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Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis

Nature Cell Biology volume 3, pages 210–214 (2001)Cite this article

Abstract

The origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria was proposed on the basis of the phylogenetic topologies of genes1,2,3. However, it was not possible to conclude whether or not the genes involved were authentic representative genes4. Furthermore, using the BLAST5 and FASTA6 programs, the similarity of open reading frame (ORF) groups between three domains (Eukarya, Archaea and Bacteria) was estimated at one threshold7,8. Therefore, their similarities at other thresholds could not be clarified. Here we use our newly developed 'homology-hit analysis' method, which uses multiple thresholds, to determine the origin of the nucleus. We removed mitochondria-related ORFs from yeast ORFs, and determined the number of yeast orthologous ORFs in each functional category to the ORFs in six Archaea and nine Bacteria at several thresholds (E-values) using the BLAST. Our results indicate that yeast ORFs related to the nucleus may share their origins with archaeal ORFs, whereas ORFs that are related to the cytoplasm may share their origins with bacterial ORFs. Our results thus strongly support the idea of nucleus symbiosis.

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Figure 1: Hit numbers of yeast ORFs to various bacterial ORFs and Zi(1) values at each threshold.
Figure 2: Origins of subcellular organs and functions as determined by homology-hit analysis.

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Acknowledgements

We wish to thank Y. Tateno (National Institute of Genetics, Japan) and H. Watanabe (Institute of Medical, Physical and Chemical Research, Univ. Tokyo) for valuable suggestions. We also thank W. Bayar and K. Mizuno for their assistance in the analyses.

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Authors and Affiliations

  1. Department of Biological and Chemical Engineering, Faculty of Engineering, Gunma University, Kiryu, 376-8515, Gunma, Japan

    Tokumasa Horiike, Kazuo Hamada & Takao Shinozawa

  2. Department of Bio-system Engineering, Faculty of Engineering, Yamagata University, Yonezawa, 992-0038, Yamagata, Japan

    Shigehiko Kanaya

Authors
  1. Tokumasa Horiike
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  2. Kazuo Hamada
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  3. Shigehiko Kanaya
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  4. Takao Shinozawa
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Correspondence to Takao Shinozawa.

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Horiike, T., Hamada, K., Kanaya, S. et al. Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nat Cell Biol 3, 210–214 (2001). https://doi.org/10.1038/35055129

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