A recently-discovered
protein post-translational modification,
lysine polyphosphorylation (K-PPn), consists of the covalent attachment of inorganic
polyphosphate (
polyP) to
lysine residues. The nonenzymatic nature of K-PPn means that the degree of this modification depends on both
polyP abundance and the
amino acids surrounding the modified
lysine. K-PPn was originally discovered in budding yeast (Saccharomyces cerevisiae), in which
polyP anabolism and catabolism are well-characterized. However, yeast vacuoles accumulate large amounts of
polyP, and upon cell lysis, the release of the vacuolar
polyP could nonphysiologically cause K-PPn of nuclear and cytosolic targets. Moreover, yeast vacuoles possess two very active endopolyphosphatases, Ppn1 and Ppn2, that could have opposing effects on the extent of K-PPn. Here, we characterized the contribution of vacuolar
polyP metabolism to K-PPn of two
yeast proteins, Top1 (
DNA topoisomerase 1) and Nsr1 (nuclear signal recognition 1). We discovered that whereas Top1-targeting K-PPn is only marginally affected by vacuolar
polyP metabolism, Nsr1-targeting K-PPn is highly sensitive to the release of
polyP and of endopolyphosphatases from the vacuole. Therefore, to better study K-PPn of cytosolic and nuclear targets, we constructed a yeast strain devoid of vacuolar
polyP by targeting the
exopolyphosphatase Ppx1 to the vacuole and concomitantly depleting the two endopolyphosphatases (ppn1Δppn2Δ, vt-Ppx1). This strain enabled us to study K-PPn of cytosolic and nuclear targets without the interfering effects of cell lysis on vacuole
polyP and of endopolyphosphatases. Furthermore, we also define the fundamental nature of the
acidic amino acid residues to the K-PPn target domain.