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DNA repair [was RE: the fountain of youth]

Robert Bradbury rbradbur at hardy.u.washington.edu
Thu May 7 09:23:35 EST 1992

The first copy of this did not appear to reach USENET, apologies to BIONET
people who have seen it already.

In article <1992Apr15.204621.4205 at alw.nih.gov> donnel at helix.nih.gov
> (Donald A. Lehn) writes:
>I've been reading the posts on this subject and would like to pose a
>Why does ageing necessarily have anything to do with DNA damage?  Not
>all of the information content of DNA is contained in the nucleotide

I will quoteth from Arthur Kornberg in the 2nd Ed. of DNA Replication (1992):

  A striking correlation has been noted, in animals from seven species with
  a 20-fold range in life span, between the capacity to repair UV lesions
  (in DNA) and longevity. (1)

  Furthermore, the error frequencies of DNA polymerases alpha and gamma from
  senescent human fibroblasts are significantly greater than those from
  "young" cells. (2)

    To this I would add that in (3), it was found that "Polymerases isolated
    from ad libitum (fed) mice exhibited a greater loss of enzyme fidelity
    with increased age than did polymerase from dietary restricted animals."
     - one more reason for expecting dietary restriction to extend life
  An accumulation of DNA of 8-hydroxyguanine, a guage of oxidative damage,
  increases in some tissues of aged rats (4), possibly due to the loss of
  repair activity.

    I will add that this reference make the interesting observation that
    there are fewer damaged bases in the testes and the brain compared
    to the liver, kidney and intestine and that the estimated numbers
    of oxidative modification to DNA are 10^4 and 10^5 per cell per day
    in humans and rodents respectively.  Does it not make sense that
    nature will protect most the organs with the highest O2 consumption
    (the brain) and the location of the next generation (the testes)?
    Shouldn't lower DNA damage be required in longer lived organisms?

Now, to present a balanced analysis he says:

  Increased deficiencies in replication are not apparent in peripheral
  lymphocytes of older people. (5)
    - Of course not, any cells with severe replication deficiencies
      are no longer in the cell population!  There are lots of studies
      which do show decline in various functions of "older" cells/tissues.

  No difference was detected in excision-repair capacity in three cold-
  blooded vertebrates with life spans ranging from 3 to over 118 years, (6)
  nor were significant correlations between repair capacity and aging
  seen among 34 species in 11 orders of mammals. (7)
    - Both of these studies are 10+ years old and do not have the benefit
      of our better understanding of the evolutionary forces which act
      on species to determine longevity.  I suspect these studies need to
      be corrected for warm vs. cold blood, O2 consumption, fertility and
      environmental stresses which impact on the aging rate to be meaningful.

  Excision-repair capacity also does not differ significantly in UV-irradiated
  human skin cells from newborns and from donors up to 88 years of age. (8)
   - Skin cells are designed to divide many times and be subjected to
     a lot of UV irradiation.  It isn't surprising that they maintain their
     repair capacity.  Again, those cells that don't are not going to be
     around to be tested.

>It may also be likely that ageing is due to a disruption of
>chromatin structure.  Perhaps even with something like when a gene
>is replicated in mitosis.  I think ageing is a far more complex than
>can be described in narrow terms.
Is there any evidence for this?  Chromosomes do get crunched
in tumor cells but I would attribute this to a defective DNA
repair of double strand breaks.  There is certainly some
evidence for decreased speed in turning genes on and off
but you could easily attribute this to "minor" variations
in proteins (such as DNA Pol above) altering the affinity of
histones for DNA or ribosome attraction to and scanning of mRNA.
All of these can be traced back to minor changes to the DNA.

So, one is left with the question of what is the rate of damage
and how does it change.  Ref (9) reviews studies of somatic
mutations in DNA.  It finds the mutation rate in the single base
in hemoglobin responsible for sickle cell anemia is 4 x 10^-8.
Mutations in the hprt locus (44,000 bases) occur at a frequency
4 x 10^-6 (avg).  They also document an increase in this
mutation frequency of 2-5% / year (0.26 x 10^-6).  (A mutation
frequency of 1 x 10^-6 cells means that 1 cell in million has
that gene broken).

Speculation on...  This means by the time you hit 80, your mutation
frequency is 2.2 x 10^-5 in a single gene.  Multiply by 5000 active
genes per cell and you have 1 in 10 cells with a broken gene.
If we assume that hits on hprt are happening at a rate similar to those
on HbS, [doubtful but we are in speculation mode :-)], we can compute
how much of the hprt gene is critical to proper functioning:
    (10^-6 * 44000) / 10^-8 = .2%
Hmmmm, so damaging .2% of a gene makes it non-functional.  Due to the
degenerate code from DNA to proteins and the large portions of proteins
which aren't critical to structure/function you can make a case that a
large fraction of the DNA for a protein can be damaged without harming the
protein.  *However*, someplace between .2% and and a "large fraction" is an
area where you degrade enzyme function without breaking it.  If we say
that 10x the critical active area is important for general functioning
then every cell in the body has a gene suffering a loss of function due
to DNA damage!  Of course this ignores things like varying gene sizes and
hot spots for mutations and lots of other things but it provides a good 
reason to point to DNA damage as being a major portion of the problem in aging.

If the last "speculation" has any basis then it is no surprise that aging
is a "complex" process.  I would argue the *cause* of aging is a "simple"

If anyone has any further data/refs on ratios of protein areas critical
to enzyme functioning vs. velocity please send them to me.

Robert Bradbury					uunet!sftwks!bradbury
1. RW Hart, RB Setlow, 1974, PNAS 71:2169
2. V Murray, R Holliday, 1981, JMB 146:55
   SW Krauss, S Linn, 1982, Biochemistry 21:1002
3. VK Srivastava, RD Tilley, RW Hart, DL Busbee, 1991, Exp Gerontol 26:453
4. CG Fraga, MK Shigenaga, JW Park, P Degan, BN Ames, 1990, PNAS 87:4533
5. SS Agarwal, M Tuffner, LA Loeb, 1978, J Cell Physiol, 96:235
6. AD Woodhead, RB Setlow, E Grist, 1980, Exp Gerontol 15:301
7. H Kato, M Harada, K Tsuchiya, K Moriwaki, 1980, Jpn J Genet 55:99
8. S Liu, PC Hanawalt, personal communciation
9. RJ Albertini, et al, 1990, Ann Rev Genet. 24:305

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