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Plant and Cell Physiology Advance Access originally published online on February 18, 2009
Plant and Cell Physiology 2009 50(4):773-788; doi:10.1093/pcp/pcp027
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© The Author 2009. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Plant and Cell Physiology issue: Special Issue Articles: Photosynthesis [View the issue table of contents]

Special Issue - Regular Paper

Orthogenomics of Photosynthetic Organisms: Bioinformatic and Experimental Analysis of Chloroplast Proteins of Endosymbiont Origin in Arabidopsis and Their Counterparts in Synechocystis

Masayuki Ishikawa1, Makoto Fujiwara1, Kintake Sonoike2 and Naoki Sato1,*

1Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902 Japan
2Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba, 277-8562 Japan

*Corresponding author: E-mail, naokisat{at}bio.c.u-tokyo.ac.jp


  Abstract

Chloroplasts are descendents of a cyanobacterial endosymbiont, but many chloroplast protein genes of endosymbiont origin are encoded by the nucleus. The chloroplast–cyanobacteria 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.

Keywords: Arabidopsis thaliana - Chloroplast protein - Comparative genomics - Endosymbiogenesis - Photosynthetic gene - Synechocystis sp. PCC 6803

Abbreviations: CPRENDO, chloroplast protein of endo-symbiont origin; GFP, green fluorescent protein; PAM, pulse amplitude modulation.

(Received January 8, 2009; Accepted February 12, 2009)
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