Functional modeling of NMIHBA-causingPRUNE1variants reveals a requirement for its exopolyphosphatase activity

Abstract

Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies (NMIHBA) is an autosomal recessive neurodevelopmental and neurodegenerative disorder characterized by global developmental delay and severe intellectual disability. Microcephaly, progressive cortical atrophy, cerebellar hypoplasia and delayed myelination are neurological hallmarks in affected individuals. NMIHBA is caused by biallelic variants in PRUNE1 encoding prune exopolyphosphatase 1. We provide in-depth clinical description of two affected siblings harboring compound heterozygous variant alleles, c.383G>A (p.Arg128Gln), c.520G>T (p.Gly174*) in PRUNE1. To gain insights into disease biology, we biochemically characterized missense variants within the conserved N-terminal aspartic acid-histidine-histidine (DHH) motif and provide evidence that they result in the destabilization of protein structure and/or loss of exopolyphosphatase activity. Genetic ablation of Prune1 results in midgestational lethality in mice, associated with perturbations to embryonic growth and vascular development. Our findings suggest that NMIHBA results from hypomorphic variant alleles in humans and underscore the potential key role of PRUNE1 exopolyphoshatase activity in neurodevelopment. 4 Introduction:

Ddp1 cooperates with Ppx1 to counter a stress response initiated by non-vacuolar polyphosphate

“…However, expressing either Prune or DIPP1-DIPP3 in yeast resulted in no appreciable change in viability and no obvious decrease in PPK-synthesized polyP. We note that the in vitro exopolyphosphatase activity of Prune is mostly against very short chains (3-4 phosphate units in length) [41,63] . In our experiments, Prune was also expressed at substantially lower levels than the DIPP1-DIPP3 proteins in yeast, despite the fact that both constructs used the GPD promoter.…”

“…Mammalian polyphosphatases may also play a role in degrading long-chain polyP made by pathogenic bacteria, which has been suggested to enter cells during infection to reprogram macrophages and thereby subvert host defense mechanisms [49] . The identities of intracellular human polyphosphatases had long remained unknown, but Prune and DIPP1-DIPP3 have emerged as candidates based on their in vitro activities [40,41,63] . Notably, mutations that reduce Prune activity in vitro give rise to the rare disease called Neurodevelopmental disorder with microcephaly, hypotonia and variable brain anomalies (NMIHBA) [63] .…”

“…The identities of intracellular human polyphosphatases had long remained unknown, but Prune and DIPP1-DIPP3 have emerged as candidates based on their in vitro activities [40,41,63] . Notably, mutations that reduce Prune activity in vitro give rise to the rare disease called Neurodevelopmental disorder with microcephaly, hypotonia and variable brain anomalies (NMIHBA) [63] . However, expressing either Prune or DIPP1-DIPP3 in yeast resulted in no appreciable change in viability and no obvious decrease in PPK-synthesized polyP.…”