Assessing chronological aging in bacteria

Methods in Molecular Biology

Volumn 965, Issue , 2013, Pages 421-437

  Gonidakis, Stavros ^a   Longo, Valter D ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Aging; Escherichia coli; Oxidative DNA damage; Protein carbonylation; Rifampicin; Stress resistance; Time lapse microscopy

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL SURVIVAL; BACTERIUM; BACTERIUM CULTURE; CELL AGING; CELL DENSITY; CELL VIABILITY; DNA DAMAGE; ESCHERICHIA COLI; LIFE CYCLE; LIMIT OF QUANTITATION; NONHUMAN; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN CARBONYLATION; STRESS; TIME-LAPSE VIDEO MICROSCOPY; CYTOLOGY; GENETICS; METABOLISM; MICROBIAL VIABILITY; MICROSCOPY; MOLECULAR EVOLUTION; PHYSIOLOGY; TIME;

DNA DAMAGE; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; MICROBIAL VIABILITY; MICROSCOPY; OXIDATIVE STRESS; PROTEIN CARBONYLATION; TIME FACTORS;

MLCS; MLOWN;

EID: 84878821637     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-239-1_28     Document Type: Article

References (50)

1. Finkel SE (2006) Long-term survival during stationary phase: evolution and the GASP phenotype. Nat Rev Microbiol 4:113-120
2. Gonidakis S (2010) Molecular genetics of longevity in Escherichia coli . Ph.D. thesis. University of Southern California, Los Angeles
3. Pin C, Baranyi J (2008) Single-cell and population lag times as a function of cell age. Appl Environ Microbiol 74:2534-2536
4. Zambrano MM, Siegele DA, Almiron M, Tormo A, Kolter R (1993) Microbial competition: Escherichia coli mutants that take over stationary phase cultures. Science 259:1757-1760
5. Nystrom T, Larsson C, Gustafsson L (1996) Bacterial defense against aging: role of the Escherichia coli ArcA regulator in gene expression, readjusted energy flux and survival during stasis. EMBO J 15:3219-3228
6. Farrell MJ, Finkel SE (2003) The growth advantage in stationary-phase phenotype conferred by rpoS mutations is dependent on the pH and nutrient environment. J Bacteriol 185:7044-7052
7. Wei Y, Lee JM, Richmond C, Blattner FR, Rafalski JA, LaRossa RA (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 183:545-556
8. Hartl DL, Dykhuizen DE (1984) The population genetics of Escherichia coli. Annu Rev Genet 18:31-68
9. Doran JW, Linn DM (1979) Bacteriological quality of runoff water from pastureland. Appl Environ Microbiol 37:985-991
10. Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51:365-379
11. Bogosian G, Sammons LE, Morris PJ, O'Neil JP, Heitkamp MA, Weber DB (1996) Death of the Escherichia coli K-12 strain W3110 in soil and water. Appl Environ Microbiol 62:4114-4120
12. Garcia-Lara J, Martinez J, Vilamu M, Vives-Rego J (1993) Effect of previous growth conditions on the starvation-survival of Escherichia coli in seawater. J Gen Microbiol 139:1425-1431
13. Morinigo MA, Cornax R, Castro D, Martinez-Manzanares E, Borrego JJ (1990) Viability of Salmonella spp and indicator microorganisms in seawater using membrane diffusion chambers. Antonie Van Leeuwenhoek 57:109-117
14. Rozen Y, Belkin S (2001) Survival of enteric bacteria in seawater. FEMS Microbiol Rev 25:513-529
15. Ericsson M, Hanstorp D, Hagberg P, Enger J, Nystrom T (2000) Sorting out bacterial viability with optical tweezers. J Bacteriol 182: 5551-5555
16. Gonidakis S, Finkel SE, Longo VD (2010) Genome-wide screen identifies Escherichia coli TCA-cycle-related mutants with extended chronological lifespan dependent on acetate metabolism and the hypoxia-inducible transcription factor ArcA. Aging Cell 9:868-881
17. Wei M, Fabrizio P, Madia F, Hu J, Ge H, Li LM, Longo VD (2009) Tor1/Sch9-regulated carbon source substitution is as effective as calorie restriction in life span extension. PLoS Genet 5:e1000467
18. Rea S, Johnson TE (2003) A metabolic model for life span determination in Caenorhabditis elegans. Dev Cell 5:197-203
19. Chen D, Thomas EL, Kapahi P (2009) HIF-1 modulates dietary restriction-mediated lifespan extension via IRE-1 in Caenorhabditis elegans. PLoS Genet 5:e1000486
20. Mehta R, Steinkraus KA, Sutphin GL, Ramos FJ, Shamieh LS, Huh A, Davis C, Chandler-Brown D, Kaeberlein M (2009) Proteasomal regulation of the hypoxic response modulates aging in C. elegans. Science 324:1196-1198
21. Zhang Y, Shao Z, Zhai Z, Shen C, Powell-Coffman JA (2009) The HIF-1 hypoxiainducible factor modulates lifespan in C. elegans. PLoS One 4:e6348
22. Nystrom T (2005) Role of oxidative carbonylation in protein quality control and senescence. EMBO J 24:1311-1317
23. Dukan S, Nystrom T (1998) Bacterial senescence: stasis results in increased and differential oxidation of cytoplasmic proteins leading to developmental induction of the heat shock regulon. Genes Dev 12:3431-3441
24. Dukan S, Nystrom T (1999) Oxidative stress defense and deterioration of growth-arrested Escherichia coli cells. J Biol Chem 274: 26027-26032
25. Desnues B, Cuny C, Gregori G, Dukan S, Aguilaniu H, Nystrom T (2003) Differential oxidative damage and expression of stress defence regulons in culturable and non-culturable Escherichia coli cells. EMBO Rep 4:400-404
26. Gonidakis S, Finkel SE, Longo VD (2010) E. coli hypoxia-inducible factor ArcA mediates lifespan extension in a lipoic acid synthase mutant by suppressing acetyl-CoA synthetase. Biol Chem 391:1139-1147
27. Harman D (1956) Aging: a theory based on free radical and radiation chemistry. J Gerontol 11:298-300
28. Muller FL, Lustgarten MS, Jang Y, Richardson A, Van Remmen H (2007) Trends in oxidative aging theories. Free Radic Biol Med 43:477-503
29. Van Raamsdonk JM, Hekimi S (2009) Deletion of the mitochondrial superoxide dismutase sod-2 extends lifespan in Caenorhabditis elegans. PLoS Genet 5:e1000361
30. Hu D, Cao P, Thiels E, Chu CT, Wu GY, Oury TD, Klann E (2007) Hippocampal long-term potentiation, memory, and longevity in mice that overexpress mitochondrial superoxide dismutase. Neurobiol Learn Mem 87:372-384
31. Longo VD, Finch CE (2003) Evolutionary medicine: from dwarf model systems to healthy centenarians? Science 299:1342-1346
32. Jobson RW, Nabholz B, Galtier N (2009) An evolutionary genome scan for longevity-related natural selection in mammals. Mol Biol Evol 27:840-847
33. Jin DJ, Gross CA (1988) Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J Mol Biol 202:45-58
34. Garibyan L, Huang T, Kim M, Wolff E, Nguyen A, Nguyen T, Diep A, Hu K, Iverson A, Yang H, Miller JH (2003) Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome. DNA Repair (Amst) 2:593-608
35. Benov L, Fridovich I (1995) A superoxide dismutase mimic protects sodA sodB Escherichia coli against aerobic heating and stationary-phase death. Arch Biochem Biophys 322:291-294
36. Farr SB, D'Ari R, Touati D (1986) Oxygendependent mutagenesis in Escherichia coli lacking superoxide dismutase. Proc Natl Acad Sci U S A 83:8268-8272
37. Jenkins DE, Schultz JE, Matin A (1988) Starvation-induced cross protection against heat or H2O2 challenge in Escherichia coli. J Bacteriol 170:3910-3914
38. Hengge-Aronis R (2002) Stationary phase gene regulation: what makes an Escherichia coli promoter sigmaS-selective? Curr Opin Microbiol 5:591-595
39. Hengge-Aronis R, Klein W, Lange R, Rimmele M, Boos W (1991) Trehalose synthesis genes are controlled by the putative sigma factor encoded by rpoS and are involved in stationaryphase thermotolerance in Escherichia coli. J Bacteriol 173:7918-7924
40. Conter A, Gangneux C, Suzanne M, Gutierrez C (2001) Survival of Escherichia coli during long-term starvation: effects of aeration, NaCl, and the rpoS and osmC gene products. Res Microbiol 152:17-26
41. Hengge-Aronis R, Fischer D (1992) Identification and molecular analysis of glgS, a novel growth-phase-regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli. Mol Microbiol 6:1877-1886
42. Hassan HM, Fridovich I (1977) Regulation of the synthesis of superoxide dismutase in Escherichia coli. Induction by methyl viologen. J Biol Chem 252:7667-7672
43. Miller RA (2009) Cell stress and aging: new emphasis on multiplex resistance mechanisms. J Gerontol A Biol Sci Med Sci 64: 179-182
44. Longo VD, Mitteldorf J, Skulachev VP (2005) Programmed and altruistic ageing. Nat Rev Genet 6:866-872
45. Stewart EJ, Madden R, Paul G, Taddei F (2005) Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol 3:e45
46. Lindner AB, Madden R, Demarez A, Stewart EJ, Taddei F (2008) Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc Natl Acad Sci U S A 105:3076-3081
47. Steinkraus KA, Kaeberlein M, Kennedy BK (2008) Replicative aging in yeast: the means to the end. Annu Rev Cell Dev Biol 24: 29-54
48. Fabrizio P, Longo VD (2003) The chronological life span of Saccharomyces cerevisiae. Aging Cell 2:73-81
49. Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297:1183-1186
50. Slonczewski JL, Rosen BP, Alger JR, Macnab RM (1981) pH homeostasis in Escherichia coli: measurement by 31P nuclear magnetic resonance of methylphosphonate and phosphate. Proc Natl Acad Sci U S A 78:6271-6275