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Biochemical Society Transactions (2005) Volume 33, part 6
Transcriptional control by chromosome-associated
protein phosphatase-1
D. Bennett1
Department of Zoology, Oxford University, South Parks Road, Oxford OX1 3PS, U.K.
Abstract
Tight regulation of gene expression is critical for cells to respond normally to physiological and environmental
cues and to allow cell specialization. Reversible phosphorylation of key structural and regulatory proteins,
from histones to the transcriptional machinery, is acknowledged to be an important mechanism of regulating
spatial and temporal patterns of gene expression. PP1 (protein phosphatase-1), a major class of serine/
threonine protein phosphatase, is found at many sites on Drosophila polytene chromosomes where it is
involved in controlling gene expression and chromatin structure. PP1 is targeted to different chromosomal
loci through interaction with a variety of different regulatory subunits, which modify PP1’s activity towards
specific substrates. This mini-review gives an overview of known chromosome-associated PP1 complexes,
their role in transcriptional control and the prospects for future analysis.
Introduction
Protein phosphatase-1 (PP1) has been found in organisms
from yeast to human and is one of the most conserved enzymes known. PP1 is involved in the regulation of many
cellular processes including glycogen metabolism, cell division and signal transduction [1,2]. Metazoans from Drosophila to humans have multiple genes encoding PP1c (PP1
catalytic subunit) isoforms [3]. Biochemical and genetic
analysis suggests that the different isoforms have overlapping
and pleiotropic functions. In vitro, the catalytic subunits
dephosphorylate a wide range of substrates, but in vivo the
catalytic subunits are associated with regulatory subunits that
target PP1c to particular loci and regulate their activity and
substrate specificity. Many regulatory subunits share a common PP1c-binding motif (Lys/Arg, Val/Ile, Xaa and Phe/Trp/
Tyr), leading to the formation of different PP1 holoenzymes
with distinct functional properties despite sharing the same
catalytic subunit [1,2]. An idea that has emerged from the
study of PP1 holoenzymes is that they often function to
promote basal and/or energy conserving states [4]. Accordingly, in transcriptional control, PP1 is implicated in promoting repressive epigenetic states, attenuating transcriptional
activators and recycling transcriptional machinery.
Chromosome-associated PP1 complexes
On Drosophila polytene chromosomes, PP1c is found at
many discrete sites, which are widely distributed along the
chromosomes (Figure 1) [5]. This distribution probably
reflects PP1c’s ability to interact with a number of different
Key words: Drosophila, polytene chromosome, protein phosphatase-1 catalytic subunit,
protein phosphatase-1 regulatory subunit, reversible phosphorylation, serine/threonine protein
phosphatase-1.
Abbreviations used: EED, embryonic ectoderm development; HDAC, histone deacetylase; PP1,
protein phosphatase-1; NIPP1, nuclear inhibitor of PP1; PNUTS, PP1 nuclear targeting subunit;
PP1c, PP1 catalytic subunit; Trx, trithorax.
1
email [email protected]
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Biochemical Society
chromosome-associated protein complexes. Complexes that
have been identified either in Drosophila or in mammals are
shown in Figure 2. A significant feature of many of these complexes is that they contain various histone-modifying or
chromatin-remodelling enzymes, providing a link between
alterations in chromatin structure and transcriptional control.
For instance, trithorax (trx) encodes a SET (suppressor of
variegation 3–9, enhancer of zest and trithorax) domain protein in Drosophila with histone methyltransferase activity. trx
belongs to the trx group of genes that is involved in maintaining active transcription of homoeotic genes and other genes
after their initial activation [6]. PP1c binds directly to Trx
protein, co-localizes with Trx on polytene chromosomes
(Figure 1) and antagonizes trx function in vivo [5]. Genetic
analysis with different isoforms of PP1c indicates that there
may be specific roles for different PP1c–Trx complexes [7]. In
mammals, PP1c is also a member of a trimeric complex containing PP1c, Gadd34 and SNF5, a component of the SWI/
SNF chromatin-remodelling complex that repositions nucleosomes [8,9]. SNF5/Snr1 and Gadd34 have been shown to
bind Trx and Hrx (a human Trx homologue) respectively,
suggesting the potential for functional interactions between
these complexes. PP1c has also been shown to be part of a
repressive complex consisting of NIPP1 (nuclear inhibitor of
PP1) and EED (embryonic ectoderm development), a member of the Polycomb group proteins that act antagonistically
to Trx and maintain transcriptional repression of homoeotic
genes. Like EED, NIPP1 can function as a transcriptional
repressor of targeted genes [10]. The class I HDAC2 (histone deacetylase 2), which has been suggested to mediate,
at least in part, the transcriptional repression by EED, is
also a component of this complex. In another context, PP1
is a component of a class I HDAC complex containing
HDAC2 and HDAC1, which functions to promote dephosphorylation and inactivation of CREB (cAMPresponse-element-binding protein) [11], indicating that PP1
has the potential to modify the activity of transcription factors
The Nucleus and Gene Expression
Figure 1 PP1c co-localizes with Trx on salivary-gland polytene chromosomes
Merging of (A) the green signal representing Trx with (B) the red signal representing HA (haemagglutinin)-tagged PP1c
identified sites where these proteins co-localize (C). Inset shows an enlarged view of one chromosomal region (indicated by
arrows) showing co-localization of Trx and PP1c staining. Figure reprinted by permission from EMBO Reports 4, pp. 59–63,
Rudenko, A., Bennett, D. and Alphey, L. ‘Trithorax interacts with type 1 serine/threonine protein phosphatase in Drosophila.’,
c 2003 Macmillan Publishers Ltd. http://www.nature.com/embor/
Figure 2 Model of potential chromosome-associated PP1 complexes, which may account for localization of PP1c to many different loci
on polytene chromosomes (Figure 1)
Known PP1 regulatory proteins in these complexes include Gadd34, NIPP1 and PNUTS. Transcriptional repressors are
represented by large circles; transcriptional activators are represented by hexagons. See main text for additional details.
Other chromosome-associated proteins that potentially interact with these complexes are not shown for clarity. CREB,
cAMP-response-element-binding protein.
associated with chromosome-associated complexes. PP1
binds directly to the class II HDAC, HDAC6 [12]. However,
targeting of PP1 to HDAC1 may be performed by a regulatory protein such as the PNUTS (PP1 nuclear targeting subunit), an abundant chromatin-associated PP1-binding protein, which is also a member of the HDAC1–PP1 complex
[11]. The in vivo role of PNUTS is not known, but recent
in vitro studies suggest a role for it in chromatin decondensation [13].
Future directions
Despite much progress over the past few years in identifying
chromosome-associated regulatory subunits of PP1 and associated complexes, many questions regarding the role and
regulation of PP1 have yet to be answered. For instance,
the effects of PP1 on the phosphorylation state and biochemical activity of the associated complexes, or on posttranslational modifications to the underlying chromatin,
have not been fully examined. Non-binding mutants of the
PP1-interacting proteins (in which the canonical PP1-bind-
ing motif is disrupted) offer a way to dissect and independently manipulate PP1’s various roles [14,15]. Genetic and
biochemical analysis of complexes with and without PP1 will
allow the identification of relevant substrates of PP1 and
will reveal the functional effects of reversible phosphorylation from the level of the whole organism down to specific
gene loci on chromosomes. The wealth of genetic and developmental information and techniques such as the visualization of locus-specific distributions of chromatin-associated proteins on polytene chromosomes makes Drosophila
the organism of choice to address these questions. Misappropriation, deregulation or disruption of chromosome-associated complexes is thought to play an important role in
the molecular pathogenesis of a variety of diseases such
as cancer. Therefore the analysis of chromosome-associated
PP1 complexes will not only help us to understand the role
of PP1 in transcriptional programmes underlying normal
development but also may ultimately provide new insights
into molecular processes underlying disease states and
provide novel strategies for therapeutic intervention.
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Biochemical Society Transactions (2005) Volume 33, part 6
This work is supported by the Biotechnology and Biological Sciences
Research Council with additional support from the Royal Society. D.B.
is Todd-Bird Research Fellow at New College, Oxford.
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Received 5 July 2005