An age-dependent feedback control model of calcium dynamics in yeast cells

Journal of Mathematical Biology

Volumn 60, Issue 6, 2010, Pages 849-879

  Tang, Fusheng ^a   Liu, Weijiu ^b  

^a University of Arkansas at Little Rock ^*  (United States)

^b UNIVERSITY OF CENTRAL ARKANSAS   (United States)

Author keywords

Aging; Calcium oscillation; Feedback control; Mathematical modeling; Pmr1p

Indexed keywords

ADENOSINE TRIPHOSPHATASE (CALCIUM); CALCIUM; CHAPERONE; PLASMA MEMBRANE CALCIUM TRANSPORTING ADENOSINE TRIPHOSPHATASE; PMC1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SSC1 PROTEIN, S CEREVISIAE;

ARTICLE; BIOLOGICAL MODEL; CALCIUM SIGNALING; CELL AGING; CELL CYCLE; COMPUTER SIMULATION; FEEDBACK SYSTEM; GENE DELETION; GENETICS; HOMEOSTASIS; METABOLISM; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE;

CALCIUM; CALCIUM SIGNALING; CALCIUM-TRANSPORTING ATPASES; CELL AGING; CELL CYCLE; COMPUTER SIMULATION; FEEDBACK, PHYSIOLOGICAL; GENE DELETION; HOMEOSTASIS; MODELS, BIOLOGICAL; MOLECULAR CHAPERONES; PLASMA MEMBRANE CALCIUM-TRANSPORTING ATPASES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

EID: 77951879786     PISSN: 03036812     EISSN: 14321416     Source Type: Journal    
DOI: 10.1007/s00285-009-0289-0     Document Type: Article

References (82)

1. 2+ homeostasis in Saccharomyces cerevisiae. J Biol Chem 277(48): 45751-45758.
2. Ashrafi K, Sinclair D, Gordon JI, Guarente L (1999) Passage through stationary phase advances replicative aging in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 96(16): 9100-9105.
3. Bagnat M, Keranen S, Shevchenko A, Shevchenko A, Simons K (2000) Lipid rafts function in biosynthetic delivery of proteins to the cell surface in yeast. Proc Natl Acad Sci USA 97(7): 3254-3259.
4. Baran I (1996) Calcium and cell cycle progression: possible effects of external perturbations on cell proliferation. Biophys J 70(3): 1198-1213.
5. 2+ from vacuolar membrane vesicles of Saccharomyces cerevisiae. FEBS Lett 323(1-2): 113-118.
6. Bonilla M, Nastase KK, Cunningham KW (2002) Essential role of calcineurin in response to endoplasmic reticulum stress. EMBO J 21: 2343-2353.
7. Boustany LM, Cyert MS (2002) Calcineurin-dependent regulation of Crz1p nuclear export requires Msn5p and a conserved calcineurin docking site. Genes Dev 16: 608-619.
8. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11: 369-391.
9. Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ (2004) Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 15: 3841-3862.
10. Cho JH, Ko KM, Singaravelu G, Ahnn J (2005) Caenorhabditis elegans PMR1, a P-type calcium ATPase, is important for calcium/manganese homeostasis and oxidative stress response. FEBS Lett 579(3): 778-782.
11. 2+-sensitive G1/s transitions in vascular smooth muscle cells. Circ Res 98(10): 1273-1281.
12. Ciapa B, Pesando D, Wilding M, Whitaker M (1994) Cell-cycle calcium transients driven by cyclic changes in inositol trisphosphate levels. Nature 368(6474): 875-878.
13. Courchesne WE, Ozturk S (2003) Amiodarone induces a caffeine-inhibited, MID1-depedent rise in free cytoplasmic calcium in Saccharomyces cerevisiae. Mol Microbiol 47(1): 223-234.
14. Crabtree GR (2001) Calcium, calcineurin, and the control of transcription. J Biol Chem 276(4): 2313-2316.
15. 2+ homeostasis. J Cell Biol 157(6): 1017-1028.
16. Cui J, Kaandorp JA (2006) Mathematical modeling of calcium homeostasis in yeast cells. Cell Calcium 39: 337-348.
17. Cui J, Kaandorp JA, Ositelu OO, Beaudry V, Knight A, Nanfack YF, Cunningham KW (2009) Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium 45: 123-132.
18. 2+ ATPases. J Cell Biol 124(3): 351-363.
19. 2+ ATPases in Saccharomyces cerevisiae. Mol Cell Biol 16(5): 2226-2237.
20. Cyert MS (2001) Genetic analysis of calmodulin and its targets in Sacchromyces cerevisiae. Annu Rev Genet 35: 647-672.
21. 2+ release in yeast is triggered by hypertonic shock and mediated by a TRP channel homologue. J Cell Biol 156(1): 29-34.
22. 2+ and MAPK signaling systems in the Xenopus blastomere: a possible frequency encoding mechanism for the control of the Xbra gene expression. Bull Math Biol 67(3): 433-465.
23. 2+ by yeast vacuoles. J Biol Chem 269: 7273-7278.
24. Flanagan WM, Corthesy B, Bram RJ, Crabtree GR (1991) Nuclear association of a T-cell transcription factor blocked by FK-506 and cyclosporin A. Nature 352: 803-807.
25. 2+ homeostasis is a constitutive function of the V-ATPase in Saccharomyces cerevisiae. J Biol Chem 275(49): 38245-38253.
26. Foster TC (2007) Calcium homeostasis and modulation of synaptic plasticity in the aged brain. Aging Cell 6(3): 319-325.
27. Funakoshi M, Kajiwara R, Goda T, Nishimoto T, Kobayashi H (2000) Isolation and characterisation of a mutation in the PMR1 gene encoding a Golgi membrane ATPase, which causes hypersensitivity to over-expression of Clb3 in Saccharomyces cerevisiae. Mol Gen Genet 264(1-2): 29-36.
28. Gillespie CS, Proctor CJ, Boys RJ, Shanley DP, Wilkinson DJ, Kirkwood TB (2004) A mathematical model of ageing in yeast. J Theor Biol 229(2): 189-196.
29. Gourlay CW, Ayscough KR (2005) The actin cytoskeleton: a key regulator of apoptosis and ageing? Nat Rev Mol Cell Biol 6(7): 583-589.
30. 2+ in Saccharomyces cerevisiae. J Biol Chem 265(34): 21216-21222.
31. Jain J, McCaffrey PG, Miner Z, Kerppola TK, Lambert JN, Verdine GL, Curran T, Rao A (1993) The T-cell transcription factor NFATp is a substrate for calcineurin and interacts with Fos and Jun. Nature 365: 352-355.
32. Kaeberlein M, Kennedy BK (2005) Large-scale identification in yeast of conserved ageing genes. Mech Ageing Dev 126(1): 17-21.
33. Kaeberlein M, Kirkland KT, Fields S, Kennedy BK (2004) Sir2-independent life span extension by calorie restriction in yeast. PLoS Biol 2(9): E296.
34. Kaeberlein M, Powers RW 3rd, Steffen KK, Westman EA, Hu D, Dang N, Kerr EO, Kirkland KT, Fields S, Kennedy BK (2005) Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science 310(5751): 1193-1196.
35. 2+ oscillations. Biophys J 61: 649-660.
36. 2+ accumulation and vacuolar fragmentation in a pmr1 Δ mutant of S. cerevisiae. J Cell Sci 116: 1637-1646.
37. Klemm RW, Ejsing CS, Surma MA, Kaiser HJ, Gerl MJ, Sampaio JL, de Robillard Q, Ferguson C, Proszynski TJ, Shevchenko A, Simons K (2009) Segregation of sphingolipids and sterols during formation of secretory vesicles at the trans-Golgi network. J Cell Biol 185(4): 601-612.
38. Kowald A, Kirkwood TB (2000) Accumulation of defective mitochondria through delayed degradation of damaged organelles and its possible role in the ageing of post-mitotic and dividing cells. J Theor Biol 202(2): 145-160.
39. Kuepfer L, Peter M, Sauer U, Stelling J (2007) Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol 25(9): 1001-1006.
40. 2+-dependent redox modulation of SERCA 2b by ERp57. J Cell Biol 164(1): 35-46.
41. Liu W, Tang F (2008) Modeling a simplified regulatory system of blood glucose at molecular levels. J Theor Biol 252: 608-620.
42. 2+ in yeast. Mol Cell Biol 20(18): 6686-6694.
43. Mao L, Zabel C, Wacker MA, Nebrich G, Sagi D, Schrade P, Bachmann S, Kowald A, Klose J (2006) Estimation of the mtDNA mutation rate in aging mice by proteome analysis and mathematical modeling. Exp Gerontol 41(1): 11-24.
44. Matsuura I, Kimura E, Tai K, Yazawa M (1993) Mutagenesis of the fourth calcium-binding domain of yeast calmodulin. J Biol Chem 169: 13267-13273.
45. 2+ efflux from the yeast vacuole lumen. J Cell Biol 164(2): 195-206.
46. 2+ levels in S. cerevisiae. FEBS Lett 451: 132-136.
47. 2+ homeostasis in the vps33Δ vacuolar biogenesis mutant of Saccharomyces cerevisiae. J Biol Chem 274(9): 5939-5947.
48. Miyakawa T, Mizunuma M (2007) Physiological roles of calcineurin in Saccharomyces cerevisiae with special emphasis on its roles in G2/M cell-cycle regulation. Biosci Biotechnol Biochem 71(3): 633-645.
49. Mouillac B, Balestre MN, Guillon G (1990) Positive feedback regulation of phospholipase C by vasopressin-induced calcium mobilization in WRK1 cells. Cell Signal 2: 497-507.
50. Murchison D, Griffith WH (2007) Calcium buffering systems and calcium signaling in aged rat basal forebrain neurons. Aging Cell 6(3): 297-305.
51. Norel R, Agur Z (1991) A model for the adjustment of the mitotic clock by cyclin and MPF levels. Science 251(4997): 1076-1078.
52. Ohsumi Y, Anraku Y (1983) Calcium transport driven by a proton motive force in vacuolar membrane vesicles of Saccharomyces cerevisiae. J Biol Chem 258: 5614-5617.
53. 2+-permeable channel in the yeast vacuolar membrane. Proc Natl Acad Sci USA 98: 7801-7805.
54. 2+ store, with functional properties distinct from those of the endoplasmic reticulum. EMBO J 17(18): 5298-5308.
55. 2+ exchangers. Mol Cell Biol 16(7): 3730-3741.
56. Putney JW Jr (1986) A model for receptor-regulated calcium entry. Cell Calcium 7: 1-12.
57. Putney JW Jr (2007) Recent breakthroughs in the molecular mechanism of capacitative calcium entry (with thoughts on how we got here). Cell Calcium 42(2): 103-110.
58. Putney JW Jr, McKay RR (1999) Capacitative calcium entry channels. Bioessays 21: 38-46.
59. Ryu JH, Lee Y, Han SK, Kim HY (2003) The role of hydrogen peroxide produced by polychlorinated biphenyls in PMR1-deficient yeast cells. J Biochem 134(1): 137-142.
60. Salazar C, Höfer T (2003) Allosteric regulation of the transcription factor NFAT1 by multiple phosphorylation sites: a mathematical analysis. J Mol Biol 327: 31-45.
61. Schomerus C, Kntzel H (1992) CDC25-dependent induction of inositol 1, 4, 5-trisphosphate and diacylglycerol in Saccharomyces cerevisiae by nitrogen. FEBS Lett 307(3): 249-252.
62. Shaw KT, Ho AM, Raghavan A, Kim J, Jain J, Park J, Sharma S, Rao A, Hogan PG (1995) Immunosuppressive drugs prevent a rapid dephosphorylation of transcription factor NFAT1 in stimulated immune cells. Proc Natl Acad Sci 92: 11205-11209.
63. Shukla N, Rowe D, Hinton J, Angelini GD, Jeremy JY (2005) Calcium and the replication of human vascular smooth muscle cells: studies on the activation and translocation of extracellular signal regulated kinase (ERK) and cyclin D1 expression. Eur J Pharmacol 509(1): 21-30.
64. Sible JC, Tyson JJ (2007) Mathematical modeling as a tool for investigating cell cycle control networks. Methods 41(2): 238-247.
65. 2+-ATPase in yeast Golgi, has properties distinct from sarco/endoplasmic reticulum and plasma membrane calcium pumps. J Biol Chem 272(15): 9895-9901.
66. Squier TC, Bigelow DJ (2000) Protein oxidation and age-dependent alterations in calcium homeostasis. Front Biosci 5: D504-D526.
67. Starovasnik MA, Davis TN, Klevit RE (1993) Similarities and differences between yeast and vertebrate calmodulin: an examination of the calcium-binding and structural properties of calmodulin from the yeast Saccharomyces cerevisiae. Biochemistry 32: 3261-3270.
68. 2+ in the yeast endoplasmic reticulum reaches only 10 mM and is mainly controlled by the secretory pathway pump Pmr1. EMBO J 18(17): 4733-4743.
69. 2+ pump. Hum Mol Genet 9(7): 1131-1140.
70. 2+-ATPase Pmc1p by the v-SNARE Protein Nyv1p. J Biol Chem 276(9): 6200-6206.
71. Tan Y, Bush JM, Liu W, Tang F (2008) Identification of longevity genes with systems biology approaches. Comput Biol Chem Adv Appl 2(2009): 49-56.
72. Tang F, Kauffman EJ, Novak JL, Nau JJ, Catlett NL, Weisman LS (2003) Regulated degradation of a class V myosin receptor directs movement of the yeast vacuole. Nature 422(6927): 87-92.
73. Tang F, Watkins W, Bermudez M, Gray R, Gaban A, Portie K, Grace S, Kleve M, Craciun G (2008) A life span-extending form of autophagy employs the vacuole-vacuole fusion machinery. Autophagy 4(7): 874-886.
74. 2+ homeostasis of yeast cells. J Biol Chem 270(17): 10113-10119.
75. Thibault O, Gant JC, Landfield PW (2007) Expansion of the calcium hypothesis of brain aging and Alzheimer's disease: minding the store. Aging Cell 6(3): 307-317.
76. Tisi R, Belotti F, Wera S, Winderickx J, Thevelein JM, Martegani E (2004) Evidence for inositol triphosphate as a second messenger for glucose-induced calcium signalling in budding yeast. Curr Genet 45(2): 83-89.
77. Ward JPT, Robertson TP, Aaronson PI (2005) Capacitative calcium entry: a central role in hypoxic pulmonary vasoconstriction? Am J Physiol Lung Cell Mol Physiol 289: L2-L4.
78. 2+-ATPase. Biochemistry 38: 14534-14541.
79. Weisman LS, Wickner W (1988) Intervacuole exchange in the yeast zygote: a new pathway in organelle communication. Science 241(4865): 589-591.
80. Zamponi GW (2003) The L-type calcium channe C-terminus: sparking interest beyond its role in calcium-dependent inactivation. J Physiol 552: 333.
81. Zinser E, Paltauf F, Daum G (1993) Sterol composition of yeast organelle membranes and subcellular distribution of enzymes involved in sterol metabolism. J Bacteriol 175(10): 2853-2858.
82. Zhou X-L, Batiza AF, Loukin SH, Palmer CP, Kung C, Saimi Y (2003) The transient receptor potential channel on the yeast vacuole is mechanosensitive. Proc Natl Acad Sci USA 100: 7105-7110.