Inhibitor-1 (I-1), a cyclic AMP-regulated
phosphoprotein, inhibits protein phosphatase-1 (PP1) activity in
response to hormones. The molecular mechanism for PP1 inhibition by I-1
remains unknown. Mutation of nine acidic residues lining a proposed
I-1-binding channel in rabbit PP1
yielded one mutant (E256A)
slightly impaired in its inhibition by I-1, with the
IC50 increased by 3-fold, and one mutant (E275R)
located in the
12-
13 loop that showed 4-fold enhanced inhibition
by I-1. Substituting Tyr-272, a proposed binding site for the toxins
okadaic acid and microcystin-LR, in the
12-
13 loop with Trp,
Phe, Asp, Arg, or Ala impaired PP1
inhibition by I-1 by 8-10-fold.
Chemical mutagenesis of the Saccharomyces cerevisiae PP1
gene (GLC7) yielded 20 point mutations in the PP1 coding
region. Two-hybrid analyses and biochemical assays of these yeast
enzymes identified four additional residues in the
12-
13 loop
that were required for PP1 binding and inhibition by I-1. Ten-fold
higher concentrations of I-1 were required to inhibit these mutants.
Finally, deletion of the
12-
13 loop from PP1
maintained full
enzyme activity, but attenuated inhibition by I-1 by >100-fold. These
data identified the
12-
13 loop in the PP1 catalytic subunit as a
domain that mediates binding and enzyme inhibition by I-1.
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INTRODUCTION |
Protein phosphatase-1
(PP1)1 is a major eukaryotic
protein-serine/threonine phosphatase that regulates a multitude of
physiological processes, including cell cycle, gene expression, protein
synthesis, carbohydrate and lipid metabolism, and muscle contraction
(1-3). Control of these functions, in response to hormones and growth factors, is likely to be mediated by interaction of the PP1 catalytic subunit with a growing number of regulatory subunits (4). To date,
physiological evidence suggests that hormones control PP1 activity
through changes in the endogenous protein inhibitors, such as
inhibitor-1 (I-1) and its structural homologue, DARPP-32 (5). I-1 has
been implicated in hormone signaling in many tissues, including
skeletal muscle (6, 7), heart (8), adipose tissue (9), brain (10), and
liver (11). Among the physiological processes controlled by I-1 are
glycogen metabolism in skeletal muscle (12), neuronal plasticity in the
hippocampal neurons (13), and proliferation of pituitary cells
(14).
Despite the physiological evidence in favor of I-1 as a
hormone-regulated PP1 inhibitor, the molecular basis for the selective and potent PP1 inhibition by I-1 remains unknown. Here, we describe a
mutagenic approach that was taken to identify domain(s) in the PP1
catalytic subunit that associate with I-1 and mediate enzyme inhibition. Initially, we were guided by the x-ray crystallography of
the PP1
catalytic subunit that had predicted an ionic interaction of
the I-1 phosphorylation site sequence with several acidic residues that
lined a putative substrate-binding channel (15). Mutagenesis of nine
acidic amino acids was undertaken to eliminate their negative charge
and to assess the impact on PP1 inhibition by I-1. The observation that
I-1 competes with the toxins okadaic acid and microcystin-LR for PP1
inhibition (16) led to the suggestion of a common binding site for PP1
inhibitors. In this regard, a number of mutations in the
12-
13
loop drastically reduced the sensitivity of PP1 to toxins (17, 18).
These mutants were also analyzed for their inhibition by I-1. Finally,
we exploited the budding yeast Saccharomyces cerevisiae,
which contains a single PP1 gene (GLC7) that is also
essential for viability. This property allowed us to develop a novel
mutagenic screen that eliminated inactive PP1 enzymes (19, 20) and
focused on the structural determinants required for PP1 regulation.
Random mutagenesis combined with biochemical assays of mutant PP1
enzymes identified a domain essential for PP1 inhibition and generated
an I-1-resistant catalytic subunit that may be used to establish the
physiological relevance of this signaling mechanism.
 |
EXPERIMENTAL PROCEDURES |
Materials--
DNA was routinely purified using Wizard Miniprep
(Promega) or Qiaprep Spin (QIAGEN Inc.) kits. Restriction enzymes, T4
polynucleotide kinase, T4 DNA ligase, T4 DNA polymerase, and
isopropyl-
-D-thiogalactopyranoside were obtained from
either New England Biolabs Inc. or Boehringer Mannheim.
[
-32P]ATP, [
-32P]dCTP, and
-35S-ATP were purchased from Amersham Biotech Inc.
Protein concentration was estimated using the Bio-Rad protein Assay
with bovine serum albumin (Sigma) as standard.
Yeast Strains and Media--
Yeast strains and plasmids are
listed in Table I. Plasmids that express
mutant Glc7p (pKC886-X) or Gal4p-Glc7p (pAS1-GLC7-X) fusions
were described by Ramaswamy et al. (20). As the chromosomal wild-type GLC7 locus was disrupted by insertion of the HIS3
nutritional marker, the JC821A/pKC886-X strains expressed Glc7p
proteins exclusively from the pKC886 plasmid. YEPD medium contained 1%
(w/v) yeast extract (Difco), 2% (w/v) glucose, and 2% (w/v)
Bacto-peptone (Difco). Filter-sterilized 3-aminotriazole was added
after autoclaving the media. Other selected media were used as
described by Sherman et al. (24). Plasmid JZ303 was made by
cloning a NcoI-SalI fragment from
pGEM3ZF(
)-hI-1 into pACT2 digested with NcoI and
XhoI.
Expression and Purification of Recombinant hI-1--
hI-1
cDNA was excised from pGEM3ZF(
)-hI-1 using a
NcoI-SalI digest. The insert was excised from a
0.8% (w/v) agarose gel, purified using a QIAGEN column, and inserted
into pT7-7 cut with NdeI-SalI. The ligated vector
was transformed into Escherichia coli BL21(DE3). A seed
culture of transformed BL21 bacteria grown overnight in LB medium (5 ml) containing ampicillin (50 µg/ml) at 37 °C was used to
inoculate 250 ml of LB medium containing ampicillin. When the
absorbance of the culture at 600 nm reached 0.6, hI-1 was induced by
addition of 1 mM
isopropyl-
-D-thiogalactopyranoside, and growth was
continued at 37 °C for 3 h. Bacteria were sedimented at
3000 × g for 15 min, resuspended in 20 ml of ice-cold
lysis buffer (50 mM Tris-HCl, pH 7.5, containing 1%
Nonidet P-40, 5 mM EDTA, 5 mM EGTA, 5 mM benzamidine, and 1 mM phenylmethylsulfonyl fluoride), and sonicated for 4 × 10 s using a Branson
sonifier (30% duty cycle and 0.5 output power). The cell lysate was
centrifuged at 3000 × g, and trichloroacetic acid was
added to the supernatant to a final concentration of 1% (w/v). The
mixture was centrifuged at 12,000 × g for 20 min at
4 °C, and the supernatant was adjusted to 15% (w/v) trichloroacetic
acid. The 12,000 × g pellet was resuspended in 3 ml of
500 mM Tris-HCl, pH 7.5, and dialyzed overnight against 0.5 mM Tris-HCl, pH 7.5, containing 0.005% (w/v) Brij 35. Preparative SDS-polyacrylamide gel electrophoresis was used to obtain
pure hI-1 (25). Purified hI-1 was lyophilized and stored at
80 °C.
Expression and Purification of Recombinant PP1
Catalytic
Subunits--
Mutations in PP1
were made using double-stranded
polymerase chain reaction (26) or Altered Site II mutagenesis
(Promega). In the latter method, PP1 cDNA was inserted into
pALTER-Ex1. The mutagenic oligonucleotide, the ampicillin repair
oligonucleotide, and the tetracycline knockout oligonucleotide were
phosphorylated and annealed to the template. Second strand DNA was
initiated using T4 DNA polymerase and T4 DNA ligase in 10 mM Tris HCl, pH 7.5, containing 0.5 mM dNTPs, 1 mM ATP, and 2 mM dithiothreitol. The resulting
heteroduplex double-stranded DNA was transformed into E. coli BMH71-18 or ES1301 mutS and grown on agar plates containing ampicillin (50 µg/ml). Plasmid DNA was isolated from individual colonies and transformed into JM109 to propagate the mutant plasmids. Mutations were confirmed by double-stranded
sequencing (Sequenase II, U. S. Biochemical Corp.) and subcloned into
pTACTAC for PP1 expression (27).
The cDNA for the rabbit skeletal muscle PP1
catalytic subunit
was expressed in E. coli. Briefly, bacteria were grown in
Terrific Broth containing 0.2 mM MnCl2 and 50 µg/ml ampicillin at 37 °C until the absorbance of the culture at
600 nm reached 0.3. Protein expression was initiated with 0.5 mM isopropyl-
-D-thiogalactopyranoside, and
bacterial growth was continued at 27 °C for 20 h. Cells were pelleted by centrifugation at 5000 × g for 20 min and
lysed in 50 mM imidazole, pH 7.4, containing 1 mM EDTA, 2 mM dithiothreitol, and 2 mM MnCl2 using a French press (at 1000 p.s.i). The PP1 catalytic subunits were then purified to homogeneity
according to Zhang et al. (27).
Isolation of Mutant PP1 (GLC7) Alleles--
pKC886 plasmid was
mutagenized as described (20). Briefly, pKC886 was treated with
hydroxylamine and transformed into JC821A. Transformants were
replica-plated on media lacking tryptophan or uracil as well as on two
YEPD plates. The YEPD plates were incubated at 30 and 37 °C and
scored for glycogen accumulation and temperature sensitivity. DNA was
prepared from uracil-minus colonies that also exhibited either altered
glycogen accumulation or temperature sensitivity compared with the wild
type. Mutant pKC886 was amplified in E. coli DH5
.
Purification of Yeast PP1--
Overnight cultures (100 ml) of
JC821A/pKC886-X strains were inoculated into 1 liter of YEPD medium.
Cells were grown to late log phase, harvested by centrifugation, and
resuspended in 10 ml of 50 mM Tris-HCl, pH 7.5, containing
1 mM EDTA and 15 mM 2-mercaptoethanol. Cells
were lysed using either Bead-Beater-6 or a French press at 1000 p.s.i. Extracts were centrifuged at 800 × g for 15 min, and the supernatant was brought to 70% saturation with ammonium sulfate. The pellet, obtained from centrifugation at 100,000 × g for 20 min, was resuspended in 10 ml of 50 mM
Tris-HCl, pH 7.5, containing 1 mM EDTA and 15 mM 2-mercaptoethanol and dialyzed overnight against the
same buffer. The dialyzed sample was applied to heparin-Sepharose
(Amersham Pharmacia Biotech) equilibrated in the dialysis buffer. The
column was washed with 10 volumes of the dialysis buffer containing 100 mM NaCl, and PP1 activity was eluted with buffer containing
250 mM NaCl and 10% (v/v) glycerol. The eluate was
dialyzed against 50 mM Tris-HCl, pH 7.5, containing 1 mM EDTA, 15 mM 2-mercaptoethanol, and 40%
(v/v) glycerol and stored at
20 °C. This procedure consistently
yielded a preparation containing the 37-kDa PP1 catalytic subunit as
~30% of the total protein.
Analysis of I-1 as a PP1 Inhibitor--
hI-1 was phosphorylated
with the protein kinase A catalytic subunit (28) using either ATP or
ATP
S (25). Activated I-1 was analyzed for the inhibition of 0.02 unit of PP1 catalytic subunit using [32P]phosphorylase
a as substrate. One unit of PP1 activity is defined as
hydrolyzing 1 nmol of phosphorylase a in 1 min in this
assay.
Two-hybrid Interactions--
Three methods were used to assay
two-hybrid interactions in yeast. In the first method, Y190 was
transformed with pAS1-GLC7 and pJZ203 (pACT2-hI-1)
containing wild-type hI-1; derivatives containing the T35A or T35D
mutant (Table I); or pCV6 (23), which expresses Gac1p fused to the
Gal4p activation domain. Transformants bearing both plasmids were
selected on media deficient in tryptophan and leucine. Y190 contained a
GAL1 promoter-driven HIS3 gene that was activated
following the association of two Gal4p fusion proteins. Positive
interaction was noted as resistance to growth in the presence of the
histidine analogue 3-aminotriazole (22).
The second method assayed for
-galactosidase activity in diploids
produced by mating JC981 with JC993. The GAL1
promoter-driven lacZ gene was activated in these strains on
the reconstitution of Gal4p activity. JC981 × JC993 diploids
containing two-hybrid plasmids were grown on solid sucrose minimal
medium lacking tryptophan and leucine for 48 h. Equivalent amounts
of cells were transferred to a nitrocellulose filter using a dot-blot
manifold. Filters were floated in liquid nitrogen for 5 s and
placed on Whatman No. 3MM filters soaked with Z buffer (29) containing
5-bromo-4-chloro-3-indolyl
-D-galactopyranoside (1 mg/ml). The filters were incubated at 37 °C for 2-24 h before
drying and photography.
In the third method, the JC981 × JC993 diploids were grown in
liquid glucose minimal medium lacking leucine and tryptophan until the
absorbance of the culture reached ~1.0. The cells were harvested,
permeabilized with chloroform and SDS, and assayed using
o-nitrophenyl
-D-galactoside as substrate
(30). Units of
-galactosidase activity were calculated in triplicate
from independent cultures and varied by <10%.
 |
RESULTS |
Mutation of Surface Acidic Residues in PP1
--
Surface
channels emanating from the PP1 catalytic center were widely speculated
to function as sites for binding phosphoprotein substrates and
inhibitors (15). Modeling a phosphopeptide conserved in I-1 and
DARPP-32 suggested that the four basic residues preceding the
phosphothreonine in these PP1 inhibitors made ionic interactions with
some of the nine acidic amino acids lining this putative substrate/inhibitor-binding channel. Thus, we mutated Asp-208, Asp-210,
Asp-212, Glu-218, Asp-220, Glu-252, Asp-253, Glu-256, and Glu-275 to
alanines (Fig. 1), expressed the mutant
PP1
proteins in E. coli, and analyzed the inhibition of
the purified enzymes by hI-1. As noted by Zhang and Lee (26), the
specific activities of the six mutants D210A, D212A, E252A, D253N,
E256A, and E275R were identical to that of wild-type PP1
using
phosphorylase a and other substrates.
Dose-dependent inhibition of mutants D210A and D212A (Fig.
2A) and mutants E252A and
D253N (Fig. 2B) by hI-1 was also identical to that of
wild-type PP1
. Only E256A showed a 3-fold right shift in its dose
response for hI-1 (Fig. 2B). The double mutants D210N/D212N
and E252N/D253N also showed no change in their IC50 for
hI-1 (Fig. 2C). The one surprising finding was that mutant
E275R increased the sensitivity of PP1 to I-1 by ~4-fold (data not
shown).

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Fig. 1.
Location of the acidic groove in the PP1
catalytic subunit. The crystal structure of the recombinant PP1
catalytic subunit (15) is shown. Nine acidic residues (numbered) line
the putative substrate-binding groove that is postulated to interact
with four consecutive arginines near the phosphorylation site in I-1.
Two partially hidden metals (filled spheres) locate the
catalytic center of PP1 .
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Fig. 2.
Analysis of PP1 with mutations in the
acidic groove. Oligonucleotide-directed mutagenesis of rabbit
PP1 cDNA was carried out as described under "Experimental
Procedures." Mutant cDNAs were inserted in the pTACTAC vector and
expressed in E. coli (27). Dose-dependent
inhibition of PP1 enzymes with charged-to-alanine substitutions, D210A
and D212A (A) and E252A, D253A, and D256A (B), is
shown using thiophosphorylated hI-1. The double mutations D210N/D212N
and E252N/D253N were also analyzed (C). The
symbols, shown in the insets, identify the
individual mutants. Each point represents the average of
three values and varied by <10%. wt, wild type.
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The other mutants, D208A, E218A, and D220A, possessed 7-10-fold lower
specific activity than wild-type PP1
. D208A, in particular, was
highly unstable. Overnight storage under conditions (0.1 mg/ml protein
in buffers containing 10% glycerol at 4 °C) that maintained 100%
wild-type activity resulted in complete loss of D208A activity. E218A
and D220A showed no difference in their IC50 values for hI-1 compared with the wild type. Freshly prepared D208A, on the other
hand, showed a 10-fold increased sensitivity to hI-1 (data not
shown).
Toxin-resistant PP1 Catalytic Subunits--
Numerous toxins
inhibit PP1 and PP2A (31), with PP2A being 10-100-fold more sensitive
to okadaic acid than PP1. PP2A is also characterized by its complete
insensitivity to I-1. A mutation (C269G) in the PP2A catalytic subunit
was identified in an okadaic acid-resistant cell line (32). To test the
possibility that Cys-269 and the surrounding sequence may represent a
toxin-binding site, Zhang et al. (17) substituted the
corresponding sequence, GEFD, in PP1
with YRC269G, the
PP2A sequence. This enhanced the sensitivity of PP1 to okadaic acid,
making it more PP2A-like (17). Okadaic acid competes with other PP1
inhibitors (33), suggesting a common inhibitor-binding site. Thus, we
postulated that the chimeric PP1 enzyme may also be more PP2A-like in
showing reduced sensitivity or no inhibition by I-1. We analyzed
YRCG-containing chimeric PP1
, but found no difference in its
dose-response curve for hI-1 compared with wild-type PP1
(data not
shown). Mutations of individual residues within this sequence (F276A
and D277G) also had no effect on the sensitivity of PP1
to hI-1
(data not shown).
In later studies, Zhang et al. (18) undertook a systematic
mutagenesis of the
12-
13 loop in PP1
and identified Tyr-272 as the primary determinant of PP1 inhibition by toxins. Substituting Tyr-272 with other amino acids reduced the sensitivity of PP1 to toxins
by several hundred- to thousand-fold. These mutants also showed small
reductions in their sensitivity to I-2, suggesting that the protein
inhibitors of PP1 may also recognize Tyr-272. Thus, we also analyzed
several different substitutions in place of Tyr-272 for their effects
on PP1
inhibition by hI-1. Conservative substitutions, Y272W (Fig.
3A) and Y272F, as well as
nonconservative mutations, Y272A, Y272E, and Y272D, all impaired PP1
inhibition by hI-1 (Fig. 3B), increasing the
IC50 by 8-10-fold (data not shown).

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Fig. 3.
Mutations of tyrosine 272 in PP1 .
Site-directed mutagenesis substituted several amino acids in place of
Tyr-272 in PP1 . The mutant enzymes were expressed in E. coli and purified to homogeneity. A shows dose-response
curves for the inhibition of the Y272W mutant (solid line)
and wild-type PP1A (shaded line) by hI-1. B shows
the comparison of several substitutions in place of Tyr-272 at a fixed
concentration of hI-1 (3.0 µM). The average of three
independent experiments is shown with S.E.
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Mutations of Yeast PP1 with Altered Interactions with
hI-1--
S. cerevisiae is unique among eukaryotes in
having a single PP1 gene. The GLC7 gene encodes a PP1
catalytic subunit with >80% identity to mammalian PP1
(34) and is
essential for yeast viability (35). A GLC7-containing
plasmid, randomly mutagenized with hydroxylamine, was screened in a
strain that contained a disruption in the chromosomal copy of the
GLC7 gene. We analyzed 20 different alleles that maintained yeast viability but resulted in a wide range of phenotypes, suggesting altered Glc7p function or regulation (20). Two-hybrid analysis of
mutant GLC7 cDNAs inserted in the pAS1 vector with the
hI-1 cDNA in pACT2 (22) showed effective PP1/I-1 binding with most alleles. Insertion of these cDNAs in the opposing vectors showed no
significant binding, suggesting that the fusion of the Gal4p DNA-binding domain to the N terminus of hI-1 and/or of the
transactivation domain to the C terminus of PP1 impaired PP1/I-1
binding. The Glc7p/hI-1 association was first monitored by the ability
of Y190 diploid strains to grow in the presence of 30 mM
3-aminotriazole, indicating the activation of the GAL1
promoter-driven HIS3 gene (Fig.
4). In this growth assay, wild-type Glc7p
interacted with hI-1 with equal avidity compared with Gac1p (23, 37), a
yeast homologue of the PP1 glycogen-targeting subunit. Substitution of
threonine 35, whose phosphorylation by protein kinase A is essential
for PP1 inhibition in vitro (25), with either alanine or
aspartic acid abolished Glc7p/hI-1 interaction, suggesting that
threonine 35 phosphorylation was also necessary for the binding of hI-1
to Glc7p in intact yeast. We have overexpressed hI-1 in yeast and,
using a phospho-specific antibody (38), have shown that threonine 35 is
phosphorylated (data not shown).

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Fig. 4.
Association of S. cerevisiae PP1
(Glc7p) with hI-1 in the two-hybrid assay. Interaction of Glc7p
with hI-1 was analyzed using the two-hybrid assay as described under
"Experimental Procedures." Association of wild-type (wt)
hI-1 with Glc7p was defined by growth of Y190 transformants on control
YEPD plates (A) and on plates containing 30 mM
3-aminotriazole (B). The role of threonine 35 phosphorylation in Glc7p/I-1 binding was assessed by substituting the
non-phosphorylated residues alanine (T35A) and aspartic acid
(T35D). Yeast growth resulting from Glc7p binding to Gac1p, a known
yeast PP1 regulator, was used as a control.
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We also monitored the expression of a
-galactosidase reporter
construct (GAL1 promoter-driven lacZ) in the
two-hybrid assay using a convenient solid-phase or dot-blot assay (Fig.
5A). In this assay, wild-type
hI-1 bound Glc7p with equal or better avidity than Snf1p and Snf4p, two
well characterized interacting proteins. We identified eight Glc7p
mutants that showed impaired binding to hI-1. These proteins were also
analyzed for binding to two other PP1 regulators: Glc8p, a yeast I-2
homologue (39), and Gac1p (Fig. 5B). Three mutants (P82S,
P195F, and R245Q) failed to bind all three baits (hI-1, Glc8p, and
Gac1p), but, in other studies (20), were shown to bind Sds22p, a
nuclear PP1 regulator. Two Glc7p mutants (R42K and Q48K) showed
enhanced hI-1 binding. The particular focus of these studies was the
five negative or weak I-1-interacting Glc7p proteins that represented
point mutations near the C terminus (domain III in Fig.
5B). Quantitative analysis of hI-1 binding to all Glc7p
mutants using a more sensitive permeabilized cell assay emphasized the
complete inability of some C-terminal Glc7p mutants to interact with
hI-1 in the two-hybrid assay (Fig. 6,
asterisks). Four of these mutations (A268T, P269L, A278V,
and G279S) were localized to the
12-
13 loop and flanked
Tyr-272.

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Fig. 5.
Comparison of Glc7p binding to
hI-1 and yeast PP1 regulators. Association of the 19 mutant Glc7p
proteins (the modified amino acids shown in the left panel),
generated by hydroxylamine mutagenesis, with hI-1 was analyzed by the
dot-blot assay (A) as described under "Experimental
Procedures." ts120 is a temperature-sensitive GLC7 allele
that results from conversion of the consensus TACTAAC intron splice
sequence to TAATAAC. Association of Snf1p and Snf4p was used as a
positive control, and Glc7p and Snf4p were used as a negative control.
The dot-blot assay was also used to compare Glc7p binding to hI-1 as
well as Glc8p and Gac1p, two known yeast PP1 regulators (B). + represents wild-type signal; +/ represents inconsistent or weak
signal; and indicates no signal in four independent assays. The
primary structure of yeast PP1 is schematically shown, with the
locations of the individual mutations marked by asterisks.
The central or core domain of PP1 (shown as a broad bar) is
highly conserved in all eukaryotes, with greater diversity present at
their N and C termini (shown by thin lines). Three domains
(indicated by roman numerals) were assigned by the
preponderance of PP1 mutations that increased hI-1 binding
(domain I), resulted in little or no change (domain
II), or significantly reduced Glc7p binding to hI-1 (domain
III). WT, wild type.
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Fig. 6.
Quantitation of -galactosidase expression
and Glc7p/hI-1 binding. Quantitative analysis of reporter gene
expression following Glc7p/hI-1 binding was undertaken using a liquid
assay as described under "Experimental Procedures." Assays were
carried out in triplicate. Asterisks indicate diploid
strains that failed to induce -galactosidase. The ts120 allele,
described in the legend for Fig. 5, is indicated here as
intron. WT, wild type.
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To determine whether loss of PP1/I-1 binding in the two-hybrid assay
was synonymous with defective PP1 inhibition, we purified wild-type and
mutant yeast PP1 enzymes for in vitro biochemical assays. In
the absence of divalent cations, wild-type Glc7p was inhibited by hI-1
with IC50 = 2 nM, a value similar to that for PP1 from mammalian tissues (Fig.
7A). Mutants P269L and A278V showed a significant loss of inhibition by hI-1, with 10-fold right
shifts in their dose-response curves (Fig. 7A). Similar results were obtained with A268T and G279S (data not shown).

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Fig. 7.
Inhibition of mutant Glc7p phosphatases by
hI-1. Glc7p proteins that failed to bind or weakly bound hI-1 in
the yeast two-hybrid assay were purified as described under
"Experimental Procedures." The purified yeast enzymes were assayed
for inhibition by thiophosphorylated hI-1 using phosphorylase
a as substrate. Results for two mutants (A278V
(closed diamonds) and P269L (open
diamonds)) and wild-type Glc7p (wt; open
squares) are shown in A. Each data point
represents the average of three values. These studies identified the
12- 13 loop (highlighted in black in B) as
a determinant of hI-1-mediated PP1 inhibition.
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I-1-resistant PP1
Catalytic Subunit--
The central core of
the PP1 catalytic subunit has been highly conserved through evolution
(34). Attempts to truncate the N or C termini in mammalian (40) or
yeast (19) PP1 failed to yield active enzymes. Ansai et al.
(41) combined N- or C-terminal truncations to successfully express an
active PP1
core in E. coli. This enzyme lacked the
12-
13 loop, a potential mediator of PP1 inhibition by hI-1. We
expressed the recombinant PP1
core in E. coli and
analyzed the purified enzyme for its regulation by I-1. The specific
activity of the core enzyme was indistinguishable from that of
wild-type PP1
with phosphorylase a as substrate (Fig.
8A). Wild-type PP1 and the
core also dephosphorylated I-1 at similar rates (Fig. 8B).
In contrast to wild-type PP1
, which was inhibited by
thiophosphorylated hI-1 with an IC50 of ~300 nM, the PP1 core was not significantly inhibited by I-1
concentrations up to 20 µM (Fig. 8C). Use of
thiophosphorylated hI-1 precluded the possibility that
dephosphorylation and inactivation of hI-1 accounted for the apparent
insensitivity of the PP1
core to I-1. The PP1
core was not
inhibited by several other phosphatase inhibitors, including 10 µM okadaic acid, 1.0 µM microcystin-LR, and
2 µM I-2 (data not shown).

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Fig. 8.
Inhibition of the PP1 core by hI-1.
The core structure of PP1 (residues 41-269) is conserved in all
eukaryotic PP1 catalytic subunits and is equivalent to the smallest
active protein phosphatase identified, that from bacteriophage (41). The specific activities of the PP1 core and wild-type
(wt) PP1 were compared using phosphorylase a
as substrate (A). The time-dependent
dephosphorylation of hI-1 (B) was also compared using the
core (closed diamonds) and wild-type PP1 (open
squares). The dose-dependent inhibition of
phosphorylase phosphatase activity (C) of wild-type PP1
(open squares) and the PP1 core (closed diamonds)
was undertaken using thiophosphorylated hI-1. All experiments were
carried out in triplicate.
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 |
DISCUSSION |
Several endogenous inhibitors control PP1 activity in mammalian
cells. These include I-1 (42), DARPP-32 (43), I-2 (33), the ribosomal
protein RIPP-1 (44), and the nuclear protein NIPP-1 (45). To define the
molecular mechanism for PP1 inhibition, early attention focused on I-1
and its neuronal homologue, DARPP-32, two proteins that control PP1
activity in response to both hormones and neurotransmitters (5).
Structure-function studies of I-1 (46, 47) and DARPP-32 (43, 48, 49)
established that protein kinase A phosphorylation of a conserved
threonine was required but not sufficient for PP1 inhibition. The
phosphorylated threonine acts in concert with an N-terminal
tetrapeptide sequence (KIQF) to inhibit PP1 activity. The KIQF sequence
represents a PP1-binding motif present in other PP1 regulators (47, 49, 50). Synthetic peptides modeled on this motif in skeletal muscle glycogen-binding subunit GM or smooth muscle myosin-binding
subunit M110 partially mimic the ability of the parent
proteins to modulate PP1 activity (51). Co-crystallization of the
GM decapeptide with PP1 (50) showed that it binds some
distance from the catalytic site and suggested that the peptide induces
a conformational change that modifies the substrate specificity of PP1.
However, the three-dimensional structure of PP1 in the PP1-peptide
complex is virtually identical to that of the isolated catalytic
subunit (52). So, the molecular basis for functional effects induced by
PP1-binding peptides remains unknown. Whereas both DARPP-32 (49, 53)
and I-1 (25), in their dephosphorylated state, bind the PP1 catalytic
subunit, most likely through the KIQF sequence, only dephospho-DARPP-32 inhibits the phosphatase (49). Dephosphorylated hI-1, even at much
higher concentrations, has no effect on PP1 activity (25). This places
greater emphasis on the region of I-1 near the phosphothreonine as
critical for PP1 inhibition.
X-ray crystallography of human PP1
1 localized the catalytic site by
the presence of a metal-bound tungstate (52). Co-crystallization of
rabbit PP1
with microcystin-LR identified the same region as the
catalytic site (15). To define the interactions of phospho-I-1 at or
near the catalytic site, we first examined the model of the DARPP-32
phosphopeptide bound within the PP1 catalytic site (15). Four
consecutive arginines that precede the phosphothreonine in I-1 and
DARPP-32 were proposed to interact with multiple acidic residues lining
a groove that emanates from the catalytic center. By site-directed
mutagenesis, we eliminated the negative charge at six of these residues
(at positions 210, 212, 218, 220, 252 and 253), but found no measurable
change in the sensitivity of PP1 to hI-1. Indeed, the double mutants
D210N/D212N and E252N/D253N, which lacked adjacent charged residues,
also showed no detriment in their regulation by I-1. This result was in
contrast to the findings of Huang et al. (54), who showed
that the double mutation E252A/D253A right-shifted the dose-response
curve for DARPP-32 by 10-fold, suggesting that the loss of negative
charge impaired the interaction of PP1 with the I-1 homologue.
The more remarkable finding was that PP1 mutants D208A and E275R showed
enhanced sensitivity to hI-1 (10- and 3-fold, respectively). The same
mutations also enhanced PP1 inhibition by DARPP-32 by 30- and 50-fold,
respectively (54). This unexpected increase in affinity for hI-1 and
DARPP-32 may, at least for Asp-208, be due to its contribution to
packing or organization of the PP1 metal-binding centers. Asp-208 is
partially buried and participates in the architecture of metal-binding
site 2 (15, 52). This may explain why D208A lowers enzyme activity and
was unstable. The other mutation, E275R, is located in the
12-
13
loop and is more difficult to explain. Glu-275 is not predicted to
interact with the four basic residues in I-1 and DARPP-32. Moreover,
the chimeric enzyme that exchanged the sequence GEFD in PP1 for YRCG in
PP2A also incorporated E275R, but had no effect on the sensitivity of
PP1 to I-1. Point mutations in the flanking residues (F276C and D277G)
also had no effect on PP1 inhibition by I-1. So, at this time, it is
unclear why E275R enhanced PP1 inhibition by I-1 and DARPP-32.
Only one mutation (E256A) lining the proposed I-1/DARPP-32-binding
groove reduced the sensitivity of PP1 to I-1, and then only by a modest
3-fold. This result also contrasted with the findings of Huang et
al. (54), who introduced a more drastic change in this position
(E256R) and found the opposite result, namely a 10-fold increase in the
potency of DARPP-32 as a PP1
inhibitor. Examination of PP1 structure
provides no clues to the differing effects of the Glu-256 mutations on
the sensitivity of PP1 to DARPP-32 and I-1, and it may take the
co-crystallization of these proteins to resolve this issue.
X-ray crystallography of two protein-serine/threonine phosphatases, PP1
(15, 52) and PP2B/calcineurin (55), drew attention to grooves emanating
from the catalytic centers as potential sites for phosphoprotein
binding (56). Our studies focused on the acidic groove in PP1
that
was postulated to be particularly important for accommodating the
multiple basic residues near the phosphorylation site of I-1. However,
mutations in all nine acidic residues failed to provide convincing
evidence for their role in either substrate (phosphorylase) or
inhibitor (I-1) binding. These experiments did highlight differences in
the structurally related PP1 inhibitors (I-1 and DARPP-32) and could
indicate that the two proteins, which are regulated differently by
protein kinases and phosphatases (48), may also interact differently
with the PP1 catalytic subunit.
Co-crystallization of PP1
with microcystin-LR (15) positioned this
cyclic heptapeptide toxin in close proximity to the
12-
13 loop,
where it forms a covalent link with cysteine 273. Docking the
three-dimensional structure of okadaic acid, a structurally distinct
inhibitor, into the PP1
catalytic site also suggests key
interactions with the
12-
13 loop (57). PP1/PP2A chimeras that
interchanged segments of the
12-
13 loop (18) and systematic mutagenesis of the
12-
13 loop (40) confirmed that selected residues in this domain play crucial roles in defining the sensitivity of PP1 to okadaic acid, microcystin, and other xenobiotic inhibitors. Competition between microcystin-LR and okadaic acid for PP1 binding (58) or with I-1 for PP1 inhibition (16) fostered the idea of a common
binding site for PP1 inhibitors. We analyzed numerous mutations in the
12-
13 loop. The chimeric PP1
that exchanged a tetrapeptide
sequence in the
12-
13 loop with that present in the
I-1-insensitive phosphatase (PP2A) showed no change in its I-1
sensitivity. We also examined several substitutions of tyrosine 272, a
key residue for toxin binding. All of these substitutions, conservative
or nonconservative, impaired PP1 regulation by I-1 and pointed to a
unique role for tyrosine 272 in binding I-1 and other PP1
inhibitors.
PP1 regulates numerous processes in S. cerevisiae, including
glycogen metabolism, protein synthesis, glucose repression,
sporulation, and cell cycle, and is encoded by a single essential
GLC7 gene (36). This offered a unique opportunity to develop
mutagenesis screens (19, 20) and to identify structural determinants
for PP1 regulators. In this regard, yeast PP1, like the mammalian enzyme, is potently inhibited by I-1 (59). Chemical mutagenesis of the
GLC7 gene yielded numerous low glycogen mutants (20), some
of which were impaired in their interaction with hI-1 in two-hybrid
analyses. Biochemical assays of these mutant PP1 enzymes identified
four residues (Ala-268, Pro-269, Ala-278, and Gly-279) in the
12-
13 loop required for both PP1 binding and inhibition by I-1.
Surprisingly, Glc7p proteins incapable of binding to hI-1 in the
two-hybrid assay were still inhibited by this protein in the in
vitro biochemical assays. Several factors may contribute to this.
First, N-terminal fusion of GAL4 to hI-1, like glutathione S-transferase fusion (25), may reduce the potency of I-1 as a PP1 inhibitor. Second, the failure of hI-1 mutants T35A and T35D to
bind PP1 points to the fact that as in the enzyme assay, hI-1 must be
phosphorylated on this threonine to interact with PP1 in yeast. Here,
we took no specific steps to enhance hI-1 phosphorylation, and so the
protein may be only partially phosphorylated in yeast. The combined
effect would be to increase the sensitivity of the two-hybrid assay to
mutations that impair PP1/hI-1 interactions. In any case, we analyzed 9 of the 12 amino acids that compose the
12-
13 loop (Table
II) and identified six residues that
modified the sensitivity of PP1 to I-1.
View this table:
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Table II
Functional analysis of the 12- 13 loop in the PP1 catalytic
subunit
Residues 268-279 form a loop connecting the 12 and 13 strands in
the PP1 catalytic subunit and are conserved in all PP1 enzymes. The
N-terminal half of this sequence is also conserved (indicated by
colons) in other protein phosphatases, PP2A and PP2B (Part A).
Mutagenesis of rabbit PP1 (Part B) and S. cerevisiae GLC7
(Part C) analyzed many of these residues for their role in PP1
regulation by hI-1. Substitution of five residues (shown in boldface)
attenuated PP1 inhibition by hI-1, whereas one mutation, E275R
(boldface and underlined), enhanced PP1 inhibition.
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An interesting finding of these studies is that yeast PP1 is active
in vitro in the absence of divalent cations. Thus, it resembles PP1 isolated from mammalian tissues rather than the enzymes
expressed in bacteria, which are inactive in the absence of added
cations. Moreover, Glc7p is inhibited by hI-1 with an IC50
of 1-2 nM, a value similar to that for mammalian PP1 (25). In contrast, bacterially expressed PP1 appears to be partially compromised, displaying IC50 values for I-1 of 50-600
nM (47, 60). This suggests that yeast is an excellent
system for expressing mutant PP1 enzymes. However, budding yeast is
highly sensitive to changes in Glc7p, such that both reduction and
elevation of PP1 activity inhibit growth. This makes yeast less
suitable for large-scale expression of PP1 enzymes and ideal for
mutagenic screens for novel GLC7 alleles. Combining the
speed and convenience of such screens with subsequent expression of
specific mutants in bacteria or insect cells for more detailed
biochemical studies may provide the most effective approach to analyze
PP1 regulators like I-1.
To establish the functional importance of the
12-
13 loop in PP1
inhibition, we expressed a truncated PP1
(41) that lacked all but
one residue in this loop. The resulting "core" enzyme was
essentially insensitive to I-1 and several other PP1 inhibitors. As the
PP1 core still recognized I-1 as a substrate, it clearly retained a
subset of interactions with I-1 at or near the catalytic site, but
lacking the
12-
13 loop, was poorly inhibited. This confirmed a
pivotal role for the
12-
13 loop in PP1 inhibition and
demonstrated that I-1 and the toxin inhibitors recognized elements of
this domain to mediate their inhibitory effects. As the PP1 core was
insensitive to high micromolar concentrations of hI-1, and the highest
levels of I-1 in mammalian tissue is ~1 µM (42), the
core may be classified as an "I-1-resistant" PP1 and could be
useful in elucidating the physiological importance of this regulator in
hormone signaling.
Finally, a host of targeting proteins dictate the subcellular
localization and substrate specificity of PP1 (61). These include
several glycogen-binding proteins: GM in skeletal muscle (62), GL in liver (63), PTG (protein
targeting to glycogen) in adipose tissue
(64), and the myosin-binding complex in smooth muscle (65). PP1 also
binds to ribosomal protein L5 (66); an RNA splicing factor (67); and
three nuclear proteins, p53BP2 (68), Sds22p (69), and the
retinoblastoma gene product pRB (22). Affinity purification of PP1
complexes (70) and interaction cloning with PP1 as bait (71) suggest
that many PP1-binding proteins remain undiscovered. Libraries of PP1
mutants might be used to analyze the unique elements that mediate
binding of potential PP1 regulators and provide new tools to establish
their physiological role.
We thank our many colleagues, in particular
John York (Duke University), for thoughtful comments on the manuscript
and John Kuriyan (Rockefeller University) for providing the coordinates for the PP1
crystal structure. We also thank Miriam Khalil for help
with some of the yeast two-hybrid experiments.