Tandem inactivation of inositol pyrophosphatases Asp1, Siw14, and Aps1 illuminates functional redundancies in inositol pyrophosphate catabolism in fission yeast
Inositol pyrophosphates 5-IP$_7$, 1-IP$_7$, and 1,5-IP$_8$ are eukaryal signaling molecules that influence cell physiology, especially phosphate homeostasis. In fission yeast, 1,5-IP$_8$ and 1-IP$_7$ impact gene expression by acting as agonists of RNA 3'-processing and transcription termination. 1,5-IP$_8$ is synthesized by position-specific kinases Kcs1 and Asp1 that convert IP$_6$ to 5-IP$_7$ and 5-IP$_7$ to 1,5-IP$_8$, respectively. Inositol pyrophosphatase enzymes Asp1 (a histidine acid phosphatase), Siw14 (a cysteinyl phosphatase), and Aps1 (a Nudix hydrolase) are agents of inositol pyrophosphate catabolism in fission yeast. Whereas Asp1, Siw14, and Aps1 are individually inessential, double pyrophosphatase mutants $asp1-H397A aps1 \Delta$ and $siw14\Delta aps1\delta$ display severe growth defects caused by overzealous 3'-processing/termination. By applying CE-ESI-MS to profile the inositol pyrophosphate content of fission yeast mutants in which inositol pyrophosphate toxicity is genetically suppressed, we elucidated the functional redundancies of the Asp1, Siw14, and Aps1 pyrophosphatases. Asp1, which exclusively cleaves the 1-$\beta$-phosphate, and Aps1, which prefers to cleave the 1-$\beta$-phosphate, play essential overlapping roles in guarding against the accumulation of toxic levels of 1-IP$_7$. Aps1 and Siw14 together catabolize the inositol-5-pyrophosphates, and their simultaneous inactivation results in overaccumulation of 5-IP$_7$. Cells lacking all three pyrophosphatases amass high levels of 1,5-IP$_8$ and 1-IP$_7$, with concomitant depletion of IP$_6$. A genetic screen identified three missense mutations in the catalytic domain of Kcs1 kinase that suppressed inositol-1-pyrophosphate toxicosis. The screen also implicated the 3'-processing factor Swd22, the inositol pyrophosphate sensor Spx1, and the nuclear poly(A)-binding protein Nab2 as mediators of inositol-1-pyrophosphate toxicity.