Distributional gradient of amino acid repeats in plant proteins

A computer-based analysis was conducted to assess the characteristics of amino acid repeats in Arabidopsis and rice. Our analysis showed a negative gradient in amino acid repeat distribution along the direction of translation in plants. Repeat occurrences are obviously associated with position in plant proteins but are not consistent with the corresponding amino acid contents. These repeats are encoded by the mixed synonymous codons rather than the uninterrupted reiterations of a single codon, and both Arabidopsis and rice have gradients in their distribution. Functional investigation showed that these repeat-containing proteins are preferentially involved in transcription regulation and protein ubiquitination but significantly underrepresented in the processes of DNA recombination and DNA replication. These data reveal that the direction-related mutation bias and functional selection have influenced the distribution of amino acid repeats in plants.Key words: amino acid repeats, amino acid usage, distributional gradient, regulation of transcription, protein ubiquitination.