Inositol pyrophosphates impact phosphate homeostasis via modulation of RNA 3′ processing and transcription termination

• Published in: Nucleic acids research Vol. 47; no. 16; pp. 8452 - 8469
• Main Authors: Sanchez, Ana M, Garg, Angad, Shuman, Stewart, Schwer, Beate
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19.09.2019
• Subjects: Acid Phosphatase - genetics; Acid Phosphatase - metabolism; Cleavage And Polyadenylation Specificity Factor - genetics; Cleavage And Polyadenylation Specificity Factor - metabolism; Cytoskeletal Proteins - deficiency; Cytoskeletal Proteins - genetics; Gene Deletion; Gene Expression Regulation, Fungal; Gene regulation, Chromatin and Epigenetics; Inositol Phosphates - metabolism; Membrane Transport Proteins - genetics; Membrane Transport Proteins - metabolism; Nuclear Proteins - genetics; Nuclear Proteins - metabolism; Protein Isoforms - genetics; Protein Isoforms - metabolism; Pyrophosphatases - deficiency; Pyrophosphatases - genetics; Regulon; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Schizosaccharomyces - genetics; Schizosaccharomyces - metabolism; Schizosaccharomyces pombe Proteins - genetics; Schizosaccharomyces pombe Proteins - metabolism; Transcription Termination, Genetic
• DOI: 10.1093/nar/gkz567
• ISSN: 0305-1048; 1362-4962

Fission yeast phosphate acquisition genes pho1, pho84, and tgp1 are repressed in phosphate-rich medium by transcription of upstream lncRNAs. Here, we show that 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 the Asp1 and Aps1 IPP pyrophosphatases 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 asp1Δ 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.