Breaking News: Oxidation of Proteins Leads to DNA Cleavage

Oxygen is a double-edge sword for cells: It is necessary for life, but at the same time it is the source of damaging free radicals that attack DNA, proteins and cell membranes. Reactive oxygen species are known to directly damage DNA, but a new study published today in Chemistry and Biology suggests that they also harm genes via the oxidation of proteins that cling to DNA. Shana Kelley and colleagues from Boston College in Massachusetts show that singlet oxygen reacts with DNA-bound proteins to form amino acid peroxides, which then proceed to chemically cleave the DNA sugar-phosphate backbone, introducing single-strand breaks. Since cellular DNA is invariably coated with proteins, the production and activity of amino acid peroxides could be a major source of the DNA damage that is associated with aging (see ARF related news story), which remains the biggest risk factor for Alzheimer disease and other neurodegenerative diseases.

To compound the ravages of aging, old brains may lose the ability to repel the assault by oxygen and time, says another new report from Diego Ruano and colleagues in Seville, Spain. In their paper, which appeared online on June 17 in Neurobiology of Aging, they show that hippocampi from aged rats display defects in the pathways that normally handle damaged, unfolded proteins. These age-related alterations could set up older brains for any one of several neurodegenerative protein aggregation diseases, they conclude.

To look at the role of oxidized amino acids in DNA damage, Kelley’s graduate students and co-first authors Erin Prestwich and Marc Roy tested DNA-binding tripeptides of the sequence lys-X-lys for their ability to cleave plasmid DNA in vitro in the presence of singlet oxygen. When the middle residue was cysteine, histidine, tyrosine or tryptophan, the peptides caused significant strand breaks, corresponding to their ability to form peroxides with oxygen. The ability of different peptides to mediate DNA cleavage was dependent on the formation and stability of peroxides on the different side chains, with tryptophan (W) being the most effective. The mechanism of cleavage was different from the alkaline-labile base damage typical of direct oxygen attack on DNA, and involved a cut in the sugar-phosphate backbone. In fact, the presence of the W-containing tripeptide protected the DNA from direct base damage by oxygen, leading the authors to characterize tryptophan as a “molecular ‘double-edged sword’ that can both suppress and induce DNA damage.”

These experiments were all carried out in vitro on plasmid or oligonucleotide DNA, but Kelley’s group has published evidence that protein-mediated DNA damage probably occurs in vivo, as well. In the April 22 Angewandte Chemie, first author Lisa Wittenhagen and colleagues conjugated a tryptophan-containing version of the DNA-binding Tat peptide from HIV with a photoactivatable dye that generates singlet oxygen. With this complex, they were able to bring together in close proximity cellular DNA, a tryptophan residue, and reactive oxygen. When the authors introduced the complex into HeLa cells, light induced cell death, but only when the tryptophan-containing Tat was used—when glycine was substituted for the tryptophan, light had no effect on cell viability. “We are working on follow-up studies that will characterize the chemical products of the DNA damage caused by these agents. In addition, we plan to examine cell lines that lack repair factors that typically take care of this type of damage naturally, which would accurately mimic aged or diseased cells,” Kelley said.

Moving from damage to defense, the second paper investigated the response of brain to misfolded proteins in young and aged rats. Accumulation of misfolded proteins in the endoplasmic reticulum triggers a set of compensatory changes, inducing upregulation of chaperone proteins, attenuation of protein translation, and degradation of proteins by the proteasome. These changes constitute the unfolded protein response (UPR), and first author M. Paz Gavilan and his colleagues show that the response does not work so well in the hippocampus of old rats. Gavilan found that, compared to young (4- to 6-month-old) rats, aged (23- to 26-month-old), rats had lower levels of three of the four chaperone proteins measured, and had higher levels of ubiquitinated proteins. To measure the UPR under stress, the researchers injected the proteasome inhibitor lactacystin directly into the hippocampus of young or aged rats. They saw increased ubiquitinated protein levels after 24 hours in young rats, which decreased back to normal after four days. Older rats showed greater increases, and failed to upregulate two chaperones, Grp78 and PDI, that are considered central to the UPR. At the same time, markers of apoptosis increased—an effect not seen in the young animals. According to the authors, the results “reveal, for the first time in vivo, a dysfunction in the ability of aged rats to solve the stress conditions induced by protein accumulation.” Similar reductions in the Grp78 chaperone (see ARF related news story) and proteasome function (Keller et al., 2000) have been observed in AD, and the new work serves to further illuminate the intriguing links among aging, protein mishandling, and neurodegenerative disorders.—Pat McCaffrey

Comments

    • User Profile Image Robert Peers
      Solo practitioner and independent researcher; Founder, National Institute of Good Health
    • Posted:

    I have a scientific question: How can aging be a risk factor for Alzheimer's? Diseases have causes, don't they?

    1. Most aging humans don't get AD, and no wild animals, eating natural foods, get it, whatever their age. That includes chimps. The aging process does not cause this disease. Villagers in India who use unrefined mustard oil in their cooking do not get AD, but they age like anyone else. Sporadic AD is seen only where refined food oils are available.

    2. If sporadic (non-genetic) AD takes 30-40 years to develop, then the disease must start somewhere between 30 and 40, possibly even earlier, i.e., it does not begin in old age; it begins in relatively young people, so aging may be a risk factor for the eventual outcome, but is not a factor in the origin and aetiology of the disease; AD may be time-related (slow to develop), but is clearly not age-related, in the sense that the aging process causes it.

    3. Hugh Hendrie has shown that African-Americans in Indiana have 3-4 times the risk of getting AD, compared to genetically similar West Africans, so how do the latter manage to get older with much less risk of getting AD, unless they are lucky enough to avoid some dietary or toxic factor that is more common in the USA?

    4. Twin discordance is common in sporadic AD; twins age at the same rate, so how come only one of them is getting AD? The most startling example of this, which triggered my investigations into diet and AD in 1990, was a discordant pair of Scottish twins, one showing plaques and tangles at autopsy, the other being completely clear of AD pathology at autopsy. Both were aging, yet only one got AD. I concluded that diet entered the picture, eventually pinning down refined, vitamin E-deficient food oils as a likely cause.

    There is even suggestive evidence that sporadic AD incidence declines after the age of 90, as does the risk of breast cancer and osteoarthritis; the reason might be that most folks who were going to get these diseases have already developed them before 90, while those who are not exposed to the actual causes live on free of risk. How often do we hear of diabetes and atherosclerosis being age-related, yet there are heaps of 10-20-year-olds with type 2 diabetics in the USA, and plenty of 3-year-olds with yellow-streaked arteries!

    Finally, so-called age-related macular degeneration (AMD) turns out to be mostly due to chronic dietetic deficiency of the macular pigments lutein and zeaxanthin, which are now known to improve vision, despite the person's age.

    View all comments by Robert Peers

  2. DNA Fragmentation Mechanism Involving Oxidative Stress: Relevance to Alzheimer Disease
    While DNA strand breaks are stereotypical of an apoptotic program, their presence in Alzheimer disease (AD) is of such a widespread nature and numerically high scale (Su et al., 1994) that we previously argued that DNA breakage in AD did not define apoptosis and that apoptosis was unlikely to play a major role in the disease (Perry et al., 1998a,b). Supporting this, the cardinal feature of apoptosis, i.e., activation of executioner caspases, is absent in the disease (Raina et al., 2001). Therefore, rather than an apoptotic mechanism, DNA fragmentation in AD is more likely a consequence of oxidative stress (Su et al., 1997). Recently, an intriguing mechanism by which oxidative stress promotes DNA fragmentation was reported in Chemistry and Biology (Prestwich et al., 2005). Specifically, these new studies show that reactive oxygen species convert protein residues into peroxides that cleave DNA via hydrogen abstraction. Since direct oxidation of proteins is known to be an invariant feature of AD (Smith, 1996) and is, like DNA fragmentation, widespread and chronic (Smith et al., 2002), these studies likely have great relevance to the pathogenesis of AD. Moreover, these studies should serve to further emphasize the promiscuous nature of oxidative stress that, in AD, involves damage to all of the major macromolecules of the cell (Casadesus et al., 2004) and is one of the earliest cytopathological changes in disease (Nunomura et al., 2001).

    References:

    Casadesus G, Smith MA, Zhu X, Aliev G, Cash AD, Honda K, Petersen RB, Perry G. Alzheimer disease: evidence for a central pathogenic role of iron-mediated reactive oxygen species. J Alzheimers Dis. 2004 Apr;6(2):165-9. PubMed.

    Nunomura A, Perry G, Aliev G, Hirai K, Takeda A, Balraj EK, Jones PK, Ghanbari H, Wataya T, Shimohama S, Chiba S, Atwood CS, Petersen RB, Smith MA. Oxidative damage is the earliest event in Alzheimer disease. J Neuropathol Exp Neurol. 2001 Aug;60(8):759-67. PubMed.

    Perry G, Nunomura A, Lucassen P, Lassmann H, Smith MA. Apoptosis and Alzheimer's disease. Science. 1998 Nov 13;282(5392):1268-9. PubMed.

    Perry G, Nunomura A, Smith MA. A suicide note from Alzheimer disease neurons?. Nat Med. 1998 Aug;4(8):897-8. PubMed.

    Prestwich EG, Roy MD, Rego J, Kelley SO. Oxidative DNA strand scission induced by peptides. Chem Biol. 2005 Jun;12(6):695-701. PubMed.

    Raina AK, Hochman A, Zhu X, Rottkamp CA, Nunomura A, Siedlak SL, Boux H, Castellani RJ, Perry G, Smith MA. Abortive apoptosis in Alzheimer's disease. Acta Neuropathol. 2001 Apr;101(4):305-10. PubMed.

    Smith MA, Casadesus G, Joseph JA, Perry G. Amyloid-beta and tau serve antioxidant functions in the aging and Alzheimer brain. Free Radic Biol Med. 2002 Nov 1;33(9):1194-9. PubMed.

    Smith MA, Perry G, Richey PL, Sayre LM, Anderson VE, Beal MF, Kowall N. Oxidative damage in Alzheimer's. Nature. 1996 Jul 11;382(6587):120-1. PubMed.

    Su JH, Anderson AJ, Cummings BJ, Cotman CW. Immunohistochemical evidence for apoptosis in Alzheimer's disease. Neuroreport. 1994 Dec 20;5(18):2529-33. PubMed.

    Su JH, Deng G, Cotman CW. Neuronal DNA damage precedes tangle formation and is associated with up-regulation of nitrotyrosine in Alzheimer's disease brain. Brain Res. 1997 Nov 7;774(1-2):193-9. PubMed.

    View all comments by Gemma Casadesus

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References

News Citations

  1. After 40, DNA Damage Accrues in Genes, Hampering Expression
  2. Presenilin-1 Interferes with Protein Folding

Paper Citations

  1. Keller JN, Hanni KB, Markesbery WR. Impaired proteasome function in Alzheimer's disease. J Neurochem. 2000 Jul;75(1):436-9. PubMed.

Further Reading

No Available Further Reading

Primary Papers

  1. Paz Gavilán M, Vela J, Castaño A, Ramos B, del Río JC, Vitorica J, Ruano D. Cellular environment facilitates protein accumulation in aged rat hippocampus. Neurobiol Aging. 2006 Jul;27(7):973-82. PubMed.
  2. Wittenhagen P, Kronborg G, Weis N, Nielsen H, Obel N, Pedersen SS, Eugen-Olsen J. The plasma level of soluble urokinase receptor is elevated in patients with Streptococcus pneumoniae bacteraemia and predicts mortality. Clin Microbiol Infect. 2004 May;10(5):409-15. PubMed.
  3. Prestwich EG, Roy MD, Rego J, Kelley SO. Oxidative DNA strand scission induced by peptides. Chem Biol. 2005 Jun;12(6):695-701. PubMed.

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