Takuro Nakayama

Differential Gene Retention in Plastids of Common Recent Origin

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 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

Summary The birth of plastids brought photosynthesis to eukaryotes and had a huge impact on their evolution. Despite its importance, details of the plastid acquisition process through primary endosymbiosis are not well understood. Recently, a cercozoan testate amoeba, Paulinella chromatophora, has received considerable attention because it may be able to provide insights into the transition from a cyanobacterial endosymbiont to a photosynthetic organelle [1–3]. The P. chromatophora cell contains two chromatophores that look like cylindrical cyanobacteria [4,5], and it has been debated whether these chromatophores are endosymbiotic cyanobacteria or photosynthetic organelles [4–7]. The chromatophore genome of P. chromatophora strain M0880/a was recently sequenced, revealing that its size (∼1 Mbp) has been reduced and that it lacks several genes important to cyanobacteria, including a few photosynthetic genes [3]. Here, we obtained concrete evidence that psaE , one of the photosynthetic genes, is expressed from the nuclear genome of P. chromatophora . This indicates that the psaE gene has been transferred into the nuclear genome from the chromatophore. Thus, another primary endosymbiotic acquisition of a photosynthetic organelle is under way.

Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle

Significance Members of the diatom family Rhopalodiaceae possess a cyanobacterial endosymbiont called a “spheroid body.” The spheroid body evolved much more recently than did mitochondria or plastids and is predicted to fix nitrogen. Here we present what is, to our knowledge, the first completely sequenced spheroid body genome from a rhopalodiacean diatom. Comparative analyses revealed that the endosymbiont is metabolically reduced, confirming its status as an obligate endosymbiont. The genome possesses genes for nitrogen fixation, and, to our surprise, no essential genes for photosynthesis. Thus, the spheroid body is, to our knowledge, the first known example of a nonphotosynthetic cyanobacterium, free-living or symbiotic. Rhopalodiacean diatoms have the potential to provide unique insight into the evolution of bacterial endosymbionts and their hosts. The evolution of mitochondria and plastids from bacterial endosymbionts were key events in the origin and diversification of eukaryotic cells. Although the ancient nature of these organelles makes it difficult to understand the earliest events that led to their establishment, the study of eukaryotic cells with recently evolved obligate endosymbiotic bacteria has the potential to provide important insight into the transformation of endosymbionts into organelles. Diatoms belonging to the family Rhopalodiaceae and their endosymbionts of cyanobacterial origin (i.e., “spheroid bodies”) are emerging as a useful model system in this regard. The spheroid bodies, which appear to enable rhopalodiacean diatoms to use gaseous nitrogen, became established after the divergence of extant diatom families. Here we report what is, to our knowledge, the first complete genome sequence of a spheroid body, that of the rhopalodiacean diatom Epithemia turgida. The E. turgida spheroid body (EtSB) genome was found to possess a gene set for nitrogen fixation, as anticipated, but is reduced in size and gene repertoire compared with the genomes of their closest known free-living relatives. The presence of numerous pseudogenes in the EtSB genome suggests that genome reduction is ongoing. Most strikingly, our genomic data convincingly show that the EtSB has lost photosynthetic ability and is metabolically dependent on its host cell, unprecedented characteristics among cyanobacteria, and cyanobacterial symbionts. The diatom–spheroid body endosymbiosis is thus a unique system for investigating the processes underlying the integration of a bacterial endosymbiont into eukaryotic cells.

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

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 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.

Detailed Process of Shell Construction in the Photosynthetic Testate Amoeba Paulinella chromatophora (Euglyphid, Rhizaria)

Most euglyphids, a group of testate amoebae, have a shell that is constructed from numerous siliceous scales. The euglyphid Paulinella chromatophora has photosynthetic organelles (termed cyanelles or chromatophores), allowing it to be cultivated more easily than other euglyphids. Like other euglyphids, P. chromatophora has a siliceous shell made of brick‐like scales. These scales are varied in size and shape. How a P. chromatophora cell makes this shell is still a mystery. We examined shell construction process in P. chromatophora in detail using time‐lapse video microscopy. The new shell was constructed by a specialized pseudopodium that laid out each scale into correct position, one scale at a time. The present study inferred that the sequence of scale production and secretion was well controlled.

Broad Distribution of TPI-GAPDH Fusion Proteins among Eukaryotes: Evidence for Glycolytic Reactions in the Mitochondrion?

Glycolysis is a central metabolic pathway in eukaryotic and prokaryotic cells. In eukaryotes, the textbook view is that glycolysis occurs in the cytosol. However, fusion proteins comprised of two glycolytic enzymes, triosephosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were found in members of the stramenopiles (diatoms and oomycetes) and shown to possess amino-terminal mitochondrial targeting signals. Here we show that mitochondrial TPI-GAPDH fusion protein genes are widely spread across the known diversity of stramenopiles, including non-photosynthetic species (Bicosoeca sp. and Blastocystis hominis). We also show that TPI-GAPDH fusion genes exist in three cercozoan taxa (Paulinella chromatophora, Thaumatomastix sp. and Mataza hastifera) and an apusozoan protist, Thecamonas trahens. Interestingly, subcellular localization predictions for other glycolytic enzymes in stramenopiles and a cercozoan show that a significant fraction of the glycolytic enzymes in these species have mitochondrial-targeted isoforms. These results suggest that part of the glycolytic pathway occurs inside mitochondria in these organisms, broadening our knowledge of the diversity of mitochondrial metabolism of protists.

Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp. nov. and the Chromatophore Genome Sequence for strain KR01

The thecate filose amoeba Paulinella chromatophora is a good model organism for understanding plastid organellogenesis because its chromatophore was newly derived from an alpha-cyanobacterium. Paulinella chromatophora was the only known photosynthetic Paulinella species until recent studies that suggested a species level of diversity. Here, we described a new photosynthetic species P. micropora sp. nov. based on morphological and molecular evidence from a newly established strain KR01. The chromatophore genome of P. micropora KR01 was fully determined; the genome was 976,991bp in length, the GC content was 39.9%, and 908 genes were annotated. A pairwise comparison of chromatophore genome sequences between strains KR01 and FK01, representing two different natural populations of P. micropora, showed a 99.85% similarity. Differences between the two strains included single nucleotide polymorphisms (SNPs) in CDSs, which resulted in 357 synonymous and 280 nonsynonymous changes, along with 245 SNPs in non-coding regions. Indels (37) and microinversions (14) were also detected. Species diversity for photosynthetic Paulinella was surveyed using samples collected from around the world. We compared our new species to two photosynthetic species, P. chromatophora and P. longichromatophora. Phylogenetic analyses using four gene markers revealed three distinct lineages of photosynthetic Paulinella species including P. micropora sp. nov.

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites

The fornicata (fornicates) is a eukaryotic group known to consist of free-living and parasitic organisms. Genome datasets of two model fornicate parasites Giardia intestinalis and Spironucleus salmonicida are well annotated, so far. The nuclear genomes of G. intestinalis assemblages and S. salmonicida are small in terms of the genome size and simple in genome structure. However, an ancestral genomic structure and gene contents, from which genomes of the fornicate parasites have evolved, remains to be clarified. In order to understand genome evolution in fornicates, here, we present the draft genome sequence of a free-living fornicate, Kipferlia bialata, the divergence of which is earlier than those of the fornicate parasites, and compare it to the genomes of G. intestinalis and S. salmonicida. Our data show that the number of protein genes and introns in K. bialata genome are the most abundant in the genomes of three fornicates, reflecting an ancestral state of fornicate genome evolution. Evasion mechanisms of host immunity found in G. intestinalis and S. salmonicida are absent in the K. bialata genome, suggesting that the two parasites acquired the complex membrane surface proteins on the line leading to the common ancestor of G. intestinalis and S. salmonicida after the divergence from K. bialata. Furthermore, the mitochondrion related organelles (MROs) of K. bialata possess more complex suites of metabolic pathways than those in Giardia and in Spironucleus. In sum, our results unveil the process of reductive evolution which shaped the current genomes in two model fornicate parasites G. intestinalis and S. salmonicida.

Evolution of UhpC‐type hexose‐phosphate transporters in dinoflagellates

Primary plastids of the group Archaeplastida are descendants of a single cyanobacterial endosymbiont, while many other algal groups have obtained complex plastids, the so‐called secondary plastids, via several parallel endosymbiotic uptakes of primary plastid‐bearing algae. Integration of the endosymbiont into its host during primary and secondary endosymbiosis necessitated the establishment of transport mechanisms for metabolites, inorganic ions, and proteins across plastid envelope membranes. As a potential protein for exporting photosynthates out of primary plastids, homologs of bacterial UhpC‐type hexose‐phosphate transporters were found in algal members of the Archaeplastida. It has been proposed that plastidic UhpC‐type transporters have been acquired in the common ancestor of Archaeplastida by the lateral gene transfer from a bacterial lineage closely related to Chlamydiae. However, it remains unknown whether secondary plastid‐bearing organisms possess UhpC‐type transporters. In the present study, we investigated homologous genes of UhpC in diverse algae using available genome and transcriptome data. Our homology survey and phylogenetic analyses revealed that only dinoflagellates possess UhpC‐type transporters derived from an archaeplastidal lineage, whereas many other secondary plastid‐bearing organisms lack them. It is possible that UhpC‐type transporters are not essential in many secondary plastids because of the existence of other families of sugar phosphate transporters.