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The draft genome sequence of Lactobacillus paracasei strain LC-Ikematsu, isolated from a pineapple in Okinawa, was determined. The total length of the 87 contigs was 3.08 Mb with a G+C content of 46.2% and 2,946 coding sequences. The genome analysis revealed its biosynthetic ability of 11 amino acids.
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A free-living ciliate, Trimyema compressum, found in anoxic freshwater environments harbors methanogenic archaea and a bacterial symbiont named TC1 in its cytoplasm. Here, we report the complete genome sequence of the TC1 symbiont, consisting of a 1.59-Mb chromosome and a 35.8-kb plasmid, which was determined using the PacBio RSII sequencer.
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We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 32 and 36 operational taxonomic units (defined at a 90% sequence similarity threshold) were recovered from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities, after normalization by using a species as the internal control, showed good correlation with the number of individuals in the samples (R = 0.91-0.99), although relative species abundances within a mock community sample estimated from sequences were skewed from community composition in terms of the number of individuals or biomass of the species. Thus, this protocol enables the comparison of collembolan communities in a quantitative manner by metabarcoding.
Assuntos
Artrópodes/classificação , Artrópodes/genética , Código de Barras de DNA Taxonômico , Animais , Biodiversidade , Complexo IV da Cadeia de Transporte de Elétrons/genética , Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Controle de Qualidade , RNA Ribossômico 16S/genéticaRESUMO
Isoprene emission from plants is very sensitive to environmental temperature both at short-term and long-term scales. Our previous study demonstrated suppression of isoprene emission by cold temperatures in a high emitting tropical tree Ficus septica and revealed a strong correlation of emission to isoprene synthase (IspS) protein levels. When challenged with decreasing daily temperatures from 30 to 12 °C, F. septica completely stopped isoprene emission at 12 °C, only to recover on the second day after re-exposure to 30 °C. Here, we explored this regulation of isoprene emission in response to environmental temperature by a comprehensive analysis of transcriptome data, gene expressions and metabolite pools of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. MEP pathway genes and metabolites dynamics did not support substrate-level limitations as major control over observed basal emission, but transcriptome data, network inferences and putative regulatory elements on IspS promoter suggested transcriptional regulation of IspS gene through circadian rhythm and phytohormone signalling processes. Expression levels of 29 genes involved in these pathways were examined by quantitative real-time PCR. We propose that temperature controls over basal isoprene emission at a time-scale of hours to few days are regulated by phytohormone-mediated transcriptional modulation of IspS gene under synchronization by the circadian clock.
Assuntos
Butadienos/metabolismo , Ficus/fisiologia , Hemiterpenos/metabolismo , Redes e Vias Metabólicas , Pentanos/metabolismo , Temperatura , Ritmo Circadiano , Ficus/genética , Ficus/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Fotossíntese , Reguladores de Crescimento de Plantas/genética , Reguladores de Crescimento de Plantas/metabolismo , Reguladores de Crescimento de Plantas/fisiologia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/fisiologia , Análise de Sequência de DNA , Estresse FisiológicoRESUMO
Isoprene is the most abundant type of nonmethane, biogenic volatile organic compound in the atmosphere, and it is produced mainly by terrestrial plants. The tropical tree species Ficus septica Burm. F. (Rosales: Moraceae) has been shown to cease isoprene emissions when exposed to temperatures of 12â °C or lower and to re-induce isoprene synthesis upon subsequent exposure to temperatures of 30â °C or higher for 24â h. To elucidate the regulation of genes underlying the disabling and then induction of isoprene emission during acclimatization to ambient temperature, we conducted gene expression analyses of F. septica plants under changing temperature using quantitative real-time polymerase chain reaction and western blotting. Transcription levels were analyzed for 17 genes that are involved in metabolic pathways potentially associated with isoprene biosynthesis, including isoprene synthase (ispS). The protein levels of ispS were also measured. Changes in transcription and protein levels of the ispS gene, but not in the other assessed genes, showed identical temporal patterns to isoprene emission capacity under the changing temperature regime. The ispS protein levels strongly and positively correlated with isoprene emission capacity (R(2)â =â 0.92). These results suggest that transcriptional regulation of ispS gave rise to the temporal variation in isoprene emission capacity in response to changing temperature.
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Aclimatação/genética , Alquil e Aril Transferases/genética , Butadienos/metabolismo , Temperatura Baixa , Ficus/fisiologia , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Hemiterpenos/metabolismo , Pentanos/metabolismo , Alquil e Aril Transferases/metabolismo , Ficus/metabolismo , Redes e Vias Metabólicas/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Estresse Fisiológico , Transcrição Gênica , Árvores/metabolismo , Árvores/fisiologia , Clima TropicalRESUMO
We sequenced a complete mitochondrial genome of the marine sponge, Cacospongia mycofijiensis, which is the first report for the family Thorectidae in the class Demospongiae. The mitogenome was obtained from a de novo assembly of shotgun genome sequencing using Illumina Miseq technology, which reconstructed a circular genome with 97 × of sequence coverage. The assembled mitochondrial genome consisting of 16,227 bp includes 14 protein-coding genes, 2 rRNAs and 2 tRNAs. This complete mitogenome sequence will be useful especially for the phylogenic studies of Demospongiae.
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Whole-genome sequencing has emerged as one of the most effective means to elucidate the biological roles and molecular features of obligate intracellular symbionts (endosymbionts). However, the de novo assembly of an endosymbiont genome remains a challenge when host and/or mitochondrial DNA sequences are present in a dataset and hinder the assembly of the genome. By focusing on the traits of genome evolution in endosymbionts, we herein developed and investigated a genome-assembly strategy that consisted of two consecutive procedures: the selection of endosymbiont contigs from an output obtained from a de novo assembly performed using a TBLASTX search against a reference genome, named TBLASTX Contig Selection and Filtering (TCSF), and the iterative reassembling of the genome from reads mapped on the selected contigs, named Iterative Mapping and ReAssembling (IMRA), to merge the contigs. In order to validate this approach, we sequenced two strains of the cockroach endosymbiont Blattabacterium cuenoti and applied this strategy to the datasets. TCSF was determined to be highly accurate and sensitive in contig selection even when the genome of a distantly related free-living bacterium was used as a reference genome. Furthermore, the use of IMRA markedly improved sequence assemblies: the genomic sequence of an endosymbiont was almost completed from a dataset containing only 3% of the sequences of the endosymbiont's genome. The efficiency of our strategy may facilitate further studies on endosymbionts.
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Bacteroidetes/isolamento & purificação , Baratas/microbiologia , Genoma Bacteriano , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Simbiose , Animais , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/fisiologia , Baratas/classificação , Baratas/fisiologia , Corpo Adiposo/microbiologia , Especificidade de Hospedeiro , Dados de Sequência Molecular , FilogeniaRESUMO
The mixed segment is a unique part of the gut present only in the most apical lineage of termites and consists of a complex of overlapping mesenteric and proctodeal epithelia. In spite of its unique structure, the physiological functions of the mixed segment have been poorly studied. We performed transcriptome analysis to identify functional enzymes acting in the mixed segment of the wood-feeding higher termite Nasutitermes takasagoensis. We sequenced the transcripts (4563 isotigs) of the mixed segment and compared them with those of the midgut (4813 isotigs) and the first proctodeal segment (3629 isotigs). We found that vacuolar H(+)-ATPase (V-ATPase) subunits were predominant in the mixed segment, which was confirmed by RT-qPCR analysis. The V-ATPase activity in these three tissues was in a good agreement with the expression patterns, suggesting that V-ATPase is a prevalent enzyme in the mixed segment of the termites. The results confirmed the proposed role of the mixed segment as a transporting epithelium.
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Proteínas de Insetos/metabolismo , Isópteros/enzimologia , ATPases Vacuolares Próton-Translocadoras/metabolismo , Animais , Trato Gastrointestinal/enzimologia , Expressão Gênica , Especificidade de Órgãos , TranscriptomaRESUMO
The unicellular green alga Chlamydomonas reinhardtii has a haplontic life cycle, and forms diploid zygotes for reproduction. The zygospore, a sporulating zygote, begins germination in response to light signals, generating haploid progenies and inducing several cell-biological events; e.g., DNA synthesis and meiotic division, successively. Their regulatory mechanisms remain largely unknown, so we focused on the early stages of germination and analyzed the dynamics of gene expression associated with the germination process. The gene expression levels of zygospores at 1 and 6h after light exposure were analyzed by a next-generation sequencing platform, the 454 GS Junior. At 6h, the photosynthesis pathway, including its antenna proteins and two methionine metabolism-related genes (methionine synthase and sulfite reductase), were up-regulated compared to 1h after light exposure. Meanwhile, three uncharacterized genes that contained an antibiotic biosynthesis monooxygenase domain and an HSP20/alpha crystallin family protein were specifically expressed at 1h after light exposure. These gene expressions were also verified by quantitative real-time PCR analysis. These results suggest that the photosynthesis and methionine synthesis pathways, both of which occur in the chloroplast, are activated in zygospores at around 6h after light exposure, and that some polyketides and/or a small heat shock protein may be related to the initiation of zygospore germination.
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Chlamydomonas reinhardtii/fisiologia , Germinação , RNA Mensageiro/genética , Sequência de Bases , Chlamydomonas reinhardtii/genética , Primers do DNA , Genes de Plantas , Reação em Cadeia da Polimerase em Tempo Real , TranscriptomaRESUMO
This paper describes the existence of temperature threshold in isoprene emission from tropical trees for the first time. Isoprene emission capacity of Ficus virgata leaves kept outdoors were measured over a period of 20 d in the wintertime. When the plants experienced the low temperature below 12 °C in the daytime, isoprene emission was completely suppressed, and re-activated by elevated temperature above the threshold of 12 °C. Photosynthesis is also decreased similarly, but too much smaller extent compared to the reduction observed for isoprene emission. The cut off level of accumulated temperature to shut off the isoprene emission was roughly estimated to be 300 degree/d. The shut off in the isoprene emission by the low temperature was confirmed experimentally by use of phytotron with tropical trees of F. virgata and F. septica. Isoprene emission of both species ceased at 12 °C, and re-activated by raising the temperature above the threshold level. Photosynthesis was lowered slightly as was the case for the field observation, and no close association between photosynthesis and isoprene emission was noted. The expression of isoprene synthase gene showed much greater variation after exposure to the cold temperature compared to those involved in photosynthesis. These observations therefore suggested the existence of putative direct connection between perception of temperature and isoprene emission in tropical trees, which may merit further investigation to estimate the net output of isoprene from subtropical or tropical forest.
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Butadienos/metabolismo , Ficus/metabolismo , Hemiterpenos/metabolismo , Pentanos/metabolismo , Alquil e Aril Transferases/metabolismo , Butadienos/análise , Hemiterpenos/análise , Pentanos/análise , Fotossíntese , Folhas de Planta/metabolismo , TemperaturaRESUMO
Bacteria of the genus Rhodococcus (Actinomycetes) have the ability to catabolize various organic compounds and are therefore considered potential genetic resources for applications such as bioremediation. We investigated a next-generation sequencing-based procedure to rapidly identify candidate functional gene(s) from rhodococci on the basis of their frequent genome recombination. The Rhodococcus rhodochrous strain B-276 and its alkene monooxygenase (AMO) gene cluster were the focus of our investigation. Firstly, 2 types of cultures of the R. rhodochrous strain B-276 were prepared, one of which was supplied with propene, which requires AMO genes for its assimilation, whereas the other was supplied with glucose as the sole energy source. The latter culture was anticipated to have a lower gene frequency of AMO genes because of their deletion during cultivation. We then conducted whole genome shotgun sequencing of the genomic DNA extracted from both cultures. Next, all sequence data were pooled and assembled into contiguous sequences (contigs). Finally, the abundance of each contig was quantified in order to detect contigs that were highly biased between the 2 cultures. We identified contigs that were overrepresented by 2 orders of magnitude in the AMO-required culture and successfully identified an AMO gene cluster among these contigs. We propose this procedure as an efficient method for the rapid detection and sequencing of deleted region, which contributes to identification of functional genes in rhodococci.
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Deleção de Genes , Genômica , Rhodococcus/genética , Mapeamento de Sequências Contíguas , Genes Bacterianos/genética , Genoma Bacteriano/genética , Família Multigênica/genética , Oxigenases/genética , Rhodococcus/classificação , Rhodococcus/enzimologia , Rhodococcus/metabolismo , Análise de Sequência de DNARESUMO
In addition to harbouring intestinal symbionts, some animal species also possess intracellular symbiotic microbes. The relative contributions of gut-resident and intracellular symbionts to host metabolism, and how they coevolve are not well understood. Cockroaches and the termite Mastotermes darwiniensis present a unique opportunity to examine the evolution of spatially separated symbionts, as they harbour gut symbionts and the intracellular symbiont Blattabacterium cuenoti. The genomes of B. cuenoti from M. darwiniensis and the social wood-feeding cockroach Cryptocercus punctulatus are each missing most of the pathways for the synthesis of essential amino acids found in the genomes of relatives from non-wood-feeding hosts. Hypotheses to explain this pathway degradation include: (i) feeding on microbes present in rotting wood by ancestral hosts; (ii) the evolution of high-fidelity transfer of gut microbes via social behaviour. To test these hypotheses, we sequenced the B. cuenoti genome of a third wood-feeding species, the phylogenetically distant and non-social Panesthia angustipennis. We show that host wood-feeding does not necessarily lead to degradation of essential amino acid synthesis pathways in B. cuenoti, and argue that ancestral high-fidelity transfer of gut microbes best explains their loss in strains from M. darwiniensis and C. punctulatus.
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Aminoácidos/biossíntese , Baratas/fisiologia , Simbiose , Animais , Baratas/genética , Baratas/metabolismo , Comportamento Alimentar , Genoma , Nitrogênio/metabolismo , FilogeniaRESUMO
The effectiveness of cancer chemotherapy is often limited by the toxicity to other tissues in the body. Therefore, the identification of non-toxic chemotherapeutics from herbal medicines remains to be an attractive goal to advance cancer treatments. This study evaluated the cytotoxicity profiles of 364 herbal plant extracts, using various cancer and normal cell lines. The screening found occurrence of A549 (human lung adenocarcinoma) specific cytotoxicity in nine species of herbal plants, especially in the extract of Arctium lappa L. Moreover, purification of the selective cytotoxicity in the extract of Arctium lappa L. resulted in the identification of arctigenin as tumor specific agent that showed cytotoxicity to lung cancer (A549), liver cancer (HepG2) and stomach cancer (KATO III) cells, while no cytotoxicity to several normal cell lines. Arctigenin specifically inhibited the proliferation of cancer cells, which might consequently lead to the induction of apoptosis. In conclusion, this study found that arctigenin was one of cancer specific phytochemicals, and in part responsible for the tumor selective cytotoxicity of the herbal medicine.
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Arctium/química , Furanos/farmacologia , Lignanas/farmacologia , Extratos Vegetais/farmacologia , Antineoplásicos , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Furanos/química , Células Hep G2 , Humanos , Lignanas/química , Extratos Vegetais/químicaRESUMO
Research on the soft coral genus Sarcophyton extends over a wide range of fields, including marine natural products and the isolation of a number of cembranoid diterpenes. However, it is still unknown how soft corals produce this diverse array of metabolites, and the relationship between soft coral diversity and cembranoid diterpene production is not clear. In order to understand this relationship, we examined Sarcophyton specimens from Okinawa, Japan, by utilizing three methods: morphological examination of sclerites, chemotype identification, and phylogenetic examination of both Sarcophyton (utilizing mitochondrial protein-coding genes MutS homolog: msh1) and their endosymbiotic Symbiodinium spp. (utilizing nuclear internal transcribed spacer of ribosomal DNA: ITS- rDNA). Chemotypes, molecular phylogenetic clades, and sclerites of Sarcophyton trocheliophorum specimens formed a clear and distinct group, but the relationships between chemotypes, molecular phylogenetic clade types and sclerites of the most common species, Sarcophyton glaucum, was not clear. S. glaucum was divided into four clades. A characteristic chemotype was observed within one phylogenetic clade of S. glaucum. Identities of symbiotic algae Symbiodinium spp. had no apparent relation to chemotypes of Sarcophyton spp. This study demonstrates that the complex results observed for S. glaucum are due to the incomplete and complex taxonomy of this species group. Our novel method of identification should help contribute to classification and taxonomic reassessment of this diverse soft coral genus.