Ryoma Kamikawa

Ryoma Kamikawa
Kyoto University | Kyodai · Graduate School of Human and Environmental Studies

About

98
Publications
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1,786
Citations
Additional affiliations
April 2013 - present
Kyoto University
December 2012 - March 2013
University of Tsukuba
January 2009 - November 2012
University of Tsukuba
Position
  • Evolutionary Microbiology

Publications

Publications (98)
Article
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary conseque...
Article
Full-text available
Ni-containing carbon monoxide dehydrogenase (Ni-CODH) plays an important role in the CO/CO 2 -based carbon and energy metabolism of microbiomes. Ni-CODH is classified into distinct phylogenetic clades, A–G, with possibly distinct cellular roles. However, the types of Ni-CODH clade used by organisms in different microbiomes are unknown. Here, we con...
Article
Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by t...
Preprint
Full-text available
Diatoms are a major phytoplankton group responsible for about 20% of Earth's primary production. They carry out photosynthesis inside the plastid, an organelle obtained through eukaryote-eukaryote endosymbiosis. Recently, microbial rhodopsin, a photoreceptor distinct from chlorophyll-based photosystems, has been identified in certain diatoms. Howev...
Article
Full-text available
Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton,1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 which is responsible for around 50% of global net primary production.¹²,¹³ However, the phenotypic identity of many of the organisms distinguished by e...
Preprint
Full-text available
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary conseque...
Article
Full-text available
Organisms that have lost their photosynthetic capabilities are present in a variety of eukaryotic lineages, such as plants and disparate algal groups. Most of such non-photosynthetic eukaryotes still carry plastids, as these organelles retain essential biological functions. Most non-photosynthetic plastids possess genomes with varied protein-coding...
Article
Full-text available
Background: Plastid electron transport systems are essential not only for photosynthesis but also for dissipating excess reducing power and sinking excess electrons generated by various redox reactions. Although numerous organisms with plastids have lost their photoautotrophic lifestyles, there is a spectrum of known functions of remnant plastids...
Article
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Nucleomorphs, relic endosymbiont nuclei, have been studied as a model to elucidate the evolutionary process of integrating a eukaryotic endosymbiont into a host cell organelle. Recently, we reported two new dinoflagellates possessing nucleomorphs, and proposed them as new models in this research field based on the following findings: genome integra...
Article
Full-text available
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggest that DNA transfer from the endosymbiont to host nuclei ha...
Article
The difficult-to-cultivate katablepharid Hatena arenicola ingests green algae, Nephroselmis spp., and temporarily retains a Nephroselmis-derived cell compartment (kleptochloroplast), including a chloroplast within a phagocytotic vacuole. H. arenicola has a unique life history; during cell division, the Nephroselmis-derived cell compartment is only...
Article
Full-text available
The triose phosphate transporter (TPT) is one of the prerequisites to exchange metabolites between the cytosol and plastids. In this study, we demonstrated that the four plastid TPT homologues in the non-photosynthetic diatom Nitzschia sp. NIES-3581 were highly likely integrated into plastid envelope membranes similar to counterparts in the model p...
Article
Full-text available
Loss of photosynthesis is a recurring theme in eukaryotic evolution. In organisms that have lost the ability to photosynthesize, non-photosynthetic plastids are retained because they play essential roles in processes other than photosynthesis. The unicellular algal genus Cryptomonas contains both photosynthetic and non-photosynthetic members, the l...
Preprint
Chloroplasts in photosynthetic eukaryotes originated from a cyanobacterial endosymbiosis far more than 1 billion years ago1-3. Due to this ancientness, it remains unclear how this evolutionary process proceeded. To unveil this mystery, we analysed the whole genome sequence of a photosynthetic rhizarian amoeba4, Paulinella micropora5,6, which has a...
Preprint
Full-text available
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process integrating an endosymbiont alga into be a host-governed plastid (organellogenesis). Nevertheless, past studies suggested that DNA transfer from the endosymbiont to host nu...
Article
The division of life into producers and consumers is blurred by evolution. For example, eukaryotic phototrophs can lose the capacity to photosynthesize, although they may retain vestigial plastids that perform other essential cellular functions. Chrysophyte algae have undergone a particularly large number of photosynthesis losses. Here, we present...
Article
Full-text available
Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis)....
Article
We determined the complete sequences of the plastid and mitochondrial genomes of three non-photosynthetic Nitzschia spp., as well as those of a photosynthetic close relative, Nitzschia palea. All the plastid genomes and the three mitochondrial genomes determined were found to be circularly mapping, and the other mitochondrial genomes were predicted...
Article
Full-text available
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 simpl...
Data
Phylogenetic trees inferred from mitochondrion-related organelle proteins. (PDF)
Data
BUSCO assessment results. (PDF)
Data
Predictable ATP transporters in Kipferlia bialata. The left column indicates the protein IDs of K. bialata ATP transporter candidates. The second left column shows the number of transmembrane domains predicted by TMHMM 2.0c. Remaining columns display results of the tblanstn search. Each of the query proteins from human or mouse used for the search...
Article
Full-text available
The ancestral kareniacean dinoflagellate has undergone tertiary endosymbiosis, in which the original plastid is replaced by a haptophyte endosymbiont. During this plastid replacement, the endosymbiont genes were most likely flowed into the host dinoflagellate genome (endosymbiotic gene transfer or EGT). Such EGT may have generated the redundancy of...
Article
Full-text available
Recent phylogenetic analyses position certain ‘orphan’ protist lineages deep in the tree of eukaryotic life, but their exact placements are poorly resolved. We conducted phylogenomic analyses that incorporate deeply sequenced transcriptomes from representatives of collodictyonids (diphylleids), rigifilids, Mantamonas and ancyromonads (planomonads)....
Article
Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral org...
Article
The non-photosynthetic diatoms Nitzschia spp. are known to have evolved from photosynthetic species to heterotrophic species by the loss of photosynthesis. We investigated their ability to tolerate wide ranges of temperatures and salinities. Nitzschia spp. were capable of surviving or thriving even at 5°C and 35°C. In addition, these diatoms were a...
Article
Non-photosynthetic plastids retain important biological functions and are indispensable for cell viability. However, the detailed processes underlying the loss of plastidal functions other than photosynthesis remain to be fully understood. In this study, we used transcriptomics, subcellular localization, and phylogenetic analyses to characterize th...
Article
Full-text available
Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third main group of Discoba. Here, we...
Article
The egg capsules of some amphibians' eggs are known to become green colored before hatching. This is due to the increase of green symbionts in the egg capsule surrounding the embryo. The green symbionts in North American amphibian eggs were reported to be unicellular green algae in the Oophila-clade of Volvocales, Chlorophyceae. However, it remains...
Article
Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitoso...
Article
Mitochondria exist on a functional and evolutionary continuum that includes anaerobic mitochondrion related organelles (MROs), such as hydrogenosomes. Hydrogenosomes lack many classical mitochondrial features, including conspicuous cristae, mtDNA, the tricarboxylic acid (TCA) cycle, and ATP synthesis powered by an electron transport chain (ETC); in...
Article
Full-text available
We here reported the mitochondrial (mt) genome of one of the heterotrophic microeukaryotes related to cryptophytes, Palpitomonas bilix. The P. bilix mt genome was found to be a linear molecule composed of ‘single copy region’ (~16 Kb) and repeat regions (~30 Kb) arranged in an inverse manner at both ends of the genome. Linear mt genomes with large...
Article
Full-text available
Although mitochondria have evolved from a single endosymbiotic event, present day mitochondria of diverse eukaryotes display a great range of genome structures, content and features. Group I and group II introns are two features that are distributed broadly but patchily in mitochondrial genomes across branches of the tree of eukaryotes. While group...
Article
In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluorescence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electro...
Article
Full-text available
Phosphoenolpyruvate carboxykinase (PEPCK) is one of the pivotal enzymes, which regulates the carbon flow of the central metabolism by fixing CO2 to phosphoenolpyruvate (PEP) to produce oxaloacetate or vice versa. While ATP- and GTP-type PEPCKs have been well studied and their protein identities are established, inorganic pyrophosphate (PPi)-type PE...
Article
Full-text available
Bacteria require two class-I release factors, RF1 and RF2, that recognize stop codons and promote peptide release from the ribosome. RF1 and RF2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. This scenario expects that the two RF gene families have...
Article
Full-text available
The Myxozoa are oligo-cellular parasites with alternate hosts—fish and annelid worms— and some myxozoan species harm farmed fish. The phylum Myxozoa, comprising 2,100 species, was difficult to position in the tree of life, due to its fast evolutionary rate. Recent phylogenomic studies utilizing an extensive number of nuclear-encoded genes have conf...
Article
Full-text available
Organisms with nonphotosynthetic plastids often retain genomes; their gene contents provide clues as to the functions of these organelles. Yet the functional roles of some retained genes - such as those coding for ATP synthase - remain mysterious. In this study, we report the complete plastid genome and transcriptome data of a nonphotosynthetic dia...
Article
Full-text available
Unlike many other photosynthetic dinoflagellates, whose plastids contain a characteristic carotenoid peridinin, members of the genus Lepidodinium are the only known dinoflagellate species possessing green alga-derived plastids. However, the precise origin of Lepidodinium plastids has hitherto remained uncertain. In this study, we completely sequenc...
Article
Full-text available
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 endosymbioti...
Article
Full-text available
Background Giardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered. However, we anticipate that more cis- and trans-spliced introns likely remain unidentified in genes encoding hypothetical proteins that occupy ca. 2/3 of all of the ope...
Article
Full-text available
Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-133...
Article
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Phylogenetic position of the marine biflagellate Palpitomonas bilix is intriguing, since several ultrastructural characteristics implied its evolutionary connection to Archaeplastida or Hacrobia. The origin and early evolution of these two eukaryotic assemblages have yet to be fully elucidated, and P. bilix may be a key lineage in tracing those gro...
Article
Full-text available
The unicellular eukaryotic assemblage Discoba (Excavata) comprises four lineages: the Heterolobosea, Euglenozoa, Jakobida, and Tsukubamonadida. Discoba has been considered as a key assemblage for understanding the early evolution of mitochondrial (mt) genomes, as jakobids retain the most gene-rich (i.e., primitive) genomes compared with any other e...
Article
Full-text available
Elongation factor-1alpha (EF-1alpha) and elongation factor-like (EFL) proteins are functionally homologous to one another, and are core components of the eukaryotic translation machinery. The patchy distribution of the two elongation factor types across global eukaryotic phylogeny is suggestive of a 'differential loss' hypothesis that assumes that...
Article
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A novel thermophilic, chemoheterotrophic, Gram-negative, multicellular filamentous bacterium, designated strain 110S(T), was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequence nested strain 110S(T) in a novel class-level clon...
Article
Elongation factor 1α (EF-1α) and elongation factor-like (EFL) proteins are considered to carry out equivalent functions in translation in eukaryotic cells. Elongation factor 1α and EFL genes are patchily distributed in the global eukaryotic tree, suggesting that the evolution of these elongation factors cannot be reconciled without multiple lateral...
Article
Full-text available
Mitochondria are descendants of the endosymbiotic α-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contribut...
Data
Putative secondary structures of group I intron RNAs. A. Schematic structures of Leucocryptos, Chlorokybus, and Nephroselmis cob introns. LAGLIDADG_2-type homing endonucleases are encoded in the region between P1 and P2 in the three introns (shown as closed boxes). B. Schematic structures o