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Biodegradation of PHB/PBAT bilayer films by soil

ABSTRACT: Biodegradation of PHB/PBAT

PROVIDER: PRJEB60405 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10962376_1.fastq.gz	Fastqsanger.gz
	ERR10962376_2.fastq.gz	Fastqsanger.gz
	ERR10962377_1.fastq.gz	Fastqsanger.gz
	ERR10962377_2.fastq.gz	Fastqsanger.gz
	ERR10962378_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of PHB-knockdown and PHB-knockout Spermatocytes Transcriptomes

Project description:We analyzed the transcriptomic differences of cultured mouse spermatocytes (GC2 cells) stably transfected with PHB-targeting shRNA (called PHB KD GC2) from those with a control shRNA (called Ctrl GC2). Furthermore, we also analyzed the difference in the transcriptomes of spermatocytes between Phb conditional knock-out and control mice.

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Snai2-mediated upregulation of NADSYN1 promotes bladder cancer progression by interacting with PHB

Project description:Prohibitin (PHB) plays a significant role in cancer processes whereas its mechanism in bladder cancer (BC) aggressiveness is not fully understood. This study aimed to investigate the role of PHB in BC aggressiveness. The study employed a range of in vivo and in vitro assays to elucidate the interaction between PHB-NADSYN1 and its underlying function in BC progression. We found that PHB was upregulated in muscle-invasive bladder cancer tissues, and bound to NADSYN1 mRNA in BC tissues more than in adjacent normal tissues. NADSYN1 and PHB were upregulated and positively correlated both in BC tissues and cell lines. We further revealed that deleting NADSYN1 prevented PHB-mediated cell invasiveness of BC in vivo and in vitro. PHB could directly bind to NADSYN1 mRNA, and it was found that the PHB domain was responsible for the PHB-NADSYN1 interaction. Depletion of NADSYN1 expression significantly decreased the protein level of PHB. In addition, Snai2 positively correlated with NADSYN1 and depletion or mutation of Snai2 binding sites inhibited NADSYN1-PHB-mediated BC progression. The study highlights a novel Snai2-NADSYN1-PHB mechanism in BC progression and indicates that PHB and NADSYN1 could serve as a therapeutic target for BC

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A systems-level insight into PHB-driven metabolic adaptation orchestrated by the PHB-binding transcriptional regulator AniA (PhaR)

Project description:Polyhydroxybutyrate (PHB) is a carbon and energy storage polymer, whose accumulation under nutrient imbalances with excess carbon is a widespread phenomenon in bacteria. PhaR is a conserved transcriptional regulator found to be associated to PHB granules in several species. Although its role in modulating PHB storage and metabolism has been extensively studied across the bacterial phylogeny, a comprehensive analysis of the PhaR regulon within the context of its dual role as a metabolic sensor and regulator remains missing. To bridge this gap, we integrated co-expression network analysis with proteome profiling across multiple mutant backgrounds (lack of PhaR (AniA) and/or PHB synthesis) in the free-living state of the PHB-accumulating alphaproteobacterial root nodule symbiont Sinorhizobium meliloti. This analysis was enriched by identifying direct regulatory targets of PhaR through a regulon-centric computational multi-step search for DNA binding site motifs combined with PhaR-DNA binding and promoter-reporter assays. We confirmed that the model of accumulated PHB sequestering PhaR and thereby relieving phasin and PHB depolymerase gene repression to control cellular PHB levels also applies to S. meliloti, and showed that PhaR-mediated regulation also occurs the symbiotic state. A comprehensive picture of the impact of PHB-mediated PhaR titration on cellular functions revealed exopolysaccharide production as well as central carbon metabolism (pdh and bkd), gluconeogenesis (ppdK and pyc), entry into the TCA cycle (gltA), and the initial steps of the Entner-Doudoroff pathway (zwf, pgl and edd) as major regulatory targets, and beyond carbon metabolism several target genes of yet unknown function. Our findings highlight a pivotal role for PhaR in orchestrating carbon metabolism.

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Project description:Cellular metabolism and chromatin landscape both contribute to cell fate determination. However, their interplay remains poorly understood. Here we show that Prohibitin (PHB), an evolutionarily conserved protein, involves in a histone variant H3.3 chaperon HIRA complex-dependent epigenetic and metabolic circuitry to maintain the identity of human embryonic stem cells (hESCs). We found that silencing of PHB triggers hESC differentiation with concomitant enhancements of histone 3 (H3) lysine (K) methyl modifications as a result of the reduced production of Î±-ketoglutarate (Î±-KG), a metabolite required for activities of many dioxygenase and in turn chromatin structure1,2. Mechanistically, PHB acts as a functional member of the HIRA complex3,4. Resembling PHB deficiency, loss of HIRA in hESCs leads to massive differentiation and aberrant histone modifications, although it was previously found not to disrupt the self-renewal in mouse ESCs (mESCs)5. Genome-wide H3.3 ChIP- sequence analyses indicate that reduction of H3.3 deposition caused by PHB knock down is extremely similar to that induced by HIRA knock down. Specifically, silencing either HIRA or PHB leads to repressive chromatin characters at promoters of pluripotency genes and isocitrate dehydrogenases (IDHs), the enzyme responsible for Î±-KG production, but active chromatin features at promoters of developmental genes, paralleling to transcript levels of these genes. Our results identify PHB as an essential factor not only for hESC self-renewal but also for the proper function of the HIRA complex, linking the HIRA complex-dependent H3.3 deposition to the production of a critical metabolite required for shaping chromatin structure, and demonstrating the importance of the interplay between epigenetic state and metabolic regulation in cell fate determination. Examination of H3.3 deposition in NT, PHB, and HIRA siRNA treated hESCs respectively.

2016-08-11 | E-GEOD-72143 | biostudies-arrayexpress

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