Kensuke Toyoda

Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment.

MutS proteins are ubiquitous in cellular organisms and have important roles in DNA mismatch repair or recombination. In the virus world, the amoeba-infecting Mimivirus, as well as the recently sequenced Cafeteria roenbergensis virus are known to encode a MutS related to the homologs found in octocorals and ɛ-proteobacteria. To explore the presence of MutS proteins in other viral genomes, we performed a genomic survey of four giant viruses (‘giruses’) (Pyramimonas orientalis virus (PoV), Phaeocystis pouchetii virus (PpV), Chrysochromulina ericina virus (CeV) and Heterocapsa circularisquama DNA virus (HcDNAV)) that infect unicellular marine algae. Our analysis revealed the presence of a close homolog of Mimivirus MutS in all the analyzed giruses. These viral homologs possess a specific domain structure, including a C-terminal HNH-endonuclease domain, defining the new MutS7 subfamily. We confirmed the presence of conserved mismatch recognition residues in all members of the MutS7 subfamily, suggesting their role in DNA mismatch repair rather than DNA recombination. PoV and PpV were found to contain an additional type of MutS, which we propose to call MutS8. The MutS8 proteins in PoV and PpV were found to be closely related to homologs from ‘Candidatus Amoebophilus asiaticus’, an obligate intracellular amoeba-symbiont belonging to the Bacteroidetes. Furthermore, our analysis revealed that MutS7 and MutS8 are abundant in marine microbial metagenomes and that a vast majority of these environmental sequences are likely of girus origin. Giruses thus seem to represent a major source of the underexplored diversity of the MutS family in the microbial world.

Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus

Heterocapsa circularisquama DNA virus (HcDNAV; previously designated as HcV) is a giant virus (girus) with a ~356-kbp double-stranded DNA (dsDNA) genome. HcDNAV lytically infects the bivalve-killing marine dinoflagellate H. circularisquama, and currently represents the sole DNA virus isolated from dinoflagellates, one of the most abundant protists in marine ecosystems. Its morphological features, genome type, and host range previously suggested that HcDNAV might be a member of the family Phycodnaviridae of Nucleo-Cytoplasmic Large DNA Viruses (NCLDVs), though no supporting sequence data was available. NCLDVs currently include two families found in aquatic environments (Phycodnaviridae, Mimiviridae), one mostly infecting terrestrial animals (Poxviridae), another isolated from fish, amphibians and insects (Iridoviridae), and the last one (Asfarviridae) exclusively represented by the animal pathogen African swine fever virus (ASFV), the agent of a fatal hemorrhagic disease in domestic swine. In this study, we determined the complete sequence of the type B DNA polymerase (PolB) gene of HcDNAV. The viral PolB was transcribed at least from 6 h post inoculation (hpi), suggesting its crucial function for viral replication. Most unexpectedly, the HcDNAV PolB sequence was found to be closely related to the PolB sequence of ASFV. In addition, the amino acid sequence of HcDNAV PolB showed a rare amino acid substitution within a motif containing highly conserved motif: YS DTDS was found in HcDNAV PolB instead of YG DTDS in most dsDNA viruses. Together with the previous observation of ASFV-like sequences in the Sorcerer II Global Ocean Sampling metagenomic datasets, our results further reinforce the ideas that the terrestrial ASFV has its evolutionary origin in marine environments.

Fine-structure of the vegetative frustule, perizonium and initial valve of Achnanthes yaquinensis (Bacillariophyta)

This study clarifies the fine structure of the vegetative and initial valves of Achnanthes yaquinensis and briefly compares them to other Achnanthes species. It also elucidates the structure of the perizonium, based on auxospore development in short-term cultures. The araphid valve has marginal ridges and terminal spines that allow connecting valves to form a chain. The terminal spines develop from the rapheless sternum. The complete cingulum consists of 3–5 split bands with two rows of areolae. These features can be used to discriminate species within the genus. Sexual reproduction is isogamous with two mother cells producing two auxospores, which are enclosed in mucilage. The perizonium develops on one side of an auxospore only, comprising one large central longitudinal band and four closed bands. There are no transverse perizonial bands. The raphid valve of the initial cell forms first, underneath the longitudinal perizonium, followed by the araphid valve, which is not covered by any perizonial bands. The araphid valve of the initial cells lacks a marginal spine, and the rapheless sternum lies more centrally than in the vegetative cell. The relationship of the genus Achnanthes to other monoraphid diatoms is discussed briefly.

First evidence for the existence of pennate diatom viruses.

Diatoms are considered the most successful and widespread group of photosynthetic eukaryotes. Their contribution to primary production is remarkably significant to the earths ecosystems. Diatoms are composed of two orders: Centrales and Pennales. Thus far, viruses infecting centric diatom species have been isolated and characterized; however, viruses infecting pennates have not been reported. Here, we describe the first isolations and preliminary characterizations of two distinct pennate diatom viruses, AglaRNAV (31 nm in diameter, accumulates in the host cytoplasm) and TnitDNAV (35 nm in diameter, accumulates in the host nuclei) infecting Asterionellopsis glacialis and Thalassionema nitzschioides, respectively. Their genomes contain a single-stranded RNA of approximately 9.5 kb, and a closed, circular single-stranded DNA of approximately 5.5 kb harboring a partially double-stranded region, respectively. Further analysis of these viruses may elucidate many aspects of diatom host–virus relationships.

Morphological investigations of the frustule, perizonium and initial valves of the freshwater diatom Achnanthes crenulata Grunow (Bacillariophyceae)

The present study clarifies the fine structure of the vegetative frustules, initial valves and perizonium of Achnanthes crenulata Grunow. The valves of the vegetative cell are distinctly linear‐lanceolate with an undulate margin. The valve face is quite flat and in girdle view is smoothly curved as in species of Gephyria (Bacillariophyceae). However, the valve face of the initial cells is slightly rounded and does not have an undulate margin. Furthermore, the rapheless sternum is centrally positioned along the apical axis of the araphid initial valve. As this taxon develops from auxospore to initial valve, it forms only longitudinal perizonial bands; no transverse bands arise. The perizonium consists of three silicified bands: one large, central longitudinal plate and two bands that underlie this plate; these two bands are either open or closed. This taxon has several conspicuous structures compared to other marine species of Achnanthes, but the structure of the perizonium supports the position of A. crenulata within Achnanthes sensu stricto.

Gametogenesis and auxospore development in Actinocyclus (Bacillariophyta).

cGametogenesis and auxospore development have been studied in detail in surprisingly few centric diatoms. We studied the development of sperm, eggs and auxospores in Actinocyclus sp., a radially symmetrical freshwater diatom collected from Japan, using LM and electron microscopy of living cultures and thin sections. Actinocyclus represents a deep branch of the ‘radial centric’ diatoms and should therefore contribute useful insights into the evolution of sexual reproduction in diatoms. Spermatogenesis was examined by LM and SEM and involved the formation of two spermatogonia (sperm mother-cells) in each spermatogonangium through an equal mitotic division. The spermatogonia produced a reduced ‘lid’ valve, resembling a large flat scale with irregular radial thickenings. Sperm formation was merogenous, producing four sperm per spermatogonium, which were released by dehiscence of the ‘lid’ valve. The sperm were spindle-shaped with numerous surface globules and, as usual for diatoms, the single anterior flagellum bore mastigonemes. One egg cell was produced per oogonium. Immature eggs produced a thin layer of circular silica scales before fertilization, while the eggs were still contained within the oogonium. Sperm were attracted in large numbers to each egg and were apparently able to contact the egg surface via a gap formed between the long hypotheca and shorter epitheca of the oogonium and a small underlying hole in the scale-case. Auxospores expanded isodiametrically and many new scales were added to its envelope during expansion. Finally, new slightly-domed initial valves were produced at right angles to the oogonium axis, after a strong contraction of the cell away from the auxospore wall. At different stages, Golgi bodies were associated with chloroplasts or mitochondria, contrasting with the constancy of Golgi–ER–mitochondrion (G-ER-M) units in some other centric diatoms, which has been suggested to have phylogenetic significance. Electron-dense bodies in the vacuole of Actinocyclus are probably acidocalcisomes containing polyphosphate.

Three extant species of Paralia (Bacillariophyceae) along the coast of Japan

Y. Sawai, T. Nagumo and K. Toyoda. 2005. Three extant species of Paralia (Bacillariophyceae) along the coast of Japan. Phycologia 44: 517–529. Three extant species of the genus Paralia (Bacillariophyceae) occur along the coast of Japan, two of them are new species. Observations of living populations suggested that significant characters for separating Paralia species are (1) structure of the mantle of the separation valve; (2) shape of the linking spines; (3) topography and morphology of valve face on the separation valve, and possibly (4) cingulum structures; and (5) rimoportula morphology. Some features vary but the structure of the separation valves in girdle view was stable in all specimens. Based on these criteria, we identified Paralia sulcata (Ehrenberg) Cleve and two new species, P. fenestrata Sawai & Nagumo sp. nov., and P. capitata Sawai & Nagumo sp. nov. from coast of Japan.

New single-stranded DNA virus with a unique genomic structure that infects marine diatom Chaetoceros setoensis

Diatoms are among the most abundant organisms in nature; however, their relationships with single-stranded DNA (ssDNA) viruses have not yet been defined in detail. We report the isolation and characterisation of a virus (CsetDNAV) that lytically infects the bloom-forming diatom Chaetoceros setoensis. The virion is 33 nm in diameter and accumulates in the nucleus of its host. CsetDNAV harbours a covalently closed-circular ssDNA genome comprising 5836 nucleotides and eight different short-complementary fragments (67–145 nucleotides), which have not been reported in other diatom viruses. Phylogenetic analysis based on the putative replicase-related protein showed that CsetDNAV was not included in the monophyly of the recently established genus Bacilladnavirus. This discovery of CsetDNAV, which harbours a genome with a structure that is unique among known viruses that infect diatoms, suggests that other such undiscovered viruses possess diverse genomic architectures.

The typification of Achnanthes Bory based on Echinella stipitata Lyngbye, with an account of the morphology and fine structure of Lyngbye's species

Achnanthes was described by Bory to include three species, A. adnata, A. dubia and A. baccillarioides, formerly included under Echinella stipitata Lyngbye. Boyer typified the genus Achnanthes using A. adnata and this typification has been accepted by subsequent authors. However no extant material of A. adnata is known. Since this species was based on E. stipitata, Lyngbye material was sought and examined. This material contains specimens of Achnanthes sensu stricto and can be used as the generitype of that genus. Light and electron microscopical observations of this material are presented. C. A. Agardh created the name Achnanthes brevipes as an avowed substitution for A. adnata and this is the name that has generally been used. There is little doubt that E. stipitata, A. adnata and A. brevipes refer to the same species. Since A. brevipes has been used most extensively in the literature there is a case for conserving this name. Based on our observations we propose that Lyngbyes material be accepted as the type for Achnanthes but that the name A. brevipes be considered for conservation against E. stipitata and A. adnata.

Isolation and characterization of a single-stranded RNA virus that infects the marine planktonic diatom Chaetoceros sp. (SS08-C03)

Diatoms are the major primary producers in the worlds aquatic environment; hence, their dynamics are an important focus in current studies. Viruses, along with other physical, chemical, and biological factors, have recently been recognized as potential factors of diatom mortality. We isolated and characterized a new diatom virus (Csp03RNAV) that causes lysis of the marine planktonic diatom Chaetoceros sp. strain SS08‐C03 isolated from Hiroshima Bay, Japan. Here, we present the physiology, morphology, and genome characteristics of this virus. Csp03RNAV was isolated from surface waters of Yatsushiro Sea, Japan. Virions were icosahedral and 32 nm in diameter, and accumulated in the cytoplasm of the host cells. The latent period was estimated to be <48 h. Csp03RNAV harbors a single‐stranded RNA genome, which has 9417 bases encoding two open reading frames that code for putative replication‐related proteins and putative structural proteins, respectively. The monophyly of Csp03RNAV and the other known diatom‐infecting single‐stranded RNA viruses (genus Bacillarnavirus), Rhizosolenia setigera RNA virus, Chaetoceros socialis f. radians RNA virus, and Chaetoceros tenuissimus RNA virus was strongly supported by phylogenetic analysis based on the amino acid sequence of the RNA‐dependent RNA polymerase domain. On the basis of these results, Csp03RNAV is considered to be a new member of the genus Bacillarnavirus.