Project description:The Candidatus phylum Omnitrophica (candidate division OP3) occurs ubiquitous in anaerobic habitats, but is currently characterized only by draft genomes from metagenomes and single cells. We had visualized cells of the phylotype OP3 LiM in methanogenic cultures on limonene as small epibiontic cells. In this study, we enriched OP3 cells by double density centrifugation and obtained the first closed genome of an apparently clonal OP3 cell population applying metagenomics and PCR for gap closure. Filaments of acetoclastic Methanosaeta, the largest morphotype in limonene enrichment cultures, contained empty cells, dead cells and cells devoid of rRNA or both rRNA and DNA according to TEM, thin-section TEM, SEM, CARD-FISH and Live/Dead images. OP3 LiM cells were ultramicrobacteria (200-300 nm in diameter) and showed two physiological stages in CARD-FISH fluorescence signals: strong signals indicated many rRNA molecules and an active metabolism of OP3 LiM cells attached to Bacteria and to Archaea, whereas free-living OP3 cells had weak signals. Metaproteomics revealed that OP3 LiM lives with highly expressed secreted proteins involved in depolymerization and uptake of macromolecules, an active glycolysis and energy conservation by the utilization of pyruvate via a pyruvate:ferredoxin oxidoreductase and an RNF complex (Ferredoxin:NAD oxidoreductase). Besides sugar fermentation, a nucleotidyl transferase may contribute to energy conservation by phosphorolysis, the phosphate-dependent depolymerization of nucleic acids. Thin section TEM showed distinctive structures of predation that had been previously observed for “Velamenicoccus”. Our study demonstrated a predatory metabolism for OP3 LiM cells and we propose as name for OP3 LiM Candidatus Velamenicoccus archaeovorus gen. nov., sp. nov..
Project description:The dataset provides the whole proteome of the anammox bacterium "Candidatus Kuenenia Stuttgartiensis" strain CSTR1 growing planctonically in semi-CSTR reactor. The bacteria were growing at high growth rate (0.33 d-1) (reactor HRT 3d).
Project description:The global transcriptional responses of the adult potato psyllid gut upon infection of the two Candidatus Liberibacter solanacearum (Lso) haplotypes using Illumina sequencing
Project description:HLB is suggested to be caused by the phloem-limited fastidious prokaryotic α-proteobacterium “Candidatus Liberibacter spp.” Previous studies focused on the proteome and transcriptome analyses of citrus 5 to 35-week-after “Ca. L. spp.” inoculation. In this study, gene expression profiles was analyzed using mandarin of Citrus reticulate Blanco cv. jiaogan leaves after 2-year infection with “Ca. L. asiaticus”. The Affymetrix GeneChip® citrus genome were applied to study the molecular pathways mediated by “Ca. L. asiaticus” inoculated 3-year-old jiaogan seedlings. Each of them was graft-inoculated with one sweet orange scions with or without “Ca. L. asiaticus” in Dectember, 2009. RNA samples from three mandarin trees infected with 'Candidatus Liberibacter asiaticus' and three uninfected trees were used for affymatrix genochip
Project description:The motor neuron (MN)–hexamer complex consisting of LIM homeobox 3, Islet-1, and nuclear LIM interactor is a key determinant of motor neuron specification and differentiation. To gain insights into the transcriptional network in motor neuron development, we performed a genome-wide ChIP-sequencing analysis and found that the MN–hexamer directly regulates a wide array of motor neuron genes by binding to the HxRE (hexamer response element) shared among the target genes. Interestingly, STAT3-binding motif is highly enriched in the MN–hexamer–bound peaks in addition to the HxRE. We also found that a transcriptionally active form of STAT3 is expressed in embryonic motor neurons and that STAT3 associates with the MN–hexamer, enhancing the transcriptional activity of the MN–hexamer in an upstream signal-dependent manner. Correspondingly, STAT3 was needed for motor neuron differentiation in the developing spinal cord. Together, our studies uncover crucial gene regulatory mechanisms that couple MN–hexamer and STAT-activating extracellular signals to promote motor neuron differentiation in vertebrate spinal cord.
Project description:This study evaluated the transcriptional reprogramming of a susceptible genotype (Pera sweet orange) challenged with the pathogenic bacteria Candidatus Liberibacter americanus (CaLam), using a customized 385K microarray containing about 32,000 unigene transcripts. For the microarray experiment were used symptomatic leaves from two Pera sweet orange plants inoculated with either bark or bud pieces infected with Candidatus Liberibacter americanus and two non-infected control plants.
Project description:We seqeunced mRNA from the bacterial pathogen 'Candidatus Liberibacter solanacearum" during its association with the psyllid vector Bactericera cockerelli.
Project description:In this study we compare the transcriptome response of two potato varieties Atlantic and NY138 to the infection by Candidatus Liberibacter solanacearum. Four weeks old potato plant grown in growth chamber were infested with potato psyllid to transmit the pathogen Candidatus Liberibacter solanacearum. Three weeks after infestation leaf samples were collected for RNA extraction and transcriptome analysis. This is the first transcriptome study on this potato disease.
Project description:We sequenced mRNA from the bacterial pathogen 'Candidatus Liberibacter solanacearum" during its association with the psyllid vector Bactericera cockerelli.