Gene, 172 (1996) 25-31 0 1996 Elsevier Science B.V. All rights reserved.
GENE
25
037%1119/96/$15.00
09774
Heterodimerization between two classes of homeodomain proteins in the mushroom Coprinus cinereus brings together potential DNA-binding and activation domains (Transcriptional
activation;
transcriptional
Rachel N. Asante-Owusua,*, Lorna A. Casseltona
repression)
Alison H. Banhama,*
,
Heidi U. Biihnert”,
E. Jane C. Mellorb and
“Department ofPlant Sciences, University of Oxford, Oxford OX1 3RB, UK; and bMicrohiology Oxford OX1 3QU, UK. Tel. (44-1865) 175109
Unit, Department of Biochemistry,
Received by J.R. Kinghorn:
1995; Received at publishers:
20 November
1995; Revised/Accepted:
19 December/24
December
University of Oxford,
22 February
1996
SUMMARY
The A mating type-genes of the mushroom, Coprinus cineveus, encode two classes of homeodomain-containing distinguished as HDl and HD2 on the basis of conserved, but distinctly different motifs. Compatible mating
proteins partners
bring together versions of the proteins that can heterodimerize, thereby generating an active transcription factor complex that commits mated cells to sexual development. We have previously described a rare mutation in which an HD2::HDI gene fusion generates a ‘fused dimer’ lacking much of HDl including the homeodomain yet capable of constitutively promoting development [Kties et al., EMBO J. 13 (1994b) 4054440591. Here, we exploit this mutation to help identify contributions made by each protein class to normal heterodimer function. We show that the HD2 homeodomain is essential; deletion within the HDl homeodomain can be tolerated in a normal heterodimer, as well as in the mutant fusion protein, but not substitution of a critical amino acid. We define, by deletion analysis, an essential C-terminal region of the HDl and demonstrate its potential activation function by the ability to activate transcription in yeast when fused to the GAL4 DNA-binding domain. We also identify a potential role in transcriptional repression for the predicted C-terminal helix of HDl proteins.
INTRODUCTION
Mating in the basidiomycete fungus Coprinus cinereus (Cc) triggers early steps in sexual development. Provided mates have different alleles of genes at the A and B mating-type loci, somatic cell fusion is sufficient to convert the asexual monokaryon with uninucleate cells into
Correspondence to: Dr. L.A. Casselton, Department of Plant South Parks Road, Oxford OX1 3RB, UK. Tel. (+44-1865) Fax (+44-1865) 275074; e-mail:
[email protected] * Equal first authors.
Sciences, 275109;
Abbreviations: aa, amino acid(s); bp, base pair(s); BGal, p-galactosidase (product of lacZ); Cc, Coprinus cinereus; GAL4, SC galactose regulatory PII SO378-1119(96)00177-1
a binucleate-celled dikaryon on which mushroom fruit bodies develop. A characteristic feature of the dikaryon is the formation of structures known as clamp connections which play an essential role in maintaining the binucleate condition of the cells. Both sets of genes play a role in forming these structures; different A genes promote clamp cell formation and different B genes
gene encoding Gal4 regulatory protein; kb, kilobase or 1000 bp; Hd, homeodomain (s); HD, Hd-containing protein; HD, gene (DNA, RNA) encoding HD; NLS, nuclear localization signal(s); ::, novel junction (fusion or insertion); nt, nucleotide(s); PCR, polymerase chain reaction; SC, Saccharomyces cerevisiae; Urn, U&ago maydis; XGal, 5-bromo-4chloro-3-indoyl-p-D-galactopyranoside.
26 their
fusion
to the adjacent
cell (Swiezynski
1960). The A locus of Cc, the subject several
genes that encode
1
of this report,
two classes
tran-
(Kties et al., 1992; 1994a). In the simpler b locus of the hemibasidiomycete fungus
Ustilago maydis (Urn) there are just two genes encoding analogous proteins of each class (Gill&en These basidiomycete fungi have multiple There
are some 33 versions
estimated mediated
et al., 1992). mating-types.
of the Urn b locus
classes, plays an essential role in self nonself recognition. A compatible mating brings together different allelic forms of HDl and HD2 proteins and in both Cc and (Banham et al., proteins encoded
that these can form heterodimers
1995; Kamper et al., 1995) whereas by genes within the same locus, and
there may be as many as five in Cc, are unable to heterodimerize. We have described a mutation in the A6 locus of Cc that has generated a chimeric gene, part HD2 and part HDI, that can be translated into a ‘fused dimer’ which constitutively promotes A-regulated development in the absence of any other A protein (Kties et al., 1994b). The chimeric protein no longer needs to recognise a compatible dimerization partner, and by deleting the 5’ end of the fusion gene, we showed that the discriminating N-terminal dimerization domain is not essential for heterodimer regulation of clamp cell development (Banham et al., 1995). The integrity of the fused dimeric complex is, however, showing that heterodimerization plays other critical roles in regulating the activity of the HDl and HD2 proteins. In this report we investigate some of the contributions made by each protein class to the function of the heterodimer.
RESULTS
N
::
II
/
1
632
/
HO2
\
,,,/
_ 'N ’N
l,,,,,
VAWrnEl 1
A6m
,,,,,,,,,, I ,,,,,,
:::
11,
A6md4
A6md5
A6md6
I
:::
1
597
381 ,,,, ,,,,,, ,,,,,,,,, ,, ,,l l,, l,,
MwDsr
1
N N
1
I
687
and an
160 of the Cc A locus. Heterodimerization via an N-terminal domain in both protein
Urn, it has been shown
520
\
contains
of putative
scription factors distinguished as HDl and HD2 on the basis of conserved but distinctly different homeodomain (Hd) motifs mating-type
N
HOI
HOZ
and Day,
AND DISCUSSION
Several of the A mating-type Cc genes have been sequenced and whilst different versions of the proteins have as little as 55% aa sequence similarity, the overall predicted structures are very conserved (Kties et al., 1994a). Fig. 1 illustrates the essential domains of each protein class, the derivation of the constitutive fusion protein and several deletions that we have generated by engineering the fusion gene. We will describe the effects of these deletions on A-regulated development following transformation of these constructs into suitable host strains.
?~a-hel,cal ?
regmns
OSer
(S), Thr CT), Pro (P) enrlched
Hod
? S,T,P ?
enriched.
posltlvely
charged
N NLS
fl S.T.P
ennched,
negatively
charged
1
Fig. 1. Predicted structural features of the HD2 and HDI A mating type proteins of Coprinus cinereus (Cc) and the constitutive fusion proteins generated
by gene fusion and engineering.
aa are numbered
from
the N terminus. The fusion gene, A6m, in pWFR1 (Kties et al., 1994b) was deleted internally using naturally occurring restriction sites, StuI in the HD2 sequence
derived from d-1
and either BglII or AsuII in the
HDl sequence derived from dl-1 to generate proteins A6md4 and A6md5, respectively. The C-terminal 94 aa of A6m were removed to generate A42mdl
protein A6md6 by digesting the genomic is encoded by an artificially generated
sequence with PstI. fusion between the
HDZgene (G-1 and the HD1 gene hl-1 which occurs in the A42 locus. The point of fusion in the naturally occurring mutant was reproduced exactly because hl-1 and dl-1 have a conserved sequence in this region. ~2-1 and hl-I were first fused using available restriction sites, and reverse PCR then used to delete the requisite number of bp to make the correct fusion point. pAMT2 (Tymon et al., 1992) was used to provide the hl-I sequence because this contains a truncated gene encoding a protein lacking the C-terminal 38 aa. Plasmids containing the genes encoding the proteins illustrated were introduced into Cc strain LT2 (A6B6 trp-l.l.l.6) by co-transformation with pCclOO1 which contains the Cc ~rp-I + gene. pFGC5, containing the a?-l:bJ-l fusion was tested in an A42 host (LN118, A42B42 trp-1.1,1.6) which represented the exact self background in which the self-compatible phenotype could be monitored. At least 50 tvp’ transformants were isolated from each experiment and screened microscopically for the presence ofclamp ceils. Media for Cc were those described by Mutasa et al. (1990). The transformation (1989).
procedure
was based on Casselton
and de la Fuente
Herce
(a) The HD2 but not the HDl homeodomain (Hd) is essential for dimer function The most striking feature of the fusion protein is that it has retained only the Hd of the HD2 as its potential DNA binding domain. This prompts the question of whether only a single Hd is necessary for the function of the heterodimer formed by individual HDl and HD2 proteins, and if so, whether the HDl and HD2 Hd are equally effective. The Hd comprises three M helices, the second two of which adopt a helix-turn-helix (HTH) structure (Kissinger et al., 1990; Wolberger et al., 1991). Crystal structures show that most of the invariant aa which are critical for making contacts with the major groove of
27 DNA
helix.
one of the resident
genes leads to A-regulated
The Cc HD2 has a typical Hd with the conserved WFXNXR residues in the recognition helix whereas the
ment; the formation
of unfused
HDl
occur
in helix
3, the so-called
Hd is classified as atypical
recognition
with WFXDXR
(Btirglin,
1994) (Fig. 2). The Trp residue (W) is the first invariant aa of the recognition helix and is situated at the hydrophobic
core where,
although
it does not make
with DNA, it plays a critical
stabilizing
contact
role in determin-
ing how helix 1 packs against helix 3. Using site directed mutagenesis we changed the conserved Trp residue in both
Hd to Ala (A). We also used PCR
to delete 9 aa
from the recognition helix of the HDl Hd and 8 aa from the HD2 Hd. The latter deletion was introduced into the protein
that contributes
fusion protein. the mutated
the single Hd of the constitutive
By replacing sequence
the normal
gene sequence
into
a
we were able to test the effect of
between
the proteins
suitable
host.
encoded
Heterodimerization
by the introduced
gene and
Clamp homeodomain
modification
cells
A5 host
HO1 gene bl-1
KDIDAWFIDARRRIGW
bl-lWa
KDIDAAFIDARRRIGW
bl-lhd
KDIDA -GW
HO2
b2-3 a2- 1
A
gene
b2-3/a2wa hd
1
RQIEVWFQNHRRRAR RQIEVAFQNHRRRAR RQIEV
AR I
I A
HD2:HDl
fusion
gene
A6m
RQIEVWFQNHRRRAR
A6m hd
RQIEV,
would normally
, AR A
Fig. 2. Mutational analysis of the HDl and HD2 Hd. A Trp to Ala change was effected using the CLONTECH transformerTM site-directed mutagenesis kit to convert the TGG codon in bl-f and b2-3 to GCG and generate bl-1”” and b2-3”“. Plasmids used for subcloning mutagenized regions were pAMT2 (Tymon et al., 1992) for bl-1 creating pB1 W and ~A625 for b2-3 (Banham et al., 1995) creating pB2W. Deletions were effected using reverse PCR; deleting nt 4955520 in the bl-1 gene to give bl-lhd and nt 580-651 in the a2-1 gene to give a2-lhd and A6mhd. Mutated regions were sequenced and then subcloned to replace the appropriate wild-type sequence in bl-1 (pBHl), ~2-1 (pAH1) and the mutant fusion gene A6m (pA6d3). Genes were tested for their ability to promote clamp cell development in the host FA2222 (ASB6 trp-1.1,1.6) by cotransformation with pCclOO1 as described in the legend to Fig. 1.
clamp cells (Tymon
et al.,
genes together with wild-type into a host strain in which they
meet a compatible
dimerization
partner
(a host with an A5 locus) and promote clamp cell development (Fig. 2). The control genes were able to promote clamp cells as expected. lated
HD2
coding
None
domains,
fusion gene, promoted
of the genes with manipuincluding
the constitutive
clamp cell development.
We con-
clude that the HD2 Hd is essential for A protein function. Changing the critical W residue to A in the HDl Hd led to loss of function whereas removal of the entire recognition
by
this deletion on the constitutive protein (Fig. 2). The activity of a cloned A gene can be tested by transformation
1992). The manipulated controls were introduced
develop-
helix
left a fully functional
protein.
As with
the
mutant fusion protein, the potential DNA-binding properties of the HDl Hd are not the essential contribution of the HDl
to the heterodimer.
The W to A change within
the Hd is likely to cause a steric effect that could prevent a normal interaction with DNA. The target site of the HDZHDl dimer is, as yet, unknown and we do not know how dimerization affects DNA binding activity. Our data allow us to predict that in a normal heterodimer both Hd normally contact DNA but that the binding of the HD2 Hd is more critical. Our conclusions are different from those of Luo et al. (1994) who tested the effect of more extensive deletions in the HDl Hd of an A mating type protein (AclZ3) from another mushroom species, S. commune. As with the deletion we describe, these had no detectable effect on protein activity. The authors concluded that the HDl function relies simply on its dimerization with its HD2 partner and that its Hd has no role in DNA-binding. However, no single aa substitutions analogous to the one we describe were made. Relevant to our experiments are those with the homeodomain mating type proteins al and a2 of Saccharomyces cerevisiae (SC). These proteins, encoded by genes in the alternative versions of the MAT locus, have Hd motifs analogous to the basidiomycete HD2 and HDl motifs, respectively. Subunits al and a2 heterodimerize following mating and generate a new transcription factor complex that binds unique sites upstream from developmentally regulated genes. Neither Hd alone has strong affinity for DNA, but interaction between a C-terminal domain of the a2 protein with the al Hd increases both the affinity for DNA-binding and the specificity of operator site selection (reviewed by Johnson, 1995). Interestingly, mutational alteration of critical aa residues in the recognition helix of the a2 Hd had no effect on dimer function (Vershon et al., 1995) suggesting that the contacts of the al Hd are more important. This is further suggested by the fact that the specificity conferred by cooperative binding with ~12 could be reconstituted in vitro if the al Hd was fused to just the C-terminal 22 aa tail from a2 (Stark
28 and Johnson,
1994). The recent
resolution
of the crystal
structure of the al/a2 heterodimer bound to DNA confirms that both Hd contact DNA (Li et al., 1995). It reveals
that the C-terminal
an amphipathic this interaction permits
tail of the a2 protein
helix that contacts introduces a bend
protein-protein
forms
the al Hd and that into the DNA that
and protein-DNA
contacts
that
Tymon
et
C-terminal
al.
(1992)
together
dimerization
with
domain.
the
potential
In this study we have
not tried to assess the importance It is interesting to note, however,
of this internal region. that we are unable to
predict NLS in the HD2 sequence and it may be that heterodimerization plays an important role in targeting a functional HDZ/HDl heterodimer to the nucleus and
are not possible on straight DNA. The artificial reconstitution of DNA-binding site specificity with just the
that both NLS are required
HD2-type al Hd may well reflect what has occurred in the fused Cc A protein dimer. The regions just C-terminal
final 38 aa which are predicted to form a C-terminal helix. This has previously been shown to be non-essential for
to the homeodomains
HDl
in both HDl
and HD2 A proteins
Of the two C-terminal
function
constitutive
ization
C-terminal
domain
that
serves
a similar
function
to the
mutant protein.
fusion
protein
and
in the
Hd
deleted
HDl
(b) The HDl C terminus contains an essential region which enables the mutant fusion protein to constitutively promote clamp cell development The constitutive fusion protein contains the first 387 aa of an HD2 fused to the C-terminal 394 aa of an HDl. The HDl sequence is essential for constitutive function (Kties et al., 1994b). Here we define more precisely the essential regions of this sequence by making two internal and two C-terminal deletions of the fusion protein (Fig. 1). The constitutive protein function was tested by introducing the gene into a host strain that has an A6 locus. The mutation arose in this locus and an A6 host contains no A proteins that could be compatible dimerization partners for the manipulated protein. This is important because the HD2 region of the fusion protein can still interact with a compatible HDl (Kties et al., 1994b). One of the constructs (see legend to Fig. 1) was an artificially derived fusion between two genes from the A42 locus and this was tested in an A42 host. The two internal deletions in the fusion protein lacked an additional 6 aa from the C-terminal domain of the HD2 (a2-1) that have previously been shown to be nonessential (Kties et al., 1994a) and either 116 aa or 210 aa from the HDl (dl-1). The shorter deletion resulted in a protein that retained its constitutive function but the clamp cell phenotype was poorly expressed with only a few cells producing these structures. We conclude that this protein is very inefficient at binding its target sites. The longer deletion led to complete loss of function. This allowed us to define the region beyond aa 503 as being absolutely essential for HDl function. The deletions removed either one or both of the bipartite nuclear localization signals (NLS) predicted by
using the clamp
the first removed
cell assay (Tymon
1992) and we now show that it is also inessential
are predicted to form amphipathic helices and we have previously suggested that these might constitute a dimerC-terminal interaction of al and a2 (Kties et al., 1994a). Significantly these helical regions are retained in both the
for efficient transport.
deletions,
activity
of the fusion protein.
94 aa, however,
removed
Removal
a negatively
the
et al., for the of the charged
domain adjacent to the terminal helix and lack of clamp cell development shows that this must be essential for heterodimer function. (c) The essential region of the HDl C terminus contains a region which can activate transcription in yeast Deletion analysis essential C-terminal
of the fusion protein identified an domain in normal HDl proteins
between aa 386 and 593. We have asked whether this region contributes an essential activation domain. We fused regions of an HDl gene (bl-1) to sequences encoding the DNA binding domain of the SC Gal4 protein. The translated fusion proteins bind the GAL4 target site and by using different reporters (Fig. 3) we assessed whether
Yeast
Integrated
strain
Repotter
,
310bp GGY1:171 UAS G
40bp
72bp I
SS38-G4
17mers
site
NJAS,l I
ss19-8
I HISIUAS
I
l-l GCN4
1
48bp
,
3Zbp
,
A
17mer DJASG]
Fig. 3. Succharomyces cereoisiae (SC) strains used to assay transcriptional regulation by Gal4 fusion proteins. GGYl:171, a strain for assaying transcriptional activation, was described by Gill and Ptashne (1987). Plasmids SS38’-G4 and SS19-8, for measuring transcriptional repression (Saha et al., 1993), and strain MLY530/18 were gifts from S. Saha and M. Ptashne. The plasmids were linearized with StuI and integrated into the URA3 locus of strain MLY530/18 (MATa, d&4, Agal80, leu2, uru3, trp, his) to give strains SS38-G4 and SS19-8. UAS, is the upstream activation site or binding site for the Gal4 regulatory protein. The 17.mers represent consensus Gal4-binding sites and are designated [UAS,]. HIS4 UAS is the binding site of the HIS4 regulatory protein.
29 the fusion proteins and Ptashne, et al., 1993). The fusion
had any ability
1987) or repress constructs
to either activate
(Gill
gene transcription
illustrated
dieted C-terminal
(Saha
helix which gave negative
results in the
activation assay and is dispensable in vivo. The C-terminal domain is highly conserved
in Fig. 4 were trans-
proteins
for which the sequence
in all HDl
has been predicted
(Kiies
formed into the SC strain GGY1:171 and assayed for their ability to activate transcription of the 1ac.Zreporter gene.
et al., 1994b; Gieser and May, 1994; Gottgens, 1994) as is the HDl Hd. Our deletion analysis of an HDl, how-
The data, summarized in Fig. 4A, indicated that certain regions of the HDl protein could activate transcription
ever, showed that both these domains
of lacZ. The different
levels of BGal activity
detected
regulating the phenotype function of the HDl/HD2
in
transformants are probably not significant because problems may arise due to different stability and conformation
opment).
of partial
is required
proteins
(Fields
and
Sternglanz,
constructs used defined a potential between aa 486 and 593.
1994). The
activation
domain
SS38-G4
(Fig. 4B)
or
strain
SS19-8
which we currently
lower than
those observed
for the vector
control
(p13H). This occurred when placed downstream (SS19-8) and more significantly, upstream (SS38-G4) of the promoter. This region of the HDl protein encodes the pre-
A bl-1
I
protem
tragment
:olour 1, :: v632
pAB32
++
IJ 1500
that
HDl
target
have
~12protein
site upstream
cells. This it does in the general transcrip-
have no phenotypic
assay.
C
plasmid pAB44 pALI
l-163
0 pAB2
pAE21 pAtI pAtl29 pAB22
a different
B
cDNA~ pl99mla
therefore,
(e) Conclusions between the HDl and HD2 Hd (I) Heterodimerization mating-type proteins of Cc brings together two proteins with potential DNA binding properties. Our mutational analysis of the Hd sequences indicates that the HD2 domain is critical for heterodimer function and that the HDl Hd is inessential but probably participates in binding the target site. Our observations suggest that there may be a parallel with the analogous al and a2 Hd
These
strains constitutively express PGal activated by the promoters illustrated in Fig. 3. Only one construct, pAB29, was able to repress transcription of 1acZ to levels significantly
for binding
for
tion factor MCMl (reviewed by Johnson, 1995). Like a2, HDl proteins might bind other DNA target sites to regulate genes not involved in the clamp cell pathway and for
gene the coninto SC strain
(Fig. 4C).
possible,
In SC the Hd of the HDl-like
from genes expressed in unmated association with another protein,
(d) The non-essential C-terminal helix from the HDl protein bl-1 can repress transcription in vitro To test whether any of the fusion proteins were able to repress transcription of a 1acZ reporter structs shown in Fig. 4A were transformed
It seems
other functions.
are dispensable
that enables us to assess the heterodimer (clamp cell devel-
593
?632 ?
++
1300
+
0.5 0
164m262
pAB31
30.5
-’
pAB33
305~381
kva
pAB30
366ma632
pAB34
486
632
++
1
pAB24 pAB29 pAB22
0
pAB3 1
4800
pAB33
0
pAB34
++
NT
++
2300
pl3H “One
ma632
0
0 ::
z !z
pGal activity
8 ” (units)
8
: N
z “7
:: r-
:: pGal activity
z z
(units)
Fig. 4. Identification of putative activation and repression domains in the HDl protein bl-1. (A) Transcriptional activation by Ga14::bl-1 fusion proteins. The restriction sites in 62-l cDNA are represented by: C, ClaI; M, MU; N, NruI: Pv, PuuII; P, PstI and aa in protein fragments by numbers, cDNA sequences were fused in frame to the region of the GAL4 gene encoding the DNA binding domain in p13H (the ADH promoter driving expression of amino acids l-147 of the Gal4p). Plasmids were transformed into SC strain GGY:171 and cells assayed for ability to produce l3Gal both on XGal plates and by enzyme assay. The expression product of pAB30 was toxic and although blue colour was observed on XGal plates the transformants were not tested (NT) for BGal activity because they did not grow sufficiently. (B) and (C). Transcriptional repression by Gal4::bl-1 fusion proteins. Constructs illustrated in (A) were transformed into SC strains SS38-G4 (B) and SS19-8 (C) and assayed for BGal synthesis. /3Gal activity was quantitated using a permeabilized cell assay (Guarente, 1983). Three transformants were assayed in duplicate for each plasmid transformed and results are expressed as mean activity obtained. ADH = gene encoding alcohol dehydrogenase.
30 mating-type correct
proteins
DNA
target
from SC. The al Hd is sufficient site selection
providing
for
it is associ-
ated with an essential part of the ~12protein which affects its conformation (Stark and Johnson, 1994; Vershon et al., 1995). The ability of one class of protein
to function
without an Hd implies that protein-protein interactions in a heterodimeric association can be more critical than contacts
made to DNA.
(2) We have demonstrated terminus
of the HDl
protein
experimentally contains
that the C
a region
between
aa 386 and 593 that can activate transcription in SC. This region has been shown to be essential in vivo for the constitutive activity of the mutant fusion protein in promoting clamp cell development. Our data is thus consistent with the conclusion that in the HD2/HDl heterodimer,
the
HD2
contributes
binding domain and the HDl activation domain.
an
provides
essential
DNA
a transcriptional
(3) Two features of the Cc HDl/HD2 heterodimer are puzzling in the light of our deletion analysis; the extreme conservation of the apparently dispensable HDl Hd and the presence of an equally conserved and apparently dispensable C-terminal domain in HDl proteins that has a potential role in transcriptional repression. This C-terminal domain is also conserved in the corresponding HDl mating-type proteins of another mushroom S. commune (Stankis et al., 1992). This leads us to suggest that HDl proteins might bind more than one target site and, by having a different transcriptional role, employ functional domains not required by the HD2/HDl heterodimer.
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568-577.
ACKNOWLEDGEMENTS
We thank Dr. S. Saha and Dr. M. Ptashne for sending us plasmids SS19-8, SS38-G4 and SC strain MLY530/18. We thank Drs. Ian Connerton and Ursula Kties for help with PCR strategies and site directed mutagenesis, respectively. H.U.B. thanks the Gatsby Charitable Foundation for a summer studentship and E.J.C.M. the Welcome Trust for a Senior Research Fellowship. This work was supported by Biotechnology and Biological Sciences Research Council grant No. PG043/0564 to L.A.C. and E.J.C.M., a research studentship to R.N. A.-O., and a postdoctoral fellowship to L.A.C.
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