Elucidation of spore-photoproduct formation by isotope labeling

Article abstract of DOI:10.1002/anie.201005228

Doing some damage: Spore photoproduct (SP) is the major DNA photodamage product in bacterial endospores. NMR spectroscopic studies of deuterium-labeled TpT dinucleotides have revealed details of the mechanism for SP formation (see scheme). Upon UV irradia

Full text of DOI:10.1002/anie.201005228

Communications
DOI: 10.1002/anie.201005228
DNA Photochemistry
Elucidation of Spore-Photoproduct Formation by Isotope Labeling**
Gengjie Lin and Lei Li*
UV light is lethal to most microorganisms owing to its
relatively high energy and efficient absorption by biomacro-
molecules. However, bacterial endospores, which are respon-
sible for a number of human diseases, such as anthrax and
tetanus, are extremely resistant to UV radiation. For example,
some Bacillus spores can be 100 times more resistant to UV
light than the corresponding vegetative cells.[1] The highly
unusual UV resistance is due to unique DNA photochemistry
coupled with efficient damage repair in endospores.[2–8]
Scheme 1. Formation of spore photoproduct upon the exposure of
endospore DNA to UV radiation, and subsequent DNA repair by spore
photoproduct lyase.
Progress has been made in the elucidation of the damage-
repair process.[6–9] However, although SP was discovered
nearly half a century ago,[10] and despite the strong interest of
the scientific community in how it is formed,[2,11] little is
known about the mechanism of spore-DNA photochemis-
the CD3 moiety migrated to the 6-position; such a conclusion
was seriously undermined by the incomplete deuterium
incorporation observed, which led Cadet and co-workers to
conclude that the origin of the two C6 hydrogen atoms was
unclear.[12] On the basis of these results, a concerted reaction
mechanism involving the methyl group of one T residue and
try.[12]
Thymine (T) is the most UV-sensitive nucleobase.[12] In
typical cells after photochemical excitation, a T residue can
dimerize with an adjacent T residue to generate cyclobutane
pyrimidine dimers and pyrimidine (6–4) photoproducts. In
contrast, the dominant DNA photoproduct in endospores is a
unique thymine dimer, 5-thyminyl-5,6-dihydrothymine, also
called spore photoproduct or SP.[13] Spores express a specific
enzyme, spore photoproduct lyase (SPL), which effectively
reverses SP-dimer formation at the early germination phase
and thus enables spores to resume their normal life cycle
(Scheme 1).[2,13]
Although two mechanisms were proposed previously to
explain SP formation, neither of them seemed to solve the
problem unambiguously.[2,12] Varghese and Wang suggested
that the SP was formed by a consecutive mechanism through
recombination of a 5-a-thyminyl and a 5,6-dihydrothymin-5-
yl radical;[14,15] however, how these two radicals were gen-
erated was unknown. By employing [D3]thymidine containing
a CD3 moiety, Cadet and co-workers isolated the SP as a
mixture of the 5S and 5R diastereomers after the photo-
reaction. More importantly, two thirds of the generated SP
contained a deuterium atom on carbon atom C6. Although
this finding appeared to suggest that a deuterium atom from
À
the C5 C6 double bond of the other T residue was pro-
posed.[2,12]
Recently, the steric configuration of SP was determined by
using the dinucleotide thymine dinucleoside monophosphate
(TpT) instead of thymidine in a dry-film reaction.[11] The
phosphate linker and the deoxyribose groups in TpT restrict
the relative position of the Tresidues. Consequently, only one
SP TpT species, formed through the addition of the CH3
group of the 3’-T residue to the C5 atom of the 5’-T residue,
was observed by NMR spectroscopy, whereby the newly
formed C5 stereocenter adopted an R configuration.[11] The
SP TpT species generated in this manner exhibited identical
properties to those of the compound obtained by the photo-
irradiation of calf-thymus DNA, followed by enzyme diges-
tion.[6] Furthermore, only the SP with the 5R configuration,
and not the isomer (prepared by chemical synthesis) with the
5S configuration, is repaired by SPL.[16] All these results
suggest that the 5R TpT SP is truly the biologically relevant
species.
Now that the steric configuration of SP has been revealed,
the photoreaction mechanism through which it is generated
remains to be elucidated. In SP, the C6 atom of 5’-T is bonded
to two hydrogen atoms and is prochiral. As the formation of
this prochiral center constitutes a major structural change
during the photoreaction, it should be possible to shed light
on the mechanism by deciphering the origins of these
hydrogen atoms. Although we were puzzled by the observa-
tion of only 60% deuterium incorporation in the study by
Cadet and co-workers, we felt that it was a reasonable
assumption that one H atom is retained from the original 5’-T
residue, whereas the other is derived from the methyl group
of 3’-T during the photochemical formation of SP. To test this
hypothesis, we prepared two deuterium-labeled TpT dinu-
[*] Dr. G. Lin, Prof. Dr. L. Li
Department of Chemistry and Chemical Biology
Indiana University-Purdue University Indianapolis (IUPUI)
402 North Blackford Street, Indianapolis, IN 46202 (USA)
Fax: (+1)317-274-4701
E-mail: lilei@iupui.edu
[**] We thank Prof. Eric Long at IUPUI for helpful discussions, and the
National Institute of Environmental Health Sciences
(R00ES017177) as well as the IUPUI startup fund for financial
support. The NMR and MS facilities are supported by National
Science Foundation MRI grants CHE-0619254 and DBI-0821661,
respectively.
Supporting information for this article is available on the WWW
under http://dx.doi.org/10.1002/anie.201005228.
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Chemie
which suggested that all three deuterium atoms in [D3]TpT
were retained after the photoreaction. Interestingly, a singlet
signal at d = 3.01 ppm was observed in the 1H NMR spectrum
of the obtained SP [D3]TpT (Figure 1b). In contrast, the
synthesized SP TpT exhibited two doublets at d = 3.15 and
3.02 ppm (Figure 1b), which were assigned to the 5’-T 6-Hpro-S
and 6-Hpro-R hydrogen atoms, respectively.[11] It thus appears
that during the photoreaction, a methyl deuterium atom is
transferred to the 5’-T 6-Hpro-S position, whereas the hydrogen
atom from the original 5’-T residue remains at 6-Hpro-R
2
(Scheme 2a). The lack of JH,H coupling at C6 in 5’-T as a
result of the replacement of a hydrogen atom by a deuterium
atom changes the NMR signal from two doublets in SP TpT to
a singlet in SP [D3]TpT.
To further validate the observed hydrogen-atom transfer,
we also prepared a [D4]TpT dinucleotide with all four carbon-
bonded hydrogen atoms in 5’-T replaced with deuterium
atoms (Scheme 2b).[17] In this compound, we incorporated a
Scheme 2. UV irradiation of the isotope-
labeled thymine dinucleotides a) [D3]TpT
and b) [D4]TpT to give the corresponding
SP derivatives.
cleotides and monitored the hydro-
gen-/deuterium-atom transfer after
UV irradiation by 1H NMR spec-
troscopy (500 MHz). The results
showed that
a hydrogen atom
from the methyl group of 3’-T is
transferred intramolecularly to the
C6 atom of 5’-T in SP in a highly
diastereoselective manner. This
result, together with the previous
assignment of the configuration C5
in SP,[11] now enables us to propose
a detailed mechanism for the SP
photoreaction.
We started our investigation
with a selectively labeled [D3]TpT
dinucleotide
containing
a
[D3]methyl group in the 3’-Tresidue
(Scheme 2a).[17] [D3]TpT was dis-
solved in methanol and transferred
to a 10 cm petri dish; solvent eva-
poration yielded a good thin film.[18]
UV irradiation of the film for
45 min produced the labeled SP in
approximately 0.1% yield.[19] After
multiple reactions and HPLC sepa-
ration, 5 mg of the labeled SP TpT
product was obtained from 3.5 g of
[D3]TpT. For structural compari-
son, nonlabeled SP TpT was also
prepared by organic synthesis.[20]
The ESI mass spectrum of the
Figure 1. a) Structure of isolated SP [D4]TpT. b) Zoom-in view of the 1H NMR signals for the 5’-T
6-Hpro-S and 6-Hpro-R hydrogen atoms in SP [D3]TpT, SP [D4]TpT, and SP TpT. c) Zoom-in view of the
ROESY spectra of SP TpT and SP [D4]TpT dissolved in [D6]dimethyl sulfoxide. The signals associated
with 6-Hpro-S are indicated by red arrows; these signals are observed for both SP species. The signals
associated with 6-Hpro-R or CH3 are indicated by black arrows; these signals are not present in the
spectrum for SP [D4]TpT as a result of the deuterium substitution. The interaction between the 5’-T
6-Hpro-S and 3’-T 6-H atoms yields a ROESY signal at d=3.14–7.51 ppm, which is outside the range of
the zoom-in view. The full 1D and 2D NMR spectra for these SP species can be found in the
labeled SP TpT species exhibited an
[M+H]+ signal at m/z 550.2,[17] Supporting Information.
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Communications
deuterium atom at C6 in 5’-T to distinguish the original
hydrogen atom at this position from the transferred hydrogen
atom after the photoreaction. The photoreaction was carried
out by using a [D4]TpT thin film prepared by a similar
procedure to that described above. However, the SP was
formed much faster than for the [D3]TpT system. The
increased reaction rate is probably due to the lack of a
primary kinetic isotope effect (KIE) after the replacement of
CD3 with CH3 in 3’-T. UV irradiation of [D4]TpT for 45 min
afforded the corresponding SP in approximately 0.4% yield.
After multiple reactions and HPLC separation, 18 mg of the
labeled photoproduct was isolated from 1.6 g of [D4]TpT.
ESIMS analysis revealed that the isolated SP TpT product
had again retained all deuterium atoms. Furthermore, the
photoproduct exhibited a singlet signal at d = 3.14 ppm in the
1H NMR spectrum (Figure 1b), wich suggested that a methyl
hydrogen atom had been transferred to the 5’-T 6-Hpro-S
position in the formed SP [D4]TpT (Scheme 2b).
To completely exclude the possibility that the transferred
hydrogen atom comes from trace methanol left in the dry
film, we prepared the film with [D4]methanol and irradiated
the film with UV light. The resulting SP TpT had an [M+H]+
signal at m/z 551.2,[17] which corresponds to the formation of
SP [D4]TpT. This observation confirms that the transferred
hydrogen atom is from the 3’-T CH3 moiety, and not from the
trace solvent in the film.
To further verify the observation that a hydrogen atom is
transferred to the 5’-T 6-Hpro-S position in the photoreaction,
we determined the hydrogen-atom correlations through space
in ROESY experiments for both SP TpT and SP [D4]TpT. In
SP TpT, the 6-Hpro-R atom mainly interacts with 3’A-H and the
CH3 moiety, whereas 6-Hpro-S associates with 2’A-H/2’’A-H,
3’A-H, and 6-H in 3’-T.[11] In contrast, for SP [D4]TpT, the
NMR signals associated with 5’-T 6-Hpro-R and/or CH3
disappear as a result of deuterium substitution, whereas the
signals associated with 6-Hpro-S remain (Figure 1c). These
observations agree with our 1D NMR spectroscopic results
and establish that a hydrogen atom from the methyl group of
3’-T is transferred to the 5’-T 6-Hpro-S position in the photo-
reaction.
Figure 2. ESIMS spectrum of the isolated SP [D3]TpT and SP [D4]TpT
complexes in the negative ionization mode. The ESIMS spectrum
recorded in the positive mode can be found in the Supporting
Information. The [MÀH]À signal at m/z 548.1 corresponds to the SP
[D3]TpT species. The [MÀH]À signal at m/z 549.2 corresponds to a
combination of SP [D4]TpT and the first isotopic peak of SP [D3]TpT,
which is predicted to be 22.4% of the signal intensity of the SP [D3]TpT
species. Subtraction of the isotopic contribution of SP [D3]TpT from
the signal strength of the peak at m/z 549.2 resulted in the contribu-
tion of SP [D4]TpT to the signal intensity. Comparison of this number
with the intensity of the peak at m/z 548.1 yielded the primary isotope
effect of 3.5.
that the MS signal ratio truly represents the kinetic isotope
effect.
These results provide mechanistic insight into the photo-
chemical formation of SP. Thus, in agreement with our
=
observations, UV light first excites the C C bond of 5’-T to
form a pair of radicals (intermediate I; Scheme 3). Abstrac-
tion of a hydrogen atom from the 3’-T methyl group by the C6
radical then leads to the formation of a 5-a-thyminyl and a
5,6-dihydrothymin-5-yl radical (intermediate II). This step is
potentially rate-limiting, as indicated by the observed primary
isotope effect of 3.5 after deuterium substitution at the 3’-T
methyl group. The resulting two radicals subsequently
recombine to yield the final product SP.
The faster photoreaction when [D4]TpT was employed
suggested the likely existence of a primary kinetic isotope
effect (KIE). To determine the KIE, we prepared a film by
using equal amounts of [D3]TpT and [D4]TpT, carried out the
photoreaction, and isolated the SP TpT photoproduct by
HPLC. ESIMS analysis of the obtained SP TpT products
revealed the presence of both D3- and D4-labeled SP TpT
species. The signal intensity of the D4 species was 3.5 Æ 0.3
times as strong as that of the D3-labeled SP in both positive
and negative ion modes (Figure 2).[17] This result suggests a
primary KIE of 3.5 for the photochemical SP formation.
To test whether the detected MS-signal intensities truly
reflected the yields of the SP products, we mixed authentic
samples of SP [D3]TpT and SP [D4]TpT in a 1:3.5 ratio and
injected the mixture into the ESI mass spectrometer. As
expected, the D4 species exhibited a MS signal that was about
3.5 times as strong as that of the D3 species. This observation
excludes the influence of the ionization and ion-detection
processes in the determination of the KIE and demonstrates
Scheme 3. Proposed mechanism for the formation of SP.
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This mechanism accounts for the observed steric config-
uration of the SP molecule. It has been suggested that, to form
SP, the DNA in spores adopts an A-like conformation,[21]
whereby thymine adopts an anti configuration relative to the
deoxyribose moiety.[2,12] This proximity dictates that the
H atom from the 3’-T CH3 group can only be transferred to
the 6-Hpro-S position. Owing to the ultrafast nature of the
photoreaction,[22] the two radicals in intermediate II have no
time to change their relative positions, and 5R remains the
sole configuration after they recombine to form SP.
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[19] This yield is in line with the previously reported yields in
reference [11]. The reason for this seemingly low yield is that
only thymine residues in the “right” conformation at the instant
of excitation dimerize, and the vast majority of excited molecules
are thermally quenched.[11] The dry film further restricts the
thermal motion of TpTand its ability to undergo conformational
changes; thus, only a very small portion of TpT can form SP TpT.
Unreacted TpT (80–90%) was recovered after HPLC separation
and reused for the SP photoreaction.
Although organic radicals are known to undergo H-atom-
abstraction reactions, to the best of our knowledge, it is the
À
first time that the C5 C6 double bond has been observed to
participate in such a reaction in thymine photochemistry. We
tentatively propose that the relative position of the Tresidues
in the dry film or A-form spore DNA facilitates this novel
photochemistry, as it was suggested recently that during
thymine photodimerization, the static TT conformation and
not the conformational motion at the instant of excitation
governs the outcome of the photoreaction.[22] Although our
data appear to support the consecutive mechanism proposed
in Scheme 3, the concerted mechanism suggested by Cadet
and co-workers cannot be ruled out at this point.
The proposed biradical intermediates I and II have not
been observed directly in SP formation; however, their
existence is well-documented in photochemical studies of
DNA: Species I is responsible for the formation of cyclo-
butane pyrimidine dimers (CPDs), and it has been suggested
that SP and CPD share a similar triplet excited state.[3] The
radicals in intermediate II have been generated by UV
irradiation and observed by EPR spectroscopy.[23–25] Further
studies to trap and characterize these radical intermediates in
SP formation in an attempt to confirm the proposed consec-
utive mechanism are in progress.
[20] S. J. Kim, C. Lester, T. P. Begley, J. Org. Chem. 1995, 60, 6256.
[21] K. S. Lee, D. Bumbaca, J. Kosman, P. Setlow, M. J. Jedrzejas,
Proc. Natl. Acad. Sci. USA 2008, 105, 2806.
Received: August 20, 2010
Published online: November 23, 2010
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Crespo-Hernꢀndez, V. N. Swaminathan, T. Carell, W. Zinth, B.
Kohler, Science 2007, 315, 625.
[23] P. S. Pershan, R. G. Shulman, B. J. Wyluda, J. Eisinger, Science
1965, 148, 378.
Keywords: DNA damage · photochemistry ·
reaction mechanisms · spore photoproduct · thymine
.
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