241 human active and 13 inactive phosphatases in total;
194 phosphatases have substrate data;
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336 protein substrates;
83 non-protein substrates;
1215 dephosphorylation interactions;
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299 KEGG pathways;
876 Reactome pathways;
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last scientific update: 11 Mar, 2019
last maintenance update: 01 Sep, 2023
Nucleus inner membrane; Lipid-anchor;Nucleoplasmic side
Function (UniProt annotation)
Lamins are components of the nuclear lamina, a fibrouslayer on the nucleoplasmic side of the inner nuclear membrane,which is thought to provide a framework for the nuclear envelopeand may also interact with chromatin
Apoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled by numerous interrelating processes. The 'extrinsic' pathway involves stimulation of members of the tumor necrosis factor (TNF) receptor subfamily, such as TNFRI, CD95/Fas or TRAILR (death receptors), located at the cell surface, by their specific ligands, such as TNF-alpha, FasL or TRAIL, respectively. The 'intrinsic' pathway is activated mainly by non-receptor stimuli, such as DNA damage, ER stress, metabolic stress, UV radiation or growth-factor deprivation. The central event in the 'intrinsic' pathway is the mitochondrial outer membrane permeabilization (MOMP), which leads to the release of cytochrome c. These two pathways converge at the level of effector caspases, such as caspase-3 and caspase-7. The third major pathway is initiated by the constituents of cytotoxic granules (e.g. Perforin and Granzyme B) that are released by CTLs (cytotoxic T-cells) and NK (natural killer) cells. Granzyme B, similarly to the caspases, cleaves its substrates after aspartic acid residues, suggesting that this protease has the ability to activate members of the caspase family directly. It is the balance between the pro-apoptotic and anti-apoptotic signals that eventually determines whether cells will undergo apoptosis, survive or proliferate. TNF family of ligands activates anti-apoptotic or cell-survival signals as well as apoptotic signals. NGF and Interleukin-3 promotes the survival, proliferation and differentiation of neurons or hematopoietic cells, respectively. Withdrawal of these growth factors leads to cell death, as described above.
Meiotic synapsis is the stable physical pairing of homologous chromosomes that begins in leptonema of prophase I and lasts until anaphase of prophase I. First, short segments of axial elements form along chromosomes. Telomeres then cluster at a region of the inner nuclear membrane and axial elements extend and fuse along the length of the chromosomes. Subsequent to the initiation of recombination transverse filaments of SYCP1 link axial/lateral elements to a central element containing SYCE1 and SYCE2, thus forming the synaptonemal complex (reviewed in Yang and Wang 2009).Unsynapsed regions are silenced during pachynema by recruitment of BRCA1 and ATR, which phosphorylates histone H2AX (reviewed in Inagaki et al. 2010)
The process of DNA damage/telomere stress induced senescence culminates in the formation of senescence associated heterochromatin foci (SAHF). These foci represent facultative heterochromatin that is formed in senescent cells. They contribute to the repression of proliferation promoting genes and play an important role in the permanent cell cycle exit that characterizes senescence (Narita et al. 2003 and 2006). SAHF appear as compacted, punctate DAPI stained foci of DNA. Each chromosome is condensed into a single SAH focus, with telomeric and centromeric chromatin located predominantly at its periphery (Funayama et al. 2006, Zhang et al. 2007).
An evolutionarily conserved protein complex of HIRA, ASF1A, UBN1 and CABIN1 plays a crucial role in the SAHF formation. As cells approach senescence, HIRA, ASF1A, UBN1 and CABIN1 accumulate at the PML bodies (Zhang et al. 2005, Banumathy et al. 2009, Rai et al. 2011). PML bodies are punctate nuclear structures that contain PML protein and numerous other proteins and are proposed to be the sites of assembly of macromolecular regulatory complexes and protein modification (Fogal et al. 2000, Guo et al. 2000, Pearson et al. 2000). Recruitment of HIRA to PML bodies coincides with altered chromatin structure and deposition of macroH2A histone H2A variant onto chromatin. As cells become senescent, HIRA, ASF1A, UBN1 and CABIN1 relocate from PML bodies to SAHF. HIRA accumulation at PML bodies is RB1 and TP53 independent, but may require phosphorylation of HIRA serine S697 by GSK3B (Ye, Zerlanko, Kennedy et al. 2007). SAHF formation itself, however, requires functional RB1 and TP53 pathways (Ye, Zerlanko, Zhang et al. 2007).
SAHF contain H3K9Me mark, characteristic of trancriptionally silent chromatin, and HP1, marcoH2A histone H2A variant and HMGA proteins are also components of SAHF (Narita et al. 2006), besides the HIRA:ASF1A:UBN1:CABIN1 complex. A yet unidentified H3K9Me histone methyltransferase may be recruited to SAHF by UBN1 (Banumathy et al. 2009). One of the functions of the HIRA:ASF1A:UBN1:CABIN1 complex is to deposit histone H3.3. variant to chromatin, which influences gene expression (Zhang et al. 2007, Rai et al. 2011).
Further studies are needed to fully elucidate the mechanism of SAHF formation and mechanism by which SAHF promote cell senescence
In mitotic prophase, chromatin detaches from the nuclear envelope, and this contributes to the nuclear envelope breakdown. VRK1 (and possibly VRK2) mediated phosphorylation of BANF1 (BAF), a protein that simultaneously interacts with DNA, LEM-domain inner nuclear membrane proteins, and lamins (Zheng et al. 2000, Shumaker et al. 2001, Haraguchi et al. 2001, Mansharamani and Wilson 2005, Brachner et al. 2005) is considered to be one of the key steps in the detachment of the nuclear envelope from chromatin (Bengtsson and Wilson 2006, Nichols et al. 2006, Gorjanacz et al. 2007)
Reassembly of the nuclear envelope is initiated at late anaphase/early telophase when BANF1 (BAF) accumulates on the decondensing chromosome mass close to the spindle ('core' region), together with EMD (emerin), TMPO (LAP2beta), LEMD3 (MAN1), LEMD2 (LEM2) and lamin A (Haraguchi et al. 2008, reviewed by Guttinger et al. 2009)
The nuclear envelope breakdown in mitotic prophase involves depolymerisation of lamin filaments, the main constituents of the nuclear lamina. The nuclear lamina is located at the nuclear face of the inner nuclear membrane and plays and important role in the structure and function of the nuclear envelope (reviewed by Burke and Stewart 2012). Depolymerisation of lamin filaments, which consist of lamin homodimers associated through electrostatic interactions in head-to-tail molecular strings, is triggered by phosphorylation of lamins. While CDK1 phosphorylates the N-termini of lamins (Heald and McKeon 1990, Peter et al. 1990, Ward and Kirschner 1990, Mall et al. 2012), PKCs (PRKCA and PRKCB) phosphorylate the C-termini of lamins (Hocevar et al. 1993, Goss et al. 1994, Mall et al. 2012). PKCs are activated by lipid-mediated signaling, where lipins, activated by CTDNEP1:CNEP1R1 serine/threonine protein phosphatase complex, catalyze the formation of DAG (Gorjanacz et al. 2009, Golden et al. 2009, Wu et al. 2011, Han et al. 2012, Mall et al. 2012)
Post-mitotic neurons do not have an active cell cycle. However, deregulation of Cyclin Dependent Kinase-5 (CDK5) activity in these neurons can aberrantly activate various components of cell cycle leading to neuronal death (Chang et al. 2012). Random activation of cell cycle proteins has been shown to play a key role in the pathogenesis of several neurodegenerative disorders (Yang et al. 2003, Lopes et al. 2009). CDK5 is not activated by the canonical cyclins, but binds to its own specific partners, CDK5R1 and CDK5R2 (aka p35 and p39, respectively) (Tsai et al. 1994, Tang et al. 1995). Expression of p35 is nearly ubiquitous, whereas p39 is largely expressed in the central nervous system. A variety of neurotoxic insults such as beta-amyloid (A-beta), ischemia, excitotoxicity and oxidative stress disrupt the intracellular calcium homeostasis in neurons, thereby leading to the activation of calpain, which cleaves p35 into p25 and p10 (Lee et al. 2000). p25 has a six-fold longer half-life compared to p35 and lacks the membrane anchoring signal, which results in its constitutive activation and mislocalization of the CDK5:p25 complex to the cytoplasm and the nucleus. There, CDK5:p25 is able to access and phosphorylate a variety of atypical targets, triggering a cascade of neurotoxic pathways that culminate in neuronal death. One such neurotoxic pathway involves CDK5-mediated random activation of cell cycle proteins which culminate in neuronal death. Exposure of primary cortical neurons to oligomeric beta-amyloid (1-42) hyper-activates CDK5 due to p25 formation, which in turn phosphorylates CDC25A, CDC25B and CDC25C. CDK5 phosphorylates CDC25A at S40, S116 and S261; CDC25B at S50, T69, S160, S321 and S470; and CDC25C at T48, T67, S122, T130, S168 and S214. CDK5-mediated phosphorylation of CDC25A, CDC25B and CDC25C not only increases their phosphatase activities but also facilitates their release from 14-3-3 inhibitory binding. CDC25A, CDC25B and CDC25C in turn activate CDK1, CDK2 and CDK4 kinases causing neuronal death. Consistent with this mechanism, higher CDC25A, CDC25B and CDC25C activities were observed in human Alzheimer's disease (AD) clinical samples, as compared to age-matched controls
Affinity Capture-MS, Affinity Capture-Western, Proximity Label-MS, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity-dependent biotin identification, pull down, two hybrid
Affinity Capture-Western, Co-localization, PCA, Reconstituted Complex, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, bimolecular fluorescence complementation, pull down
association, direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, Proximity Label-MS, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity-dependent biotin identification, pull down, two hybrid
Affinity Capture-Western, Co-localization, PCA, Reconstituted Complex, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, bimolecular fluorescence complementation, pull down
association, direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, Proximity Label-MS, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity-dependent biotin identification, pull down, two hybrid
Affinity Capture-Western, Co-localization, PCA, Reconstituted Complex, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, bimolecular fluorescence complementation, pull down
association, direct interaction, physical, physical association