PPP1R8 (protein phosphatase 1, regulatory (inhibitor) subunit 8)

2011-05-01   Nikki Minnebo , Nele Van Dessel , Monique Beullens , Aleyde van Eynde , Mathieu Bollen 

Laboratory of Biosignaling & Therapeutics, Dept Molecular Cell Biology, University of Leuven, Herestraat 49 box 901, 3000 Leuven, Belgium

Identity

HGNC
LOCATION
1p35.3
LOCUSID
ALIAS
ARD-1,ARD1,NIPP-1,NIPP1,PRO2047
FUSION GENES

DNA/RNA

Note

ARD1 is a frequently used alias for NIPP1, however, this name actually corresponds to an alternative transcript (NIPP1gamma), which encodes a truncated form of NIPP1 encompassing residues 225-351 only. This transcript has been shown to restore endoribonuclease activity to E. coli rne gene mutants (Wang and Cohen, 1994; Claverie-Martin et al., 1997; Chang et al., 1999; Jin et al., 1999; Van Eynde et al., 1999). Moreover, note that the name ARD1 is also used for a completely unrelated protein, TRIM23 (Mishima et al., 1993).
Atlas Image
Genomic organization of the PPP1R8 gene and the alternative splice variants with their corresponding coding sequences (black line). Exons and alternative splice sites are indicated by different colors.

Description

The entire PPP1R8 gene spans 20.9 kb on the forward strand of the long arm on chromosome 1. The gene contains 7 exons of which exon 1 has 5-alternative splice sites.

Transcription

The PPP1R8 gene contains 7 exons which give rise to 5 alternative splice products (see diagram above). When speaking about NIPP1, one usually refers to the NIPP1alpha isoform (39 kDa, 351 residues) which is by far the most abundant isoform in all examined mammalian tissues. When visualized by immunoblotting with C-terminal antibodies (which recognize all isoforms except NIPP1epsilon), also smaller polypeptides are visualized albeit at a much lower intensity as compared to the alpha-isoform. However, it is not clear yet whether these represent some of the other NIPP1 isoforms or simply degradation products of NIPP1alpha (Van Eynde et al., 1999; Chang et al., 1999; Fardilha et al., 2004).

Pseudogene

A processed pseudogene, termed PPP1R8P, has been mapped to chromosome 1p33-32 (48790762-48791795 bp from pter according to hg19 - Feb 2009). Consistent with this notion, it is only 1034 bp in size, contains no introns and encodes an incomplete NIPP1-transcript due to the presence of various premature stop codons (Van Eynde et al., 1999).

Proteins

Note

Nuclear Inhibitor of PP1 (NIPP1) was first identified in bovine thymus nuclei as a potent inhibitor of the protein Ser/Thr phosphatase PP1 (Beullens et al., 1992; Beullens et al., 1993). Later on, it became clear that NIPP1 exerts various functions in the eukaryotic cell by serving as a kind of scaffold protein onto which a variety of proteins can bind. These interaction partners range from protein kinase MELK, protein phosphatase PP1 (PPP1C-a/PPP1C-b/PPP1C-c), the pre-mRNA splicing factors SAP155 (SF3B1) and CDC5L to the chromatin modifiers EED and EZH2.
Atlas Image
A schematic representation of the domain structure of NIPP1 and its interactor binding sites. The FHA-domain (red) binds the indicated interactors via a phosphorylated TP dipeptide motif. NIPP1 binds PP1 via the indicated RVXF-motif and via a C-terminal binding site (green). EED and RNA binding sites are colored blue and orange, respectively. Known phosphorylation sites are indicated in black (in vivo validated) or grey (in vitro data).

Description

NIPP1 consists of 351 amino acids and has a molecular mass of 39 kDa. However, it migrates at a size of about 45 kDa on SDS-PAGE. NIPP1 contains an N-terminal ForkHead Associated (FHA) domain. Via this established phosphothreonine-binding domain, NIPP1 interacts with protein kinase MELK, the splicing factors SAP155 and CDC5L and the histone methyltransferase EZH2. Moreover, it was shown that the NIPP1 FHA-domain binds to its ligands via phosphorylated TP-dipeptide motifs, present in the interacting proteins (Boudrez et al., 2000; Boudrez et al., 2002; Vulsteke et al., 2004; Nuytten et al., 2008).
Two additional interactors, PP1 and EED, have two separate binding sites on NIPP1: one in the central domain and the other at the C-terminus. In the central domain, the binding of NIPP1 to PP1 is mediated by a so called RVXF-motif, which is present in about two thirds of all known PP1 interacting proteins (Beullens et al., 1999; Beullens et al., 2000; Hendrickx et al., 2009). In addition, the C-terminal 22 residues can interact with nucleic acids (Jin et al., 1999).

Expression

NIPP1 is ubiquitously expressed (Van Eynde et al., 1995).

Localisation

NIPP1 is a nuclear protein and is enriched in splicing factor storage sites called speckles (Trinkle-Mulcahy et al., 1999; Jagiello et al., 2000). Although largely nuclear, some data suggest that there also exists a cytoplasmic pool of NIPP1 (Boudrez et al., 1999; Jagiello et al., 1997).

Function

NIPP1 is a scaffold protein and exerts its functions via its interacting proteins. NIPP1 was discovered as a potent inhibitor and a major nuclear interactor of the phosphatase PP1 (Beullens et al., 1999). PP1 functions as a holoenzyme in which the interacting proteins confine substrate specificity, activity and/or localization of PP1 (Bollen et al., 2010). For NIPP1, it has been shown that it acts as a physiological PP1 inhibitor for some substrates, while functioning as an activator towards other substrates (Parker et al., 2002; Lesage et al., 2004; Comerford et al., 2006; Shi and Manley, 2007). Also, the interaction between NIPP1 and PP1 can be regulated by phosphorylation (Beullens et al., 1993; Van Eynde et al., 1994; Jagiello et al., 1995; Vulsteke et al., 1997; Beullens et al., 1999).
NIPP1 is also involved in 3 other major cellular processes: splicing, transcription and development. Firstly, NIPP1 is associated with spliceosomes and splicing factor storage sites called "speckles", probably mediated by its interaction with the splicing factors CDC5L and SAP155 (Boudrez et al., 2000; Deckert et al., 2006). Pre-mRNA splicing assays showed that NIPP1 is required for late stage spliceosome formation (Beullens and Bollen, 2002). Recently it was published that NIPP1 directs associated PP1 to dephosphorylate SAP155 (Tanuma et al., 2008). Secondly, NIPP1 is a transcriptional repressor via its interaction with EED and EZH2 (Jin et al., 2003; Roy et al., 2007), two core components of the Polycomb repressive complex 2 (PRC2). Through its interaction with PRC2, NIPP1 directs it to a subset of Polycomb target genes, where the methyltransferase EZH2 will mark genes proned for silencing by trimethylating histone 3 on lysine 27 (Nuytten et al, 2008). In 2010, Van Dessel et al. showed that this targeting function of NIPP1 is dependent on associated PP1. Finally, NIPP1 is essential for embryonic development as a NIPP1 knock out mouse is embryonically lethal at the onset of gastrulation (Van Eynde et al., 2004).
The splice variant NIPP1gamma or ARD1 displays a site-specific Mg2+-dependent endoribonuclease activity, in contrast to the NIPP1alpha isoform, which does not possess this function (Wang and Cohen, 1994; Claverie-Martin et al., 1997; Chang et al., 1999; Jin et al., 1999; Van Eynde et al., 1999).

Homology

NIPP1 is highly conserved in all multicellular organisms.

Implicated in

Entity name
Hepatoma
Disease
Cancer.
Prognosis
An increase in NIPP1 mRNA is correlated with a malignant phenotype in rats (Kim et al., 2000).

Bibliography

Pubmed IDLast YearTitleAuthors
119098642002The protein phosphatase-1 regulator NIPP1 is also a splicing factor involved in a late step of spliceosome assembly.Beullens M et al
203991032010The extended PP1 toolkit: designed to create specificity.Bollen M et al
121052152002Phosphorylation-dependent interaction between the splicing factors SAP155 and NIPP1.Boudrez A et al
104284961999Identification of MYPT1 and NIPP1 as subunits of protein phosphatase 1 in rat liver cytosol.Boudrez A et al
105648111999Alternative splicing regulates the production of ARD-1 endoribonuclease and NIPP-1, an inhibitor of protein phosphatase-1, as isoforms encoded by the same gene.Chang AC et al
91532391997ARD-1 cDNA from human cells encodes a site-specific single-strand endoribonuclease that functionally resembles Escherichia coli RNase E.Claverie-Martin F et al
168265682006Regulation of protein phosphatase 1gamma activity in hypoxia through increased interaction with NIPP1: implications for cellular metabolism.Comerford KM et al
168097852006Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions.Deckert J et al
156598322004Alternatively spliced protein variants as potential therapeutic targets for male infertility and contraception.Fardilha M et al
193896232009Docking motif-guided mapping of the interactome of protein phosphatase-1.Hendrickx A et al
92683471997NIPP-1, a nuclear inhibitory subunit of protein phosphatase-1, has RNA-binding properties.Jagiello I et al
104322941999Mapping of the RNA-binding and endoribonuclease domains of NIPP1, a nuclear targeting subunit of protein phosphatase 1.Jin Q et al
127889422003The protein phosphatase-1 (PP1) regulator, nuclear inhibitor of PP1 (NIPP1), interacts with the polycomb group protein, embryonic ectoderm development (EED), and functions as a transcriptional repressor.Jin Q et al
107172442000Increased expression of NIPP-1 mRNA correlates positively with malignant phenotype in rat hepatomas.Kim SE et al
155018172004Interactor-mediated nuclear translocation and retention of protein phosphatase-1.Lesage B et al
84733241993ARD 1, a 64-kDa guanine nucleotide-binding protein with a carboxyl-terminal ADP-ribosylation factor domain.Mishima K et al
177244622008The transcriptional repressor NIPP1 is an essential player in EZH2-mediated gene silencing.Nuytten M et al
123585982002Functional interaction between nuclear inhibitor of protein phosphatase type 1 (NIPP1) and protein phosphatase type 1 (PP1) in Drosophila: consequences of over-expression of NIPP1 in flies and suppression by co-expression of PP1.Parker L et al
178040932007The transcriptional repression by NIPP1 is mediated by Polycomb group proteins.Roy N et al
179367062007A complex signaling pathway regulates SRp38 phosphorylation and pre-mRNA splicing in response to heat shock.Shi Y et al
188425822008Nuclear inhibitor of protein phosphatase-1 (NIPP1) directs protein phosphatase-1 (PP1) to dephosphorylate the U2 small nuclear ribonucleoprotein particle (snRNP) component, spliceosome-associated protein 155 (Sap155).Tanuma N et al
98584691999Nuclear organisation of NIPP1, a regulatory subunit of protein phosphatase 1 that associates with pre-mRNA splicing factors.Trinkle-Mulcahy L et al
206710312010The phosphatase interactor NIPP1 regulates the occupancy of the histone methyltransferase EZH2 at Polycomb targets.Van Dessel N et al
151991422004The nuclear scaffold protein NIPP1 is essential for early embryonic development and cell proliferation.Van Eynde A et al
146991192004Inhibition of spliceosome assembly by the cell cycle-regulated protein kinase MELK and involvement of splicing factor NIPP1.Vulsteke V et al
75240971994ard-1: a human gene that reverses the effects of temperature-sensitive and deletion mutations in the Escherichia coli rne gene and encodes an activity producing RNase E-like cleavages.Wang M et al

Other Information

Locus ID:

NCBI: 5511
MIM: 602636
HGNC: 9296
Ensembl: ENSG00000117751

Variants:

dbSNP: 5511
ClinVar: 5511
TCGA: ENSG00000117751
COSMIC: PPP1R8

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000117751ENST00000236412Q12972
ENSG00000117751ENST00000236412Q6ICT4
ENSG00000117751ENST00000311772Q12972
ENSG00000117751ENST00000373931Q12972
ENSG00000117751ENST00000431586A0A0A0MT09

Expression (GTEx)

0
10
20
30
40
50
60

Protein levels (Protein atlas)

Not detected
Low
Medium
High

References

Pubmed IDYearTitleCitations
177244622008The transcriptional repressor NIPP1 is an essential player in EZH2-mediated gene silencing.37
229405842012The molecular basis for substrate specificity of the nuclear NIPP1:PP1 holoenzyme.28
155018172004Interactor-mediated nuclear translocation and retention of protein phosphatase-1.25
188425822008Nuclear inhibitor of protein phosphatase-1 (NIPP1) directs protein phosphatase-1 (PP1) to dephosphorylate the U2 small nuclear ribonucleoprotein particle (snRNP) component, spliceosome-associated protein 155 (Sap155).22
168265682006Regulation of protein phosphatase 1gamma activity in hypoxia through increased interaction with NIPP1: implications for cellular metabolism.10
119098642002The protein phosphatase-1 regulator NIPP1 is also a splicing factor involved in a late step of spliceosome assembly.9
298989192018Overexpression of PP1-NIPP1 limits the capacity of cells to repair DNA double-strand breaks.9
228158112012A role for PP1/NIPP1 in steering migration of human cancer cells.8
178040932007The transcriptional repression by NIPP1 is mediated by Polycomb group proteins.5
259075362015Protein phosphatase PP1-NIPP1 activates mesenchymal genes in HeLa cells.5

Citation

Nikki Minnebo ; Nele Van Dessel ; Monique Beullens ; Aleyde van Eynde ; Mathieu Bollen

PPP1R8 (protein phosphatase 1, regulatory (inhibitor) subunit 8)

Atlas Genet Cytogenet Oncol Haematol. 2011-05-01

Online version: http://atlasgeneticsoncology.org/gene/41811/ppp1r8