Ppn2 endopolyphosphatase overexpressed in Saccharomyces cerevisiae: Comparison with Ppn1, Ppx1, and Ddp1 polyphosphatases

Андреева, Н. И.; Ledova, L. A.; Ryazanova, L. P.; Tomashevsky, Alexander; Kulakovskaya, T. V.; Eldarov, M. A.

doi:10.1016/j.biochi.2019.06.001

Cited by 28 publications

(32 citation statements)

References 39 publications

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“…P13 and P14 (equivalent to P and P) conserve interaction with Mg1. The presence of P15 after the cleavable pyrophosphate (P13 to P14) suggests that we observe the substrate ready for the predominant endopolyphosphatase activity described for this enzyme (11,14). Additional interactions are seen between these phosphates and the enzyme: P1-Lys 57…”

Section: Ddp1:polyp15 Complexmentioning

confidence: 78%

“…It hydrolyzes 1-InsP 7 , 5-InsP 7 , and InsP 8 , although it hydrolyzes 1-InsP 7 faster than InsP 8 and 5-InsP 7 (13). However, ScDDP1 is not exclusively a PP-InsP phosphatase, since it also hydrolyzes polyphosphates (polyPn) (11,14) and diadenosine polyphosphates (Ap n A as Ap 5 A or Ap 6 A) (11,15). ScDDP1 participation in cytoplasmic polyPn cleavage has been already proven (16).…”

Section: Introductionmentioning

confidence: 99%

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Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping

et al. 2021

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The yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase DDP1 is a Nudix enzyme with pyrophosphatase activity on diphosphoinositides, dinucleotides, and polyphosphates. These substrates bind to diverse protein targets and participate in signaling and metabolism, being essential for energy and phosphate homeostasis, ATPase pump regulation, or protein phosphorylation. An exhaustive structural study of DDP1 in complex with multiple ligands related to its three diverse substrate classes is reported. This allowed full characterization of the DDP1 active site depicting the molecular basis for endowing multisubstrate abilities to a Nudix enzyme, driven by phosphate anchoring following a defined path. This study, combined with multiple enzyme variants, reveals the different substrate binding modes, preferences, and selection. Our findings expand current knowledge on this important structural superfamily with implications extending beyond inositide research. This work represents a valuable tool for inhibitor/substrate design for ScDDP1 and orthologs as potential targets to address fungal infections and other health concerns.

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Section: Ddp1:polyp15 Complexmentioning

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping

et al. 2021

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“…For the enzymatic assay, the samples of polyP fractions polyP2 and polyP3 were neutralized to pH 7,0 by HCl aliquotes and incubated with S. cerevisiae exopolyphosphatase Ppx1 obtained as described earlier [34]. The reaction mixture containing 0.5 mL of 50 mM Tris-HCl (pH 7.2), 2.5 mM MgSO4, 0.02 mL (~5 U) of Ppx1 preparation, and 0.1 mL of polyP extracts was incubated at 30 °С for 2 h with shaking, and the released Pi was assayed as previously described [32].…”

Section: Enzymatic Assay Of Polypsmentioning

confidence: 99%

Role of VTC4 in Stress Response and Regulation of Inorganic Polyphosphate Levels in Yeast

Tomashevsky¹,

Kulakovskaya²,

Trilisenko³

et al. 2020

Preprint

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Inorganic polyphosphate (polyP) is an important factor of stress tolerance in microbial cells. In yeast, the major enzyme of polyP biosynthesis is Vtc4, a subunit of the vacuole transporter chaperone (VTC) complex. In this study, we demonstrated that Vtc4 knockout in Saccharomyces cerevisiae not only decreased polyP content but also caused shifts in the composition of the intracellular polyP pool and changed the stress tolerance profile. In the mutant S. cerevisiae, the level of short-chain acid-soluble polyPs was decreased nearly 10-fold, whereas that of longer acid-insoluble polyPs was decreased only 2-fold, suggesting the existence of other enzymes compensating the production of long-chain polyPs. The Δvtc4 mutant showed inhibition of Mg2+-dependent phosphate uptake and decreased resistance to alkaline stress but increased tolerance to oxidation and heavy metal ions, especially Mn2+. Quantitative PCR revealed the upregulation of the DDR2 gene implicated in multiple stress responses and downregulation of PHO84 encoding a phosphate and Mn2+ transporter, which could account for the effects on phosphate uptake and Mn2+-related stress response in the Δvtc4 mutant. Our study indicates that short-chain polyPs, plays an important role in the regulation of stress response in yeast.

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“…To the best of our knowledge, only two ALPHs have been functionally characterised to date. One is the S. cerevisiae ALPH protein (YNL217W), a Zn 2+ dependent endopolyphosphatase of the vacuolar lumen [ 7 ] that is also active with Co 2+ and possibly Mg 2+ [ 8 ]. The enzyme’s main function is the cleavage of vacuolar poly(P).…”

Section: Introductionmentioning

confidence: 99%

Is mRNA decapping by ApaH like phosphatases present in eukaryotes beyond the Kinetoplastida?

et al. 2021

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Background ApaH like phosphatases (ALPHs) originate from the bacterial ApaH protein and have been identified in all eukaryotic super-groups. Only two of these proteins have been functionally characterised. We have shown that the ApaH like phosphatase ALPH1 from the Kinetoplastid Trypanosoma brucei is the mRNA decapping enzyme of the parasite. In eukaryotes, Dcp2 is the major mRNA decapping enzyme and mRNA decapping by ALPHs is unprecedented, but the bacterial ApaH protein was recently found decapping non-conventional caps of bacterial mRNAs. These findings prompted us to explore whether mRNA decapping by ALPHs is restricted to Kinetoplastida or could be more widespread among eukaryotes. Results We screened 827 eukaryotic proteomes with a newly developed Python-based algorithm for the presence of ALPHs and used the data to characterize the phylogenetic distribution, conserved features, additional domains and predicted intracellular localisation of this protein family. For most organisms, we found ALPH proteins to be either absent (495/827 organisms) or to have non-cytoplasmic localisation predictions (73% of all ALPHs), excluding a function in mRNA decapping. Although, non-cytoplasmic ALPH proteins had in vitro mRNA decapping activity. Only 71 non-Kinetoplastida have ALPH proteins with predicted cytoplasmic localisations. However, in contrast to Kinetoplastida, these organisms also possess a homologue of Dcp2 and in contrast to ALPH1 of Kinetoplastida, these ALPH proteins are very short and consist of the catalytic domain only. Conclusions ALPH was present in the last common ancestor of eukaryotes, but most eukaryotes have either lost the enzyme, or use it exclusively outside the cytoplasm. The acceptance of mRNA as a substrate indicates that ALPHs, like bacterial ApaH, have a wide substrate range: the need to protect mRNAs from unregulated degradation is one possible explanation for the selection against the presence of cytoplasmic ALPH proteins in most eukaryotes. Kinetoplastida succeeded to exploit ALPH as their only or major mRNA decapping enzyme. 71 eukaryotic organisms outside the Kinetoplastid lineage have short ALPH proteins with cytoplasmic localisation predictions: whether these proteins are used as decapping enzymes in addition to Dcp2 or else have adapted to not accept mRNAs as a substrate, remains to be explored.

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Ppn2 endopolyphosphatase overexpressed in Saccharomyces cerevisiae: Comparison with Ppn1, Ppx1, and Ddp1 polyphosphatases

Cited by 28 publications

References 39 publications

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping

Role of VTC4 in Stress Response and Regulation of Inorganic Polyphosphate Levels in Yeast

Is mRNA decapping by ApaH like phosphatases present in eukaryotes beyond the Kinetoplastida?

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