Skip to main content

Advertisement

SpringerLink
Log in

Inter-nucleosomal DNA fragmentation and loss of RNA integrity during seed ageing

  • Original Research
  • Published:
Plant Growth Regulation Aims and scope Submit manuscript

Abstract

The germination of viable seeds is the basis for new plant growth and development. Seeds lose viability during storage, but the biochemical mechanisms of seed death are not fully understood. This study aimed to investigate degradation patterns of nucleic acids during seed ageing and subsequent water uptake. Seeds of Pisum sativum L. were artificially aged at 50°C and 12% seed water content (WC). Nucleic acids degradation was studied during ageing and during imbibition of four seed lots with differential viability from highly viable to dead. As seeds lost viability during ageing, DNA was gradually degraded into internucleosomal fragments, resulting in ‘DNA laddering’, in conjunction with disintegration of 18S and 28S rRNA bands. During imbibition, non-aged controls had high levels of DNA and RNA integrity through to radicle protrusion. In an aged seed lot with 85% total germination (TG) DNA fragmentation decreased upon imbibition probably due to nucleosome degradation, while rRNA integrity did not improve. In an aged seed lot with 44% TG, neither DNA nor rRNA integrity improved upon imbibition. Dead seeds showed DNA degradation as laddering throughout imbibition along with extensive degradation of rRNA. We present a model in which interlinked programmed and non-programmed events contribute to seed ageing, and suggest that protection of nucleic acids during ageing is key to seed longevity.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Bailly C (2004) Active oxygen species and antioxidants in seed biology. Seed Sci Res 14:93–107

    Article  CAS  Google Scholar 

  • Bernal-Lugo I, Leopold AC (1998) The dynamics of seed mortality. J Exp Bot 49:1455–1461

    Article  CAS  Google Scholar 

  • Birtić S, Kranner I (2006) Isolation of high-quality RNA from polyphenol-, polysaccharide- and lipid-rich seeds. Phytochem Anal 17:144–148

    Article  PubMed  Google Scholar 

  • Boubriak I, Dini M, Berjak P, Osborne DJ (2000) Desiccation and survival in the recalcitrant seeds of Avicennia marina: DNA replication, DNA repair and protein synthesis. Seed Sci Res 10:307–315

    CAS  Google Scholar 

  • Bray CM, Chow TY (1976) Lesions in post-ribosomal supernatant fractions associated with loss of viability in pea (Pisum arvense) seed. Biochim Biophys Acta 442:1–13

    CAS  PubMed  Google Scholar 

  • Bray CM, Dasgupta J (1976) Ribonucleic acid synthesis and loss of viability in pea seed. Planta 132:103–108

    Article  CAS  Google Scholar 

  • Brockelhurst PA, Fraser RSS (1980) Ribosomal RNA integrity and rate of seed germination. Planta 148:417–421

    Google Scholar 

  • Brown PH, Ho THD (1986) Barley aleurone layers secrete a nuclease in response to gibberellic acid purification and partial characterization of the associated ribonuclease, deoxyribonuclease, and 3’-nucleotidase activities. Plant Physiol 82:801–806

    Article  CAS  PubMed  Google Scholar 

  • Buitink J, Leprince O (2004) Glass formation in plant anhydrobiotes: survival in the dry state. Cryobiology 48:215–228

    Article  CAS  PubMed  Google Scholar 

  • Bushell M, Stoneley M, Sarnow P, Willis AE (2004) Translation inhibition during the induction of apoptosis: RNA or protein degradation? Biochem Soc T 32:606–610

    Article  CAS  Google Scholar 

  • Cheah KSE, Osborne DJ (1978) DNA lesions occur with loss of viability in embryos of aging rye seed. Nature 272:593–599

    Article  CAS  PubMed  Google Scholar 

  • Chowdhury I, Tharakan B, Bhat GK (2006) Current concepts in apoptosis: The physiological suicide program revisited. Cell Mol Biol Lett 11:506–525

    Article  CAS  PubMed  Google Scholar 

  • Crawford DR, Lauzon RJ, Wang Y, Mazurkiewicz JE, Schools GP, Davies KJA (1997) 16S mitochondrial ribosomal RNA degradation is associated with apoptosis. Free Radical Bio Med 22:1295–1300

    Article  CAS  Google Scholar 

  • Daws MI, Davies J, Vaes E, van Gelder R, Pritchard HW (2007) Two-hundred year seed survival of Leucospermum and two other woody species from the Cape floristic region, South Africa. Seed Sci Res 17:73–79

    Article  Google Scholar 

  • Elbaz M, Avni A, Weil M (2002) Constitutive caspase-like machinery executes programmed cell death in plant cells. Cell Death Differ 9:726–733

    Article  CAS  PubMed  Google Scholar 

  • Ellis RH, Roberts EH (1980) Improved equations for the prediction of seed longevity. Ann Bot-London 45:13–30

    Google Scholar 

  • Evershed RP, Bland HA, Vanbergen PF, Carter JF, Horton MC, Rowley-Conwy PA (1997) Volatile compounds in archaeological plant remains and the Maillard reaction during decay of organic matter. Science 278:432–433

    Article  CAS  Google Scholar 

  • Faria JMR, Buitink J, van Lammeren AAM, Hilhorst HWM (2005) Changes in DNA and microtubules during loss and re-establishment of desiccation tolerance in germinating Medicago truncatula seeds. J Exp Bot 56:2119–2130

    Article  CAS  PubMed  Google Scholar 

  • Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118

    Article  CAS  PubMed  Google Scholar 

  • Hay F, Adams J, Manger K, Probert R (2008) The use of non-saturated lithium chloride solutions for experimental control of seed water content. Seed Sci Technol 36:737–746

    Google Scholar 

  • Hengartner MO (2000) The biochemistry of apoptosis. Nature 407:770–776

    Article  CAS  PubMed  Google Scholar 

  • Hoat TX, Nakayashiki H, Tosa Y, Mayama S (2006) Specific cleavage of ribosomal RNA and mRNA during victorin-induced apoptotic cell death in oat. Plant J 46:922–933

    Article  CAS  PubMed  Google Scholar 

  • Hoeberichts FA, Woltering EJ (2003) Multiple mediators of plant programmed cell death: interplay of conserved cell death mechanisms and plant-specific regulators. Bioessays 25:47–57

    Article  PubMed  Google Scholar 

  • Houge G, Doskeland SO (1996) Divergence towards a dead end? Cleavage of the divergent domains of ribosomal RNA in apoptosis. Experientia 52:963–967

    Article  CAS  PubMed  Google Scholar 

  • Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  Google Scholar 

  • Kalpana R, Rao KVM (1997) Nucleic acid metabolism of seeds of pigeonpea (Cajanus cajan (L) Millsp) cultivars during accelerated ageing. Seed Sci Technol 25:293–301

    Google Scholar 

  • Kranner I, Birtić S, Anderson KM, Pritchard HW (2006) Glutathione half-cell reduction potential: A universal stress marker and modulator of programmed cell death? Free Radical Bio Med 40:2155–2165

    Article  CAS  Google Scholar 

  • Lieber MR, Karanjawala ZE (2004) Ageing, repetitive genomes and DNA damage. Nat Rev Mol Cell Biol 5:69–75

    Article  CAS  PubMed  Google Scholar 

  • Mickelson JA, Grey WE (2006) Effect of soil water content on wild oat (Avena fatua) seed mortality and seedling emergence. Weed Sci 54:255–262

    CAS  Google Scholar 

  • Mycock DJ, Berjak P (1992) Intraseminal fungal location in maize of selected seed storage fungi in relation to some physiological-parameters. Afr J Bot 58:139–144

    Google Scholar 

  • Nadano D, Sato TA (2000) Caspase-3-dependent and–independent degradation of 28S ribosomal RNA may be involved in the inhibition of protein synthesis during apoptosis initiated by death receptor engagement. J Biol Chem 275:13967–13973

    Article  CAS  PubMed  Google Scholar 

  • Nielsen KF, Holm G, Uttrup LP, Nielsen PA (2004) Mould growth on building materials under low water activities. Influence of humidity and temperature on fungal growth and secondary metabolism. Int Biodeter Biodegr 54:325–336

    Article  CAS  Google Scholar 

  • Osborne DJ (2000) Hazards of a germinating seed: Available water and the maintenance of genomic integrity. Isr J Plant Sci 48:173–179

    Article  CAS  Google Scholar 

  • Panavas T, Walker EL, Rubinstein B (1998) Possible involvement of abscisic acid in senescence of daylily petals. J Exp Bot 49:1987–1997

    Article  CAS  Google Scholar 

  • Papoulis A, Al-Abed Y, Bucala R (1995) Identification of N2-(1-carboxyethyl)guanine (CEG) as a guanine advanced glycosylation end product. Biochemistry 34:648–655

    Article  CAS  PubMed  Google Scholar 

  • Perrin R, Lange H, Grienenberger JM, Gagliardi D (2004) AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria. Nucleic Acids Res 32:5174–5182

    Article  CAS  PubMed  Google Scholar 

  • Pritchard HW, Dickie JB (2003) Predicting seed longevity: the use and abuse of seed viability equations. In: Smith RD, Dickie JD, Linington SH, Pritchard HW, Probert RJ (eds) Seed conservation: turning science into practice. Royal Botanic Gardens, Kew, UK, pp 653–721

    Google Scholar 

  • Raff M (1998) Cell suicide for beginners. Nature 396:119–122

    Article  CAS  PubMed  Google Scholar 

  • Roberts EH (1973) Predicting the viability of seeds. Seed Sci Technol 1:499–514

    Google Scholar 

  • Sallon S, Solowey E, Cohen Y, Korchinsky R, Egli M, Woodhatch I, Simchoni O, Kislev M (2008) Germination, genetics, and growth of an ancient date seed. Science 320:1464

    Article  CAS  PubMed  Google Scholar 

  • Samali A, Gilje B, Doskeland SO, Cotter TG, Houge G (1997) The ability to cleave 28S ribosomal RNA during apoptosis is a cell-type dependent trait unrelated to DNA fragmentation. Cell Death Differ 4:289–293

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbour Laboratory Press, New York

    Google Scholar 

  • Samejima K, Earnshaw WC (2005) Trashing the genome: The role of nucleases during apoptosis. Nat Rev Mol Cell Biol 6:677–688

    Article  CAS  PubMed  Google Scholar 

  • Schafer FQ, Buettner GR (2001) Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple. Free Radical Bio Med 30:1191–1212

    Article  CAS  Google Scholar 

  • Sen S, Osborne DJ (1974) Germination of rye embryos following hydration-dehydration treatments–enhancement of protein and RNA—synthesis and earlier induction of DNA replication. J Exp Bot 25:1010–1019

    Article  CAS  Google Scholar 

  • Sen S, Osborne DJ (1977) Decline in ribonucleic acid and protein synthesis with loss of viability during the early hours of imbibition of rye (Secale cereale L.) embryos. Biochem J 166:33–38

    CAS  PubMed  Google Scholar 

  • Shen-Miller J, Mudgett MB, Schopf JW, Clarke S, Berger R (1995) Exceptional seed longevity and robust growth–ancient sacred lotus from China. Am J Bot 82:1367–1380

    Article  Google Scholar 

  • Shirkey B, McMaster NJ, Smith SC, Wright DJ, Rodriguez H, Jaruga P, Birincioglu M, Helm RF, Potts M (2003) Genomic DNA of Nostoc commune (Cyanobacteria) becomes covalently modified during long-term (decades) desiccation but is protected from oxidative damage and degradation. Nucleic Acids Res 31:2995–3005

    Article  CAS  PubMed  Google Scholar 

  • Spano C, Buselli R, Castiglione MR, Bottega S, Grilli I (2007) RNases and nucleases in embryos and endosperms from naturally aged wheat seeds stored in different conditions. J Plant Physiol 164:487–495

    Article  CAS  PubMed  Google Scholar 

  • Stewart C, Via LE (1993) A rapid CTAB DNA isolation technique useful for rapid fingerprinting and other PCR applications. Biotechniques 14:748

    CAS  PubMed  Google Scholar 

  • Strelec I, Ugarcic-Hardi Z, Hlevnjak M (2008) Accumulation of Amadori and Maillard products in wheat seeds aged under different storage conditions. Croat Chem Acta 8:131–137

    Google Scholar 

  • Sun WQ (1997) Glassy state and seed storage stability: The WLF kinetics of seed viability loss at T > T-g and the plasticization effect of water on storage stability. Ann Bot-London 79:291–297

    Article  Google Scholar 

  • Sun WQ, Leopold AC (1993) The glassy state and accelerated aging of soybeans. Physiol Plant 89:767–774

    Article  Google Scholar 

  • Thomas SG, Franklin-Tong VE (2004) Self-incompatibility triggers programmed cell death in Papaver pollen. Nature 429:305–309

    Article  CAS  PubMed  Google Scholar 

  • Thompson S, Bryant JA, Brockelhurst PA (1987) Changes in levels and integrity of ribosomal RNA during seed maturation and germination in carrot (Daucus carota L.). J Exp Bot 38:1343–1350

    Article  CAS  Google Scholar 

  • Tuteja N, Singh MB, Misra MK, Bhalla PL, Tuteja R (2001) Molecular mechanisms of DNA damage and repair: Progress in plants. Crit Rev Biochem Mol Biol 36:337–397

    Article  CAS  PubMed  Google Scholar 

  • VanBergen PF, Bland HA, Horton MC, Evershed RP (1997) Chemical and morphological changes in archaeological seeds and fruits during preservation by desiccation. Geochim Cosmochi. Acta 61:1919–1930

    Article  CAS  Google Scholar 

  • Vertucci CW, Roos EE (1990) Theoretical basis of protocols for seed storage. Plant Physiol 94:1019–1023

    Article  CAS  PubMed  Google Scholar 

  • Vertucci CW, Roos EE (1993) Theoretical basis of protocols for seed storage II. The influence of temperature on optimal moisture levels. Seed Sci Res 3:201–213

    Google Scholar 

  • Viannelo A, Zancani M, Peresson C, Petrussa E, Casolo V, Krajnakova J, Patui S, Braidot E, Macri F (2007) Plant mitochondrial pathway leading to programmed cell death. Physiol Plant 129:242–252

    Article  Google Scholar 

  • Walters C (1998) Understanding the mechanisms and kinetics of seed aging. Seed Sci Res 8:223–244

    Article  CAS  Google Scholar 

  • Walters C, Wheeler L, Stanwood PC (2004) Longevity of cryogenically stored seeds. Cryobiology 48:229–244

    Article  PubMed  Google Scholar 

  • Walters C, Hill LM, Wheeler LJ (2005) Dying while dry: Kinetics and mechanisms of deterioration on desiccated organisms. Integr Comp Biol 45:751–758

    Article  Google Scholar 

  • Walters C, Reilley AA, Reeves PA, Baszaszak J (2006) The utility of aged seeds in DNA banks. Seed Sci Res 16:169–178

    Article  CAS  Google Scholar 

  • Whitaker C, Berjak P, Pammenter NW (2008) Abnormal morphology of the embryo and seedling of Welwitschia mirabilis, and some observations on seed-associated fungi. S Afr J Bot 74:338–340

    Article  Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: A guide to methods and applications. Academic Press, New York, pp 315–322

    Google Scholar 

  • Williams RJ, Leopold AC (1989) The glassy state in corn embryos. Plant Physiol 89:977–981

    Article  CAS  PubMed  Google Scholar 

  • Xu Y, Hanson MR (2000) Programmed cell death during pollination-induced petal senescence in petunia. Plant Physiol 122:1323–1333

    Article  CAS  PubMed  Google Scholar 

  • Zangger H, Mottram JC, Fasel N (2002) Cell death in Leishmania induced by stress and differentiation: programmed cell death or necrosis? Cell Death Differ 9:1126–1139

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Prof Martin Grube, University of Graz, Austria, for helpful discussions regarding primer design. The Seed Conservation Department’s Millennium Seed Bank Project was supported by the Millennium Commission, the Welcome Trust, Orange Plc., and Defra. The Royal Botanic Gardens, Kew, receive grant-in-aid from Defra.

Author information

Authors and Affiliations

  1. Seed Conservation Department, Royal Botanic Gardens, Kew, Wakehurst Place, West Sussex, RH17 6TN, UK

    Ilse Kranner, Hongying Chen, Hugh W. Pritchard & Simona Birtić

  2. Kunming Institute of Botany, Chinese Academy of Sciences, 661100, Kunming, People’s Republic of China

    Hongying Chen

  3. School of Life-Sciences, University of Sussex, Brighton, East Sussex, BN1 9QG, UK

    Stephen R. Pearce & Simona Birtić

Authors
  1. Ilse Kranner
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hongying Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hugh W. Pritchard
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stephen R. Pearce
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Simona Birtić
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ilse Kranner.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kranner, I., Chen, H., Pritchard, H.W. et al. Inter-nucleosomal DNA fragmentation and loss of RNA integrity during seed ageing. Plant Growth Regul 63, 63–72 (2011). https://doi.org/10.1007/s10725-010-9512-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10725-010-9512-7

Keywords

Search

Navigation