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First published online February 27, 2009
Journal of Experimental Biology 212, 785-789 (2009)
Published by The Company of Biologists 2009
doi: 10.1242/jeb.023663
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Ametabolic embryos of Artemia franciscana accumulate DNA damage during prolonged anoxia
Cell Regulation and Signalling Division, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
e-mail: agmclen{at}liv.ac.uk
Accepted 6 January 2009
| Summary |
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Key words: Artemia, anoxia, DNA damage, depurination
| INTRODUCTION |
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One form of molecular damage that would clearly have to be prevented or
repaired before development could properly resume is DNA damage. DNA is known
to undergo a number of spontaneous hydrolytic reactions, including
depurination (and to a lesser extent depyrimidination) and cytosine and
adenine deamination (Lindahl,
1993
). Abasic sites (AP sites, apurinic/apyrimidinic sites) arise
through the hydrolysis of the N-glycosylic linkage between the bases and
sugars in DNA and RNA and are both potentially mutagenic and lethal
(Boiteux and Guillet, 2004
;
Lhomme et al., 1999
;
Yu et al., 2003
). They have
been estimated to occur in mammalian cells at 37°C and pH 7.4 at a rate of
up to 10,000 per cell per generation
(Lindahl and Nyberg, 1972
).
Using data from that paper on the temperature and pH-dependence of DNA
depurination, an empirical rate constant for depurination of
8.4x10–11 s–1 can be estimated for
Artemia DNA at 23°C and pH 6.3, the intracellular pH of anoxic
cysts (Busa et al., 1982
). With
a genome size of 2.9x109 bp
(Rheinsmith et al., 1974
),
this corresponds to 40,000 bases lost per day or 0.25% of the total genomic
code per year if uncorrected. This rises to 0.5% and 2.5% at 28°C and
40°C, respectively, temperatures that could be experienced at least
temporarily by cysts in their natural habitat. In an actively metabolising
cell, AP sites arising spontaneously and by enzymatic removal of damaged bases
are efficiently and continuously repaired by the process of excision repair.
However, this requires energy in the form of ATP for ligation and dNTPs for
base replacement, both of which would be quickly depleted in the absence of
restorative metabolism. Thus, to prevent a catastrophic genetic loss,
Artemia embryos must somehow severely restrict depurination or else
allow AP sites and other hydrolytic damage to accumulate and then rely on
efficient post-anoxia repair. To investigate these alternatives, we have
measured the number of AP sites in DNA purified from anoxic cysts stored at
28°C and 40°C for periods up to 36 weeks and from larvae hatched from
these cysts.
| MATERIALS AND METHODS |
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Calf thymus DNA (Sigma Chemical Co., St Louis, MO, USA) was dissolved in TE buffer (10 mmol l–1 Tris-HCl pH 7.5, 1 mmol l–1 EDTA) and adjusted to 0.8 mg ml–1. It was then dialysed extensively at 4°C against 20 mmol l–1 MES-KOH pH 6.3, 0.15 mol l–1 KCl, 1 mmol l–1 EDTA and sodium azide finally added to 0.1%. Portions (5 ml) were transferred to greased, ground-glass stoppered tubes and bubbled with N2 for 8 h. The tubes were then sealed and incubated as above. Periodically, the tubes were sampled (250 µl) under N2.
Preparation of DNA from Artemia cysts and larvae
A tube of hydrated, anoxic cysts was shaken, allowed to settle and any
floating material removed by aspiration. The remaining cysts were decapsulated
as previously described (McLennan and
Prescott, 1984
) and finally collected by vacuum filtration. Each
tube yielded six 0.5 g portions, which were frozen at –20°C. Each
portion of frozen cysts was transferred to a pre-cooled mortar and liquid
N2 added. After grinding the cysts to a fine powder, 5 ml DNAzol
(Invitrogen, Carlsbad, CA, USA) was added and homogenization continued
briefly. The contents were transferred to a tube, 100 µl proteinase K
(Sigma Chemical Co., 10 mg ml–1 in water) added and the tube
incubated with rolling at room temperature (RT) for 2–3 h.
After centrifugation (13,000 g, 5 min), 2.5 ml of 100% ethanol was added to the supernatant, the mixture shaken gently for 1 min and the DNA (heavily contaminated with orange lipid) removed by spooling into 2.8 ml 10 mmol l–1 Tris base. Once the DNA had dissolved, it was extracted three times with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1 saturated with TE buffer, pH 8.0). 1/10 volume 3 mol l–1 sodium acetate pH 5.2 was added to the final aqueous layer followed by 2.5 volumes of cold 100% ethanol. After gentle mixing, the DNA was allowed to precipitate at –20°C for at least 10 min. The DNA was washed twice in 70% ethanol, once in 100% ethanol, dissolved in 1 ml TE buffer and adjusted to 200 µg ml–1 with TE. The final yield was typically 0.4 mg DNA per 0.5 g portion of hydrated cysts.
To prepare DNA from larvae, anoxic cysts (1.5 g wet mass) were hatched and
the swimming larvae separated from unhatched cysts and other material by
attraction to a light source in a separator box
(Persoone and Sorgeloos,
1972
). After collection by vacuum filtration through a small piece
of cheesecloth, larvae were frozen in liquid N2 and weighed. DNA
was then prepared as described above, with appropriate volume adjustments.
Preparation of depurinated DNA standards
Depurinated calf thymus DNA was prepared as previously described
(Asaeda et al., 1998
;
Mohsin Ali et al., 2004
).
Briefly, RNAase A (Sigma Type II) was added to a 0.8 mg ml–1
solution of calf thymus DNA (Sigma Chemical Co.) in TE buffer to final
concentration of 100 µg ml–1 and incubated for 1 h at
37°C. Existing abasic sites were removed by addition of NaBH4
to 100 mmol l–1 and incubation for 1 h at RT. DNA was then
purified by extracting three times with an equal volume of
phenol:chloroform:isoamyl alcohol (25:24:1 saturated with TE buffer, pH 8.0).
The DNA was dialysed extensively at 4°C against 10 mmol
l–1 sodium citrate pH 5.0, 100 mmol l–1 NaCl
then heated at 70°C for various times up to 90 min. Samples were removed
every 9 min, purified by ethanol precipitation and redissolved in TE buffer at
200 µg ml–1. DNA heated in this way for 9 min contains two
AP sites per 104 bp, etc.
(Lindahl and Nyberg, 1972
;
Mohsin Ali et al., 2004
).
Assay for AP sites
AP sites were assayed using a modification of the aldehyde reactive probe
(ARP) assay previously described (Asaeda et
al., 1998
; Mohsin Ali et al.,
2004
). This assay tags the free aldehyde group of AP sites with
biotin and these are then detected with high sensitivity using
peroxidase-conjugated streptavidin. ARP-DNA samples were prepared from cyst,
anoxic calf thymus and depurinated calf thymus DNA by incubating 50 µl (10
µg) DNA in TE buffer with 50 µl 10 mmol l–1 ARP
(Dojindo, Rockville, MD, USA) for 2 h at 37°C. Unreacted ARP was removed
by sequential dilution and concentration three times using Microcon 30
centrifugal concentrators (Millipore, Watford, UK). The final ARP-DNA was
adjusted to 1 µg ml–1 with TE buffer.
ARP-DNA samples (200 µl) were added to the wells of a protamine-coated
96-well EIA plate (Bio-Rad, Hercules, CA, USA) and incubated at 37°C for
at least 1 h (Asaeda et al.,
1998
). Excess DNA was removed by suction and the wells washed five
times with 350 µl PBS–0.1% Tween (137 mmol l–1 NaCl,
2.7 mmol l–1 KCl, 4.3 mmol l–1
Na2HPO4 7H2O, 1.4 mmol l–1
KH2PO4, 0.1% Tween 20). Wells were blocked with 350
µl SuperBlock buffer (Thermo Fisher, Loughborough, UK) for 30 min at RT,
then this was replaced by 100 µl of a 1:2000 dilution of
streptavidin–peroxidase polymer (Sigma Chemical Co.) in SuperBlock
buffer containing 0.5% Tween. After 30 min at RT, the conjugate was removed
and the wells washed 10 times with 350 µl PBS–0.5% Tween as follows:
4x1 min; 1x5 min; 4x1 min; 1x5 min, followed by one
wash with 350 µl PBS–0.1% Tween.
Peroxidase substrate was freshly made by adding 20 µl of 35 mg ml–1 o-phenylenediamine and 0.5 µl 30% H2O2 per ml of buffer (51 mmol l–1 Na2HPO4, 24 mmol l–1 citric acid). 160 µl of this was added to each well and incubated for 30 min at 28°C with occasional shaking. After adding 40 µl 4 mol l–1 H2SO4, the absorbance was measured at 495 nm.
| RESULTS |
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The % viability of anoxic embryos stored at 28°C (but not 40°C) was
tested by measuring the hatch rate 64 h after reintroduction to oxygenated
seawater. These were found to be 85, 83, 75 and 67% after 0, 8, 20 and 36
weeks anoxia. Although impressive, these rates are considerably lower than
those reported by Clegg for San Francisco Bay cysts, which maintained almost
full hatchability for two years (Clegg,
1997
). However, the cysts were not dried before hatching, which
may improve the hatch by helping to break the anoxia-induced diapause, so the
unhatched cysts may not be dead but still locked in diapause
(Abatzopolous et al., 1994
;
Clegg, 1994
). To find evidence
that accumulated DNA damage is repaired before hatching, the number of AP
sites was measured in samples of cysts and in larvae hatched from cysts stored
under N2 for 30 weeks at 28°C followed by incubation in
oxygenated seawater for up to 72 h. A marked reduction in AP sites per
104 bp from 21.1±4.0 to 9.8±2.0 was observed in cysts
12 h after reoxygenation, with a further reduction to 6.2±2.1 by 24 h,
when 4% of the cysts had hatched (Fig.
3). However, as only 71% of the cysts hatched by 72 h, and this
number did not increase significantly beyond this time, the level of DNA
damage remaining in `24 h' cysts (30% of that in `0 h' cysts) may represent
that specifically in dead and diapause-arrested cysts and so the damage in
viable, hatchable cysts may have been fully repaired by this stage.
Unfortunately, insufficient larvae had hatched by 24 h to test this directly;
however, the level of AP sites per 104 bp present in larvae hatched
after 48 and 72 h was much lower (0.59±0.17 and 0.48±0.07,
respectively) and was comparable with that found in 48 h larvae hatched from
cysts that had not been exposed to anoxia (0.60±0.23 per 104
bp, N=6), indicating that full repair had taken place by 48 h.
|
| DISCUSSION |
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In prokaryotes, DNA-binding proteins such as HU and the ferritin-like Dps
proteins protect the bacterial DNA from radiation and oxidative damage
(Nair and Finkel, 2004
)
whereas small, acid-soluble spore proteins are known to provide protection
against wet heat and to reduce the rate of DNA depurination in Bacillus
subtilis spores by a factor of 20
(Setlow and Setlow, 1994
;
Setlow, 2007
). We have found
no evidence for a similar degree of protection in Artemia despite the
existence of high levels of various diapause-specific proteins and chaperones
in cysts that are believed to impart stress tolerance. The small heat
shock/
-crystallin protein p26 translocates to the nucleus during anoxia
and may stabilize proteins and nucleoprotein structures towards thermal and
oxidative denaturation and aggregation
(Clegg, 2007
;
Clegg et al., 1994
;
Collins and Clegg, 2004
;
Willsie and Clegg, 2001
)
whereas the ferritin homolog, artemin, has also been proposed as a protein and
RNA protectant during diapause and encystment
(Chen et al., 2007
;
Warner et al., 2004
). Small
heat shock proteins, ArHsp21 and ArHsp22 (nuclear)
(Qiu and MacRae, 2008a
;
Qiu and MacRae, 2008b
), and
homologs of the plant anti-aggregation LEA proteins
(Hand et al., 2007
;
Wang et al., 2007
) have also
recently been found in Artemia. However, none of these proteins has
been reported to bind DNA. In Artemia and other eukaryotes, it is
likely that histones are the major protectant from radiation and oxidative
stress by simply acting as local competitors for photon and free radical
attack (Enright et al., 1992
)
but they appear to be of limited value at excluding water from the DNA. By
acting as water replacements and hydrogen bonding to the DNA, trehalose and
glycerol might be expected to reduce hydrolytic base loss and the modest
reduction seen could in part be due to these compounds. However, it appears
that in fully hydrated cysts, this effect is equally limited. The increase in
developmental defects seen in larvae after long periods of anoxia
(Clegg, 1997
) suggests that
unrepaired lesions can have a detrimental effect, probably as a result of
mutagenic transcription during the post-anoxia emergence period.
Dry cysts that have not been exposed to anoxic conditions also display a
delay between rehydration and hatching, typically 16–20 h, known as
pre-emergence development (PED). During this time there is continued
transcription, translation and cellular differentiation but no DNA replication
or cell division (McLean and Warner,
1971
; Tate and Marshall,
1991
). It is possible that hydrolytic DNA damage accumulates
during the period of diapause when the cysts are arrested in a hydrated state
before desiccation and that PED offers the opportunity to repair this before
replication. The more prolonged pre-emergence period displayed by anoxic cysts
would then reflect the increased amount of accumulated molecular damage. We
have previously observed a loss of alkali-labile sites in DNA from normoxic
cysts during PED, which is consistent with the repair of abasic lesions
(Slater and McLennan, 1982
).
Studies are now under way to test this directly.
In conclusion, despite their extensive armory of factors dedicated to the prevention of molecular damage under conditions of extreme physiological stress, Artemia cysts do not appear to have mechanisms beyond those available to all eukaryotes to prevent spontaneous hydrolytic DNA damage. In the dehydrated state, water replacement by trehalose and glycerol will clearly limit this damage but when hydrated, compaction of the DNA into chromatin, which may exclude the possibility of DNA binding by more specific protective proteins, may be the only mechanism available. Therefore, developing embryos must rely on efficient pre-hatching systems to repair this damage before DNA replication can resume.
LIST OF ABBREVIATIONS
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