Takuro Nakayama

Publications of Takuro Nakayama

• Spheroid bodies in rhopalodiacean diatoms were derived from a single endosymbiotic cyanobacterium.

  Authors: Takuro Nakayama, Yuko Ikegami, Takeshi Nakayama, Ken-Ichiro Ishida, Yuji Inagaki, Isao Inouye

  Journal of plant research. 01/2011; 124(1):93-7.

  Members of the diatom family rhopalodiaceae possess cyanobacteria-derived intracellular structures called spheroid bodies (SBs) that very likely carry out nitrogen fixation. Due to the shortage ofMembers of the diatom family rhopalodiaceae possess cyanobacteria-derived intracellular structures called spheroid bodies (SBs) that very likely carry out nitrogen fixation. Due to the shortage of molecular data from SBs and rhopalodiacean diatoms, it remains unclear how SBs were established and spread in rhopalodiacean diatoms. We here amplified the small subunit ribosomal DNA sequences from both host and SB in three rhopalodiacean diatom species, Epithemia turgida, E. sorex, and Rhopalodia gibba. Phylogenetic analyses considering these new sequences clearly indicate that the SBs were acquired by a common ancestor of rhopalodiacean diatoms and have been retained during host speciation.

• Cercozoa comprises both EF-1α-containing and EFL-containing members.

  Authors: Ryoma Kamikawa, Akinori Yabuki, Takuro Nakayama, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji Inagaki

  European journal of protistology. 11/2010; 47(1):24-8.

  Elongation factor 1α (EF-1α) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided intoElongation factor 1α (EF-1α) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided into 'EF-1α-containing' and 'EFL-containing' types. Recently, EF-1α and EFL genes have been surveyed across the diversity of eukaryotes to explore the origin and evolution of EFL genes. Although the phylum Cercozoa is a diverse group, gene data for either EFL or EF-1α are absent from all cercozoans except chlorarachniophytes which were previously defined as EFL-containing members. Our survey revealed that two members of the cercozoan subphylum Filosa (Thaumatomastix sp. and strain YPF610) are EFL-containing members. Importantly, we identified EF-1α genes from two members of Filosa (Paracercomonas marina and Paulinella chromatophora) and a member of the other subphylum Endomyxa (Filoreta japonica). All cercozoan EFL homologues could not be recovered as a monophyletic group in maximum-likelihood and Bayesian analyses, suggesting that lateral gene transfer was involved in the EFL evolution in this protist assemblage. In contrast, EF-1α analysis successfully recovered a monophyly of three homologues sampled from the two cercozoan subphyla. Based on the results, we postulate that cercozoan EF-1α genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1α genes.

• Differential gene retention in plastids of common recent origin.

  Authors: Adrian Reyes-Prieto, Hwan Su Yoon, Ahmed Moustafa, Eun Chan Yang, Robert A Andersen, Sung Min Boo, Takuro Nakayama, Ken-ichiro Ishida, Debashish Bhattacharya

  Molecular biology and evolution. 07/2010; 27(7):1530-7.

  The cyanobacterium-derived plastids of algae and plants have supported the diversification of much of extant eukaryotic life. Inferences about early events in plastid evolution must rely onThe cyanobacterium-derived plastids of algae and plants have supported the diversification of much of extant eukaryotic life. Inferences about early events in plastid evolution must rely on reconstructing events that occurred over a billion years ago. In contrast, the photosynthetic amoeba Paulinella chromatophora provides an exceptional model to study organelle evolution in a prokaryote-eukaryote (primary) endosymbiosis that occurred approximately 60 mya. Here we sequenced the plastid genome (0.977 Mb) from the recently described Paulinella FK01 and compared the sequence with the existing data from the sister taxon Paulinella M0880/a. Alignment of the two plastid genomes shows significant conservation of gene order and only a handful of minor gene rearrangements. Analysis of gene content reveals 66 differential gene losses that appear to be outright gene deletions rather than endosymbiotic gene transfers to the host nuclear genome. Phylogenomic analysis validates the plastid ancestor as a member of the Synechococcus-Prochlorococcus group, and the cyanobacterial provenance of all plastid genes suggests that these organelles were not targets of interphylum gene transfers after endosymbiosis. Inspection of 681 DNA alignments of protein-encoding genes shows that the vast majority have dN/dS ratios <1, providing evidence for purifying selection. Our study demonstrates that plastid genomes in sister taxa are strongly constrained by selection but follow distinct trajectories during the earlier phases of organelle evolution.

• Another acquisition of a primary photosynthetic organelle is underway in Paulinella chromatophora.

  Authors: Takuro Nakayama, Ken-Ichiro Ishida

  Current biology : CB. 05/2009; 19(7):R284-5.

• A single origin of the photosynthetic organelle in different Paulinella lineages.

  Authors: Hwan Su Yoon, Takuro Nakayama, Adrian Reyes-Prieto, Robert A Andersen, Sung Min Boo, Ken-Ichiro Ishida, Debashish Bhattacharya

  BMC evolutionary biology. 02/2009; 9:98.

  BACKGROUND: Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines ofBACKGROUND: Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines of photosynthesis are plastids (e.g., chloroplast in plants) that evolved from cyanobacteria through primary endosymbiosis. Our knowledge of plastid evolution, however, remains limited because the primary endosymbiosis occurred more than a billion years ago. In this context, the thecate "green amoeba" Paulinella chromatophora is remarkable because it very recently (i.e., minimum age of approximately 60 million years ago) acquired a photosynthetic organelle (termed a "chromatophore"; i.e., plastid) via an independent primary endosymbiosis involving a Prochlorococcus or Synechococcus-like cyanobacterium. All data regarding P. chromatophora stem from a single isolate from Germany (strain M0880/a). Here we brought into culture a novel photosynthetic Paulinella strain (FK01) and generated molecular sequence data from these cells and from four different cell samples, all isolated from freshwater habitats in Japan. Our study had two aims. The first was to compare and contrast cell ultrastructure of the M0880/a and FK01 strains using scanning electron microscopy. The second was to assess the phylogenetic diversity of photosynthetic Paulinella to test the hypothesis they share a vertically inherited plastid that originated in their common ancestor. RESULTS: Comparative morphological analyses show that Paulinella FK01 cells are smaller than M0880/a and differ with respect to the number of scales per column. There are more distinctive, multiple fine pores on the external surface of FK01 than in M0880/a. Molecular phylogenetic analyses using multiple gene markers demonstrate these strains are genetically distinct and likely comprise separate species. The well-supported monophyly of the Paulinella chromatophora strains analyzed here using plastid-encoded 16S rRNA suggests strongly that they all share a common photosynthetic ancestor. The strain M0880/a is most closely related to Japanese isolates (Kanazawa-1, -2, and Kaga), whereas FK01 groups closely with a Kawaguchi isolate. CONCLUSION: Our results indicate that Paulinella chromatophora comprises at least two distinct evolutionary lineages and likely encompasses a broader taxonomic diversity than previously thought. The finding of a single plastid origin for both lineages shows these taxa to be valuable models for studying post-endosymbiotic cell and genome evolution.

• A single origin of the photosynthetic organelle in different Paulinella lineages

  Authors: Yoon Hwan Su, Takuro Nakayama, Adrian Reyes-Prieto, Robert Andersen, Boo Sung Min, Ken-Ichiro Ishida, Debashish Bhattacharya

  BMC Evolutionary Biology. 01/2009;

  Abstract Background Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines ofAbstract Background Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines of photosynthesis are plastids (e.g., chloroplast in plants) that evolved from cyanobacteria through primary endosymbiosis. Our knowledge of plastid evolution, however, remains limited because the primary endosymbiosis occurred more than a billion years ago. In this context, the thecate "green amoeba" Paulinella chromatophora is remarkable because it very recently (i.e., minimum age of ≈ 60 million years ago) acquired a photosynthetic organelle (termed a "chromatophore"; i.e., plastid) via an independent primary endosymbiosis involving a Prochlorococcus or Synechococcus -like cyanobacterium. All data regarding P. chromatophora stem from a single isolate from Germany (strain M0880/a). Here we brought into culture a novel photosynthetic Paulinella strain (FK01) and generated molecular sequence data from these cells and from four different cell samples, all isolated from freshwater habitats in Japan. Our study had two aims. The first was to compare and contrast cell ultrastructure of the M0880/a and FK01 strains using scanning electron microscopy. The second was to assess the phylogenetic diversity of photosynthetic Paulinella to test the hypothesis they share a vertically inherited plastid that originated in their common ancestor. Results Comparative morphological analyses show that Paulinella FK01 cells are smaller than M0880/a and differ with respect to the number of scales per column. There are more distinctive, multiple fine pores on the external surface of FK01 than in M0880/a. Molecular phylogenetic analyses using multiple gene markers demonstrate these strains are genetically distinct and likely comprise separate species. The well-supported monophyly of the Paulinella chromatophora strains analyzed here using plastid-encoded 16S rRNA suggests strongly that they all share a common photosynthetic ancestor. The strain M0880/a is most closely related to Japanese isolates (Kanazawa-1, -2, and Kaga), whereas FK01 groups closely with a Kawaguchi isolate. Conclusion Our results indicate that Paulinella chromatophora comprises at least two distinct evolutionary lineages and likely encompasses a broader taxonomic diversity than previously thought. The finding of a single plastid origin for both lineages shows these taxa to be valuable models for studying post-endosymbiotic cell and genome evolution.

• Cercozoa comprises both EF-1α-containing and EFL-containing members

  Authors: Ryoma Kamikawa, Akinori Yabuki, Takuro Nakayama, Ken-ichiro Ishida, Tetsuo Hashimoto, Yuji Inagaki

  European Journal of Protistology.

  Elongation factor 1α (EF-1α) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided intoElongation factor 1α (EF-1α) and elongation factor-like protein (EFL) are considered to be functionally equivalent proteins involved in peptide synthesis. Eukaryotes can be fundamentally divided into ‘EF-1α-containing’ and ‘EFL-containing’ types. Recently, EF-1α and EFL genes have been surveyed across the diversity of eukaryotes to explore the origin and evolution of EFL genes. Although the phylum Cercozoa is a diverse group, gene data for either EFL or EF-1α are absent from all cercozoans except chlorarachniophytes which were previously defined as EFL-containing members. Our survey revealed that two members of the cercozoan subphylum Filosa (Thaumatomastix sp. and strain YPF610) are EFL-containing members. Importantly, we identified EF-1α genes from two members of Filosa (Paracercomonas marina and Paulinella chromatophora) and a member of the other subphylum Endomyxa (Filoreta japonica). All cercozoan EFL homologues could not be recovered as a monophyletic group in maximum-likelihood and Bayesian analyses, suggesting that lateral gene transfer was involved in the EFL evolution in this protist assemblage. In contrast, EF-1α analysis successfully recovered a monophyly of three homologues sampled from the two cercozoan subphyla. Based on the results, we postulate that cercozoan EF-1α genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1α genes.

• Comprehensive SSU rRNA Phylogeny of Eukaryota

  Authors: Ken-ichiro Ishida, Yuji Inagaki, Miako Sakaguchi, Atsushi Oiwa, Atsushi Kai, Masahiro Suzuki, Takuro Nakayama, Tomoko Chikuni, Akinori Yabuki, Haruyo Yamaguchi, Naoji Yubuki, Masaki Yoshi- da, Takeshi Nakayama, Isao Inouye, Tetsuo Hashimoto

  20:81-88.

  The SSU rRNA gene has been the most sequenced mo­ lecule from various eukaryotes and the SSU rRNA phy­ logeny is still a useful tool for tracing the evolutionary history of eukaryotes and forThe SSU rRNA gene has been the most sequenced mo­ lecule from various eukaryotes and the SSU rRNA phy­ logeny is still a useful tool for tracing the evolutionary history of eukaryotes and for elucidating phylogenetic positions of newly discovered organisms and environ­ mental sequences. However, SSU rRNA tree with com­ prehensive taxon­sampling from eukaryotes hasn’t been reported for a decade. Here, an updated compre­ hensive SSU rRNA phylogeny of Eukaryota was recon­ structed using the maximum likelihood method for the first time. The resulted tree roughly agreed with those that have recently been reconstructed with various multi­gene datasets and recovered many of major eu­ karyotic groups as monophyletic lineages, though some of those did not gain good support by bootstrap proba­ bility value and the relationship among major lineages was not well resolved. The major eukaryotic groups that were not recovered were Excavata, Hacrobia, Amoebozoa, and Archaeplastida. The present updated SSU rRNA tree provides a current version of SSU rRNA phlogeny and can be used as a reference tree for vari­ ous researches on the phylogeny, evolution and diversi­ ty of eukaryotes.

• Comprehensive SSU rRNA Phylogeny of Eukaryota

  Authors: Ken-ichiro Ishida, Yuji Inagaki, Miako Sakaguchi, Atsushi Oiwa, Atsushi Kai, Masahiro Suzuki, Takuro Nakayama, Tomoko Chikuni, Akinori Yabuki, Haruyo Yamaguchi, Naoji Yubuki, Masaki Yoshi- da, Takeshi Nakayama, Isao Inouye, Tetsuo Hashimoto

  Journal of Endocytobiosis and Cell Research. 20:81-88.