological factors (6,(10)(11)(12)(13).…”

Section: Introductionmentioning

confidence: 99%

Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene

et al. 2013

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Background: Little knowledge of synonymous codon usage pattern of pseudorabies virus (PRV) genome, especially the UL31 gene in the process for its evolution is available. Objectives: In the present study, the codon usage bias between PRV UL31 sequence and the UL31-like sequences was identified. Materials and Methods:We used a comprehensive analysis on codon usage pattern in the PRV UL31 gene and the UL31-like genes of 48 reference herpesviruses by calculating codon adaptation index, ENc, RSCU and EMBOSS assays. Results: Cluster analysis demonstrated that the codon usage bias of UL31-like genes of 49 herpesviruses had a very close relation to their gene functions. In addition, comparison of codon preferences in the UL31 gene of PRV with those of E. coli, yeast and human showed that there were 33 codons showing discrete usage differences between PRV and yeast, 24 between PRV and E. coli, but 22 between PRV and human. Although there were slightly fewer differences in codon usages between PRV and human, the difference is unlikely to be statistically significant, and experimental studies are necessary to establish the most suitable expression system for PRV UL31. Conclusions: These results may further our comprehending of the evolution, pathogenesis and functional studies of PRV.

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An Evaluation of Measures of Synonymous Codon Usage Bias

Cited by 302 publications

References 20 publications

cDNA Cloning, Sequencing, and Characterization of Male and Female Rat Liver Aldehyde Oxidase (rAOX1)

cDNA Cloning, Sequencing, and Characterization of Male and Female Rat Liver Aldehyde Oxidase (rAOX1)

Codon Optimization, Cloning and Expression of the Human Leukemia Inhibitory Factor (hLIF) in E. coli

Identification of Synonymous Codon Usage Bias in the Pseudorabies Virus UL31 Gene

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