Correction: A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserina (PLoS ONE) (2013) 8, 12 (e83109) DOI: 10.1371/journal.pone.0083109);A genome-wide longitudinal transcriptome analysis of the aging model Podospora anserine

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Philipp, Oliver ^a   Hamann, Andrea ^a   Servos, Jörg ^a   Werner, Alexandra ^a   Koch, Ina ^a   Osiewacz, Heinz D ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COPPER; FUNGAL RNA; PROTEASOME; TRANSCRIPTOME;

AGING; ARTICLE; AUTOPHAGY; CONTROLLED STUDY; COPPER METABOLISM; DOWN REGULATION; ENERGY METABOLISM; FUNGAL GENOME; FUNGUS MUTANT; GENOME ANALYSIS; LONGITUDINAL STUDY; MITOCHONDRION; NONHUMAN; PODOSPORA ANSERINA; RIBOSOME; WILD TYPE;

AGING; AUTOPHAGY; COPPER; ENERGY METABOLISM; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MITOCHONDRIA; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; PODOSPORA; RIBOSOMES; TIME FACTORS; TRANSCRIPTOME;

EID: 84893364380     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0091590     Document Type: Erratum

References (91)

1. Osiewacz HD (1997) Genetic regulation of aging. J Mol Med 75: 715-727.
2. Kirkwood TB, Austad SN (2000) Why do we age? Nature 408: 233-238.
3. Kenyon CJ (2010) The genetics of ageing. Nature 464: 504-512.
4. Esser K (1974) Podospora anserina. In: King RC, editors. Handbook of Genetics. New York: Plenum Press. 531-551.
5. Osiewacz HD, Hamann A, Zintel S (2013) Assessing organismal aging in the filamentous fungus Podospora anserina. Methods Mol Biol 965: 439-462.
6. Scheckhuber CQ, Osiewacz HD (2008) Podospora anserina: a model organism to study mechanisms of healthy ageing. Mol Genet Genomics 280: 365-374.
7. Rizet G (1953) Sur l'impossibilité d'obtenir la multiplication végétative ininterrompue et illimitée de l'ascomycète Podospora anserina. C R Acad Sci Paris 237: 838-855.
8. Nitsche BM, Burggraaf-van Welzen AM, Lamers G, Meyer V, Ram AF (2013) Autophagy promotes survival in aging submerged cultures of the filamentous fungus Aspergillus niger. Appl Microbiol Biotechnol 97: 8205-8218.
9. Fabrizio P, Longo VD (2003) The chronological life span of Saccharomyces cerevisiae. Aging Cell 2: 73-81.
10. Longo VD, Shadel GS, Kaeberlein M, Kennedy B (2012) Replicative and chronological aging in Saccharomyces cerevisiae. Cell Metab 16: 18-31.
11. Osiewacz HD, Kimpel E (1999) Mitochondrial-nuclear interactions and lifespan control in fungi. Exp Gerontol 34: 901-909.
12. Osiewacz HD (2002) Aging in fungi: role of mitochondria in Podospora anserina. Mech Ageing Dev 123: 755-764.
13. Osiewacz HD (2011) Mitochondrial quality control in aging and lifespan control of the fungal aging model Podospora anserina. Biochem Soc Trans 39: 1488-1492.
14. Osiewacz HD (1992) Genetic control of aging in the ascomycete Podospora anserina. Berlin; Heidelberg: Springer. 164 p.
15. Espagne E, Lespinet O, Malagnac F, Da SC, Jaillon O, et al. (2008) The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol 9: R77.
16. Osiewacz HD, Clairmont A, Huth M (1990) Electrophoretic karyotype of the ascomycete Podospora anserina. Curr Genet 18: 481-483.
17. Osiewacz HD, Skaletz A, Esser K (1991) Integrative transformation of the ascomycete Podospora anserina: identification of the mating-type locus on chromosome VII of electrophoretically separated chromosomes. Appl Microbiol Biotechnol 35: 38-45.
18. Osiewacz HD (1994) A versatile shuttle cosmid vector for the efficient construction of genomic libraries and for the cloning of fungal genes. Curr Genet 26: 87-90.
19. Molina C, Rotter B, Horres R, Udupa SM, Besser B, et al. (2008) SuperSAGE: the drought stress-responsive transcriptome of chickpea roots. BMC Genomics 9: 553.
20. Kumar L, Futschik M (2007) Mfuzz: A software package for soft clustering of microarray data. Bioinformation 2: 5-7.
21. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29. (Pubitemid 30257031)
22. Servos J, Hamann A, Grimm C, Osiewacz HD (2012) A differential genome-wide transcriptome analysis: impact of cellular copper on complex biological processes like aging and development. PLoS ONE 7: e49292.
23. Rexroth S, Poetsch A, Rögner M, Hamann A, Werner A, et al. (2012) Reactive oxygen species target specific tryptophan site in the mitochondrial ATP synthase. Biochim Biophys Acta 1817: 381-387.
24. Brust D, Hamann A, Osiewacz HD (2010) Deletion of PaAif2 and PaAmid2, two genes encoding mitochondrial AIF-like oxidoreductases of Podospora anserina, leads to increased stress tolerance and lifespan extension. Curr Genet 55: 225-235.
25. Borghouts C, Kerschner S, Osiewacz HD (2000) Copper-dependence of mitochondrial DNA rearrangements in Podospora anserina. Curr Genet 37: 268-275. (Pubitemid 30224123)
26. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, et al. (2013) ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Res 41: D987-D990.
27. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. (Pubitemid 27359211)
28. The UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-D75.
29. R Core Team (2013) R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing.
30. Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258. (Pubitemid 46189622)
31. Merico D, Isserlin R, Stueker O, Emili A, Bader DB (2010) Enrichment Map: A network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5: e13984.
32. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, et al. (2012) A travel guide to Cytoscape plugins. Nat Methods 9: 1069-1076.
33. Lin WD, Liao YY, Yang TJ, Pan CY, Buckhout TJ, et al. (2011) Coexpression-based clustering of Arabidopsis root genes predicts functional modules in early phosphate deficiency signaling. Plant Physiol 155: 1383-1402.
34. Wang S, Yin Y, Ma Q, Tang X, Hao D, et al. (2012) Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis. BMC Plant Biol 12: 138.
35. Nikhil RP, Bezdek JC, Hathaway RJ (1996) Sequential competitive learning and the fuzzy c-means clustering algorithms. Neural Networks 9: 787-796. (Pubitemid 26264491)
36. Xie XL, Beni G (1991) A validity measure for fuzzy clustering. TPAMI 13: 841-847.
37. Scheckhuber CQ, Erjavec N, Tinazli A, Hamann A, Nyström T, et al. (2007) Reducing mitochondrial fission results in increased life span and fitness of two fungal ageing models. Nat Cell Biol 9: 99-105. (Pubitemid 46024203)
38. Borghouts C, Scheckhuber CQ, Stephan O, Osiewacz HD (2002) Copper homeostasis and aging in the fungal model system Podospora anserina : differential expression of PaCtr3 encoding a copper transporter. Int J Biochem Cell Biol 34: 1355-1371. (Pubitemid 35245395)
39. Averbeck NB, Borghouts C, Hamann A, Specke V, Osiewacz HD (2001) Molecular control of copper homeostasis in filamentous fungi: increased expression of a metallothionein gene during aging of Podospora anserina. Mol Gen Genet 264: 604-612.
40. Borghouts C, Werner A, Elthon T, Osiewacz HD (2001) Copper-modulated gene expression and senescence in the filamentous fungus Podospora anserina. Mol Cell Biol 21: 390-399. (Pubitemid 32037360)
41. Stahl U, Lemke PA, Tudzynski P, Kück U, Esser K (1978) Evidence for plasmid like DNA in a filamentous fungus, the ascomycete Podospora anserina. Mol Gen Genet 162: 341-343. (Pubitemid 8375766)
42. Esser K, Tudzynski P, Stahl U, Kück U (1980) A model to explain senescence in the filamentous fungus Podospora anserina by the action of plasmid like DNA. Mol Gen Genet 178: 213-216. (Pubitemid 10079083)
43. Esser K, Kück U, Stahl U, Tudzynski P (1981) Mitochondrial DNA and senescence in Podospora anserina. Curr Genet 4: 83.
44. Sellem CH, Lecellier G, Belcour L (1993) Transposition of a group II intron. Nature 366: 176-178. (Pubitemid 23351824)
45. Osiewacz HD, Esser K (1984) The mitochondrial plasmid of Podospora anserina: A mobile intron of a mitochondrial gene. Curr Genet 8: 299-305. (Pubitemid 14079441)
46. Kil IS, Huh TL, Lee YS, Lee YM, Park JW (2006) Regulation of replicative senescence by NADP+ -dependent isocitrate dehydrogenase. Free Radic Biol Med 40: 110-119. (Pubitemid 41759408)
47. Osiewacz HD, Hermanns J (1992) The role of mitochondrial DNA rearrangements in aging and human diseases. Aging (Milano) 4: 273-286.
48. Osiewacz HD, Hermanns J, Marcou D, Triffi M, Esser K (1989) Mitochondrial DNA rearrangements are correlated with a delayed amplification of the mobile intron (plDNA) in a long-lived mutant of Podospora anserina. Mutat Res 219: 9-15. (Pubitemid 19003362)
49. Osiewacz HD, Hamann A (1997) DNA reorganization and biological aging. A review. Biochemistry (Mosc) 62: 1275-1284. (Pubitemid 127665916)
50. Scheckhuber CQ, Mack SJ, Strobel I, Ricciardi F, Gispert S, et al. (2010) Modulation of the glyoxalase system in the aging model Podospora anserina: effects on growth and lifespan. Aging (Albany NY) 2: 969-980.
51. Nissan TA, Baßler J, Petfalski E, Tollervey D, Hurt E (2002) 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm. EMBO J 21: 5539-5547.
52. Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, et al. (2011) Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet 7.
53. Averbeck NB, Jensen ON, Mann M, Schägger H, Osiewacz HD (2000) Identification and characterization of PaMTH1, a putative o-methyltransferase accumulating during senescence of Podospora anserina cultures. Curr Genet 37: 200-208. (Pubitemid 30198933)
54. Groebe K, Krause F, Kunstmann B, Unterluggauer H, Reifschneider NH, et al. (2007) Differential proteomic profiling of mitochondria from Podospora anserina, rat and human reveals distinct patterns of age-related oxidative changes. Exp Gerontol 42: 887-898. (Pubitemid 47268737)
55. Kunstmann B, Osiewacz HD (2009) The S-adenosylmethionine dependent O-methyltransferase PaMTH1: a longevity assurance factor protecting Podospora anserina against oxidative stress. Aging (Albany NY) 1: 328-334.
56. Zhu BT, Ezell EL, Liehr JG (1994) Catechol-O-methyltransferase-catalyzed rapid O-methylation of mutagenic flavonoids. Metabolic inactivation as a possible reason for their lack of carcinogenicity in vivo. J Biol Chem 269: 292-299.
57. Nappi AJ, Vass E (1998) Hydroxyl radical formation via iron-mediated Fenton chemistry is inhibited by methylated catechols. Biochim Biophys Acta 1425: 159-167. (Pubitemid 28479722)
58. Knab B, Osiewacz HD (2010) Methylation of polyphenols with vicinal hydroxyl groups: A protection pathway increasing organismal lifespan. Cell Cycle 9: 3387-3388.
59. Kunstmann B, Osiewacz HD (2008) Over-expression of an S-adenosylmethionine-dependent methyltransferase leads to an extended lifespan of Podospora anserina without impairments in vital functions. Aging Cell 7: 651-662.
60. Eriksen JL, Wszolek Z, Petrucelli L (2005) Molecular pathogenesis of Parkinson disease. Arch Neurol 62: 353-357. (Pubitemid 40349469)
61. Ding Q, Dimayuga E, Keller JN (2006) Proteasome regulation of oxidative stress in aging and age-related diseases of the CNS. Antioxid Redox Signal 8: 163-172. (Pubitemid 43324543)
62. Scheckhuber CQ, Grief J, Boilan E, Luce K, Debacq-Chainiaux F, et al. (2009) Age-related cellular copper dynamics in the fungal ageing model Podospora anserina and in ageing human fibroblasts. PLoS One 4: e4919.
63. Chondrogianni N, Stratford FL, Trougakos IP, Friguet B, Rivett AJ, et al. (2003) Central role of the proteasome in senescence and survival of human fibroblasts: induction of a senescence-like phenotype upon its inhibition and resistance to stress upon its activation. J Biol Chem 278: 28026-28037. (Pubitemid 36899999)
64. Yiu G, McCord A, Wise A, Jindal R, Hardee J, et al. (2008) Pathways change in expression during replicative aging in Saccharomyces cerevisiae. J Gerontol A Biol Sci Med Sci 63: 21-34. (Pubitemid 351738460)
65. Pinan-Lucarré B, Iraqui I, Clavé C (2006) Podospora anserina target of rapamycin. Curr Genet 50: 23-31.
66. Martin DE, Soulard A, Hall MN (2004) TOR regulates ribosomal protein gene expression via PKA and the Forkhead transcription factor FHL1. Cell 119: 969-979. (Pubitemid 40037610)
67. Reiter A, Steinbauer R, Philippi A, Gerber J, Tschochner H, et al. (2011) Reduction in ribosomal protein synthesis is sufficient to explain major effects on ribosome production after short-term TOR inactivation in Saccharomyces cerevisiae. Mol Cell Biol 31: 803-817.
68. Osiewacz HD, Nuber U (1996) GRISEA, a putative copper-activated transcription factor from Podospora anserina involved in differentiation and senescence. Mol Gen Genet 252: 115-124.
69. Borghouts C, Osiewacz HD (1998) GRISEA, a copper-modulated transcription factor from Podospora anserina involved in senescence and morphogenesis, is an ortholog of MAC1 in Saccharomyces cerevisiae. Mol Gen Genet 260: 492-502. (Pubitemid 29015291)
70. Borghouts C, Scheckhuber CQ, Werner A, Osiewacz HD (2002) Respiration, copper availability and SOD activity in P. anserina strains with different lifespan. Biogerontology 3: 143-153. (Pubitemid 34678892)
71. Brust D, Daum B, Breunig C, Hamann A, Kühlbrandt W, et al. (2010) Cyclophilin D links programmed cell death and organismal aging in Podospora anserina. Aging Cell 9: 761-775.
72. Voigt O, Herzog B, Jakobshagen A, Pöggeler S (2013) Autophagic kinases SmVPS34 and SmVPS15 are required for viability in the filamentous ascomycete Sordaria macrospora. Microbiol Res.
73. Kundu M, Thompson CB (2008) Autophagy: basic principles and relevance to disease. Annu Rev Pathol 3: 427-455. (Pubitemid 351488288)
74. Powers RW III, Kaeberlein M, Caldwell SD, Kennedy BK, Fields S (2006) Extension of chronological life span in yeast by decreased TOR pathway signaling. Genes Dev 20: 174-184. (Pubitemid 43112936)
75. Jia K, Chen D, Riddle DL (2004) The TOR pathway interacts with the insulin signaling pathway to regulate C. elegans larval development, metabolism and life span. Development 131: 3897-3906. (Pubitemid 39232150)
76. Kapahi P, Zid BM, Harper T, Koslover D, Sapin V, et al. (2004) Regulation of lifespan in Drosophila by modulation of genes in the TOR signaling pathway. Curr Biol 14: 885-890. (Pubitemid 38800910)
77. Kück U, Osiewacz HD, Schmidt U, Kappelhoff B, Schulte E, et al. (1985) The onset of senescence is affected by DNA rearrangements of a discontinuous mitochondrial gene in Podospora anserina. Curr Genet 9: 373-382.
78. Pollack JK, Harris SD, Marten MR (2009) Autophagy in filamentous fungi. Fungal Genet Biol 46: 1-8.
79. Voigt O, Pöggeler S (2013) Self-eating to grow and kill: autophagy in filamentous ascomycetes. Appl Microbiol Biotechnol.
80. Tatsuta T, Langer T (2008) Quality control of mitochondria: Protection against neurodegeneration and ageing. EMBO J 27: 306-314. (Pubitemid 351161660)
81. Weber TA, Reichert AS (2010) Impaired quality control of mitochondria: aging from a new perspective. Exp Gerontol 45: 503-511.
82. Fischer F, Hamann A, Osiewacz HD (2012) Mitochondrial quality control: An integrated network of pathways. Trends Biochem Sci 37: 284-292.
83. Pan T, Kondo S, Zhu W, Xie W, Jankovic J, et al. (2008) Neuroprotection of rapamycin in lactacystin-induced neurodegeneration via autophagy enhancement. Neurobiol Dis 32: 16-25.
84. Pandey UB, Nie Z, Batlevi Y, McCray BA, Ritson GP, et al. (2007) HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS. Nature 447: 859-863. (Pubitemid 46920134)
85. Gamerdinger M, Hajieva P, Kaya AM, Wolfrum U, Hartl FU, et al. (2009) Protein quality control during aging involves recruitment of the macroautophagy pathway by BAG3. EMBO J 28: 889-901.
86. Lilienbaum A (2013) Relationship between the proteasomal system and autophagy. Int J Biochem Mol Biol 4: 1-26.
87. Harman D (1972) The biologic clock: the mitochondria? J Am Geriatr Soc 20: 145-147.
88. Osiewacz HD, Stumpferl SW (2001) Metabolism and aging in the filamentous fungus Podospora anserina. Arch Gerontol Geriatr 32: 185-197. (Pubitemid 32505685)
89. Osiewacz HD (2002) Mitochondrial functions and aging. Gene 286: 65-71.
90. Wallace DC (2001) A mitochondrial paradigm for degenerative diseases and ageing. Novartis Found Symp 235: 247-263.
91. Korolchuk VI, Menzies FM, Rubinsztein DC (2010) Mechanisms of cross-talk between the ubiquitin-proteasome and autophagy-lysosome systems. FEBS Lett 584: 1393-1398.