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Inositol pyrophosphate dynamics impact fission yeast phosphate homeostasis via modulation of RNA 3' processing and transcription termination

ABSTRACT: Inositol pyrophosphate dynamics impact fission yeast phosphate homeostasis via modulation of RNA 3' processing and transcription termination

PROVIDER: PRJNA543029 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9057310_1.fastq.gz	Fastqsanger.gz
	SRR9057310_2.fastq.gz	Fastqsanger.gz
	SRR9057311_1.fastq.gz	Fastqsanger.gz
	SRR9057311_2.fastq.gz	Fastqsanger.gz
	SRR9057312_1.fastq.gz	Fastqsanger.gz

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Inositol pyrophosphate dynamics impact fission yeast phosphate homeostasis via modulation of RNA 3' processing and transcription termination

Project description:This RNA-Seq analysis compares gene expression of the Inositol pyrophosphate phosphatase mutant aps1∆ and Inositol pyrophsophate kinase mutant asp1-D333A contrasting to the WT in the fission yeast S. pombe

2019-06-16 | GSE131237 | GEO

Inositol pyrophosphate dynamics impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination

Project description:Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here we show phosphate homeostasis is subject to metabolite control by inositol pyrophosphates (IPPs), exerted through the 3'-processing/termination machinery and the Pol2 CTD code. Increasing IP8 (via Asp1 IPP pyrophosphatase mutation) de-represses the PHO regulon and leads to precocious termination of prt lncRNA synthesis. pho1 de-repression by IP8 depends on cleavage-polyadenylation factor (CPF) subunits, termination factor Rhn1, and the Thr4 letter of the CTD code. pho1 de-repression by mutation of the Ser7 CTD letter depends on IP8. Simultaneous inactivation of Asp1 and Aps1 pyrophosphatases (i.e., too much IP8) is lethal, but this lethality is suppressed by mutations of CPF subunits Ppn1, Swd22, Ssu72, and Ctf1 and CTD mutation T4A. Failure to synthesize IP8 (via Asp1 IPP kinase mutation) results in pho1 hyper-repression. Synthetic lethality of asp1∆ with Ppn1, Swd22, and Ssu72 mutations argues that IP8 plays an important role in essential 3'-processing/termination events, albeit in a manner genetically redundant to CPF. Transcriptional profiling delineates an IPP-responsive regulon composed of genes overexpressed when IP8 levels are increased. Our results establish a novel role for IPPs in cell physiology.

2019-06-16 | GSE127550 | GEO

Inositol pyrophosphate dynamics impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination

Project description:Inositol pyrophosphate dynamics impact phosphate homeostasis via modulation of RNA 3' processing and transcription termination

| PRJNA524918 | ENA

SPX domain proteins are agents of inositol pyrophosphate toxicosis in fission yeast

Project description:SPX domain proteins are agents of inositol pyrophosphate toxicosis in fission yeast

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Inositol pyrophosphate InsP8 acts as intracellular phosphate signal in Arabidopsis

Project description:The maintenance of cellular phosphate (Pi) homeostasis is of paramount importance in living organisms. Little is known about how cells sense intracellular Pi status in multi-cellular eukaryotes. Here, we report the identification of inositol pyrophosphate InsP8, a ligand that binds to the Pi sensor protein SPX1 to inhibit PHR1, the central regulator of Pi starvation responses in Arabidopsis. The concentration of InsP8, synthesized by diphosphoinositol pentakisphosphate kinases VIH1 and VIH2, depends on cellular Pi level and the double mutants accumulated higher amounts of Pi. The paradox of Pi toxicity and induction of Pi starvation inducible genes indicated that the cells could not sense cellular Pi without InsP8. Our study reveals that InsP8 acts as a Pi signaling molecule and binds to the receptor SPX1 to regulate Pi homeostasis.

2022-02-22 | GSE126927 | GEO

Inositol pyrophosphate InsP8 acts as intracellular phosphate signal in Arabidopsis

Project description:Inositol pyrophosphate InsP8 acts as intracellular phosphate signal in Arabidopsis

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SPX domain proteins are agents of inositol pyrophosphate toxicosis in fission yeast

Project description:This RNA-Seq analysis compares gene expression of spx1∆ mutant contrasting to the WT fission yeast S. pombe

2021-12-08 | GSE185441 | GEO

A GAF domain mediates inositol pyrophosphate substrate channeling in PPIP5K phosphatases

Project description:Inositol pyrophosphates are highly phosphorylated nutrient messengers. The final step of their biosynthesis is catalyzed by diphosphoinositol pentakisphosphate kinase (PPIP5K) enzymes, which are conserved among fungi, plants, and animals. PPIP5Ks contain an N-terminal kinase domain that generates the active messenger 1,5-InsP8 and a C-terminal phosphatase domain that participates in PP-InsP catabolism. The balance between kinase and phosphatase activities controls the cellular levels and signaling capacity of 1,5- InsP8. Here, we present crystal structures of the apo and substrate-bound Vip1 phosphatase domain from S. cerevisiae (ScVip1PD). ScVip1PD is a phytase-like inositol 1-pyrophosphate phosphatase with two conserved histidine phosphatase catalytic motifs. The enzyme has a strong preference for 1,5-InsP8 and is inhibited by inorganic phosphate. ScVip1PD has an α-helical insertion domain stabilized by a structural Zn2+ binding site, and a unique GAF domain that exists in an open and closed state, allowing channeling of the 1,5-InsP 8 substrate to the active site. Mutations that alter the active site, that restrict the movement of the GAF domain or that modify the charge of the substrate channel significantly inhibit the activity of the yeast enzyme in vitro, and the function of the Arabidopsis PPIP5K VIH2 in planta. Structural analyses of full-length PPIP5Ks suggest that the kinase and phosphatase are independent enzymatic modules. Taken together, our work reveals the structure, enzymatic mechanism and regulation of eukaryotic PPIP5K phosphatases

2024-10-07 | PXD056020 | Pride

Genetic suppressor screen identifies Tgp1 (glycerophosphocholine transporter), Plc1 (phospholipase C), and Kcs1 (IP6 kinase) as determinants of inositol pyrophosphate toxicosis in fission yeast

Project description:Genetic suppressor screen identifies Tgp1 (glycerophosphocholine transporter), Plc1 (phospholipase C), and Kcs1 (IP6 kinase) as determinants of inositol pyrophosphate toxicosis in fission yeast

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Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast

Project description:Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Unexpectedly, we show here that NNS-like transcription termination is not conserved in fission yeast. Instead, genome-wide location analyses show global recruitment of mRNA 3’ end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We further show that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.

2018-08-10 | GSE115595 | GEO

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