title: Evolution of Drosophila ribosomal protein gene core promoters.
abstract: The coordinated expression of ribosomal protein genes (RPGs) has been well documented in many species. Previous analyses of RPG promoters focus only on Fungi and mammals. Recognizing this gap and using a comparative genomics approach, we utilize a motif-finding algorithm that incorporates cross-species conservation to identify several significant motifs in Drosophila RPG promoters. As a result, significant differences of the enriched motifs in RPG promoter are found among Drosophila, Fungi, and mammals, demonstrating the evolutionary dynamics of the ribosomal gene regulatory network. We also report a motif present in similar numbers of RPGs among Drosophila species which does not appear to be conserved at the individual RPG gene level. A module-wise stabilizing selection theory is proposed to explain this observation. Overall, our results provide significant insight into the fast-evolving nature of transcriptional regulation in the RPG module.
authors.affiliation: Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Xiaotu
authors.initials: X
authors.lastname: Ma
authors.forename: Kangyu
authors.initials: K
authors.lastname: Zhang
authors.forename: Xiaoman
authors.initials: X
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence; D004261:DNA Replication / Q000235:genetics; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics; D017344:Genes, Insect; D008322:Mammals / Q000235:genetics; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D017434:Protein Structure, Tertiary; D012269:Ribosomal Proteins / Q000235:genetics*; D012641:Selection, Genetic; D013045:Species Specificity; D014157:Transcription Factors / Q000737:chemistry
chemical_list: D003062:Codon; D029721:Drosophila Proteins; D012269:Ribosomal Proteins; D014157:Transcription Factors