title: Eukaryotic Components Remodeled Chloroplast Nucleoid Organization during the Green Plant Evolution.
abstract: Chloroplast (cp) DNA is thought to originate from the ancestral endosymbiont genome and is compacted to form nucleoprotein complexes, cp nucleoids. The structure of cp nucleoids is ubiquitously observed in diverse plants from unicellular algae to flowering plants and is believed to be a multifunctional platform for various processes, including cpDNA replication, repair/recombination, transcription, and inheritance. Despite its fundamental functions, the protein composition for cp nucleoids in flowering plants was suggested to be divergent from those of bacteria and algae, but the evolutionary process remains elusive. In this research, we aimed to reveal the evolutionary history of cp nucleoid organization by analyzing the key organisms representing the three evolutionary stages of eukaryotic phototrophs: the chlorophyte alga Chlamydomonas reinhardtii, the charophyte alga Klebsormidium flaccidum, and the most basal land plant Marchantia polymorpha. To clarify the core cp nucleoid proteins in C. reinhardtii, we performed an LC-MS/MS analysis using highly purified cp nucleoid fractions and identified a novel SAP domain-containing protein with a eukaryotic origin as a constitutive core component. Then, homologous genes for cp nucleoid proteins were searched for in C. reinhardtii, K. flaccidum, and M. polymorpha using the genome databases, and their intracellular localizations and DNA binding activities were investigated by cell biological/biochemical analyses. Based on these results, we propose a model that recurrent modification of cp nucleoid organization by eukaryotic factors originally related to chromatin organization might have been the driving force for the diversification of cp nucleoids since the early stage of green plant evolution.
authors.affiliation: Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kobayashi
authors.affiliation: Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan Department of Biological Science and Chemistry, Faculty of Science, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan.
authors.forename: Mari
authors.initials: M
authors.lastname: Takusagawa
authors.affiliation: Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan.
authors.forename: Naomi
authors.initials: N
authors.lastname: Harada
authors.affiliation: Plant Global Educational Project, and Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Japan Department of Bioinformatics, Ritsumeikan University, Kusatsu, Shiga, Japan.
authors.forename: Yoichiro
authors.initials: Y
authors.lastname: Fukao
authors.affiliation: Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
authors.forename: Shohei
authors.initials: S
authors.lastname: Yamaoka
authors.affiliation: Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
authors.forename: Takayuki
authors.initials: T
authors.lastname: Kohchi
authors.affiliation: Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama City, Kanagawa, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Hori
authors.affiliation: Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, Yokohama City, Kanagawa, Japan Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-Ku, Tokyo, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ohta
authors.affiliation: Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan.
authors.forename: Toshiharu
authors.initials: T
authors.lastname: Shikanai
authors.affiliation: Laboratory of Plant Molecular Genetics, Department of Botany, Kyoto University, Oiwake-Cho, Kita-Shirakawa, Kyoto, Japan yoshiki@pmg.bot.kyoto-u.ac.jp.
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Nishimura
mesh_terms: D016825:Chlamydomonas reinhardtii / Q000235:genetics; D060365:Chloroplast Proteins / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D054628:Genome, Chloroplast; D047008:Marchantia / Q000235:genetics
chemical_list: D060365:Chloroplast Proteins
keywords: chloroplast; endosymbiosis; evolution; nucleoid