title: Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment.
abstract: BACKGROUND
  Chloroplasts and mitochondria evolved from the endosymbionts of once free-living eubacteria, and they transferred most of their genes to the host nuclear genome during evolution. The mechanisms used by plants to coordinate the expression of such transferred genes, as well as other genes in the host nuclear genome, are still poorly understood.
  
  
  RESULTS
  In this paper, we use nuclear-encoded chloroplast (cpRPGs), as well as mitochondrial (mtRPGs) and cytoplasmic (euRPGs) ribosomal protein genes to study the coordination of gene expression between organelles and the host. Results show that the mtRPGs, but not the cpRPGs, exhibit strongly synchronized expression with euRPGs in all investigated land plants and that this phenomenon is linked to the presence of a telo-box DNA motif in the promoter regions of mtRPGs and euRPGs. This motif is also enriched in the promoter regions of genes involved in DNA replication. Sequence analysis further indicates that mtRPGs, in contrast to cpRPGs, acquired telo-box from the host nuclear genome.
  
  
  CONCLUSIONS
  Based on our results, we propose a model of plant nuclear genome evolution where coordination of activities in mitochondria and chloroplast and other cellular functions, including cell cycle, might have served as a strong selection pressure for the differential acquisition of telo-box between mtRPGs and cpRPGs. This research also highlights the significance of physiological needs in shaping transcriptional regulatory evolution.
authors.affiliation: Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wang
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.forename: Xin-Guang
authors.initials: XG
authors.lastname: Zhu
authors.forename: Xiaotu
authors.initials: X
authors.lastname: Ma
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D002736:Chloroplasts / Q000235:genetics*; D032461:Chromosomes, Plant; D003600:Cytosol / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D024101:Mitochondrial Proteins / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012269:Ribosomal Proteins / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D024101:Mitochondrial Proteins; D010940:Plant Proteins; D012269:Ribosomal Proteins; D014157:Transcription Factors