title: Distributional gradient of amino acid repeats in plant proteins.
abstract: 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.
authors.affiliation: Plant Biotechnology Research Center, Institute of Systems Biology, Shanghai Key Laboratory of Agrobiotechnology, Fudan-SJTU-Nottingham Plant Biotechnology R & D Center, School of Agriculture, Shanghai, China.
authors.forename: Lida
authors.initials: L
authors.lastname: Zhang
authors.forename: Shunwu
authors.initials: S
authors.lastname: Yu
authors.forename: Youfang
authors.initials: Y
authors.lastname: Cao
authors.forename: Jiang
authors.initials: J
authors.lastname: Wang
authors.forename: Kaijing
authors.initials: K
authors.lastname: Zuo
authors.forename: Jie
authors.initials: J
authors.lastname: Qin
authors.forename: Kexuan
authors.initials: K
authors.lastname: Tang
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000502:physiology; D003062:Codon / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030562:Databases, Protein; D012275:Oryza / Q000235:genetics / Q000502:physiology; D010940:Plant Proteins / Q000235:genetics* / Q000502:physiology; D020449:Repetitive Sequences, Amino Acid
chemical_list: D029681:Arabidopsis Proteins; D003062:Codon; D018076:DNA, Complementary; D018744:DNA, Plant; D010940:Plant Proteins