An in silico model of the ubiquitin-proteasome system that incorporates normal homeostasis and age-related decline

BMC Systems Biology

Volumn 1, Issue , 2007, Pages

  Proctor, Carole J ^a   Tsirigotis, Maria ^b   Gray, Douglas A ^b,c  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b OTTAWA HOSPITAL RESEARCH INSTITUTE   (Canada)

^c UNIVERSITY OF OTTAWA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEASOME; UBIQUITIN; UBIQUITIN PROTEIN LIGASE;

AGING; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CELL STRAIN 3T3; CHO CELL; COMPUTER SIMULATION; CRICETULUS; DRUG ANTAGONISM; GENETICS; HAMSTER; HOMEOSTASIS; HUMAN; METABOLISM; MOUSE; PROTEIN FOLDING; TUMOR CELL LINE;

AGING; ANIMALS; CELL LINE, TUMOR; CHO CELLS; COMPUTER SIMULATION; CRICETINAE; CRICETULUS; HOMEOSTASIS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MICE; MODELS, BIOLOGICAL; NIH 3T3 CELLS; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEIN FOLDING; UBIQUITIN; UBIQUITIN-ACTIVATING ENZYMES;

EID: 38149065992     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-1-17     Document Type: Article

References (48)

1. Kirkwood TBL Evolution of ageing Nature 1977, 270:301-304. 10.1038/ 270301a0 593350
2. Brunk UT Terman A The mitochondrial-lysosomal axis theory of aging - Accumulation of damaged mitochondria as a result of imperfect autophagocytosis Eur J Biochem 2002, 269(8):1996-2002. 10.1046/ j.1432-1033.2002.02869.x 11985575
3. Terman A Garbage catastrophe theory of aging: Imperfect removal of oxidative damage? Redox Rep 2001, 6(1):15-26. 10.1179/135100001101535996 11333111
4. Smith CD Carney JM Starke-Reed PE Oliver CN Stadtman ER Floyd RA Markesbery WR Excess Brain Protein Oxidation and Enzyme Dysfunction in Normal Aging and in Alzheimer Disease PNAS 1991, 88(23):10540-10543. 52964 1683703 10.1073/pnas.88.23.10540
5. Terman A Brunk UT Lipofuscin: Mechanisms of formation and increase with age Apmis 1998, 106(2):265-276. 9531959
6. Martin K Kirkwood TBL Potten CS Age changes in stem cells of murine small intestinal crypts Exp Cell Res 1998, 241(2):316-323. 10.1006/ excr.1998.4001 9637773
7. Wickner S Maurizi MR Gottesman S Posttranslational quality control: Folding, refolding, and degrading proteins Science 1999, 286(5446):1888-1893. 10.1126/science.286.5446.1888 10583944
8. Martinez-Vicente M Sovak G Cuervo AM Protein degradation and aging Experimental Gerontology 2005, 40(8-9):622-633. 10.1016/ j.exger.2005.07.005 16125351
9. Bjorkoy G Lamark T Brech A Outzen H Perander M Overvatn A Stenmark H Johansen T p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death J Cell Biol 2005:jCb.200507002.
10. Friguet B Bulteau AL Chondrogianni N Conconi M Petropoulos Protein degradation by the proteasome and its implications in aging The Annals of the New York Academy of Sciences 2000, 908:143-154.
11. Szweda PA Friguet B Szweda LI Proteolysis, free radicals, and aging Free Radic Biol Med 2002, 33(1):29-36. 10.1016/S0891-5849(02)00837-7 12086679
12. Sitte N Merker K Von Zglinicki T Davies KJA Grune T Protein oxidation and degradation during cellular senescence of human BJ fibroblasts: Part II - aging of nondividing cells Faseb J 2000, 14(15):2503-2510. 10.1096/ fj.00-0210com 11099468
13. Sitte N Merker K Von Zglinicki T Grune T Davies KJA Protein oxidation and degradation during cellular senescence of human BJ fibroblasts: Part I - effects of proliferative senescence Faseb J 2000, 14(15):2495-2502. 10.1096/fj.00-0209com 11099467
14. Gredilla R Sanz A Lopez-Torres M Barja G Caloric restriction decreases mitochondrial free radical generation at complex I and lowers oxidative damage to mitochondrial DNA in the rat heart Faseb J 2001, 15(9):1589-1591. 11427495
15. Miwa S Riyahi K Partridge L Brand MD Lack of correlation between mitochondrial reactive oxygen species production and life span in Drosophila Strategies for Engineered Negligible Senescence: Why Genuine Control of Aging May Be Foreseeable Annals of the New York Academy of Sciences 2004, 1019:388-391.
16. Sitte N Huber M Grune T Ladhoff A Doecke WD Von Zglinicki T Davies KJA Proteasome inhibition by lipofuscin/ceroid during postmitotic aging of fibroblasts Faseb J 2000, 14(11):1490-1498. 10.1096/fj.14.11.1490 10928983
17. Chiti F Calamai M Taddei N Stefani M Ramponi G Dobson CM Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases Proc Natl Acad Sci U S A 2002, 99:16419-16426. 139903 12374855 10.1073/pnas.212527999
18. Chondrogianni N Gonos ES Proteasome dysfunction in mammalian aging: Steps and factors involved Experimental Gerontology 2005, 40(12):931-938. 10.1016/j.exger.2005.09.004 16246514
19. Bence NF Sampat RM Kopito RR Impairment of the ubiquitin-proteasome system by protein aggregation Science 2001, 292(5521):1552-1555. 10.1126/ science.292.5521.1552 11375494
20. Bennett EJ Bence NF Jayakumar R Kopito RR Global impairment of the ubiquitin-proteasome system by nuclear or cytoplasmic protein aggregates precedes inclusion body formation Mol Cell 2005, 17(3):351-365. 10.1016/ j.molcel.2004.12.021 15694337
21. Johnston JA Ward CL Kopito RR Aggresomes: A cellular response to misfolded proteins J Cell Biol 1998, 143(7):1883-1898. 10.1083/ jcb.143.7.1883 9864362
22. Ardley HC Hung CC Robinson PA The aggravating role of the ubiquitin-proteasome system in neurodegeneration FEBS Lett 2005, 579(3):571-576. 10.1016/j.febslet.2004.12.058 15670810
23. Arrasate M Mitra S Schweitzer ES Segal MR Finkbeiner S Inclusion body formation reduces levels of mutant huntingtin and the risk of neuronal death Nature 2004, 431(7010):805-810. 10.1038/nature02998 15483602
24. Semple CAM RIKEN GER Group GSL Members The Comparative Proteomics of Ubiquitination in Mouse Genome Res 2003, 13(6b):1389-1394. 403670 12819137 10.1101/gr.980303
25. Robinson PA Ardley HC Ubiquitin-protein ligases Journal of Cell Science 2004, 117:5191-5194. 10.1242/jcs.01539 15483315
26. Pickart CM Fushman D Polyubiquitin chains: Polymeric protein signals Current Opinion in Chemical Biology 2004, 8(6):610-616. 10.1016/ j.cbpa.2004.09.009 15556404
27. Hochstrasser M Lingering Mysteries of Ubiquitin-Chain Assembly Cell 2006, 124(1):27-34. 10.1016/j.cell.2005.12.025 16413479
28. Hoppe T Multiubiquitylation by E4 enzymes: 'one size' doesn't fit all Trends in Biochemical Sciences 2005, 30(4):183-187. 10.1016/ j.tibs.2005.02.004 15817394
29. Wilkinson KD Regulation of ubiquitin-dependent processes by deubiquitinating enzymes Faseb J 1997, 11(14):1245-1256. 9409543
30. Proctor CJ Söti C Boys RJ Gillespie CS Shanley DP Wilkinson DJ Kirkwood TBL Modelling the actions of chaperones and their role in ageing Mechanisms of Ageing and Development 2005, 126:119-131. 10.1016/ j.mad.2004.09.031
31. Kulka RG Raboy B Schuster R Parag HA Diamond G Ciechanover A Marcus M A Chinese hamster cell cycle mutant arrested at G2 phase has a temperature-sensitive ubiquitin-activating enzyme, E1 J Biol Chem 1988, 263(30):15726-15731. 3049611
32. Nichols WW Murphy DG Cristofalo VJ Toji LH Greene AE Dwight SA Characterization of a new human diploid cell strain, IMR-90 1977, 196(4285):60-63. 841339
33. Sohal RS Role of oxidative stress and protein oxidation in the aging process Free Radic Biol Med 2002, 33(1):37-44. 10.1016/ S0891-5849(02)00856-0 12086680
34. Princiotta MF Finzi D Qian SB Gibbs J Schuchmann S Buttgereit F Bennink JR Yewdell JW Quantitating Protein Synthesis, Degradation, and Endogenous Antigen Processing Immunity 2003, 18(3):343-354. 10.1016/ S1074-7613(03)00051-7 12648452
35. Ravikumar B Rubinsztein DC Role of autophagy in the clearance of mutant huntingtin: A step towards therapy? Molecular Aspects of Medicine 2006, 27(5-6):520-527. 10.1016/j.mam.2006.08.008 16973207
36. Bender A Krishnan KJ Morris CM Taylor GA Reeve AK Perry RH Jaros E Hersheson JS Betts J Klopstock et High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease Nature Genetics 2006, 38(5):515-517. 10.1038/ng1769 16604074
37. Wilkinson DJ Stochastic Modelling for Systems Biology Chapman & Hall/ CRC Press 2006
38. Hucka M Finney A Sauro HM Bolouri H Doyle JC Kitano H and the rest of the SBML Forum: Arkin AP Bornstein BJ Bray D Cornish-Bowden A Cuellar AA Dronov S Gilles ED Ginkel M Gor V Goryanin II Hedley WJ Hodgman TC Hofmeyr JH Hunter PJ Juty NS Kasberger JL Kremling A Kummer U Le Novere N Loew LM Lucio D Mendes P Minch E Mjolsness ED Nakayama Y Nelson MR Nielsen PF Sakurada T Schaff JC Shapiro BE Shimizu TS Spence HD Stelling J Takahashi K Tomita M Wagner J Wang J The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models Bioinformatics 2003, 19(4):524-531. 10.1093/ bioinformatics/btg015 12611808
39. Basis http://www.basis.ncl.ac.uk
40. Kirkwood TBL Boys RJ Gillespie CS Proctor CJ Shanley DP Wilkinson DJ Towards an e-biology of ageing: Integrating theory and data Nat Rev Mol Cell Biol 2003, 4(3):243-249. 10.1038/nrm1051 12612643
41. Gillespie DT Exact stochastic simulation of coupled chemical reactions The Journal of Physical Chemistry 1977, 31:2340-2361. 10.1021/j100540a008
42. Biomodels http://www.ebi.ac.uk/biomodels/
43. Le Novere N Bornstein B Broicher A Courtot M Donizelli M Dharuri H Li L Sauro H Schilstra M Shapiro B Snoep JL Hucka M BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems Nucleic Acids Research 2006, 34(suppl 1):D689-691. 10.1093/nar/gkj092
44. Haas AL Bright PM The dynamics of ubiquitin pools within cultured human lung fibroblasts J Biol Chem 1987, 262(1):345-351. 3025210
45. Lodish H Berk A Zipursky SL Matsudaira P Baltimore D Darnell J Molecular Cell Biology New York, W.H. Freeman and Company 4th 2000
46. Interpro http://www.ebi.ac.uk/interpro/
47. Gene Ontology http://www.geneontology.org
48. Chemical Entities of Biological Interest database http://www.ebi.ac.uk/ chebi 12365828