Identification of longevity genes with systems biology approaches

Advances and Applications in Bioinformatics and Chemistry

Volumn 2, Issue 1, 2009, Pages 49-56

  Tan, Yuanyou ^a,c   Bush, John M ^a   Liu, Weijiu ^b   Tang, Fusheng ^a  

^a University of Arkansas ^*  (United States)

^b UNIVERSITY OF CENTRAL ARKANSAS   (United States)

^c WUHAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Aging; In silico genetic manipulation; Modeling; Systems biology; Yeast

Indexed keywords

EID: 80051555220     PISSN: None     EISSN: 11786949     Source Type: Journal    
DOI: None     Document Type: Review

References (63)

1. Kaeberlein M, McVey M, Guarente L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 1999;13(19):2570-2580.
2. Longo VD, Kennedy BK. Sirtuins in aging and age-related disease. Cell. 2006;126(2):257-268.
3. Tissenbaum HA, Guarente L. Increased dosage of a sir-2 gene extends life span in Caenorhabditis elegans. Nature. 2001;410(6825): 227-230.
4. Rogina B, Helfand SL. Sir2 mediates longevity in the fly through a pathway related to calorie restriction. Proc Natl Acad Sci U S A. 2004;101(45):15998-16003.
5. Alcendor RR, Gao S, Zhai P, et al. Sirt1 regulates aging and resistance to oxidative stress in the heart. Circ Res. 2007;100(10):1512-1521.
6. Milne JC, Lambert PD, Schenk S, et al. Small molecule activators of SIRT1 as therapeutics for the treatment of type 2 diabetes. Nature. 2007;450(7170):712-716.
7. Firestein R, Blander G, Michan S, et al. The SIRT1 deacetylase suppresses intestinal tumorigenesis and colon cancer growth. PLoS ONE. 2008;3(4):e2020.
8. Pearson KJ, Baur JA, Lewis KN, et al. Resveratrol delays age-related deterioration and mimics transcriptional aspects of dietary restriction without extending life span. Cell Metab. 2008;8(2):157-168.
9. Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J, Ruvkun G. A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity. Nat Genet. 2005;33(1):40-48.
10. Hansen M, Hsu AL, Dillin A, Kenyon C. New genes tied to endocrine, metabolic, and dietary regulation of life span from a Caenorhabditis elegans genomic RNAi screen. PLoS Genet. 2005;1(1):119-128.
11. Hamilton B, Dong Y, Shindo M, et al. A systematic RNAi screen for longevity genes in C. elegans. Genes Dev. 2005;19(13):1544-1555.
12. Kaeberlein M, Powers RW 3rd, Steffen KK, et al. Regulation of yeast replicative life span by TOR and Sch9 in response to nutrients. Science. 2005;310(5751):1193-1196.
13. Tang F, Watkins W, Bermudez M, et al. A life span-extending form of autophagy employs the vacuole-vacuole fusion machinery. Autophagy. 2008;4:874-886.
14. Zahn JM, Kim SK. Systems biology of aging in four species. Curr Opin Biotechnol. 2007;18:355-359.
15. Lin SS, Manchester JK, Gordon JI. Enhanced gluconeogenesis and increased energy storage as hallmarks of aging in Saccharomyces cerevisiae. J Biol Chem. 2001;276(38):36000-36007.
16. Cheng C, Fabrizio P, Ge H, Longo VD, Li LM. Inference of transcription modification in long-live yeast strains from their expression profiles. BMC Genomics. 2007;8:219.
17. Fabrizio P, Pozza F, Pletcher SD, Gendron CM, Longo VD. Regulation of longevity and stress resistance by Sch9 in yeast. Science. 2001;292(5515):288-290.
18. Raghothama C, Harsha HC, Prasad CK, Pandey A. Bioinformatics and proteomics approaches for aging research. Biogerontology. 2005;6(4):227-232.
19. Drees BL, Sundin B, Brazeau E, et al. A protein interaction map for cell polarity development. J Cell Biol. 2001;154(3):549-571.
20. Budovsky A, Abramovich A, Cohen R, Chalifa-Caspi V, Fraifeld V. Longevity network: construction and implications. Mech Ageing Dev. 2007;128(1):117-124.
21. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature. 1999;402(6761 Suppl):C47-C52.
22. Xue H, Xian B, Dong D, et al. A modular network model of aging. Mol Syst Biol. 2007;3:147.
23. Rattan SI. Increased molecular damage and heterogeneity as the basis of aging. Biol Chem. 2008;3893:267-272.
24. Frenz LM, Lee SE, Fesquet D, Johnston LH. The budding yeast Dbf2 protein kinase localises to the centrosome and moves to the bud neck in late mitosis. J Cell Sci. 2000;19:3399-3408.
25. 2+ ATPase family. Cell. 1989;58:133-145.
26. Przulj N, Wigle DA, Jurisica I. Functional topology in a network of protein interactions. Bioinformatics. 2004;20(3):340-348.
27. Asur S, Ucar D, Parthasarathy S. An ensemble framework for clustering protein-protein interaction networks. Bioinformatics. 2007;23(13): i29-i40.
28. Mete M, Tang F, Xu X, Yuruk N. A structural approach for finding functional modules from large biological networks. BMC Bioinformatics. 2008;9(Suppl 9):S19.
29. de Lichtenberg U, Jensen LJ, Brunak S, Bork P. Dynamic complex formation during the yeast cell cycle. Science. 2005;307(5710): 724-727.
30. Maraziotis IA, Dimitrakopoulou K, Bezerianos A. Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics. 2007;8:408.
31. Antoun GR, Williamson DG. Age-dependent changes in the multiple forms of the soluble 17 beta-hydroxysteroid dehydrogenase of female rabbit liver. Biochem J. 1985;225(2):391-398.
32. Liu W, Tang F. Modeling a simplified regulatory system of blood glucose at molecular levels. J Theory Biol. 2008;252:608-620.
33. Gordeeva AV, Zvyagilskaya RA, Labas YA. Cross-talk between reactive oxygen species and calcium in living cells. Biochemistry (Moscow). 2003;68(10):1077-1080.
34. 2+)-induced damage. Arch Biochem Biophys. 2004;425(1):14-24.
35. Brookes PS, Yoon Y, Robotham JL, Anders MW, Sheu S-S. Calcium, ATP, and ROS: a mitochondrial love-hate triangle. Am J Physiol Cell Physiol. 2004;287:C817-C833.
36. Inoue M, Sato EF, Nishikawa M, Hiramoto K, Kashiwagi A, Utsumi K. Free radical theory of apoptosis and metamorphosis. Redox Rep. 2004;9(5):237-247.
37. Dröge W, Schipper HM. Oxidative stress and aberrant signaling in aging and cognitive decline. Aging Cell. 2007;6(3):361-370.
38. Muller FL, Lustgarten MS, Jang Y, Richardson A, Van Remmen H. Trends in oxidative aging theories. Free Radic Biol Med. 2007;43(4):477-503.
39. Finkel T. Oxidant signals and oxidative stress. Curr Opin Cell Biol. 2003;15:247-254.
40. Colavitti R, Finkel T. Reactive oxygen species as mediators of cellular senescence. IUBMB Life. 2005;57(4/5):277-281.
41. Kenyon C, Chang J, Gensch E, Rudner A, Tabtiang R. AC. elegans mutant that lives twice as long as wild type. Nature. 1993;366(6454): 461-464.
42. Guarente L, Kenyon C. Genetic pathways that regulate ageing in model organisms. Nature. 2000;408:255-262.
43. Tothova Z, Kollipara R, Huntly BJ, et al. FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress. Cell. 2007;128(2):325-339.
44. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Sinclair DA. Nicotinamide and PNC1 govern life span extension by calorie restriction in Saccharomyces cerevisiae. Nature. 2003;423(6936):181-185.
45. Luo J, Nikolaev AY, Imai S, et al. Negative control of p53 by Sir2alpha promotes cell survival under stress. Cell. 2001;107(2):137-148.
46. Chao C, Wu Z, Mazur SJ, et al. Acetylation of mouse p53 at lysine 317 negatively regulates p53 apoptotic activities after DNA damage. Mol Cell Biol. 2006;26(18):6859-6869.
47. Jung MS, Jin DH, Chae HD, et al. Bcl-xL and E1B-19K proteins inhibit p53-induced irreversible growth arrest and senescence by preventing reactive oxygen species-dependent p38 activation. J Biol Chem. 2004;279(17):17765-17771.
48. 2 accelerates cellular senescence by accumulation of acetylated p53 via decrease in the function of SIRT1 by NAD+ depletion. Cell Physiol Biochem. 2007;20(1-4):45-54.
49. Heeren G, Jarolim S, Laun P, et al. The role of respiration, reactive oxygen species and oxidative stress in mother cell-specific ageing of yeast strains defective in the RAS signalling pathway. FEMS Yeast Res. 2004;5(2):157-167.
50. Hlavatá L, Nachin L, Jezek P, Nyström T. Elevated Ras/protein kinase A activity in Saccharomyces cerevisiae reduces proliferation rate and life span by two different reactive oxygen species-dependent routes. Aging Cell. 2008;7(2):148-157.
51. Harman D. The biologic clock: the mitochondria? J Am Geriatric Soc. 1972;20:145-147.
52. Harman D. Free radical theory of aging: consequences of mitochondrial aging. Age. 1983;6:86-94.
53. Kowald A, Kirkwood TB. 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. 2000;202(2):145-160.
54. Sinclair DA, Guarente L. Extrachromosomal rDNA circles - a cause of aging in yeast. Cell. 1997;91:1033-1042.
55. Gillespie CS, Proctor CJ, Boys RJ, Shanley DP, Wilkinson DJ, Kirkwood TB. A mathematical model of ageing in yeast. J Theor Biol. 2004;229(2):189-196.
56. Foster TC. Calcium homeostasis and modulation of synaptic plasticity in the aged brain. Aging Cell. 2007;6(3):319-325.
57. Murchison D, Griffith WH. Calcium buffering systems and calcium signaling in aged rat basal forebrain neurons. Aging Cell. 2007;6(3): 297-305.
58. Thibault O, Gant JC, Landfield PW. Expansion of the calcium hypothesis of brain aging and Alzheimer's disease: minding the store. Aging Cell. 2007;6(3):307-317.
59. Courchesne WE, Ozturk S. Amiodarone induces a caffeine-inhibited, MID1 -depedent rise in free cytoplasmic calcium in Saccharomyces cerevisiae. Mol Microbiol. 2003;47(1):223-234.
60. Cyert MS. Genetic analysis of calmodulin and its targets in Sacchromyces cerevisiae. Annu Rev Genet. 2001;35:647-672.
61. 2+ release in yeast is triggered by hypertonic shock and mediated by a TRP channel homologue. J Cell Biology. 2002;156(1):29-34.
62. Cui J, Kaandorp JA. Mathematical modeling of calcium homeostasis in yeast cells. Cell Calcium. 2006;39:337-348.
63. Petranovic D, Nielsen J. Can yeast systems biology contribute to the understanding of human disease? Trends Biotechnol. 2008;26(11): 584-590.