Orthogenomics of photosynthetic organisms

Bioinformatic and experimental analysis of chloroplast proteins of endosymbiont origin in arabidopsis and their counterparts in synechocystis

Masayuki Ishikawa, Makoto Fujiwara, Kintake Sonoike, Naoki Sato

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Chloroplasts are descendents of a cyanobacterial endosymbiont, but many chloroplast protein genes of endosymbiont origin are encoded by the nucleus. The chloroplastcyanobacteria relationship is a typical target of orthogenomics, an analytical method that focuses on the relationship of orthologous genes. Here, we present results of a pilot study of functional orthogenomics, combining bioinformatic and experimental analyses, to identify nuclear-encoded chloroplast proteins of endosymbiont origin (CPRENDOs). Phylogenetic profiling based on complete clustering of all proteins in 17 organisms, including eight cyanobacteria and two photosynthetic eukaryotes, was used to deduce 65 protein groups that are conserved in all oxygenic autotrophs analyzed but not in non-oxygenic organisms. With the exception of 28 well-characterized protein groups, 56 Arabidopsis proteins and 43 Synechocystis proteins in the 37 conserved homolog groups were analyzed. Green fluorescent protein (GFP) targeting experiments indicated that 54 Arabidopsis proteins were targeted to plastids. Expression of 39 Arabidopsis genes was promoted by light. Among the 40 disruptants of Synechocystis, 22 showed phenotypes related to photosynthesis. Arabidopsis mutants in 21 groups, including those reported previously, showed phenotypes. Characteristics of pulse amplitude modulation fluorescence were markedly different in corresponding mutants of Arabidopsis and Synechocystis in most cases. We conclude that phylogenetic profiling is useful in finding CPRENDOs, but the physiological functions of orthologous genes may be different in chloroplasts and cyanobacteria.

Original languageEnglish
Pages (from-to)773-788
Number of pages16
JournalPlant and Cell Physiology
Volume50
Issue number4
DOIs
Publication statusPublished - 2009 Apr
Externally publishedYes

Fingerprint

Chloroplast Proteins
Synechocystis
endosymbionts
autotrophs
Computational Biology
Arabidopsis
bioinformatics
chloroplasts
Arabidopsis Proteins
Cyanobacteria
Chloroplasts
Proteins
proteins
Chloroplast Genes
Genes
Phenotype
Plastids
Photosynthesis
Protein Transport
Green Fluorescent Proteins

Keywords

  • Arabidopsis thaliana
  • Chloroplast protein
  • Comparative genomics
  • Endosymbiogenesis
  • Photosynthetic gene
  • Synechocystis sp. PCC 6803

ASJC Scopus subject areas

  • Plant Science
  • Physiology
  • Cell Biology

Cite this

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title = "Orthogenomics of photosynthetic organisms: Bioinformatic and experimental analysis of chloroplast proteins of endosymbiont origin in arabidopsis and their counterparts in synechocystis",
abstract = "Chloroplasts are descendents of a cyanobacterial endosymbiont, but many chloroplast protein genes of endosymbiont origin are encoded by the nucleus. The chloroplastcyanobacteria relationship is a typical target of orthogenomics, an analytical method that focuses on the relationship of orthologous genes. Here, we present results of a pilot study of functional orthogenomics, combining bioinformatic and experimental analyses, to identify nuclear-encoded chloroplast proteins of endosymbiont origin (CPRENDOs). Phylogenetic profiling based on complete clustering of all proteins in 17 organisms, including eight cyanobacteria and two photosynthetic eukaryotes, was used to deduce 65 protein groups that are conserved in all oxygenic autotrophs analyzed but not in non-oxygenic organisms. With the exception of 28 well-characterized protein groups, 56 Arabidopsis proteins and 43 Synechocystis proteins in the 37 conserved homolog groups were analyzed. Green fluorescent protein (GFP) targeting experiments indicated that 54 Arabidopsis proteins were targeted to plastids. Expression of 39 Arabidopsis genes was promoted by light. Among the 40 disruptants of Synechocystis, 22 showed phenotypes related to photosynthesis. Arabidopsis mutants in 21 groups, including those reported previously, showed phenotypes. Characteristics of pulse amplitude modulation fluorescence were markedly different in corresponding mutants of Arabidopsis and Synechocystis in most cases. We conclude that phylogenetic profiling is useful in finding CPRENDOs, but the physiological functions of orthologous genes may be different in chloroplasts and cyanobacteria.",
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author = "Masayuki Ishikawa and Makoto Fujiwara and Kintake Sonoike and Naoki Sato",
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T2 - Bioinformatic and experimental analysis of chloroplast proteins of endosymbiont origin in arabidopsis and their counterparts in synechocystis

AU - Ishikawa, Masayuki

AU - Fujiwara, Makoto

AU - Sonoike, Kintake

AU - Sato, Naoki

PY - 2009/4

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KW - Arabidopsis thaliana

KW - Chloroplast protein

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