Project description:Sequencing of mononucleosomal DNA during asynchronous mitosis in Schizosaccharomyces pombe, Schizosaccharomyces octosporus, Schizosaccharomyces japonicus and Saccharomyces cerevisiae Samples from mononucleosomal DNA from asynchronous mitosis of four species of budding (Saccharomyces cerevisiae W303-1a) and fission yeasts (S. pombe wild type 972h-, S. octosporus CBS1804, S. japonicus var. japonicus ade12- FY53) were sequenced (Illumina Genome Analyzer IIx and HiSeq 2500) using the single read and paired end protocol.
Project description:We presented a genome-wide characterization for H3K9 acetylation (H3K9ac) binding regions in normal temperature and heat-stress conditions via ChIP-seq. The results revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. We further identified differentially acetylated regions (DARs) under heat stress.
Project description:To identify the regulatory targets of the R2R3-Myb transcription factor, LjMyb14, the gene was constitutively over-expressed in Lotus japonicus under the Lotus ubiquitin promoter. The gene expression levels of three biological replicates of the Lotus japonicus (MG20) were averaged and compared to the the gene expression levels of three independent lines of Lotus japonicus japonicus constituitively over expressing LjMyb14 using the Lotus ubiquitin promoter.
Project description:The sea cucumber Apostichopus japonicus is a deposit-feeder and vital for marine benthic ecosystems. Hypoxia lasting for several days can lead to massive mortality in A. japonicus. It is important to understand the molecular responses of A. japonicus when exposed to acute changes in DO concentration. In the present study, RNA-seq provided a general overview of the gene expression profiles of the respiratory tree of A. japonicus exposed to dissolved oxygen (DO) of 8 mg/L (DO8), 4 mg/L (DO4) and 2 mg/L (DO2) conditions.
Project description:Microbial deconstruction of plant polysaccharides is important for environmental nutrient cycling, and bacteria proficient at this process have extensive suites of polysaccharide-specific enzymes. In the Gram-negative saprophyte Cellvibrio japonicus, genome annotation suggests that 17 genes are predicted to encode Carbohydrate-Active enZymes (CAZymes) with roles in cellulose degradation, however previous work suggested that only a subset of these genes is essential. Building upon that work, here we identify the required and minimally sufficient set of enzymes for complete degradation of cellulose using a combination of transcriptomics, gene deletion analysis, heterologous expression studies, and metabolite analysis. We identified six CAZyme-encoding required for cellulose deconstruction in C. japonicus, which are cel3B, cel5B, cel6A, lpmo10B, cbp2D, and cbp2E. These genes encode for a β-glucosidase, an endoglucanase, a cellbiohydrolase, a lytic polysaccharide mono-oxygenase, and two carbohydrate-binding proteins, respectively. These CAZyme-encoding genes are essential for growth using insoluble cellulose by C. japonicus, and sufficient using soluble cellulose when heterologously expressed in Escherichia coli. Moreover, during C. japonicus grow using insoluble cellulose we detected no cellodextrins in the medium, which suggests that cello-oligosaccharide uptake is highly efficient. RNAseq analysis corroborates these results, as we observed several genes significantly up-regulated during growth on cellulose that encode TonB-dependent and ABC transporters. Our revised model of cellulose utilization by C. japonicus suggests a greater importance for the Cbp2D and Cbp2E proteins than previously thought and that rapid cellodextrin update by C. japonicus is a mechanism to maximize the energetic return on investment for the production and secretion of CAZymes.
Project description:Investigation of whole genome gene expression level changes in Cellvibrio japonicus wild-type, comparing glucose vs cellulose. Study was purposed with determining changes in polysaccharide degradation pathways during utilization of insoluble cellulose.
