Piscinibacter sakaiensis strain:201-F6
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ABSTRACT:
PROVIDER: PRJNA1112095 | ENA |
REPOSITORIES: ENA
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Project description:Piscinibacter sakaiensis strain:201-F6 Genome sequencing
| PRJNA1130519 | ENA
Project description:Genome sequencing of Ideonella sakaiensis 201-F6
| PRJDB4046 | ENA
Project description:Piscinibacter sakaiensis Transcriptome or Gene expression
| PRJNA967349 | ENA
Project description:Poly(ethylene terephthalate) (PET)-degrading bacterium Ideonella sakaiensis produces hydrolytic enzymes that convert PET, via mono(2-hydroxyethyl) terephthalate (MHET), into the monomeric compounds, terephthalic acid (TPA) and ethylene glycol (EG). Understanding PET metabolism is critical if this bacterium is to be engineered for bioremediation and biorecycling. TPA uptake and catabolism in I. sakaiensis have previously been studied, but EG metabolism remains largely unexplored despite its importance. First, we identified two alcohol dehydrogenases (IsPedE and IsPedH) and one aldehyde dehydrogenase (IsPedI) in I. sakaiensis as the homologs of EG metabolic enzymes in Pseudomonas putida KT2440. IsPedE and IsPedH exhibited EG dehydrogenase activities with Ca2+ and a rare earth element (REE) Pr3+, respectively. We further found an upregulated dehydrogenase gene when the bacterium was grown on EG, whose gene product (IsXoxF) displays a minor EG dehydrogenase activity with Pr3+. IsPedE displayed a similar level of activity toward various alcohols. In contrast, IsPedH was more active toward small alcohols, whereas IsXoxF was the opposite. Structural analysis with homology models revealed that IsXoxF had a larger catalytic pocket than IsPedE and IsPedH, which could accommodate relatively bulkier substrates. Pr3+ regulated the protein expression of IsPedE negatively; IsPedH and IsXoxF were positively regulated. Taken together, these results indicated that the combination of IsPedH and IsXoxF complements the function of IsPedE in the presence of REEs. IsPedI exhibited dehydrogenase activity toward various aldehydes with the highest activity toward glycolaldehyde (GAD). This study demonstrated a unique alcohol oxidation pathway of I. sakaiensis, which could be efficient in EG utilization.
2022-10-17 | GSE205843 | GEO
Project description:RNA-seq of Ideonella sakaiensis 201-F6 when grown on PET, TPA·2Na, and EG
| PRJNA847936 | ENA
Project description:Purpose: In previous studies, we found that the fyuA gene plays an important role in the virulence and pathogenicity of Yersinia pestis strain 201. In order to globally observe which functions of the fyuA gene also affect Y. pestis, we performed RNA-seq on the Y. pestis wild strain 201-WT and mutant strains △fyuA and △fyuAGCAdel, hoping to find their differences at the transcription level, so that better elucidate the effect of fyuA gene on Y. pestis gene transcription. Methods: Total RNA was extracted using the PureLink™ RNA Mini Kit, and then used for creating a cDNA library and deep sequencing. According to the values of Fragments Per Kilobase of Transcript per Million Mapped Reads (FPKM), the ratio of transcript levels between WT and ΔfyuAGCAdel groups was used as the logarithm to the base 2 (twofold change). The differential values of at least a 2-fold were applied to analyze the differential expression of genes according to the Y. pestis 91001 genome annotation. The transcriptome data were verified by qPCR. Results: We found that compared with 201-WT, genes related to siderophore synthesis such as ybtS, ybtX, ybtQ, irp2, irp1, ybtU, ybtT and ybtE were significantly down-regulated at either 26 ℃ or 37 ℃. At 37 ℃, the genes related to type Ⅲ secretion system were significantly up-regulated.
2022-03-22 | GSE198937 | GEO
Project description:Piscinibacter lacus strain:Jin2 Genome sequencing and assembly
| PRJNA689939 | ENA
Project description:Piscinibacter gummiphilus Genome sequencing
| PRJNA412281 | ENA