RING Finger Ubiquitin-Protein Isopeptide Ligase Nrdp1/FLRF Regulates Parkin Stability and Activity
Bibliographic record
Abstract
Parkin is a ubiquitin-protein isopeptide ligase. It has been suggested that loss of function in parkin causes accumulation and aggregation of its substrates, leading to death of dopaminergic neurons in Parkinson disease. Using the yeast two-hybrid screen, we isolated a RING finger protein that interacted with the N terminus of parkin in a Drosophila cDNA library. Interaction between human parkin and the mammalian RING finger protein homologue Nrdp1/FLRF, a ubiquitin-protein isopeptide ligase that ubiquitinates ErbB3 and ErbB4, was validated by in vitro binding assay, co-immunoprecipitation, and immunofluorescence co-localization. Significantly, pulse-chase experiments showed that cotransfection of Nrdp1 and parkin reduced the half-life of parkin from 5 to 2.5 h. Consistent with these findings, we further observed that degradation of CDCrel-1, a parkin substrate, was facilitated by overexpression of parkin protein. However, co-transfection of Nrdp1 with parkin reversed the effects of parkin on CDCrel-1 degradation. We conclude that Nrdp1 is a parkin modifier that accelerates degradation of parkin, resulting in a reduction of parkin activity. Parkin is a ubiquitin-protein isopeptide ligase. It has been suggested that loss of function in parkin causes accumulation and aggregation of its substrates, leading to death of dopaminergic neurons in Parkinson disease. Using the yeast two-hybrid screen, we isolated a RING finger protein that interacted with the N terminus of parkin in a Drosophila cDNA library. Interaction between human parkin and the mammalian RING finger protein homologue Nrdp1/FLRF, a ubiquitin-protein isopeptide ligase that ubiquitinates ErbB3 and ErbB4, was validated by in vitro binding assay, co-immunoprecipitation, and immunofluorescence co-localization. Significantly, pulse-chase experiments showed that cotransfection of Nrdp1 and parkin reduced the half-life of parkin from 5 to 2.5 h. Consistent with these findings, we further observed that degradation of CDCrel-1, a parkin substrate, was facilitated by overexpression of parkin protein. However, co-transfection of Nrdp1 with parkin reversed the effects of parkin on CDCrel-1 degradation. We conclude that Nrdp1 is a parkin modifier that accelerates degradation of parkin, resulting in a reduction of parkin activity. Parkinson disease (PD) 1The abbreviations used are: PD, Parksinson disease; AR-JP, autosomal recessive juvenile Parkinsonism; E3, ubiquitin-protein isopeptide ligase; HA, hemagglutinin; GST, glutathione S-transferase. is the second most common neurodegenerative disorder after Alzheimer disease with ∼500,000 patients in the United States alone. PD patients experience slowness of movement, rigidity, tremor, difficulty with balance, and variable manifestation of dementia. The main pathological features of PD are the loss of the dopaminergic neurons in the substantia nigra and the presence of abnormal protein aggregates that form filamentous inclusions in neuronal cytoplasm, termed Lewy bodies or Lewy neurites (nerve fibers) in PD brains (1McKeith I.G. Galasko D. Kosaka K. Perry E.K. Dickson D.W. Hansen L.A. Salmon D.P. Lowe J. Mirra S.S. Byrne E.J. Lennox G. Quinn N.P. Edwardson J.A. Ince P.G. Bergeron C. Burns A. Miller B.L. Lovestone S. Collerton D. Jansen E.N. Ballard C. de Vos R.A. Wilcock G.K. Jellinger K.A. Perry R.H. Neurology. 1996; 47: 1113-1124Crossref PubMed Scopus (3645) Google Scholar, 2Galvin J.E. Lee V.M. Trojanowski J.Q. Arch. Neurol. 2001; 58: 186-190Crossref PubMed Scopus (395) Google Scholar, 3Lang A.E. Lozano A.M. N. Engl. J. Med. 1998; 339: 1130-1143Crossref PubMed Scopus (1009) Google Scholar, 4Lang A.E. Lozano A.M. N. Engl. J. Med. 1998; 339: 1044-1053Crossref PubMed Scopus (1787) Google Scholar). 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The discoveries of genetic linkages for PD to several loci provide promises to identify mutations in ubiquitin C-terminal hydrolase (UCH)-L1, α-synuclein, DJ-1, and Pink1 (12Valente E.M. Abou-Sleiman P.M. Caputo V. Muqit M.M. Harvey K. Gispert S. Ali Z. Del Turco D. Bentivoglio A.R. Healy D.G. Albanese A. Nussbaum R. Gonzalez-Maldonado R. Deller T. Salvi S. Cortelli P. Gilks W.P. Latchman D.S. Harvey R.J. Dallapiccola B. Auburger G. Wood N.W. Science. 2004; 304: 1158-1160Crossref PubMed Scopus (2725) Google Scholar, 13Kruger R. Kuhn W. Muller T. Woitalla D. Graeber M. Kosel S. Przuntek H. Epplen J.T. Schols L. Riess O. Nat. Genet. 1998; 18: 106-108Crossref PubMed Scopus (3344) Google Scholar, 14Athanassiadou A. Voutsinas G. Psiouri L. Leroy E. Polymeropoulos M.H. Ilias A. Maniatis G.M. Papapetropoulos T. Am. J. Hum. Genet. 1999; 65: 555-558Abstract Full Text Full Text PDF PubMed Scopus (109) Google Scholar, 15Leroy E. Boyer R. Auburger G. Leube B. Ulm G. Mezey E. Harta G. 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Autosomal recessive juvenile Parkinsonism (AR-JP) was mapped to the long arm of chromosome 6 (6q25.2-q27) and is linked strongly to the markers D6S305 and D6S253 (18Matsumine H. Saito M. Shimoda-Matsubayashi S. Tanaka H. Ishikawa A. Nakagawa-Hattori Y. Yokochi M. Kobayashi T. Igarashi S. Takano H. Sanpei K. Koike R. Mori H. Kondo T. Mizutani Y. Schaffer A.A. Yamamura Y. Nakamura S. Kuzuhara S. Tsuji S. Mizuno Y. Am. J. Hum. Genet. 1997; 60: 588-596PubMed Google Scholar). D6S305 is deleted in one Japanese AR-JP patient (19Matsumine H. Yamamura Y. Hattori N. Kobayashi T. Kitada T. Yoritaka A. Mizuno Y. Genomics. 1998; 49: 143-146Crossref PubMed Scopus (49) Google Scholar). Using the positional cloning strategy combined with the exon-trapping technology and cDNA library screening, Kitada et al. (20Kitada T. Asakawa S. Hattori N. Matsumine H. Yamamura Y. Minoshima S. Yokochi M. Mizuno Y. Shimizu N. Nature. 1998; 392: 605-608Crossref PubMed Scopus (4231) Google Scholar) identified a gene named parkin in which exons 3–7 were deleted from this Japanese patient. They also described four other AR-JP patients from three unrelated families with a deletion of exon 4 in the parkin gene, confirming that mutations in the parkin gene appear to be responsible for the pathogenesis of AR-JP. Although most mutations in the parkin gene are thought to inactivate the gene with exon deletions (20Kitada T. Asakawa S. Hattori N. Matsumine H. Yamamura Y. Minoshima S. Yokochi M. Mizuno Y. Shimizu N. Nature. 1998; 392: 605-608Crossref PubMed Scopus (4231) Google Scholar, 21Bonifati V. Lucking C.B. Fabrizio E. Periquet M. Meco G. Brice A. J. Neurol. Neurosurg. Psychiatry. 2001; 71: 531-534Crossref PubMed Scopus (20) Google Scholar, 22van de Warrenburg B.P. Lammens M. Lucking C.B. Denefle P. Wesseling P. Booij J. Praamstra P. Quinn N. Brice A. Horstink M.W. 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Minoshima S. Yokochi M. Mizuno Y. Shimizu N. Nature. 1998; 392: 605-608Crossref PubMed Scopus (4231) Google Scholar). The deduced amino acid sequence of parkin showed similarity to ubiquitin at the N terminus. The C terminus of parkin contains two RING finger motifs and in between RING finger domain. Further studies demonstrate that parkin possesses E3 ligase activity (28Shimura H. Hattori N. Kubo S. Mizuno Y. Asakawa S. Minoshima S. Shimizu N. Iwai K. Chiba T. Tanaka K. Suzuki T. Nat. Genet. 2000; 25: 302-305Crossref PubMed Scopus (1713) Google Scholar) and ubiquitinates at least eight substrates including α-synuclein, Pael receptor, CDCrel-1, tubulin, synphilin-1, synaptotagmin, cyclin E, and P38 (29Chung K.K. Zhang Y. Lim K.L. Tanaka Y. Huang H. Gao J. Ross C.A. Dawson V.L. Dawson T.M. Nat. Med. 2001; 7: 1144-1150Crossref PubMed Scopus (666) Google Scholar, 30Huynh D.P. Scoles D.R. Nguyen D. Pulst S.M. Hum. Mol. 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Mol. Genet. 2003; 12: 1427-1437Crossref PubMed Google Scholar). In PD patients, it is presumed that the ability of parkin to ubiquitinate these substrates is of mutations or deletions in the gene, leading to accumulation and aggregation that in the death of nigral identify that are in PD, we used the yeast two-hybrid We that parkin with a RING finger protein R. Mol. 2001; PubMed Scopus Google Scholar). is also ubiquitin E3 ligase that ubiquitinates ErbB3 and Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar, A.J. P.M. C. K. C. K.L. Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar). demonstrate that degradation of parkin protein and a parkin that parkin and form a that of E3 and the of The N terminus of the Drosophila parkin cDNA was by and to a protein the of of the in yeast was by of the were with the and with a Drosophila library to sequence of the in were on were for and and mammalian is with a at its N Nrdp1 was in and were from CDCrel-1 was from W. S. for or was from in is from Science. is from and and are from is from was from In in vitro binding assay, and with were the and and in binding 5 and the or was to either or and the Nrdp1 or was by and by a In a expressed was and to were with binding and with of in vitro for at 4 in binding The were with binding and in The binding to were on and by a of that to Nrdp1 were mapped with C-terminal or and or Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar) and or were was by or co-immunoprecipitation, were with to the of or of Nrdp1 and after the were or protein was in by with or two were were with 12 of CDCrel-1 was by were with and to h. or was by or were on and by a three experiments were were on and with and were in of for three with in of in for and with and in for h. The were with primary either or that been In a were with of for and with and or The of was by a identify parkin substrates or we the yeast two-hybrid The N terminus of Drosophila parkin cDNA was from and by and of the and the Drosophila cDNA three that three markers and genes in were that one of these is the homologue of mammalian Nrdp1/FLRF, a RING finger E3 ligase R. Mol. 2001; PubMed Scopus Google Scholar) that ubiquitinates ErbB3 and Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar, A.J. P.M. C. K. C. K.L. Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar). The Drosophila to interacted with in a yeast two-hybrid has of a amino acid protein. between human and Drosophila a and a and R. Mol. 2001; PubMed Scopus Google Scholar). the also with the human proteins, in vitro binding were and the were in vitro In vitro was from binding of and Nrdp1 or were by and a The Nrdp1 was observed from was by were was to the Nrdp1 C terminus in vitro between and Nrdp1 was also by of the with or protein or were to In vitro was on the by the protein binding between and Nrdp1 Further by in vitro binding mapped the binding between and Nrdp1 to the N terminus with the from the yeast two-hybrid between parkin and Nrdp1 in and were for degradation of parkin by we used Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar). was used to Nrdp1 protein from was from with and from that were with and a In a we to and The with and showed protein a of was from the in with and between these two further between parkin and and were on and with and was with and or and a in or with The of and Nrdp1 was in bodies neuronal and Nrdp1 are were on and with and was by and primary and and or a and a of Nrdp1 and parkin was by a were by for parkin and Nrdp1 are E3 (28Shimura H. Hattori N. Kubo S. Mizuno Y. Asakawa S. Minoshima S. Shimizu N. Iwai K. Chiba T. Tanaka K. Suzuki T. Nat. Genet. 2000; 25: 302-305Crossref PubMed Scopus (1713) Google Scholar, 31Zhang Y. Gao J. Chung K.K. Huang H. Dawson V.L. Dawson T.M. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 13354-13359Crossref PubMed Scopus (842) Google Scholar, 32Shimura H. Schlossmacher M.G. Hattori N. Frosch M.P. Trockenbacher A. Schneider R. Mizuno Y. Kosik K.S. Selkoe D.J. Science. 2001; 293: 263-269Crossref PubMed Scopus (955) Google Scholar, 34Imai Y. Soda M. Inoue H. Hattori N. Mizuno Y. Takahashi R. Cell. 2001; 105: 891-902Abstract Full Text Full Text PDF PubMed Scopus (933) Google Scholar, Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar, A.J. P.M. C. K. C. K.L. Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar), we Nrdp1 or parkin or activity. We a pulse-chase that were with were with for h. were for or to in with and or a was and on and a of was that the half-life of is about 5 in the of Nrdp1 in with the Y. Gao J. Chung K.K. Huang H. Dawson V.L. Dawson T.M. Proc. Natl. Acad. Sci. U. S. A. 2000; 97: 13354-13359Crossref PubMed Scopus (842) Google Scholar), overexpression of Nrdp1 parkin half-life to 2.5 that Nrdp1 accelerates parkin degradation. However, in to the Proc. Natl. Acad. Sci. U. S. A. 2002; PubMed Scopus Google Scholar), the C terminus of Nrdp1 effects on degradation of Significantly, we also by pulse-chase that degradation of CDCrel-1 was with Nrdp1 overexpression In this of and were in or in were with and to h. was on and in a A and In the of parkin the half-life of CDCrel-1 is overexpression of parkin CDCrel-1 with a half-life of 5 h. However, CDCrel-1 was and Nrdp1 were A and that Nrdp1 CDCrel-1 parkin activity. were in was used in C and We conclude that Nrdp1 also activity on its between Nrdp1 and parkin parkin activity on were with and or A and were with for and to h. was with was on and by C and were with 12 for h. CDCrel-1 was by and experiments were and were between with and Nrdp1 at 5 for parkin and its substrates synuclein and been Ibanez P. Abbas N. C. Bohme G.A. M. J. O. Pradier L. G. C. Periquet M. F. J. M.J. S. R. A. E. M. Denefle P. J. G. Rooney Brice A. de J. Hum. Mol. Genet. 2003; 12: PubMed Scopus Google Scholar, S.M. C. A. N. G.J. M. B.L. J. J. 2003; Full Text Full Text PDF PubMed Scopus Google Scholar, W.W. Nature. 2000; PubMed Scopus Google Scholar). Although in been Ibanez P. Abbas N. C. Bohme G.A. M. J. O. Pradier L. G. C. Periquet M. F. J. M.J. S. R. A. E. M. Denefle P. J. G. Rooney Brice A. de J. Hum. Mol. Genet. 2003; 12: PubMed Scopus Google Scholar, S.M. C. A. N. G.J. M. B.L. J. J. 2003; Full Text Full Text PDF PubMed Scopus Google Scholar, S.M. C. A. N. G.J. M. B.L. J. J. 2003; Full Text Full Text PDF PubMed Scopus Google Scholar), it has been that in Drosophila are more W.W. Nature. 2000; PubMed Scopus Google Scholar, J.C. A.J. L.A. Proc. Natl. Acad. Sci. U. S. A. 2003; PubMed Scopus Google Scholar). of parkin in that pathological of PD patients J.C. A.J. L.A. Proc. Natl. Acad. Sci. U. S. A. 2003; PubMed Scopus Google Scholar). The of parkin in Drosophila that synuclein or in more reduction in the of dopaminergic the other of parkin in Drosophila by overexpression of either synuclein or Y. Y. Takahashi R. B. Neuron. 2003; 37: Full Text Full Text PDF PubMed Scopus Google Scholar). that studies of parkin and its in Drosophila provide on the pathogenesis of Parkinson disease. In this we demonstrate that a Drosophila ubiquitin E3 ligase with parkin also parkin and activity. It be and to Drosophila with either Nrdp1 or of on parkin on of parkin by Nrdp1 can be by these with Drosophila for parkin, and of the most about is Nrdp1 a in the pathogenesis of Parkinson disease. We that overexpression of Nrdp1 the parkin half-life from 5 to 2.5 h. It is to that Nrdp1 activity in the of parkin resulting in accumulation of parkin substrates Although is that the Nrdp1 on chromosome R. Mol. 2001; PubMed Scopus Google Scholar) is linked to in this and the that reduction of parkin in more death of dopaminergic neurons in Drosophila with overexpression of or Y. Y. Takahashi R. B. Neuron. 2003; 37: Full Text Full Text PDF PubMed Scopus Google Scholar) a that Nrdp1 of Parkinson disease by the of parkin protein. It is also that Nrdp1 is in the pathogenesis of the disease. Parkin contains two RING and is a ubiquitin E3 ligase. Parkin ubiquitinates its substrates and degradation. It is suggested that loss of function in parkin causes accumulation and aggregation of these substrates, resulting in death of dopaminergic However, studies in with parkin that of parkin protein has effects on of its substrates, CDCrel-1, and synuclein S.M. C. A. N. G.J. M. B.L. J. J. 2003; Full Text Full Text PDF PubMed Scopus Google Scholar). In overexpression of parkin reduced of by overexpression of synuclein and by other than by reduction of its Y. Y. Takahashi R. B. Neuron. 2003; 37: Full Text Full Text PDF PubMed Scopus Google Scholar). or Lewy bodies or Lewy neurites were observed in PD patients with parkin mutations AR-JP patients with mutations in the parkin a loss of these that degradation of its substrates, parkin other in this we that of parkin and Nrdp1 in the pathogenesis of PD by pathways including the it be to of parkin and Nrdp1 in PD and We for cDNA We W. S. for for
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".