Epistemic_Statements  

CORD-19:d8c4042441e88788e26135cb83f2510ac050aae7 JSONTXT 12 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T1 2162-2264 Epistemic_statement denotes However, pADPr accumulation is transient, as it is rapidly degraded by PARG (Davidovic et al., 2001) .
T2 2265-2415 Epistemic_statement denotes Notably, the polymerase activity has been demonstrated for only six of the PARP family members (PARP1, PARP2, PARP3, PARP4/vPARP, Tankyrases 1 and 2).
T3 2416-2768 Epistemic_statement denotes Based on experimental and structural examinations, it has been proposed that the other PARP family members are either inactive (PARP9/BAL and PARP13/ ZAP) or carry a mono-ADP-ribosyl transferase activity (PARP6, TiPARP, PARP8, PARP10, PARP11, PARP12, PARP14/BAL2, PARP15/BAL3, PARP16) (Goenka et al., 2007; Hottiger et al., 2010; Kleine et al., 2008) .
T4 2769-2878 Epistemic_statement denotes Their functions are only starting to emerge, but suggest an important role for these poorly studied proteins.
T5 3385-3458 Epistemic_statement denotes Poly(ADP-ribosyl)ation can be achieved covalently or non-covalently (Fig.
T6 4220-4531 Epistemic_statement denotes Accumulating evidence indicates that pADPr actually conveys a broad spectrum of cellular signals through direct binding of a variety of protein motifs to pADPr, such as the DNA damage response, replication, chromatin structure, transcription, telomere homeostasis and cell death (Krishnakumar and Kraus, 2010) .
T7 4748-4959 Epistemic_statement denotes Indeed, the average chain length of pADPr synthesized by the PARP family members can range from very short and linear oligomers to extended molecules of up to 200 units and branched at every 20-50 residues (Fig.
T8 5094-5360 Epistemic_statement denotes There are very limited investigations conducted on the physico-chemical properties of pADPr, such as flexibility and conformation, but the formation of helical pADPr structures was postulated upon protein binding (Minaga and Kun, 1983a,b; Schultheisz et al., 2009 ).
T9 5361-5625 Epistemic_statement denotes The first experimental lines of evidence for proteins that bind pADPr in a non-covalent, yet specific, manner were given in the late 1960s and early 1970s when it was shown that histones possess high affinity for pADPr Nakaz-awa et al., 1968; Otake et al., 1969) .
T10 5626-5756 Epistemic_statement denotes However, whether the chemical nature of the bond was covalent or non-covalent was a highly debated topic (Adamietz et al., 1975) .
T11 6587-6980 Epistemic_statement denotes This paper first provides an inventory of the predominant techniques currently used to detect and measure non-covalent protein-pADPr interactions, then turns to an in-depth description of the specialized pADPr-binding modules that recognize different structural features of the pADPr, and finally, presents the functional consequences of this association in pADPr-responsive cellular pathways.
T12 7510-7631 Epistemic_statement denotes Experimental evidence suggests that other protein modules and sequence motifs can read this modification (see Section 3).
T13 7966-8108 Epistemic_statement denotes The mechanism that determines selective modification of specific residues and the functional significance of this heterogeneity are not known.
T14 8109-8221 Epistemic_statement denotes Additional ADP-ribose units are subsequently attached by O-glycosidic linkages to form linear or branched pADPr.
T15 8546-8862 Epistemic_statement denotes Polymer-blot and electrophoretic mobility shift assays (EMSA) are currently used to determine whether there is binding or not, while isothermal titration calorimetry (ITC), surface plasmon resonance (SPR) and a variation of the EMSA method allow to measure the affinity for pADPr by determining an affinity constant.
T16 10196-10287 Epistemic_statement denotes A shift in the mobility of the protein indicates the formation of a protein-ligand complex.
T17 10288-10415 Epistemic_statement denotes Since all measurements are made at equilibrium, the binding affinities can be calculated using a sigmoidal dose-response curve.
T18 11505-11673 Epistemic_statement denotes Each of these methods may also be conducted using fractionated pADPr, allowing further characterization of the binding specificity of a protein for long or short pADPr.
T19 11944-12091 Epistemic_statement denotes Collectively, these methods have therefore been critical in characterizing the pADPr binding modules that are described in the following Section 3.
T20 12709-12943 Epistemic_statement denotes Notably, the Althaus group had a strong intuition when they raised the innovative hypothesis that ''PARP-associated polymers may recruit signal proteins to sites of DNA breakage and reprogram their functions'' (Althaus et al., 1999) .
T21 14402-14548 Epistemic_statement denotes Computational PBM prediction has proven to be a powerful tool for the identification of protein regions that could mediate interaction with pADPr.
T22 14549-14617 Epistemic_statement denotes They have been shown to convey important functions in animal models.
T23 14618-14720 Epistemic_statement denotes Notably, the PBM discovered in the apoptosis-inducing factor (AIF) is critical for Macro Egloff et al.
T24 14835-15092 Epistemic_statement denotes A detailed PBM-pADPr complex has yet to be modeled but a study of the structural features of AIF's PBM showed that it occupies an area on the surface of the protein which could provide stabilizing non-covalent contacts of amino acid side chains with pADPr .
T25 15093-15276 Epistemic_statement denotes We can only speculate as to whether all PBMs possess common structural features, but a highly exposed solvent-accessible surface must be present to make contacts with pADPr molecules.
T26 15412-15541 Epistemic_statement denotes Since PBMs are located in lysine-and arginine-rich regions, it would be likely to find several of them in a helical conformation.
T27 15542-15657 Epistemic_statement denotes A summary of pADPr-binding proteins for which binding affinity constants have been determined is given in Table 2 .
T28 15658-15829 Epistemic_statement denotes Of particular interest, several reports have shown that pADPr chain length is a crucial determinant for high affinity non-covalent interactions of PBM proteins with pADPr.
T29 16136-16158 Epistemic_statement denotes b n.d. not determined.
T30 16712-16815 Epistemic_statement denotes Furthermore, the PBM often overlaps with important regulatory protein domains (Pleschke et al., 2000) .
T31 16816-17009 Epistemic_statement denotes This has triggered the idea that upon binding to pADPr, the PBM could shield a regulatory surface by steric hindrance, thus destabilizing several protein-protein or protein-ligand interactions.
T32 17010-17158 Epistemic_statement denotes Alternatively, a highly extended and flexible polymer bound to a protein domain could distort it so that perturbations of the native fold may arise.
T33 17159-17322 Epistemic_statement denotes Globally, molecular crowding by the pADPr provides the basis for the concept of ''reprogrammation'' of protein functions as suggested (Malanga and Althaus, 2005) .
T34 17323-17550 Epistemic_statement denotes Actually, the affinity of several DNA damage response factors for pADPr can modulate (I) the sensing of DNA lesions; (II) the dynamic chromatin remodeling events and (III) the assembly and functionality of DNA repair complexes.
T35 17551-17761 Epistemic_statement denotes We believe that the transient accumulation of pADPr following DNA-dependent PARP activation can result in vast pleiotropic effects on a systems-wide scale that implicates numerous DNA damage response effectors.
T36 17901-18132 Epistemic_statement denotes Indeed, DNA-and RNA-binding modules are significantly over-represented as putative pADPr-binding modules and thus represent a general class of pADPr-targeted proteins with potential for broad implication in the DNA damage response.
T37 18133-18334 Epistemic_statement denotes However, in some proteins, the PBM is distinct from the nucleic acid binding domains, such as in AIF, providing the ability of pADPr to modulate protein function in the context of nucleic acid binding.
T38 18335-18479 Epistemic_statement denotes Generally, proteins associate in multi-protein complex machineries that execute biological processes that a single protein cannot execute alone.
T39 18983-19109 Epistemic_statement denotes Indeed, in addition to the classical PBM, recent studies suggest alternative PBMs located in nucleic acid-interaction domains.
T40 20858-21069 Epistemic_statement denotes The MRE11 exonuclease activity is inhibited by pADPr in vitro, suggesting that pADPr may regulate MRE11-dependent end-resection at DSBs or at stalled replication forks, as recently reported (Ying et al., 2012) .
T41 21070-21185 Epistemic_statement denotes Interestingly, several other GARcontaining proteins participate in the DNA damage response and genome surveillance.
T42 21186-21367 Epistemic_statement denotes In view of the high pADPr level that transiently accumulates at sites of damage, it is suspected that the function of some of these GAR-bearing proteins might be regulated by pADPr.
T43 21590-21713 Epistemic_statement denotes The nucleosome remodeling and histone deacetylase (NuRD) complex comprises several core components with affinity for pADPr.
T44 21979-22126 Epistemic_statement denotes The latter two proteins are involved in the recruitment of the NuRD complex to DNA strand breaks in a pADPr-dependent manner (Lai and Wade, 2011) .
T45 22127-22324 Epistemic_statement denotes Our current understanding suggests that the presence of pADPr acts as a recruitment module for the organization of the PARP1-associated DNA repair and chromatin remodeling machinery at DNA lesions.
T46 22325-22519 Epistemic_statement denotes On the other hand, pADPr binding to the GAR domain could be considered as a DNA displacement mechanism required to reconfigure the DNA repair protein complexes and provide access to damaged DNA.
T47 22520-22697 Epistemic_statement denotes It may also interfere with other DNA damage-induced posttranslational modifications, such as PRMT1-dependent arginine methylation in the GAR domain (Bedford and Richard, 2005) .
T48 22698-22788 Epistemic_statement denotes This view supports a concept where pADPr is a key orchestrator of the DNA damage response.
T49 22789-22979 Epistemic_statement denotes Recently, it has been suggested that pADPr regulates post-transcriptional gene regulation in the cytoplasm, notably through the assembly of cytoplasmic stress granules (Leung et al., 2012) .
T50 23081-23309 Epistemic_statement denotes Importantly, G3BP1-mediated stress granule assembly is impaired by PARP inhibition during genotoxic insult, suggesting that pADPr is critical for the reprogrammation of messenger ribonucleoparticles in cellular stress responses.
T51 23466-23697 Epistemic_statement denotes These results emphasize the fact that pADPr can perform various functions in several different DNA damage-processing pathways and can enable a crosstalk between the regulation of the early and late steps of the DNA damage response.
T52 23970-24032 Epistemic_statement denotes RRMs may be found in conjunction with GAR-containing proteins.
T53 24121-24368 Epistemic_statement denotes hnRNPs are highly versatile proteins that can participate in various aspects of nucleic acid metabolism: mRNA stability and splicing, DNA replication, chromatin remodeling, telomere maintenance, DNA repair and genome stability (Han et al., 2010) .
T54 25429-25579 Epistemic_statement denotes Notably, the binding of NONO to pADPr by RRM1 is crucial for the recruitment of NONO to DNA damage sites and influences the outcome of DNA DSB repair.
T55 25822-25932 Epistemic_statement denotes These observations therefore provide further support for RRMs as biologically relevant pADPr-binding modules .
T56 25933-26145 Epistemic_statement denotes Given the frequent occurrence of RRM-containing proteins in the human proteome, interactions with pADPr are likely to have a significant impact on cell signaling through a complex network of biochemical pathways.
T57 26386-26487 Epistemic_statement denotes It has been shown that the SR protein ASF/SF2 binds pADPr with high affinity (Malanga et al., 2008) .
T58 26488-26654 Epistemic_statement denotes Two domains in ASF/SF2 can mediate the interaction with pADPr: (I) a N-terminal fragment that contains a RRM1 and (II) a C-terminal SR domain (Malanga et al., 2008) .
T59 27078-27365 Epistemic_statement denotes It remains to be determined whether the presence of a basic electrostatic patch on a protein surface could be considered as a general pADPr-protein interface or if additional structural determinants are required (such as the helical conformation of the SR domain (Sellis et al., 2012) ).
T60 27553-27765 Epistemic_statement denotes This newly identified C2H2-type ''pADPr-binding zinc finger'' (PBZ) has a consensus sequence defined as [K/R]xxCx[F/Y]GxxCxbbxxxxHxxx[F/Y]xH where b denotes a basic residue and x any residue (Ahel et al., 2008) .
T61 27843-28023 Epistemic_statement denotes The absence of PBZ motifs in prokaryote and yeast proteins parallels the absence of pADPr metabolism in those, suggesting a coevolution of the PBZ motif with the presence of PARPs.
T62 28024-28264 Epistemic_statement denotes Only three human proteins appear to carry a PBZ motif: the aprataxin and PNK-like factor (APLF, also called XIP1, PALF), the checkpoint protein with FHA and RING domains (CHFR), and the DNA cross-link repair 1A protein (DCLRE1A/SNM1A) (Fig.
T63 28290-28554 Epistemic_statement denotes Interestingly, the PBZ module was found in some non-human proteins involved in the maintenance of genome integrity or DNA repair: Ku70, Rad17, Parp and Chk2 in Dictyostelium discoideum and DNA Ligase in Caenorhabditis elegans corresponding to human DNA Ligase III.
T64 28555-28658 Epistemic_statement denotes However, the human orthologues do not contain any PBZ domain (Ahel et al., 2008; Isogai et al., 2010) .
T65 29127-29332 Epistemic_statement denotes The lack of conservation of most of these critical binding residues in the PBZ sequence of DCLRE1A suggests that it may not bind pADPr, but this has not been experimentally assessed (Oberoi et al., 2010) .
T66 29524-29647 Epistemic_statement denotes Interestingly, the affinity of APLF for pADPr is in the same range than that of CHFR, despite the fact that it has two PBZ.
T67 30000-30289 Epistemic_statement denotes These observations are in line with the structural details of CHFR and APLF, which strongly suggested that the CHFR PBZ and the PBZ1 domain of APLF are able to interact with two consecutive ADPr moieties in pADPr while the second PBZ of APLF probably binds only one (Oberoi et al., 2010) .
T68 30290-30479 Epistemic_statement denotes These observations are also consistent with the more deleterious effects of mutations in PBZ1 than in PBZ2 for the recruitment of APLF to UV-induced DNA strand breaks Rulten et al., 2008) .
T69 30480-30629 Epistemic_statement denotes PBZ1 may also interact with PARP1 as well, providing further affinity of PBZ1 for automodified PARP1 (Eustermann et al., 2010; Macrae et al., 2008) .
T70 31361-31523 Epistemic_statement denotes Both PARP1 and PARP3-dependent poly(ADP-ribosyl)ation have been shown to promote APLF responses to DNA strand breaks (Rulten et al., 2008 (Rulten et al., , 2011 .
T71 31524-31821 Epistemic_statement denotes Similar to APLF, CHFR comprises a phospho-binding FHA module but also a RING finger domain with E3 ubiquitin ligase activity that plays an essential role in the antephase checkpoint, delaying mitotic entry under certain stress conditions (Chaturvedi et al., 2002; Scolnick and Halazonetis, 2000) .
T72 32396-32500 Epistemic_statement denotes This finding further revealed that PARP1 levels must be critically controlled during cell proliferation.
T73 32501-32554 Epistemic_statement denotes The binding of DCLRE1A to pADPr has not been studied.
T74 32705-32868 Epistemic_statement denotes However, the putative PBZ does not comprise the aromatic residues needed to contact pADPr, suggesting that its functions are independent of poly(ADP-ribosyl)ation.
T75 33297-33460 Epistemic_statement denotes Determination of the 3D structure of the thermophile Archaeoglobus fulgidus macro protein Af1521 provided the first clues to the potential function of this domain.
T76 33461-33650 Epistemic_statement denotes It revealed an organization of helices and sheets reminiscent of the P-loop found in nucleotide hydrolases, suggesting a related enzymatic function for the macro fold (Allen et al., 2003) .
T77 33651-33932 Epistemic_statement denotes Additional studies with Af1521 and with the yeast macro domain protein YBR022 W supported this observation as they revealed the ability of these macro domains to hydrolyze ADP-ribose-1''-phosphate into ADPr and inorganic phosphate (Pi) (Karras et al., 2005; Martzen et al., 1999) .
T78 33933-34201 Epistemic_statement denotes Subsequent studies indicated that some macro domains could not only interact with ADPr but also with pADPr, making it a novel pADPr-interaction module (Ahel et al., 2009; Gottschalk et al., 2009; Karras et al., 2005; Neuvonen and Ahola, 2009; Timinszky et al., 2009) .
T79 34305-34639 Epistemic_statement denotes This macro domain may exist on its own (macroD1, also called MDO1 and LRP16, macroD2 also called MDO2 and C6orf130) or in association with the histone fold (macrohistones H2A), the PARP catalytic domain (PARP9, 14 and 15), the SNF2/helicase ATPase domain (ALC1/CHD1L), or the Sec14p/CRAL-TRIO protein-lipid interaction module (GDAP2).
T80 34640-34903 Epistemic_statement denotes Intriguingly, macroPARPs (also called BAL PARPs) have the unique feature of bearing two (PARP9 and PARP15) or even three (PARP14) macro domains in tandem, which, in PARP14, are further associated with two more putative pADPr binding modules, a RRM and a WWE (Fig.
T81 35079-35302 Epistemic_statement denotes It should be stressed that, out of nine macro domain-containing human proteins so far tested for pADPr binding (PARP14 and PARP15 have not been examined), only four bind pADPr (namely macroH2A1.1, CHD1L, macroD1 and PARP9).
T82 35386-35593 Epistemic_statement denotes Furthermore, the detailed structural analysis of macroH2A1.1 revealed that it is able to bind solely the terminal ADPr of the polymer, indicating that its macro domain is in practice an ADPr binding module .
T83 36433-36732 Epistemic_statement denotes The binding of viral macro domains to ADPr is at least 10-fold lower (K D of the severe acute respiratory syndrome (SARS) coronavirus is 24 lM, that of hepatitis E virus above 50 lM) but interactions with pADPr have been shown by polymer blot assays (Egloff et al., 2006; Neuvonen and Ahola, 2009) .
T84 36733-36824 Epistemic_statement denotes It remains to be determined whether this interaction is critical for viral host infections.
T85 36825-37015 Epistemic_statement denotes Collectively, these observations indicate that the presence of a macro fold hints to a possible interaction with ADPr-related metabolites, which however needs to be experimentally addressed.
T86 37421-37684 Epistemic_statement denotes Therefore, despite minimal sequence similarity between the typical macro domain and PARG, part of the PARG catalytic domain adopts this characteristic macro fold organization in which the PARG sequence signature GGG-X 6-8 -QEE lines the ADP-ribose binding pocket.
T87 37685-37901 Epistemic_statement denotes However, in the mammalian PARG, additional essential sequences extending beyond the macro domain adopt structural conformations around the macro fold that specify the catalytic pocket and the glycohydrolase activity.
T88 38186-38419 Epistemic_statement denotes These recent findings have thus highlighted that some macro domains may only be revealed once the 3D structure is determined, indicating that there may be other pADPr-binding macro proteins in mammalian cells awaiting identification.
T89 38420-38563 Epistemic_statement denotes Many of the macro domain-ADPr/pADPr interactions have been examined in vitro, using purified macro domains or proteins and purified ADPr/pADPr.
T90 38564-38768 Epistemic_statement denotes Because PARPs catalyze the addition of ADPr onto protein substrates, it will be critical to investigate whether the macro-ADPr interaction can be extended to ADPr covalently attached to acceptor proteins.
T91 38769-38960 Epistemic_statement denotes A recent study using synthetic peptides corresponding to mono-ADP-ribosylated histone H2B tail showed that it could be the case, as macroH2A1.1 did bind such peptides (Moyle and Muir, 2010) .
T92 38961-39084 Epistemic_statement denotes Recent detailed analysis of the enzymatic activity of the macro domain indicates that some deacetylate O-acetyl-ADP-ribose.
T93 39197-39427 Epistemic_statement denotes The three stand-alone macro domain proteins, namely macroD1, macroD2, and C6orf130, appear to form a subgroup of macro domain proteins showing this deacetylase activity by cleaving the ester bond between the acetyl group and ADPr.
T94 39428-39583 Epistemic_statement denotes One could envision that some macro domain proteins possessing O-acetyl-ADPr deacetylase activity may be able to hydrolyze the protein-ADPr ester bond (Fig.
T95 39590-39675 Epistemic_statement denotes Until now, the ability of PARG and ARH3 to fulfill this function has been questioned.
T96 39676-39936 Epistemic_statement denotes The existence of a distinct enzyme (an ADP-ribose lyase) able to hydrolyze the ester bond between the glutamic or aspartic acid residue of the acceptor protein and ADPr has been proposed nearly 30 years ago (Oka et al., 1984) , but remains to be characterized.
T97 39937-40084 Epistemic_statement denotes However, the recent indications that lysines could also constitute ADPr acceptor sites on PARP1 and histones, forming a ketamine in this case (Fig.
T98 40085-40163 Epistemic_statement denotes 1B) Messner et al., 2010) , suggest that there may be more than one ''lyase''.
T99 40164-40243 Epistemic_statement denotes Biological functions of macro domain proteins remain to be examined in details.
T100 40445-40754 Epistemic_statement denotes The latter macrohistones have been generally linked to transcriptional repression as they induce a more condensed chromatin state and impede access to transcription factors, although in some specific cases they can also promote transcription (reviewed by (Gamble and Kraus, 2010) ) (Muthurajan et al., 2011) .
T101 41465-41580 Epistemic_statement denotes Collectively, these examples suggest that pADPr-macro domain interactions contribute to transcriptional regulation.
T102 41872-42023 Epistemic_statement denotes 3 ) belong mostly to two functional classes of proteins, namely those associated with ubiquitylation and those associated with poly(ADP-ribosyl)ation .
T103 42108-42260 Epistemic_statement denotes pADPr binding of Iduna/RNF146 was first ascribed to a PBM which was further defined as part of the WWE domain that mediates the interaction with pADPr .
T104 42452-42549 Epistemic_statement denotes Iso-ADPr rather than ADPr is the smallest unit that can be bound by the Iduna/RNF146 domain (Fig.
T105 42747-42892 Epistemic_statement denotes This supported the idea that the WWE domain is a pADPr-binding module because at least two ADPr units are needed to generate the iso-ADPr ligand.
T106 43155-43374 Epistemic_statement denotes These residues are well conserved throughout most human WWE domains , including the putative or demonstrated ubiquitin ligases Deltex 1,2,4, HUWE1 and TRIP12, which have been shown by SPR to also bind pADPr ( Table 2 ).
T107 43375-43537 Epistemic_statement denotes The WWE domains of several PARP family members (PARP11, PARP13 and the first WWE of PARP12) also comprise the conserved residues, suggesting that they bind pADPr.
T108 43538-43683 Epistemic_statement denotes Only the binding of PARP11 has been examined, and showed interactions with ADPr and pADPr with rather low affinity (Table 2) Wang et al., 2012) .
T109 43684-43941 Epistemic_statement denotes In contrast, two of the residues are not conserved in the second WWE of PARP12, in TiPARP, PARP14 and the putative phospholipase DDHD2, suggesting that these may not bind pADPr, as shown for DDHD2 (DDHD domain containing 2) in in vitro binding experiments .
T110 43942-44130 Epistemic_statement denotes A common theme among WWE containing proteins is the association with domains of the E3 ligase type, strongly suggesting a functional link between ubiquitylation and poly(ADP-ribosyl)ation.
T111 44665-44903 Epistemic_statement denotes Interestingly, we concurrently showed that Iduna/RNF146 plays a prominent role in the context of DNA damage through its pADPr-dependent E3 ligase activity as it also ubiquitylates several DNA repair factors in a way that depends on pADPr.
T112 45061-45208 Epistemic_statement denotes The cross-talk between ubiquitylation and poly(ADP-ribosyl)ation may not be restricted to Iduna/RNF146 but awaits further experimental examination.
T113 46618-46754 Epistemic_statement denotes The importance of pADPr-binding by the WWE motif of HUWE1 and TRIP12 for their recruitment to DNA strand breaks remains to be addressed.
T114 46755-46940 Epistemic_statement denotes It is interesting to note that the members of the PARP family that carry WWE domains are most likely mono(ADPribosyl)transferases and unable to produce the iso-ADPr moiety bound by WWE.
T115 46941-46998 Epistemic_statement denotes Little is known about these proteins and their functions.
T116 46999-47140 Epistemic_statement denotes One aspect that may be of further functional relevance is the presence of classical zinc fingers associated with TiPARP, PARP12, PARP13 (Fig.
T117 47146-47245 Epistemic_statement denotes Of these, PARP13 has been examined as an antiviral protein (also named zinc antiviral protein ZAP).
T118 47484-47665 Epistemic_statement denotes The mechanistic link between poly(ADP-ribosyl)ation and the regulation of protein degradation is one of the most surprising aspects of the recent advances on poly(ADP-ribosyl)ation.
T119 47875-48020 Epistemic_statement denotes Remarkably, this pathway appears to function in several biological contexts, regulated not only by PARP1 but also by the tankyrases 1 and 2 (Fig.
T120 48639-48758 Epistemic_statement denotes Thus Iduna/RNF146's dynamic range of protein quality control in the setting of poly(ADP-ribosyl)ation may be extensive.
T121 48759-48915 Epistemic_statement denotes Because of this, there are likely to be multiple checkpoints that control Iduna/RNF146's activity and biological actions that require further investigation.
T122 48916-49219 Epistemic_statement denotes Interestingly, regulation of protein stability in a pADPr-dependent manner is not restricted to WWE-containing E3-ligases because the PBZ-bearing CHFR E3-ligase has been shown recently to ubiquitylate PARP1 to target it for proteasomal degradation in the context of mitotic stress (see Section 3.3; Fig.
T123 49473-49656 Epistemic_statement denotes Cherubism is a rare autosomal dominant human disorder characterized by inflammatory destructive bone lesions resulting in abnormal fibrous tissue growth in the lower part of the face.
T124 49804-49974 Epistemic_statement denotes Interestingly, most of these mutations lie within a six amino acid sequence (RSPPDG) that corresponds to the tankyrase substrate-recognition motif (Levaot et al., 2011) .
T125 50484-50750 Epistemic_statement denotes The abnormal accumulation of 3BP2 within cells appears to alter the signaling balance of SRC kinase multiprotein complex to which it is associated, causing systematic inflammation, and leading to the cherubism phenotype (Guettler et al., 2011; Levaot et al., 2011) .
T126 50751-50895 Epistemic_statement denotes Hence, understanding the concerted action of poly(ADP-ribosyl)ation and ubiquitylation might improve therapeutic approaches targeting cherubism.
T127 50896-51094 Epistemic_statement denotes It is tempting to speculate that the tankyrase-dependent poly(ADP-ribosyl)ation coupled to Iduna/RNF146 ubiquitylation/ degradation pathway is a widespread process to regulate protein steady states.
T128 51178-51326 Epistemic_statement denotes (2011) have identified a very large list of proteins carrying the tankyrase interaction sequence RXX(G/P)DG that could constitute potential targets.
T129 51562-51695 Epistemic_statement denotes Massive activation of PARP1 following a genotoxic stress has been long recognized as a critical event in the induction of cell death.
T130 51696-51932 Epistemic_statement denotes However, it is only in recent years that pADPr has been recognized as a death signaling molecule after the identification of In the first view, cytoplasmic ADPr and pADPr are synthesized by tankyrases and PARP12-15 upon stress exposure.
T131 52886-52949 Epistemic_statement denotes This possibly facilitates access of the DNA repair machineries.
T132 53625-53935 Epistemic_statement denotes Experiments to determine the mechanism of how PARP1 activation was intimately coupled to AIF translocation led to the discovery that pADPr translocates from the nucleus to mitochondria where it acts as an AIF releasing factor to cause the mitochondrial-nuclear translocation of AIF, initiating cell death (Fig.
T133 54367-54523 Epistemic_statement denotes Thus, agents could be designed to block this interaction serving as inhibitors of parthanatos or to enhance the release of AIF for cancer chemotherapeutics.
T134 54935-55094 Epistemic_statement denotes Iduna/ RNF146's protective properties are due to its ability to bind pADPr, consistent with the notion that pADPr can act as a death signal during parthanatos.
T135 56948-57206 Epistemic_statement denotes It has been shown that the overexpression of the SG-PARPs promotes the poly(ADP-ribosyl)ation of mRNA-associated proteins and the assembly of SGs, while PARG overexpression inhibits their appearance supporting a key role for pADPr in the assembly of SG (Fig.
T136 57753-57821 Epistemic_statement denotes The mechanism through which this occurs remains to be characterized.
T137 58342-58541 Epistemic_statement denotes This PARP-dependent function of CHD1L may be of importance during DNA damage signaling and repair of DNA strand breaks, as well as of cyclobutane pyrimidine dimers by nucleotide excision repair (Fig.
T138 58744-58968 Epistemic_statement denotes pADPr synthesis at sites of DNA lesions triggers the recruitment of many DNA damage mediators and repair factors as well as chromatin remodeling and may serve as a scaffold for the assembly of repair complexes (Table 1; Fig.
T139 59882-60020 Epistemic_statement denotes Interestingly, the exact mechanism of action of PARP inhibitors is still a matter of ongoing debate (Helleday, 2011; Patel et al., 2011) .
T140 60021-60313 Epistemic_statement denotes Large-scale sequencing projects of human genomes, such as the ENCODE project consortium, may help to reveal novel sequence variants or mutations in proteins involved in the maintenance of genomic stability with critical implications in the development of human cancers (Dunham et al., 2012) .
T141 60314-60491 Epistemic_statement denotes It is also reasonable to think that a critical mutation in a pADPr-binding motif might have deleterious consequences in signaling pathways that comprise the DNA damage response.
T142 60492-60550 Epistemic_statement denotes Such information might be positively exploited clinically.
T143 60551-60741 Epistemic_statement denotes While defective DNA damage repair pathways are one type of susceptibility to PARP inhibitors, there appear to be others for which mechanistic basis are failing to be explained at the moment.
T144 61186-61381 Epistemic_statement denotes In this case, both the transcriptional and DNA damage signaling functions of PARP1 may be involved to explain the sensitivity (Brenner et al., 2011; Garnett et al., 2012; Schiewer et al., 2012) .
T145 61813-62080 Epistemic_statement denotes With these examples in mind, and as the list of pADPr-binding proteins and pathways using poly(ADP-ribosyl)ation as signaling mechanisms is still expanding, it becomes crucial to investigate the broad spectrum of biological implications of pADPr-protein interactions.
T146 62081-62214 Epistemic_statement denotes It will undoubtedly lead to a better understanding of more applications of PARP inhibitors as single-agent and combination therapies.
T147 62215-62317 Epistemic_statement denotes For instance, several pADPr-binding proteins have been linked to cancer progression or aggressiveness.
T148 62761-63018 Epistemic_statement denotes Further investigation of the mechanistic roles of pADPr in the regulation of cancer-associated protein networks and signaling pathways will be fundamental for the development of innovative treatment strategies, and to overcome resistance to such treatments.
T149 63152-63494 Epistemic_statement denotes As described above, in humans, there are at least four pADPr-binding modules (and others perhaps waiting to be discovered), coupled to a discrete number of additional domains linking poly(ADP-ribosyl)ation to ubiquitylation and chromatin structure in several cellular contexts such as protein degradation, DNA damage responses and cell death.
T150 63622-63716 Epistemic_statement denotes While some seems to have a general affinity for the polyanionic backbone of biomolecules (i.e.
T151 64218-64394 Epistemic_statement denotes With this knowledge, we can speculate that uncharacterized variations in finger-like protrusions might provide the specificity required to recognize different pADPr structures.
T152 64395-64693 Epistemic_statement denotes Over 60 human proteins have been shown to interact with pADPr (Table 1) , but based on in silico predictions of the occurrence of the PBM sequence, there may be over 500 of them, and many more if we consider that proteins in complexes with pADPr-binding proteins are (indirectly) affected by pADPr.
T153 64694-65020 Epistemic_statement denotes Because the PBM represents a short contiguous protein segment, examination of other context criteria, such as protein surface accessibility, evolutionary conservation as well as the determination of three-dimensional PBM-bound pADPr complexes will help to establish the local structural environment required for pADPr-binding.
T154 65021-65206 Epistemic_statement denotes Because of this potential that poly(ADP-ribosyl)ation affects a significant portion of the proteome, it is crucial to pursue the extensive examination of the pADPr-protein interactions.
T155 65328-65564 Epistemic_statement denotes One may envision that there is a ''pADPr code'' where the length, complexity, and conformation adopted by pADPr covalently linked to a particular protein target, all contribute to favor some non-covalent interactions relative to others.
T156 65565-65720 Epistemic_statement denotes The remarkably high affinity and processivity of PARG for long pADPr will certainly have a role to play in the regulation of the non-covalent interactions.
T157 65852-65963 Epistemic_statement denotes Does it confer higher specificity, stronger interactions, or preference for pADPr in a particular conformation?
T158 66144-66170 Epistemic_statement denotes are now better understood.
T159 66171-66293 Epistemic_statement denotes Still, the mechanisms underlying the relocalization of pADPr to the cytoplasm after specific stresses are largely unknown.
T160 66294-66410 Epistemic_statement denotes The physiological aspects of poly(ADP-ribosyl)ation are only starting to emerge as they are more difficult to grasp.
T161 66637-66827 Epistemic_statement denotes Nonetheless, in view of their important functional outcomes in regulating protein stability and posttranslational gene expression in the cytoplasm, no doubt that it must be finely regulated.
T162 66828-67213 Epistemic_statement denotes Considering the critical functions of Iduna/RNF146 in directing poly(ADP-ribosyl)ated proteins towards proteasomal degradation, and the high catabolic activity of PARG, it is conceivable that some functional aspects of pADPr-binding proteins may consist in protecting pADPr from degradation, or in shielding the pADPr from Iduna/RNF146/CHFR to protect target proteins from degradation.
T163 67214-67321 Epistemic_statement denotes We can also wonder whether there may be pADPr-dependent deubiquitylases that further regulate this process.
T164 67322-67581 Epistemic_statement denotes It is now important to critically examine the regulation of pADPr degradation by PARG, ARH3 and possibly some macro domain proteins, in cellular contexts where pADPr-binding proteins also operate, to truly understand the extent of signaling afforded by pADPr.
T165 67582-67734 Epistemic_statement denotes Some pathways appear to rely on the generation of free pADPr molecules, requiring an endoglycosidic activity that so far, only PARG is known to display.