Bryan L Payne

Highly Abundant Proteins Are Highly Thermostable

Agusto Luzuriaga-Neira, Andrew M. Ritchie, Bryan L Payne, Oliver Carrillo et autres

Highly abundant proteins tend to evolve slowly (a trend called E-R anticorrelation), and a number of hypotheses have been proposed to explain this phenomenon. The misfolding avoidance hypothesis attributes the E-R anticorrelation to the abundance-dependent toxic effects of protein misfolding. To avoid …

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The Codon Statistics Database: A Database of Codon Usage Bias

Krishnamurthy Subramanian, Bryan L Payne, Felix Feyertag, David Alvarez‐Ponce

We present the Codon Statistics Database, an online database that contains codon usage statistics for all the species with reference or representative genomes in RefSeq (over 15,000). The user can search for any species and access two sets of tables. One set …

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The Codon Statistics Database: a Database of Codon Usage Bias

Krishnamurthy Subramanian, Bryan L Payne, Felix Feyertag, David Alvarez‐Ponce

ABSTRACT Motivation Most amino acids can be encoded by a set of synonymous codons. Often, for any given amino acid, certain codons are significantly more used than others, a phenomenon known as codon usage bias. The genomes of different species differ in …

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Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster

Bryan L Payne, David Alvarez‐Ponce

Codon usage patterns are affected by both mutational biases and translational selection. The frequency at which each codon is used in the genome is directly linked to the cellular concentrations of their corresponding tRNAs. Transfer RNA abundances-as well as the abundances of …

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Proteins of generalist and specialist pathogens differ in their amino acid composition

Luz P. Blanco, Bryan L Payne, Felix Feyertag, David Alvarez‐Ponce

Pathogens differ in their host specificities, with species infecting a unique host (specialist pathogens) and others having a wide host range (generalists). Molecular determinants of pathogen's host range remain poorly understood. Secreted proteins of generalist pathogens are expected to have a broader …

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Higher Rates of Protein Evolution in the Self-Fertilizing Plant Arabidopsis thaliana than in the Out-Crossers Arabidopsis lyrata and Arabidopsis halleri

Bryan L Payne, David Alvarez‐Ponce

The common transition from out-crossing to self-fertilization in plants decreases effective population size. This is expected to result in a reduced efficacy of natural selection and in increased rates of protein evolution in selfing plants compared with their outcrossing congeners. Prior analyses, …

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Differences in the Protein Evolutionary Rates of Arabidopsis Species and Codon Usage Biases in the Tissues of Drosophila melanogaster

Bryan L Payne