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Acknowledgements
We thank S.O. Freytag for C/EBP
b
cDNA and pWZLhygro plasmid; A.B. Lassar for pBabe-
MyoD plasmid, anti-myogenin, anti-MyoD and anti-MHC antibodies; T.M. Wilson and
S.A. Kliewer for rosiglitazone; G.P. Nolan for Phoenix retrovirus packaging cell lines;
J. Zhang, S. Malik, U. Kim, X. Ren and other members of the laboratory for critical reading
of the manuscript and discussion. This work was supported by the NIH. K.G. was
supported by a postdoctoral fellowship from Charles H. Revson Foundation. A.E.W. was
supported by the Swedish Cancer Society.
Competing interests statement
The authors declare that they have no competing financial interests.
Correspondence and requests for materials should be addressed to R.G.R.
(e-mail: roeder@mail.rockefeller.edu).
..............................................................
Functional relationship of
cytochrome c
6
and plastocyanin
in Arabidopsis
Rajeev Gupta, Zengyong He & Sheng Luan
Department of Plant and Microbial Biology, University of California, Berkeley,
California 94720, USA
.............................................................................................................................................................................
Photosynthetic electron carriers are important in converting
light energy into chemical energy in green plants. Although
protein components in the electron transport chain are largely
conserved among plants, algae and prokaryotes, there is thought
to be a major difference concerning a soluble protein in the
thylakoid lumen. In cyanobacteria and eukaryotic algae, both
plastocyanin and cytochrome c
6
mediate electron transfer from
cytochrome b
6
f complex to photosystem I
1–4
. In contrast, only
plastocyanin has been found to play the same role in higher
plants. It is widely accepted that cytochrome c
6
has been evolu-
tionarily eliminated from higher-plant chloroplasts
5,6
. Here we
report characterization of a cytochrome c
6
-like protein from
Arabidopsis (referred to as Atc6). Atc6 is a functional cytochrome
c localized in the thylakoid lumen. Electron transport reconstruc-
tion assay showed that Atc6 replaced plastocyanin in the photo-
synthetic electron transport process. Genetic analysis demon-
strated that neither plastocyanin nor Atc6 was absolutely
essential for Arabidopsis growth and development. However,
plants lacking both plastocyanin and Atc6 did not survive.
The protein cytochrome c
6
(cyt c
6
) was identified from algae
more than four decades ago
7
. However, a higher-plant cyt c
6
has
never been found, contributing to the dogma that the copper
protein plastocyanin is the only electron donor to photosystem I
in higher plants
8
. We identified an Arabidopsis cyt c
6
-like protein
during a yeast two-hybrid screening experiment searching for
interacting partners of a chloroplast immunophilin protein. One
of the putative interacting clones showed sequence homology to cyt
c
6
from cyanobacteria and algae. Southern blot analysis indicated
that the complementary DNA came from the Arabidopsis genome
(data not shown). More recently, the Arabidopsis genomic sequence
database also showed a single copy of a gene that corresponds to the
sequence of our cDNA. Figure 1 presents the cDNA-deduced
amino-acid sequence and its alignment with cyt c
6
proteins from
cyanobacteria and algae. Although the overall sequence homology is
low (20–30% identical between Atc6 and other cyt c
6
proteins), the
amino-acid residues for haem-binding are completely conserved.
These residues are located in the same relative positions in the Atc6
protein, suggesting that Atc6 may be assembled with a haem group,
like other c-type cytochromes (Fig. 1a). Further database searches
identified several expressed sequence tags (ESTs) that encode highly
similar proteins from other higher plants including soybean, maize
and rice (Fig. 1b). Clearly, genes coding for cyt c
6
-like proteins are
universally present in higher plants. Identification of ESTs in various
plant species and isolation of Atc6 cDNA indicate that genes coding
for cyt c
6
are not pseudogenes but are expressed in these plants. We
noted an interesting insertion of 12 amino acids in the Atc6
sequence (and other higher-plant sequences) as compared to cyt
c
6
proteins from cyanobacteria and algae. This insert contains two
cysteine residues that may regulate the function of the protein.
The cDNA-deduced peptide sequence of Atc6 contains a long
stretch of amino acids at the amino terminus of the protein that
does not align with cyt c
6
proteins from cyanobacteria or algae (Fig.
1a and b). This N-terminal extension may serve as a signal peptide
for targeting to a specific subcellular compartment in plant cells.
Because cyt c
6
in eukaryotic algae is located in the thylakoid lumen
of the chloroplasts, we tested the possibility of Atc6 being located in
the thylakoid lumen of chloroplasts in Arabidopsis plants. Almost all
genes coding for chloroplast proteins are expressed in a green-
tissue-specific manner
9
. To determine whether Atc6 gene expression
follows this pattern, we isolated total RNA from leaves and roots and
analysed the Atc6 messenger RNA levels by northern blot. Figure 2a
indicates that Atc6 transcript accumulated in leaves but was not
detectable in the roots. We produced recombinant Atc6 protein in
Escherichia coli as a glutathione S-transferase fusion protein, and
used it as antigen to raise antibody in a rabbit. Using a purified
antibody, we performed western blot analysis of the Atc6 protein in
Arabidopsis plants. Figure 2a shows that Atc6 protein, like its
mRNA, was produced in leaves but little was detected in the roots.
To facilitate further biochemical studies of Atc6, we overex-
pressed Atc6 precursor protein under the control of a constitutive
promoter in transgenic plants. Atc6 expression was examined at
both mRNA and protein level (Fig. 2b). Interestingly, Atc6 mRNA
accumulated at high levels in both roots and leaves, but the Atc6
protein was only produced in the leaves. This finding suggests that
Atc6 mRNA was not translated, or that the protein was degraded in
the roots. Moreover, Atc6 protein in the leaves of both wild-type and
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transgenic plants was processed into a smaller form (relative
molecular mass 11,000, M
r
11K) as compared to the cDNA-
deduced protein (19K), suggesting that Atc6 protein was processed
after translation and possible translocation. Post-translational pro-
cessing and leaf-specific accumulation of Atc6 suggest that this
protein may be located in the chloroplast. We purified chloroplasts
from both wild-type and cyt c
6
-overexpressing plants and further
fractionated chloroplasts into stromal and thylakoid lumen frac-
tions. Western blot analysis showed that Atc6 protein, like plasto-
cyanin, is located in the thylakoid lumen of both wild-type (not
shown) and cyt c
6
-overexpressing plants (Fig. 2c).
On the basis of the amino-acid sequence (Fig. 1), Atc6 protein
contains the putative haem-binding residues in the conserved
positions. To confirm that Atc6 is a functional c-type cytochrome,
we expressed Atc6 protein in Synechocystis sp. PCC 6803 cells
lacking the endogenous gene coding for cyt c
6
and examined the
recombinant protein by haem stain and absorption spectrum
analyses. As described in Methods, we constructed a plasmid that
targeted the endogenous cyt c
6
gene in Synechocystis and replaced it
with Atc6 cDNA using homologous recombination
10
. After confir-
mation of the gene replacement using Southern blot analysis (data
not shown), we cultured the transformant and the wild-type cells
Figure 2 Expression pattern and subcellular localization of Atc6 in Arabidopsis. Wild-type
Arabidopsis (a) or transgenic plants overproducing Atc6 (b) accumulated Atc6 mRNA
(middle panel) and protein (bottom panel). Upper panels in a and b show ribosomal RNA as
a loading control. L, leaves; R, roots. c, Localization of Atc6 and plastocyanin. 1, 2,
Coomassie-blue-stained proteins from stromal and lumen fraction; 3, 4, a western blot
probed with Atc6 antibody against the same proteins as in 1, 2; 5, 6, a western blot
probed by a plastocyanin antibody against the same proteins as 3 and 4. The numbers on
the left in c indicate relative molecular mass.
Figure 3 Atc6 is a functional cytochrome c. a, Haem and antibody stain of Synechocystis
cyt c
6
(Syc6) and Atc6 using Atc6 antibody. b, Light absorption analysis of Syc6 and Atc6.
For the reduced absorption spectrum, Syc6 and Atc6 was suspended in 50 mM sodium
phosphate (pH 7.2) and 100 mM sodium chloride, oxidized by 1.5 mM ferricyanide, and
subsequently reduced by 5 mM ascorbate. Reduced minus oxidized absorption spectra of
Synechocystis cyt c
6
and Atc6 are presented in the inset. In both figures, thick and thin
lines present Atc6 and Synechocystis cyt c
6
absorption spectrum, respectively.
V
Figure 1 Sequence analyses of Atc6 and other cyt c
6
proteins. a, Amino-acid sequence
alignment of Atc6 and cyt c
6
proteins from yellow-green alga (Bf; Bumilleriopsis
filiformis), green alga (Cr; Chlamydomonas reinhardtii) and cyanobacteria (Ss;
Synechococcus sp. PCC 7942). The haem-binding residues are noted by asterisks.
b, Amino-acid sequence alignment of Atc6 and putative proteins encoded by ESTs from
soybean (Gm), maize (Zm) and rice (Os). The vertical arrow in a indicates the putative start
of mature Atc6 protein. Shaded areas in a and b are identical amino-acid residues, and
dashes represent gaps introduced to optimize alignments.
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under copper-deficient conditions and purified wild-type cyt c
6
and
Atc6 protein from the cultures. A haem stain assay indicated that
both Synechocystis cyt c
6
and Atc6 proteins are assembled into
haem-bound forms (Fig. 3a). In a parallel western blot analysis,
Synechocystis cyt c
6
was not recognized by the Atc6 antibody,
consistent with a low sequence similarity between the two proteins.
Visible spectral analysis further demonstrated that Atc6 had an
absorption spectrum similar to the Synechocystis cyt c
6
protein (Fig.
3b). The visible absorption spectrum of purified Atc6 in its reduced
form exhibited the characteristic absorbency maximum at 553 nm
(
a
), 522 nm (
b
) and 416 nm (
d
or Soret band). The difference
spectra (reduced minus oxidized) of Atc6 and Sync6 are also
qualitatively identical (Fig. 3b).
A hallmark of cyt c
6
function in cyanobacteria and eukaryotic
algae is to replace plastocyanin in the photosynthetic electron
transfer process. To determine whether Atc6 retains the function
of a typical cyt c
6
protein, we tested its electron transport property
in an oxygen evolution reconstruction assay. As previously demon-
strated
11
, intact chloroplasts or thylakoids are capable of light-
dependent oxygen evolution in the presence of a terminal electron
acceptor. If inside-out vesicles of thylakoid membrane are used,
however, oxygen production is drastically reduced because such
preparations largely lack plastocyanin, the lumen electron carrier
that is lost during preparation. Addition of plastocyanin or an
equivalent electron carrier to the inside-out vesicles restores oxygen
evolution
12
. We prepared inside-out thylakoid vesicles and used this
preparation to test the function of Atc6. As shown in Table 1, intact
thylakoids evolved oxygen at high rates as expected. Inside-out
vesicles produced much less oxygen (19% of the intact thylakoids).
When recombinant Arabidopsis plastocyanin (AtPC), Synechocystis
plastocyanin, Synechocystis cyt c
6
, or Atc6 protein was added to the
preparation, oxygen evolution was restored to 89%, 72%, 73% and
74% of the level in the sample containing intact thylakoids. This
result demonstrated that Atc6 protein functionally replaces plasto-
cyanin in the photosynthetic electron transport, as a typical cyt c
6
protein does in cyanobacteria and algae. Together with the fact that
Atc6 protein is located in the thylakoid lumen, these results strongly
suggest that Atc6 functions along with plastocyanin in photosyn-
thetic electron transport.
To further determine the physiological function of Atc6 and its
relationship with plastocyanin, we used a reverse genetics method to
disrupt the function of Atc6. We identified a T-DNA insertional
allele of Atc6 gene from a collection of Agrobacterium tumefaciens-
DNA-transformed Arabidopsis lines (Fig. 4a). The Agrobacterium
T-DNAwas inserted in the second exon of the Atc6 gene, causing the
disruption of the coding sequence at a position corresponding to
amino acid residue V59 (Fig. 4a). As a result, the knockout mutant
plants did not express Atc6 mRNA or protein (Fig. 4b). The
homozygous Atc6 mutant plants did not show visible phenotypic
changes during their life cycle (Fig. 4e and f), which was expected if
Atc6 and plastocyanin are functionally equivalent. It became clear
that one must examine the function of Atc6 in the plastocyanin-null
background, which presented a technical challenge. Plants with
plastocyanin-null genetic background have not been generated
previously in Arabidopsis (or any other plant species). Therefore,
it is not known whether plastocyanin is essential for plant growth
and development despite the extensive biochemical and biophysical
studies on the function of plastocyanin in the electron transfer
process. Without a plastocyanin mutant, it prevented genetic
crosses between Atc6 mutant and plastocyanin-null plants.
Although it is theoretically possible to remove functional plasto-
cyanin from plants by copper starvation
4
, it has not been demon-
strated in higher plants. Nevertheless, we grew the wild-type and
Atc6 mutant plants in a liquid medium without copper, and
monitored the loss of plastocyanin protein and phenotypic changes.
Western blot analysis showed that our procedure reduced the
level of plastocyanin protein by 50–60% in both the wild-type and
the Atc6 mutant plants during a two-week culture (data not shown).
Reduction in plastocyanin protein abundance did not cause signifi-
cant phenotypic changes in either wild-type or Atc6 mutant (data
not shown). In addition, reduction in plastocyanin under copper-
deficient conditions did not alter the level of Atc6 protein in wild-
type plants, suggesting that Atc6 expression is not regulated by
plastocyanin abundance in plants as it is in cyanobacteria and
algae. Prolonged culture under copper-deficient condition caused
Table 1 Atc6 replaces plastocyanin in the O
2
evolution assay
Assay conditions
O
2
evolution
(
m
mol per mg chl) Percentage
.............................................................................................................................................................................
Thylakoids Buffer 228.25 ^ 23 100 (control)
Inside-out vesicles Buffer 44.5 ^ 10 19
Sync6 166.75 ^ 22 73
Atc6 169 ^ 16 74
SynPC 165.87 ^ 15 72
AtPC 202 ^ 11 89
.............................................................................................................................................................................
Sync6, Synechocystis cyt c
6
;SynPC,Synechocystis plastocyanin; AtPC, Arabidopsis
plastocyanin.
Figure 4 Genetic analysis of plastocyanin and Atc6 in Arabidopsis. a, T-DNA insertional
allele of the Atc6 gene. Black boxes and lines indicate exons and introns, respectively. The
size of T-DNA is not drawn to scale. b, Atc6 mRNA and protein in wild-type (WT) and
mutant (KO) plants. The rRNA was shown as a loading control for mRNA blot. c, PC1/PC2-
RNAi construct. Arrows indicate the 5
0
! 3
0
direction. Transcription cassette contains
partial plastocyanin cDNAs (PC1 and PC2), partial GUS gene (GUS), CaMV 35S promoter
(35S), and nopaline synthetase terminator (NOS). d, Western blot analysis of wild-type (1,
ecotype WS), Atc6 knockout mutant in WS background (2); PC1/PC2-RNAi construct in
WS background (3), and PC1/PC2-RNAi construct in Atc6 mutant background (4).
e, Phenotype of wild-type (1), Atc6 mutant (2), and wild-type background without
plastocyanin protein (3). f, Statistical analysis of plant height of three independent
transgenic lines (10 plants in each) in the same genetic background as in e. Shown as
100% of wild-type control. The error bars indicate the standard deviation in each sample.
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bleaching and death of plants, consistent with the understanding
that copper is an essential microelement for plant growth. However,
it is not possible to determine whether plant death was a result of
plastocyanin depletion or a defect in other copper-dependent
processes.
We examined the functional relationship of Atc6 and plastocya-
nin by genetically silencing plastocyanin expression in the wild-type
and Atc6-null genetic background. The Arabidopsis genome con-
tains two genes coding for plastocyanin (PC1 and PC2, Genbank
accession numbers P11490 and CAB66894) that are highly homo-
logous to each other at protein level. To disrupt the function of
plastocyanin, we must silence both genes. We achieved this goal by
the RNA interference (RNAi) approach that has been used to silence
genes in both animals and plants
13,14
. The RNAi construct contained
the separate inverted repeats of PC1 and PC2 partial cDNA
sequences with a partial
b
-glucuronidase (GUS) gene as a spacer
in between these repeats (Fig. 4c). The expression of PC1 and PC2
RNAi products was driven by a separate CaMV 35S promoter that is
highly active in most plant tissues including photosynthetic cells
15
.
This construct (named as ‘PC1/PC2-RNAi’) was introduced into
both the wild-type (WS ecotype) and the Atc6 mutant to produce
transgenic plants. The transgenic wild-type plants with PC1/PC2-
RNAi construct produced normal level of Atc6 protein, but plasto-
cyanin was not detectable by western blot analysis (Fig. 4d). The
transgenic plants expressing the RNAi construct in the Atc6 mutant
background did not express detectable levels of plastocyanin or Atc6
(Fig. 4d). Transgenic plants without detectable plastocyanin protein
were significantly smaller than wild-type plants (Fig. 4e, f). Trans-
genic plants lacking both plastocyanin and Atc6 protein (20
independent lines) did not survive under the same growth con-
dition (not shown). These plants died soon after transfer from the
agar plate to the soil. These results from genetic analyses demon-
strated that neither plastocyanin nor Atc6 is absolutely essential for
plant growth and development. While plastocyanin completely
complemented the Atc6 mutant, Atc6 partially replaces plastocyanin
under normal growth conditions. Our results also defined another
critical difference between higher plants and algae in the regulation
of Atc6 expression. The cyt c
6
protein is expressed in algae and
cyanobacteria only if plastocyanin is depleted under copper
deficiency conditions
4
. In higher plants, Atc6 protein is constitu-
tively expressed and is not regulated by plastocyanin abundance.
We have identified a functional cyt c
6
from a higher plant.
Sequence search results indicated that other plants such as soybean,
maize and rice express a similar gene, suggesting that all higher plants
possess cyt c
6
that is located in the thylakoid lumen. Biochemical and
genetic analyses demonstrated the functional relationship of Atc6
and plastocyanin in Arabidopsis. This study has added an ancient
protein to the list of electron carriers in higher plants, and provided
evidence against the accepted view of electron transport in higher
plants versus eukaryotic algae and cyanobacteria. A
Methods
Molecular cloning, transgenic plant, and genetics procedures
The Atc6 cDNAwas cloned by a yeast two-hybrid screening for interactors of a chloroplast
immunophilin protein. The Arabidopsis ACT cDNA expression library CD4-22 (ref. 16)
was screened essentially as described in ref. 17. For northern blot analysis, Arabidopsis
plants (ecotype Columbia) were grown in a greenhouse under long-day conditions to
flowering stage. Different organs were gathered and total RNA was isolated and analysed as
described
18
.
To identify a T-DNA insertional allele in the Atc6 gene, we screened 62,000 T-DNA-
transformed Arabidopsis lines using polymerase chain reaction (PCR) as previously
described
19
. The homozygous knockout plants were analysed for Atc6 mRNA and protein
levels, and were used for further genetic analyses. To produce transgenic plants
overexpressing Atc6, the coding sequence of Atc6 precursor was cloned in sense
orientation following a constitutive promoter in the binary vector pATC940
20
. To disrupt
the function of both PC1 and PC2 genes, we used the RNAi approach previously
described
14
with a modification to silence both genes with one construct. The ‘PC1/PC2-
RNAi’ construct as shown in Fig. 4c was transferred into Agrobacterium tumefaciens
GV3101pMP9 strain for Arabidopsis transformation. Arabidopsis plants (ecotype
Columbia or WS or Atc6 mutant) were transformed by the ‘floral dip’ method
21
.
To produce Atc6 antibody, the mature form of Atc6 was expressed in E. coli as a
glutathione S-transferase (GST) fusion protein that was used as antigen to immunize
rabbit. The Atc6 antibody was purified by an affinity purification method
22
. For western
blot analysis, total protein was extracted from plants, separated by SDS–polyacrylamide
gel electrophoresis (SDS–PAGE), and transferred onto nitrocellulose membrane for
antibody probing. The amount of bound antibody was detected by the ECL system
(Amersham).
For protein localization assay, chloroplasts were isolated from protoplasts according to
a previous method
23
with modifications. Protoplast suspension was passed through
15-
m
m nylon net to release chloroplasts. Chloroplasts were lysed on ice in a hypotonic
solution. The thylakoids were sonicated to release the lumen contents, and centrifuged to
separate the membrane and the soluble fraction. The stromal and lumenal fraction was
analysed by western blot to determine the distribution of plastocyanin and Atc6 proteins
in the two fractions.
Cyanobacterial genetics and biochemical procedures
Wild-type Synechocystis sp. PCC 6803 strain was obtained from A. Glazer and grown in
BG-11 medium
24
at 30 8C. Transformation of Synechocystis sp. PCC 6803 strains and
mutant selection was carried out according to ref. 10. The mutant segregation was
followed by PCR and confirmed by Southern hybridization. The genomic sequence
information was obtained from CyanoBase (http://www.kazusa.or.jp/cyano).
To express Arabidopsis cyt c
6
(Atc6) and plastocyanin (AtPC) in Synechocystis sp. PCC
6803, the petJ and petE gene encoding Synechocystis cyt c
6
(SynC6) and plastocyanin
(SynPC) was deleted and replaced by petJ and petE from Arabidopsis. To delete the petE
gene from Synechocystis sp. PCC 6803, a 4-kilobase genomic fragment containing the
0.5-kb petE coding region and 1.75 kb upstream and downstream sequences was amplified
by PCR and cloned into pUC119. The coding region for the mature protein was deleted by
PCR using the QuikChange site-directed mutagenesis kit (Stratagene) and replaced by the
kanamycin-resistance cassette from pUC4k (Pharmacia) and used to transform wild-type
Synechocystis sp. PCC 6803. Kanamycin-resistant transformants were segregated to
produce petE mutant. A similar strategy was used to create the petJ mutant. The
Synechocystis strains lacking petE and petJ, respectively, were transformed by plasmids
containing Arabidopsis plastocyanin and cyt c
6
cDNA. These two plasmids were
constructed by fusing the cDNA fragment encoding the mature region of AtPC or Atc6 to
the genomic sequence for leader peptide of Synechocystis sp. PCC 6803 petE and petJ gene.
The chlorophenicol-resistance cassette from pACYC184 was inserted downstream of the
stop codon. Transformants were selected on medium containing chlorophenicol and
segregated to homogeneity.
Wild-type Synechocystis sp. PCC 6803 strain was used to purify SynPC and SynC6
protein. The mutant strains expressing AtPC and Atc6 (as described above) were used to
purify Arabidopsis proteins. All strains were grown in BG-11 medium with (for
plastocyanin) or without (for cyt c
6
) copper according to previously described
procedures
25,26
. Purified Atc6 was confirmed by western blot, haem stain, and spectrum
analysis. The identity and purity of plastocyanin protein was verified by SDS–PAGE and
western blot. Haem-dependent peroxidase activity was determined by a procedure
described elsewhere
27
.
Inside-out thylakoid vesicles were prepared from spinach using a previously reported
method
11
. Whole chain electron transport from water to methyl viologen was followed at
25 8C using a Clark-type oxygen electrode. The assay medium contains 20 mM MES, pH
6.5, 100 mM sucrose, 5 mM KCl, 5 mM MgCl
2
, 0.1 mM methyl viologen, and intact
thylakoids or inside-out vesicles corresponding to 50 mg chlorophyll in a total volume of
2 ml. Where indicated, plastocyanin or cyt c
6
was added to the reactions to a final
concentration of 1.5 mM.
Received 11 January; accepted 25 March 2002.
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Acknowledgements
We thank R. Malkin, J. Gray and S. Merchant for discussions. This work was supported by
the National Institutes of Health and the US Department of Energy (S.L.).
Competing interests statement
The authors declare that they have no competing financial interests.
Correspondence and requests for materials should be addressed to S.L.
(e-mail: sluan@nature.berkeley.edu). The Atc6 cDNA sequence has been deposited at GenBank
under accession number AJ438488.
..............................................................
corrigendum
Isochorismate synthase is required
to synthesize salicylic acid for plant
defence
Mary C. Wildermuth, Julia Dewdney, Gang Wu & Frederick M. Ausubel
Nature 414, 562–565 (2001).
.............................................................................................................................................................................
In this Letter, the GenBank accession number for the sequence of
ICS1 cDNA was given incorrectly as AY056500. It should be
AY056055. A
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