RESUMEN
Taiwan is situated in the subtropical region and its geographical location and topographical features contribute to a rich ecological diversity and scenic landscapes. We investigated the diversity of methanogens in different environments of Taiwan using a culture-dependent method. This report presents the characterization and taxonomy of six hydrogenotrophic methanogens obtained from cold seep sediments (strain FWC-SCC1T and FWC-SCC3T), marine sediments (strain CWC-02T and YWC-01T), estuarine sediments (strain Afa-1T), and a hot spring well (strain Wushi-C6T) in Taiwan. The proposed names of the six novel species are Methanoculleus frigidifontis (type strain FWC-SCC1T=BCRC AR10056T=NBRC 113993T), Methanoculleus oceani (CWC-02T=BCRC AR10055T=NBRC 113992T), Methanoculleus methanifontis (FWC-SCC3T=BCRC AR10057T=NBRC 113994T), Methanoculleus nereidis (YWC-01T=BCRC AR10060T=NBRC 114597T), Methanoculleus formosensis (Afa-1T=BCRC AR10054T=NBRC 113995T), and Methanoculleus caldifontis (Wushi-06T=BCRC AR10059T= NBRC 114596T).
Asunto(s)
ADN de Archaea , Sedimentos Geológicos , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Taiwán , ARN Ribosómico 16S/genética , Sedimentos Geológicos/microbiología , ADN de Archaea/genética , Methanomicrobiaceae/genética , Methanomicrobiaceae/clasificación , Methanomicrobiaceae/aislamiento & purificación , Composición de Base , Manantiales de Aguas Termales/microbiologíaRESUMEN
Here, we report the complete genome sequence of Sedimentibacter sp. strain MB35-C1, which was isolated from sewage sludge at the Wastewater Treatment Plant of Sanming Steel Co. Ltd. in Fujian, China. The resulting genome of strain MB35-C1 is a single contig of 3,621,605 bp.
RESUMEN
Here, we report the complete genome sequence of Paludicola sp. strain MB14-C6, which was isolated from the lake waters of Donghu, situated at Wuhan City, Hubei Province, China. The genome of strain MB14-C6 was chosen for further species delineation and comparative genomic analysis.
RESUMEN
We report the complete genome sequence of Anaerotignum sp. strain MB30-C6, which was isolated from the dehydrated sludge collected at the wastewater treatment plant of Sanming Steel Co. Ltd. in Fujian, China. The resulting genome of strain MB30-C6 is a single contig of 3,104,838 bp with 39.49% GC content.
RESUMEN
Here, we report the complete genome sequence of Aminobacterium sp. strain MB27-C1, which was isolated from sewage sludge collected at the wastewater treatment plant of Sanming Steel Co. Ltd. in Fujian, China. The resulting genome of strain MB27-C1 is a single contig of 2,427,830 bp with 41.58% GC content.
RESUMEN
Here, we present the complete genome sequence of Kineothrix sp. MB12-C1 (= BCRC 81406), isolated from the feces of black soldier fly (Hermetia illucens) larvae. The genome of strain MB12-C1 was chosen for further species classification and comparative genomic analysis.
RESUMEN
Here, we report the complete genome sequence of Proteiniborus sp. MB09-C3 (= BCRC 81405), isolated from the feces of black soldier fly (Hermetia illucens) larvae. The genome of strain MB09-C3 was selected for further species delineation and comparative genomic analysis.
RESUMEN
Here, we report the complete genome sequence of Proteiniclasticum sp. QWL-01 (= BCRC 81396), isolated from sewage sludge of the Wastewater Treatment Plant of Sanming Steel Co. Ltd., Fujian, China. The genome of strain QWL-01 was selected for further species delineation and comparative genomic analysis.
RESUMEN
We report the complete genome sequence of Tissierella sp. strain Yu-01 (=BCRC 81391), isolated from the feces of black soldier fly (Hermetia illucens) larvae. This fly has increasingly been gaining attention because of its usefulness for recycling organic waste. The genome of strain Yu-01 was selected for further species delineation.
RESUMEN
A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C15â:â0 and C15â:â0 as the major fatty acids. The genome size of strain 14-104T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87â% 16S rRNA sequence similarity, <71â% orthologous average nucleotide identity, <76â% average amino acid identity and <68â%% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104T and P. abscessus CCUG 55929T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104T (=BCRC 81305T= NBRC 115041T).
Asunto(s)
Carcinoma de Células Escamosas , Neoplasias de Cabeza y Cuello , Neoplasias de la Boca , Humanos , Ácidos Grasos/química , Fosfolípidos/química , Filogenia , ARN Ribosómico 16S/genética , Composición de Base , Análisis de Secuencia de ADN , Carcinoma de Células Escamosas de Cabeza y Cuello , Anaerobiosis , Saliva/química , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Bacterias Anaerobias/genéticaRESUMEN
The hydrogenotrophic methanogen Methanofollis aquaemaris BCRC 16166T (= N2F9704T = DSM 14661T) was isolated from a marine aquaculture fishpond near Wang-gong (Taiwan, Republic of China). The genome of strain BCRC 16166T was selected for sequencing in order to provide further information about the species delineation and its infected virus.
RESUMEN
The family Methanocalculaceae comprises hydrogen- and formate-utilizing methanogens. Here, we report two additional draft genome sequences of Methanocalculaceae, those of Methanocalculus taiwanensis P2F9704aT (equivalent to BCRC 16182T and DSM 14663T) and Methanocalculus chunghsingensis K1F9705bT (equivalent to DSM 14646T and OCM 772T), which were selected for further species delineation and comparative genomic analyses.
RESUMEN
A Gram-stain-positive strain, 8 H-2T, was isolated from faeces of Reeves' muntjac (Muntiacus reevesi) barking deer in Taiwan. Cells of the strain were short rod-shaped, non-motile, non-haemolytic, asporogenous, facultatively anaerobic, heterofermentative and did not exhibit catalase and oxidase activities. Comparative analyses of 16S rRNA, pheS and dnaA gene sequences demonstrated that the novel strain was a member of the genus Weissella. On the basis of 16S rRNA gene sequence similarities, the type strains of Weissella oryzae (99.2â%), Weissella confusa (97.8â%), Weissella cibaria (97.6â%) and Weissella soli (97.3â%) were the closest neighbours to strain 8 H-2T. The concatenated housekeeping gene sequence (pheS and dnaA) similarities of 8 H-2T to closely related type strains were 72.5-84.9â%, respectively. The genomic DNA G+C content was 40.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values with these type strains were 70.2-75.4% and 25.1-30.1â%, respectively. Phenotypic and genotypic test results demonstrated that strain 8 H-2T represents a novel species belonging to the genus Weissella, for which the name Weissella muntiaci sp. nov. is proposed. The type strain is 8 H-2T (=BCRC 81133T=NBRC 113537T).
Asunto(s)
Ciervos/microbiología , Heces/microbiología , Filogenia , Weissella/clasificación , Animales , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Fermentación , Genes Bacterianos , Ciervo Muntjac , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Taiwán , Weissella/aislamiento & purificaciónRESUMEN
A novel lactic acid bacterium, strain MB7T, was isolated from lychee in Taiwan. MB7T is Gram-staining-positive, catalase-negative, non-motile, non-haemolytic, facultatively anaerobic, coccoid-shaped, heterofermentative and mainly produces d-lactic acid from glucose. Comparative analysis of 16S rRNA, pheS and rpoA gene sequences has demonstrated that the novel strain represented a member of the genus Leuconostoc. 16S rRNA gene sequencing results indicated that MB7T had the same sequence similarity of 99.25 % to four type strains of members of the genus Leuconostoc: Leuconostoc mesenteroides subsp. dextranicum DSM 20484T, Leuconostoc mesenteroides subsp. jonggajibkimchii DRC 1506T, Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293T and Leuconostoc suionicum DSM 20241T. Additionally, high 16S rRNA sequence similarities were also observed with Leuconostoc mesenteroides subsp. cremoris ATCC 19254T (99.12 %) and Leuconostoc pseudomesenteroides NRIC 1777T (98.69 %). When comparing the genomes of these type strains, the average nucleotide identity values and digital DNA-DNA hybridization values of MB7T with these type strains were 76.57-80.53 and 22.0-22.6â%, respectively. MB7T also showed different phenotypic characteristics to other most closely related species of the genus Leuconostoc, such as carbohydrate metabolizing ability, halotolerance and growth at various pHs. On the basis of phenotypic and genotypic properties, strain MB7T represents a novel species belonging to the genus Leuconostoc, for which the name Leuconostoc litchii sp. nov. is proposed. The type strain is MB7T (=BCRC 81077T=NBRC 113542T).
Asunto(s)
Frutas/microbiología , Leuconostoc/clasificación , Litchi/microbiología , Filogenia , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Fermentación , Ácido Láctico , Leuconostoc/aislamiento & purificación , Leuconostoc mesenteroides , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , TaiwánRESUMEN
During Drosophila melanogaster metamorphosis, arrested immature neurons born during larval development differentiate into their functional adult form. This differentiation coincides with the downregulation of two zinc-finger transcription factors, Chronologically Inappropriate Morphogenesis (Chinmo) and the Z3 isoform of Broad (Br-Z3). Here, we show that br-Z3 is regulated by two microRNAs, let-7 and miR-125, that are activated at the larval-to-pupal transition and are known to also regulate chinmo The br-Z3 3'UTR contains functional binding sites for both let-7 and miR-125 that confers sensitivity to both of these microRNAs, as determined by deletion analysis in reporter assays. Forced expression of let-7 and miR-125 miRNAs leads to early silencing of Br-Z3 and Chinmo and is associated with inappropriate neuronal sprouting and outgrowth. Similar phenotypes were observed by the combined but not separate depletion of br-Z3 and chinmo Because persistent Br-Z3 was not detected in let-7-C mutants, this work suggests a model in which let-7 and miR-125 activation at the onset of metamorphosis may act as a failsafe mechanism that ensures the coordinated silencing of both br-Z3 and chinmo needed for the timely outgrowth of neurons arrested during larval development. The let-7 and miR-125 binding site sequences are conserved across Drosophila species and possibly other insects as well, suggesting that this functional relationship is evolutionarily conserved.
Asunto(s)
Proteínas de Drosophila , MicroARNs , Neuronas , Animales , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Regulación del Desarrollo de la Expresión Génica , MicroARNs/genética , Proteínas del Tejido Nervioso/genética , Neuronas/metabolismo , Factores de TranscripciónRESUMEN
A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2T, was isolated from a brewer's grain used to make silage in Taiwan. Comparative analyses of 16S rRNA, hsp60 and pheS gene sequences demonstrated that strain 2B-2T was a member of the genus Vagococcus. On the basis of 16S rRNA gene sequence similarity, the type strains of Vagococcus teuberi (98.4â% similarity), Vagococcus carniphilus (98.4â%), Vagococcus martis (98.2â%), Vagococcus penaei (98.2â%) and Vagococcus fluvialis (98.0â%) were the closest neighbours to this novel strain. The similarity levels of concatenated housekeeping gene sequences (hsp60 and pheS) between strain 2B-2T and these closely related species ranged from 84.5 to 88.0â%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 2B-2T and its closest relatives were lower than 72.9 and 21.6â%, respectively. The DNA G+C content was 34.7 mol%. Phenotypic and genotypic features demonstrated that strain 2B-2T represents a novel species of the genus Vagococcus, for which the name Vagococcus silagei sp. nov. is proposed. The type strain is 2B-2T (=BCRC 81132T=NBRC 113536T).
Asunto(s)
Grano Comestible/microbiología , Enterococcaceae/clasificación , Filogenia , Ensilaje/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Enterococcaceae/aislamiento & purificación , Ácidos Grasos/química , Genes Bacterianos , Hibridación de Ácido Nucleico , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , TaiwánRESUMEN
Notch (N) signaling is central to the self-renewal of neural stem cells (NSCs) and other tissue stem cells. Its deregulation compromises tissue homeostasis and contributes to tumorigenesis and other diseases. How N regulates stem cell behavior in health and disease is not well understood. Here we show that N regulates bantam (ban) microRNA to impact cell growth, a process key to NSC maintenance and particularly relied upon by tumor-forming cancer stem cells. Notch signaling directly regulates ban expression at the transcriptional level, and ban in turn feedback regulates N activity through negative regulation of the Notch inhibitor Numb. This feedback regulatory mechanism helps maintain the robustness of N signaling activity and NSC fate. Moreover, we show that a Numb-Myc axis mediates the effects of ban on nucleolar and cellular growth independently or downstream of N. Our results highlight intricate transcriptional as well as translational control mechanisms and feedback regulation in the N signaling network, with important implications for NSC biology and cancer biology.
Asunto(s)
Encéfalo/metabolismo , Proteínas de Drosophila/genética , Drosophila/genética , Hormonas Juveniles/genética , MicroARNs/genética , Células Madre Neoplásicas/metabolismo , Receptores Notch/metabolismo , Animales , Encéfalo/citología , Diferenciación Celular , Procesos de Crecimiento Celular , Drosophila/citología , Drosophila/metabolismo , Proteínas de Drosophila/metabolismo , Retroalimentación Fisiológica , Hormonas Juveniles/metabolismo , Células Madre Neoplásicas/citología , Células Madre Neoplásicas/fisiología , Células-Madre Neurales/citología , Células-Madre Neurales/metabolismo , Células-Madre Neurales/fisiología , Receptores Notch/genética , Transducción de SeñalRESUMEN
Messenger RNAs (mRNAs) often contain binding sites for multiple, different microRNAs (miRNAs). However, the biological significance of this feature is unclear, since such co-targeting miRNAs could function coordinately, independently, or redundantly with one another. Here, we show that two co-transcribed Drosophila miRNAs, let-7 and miR-125, non-redundantly regulate a common target, the transcription factor Chronologically Inappropriate Morphogenesis (Chinmo). We first characterize novel adult phenotypes associated with loss of both let-7 and miR-125, which are derived from a common, polycistronic transcript that also encodes a third miRNA, miR-100. Consistent with the coordinate upregulation of all three miRNAs in aging flies, these phenotypes include brain degeneration and shortened lifespan. However, transgenic rescue analysis reveal separable roles for these miRNAs: adult miR-125 but not let-7 mutant phenotypes are associated with ectopic Chinmo expression in adult brains and are suppressed by chinmo reduction. In contrast, let-7 is predominantly responsible for regulating chinmo during nervous system formation. These results indicate that let-7 and miR-125 function during two distinct stages, development and adulthood, rather than acting at the same time. These different activities are facilitated by an increased rate of processing of let-7 during development and a lower rate of decay of the accumulated miR-125 in the adult nervous system. Thus, this work not only establishes a key role for the highly conserved miR-125 in aging. It also demonstrates that two co-transcribed miRNAs function independently during distinct stages to regulate a common target, raising the possibility that such biphasic control may be a general feature of clustered miRNAs.
Asunto(s)
Proteínas de Drosophila/genética , Longevidad/genética , MicroARNs/genética , Proteínas del Tejido Nervioso/genética , Envejecimiento/genética , Envejecimiento/patología , Animales , Sitios de Unión , Encéfalo/crecimiento & desarrollo , Encéfalo/metabolismo , Drosophila/genética , Drosophila/crecimiento & desarrollo , Proteínas de Drosophila/biosíntesis , Regulación del Desarrollo de la Expresión Génica , MicroARNs/biosíntesis , Morfogénesis/genética , Proteínas del Tejido Nervioso/biosíntesis , Sistema Nervioso/crecimiento & desarrollo , Sistema Nervioso/patología , Neuronas/metabolismoRESUMEN
Cleavage of microRNAs and mRNAs by Drosha and its cofactor Pasha/DGCR8 is required for animal development, but whether these proteins also have independent roles in development has been unclear. Known phenotypes associated with loss of either one of these two proteins are very similar and consistent with their joint function, even though both cofactors are involved with additional distinct RNA biogenesis pathways. Here, we report clear phenotypic differences between drosha and pasha/dgcr8 null alleles in two postembryonic lineages in the Drosophila brain: elimination of pasha/dgcr8 leads to defects that are not shared by drosha null mutations in the morphology of gamma neurons in the mushroom body lineage, as well as many neurons in the anterodorsal projection neuron lineage. These morphological defects are not detected in neurons that are genetically depleted of two additional microRNA pathway components, dicer-1 and argonaute1, indicating that they are not due to loss of microRNA activity. They are, however, phenocopied by a newly identified recessive gain-of-function allele in drosha that probably interferes with the microRNA independent functions of Pasha/DGCR8. These data therefore identify a general Drosha-independent DGCR8/Pasha pathway that promotes proper morphology in multiple neuronal lineages. Given that reduction of human DGCR8/Pasha may contribute to the cognitive and behavioral characteristics of DiGeorge syndrome patients, disruption of this newly described pathway could underlie human neurological disease.
Asunto(s)
Proteínas de Drosophila/fisiología , Morfogénesis , Neuronas/citología , Proteínas de Unión al ARN/fisiología , Ribonucleasa III/fisiología , Alelos , Animales , Proteínas de Drosophila/genética , MicroARNs/genética , Fenotipo , Procesamiento Postranscripcional del ARN , Proteínas de Unión al ARN/genética , Ribonucleasa III/genéticaRESUMEN
Many neural lineages display a temporal pattern, but the mechanisms controlling the ordered production of neuronal subtypes remain unclear. Here, we show that Drosophila let-7 and miR-125, cotranscribed from the let-7-Complex (let-7-C) locus, regulate the transcription factor chinmo to control temporal cell fate in the mushroom body (MB) lineage. We find that let-7-C is activated in postmitotic neurons born during the larval-to-pupal transition, when transitions among three MB subtypes occur. Loss or increase of let-7-C delays or accelerates these transitions, respectively, and leads to cell fate transformations. Consistent with our identification of let-7 and miR-125 sites in a recently identified â¼6 kb extension of the chinmo 3' UTR, Chinmo is elevated in let-7-C mutant MBs. In addition, we show that let-7-C acts upstream of chinmo and that let-7-C phenotypes are caused by elevated chinmo. Thus, these heterochronic miRNAs, originally identified in C. elegans, underlie progenitor cell multipotency during the development of diverse bilateria.