Publications

isolation and characterization of a virus (cvv-bw1) that infects symbiotic algae of paramecium bursaria in lake biwa, japan.	we performed an environmental study of viruses infecting the symbiotic single-celled algae of paramecium bursaria (paramecium bursaria chlorella virus, pbcv) in lake biwa, the largest lake in japan. the viruses detected were all chlorella variabilis virus (cvv = nc64a virus). one of them, designated cvv-bw1, was subjected to further characterization.	2010	20831832
the chlorella variabilis nc64a genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.	chlorella variabilis nc64a, a unicellular photosynthetic green alga (trebouxiophyceae), is an intracellular photobiont of paramecium bursaria and a model system for studying virus/algal interactions. we sequenced its 46-mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. nc64a exhibits variations in gc content across its genome that correlate with global expression level, average intron size, and codon usage bias. although chlore ...	2010	20852019
an in silico analysis of the mitochondrial protein import apparatus of plants.	an in silico analysis of the mitochondrial protein import apparatus from a variety of species; including chlamydomonas reinhardtii, chlorella variabilis, ectocarpus siliculosus, cyanidioschyzon merolae, physcomitrella patens, selaginella moellendorffii, picea glauca, oryza sativa and arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.	2010	21078193
evolutionary significance of an algal gene encoding an [fefe]-hydrogenase with f-domain homology and hydrogenase activity in chlorella variabilis nc64a.	[fefe]-hydrogenases (hyda) link the production of molecular h(2) to anaerobic metabolism in many green algae. similar to chlamydomonas reinhardtii, chlorella variabilis nc64a (trebouxiophyceae, chlorophyta) exhibits [fefe]-hydrogenase (hyda) activity during anoxia. in contrast to c. reinhardtii and other chlorophycean algae, which contain hydrogenases with only the hyda active site (h-cluster), c. variabilis nc64a is the only known green alga containing hyda genes encoding accessory fes cluster- ...	2011	21643991
the genome of the polar eukaryotic microalga coccomyxa subellipsoidea reveals traits of cold adaptation.	little is known about the mechanisms of adaptation of life to the extreme environmental conditions encountered in polar regions. here we present the genome sequence of a unicellular green alga from the division chlorophyta, coccomyxa subellipsoidea c-169, which we will hereafter refer to as c-169. this is the first eukaryotic microorganism from a polar environment to have its genome sequenced.	2012	22630137
cell division and density of symbiotic chlorella variabilis of the ciliate paramecium bursaria is controlled by the host's nutritional conditions during early infection process.	the association of ciliate paramecium bursaria with symbiotic chlorella sp. is a mutualistic symbiosis. however, both the alga-free paramecia and symbiotic algae can still grow independently and can be reinfected experimentally by mixing them. effects of the host's nutritional conditions against the symbiotic algal cell division and density were examined during early reinfection. transmission electron microscopy revealed that algal cell division starts 24 h after mixing with alga-free p. bursari ...	2012	22672708
phycodnavirus potassium ion channel proteins question the virus molecular piracy hypothesis.	phycodnaviruses are large dsdna, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. among the viral gene products are the smallest proteins known to form functional k(+) channels. to determine if these viral k(+) channels are the product of molecular piracy from their hosts, we compared the sequences of the k(+) channel pore modules from seven phycodnaviruses to the k(+) channels from chlorella variabilis and ectocarpus siliculosus, whose genomes have rec ...	2012	22685610
paramecium bursaria chlorella virus 1 proteome reveals novel architectural and regulatory features of a giant virus.	the 331-kbp chlorovirus paramecium bursaria chlorella virus 1 (pbcv-1) genome was resequenced and annotated to correct errors in the original 15-year-old sequence; 40 codons was considered the minimum protein size of an open reading frame. pbcv-1 has 416 predicted protein-encoding sequences and 11 trnas. a proteome analysis was also conducted on highly purified pbcv-1 virions using two mass spectrometry-based protocols. the mass spectrometry-derived data were compared to pbcv-1 and its host chlo ...	2012	22696644
homology modeling and docking studies of fabh (β-ketoacyl-acp synthase iii) enzyme involved in type ii fatty acid biosynthesis of chlorella variabilis: a potential algal feedstock for biofuel production.	the concept of using microalgae as an alternative renewable source of biofuel has gained much importance in recent years. however, its commercial feasibility is still an area of concern for researchers. unraveling the fatty acid metabolic pathway and understanding structural features of various key enzymes regulating the process will provide valuable insights to target microalgae for augmented oil content. fabh (β-ketoacyl-acyl carrier protein synthase; kas iii) is a condensing enzyme catalyzing ...	2013	22830394
virus infection of chlorella variabilis and enzymatic saccharification of algal biomass for bioethanol production.	experiments were conducted to investigate the application of virus infection and amylolytic enzyme treatment on sugar release from chlorella variabilis nc64a and bioethanol production from released sugars via escherichia coli ko11 fermentation. chlorella variabilis nc64a accumulated starch when it was cultured in a nitrogen-limited medium. the accumulated starch was not consumed during viral infection based on analysis of sugars released during infection. both amylolytic enzyme addition and viru ...	2013	23597760
insights into molecular assembly of accase heteromeric complex in chlorella variabilis--a homology modelling, docking and molecular dynamic simulation study.	acetyl-coa carboxylase (accase), a biotin-dependent enzyme that catalyses the first committed step of fatty acid biosynthesis, is considered as a potential target for improving lipid accumulation in oleaginous feedstocks, including microalgae. accase is composed of three distinct conserved domains, and understanding the structural details of each catalytic domain assumes great significance to gain insights into the molecular basis of the complex formation and mechanism of biotin transport. in th ...	2013	23677812
evaluation of higher plant virus resistance genes in the green alga, chlorella variabilis nc64a, during the early phase of infection with paramecium bursaria chlorella virus-1.	with growing industrial interest in algae plus their critical roles in aquatic systems, the need to understand the effects of algal pathogens is increasing. we examined a model algal host-virus system, chlorella variabilis nc64a and virus, pbcv-1. c. variabilis encodes 375 homologs to genes involved in rna silencing and in response to virus infection in higher plants. illumina rna-seq data showed that 325 of these homologs were expressed in healthy and early pbcv-1 infected (≤60min) cells. for e ...	2013	23701839
generation of a phage-display library of single-domain camelid vh h antibodies directed against chlamydomonas reinhardtii antigens, and characterization of vh hs binding cell-surface antigens.	single-domain antibodies (sdabs) are powerful tools for the detection, quantification, purification and subcellular localization of proteins of interest in biological research. we have generated camelid (lama pacos) heavy chain-only variable vh domain (vh h) libraries against antigens in total cell lysates from chlamydomonas reinhardtii. the sdabs in the sera from immunized animals and vh h antibody domains isolated from the library show specificity to c. reinhardtii and lack of reactivity to an ...	2013	23980604
de novo transcriptome profiling uncovers a drastic downregulation of photosynthesis upon nitrogen deprivation in the nonmodel green alga botryosphaerella sudeticus.	neutral lipid storage is enhanced by nitrogen deprivation (nd) in numbers of green microalgal species. however, little is known about the metabolic pathways whose transcription levels are most significantly altered following nd in green microalgae, especially the nonmodel species.	2013	24138407
global analysis of chlorella variabilis nc64a mrna profiles during the early phase of paramecium bursaria chlorella virus-1 infection.	the pbcv-1/chlorella variabilis nc64a system is a model for studies on interactions between viruses and algae. here we present the first global analyses of algal host transcripts during the early stages of infection, prior to virus replication. during the course of the experiment stretching over 1 hour, about a third of the host genes displayed significant changes in normalized mrna abundance that either increased or decreased compared to uninfected levels. the population of genes with significa ...	2014	24608695
deep rna sequencing reveals hidden features and dynamics of early gene transcription in paramecium bursaria chlorella virus 1.	paramecium bursaria chlorella virus 1 (pbcv-1) is the prototype of the genus chlorovirus (family phycodnaviridae) that infects the unicellular, eukaryotic green alga chlorella variabilis nc64a. the 331-kb pbcv-1 genome contains 416 major open reading frames. a mrna-seq approach was used to analyze pbcv-1 transcriptomes at 6 progressive times during the first hour of infection. the alignment of 17 million reads to the pbcv-1 genome allowed the construction of single-base transcriptome maps. signi ...	2014	24608750
comparison of gene expression of paramecium bursaria with and without chlorella variabilis symbionts.	the ciliate paramecium bursaria harbors several hundred cells of the green-alga chlorella sp. in their cytoplasm. irrespective of the mutual relation between p. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. they can easily reestablish endosymbiosis when put in contact with each other. consequently, p. bursaria is an excellent model for studying cell-cell interaction and the evolution of eukaryotic cells through secondary endosymbiosis between differ ...	2014	24612690
plastid and mitochondrion genomic sequences from arctic chlorella sp. arm0029b.	chorella is the representative taxon of chlorellales in trebouxiophyceae, and its chloroplast (cp) genomic information has been thought to depend only on studies concerning chlorella vulgaris and genbank information of c. variablis. mitochondrial (mt) genomic information regarding chlorella is currently unavailable. to elucidate the evolution of organelle genomes and genetic information of chlorella, we have sequenced and characterized the cp and mt genomes of arctic chlorella sp. arm0029b.	2014	24735464
oil accumulation mechanisms of the oleaginous microalga chlorella protothecoides revealed through its genome, transcriptomes, and proteomes.	microalgae-derived biodiesel is a promising substitute for conventional fossil fuels. in particular, the green alga chlorella protothecoides sp. 0710 is regarded as one of the best candidates for commercial manufacture of microalgae-derived biofuel. this is due not only to its ability to live autotrophically through photosynthesis, but also to its capacity to produce a large amount of biomass and lipid through fermentation of glucose. however, until the present study, neither its genome sequence ...	2014	25012212
dynamic attachment of chlorovirus pbcv-1 to chlorella variabilis.	chloroviruses infect their hosts by specifically binding to and degrading the cell wall of their algal hosts at the site of attachment, using an intrinsic digesting enzyme(s). chlorovirus pbcv-1 stored as a lysate survived longer than virus alone, suggesting virus attachment to cellular debris may be reversible. ghost cells (algal cells extracted with methanol) were used as a model to study reversibility of pbcv-1 attachment because ghost cells are as susceptible to attachment and wall digestion ...	2014	25240455
symbiotic chlorella variabilis incubated under constant dark conditions for 24 hours loses the ability to avoid digestion by host lysosomal enzymes in digestive vacuoles of host ciliate paramecium bursaria.	endosymbiosis between symbiotic chlorella and alga-free paramecium bursaria cells can be induced by mixing them. to establish the endosymbiosis, algae must acquire temporary resistance to the host lysosomal enzymes in the digestive vacuoles (dvs). when symbiotic algae isolated from the alga-bearing paramecia are kept under a constant dark conditions for 24 h before mixing with the alga-free paramecia, almost all algae are digested in the host dvs. to examine the cause of algal acquisition to the ...	2014	25348325
complete sequence and characterization of mitochondrial and chloroplast genome of chlorella variabilis nc64a.	the complete nucleotide sequences of the mitochondrial (mtdna) and chloroplast (cpdna) genomes of chlorella variabilis nc64a (trebouxiophyceae) have been determined in this study (genbank accession no. kp271968 and kp271969, respectively). the mt genome assembles as a circle of 78,500 bp and contains 62 genes, including 32 protein-coding, 27 trna and 3 rrna genes. the overall gc content is 28.2%, while the coding sequence is 34%. the cp genome forms a circle of 124,793 bp, containing 114 genes, ...	2016	25690053
organic and inorganic nitrogen impact chlorella variabilis productivity and host quality for viral production and cell lysis.	microalgae have been proposed as a potential feedstock for biofuel production; however, cell disruption is usually required for collection and utilization of cytoplasmic polysaccharides and lipids. virus infection might be one approach to disrupt the cell wall. the concentration of yeast extract and presence of kno3 in algae cultivation media were investigated to observe their effects on chlorella variabilis nc64a physiology and composition and the subsequent effect on production of chlorella vi ...	2015	25805020
optimization of cell disruption methods for efficient recovery of bioactive metabolites via nmr of three freshwater microalgae (chlorophyta).	this study demonstrates the use of nmr techniques coupled with chemometric analysis as a high throughput data mining method to identify and examine the efficiency of different disruption techniques tested on microalgae (chlorella variabilis, scenedesmus regularis and ankistrodesmus gracilis). the yield and chemical diversity from the disruptions together with the effects of pre-oven and pre-freeze drying prior to disruption techniques were discussed. hcl extraction showed the highest recovery of ...	2015	25812996
fluorescent minerals--a potential source of uv protection and visible light for the growth of green algae and cyanobacteria in extreme cosmic environments.	we propose that green algae (chlorella variabilis and dunaliella tertiolecta) and cyanobacteria (synechococcus elongatus and nostoc commune) can grow inside fluorescent rock minerals which convert damaging uv light to visible light, thereby allowing these organisms to survive and thrive in uv-rich environments without (or with limited) visible light, which would otherwise be inimical to them. the four microorganisms were incubated inside fluorescent rocks composed of fluorite, calcite and pyrite ...	2015	26256632
glutamine assimilation and feedback regulation of l-acetyl-n-glutamate kinase activity in chlorella variabilis nc64a results in changes in arginine pools.	glutamine is a metabolite of central importance in nitrogen metabolism of microorganisms and plants. the chlorella pii signaling protein controls, in a glutamine-dependent manner, the key enzyme of the ornithine/arginine biosynthesis pathway, n-acetyl-l-glutamate kinase (nagk) that leads to arginine formation. we provide evidence that glutamine promotes effective growth of c. variabilis strain nc64a. the present study shows that externally supplied glutamine directly influences the internal pool ...	2015	26356535
process design for augmentation and spectrofluorometric quantification of neutral lipid by judicious doping of pathway intermediate in the culture of marine chlorella variabilis for biodiesel application.	over the past few years microalgae have emerged as the most promising feedstock for biodiesel production. however, enhancing lipid content remains a major scientific challenge. many studies irrationally rely upon nitrogen starvation for improving lipid content at the cost of biomass. in this study, strategic enhancement of neutral lipid without compromising with biomass production was achieved in marine chlorella variabilis by supplementing the culture with triacylglycerol pathway intermediate, ...	2015	26454043
rna-seq transcriptomic analysis with bag2d software identifies key pathways enhancing lipid yield in a high lipid-producing mutant of the non-model green alga dunaliella tertiolecta.	for many years, increasing demands for fossil fuels have met with limited supply. as a potential substitute and renewable source of biofuel feedstock, microalgae have received significant attention. however, few of the current algal species produce high lipid yields to be commercially viable. to discover more high yielding strains, next-generation sequencing technology is used to elucidate lipid synthetic pathways and energy metabolism involved in lipid yield. when subjected to manipulation by g ...	2015	26613001
differences in infectivity between endosymbiotic chlorella variabilis cultivated outside host paramecium bursaria for 50 years and those immediately isolated from host cells after one year of reendosymbiosis.	chlorella variabilis strain nc64a is an intracellular photobiont of the ciliate paramecium bursaria. nc64a was isolated from p. bursaria nearly 50 years ago and was thereafter cultivated outside the host. this study was undertaken to detect changes in its infectivity to p. bursaria and its auxotrophy for growth outside the host induced during long-term cultivation. nc64a can grow in modified bold's basal medium but not in c medium, whereas another symbiotic chlorella variabilis strain, 1n, that ...	2015	26718931
lipid extracted microalgal biomass residue as a fertilizer substitute for zea mays l.	high volumes of lipid extracted microalgal biomass residues (lmbrs) are expected to be produced upon commencement of biodiesel production on a large scale, thus necessitating its value addition for sustainable development. lmbrs of chlorella variabilis and lyngbya majuscula were employed to substitute the nitrogen content of recommended rate of fertilizer (rrf) for zea mays l. the pot experiment comprised of 10 treatments, i.e., t1 (no fertilizer); t2 (rrf-120 n: 60 p2o5: 40 k2o kg ha(-1)); t3 t ...	2015	26834768
genome scale metabolic reconstruction of chlorella variabilis for exploring its metabolic potential for biofuels.	a compartmentalized genome scale metabolic network was reconstructed for chlorella variabilis to offer insight into various metabolic potentials from this alga. the model, iaj526, was reconstructed with 1455 reactions, 1236 metabolites and 526 genes. 21% of the reactions were transport reactions and about 81% of the total reactions were associated with enzymes. along with gap filling reactions, 2 major sub-pathways were added to the model, chitosan synthesis and rhamnose metabolism. the reconstr ...	2016	26995318
is chloroplastic class iia aldolase a marine enzyme?	expressed sequence tag analyses revealed that two marine chlorophyceae green algae, chlamydomonas sp. w80 and chlamydomonas sp. hs5, contain genes coding for chloroplastic class iia aldolase (fructose-1, 6-bisphosphate aldolase: fba). these genes show robust monophyly with those of the marine prasinophyceae algae genera micromonas, ostreococcus and bathycoccus, indicating that the acquisition of this gene through horizontal gene transfer by an ancestor of the green algal lineage occurred prior t ...	2016	27058504
plant phosphomannose isomerase as a selectable marker for rice transformation.	the e. coli phosphomannose isomerase (ecpmi) gene is widely used as a selectable marker gene (smg) in mannose (man) selection-based plant transformation. although some plant species exhibit significant pmi activity and active pmis were even identified in man-sensitive plants, whether plant pmis can be used as smgs remains unclear. in this study, we isolated four novel pmi genes from chlorella variabilis and oryza sativa. their isoenzymatic activities were examined in vitro and compared with that ...	2016	27174847
microalgae synthesize hydrocarbons from long-chain fatty acids via a light-dependent pathway.	microalgae are considered a promising platform for the production of lipid-based biofuels. while oil accumulation pathways are intensively researched, the possible existence of a microalgal pathways converting fatty acids into alka(e)nes has received little attention. here, we provide evidence that such a pathway occurs in several microalgal species from the green and the red lineages. in chlamydomonas reinhardtii (chlorophyceae), a c17 alkene, n-heptadecene, was detected in the cell pellet and ...	2016	27288359
induction of maltose release by light in the endosymbiont chlorella variabilis of paramecium bursaria.	the endosymbiotic green algae of paramecium bursaria are known to release a photosynthate to the host cells. the endosymbiont chlorella variabilis f36-zk isolated in japan releases maltose under acidic conditions, and such release requires both light and low ph. however, whether photosynthate release is due to light sensing by photoreceptors or is merely a consequence of active photosynthesis is unclear. herein, we studied the effect of light on maltose release from c. variabilis f36-zk; we meas ...	2016	27631277
non-isothermal pyrolysis of de-oiled microalgal biomass: kinetics and evolved gas analysis.	non-isothermal (β=5, 10, 20, 35°c/min) pyrolysis of de-oiled microalgal biomass (dmb) of chlorella variabilis was investigated by tga-ms (30-900°c, argon atmosphere) to understand thermal decomposition and evolved gas analysis (ega). the results showed that three-stage thermal decomposition and three volatilization zone (100-400°c, 400-550°c and 600-750°c) of organic matters during pyrolysis. the highest rate of weight-loss is 8.91%/min at 302°c for 35°c/min heating-rate. kinetics of pyrolysis w ...	2016	27643733
influence of iron-doped apatite nanoparticles on viral infection examined in bacterial versus algal systems.	the centers for disease control and prevention have estimated that each year, two million people in the united states become infected with antibiotic-resistant bacteria, of which, approximately 23000 die as a direct result of these infections. phage therapy, or the treatment of bacterial infection by specific, antagonistic viruses, provides one alternative to traditional antibiotics. bacteriophages, or phages, are bacteria-specific viruses that possess biological traits that allow for not only t ...	2016	27775532
characterization of a new chlorovirus type with permissive and non-permissive features on phylogenetically related algal strains.	a previous report indicated that prototype chlorovirus pbcv-1 replicated in two chlorella variabilis algal strains, nc64a and syngen 2-3, that are ex-endosymbionts isolated from the protozoan paramecium bursaria. surprisingly, plaque-forming viruses on syngen 2-3 lawns were often higher than on nc64a lawns from indigenous water samples. these differences led to the discovery of viruses that exclusively replicate in syngen 2-3 cells, named only syngen (osy) viruses. osy-ne5, the prototype virus f ...	2017	27816636
label-free quantitative proteomic analysis of harmless and pathogenic strains of infectious microalgae, prototheca spp.	microalgae of the genus prototheca (p.) spp are associated with rare algal infections of invertebrates termed protothecosis. among the seven generally accepted species, p. zopfii genotype 2 (gt2) is associated with a severe form of bovine mastitis while p. blaschkeae causes the mild and sub-clinical form of mastitis. the reason behind the infectious nature of p. zopfii gt2, while genotype 1 (gt1) remains non-infectious, is not known. therefore, in the present study we investigated the protein ex ...	2016	28036087
responses triggered in chloroplast of chlorella variabilis nc64a by long-term association with paramecium bursaria.	the unicellular green alga chlorella variabilis nc64a is an endosymbiont of the ciliate paramecium bursaria. the host's control, including the transfer of biochemical substrates from p. bursaria to c. variabilis, is involved in symbiotic relationships. c. variabilis nc64a that had been re-infected to p. bursaria for more than 1 year and isolated from the host showed higher chlorophyll levels compared to those in free-living cells. unlike the host, the expression of c. variabilis nc64a heat shock ...	2017	28074287