Inositol pyrophosphates regulate RNA polymerase I-mediated rRNA transcription in Saccharomyces cerevisiae

Abstract

Ribosome biogenesis is an essential cellular process regulated by the metabolic state of a cell. We examined whether inositol pyrophosphates, energy-rich derivatives of inositol that act as metabolic messengers, play a role in ribosome synthesis in the budding yeast, Saccharomyces cerevisiae. Yeast strains lacking the inositol hexakisphosphate (IP6) kinase Kcs1, which is required for the synthesis of inositol pyrophosphates, display increased sensitivity to translation inhibitors and decreased protein synthesis. These phenotypes are reversed on expression of enzymatically active Kcs1, but not on expression of the inactive form. The kcs1Δ yeast cells exhibit reduced levels of ribosome subunits, suggesting that they are defective in ribosome biogenesis. The rate of rRNA synthesis, the first step of ribosome biogenesis, is decreased in kcs1Δ yeast strains, suggesting that RNA polymerase I (Pol I) activity may be reduced in these cells. We determined that the Pol I subunits, A190, A43 and A34.5, can accept a β-phosphate moiety from inositol pyrophosphates to undergo serine pyrophosphorylation. Although there is impaired rRNA synthesis in kcs1Δ yeast cells, we did not find any defect in recruitment of Pol I on rDNA, but observed that the rate of transcription elongation was compromised. Taken together, our findings highlight inositol pyrophosphates as novel regulators of rRNA transcription.

Inositol hexakisphosphate kinase 1 (IP6K1) activity is required for cytoplasmic dynein-driven transport

“…One mechanism by which inositol pyrophosphates may directly influence dynein function is by serine pyrophosphorylation on dynein subunits. A consensus pyrophosphorylation site comprises one or more Ser residues flanked by Asp/Glu residues [9–11,33]. This is also a preferred site for phosphorylation by the protein kinase CK2, which is known to prephosphorylate the target Ser to prime it for pyrophosphorylation [9].…”

“…Our study also sheds light on the mechanism of protein pyrophosphorylation, revealing that a disordered protein sequence distinct from the target Ser residue is required for pyrophosphorylation. Similarly, pyrophosphorylation target sites identified in three different yeast RNA Pol I subunits also fall within highly mobile regions [33], implying that flexible secondary structures promote phosphotransfer from IP 7 to phosphoserine. As with other posttranslational modifications, pyrophosphorylation has recently been shown to be reversible [48], suggesting that dynein recruitment to vesicles via IC–p150 Glued interaction may be regulatable by yet to be identified signaling pathways.…”

Inositol polyphosphates intersect with signaling and metabolic networks via two distinct mechanisms

“…This analysis strongly implies a role for the highly phosphorylated inositols in ribosome biogenesis. Indeed, a recent report described a direct function of the PP-InsPs in ribosome biogenesis, by controlling RNA polymerase I activity (25).…”

Inositol pyrophosphates modulate cell cycle independently of alteration in telomere length

“…There are numerous ways how inositol pyrophosphates may regulate cell cycle progression, this may include events on vacuole biogenesis and cell wall integrity (Dubois et al, 2002), proper endocytic trafficking (Saiardi et al, 2002), cyclin-CDK-CDK inhibitor complex (Lee et al, 2007), chromatin remodelling (Steger et al, 2003) or RNA polymerase Imediated rRNA transcription (Thota et al, 2015) and for all of them understanding of structural analysis of diphosphoinositol polyphosphate kinase is crucial (Shears et al, 2013). Furthermore, above all of them, two might be of particular significance.…”