Download Unicellular Eukaryotes to Humans Protein Arginine

Protein Arginine Methyltransferases: from
Unicellular Eukaryotes to Humans
François Bachand
Eukaryotic Cell 2007, 6(6):889. DOI: 10.1128/EC.00099-07.
Published Ahead of Print 27 April 2007.
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EUKARYOTIC CELL, June 2007, p. 889–898
1535-9778/07/$08.00⫹0 doi:10.1128/EC.00099-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
Vol. 6, No. 6
MINIREVIEW
Protein Arginine Methyltransferases: from Unicellular Eukaryotes
to Humans䌤
François Bachand*
no enzymatic activity has yet been described for human
PRMT2 (83). As can be seen in Fig. 1B, the primary structure of each PRMT shares a conserved methyltransferase
domain that includes subdomains for binding to the methyl
donor, S-adenosyl-L-methionine (SAM) and substrate proteins.
Eukaryotic cells extend their polypeptide diversity beyond
the constraints of the encoded amino acids by means of posttranslational modifications. These modifications regulate the
stability, localization, activity, and probably other as-yet-uncharacterized protein functions. Methylated derivatives of
arginines were identified 40 years ago from acidic lysates of
nuclear extracts (69). However, the first genes encoding protein arginine methyltransferases (PRMTs) were identified only
a decade ago (29, 37, 54). Since this important discovery, the
study of protein arginine methylation has been a rapidly expanding field, and PRMT-encoding genes have been identified
from the sequenced genomes of yeasts, worm, fly, plants, and
mammals but not prokaryotes (7, 28, 60). Here, I will focus on
the current knowledge of PRMTs predicted to be expressed in
several unicellular eukaryotic species. References and comparisons to the functional roles played by these evolutionarily
conserved PRMTs in higher eukaryotes, especially humans,
will also be discussed.
PRMTs are divided into four major classes depending on the
type of methylarginine they generate (Fig. 1A). Type I and II
PRMTs both catalyze monomethylation of the guanidinium (␻)
nitrogen of specific arginine residues in proteins; yet, they differ
on the type of dimethylarginine they generate (Fig. 1A). Type I
PRMTs modify proteins by the catalysis of asymmetric NG,NGdimethylarginine, whereas type II PRMTs catalyze the formation
of symmetric NG,N⬘G-dimethylarginine. Type III enzymes catalyze only the monomethylation of arginine residues in proteins
(64). It remains unclear, however, whether such enzymes are
dedicated for the catalysis of ␻-NG-monomethylarginine or if the
modified monomethylarginine is an intermediate to additional
steps of methylation. A less common form of methylarginine is
one in which the delta (␦) nitrogen atom of arginine residues is
modified by type IV PRMTs (Fig. 1A). As yet, protein arginine
methylation by the type IV PRMTs has been characterized only
in Saccharomyces cerevisiae (67) and is less abundant than protein
arginine methylation of the guanidinium nitrogen.
In humans, nine PRMTs have so far been identified (Fig.
1B): the type I arginine methyltransferases PRMT1,
PRMT3, PRMT4, PRMT6, and PRMT8, as well as those of
type II, PRMT5, PRMT7, and PRMT9. Although PRMT2
demonstrates a significant degree of similarity to PRMT1,
PROTEIN ARGININE METHYLATION IN
UNICELLULAR EUKARYOTES
Although evidence for protein arginine methylation was reported for Leishmania (71) and Trypanosoma (103) species, the
evolutionary conservation of human PRMTs in unicellular eukaryotes has not been thoroughly investigated. With the recent
sequencing and annotation of genomes from several unicellular eukaryotes, it is now possible to identify and characterize
homologs of the different human PRMTs in various species.
Table 1 presents an overview of the evolutionary conservation
of each human PRMT in 10 unicellular eukaryotes, including
yeasts, molds, amoebae, and protozoa. This analysis reveals
that PRMT1, PRMT3, and PRMT5 are the arginine methyltransferase-encoding genes that were most strictly conserved
throughout eukaryotic evolution. Furthermore, it can be seen
that PRMT2, PRMT8, and PRMT9 do not appear to have
homologs in any of the unicellular eukaryotes shown in Table
1. These three methyltransferases may have evolved as a requirement for tissue-specific functions in multicellular organisms. Accordingly, Northern blotting analyses of PRMT2 and
PRMT8 demonstrate tissue-specific mRNA expression (46,
83). Conversely, the PRMT1, PRMT3, PRMT4, PRMT5, and
PRMT6 mRNAs are more widely expressed in human tissues,
and proteins with homology to some of these methyltransferases can be identified in unicellular eukaryotes (Table 1).
Gene products with low amino acid sequence similarity to
human PRMT7 were also found in Leishmania major and
Trypanosoma brucei (Table 1). The current state of knowledge
about the biology of the highly conserved methyltransferases
PRMT1, PRMT3, and PRMT5 will be discussed in the next
sections.
PROTEIN ARGININE METHYLTRANSFERASE 1
The first studies reporting a gene product with protein arginine methyltransferase activity were published in 1996 after
the identification of the budding yeast heterogeneous nuclear
ribonucleoprotein (hnRNP) methyltransferase 1 (HMT1, or
* Mailing address: Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada. Phone: (819) 8206868. Fax: (819) 564-5340. E-mail: [email protected].
䌤
Published ahead of print on 27 April 2007.
889
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Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
890
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RMT1) (29, 37) and of human PRMT1 (54). Amino acid
analysis by ion exchange chromatography indicates that
PRMT1 is the methyltransferase responsible for the majority
of asymmetric dimethylation (aDMA) in budding yeast (29),
trypanosomes (73), and human cells (72). Consistently, yeast
PRMT1 is an abundant protein with approximately 37,600
molecules/cell as determined by quantitative immunoblotting
(30). Such a level is comparable to the number of specific
translation initiation factors and proteins involved in ribosome
assembly (30). Structures of PRMT1 from budding yeast and
humans have also been resolved by X-ray crystallography (99,
107). Both crystals reveal the formation of a dimer ring that is
characterized by a large acidic cavity at the dimer interface.
This acidic cleft forms a binding surface that targets arginines
of positively charged arginine-rich regions of substrate proteins
for methylation. Consistently, structure-function analyses reveal that dimerization is essential for PRMT1 function, as
substitutions that replace the helix-loop-helix domain involved
in dimer formation lead to a loss of catalytic activity and
function in vivo (99). The oligomerization of PRMTs has also
been proposed to favor enzymatic processivity whereby
monomethylated arginines could be dimethylated by adjacent
active sites without substrate release (107).
PRMT1 is found in the cytoplasm and the nucleus of both
yeast and human cells (5, 30, 93). The pathway by which it is
imported into the nucleus, however, remains to be determined,
as PRMT1 appears to lack a nuclear localization signal. One
possibility is that PRMT1 is indirectly imported into the cell
nucleus via association with unmethylated substrates. Such a
model is supported by mobility assays of live human cells that
demonstrate nuclear accumulation of PRMT1 upon the inhibition of cellular methylation (38).
Our knowledge about the biochemistry and biology of
PRMT1 is best understood from studies of the budding yeast
Saccharomyces cerevisiae. In this organism, two main functions
have been ascribed to PRMT1: mRNA biogenesis and hetero-
TABLE 1. Conservation of type I and II PRMTs across simple eukaryotesa
% Of identity to human PRMTb
Organism
Cryptococcus neoformans
Schizosaccharomyces pombe
Saccharomyces cerevisiae
Candida albicans
Aspergillus nidulans
Neurospora crassa
Dictyostelium discoideum
Leishmania major
Trypanosoma brucei
Toxoplasma gondii
PRMT1
PRMT2
PRMT3
PRMT4
PRMT5
PRMT6
PRMT7
PRMT8
PRMT9
50
49
38
41
46
46
50
41
43
45
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
32
33
ND
ND
36
33
ND
ND
ND
30
?
ND
ND
ND
ND
ND
ND
ND
ND
?
38
33
27
ND
37
33
46
23
21
32
ND
ND
ND
ND
ND
ND
?
?
?
ND
ND
ND
ND
ND
ND
ND
ND
?
?
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
ND
a
The amino acid sequences of human PRMT1 to PRMT9 were used as bait for BLAST searches. The search and collection of related information was performed
at the following websites: NCBI (www.ncbi.nlm.nih.gov), the Wellcome Trust Sanger Institute (www.sanger.ac.uk), the BROAD Institute (www.broad.mit.edu/tools
/data/seq.html), the ToxoDB (www.toxodb.org/toxo/home.jsp), and the Saccharomyces Genome Database (www.yeastgenome.org).
b
The percentages of identity were derived after amino acid sequence alignments using ClustalW (www.ebi.ac.uk/services). ND, not determined. ?, a gene product
with low amino acid sequence similarity to this human PRMT has been found in this organism (see text).
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FIG. 1. Methylated arginine derivatives and PRMTs. (A) The structure of methylated arginine derivatives. (B) Schematic representation of the
nine mammalian PRMTs, all containing a conserved methyltransferase (MTase) domain. SH3, Src-homology 3; Zn, zinc finger; Myr, myristoylation; and F-box motifs of specific PRMTs are shown.
VOL. 6, 2007
891
main of the human DNA endonuclease, MRE11, is arginine
methylated by PRMT1 (12). Significantly, a decrease in
MRE11 methylation results in defective S-phase checkpoint
control (12). The evolutionary conservation of this PRMT1
function in unicellular eukaryotes seems unlikely, however, as
arginine-rich domains do not appear to be present in yeast
homologs of MRE11.
Given the important cellular roles played by PRMT1 and
the conservation of the PRMT1 gene in eukaryotes (Table
1), it is surprising to learn that expression of this gene is not
required for cell viability in yeasts and mammals (5, 29, 37,
72). Nevertheless, PRMT1 is essential during development
as mice in which PRMT1 expression has been significantly
reduced die during embryogenesis (72). PRMT1 also appears to play an important role in the Trypanosoma life
cycle. A recent chromosome-wide screen for gene function
in Trypanosoma brucei indicates growth impairment and nuclear defects in the bloodstream form of the parasites after
depletion of PRMT1 expression via RNA interference (90).
However, this growth defect is not observed in the procyclic
form of the parasites (73). It appears unlikely that this
stage-specific growth defect is explained by the role of
PRMT1 in T. brucei mitochondrial gene expression (33), as
mitochondrial activity is significantly reduced in the bloodstream form of T. brucei (8, 9).
PROTEIN ARGININE METHYLTRANSFERASE 3
The conserved methyltransferase core domain of PRMT3
was the first PRMT structure obtained (108). This structure
suggested that a putative dimer interface is involved in the
mechanism for the methylation reaction (108). As mentioned
previously, the formation of a dimer ring was later confirmed
after the structure of PRMT1 was resolved (99, 107). Human
PRMT3 was originally identified from a two-hybrid screen that
used PRMT1 as a bait protein (93). The formation of PRMT1/
PRMT3 oligomers is unlikely, however, as these methyltransferases do not appear to cofractionate as determined by gel
filtration chromatography (93). Searches for arginine methyltransferase homologs in eukaryotic lineages reveal that
PRMT3 is not as strictly conserved as PRMT1 (see Table 1).
Genes with significant homology to the PRMT3 gene are found
in S. pombe and Drosophila melanogaster but not in S. cerevisiae
and Caenorhabditis elegans (5). Homologs of PRMT3 can also
be identified in other unicellular eukaryotes, such as Cryptococcus, Aspergillus, Neurospora, and Toxoplasma species (Table
1).
PRMT3 is a cytosolic protein that contains a single C2H2type zinc finger domain in the amino-terminal part of the
protein that is conserved among rats and humans (93). The
cytoplasmic localization and the zinc finger domain are also
features of the fission yeast homolog of mammalian PRMT3
(5). Truncation of the amino-terminal region of PRMT3, including its zinc finger motif, results in an enzyme that can
methylate arginine residues of a recombinant substrate but
cannot methylate substrates from a total cell extract (25).
Based on these results, it was concluded that the zinc finger
domain is key for PRMT3 substrate selectivity. Interestingly,
amino acid sequence alignments between PRMT3 homologs
indicate that the zinc finger domain of PRMT3 is not strictly
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chromatin formation. One of the first demonstrations of the
functional consequence of PRMT1-dependent arginine methylation was on the kinetics of nucleocytoplasmic transport.
Using a temperature-sensitive strain with a substitution in a
nucleoporin that blocks only nuclear import, it was demonstrated that nuclear export of the yeast RNA-binding proteins
Npl3, Hrp1, and Nab2 is perturbed in PRMT1-null cells (34,
85). Subsequent studies with humans showed that PRMT1
affects the subcellular localization of a number of PRMT1
substrates (21, 66, 89). Additional insights into the biological
role of PRMT1 have recently been obtained from genomewide studies of yeast. A combination of chromatin immunoprecipitation assays (ChIP) and whole-genome microarrays indicate that PRMT1 is recruited to actively transcribed genes
and that arginine methylation modulates the recruitment of
different PRMT1 substrates during mRNA synthesis (104).
Accordingly, the kinetics of transcript release from sites of
transcription are delayed in PRMT1-null cells (104). Since an
important biochemical effect of arginine methylation is the
regulation of protein-protein interactions (59, 100, 104), these
studies suggest that arginine methylation by PRMT1 is involved in modulating the architecture of mRNA synthesis for
the proper release of messenger RNPs from sites of transcription and subsequent nuclear export. Therefore, the nuclear
accumulation of specific RNA-binding proteins in PRMT1-null
cells may be explained in part by the effect of PRMT1 on
mRNA production, as several PRMT1 substrates exit the nucleus in association with polyadenylated mRNAs (34, 49).
Regulation of RNA-binding proteins by PRMT1-dependent
arginine methylation was also described in fission yeast. In this
organism, PRMT1 modulates the oligomerization level and the
growth inhibitory effect of the S. pombe homolog of the human
nuclear poly(A)-binding protein (PABP2) (74). These findings
are significant, given the suspected role of PABP2 oligomerization in the formation of nuclear aggregates found in oculopharyngeal muscular dystrophy, a syndrome linked to mutations in the human PABP2 gene. Therefore, fission yeast
should prove to be a useful model system with which to understand the biological significance of PABP2 methylation at
arginines.
Recently, a role for PRMT1 in the establishment and maintenance of silent chromatin was demonstrated with budding
yeast (105). Transcription profiles from PRMT1-null cells indicate upregulation of RNAs expressed near telomere-proximal regions, mating loci, and ribosomal DNA repeats. Since
these chromosomal regions are normally condensed into silent
chromatin (80), these data suggest defects in the formation of
such chromatin structure in PRMT1-null cells. Accordingly, a
survey of silent loci occupancy by ChIP assays reveals a reduction in the recruitment of the silent information regulator 2
(Sir2) as well as a corresponding increase in acetylated histone
H4 in a strain that expresses a catalytically inactive version of
PRMT1 (105). The role of histone H4 arginine-3 methylation
in PRMT1-dependent heterochromatin formation has been
proposed (105); yet, it remains unclear whether PRMT1 is the
methyltransferase responsible for this specific modification of
histone H4 in yeast (45). A role for PRMT1 in the maintenance of genomic integrity in humans was also reported. From
a proteomic screen for arginine methylated substrates in human cells (11), it was demonstrated that the arginine-rich do-
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conserved. As can be seen in Fig. 2, the canonical cysteine and
histidine residues that constitute the zinc finger motif are not
conserved in PRMT3 from Neurospora, Aspergillus, and Cryptococcus species. Based on the lack of conservation in the zinc
finger domain, the Aspergillus nidulans RmtB methyltransferase was previously classified in a separate group within the
PRMT family (95). Despite the lack of conservation in the
zinc-binding cysteine and histidine residues of the predicted
PRMT3 homologs from N. crassa, A. nidulans, and C. neoformans, their amino-terminal domains demonstrate significant
homology in terms of amino acid identity and spacing for two
blocks of highly conserved residues. These blocks are referred
to as conserved region 1 (CR1) and CR2 (Fig. 2). In addition,
the overall percentages of identity of PRMT3 between humans
and N. crassa, A. nidulans, and C. neoformans (33, 36, and 32%,
respectively) are similar to the identity calculated after alignments of human PRMT3 and its characterized S. pombe homolog (33%). Based on the strong similarities of their aminoterminal domains and the overall percentage of identity, it is
therefore likely that the discussed methyltransferases from N.
crassa, A. nidulans, and C. neoformans are closely related to the
PRMT3 methyltransferase.
The first insight into the biological role of PRMT3 was
obtained from studies of fission yeast. Tandem affinity purification coupled with mass spectrometric protein identification
indicates that specific components of the translation machinery
copurify with S. pombe PRMT3. Accordingly, the 40S ribosomal protein S2 (rpS2) was the first physiological substrate of
PRMT3 to be identified (5). This role of PRMT3 in rpS2
methylation is evolutionarily conserved (91) and likely suggests
a significant role for PRMT3 in ribosome function among
eukaryotes. Indeed, the deletion of the PRMT3 coding sequence in fission yeast produces unmethylated rpS2 and yields
an imbalance in the 40S/60S ribosomal subunit ratio (5). Significant changes at the levels of monosomes and polysomes are
not seen, however, consistent with the absence of growth defects in PRMT3-null cells. In a recent study, the genome-wide
biological response of PRMT3-null cells to the ribosomal subunit imbalance was investigated. Whereas hardly any changes
were noted at the transcriptional level in PRMT3⌬ cells, nearly
all of the 40S ribosomal protein-encoding mRNAs showed
increased ribosome density in PRMT3-null cells (4). Sucrose
gradient analysis also indicated that PRMT3⌬ cells have reduced levels of small ribosomal subunits (4). These findings
thus suggest that PRMT3-null cells respond to a small ribosomal subunit deficit by upregulating the translational effi-
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FIG. 2. Amino acid sequence alignment of the amino-terminal domains of PRMT3 from multiple species. Identical amino acids are shown in
black, and similar amino acids are shown in gray. The predicted zinc finger domain, the conserved region 1 (CR1) and CR2, and the PRMT-specific
motif I are boxed. Asterisks are present under the canonical cysteine and histidine residues of the zinc finger motif. Sequence are from Neurospora
crassa (Nc), Aspergillus nidulans (An), Homo sapiens (Hs), Drosophila melanogaster (Dm), Schizosaccharomyces pombe (Sp), Cryptococcus
neoformans (Cn), and Toxoplasma gondii (Tg). Alignment and shading were generated using ClustalW and Boxshade software.
VOL. 6, 2007
PROTEIN ARGININE METHYLTRANSFERASE 5
Every multicellular eukaryote from which the genome has
been sequenced and annotated appears to encode the type II
methyltransferase PRMT5. As can be seen in Table 1, the
evolutionary conservation of the PRMT5 gene among unicellular eukaryotes is significant. The fungus Candida albicans
appears to be an exception, however, as a gene with homology
to PRMT5 could not be found (96 and Table 1). Given the
significant conservation of PRMT5 across eukaryotic species, it
is possible that C. albicans uses another gene product to accomplish the evolutionarily conserved function of the PRMT5
methyltransferase.
Although this evolutionary conservation suggests a key functional role for PRMT5, deciphering the biological function of
this methyltransferase has been challenging. A number of studies of PRMT5 have been published, using different model
organisms, including budding and fission yeasts, Drosophila,
Xenopus, and human; yet, an evolutionarily conserved function
for this methyltransferase remains elusive. Whereas the apparent budding and fission yeast homologs of PRMT5, histone
synthetic lethal 7 (Hsl7) and Shk1-binding protein 1 (Skb1),
respectively, demonstrate catalytic activity in vitro (6, 47, 94), a
physiological substrate for PRMT5 has yet to be identified in
these unicellular eukaryotes. Furthermore, recent evidence indicates that Hsl7 catalyzes only the formation of monomethylarginine in vitro, as the formation of symmetrical dimethylarginine was not detected using a variety of artificial substrates
(64). This is in contrast to mammalian cells where evidence
strongly supports the PRMT5-dependent formation of symmetrical dimethylarginine in several proteins, including specific
Sm proteins of the small nuclear ribonucleoprotein core par-
893
ticle (10, 27, 63), the Coilin protein (10, 36), histones H3 and
H4 (70), and the methyl-DNA binding domain protein 2 (92).
It is unclear whether any of these proteins represent evolutionarily conserved PRMT5 substrates such as rpS2 for PRMT3 (5,
91) and PABP2/PABPN1 (74, 88) or fibrillarin/Nop1 (53, 101)
for PRMT1. Therefore, the search for endogenous substrates
of the PRMT5 methyltransferase in unicellular eukaryotes is
ongoing. Alternatively, PRMT5 homologs in some unicellular
eukaryotes may have evolved functional roles independent of
methyltransferase activity, as appears to be the case with S.
cerevisiae (see discussion below).
Functionally, biochemical and genetic evidence link S. cerevisiae Hsl7 and S. pombe Skb1 to regulatory steps of the cell
cycle at the G2/M transition. However, both genes appear to
control different molecular events such that Hsl7 and Skb1
have been reported as positive and negative regulators, respectively, of the G2/M transition. The HSL7 gene was originally
identified in a genetic screen designed to identify secondary
mutations that are lethal when combined with a deletion of the
amino-terminal tail of histone H3 (57). HSL7-null cells are
viable but show elongated buds and a delay in the G2 phase of
the cell cycle (57). In S. cerevisiae, mitotic entry is promoted by
the inactivation of the Swe1 kinase, which phosphorylates and
inhibits the cyclin-dependent kinase Cdc28 (48). The current
data on Hsl7 suggest the following model: a direct interaction
between the Hsl1 kinase (identified in the same synthetic lethal
screen as Hsl7) and Hsl7 leads to the Hsl1-dependent localization of Hsl7 to bud necks (17, 87). Phosphorylation of Hsl7
by Hsl1 also appears to be important for tethering Hsl7 to bud
necks, as a kinase-dead version of Hsl1 perturbs this specific
localization of Hsl7 (94). A physical interaction between Swe1
and Hsl7 at the G2/M stage would recruit increasing concentrations of Swe1 to bud necks (17, 55, 61, 62) to trigger sequential phosphorylation of Swe1 by bud neck-localized kinases, including Cla4 and the polo-like kinase, Cdc5 (3, 81, 87).
This highly phosphorylated form of Swe1 undergoes efficient
degradation (3, 81), presumably via the ubiquitin-dependent
proteasome pathway (42). Therefore, deletion of HSL7 results
in a constitutively activated morphogenesis checkpoint control
in budding yeast due to Swe1 accumulation at the G2/M phase
and a consequent impairment in budding.
Significantly, catalytically inactive versions of Hsl7, as confirmed by in vitro methyltransferase assays, rescue the elongated bud phenotype of HSL7-null cells (17, 94). This is in
contrast to a report suggesting that the protein methyltransferase activity of human PRMT5 is required in yeast for
complementation of the budding defect of HSL7-null cells
(47). The expression of the catalytically inactive version of
human PRMT5 was not confirmed in this study, however.
Therefore, the available data for the role of Hsl7 in the morphogenesis checkpoint control would strongly suggest that the
methyltransferase activity of Hsl7 is not required.
Although the role of Hsl7 in cell cycle control is fairly well
understood, the molecular basis for the genetic interaction
between HSL7 and histones has remained unclear for over a
decade after its discovery. A recent study shed some light on
these poorly understood genetic interactions. It was shown that
a number of genes encoding chromatin-modifying enzymes,
including the acetyltransferases Gcn5 and Esa1, the deacetylase Rpd3, and the lysine methyltransferase Set1, result in
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ciency of 40S ribosomal protein mRNAs. Accordingly, such a
compensatory mechanism could explain the viable phenotype
of PRMT3-null cells by providing a sufficient number of small
subunits, and thus functional ribosomes, to accommodate
global protein synthesis and survival. Future studies are
needed to determine the nature of the 40S ribosomal subunit
deficit in the absence of PRMT3 expression in fission yeast.
Ribosomal proteins are subject to a variety of posttranslational modifications including acetylation, ubiquitination,
phosphorylation, and methylation (50, 56). In fact, asymmetric
dimethylarginine is the predominant methylated amino acid in
both the eukaryotic 40S and 60S ribosomal subunits (15). Arginine methylation of ribosomal proteins is evolutionarily conserved among eukaryotes (44, 51, 78) and fluctuates during the
cell cycle (14). Ribosomal proteins can also be modified by
lysine methylation, and methyltransferases that catalyze such
modifications in ribosomal proteins were recently identified in
eukaryotes (75, 76). Interestingly, internal ribosome entry site
(IRES)-bound ribosomes contain a different methylation pattern than native ribosomes (106), suggesting a role for methylation in translation control. It will be of great interest to study
the role of ribosomal protein methylation, given the evolutionary conservation of this modification. Similar to posttranslational modifications of nucleosomal histones (41), ribosome
heterogeneity via combinations of ribosomal protein modifications may represent a key layer of gene regulation by controlling translation of specific cellular transcripts.
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hyperosmolarity (6). Although the molecular mechanism by
which Skb1 provides an adaptive response in S. pombe under
osmostress conditions remains to be determined, evidence suggest that it may involve the methyltransferase activity of Skb1.
In vitro assays using Skb1 that was immunopurified from extracts of cells that were previously subjected to high osmolarity
indicate that the methyltransferase activity of Skb1 is stimulated under hyperosmotic conditions. As yet, this is the only
report providing evidence that the methyltransferase activity of
a PRMT is regulated in unicellular eukaryotes. In humans,
stimulation of cells in culture by the nerve growth factor has
been reported to increase the catalytic activity of PRMT1 (18).
TYPE IV PROTEIN ARGININE METHYLTRANSFERASES
Most of the characterized protein arginine methyltransferases mediate the addition of methyl groups onto the guanidino (␻) nitrogens of arginine residues of proteins (Fig. 1A).
Nevertheless, an unusual PRMT that catalyzes methylation of
the delta (␦) nitrogen atom of arginines within proteins has
been identified in S. cerevisiae (67, 109). This arginine methyltransferase, designated Rmt2, is not essential for cell viability
and accumulates in granulated and punctuated structures in
both the nucleus and the cytoplasm of yeast cells, as determined by fluorescence microscopy (67, 68). Interestingly,
whereas the ability of budding yeast PRMT1 to modify protein
substrates is not affected by translational inhibitors (101),
Rmt2 appears to act on protein substrates in a cotranslational
manner (67). Therefore, it remains to be determined whether
the nuclear pool of Rmt2 acts enzymatically. In vitro methylation assays using recombinantly expressed Rmt2 identified the
large ribosomal subunit protein rpL12 as a substrate of this
methyltransferase (16). However, the association of Rmt2 with
rpL12 and/or ribosomes, as well as the role of Rmt2 in ribosome function, remains elusive. The association between Rmt2
and specific nucleoporins was also recently demonstrated (68).
Without any functional data, however, the role of Rmt2 in
biological activities related to the ribosome and the nuclear
pore complex remains to be established.
Genes encoding products with significant amino acid identity to budding yeast Rmt2 are found in the genomes of Schizosaccharomyces, Aspergillus, Candida, Neurospora, and Cryptococcus species. Rmt2 does not appear to be conserved in
protozoa, however, as genes similar to RMT2 were not found in
Leishmania major, Trypanosoma brucei, Dictyostelium discoideum, and Toxoplasma gondii. Similarly, a protein with significant homology to yeast Rmt2 is not found in the human
genome. However, Rmt2 does share a low degree of sequence
similarity to the human guanidinoacetate N-methyltransferase
(GMAT). The enzymatic activity of GMAT is responsible for
SAM-dependent methylation of the ␦-nitrogen atom of guanidinoacetate into creatine, and therefore, the shortage in
GMAT activity leads to creatine deficiency syndromes in humans (82). Despite the existence of a human enzyme such as
GMAT that specifically modifies the ␦-nitrogen atom of guanidine derivatives, the absence of a strong candidate for an
Rmt2 homolog in protozoa and mammals suggests that a protein arginine methyltransferase with such an enzymatic activity
has not been evolutionarily conserved.
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synthetic lethality when combined with either HSL7⌬ or
HSL1⌬ (79). Whereas the enzymatic activity of Rpd3 and
Gcn5 are required in HSL7-null cells, the methyltransferase
activity of Hsl7 is dispensable in RPD3⌬, SET1⌬, and GCN5⌬
cells. Furthermore, deletion of the SWE1 gene suppresses all
of the synthetic lethal interactions between HSL7 and the
above-mentioned chromatin modifiers. These data suggest that
the molecular basis for the synthetic lethality between Hsl7 and
histones results from the inability to trigger a transcriptional
response via specific chromatin modifications to circumvent
the constitutive morphogenesis checkpoint that is activated in
HSL7-null cells. This transcriptional response would require
chromatin modifications at the amino-terminal tail of histones
H3/H4 that are mediated, at least in part, by Gcn5, Rpd3,
Esa1, and Set1 but do not appear to involve histone methylation by Hsl7. This is consistent with the lack of Hsl7-dependent methylation observed upon amino acid analyses of endogenous yeast histones (64). Therefore, whether Hsl7 acts
enzymatically in S. cerevisiae remains to be established.
In the fission yeast S. pombe, the homolog of human PRMT5
was originally identified as an Shk1-binding protein (Skb1) via
a two-hybrid screen (32). Shk1 is the fission yeast homolog of
the S. cerevisiae Ste20 and of the mammalian p21-activated
kinase (58), two kinases that are involved in Ras-dependent
signaling cascades. As for S. cerevisiae Hsl7, Skb1 expression is
not essential for cell viability. Compared to normal fission
yeast, however, SKB1-null cells have a less elongated morphology (32). Conversely, whereas overexpression of Skb1 in fission
yeast does not appear to affect growth, it leads to hyperelongated cells (31, 32). These phenotypes are consistent with Skb1
being a negative regulator of mitosis. Accordingly, Gilbreth
et al. (31) demonstrated that deletion of the SKB1 gene partly
suppresses the cell cycle block in G2 that normally occurs upon
inactivation of Cdc25, the phosphatase targeting Wee1 (Wee1
is the homolog of the S. cerevisiae Swe1). Furthermore, the
hyperelongated cell phenotype observed upon increasing SKB1
gene dosage is dependent on the mitotic regulator Wee1 (31).
Because catalytically inactive versions of Skb1 were not assayed in these experiments, it remains unknown whether the
methyltransferase activity of Skb1 is required for cell cycle
control in fission yeast. Therefore, despite the observations
where Skb1 and Hsl7 both regulate the transition between the
G2 and M phases of the cell cycle, they appear to have evolved
to control opposite checkpoint mechanisms of mitotic entry. In
Xenopus laevis, PRMT5 was also shown to regulate the stability
of Xenopus Swe1 in a methyltransferase-independent fashion
(102). As opposed to budding yeast, where Hsl7 regulates the
morphogenesis checkpoint, Xenopus PRMT5 is involved in the
DNA replication checkpoint. Collectively, the available data
indicate that the PRMT5-Wee1 regulatory module appears
evolutionarily conserved, but has evolved to function in different cell cycle-dependent checkpoints in a species-specific
manner.
The Hsl7-Swe1 module of budding yeast also appears to be
sensitive to stress signals, including high osmolarity. Under
osmostress conditions, Hsl1 phosphorylation by the stress-activated Hog1 kinase prevents Hsl7 localization to bud necks,
leading to Swe1 accumulation and cell cycle arrest at G2 (19).
Similarly, it was previously demonstrated that Skb1 expression
in fission yeast is important for cell survival under conditions of
EUKARYOT. CELL
VOL. 6, 2007
MINIREVIEW
PREDICTED PROTEIN ARGININE
METHYLTRANSFERASES
IS PROTEIN ARGININE METHYLATION DYNAMIC IN
UNICELLULAR EUKARYOTES?
Circumstantial evidence over the past 40 years depicted
arginine methylation as an irreversible posttranslational
modification. The experimental evidence includes data that
demonstrate similar half-lives of bulk histones and their
methylarginine derivatives (13, 24) as well as the substantial
metabolic cost of arginine methylation (12 ATPs for catalysis), making this modification energetically unfavorable if
rapid turnover is needed (28). Recent studies, however,
have reported the identification of an enzymatic activity in
mammalian cells that can convert methylarginines within
histones to citrullines (22, 98), consistent with the previous
identification of citrullinated histones (35, 65). Peptidylarginine deiminases (PADs), a family of enzymes that were
previously characterized for the conversion of arginines
within proteins to citrullines, are responsible for such modifications. Structures of PAD4 as determined by X-ray crystallography (1, 2) also suggest that the active site of this
enzyme can accommodate arginine or monomethylarginine
but not dimethylarginines. There are conflicting data about
the ability of PADs to use monomethylarginine-containing
substrates, however. A number of studies have indeed reported that arginine-methylated peptides, including methylated peptides derived from the N-terminal tail of histones,
are poor substrates for PAD enzymes in vitro (39, 43, 77).
Hence, the reversibility of histone arginine methylation and
the underlying mechanism by which it is turned over remain
elusive.
PADs are apparently not evolutionarily conserved in unicellular eukaryotes. BLAST searches reveal PAD-encoding genes
in mammals and some nonmammalian vertebrates (97), including Xenopus and zebrafish, but not in unicellular eukaryotes. Therefore, it appears unlikely that PAD-dependent
regulation of arginine methylation occurs in unicellular eukaryotes. In contrast, lysine demethylases have recently been
identified in budding and fission yeasts that can reverse mono-,
di-, and trimethyl lysines in histones (52, 84, 86). Given the
recent evidence that histone lysine methylation is regulated in
a dynamic fashion in yeast, it is likely that protein arginine
methylation is also actively controlled in unicellular eukaryotes.
PERSPECTIVES FOR FUTURE STUDIES
Future studies of PRMTs in unicellular eukaryotes will
hopefully resolve some of the outstanding questions about the
mechanism of action of these methyltransferases. First, it remains unclear whether the catalytic activity of PRMTs is regulated or constitutive. Although proteins with regulatory action toward PRMT1 in yeast (40) and mammals (54) have been
reported, the biological significance of these proteins in any
PRMT1-dependent function remains to be determined. The
amenability of some unicellular eukaryotic model systems to
genetic screens may also reveal novel regulatory pathways that
control the methylation status of arginine methylated proteins.
Last, whereas several methyl lysine-reading proteins have been
identified (23), much remains to be elucidated about effectors
for arginine-methylated proteins. Such studies will surely further our understanding of the biological significance of protein
arginine methylation and provide additional challenges and
surprises about this evolutionarily conserved posttranslational
modification.
ACKNOWLEDGMENTS
I thank Stéphane Richard, Anne McBride, Michael Yu, and Laurie
Read for critical reading of the manuscript. I also apologize to those
whose work was not cited due to space limitation.
Work from my laboratory is supported by a grant from the Canadian
Institutes of Health Research (CIHR). F.B. is a Chercheur-Boursier of
the Fonds de la Recherche en Santé du Québec (FRSQ) and a New
Investigator of the CIHR.
REFERENCES
1. Arita, K., H. Hashimoto, T. Shimizu, K. Nakashima, M. Yamada, and M.
Sato. 2004. Structural basis for Ca(2⫹)-induced activation of human PAD4.
Nat. Struct. Mol. Biol. 11:777–783.
2. Arita, K., T. Shimizu, H. Hashimoto, Y. Hidaka, M. Yamada, and M. Sato.
2006. Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4. Proc. Natl. Acad. Sci. USA 103:5291–5296.
3. Asano, S., J. E. Park, K. Sakchaisri, L. R. Yu, S. Song, P. Supavilai, T. D.
Veenstra, and K. S. Lee. 2005. Concerted mechanism of Swe1/Wee1 regulation by multiple kinases in budding yeast. EMBO J. 24:2194–2204.
4. Bachand, F., D. H. Lackner, J. Bahler, and P. A. Silver. 2006. Autoregu-
Downloaded from http://ec.asm.org/ on February 23, 2013 by PENN STATE UNIV
Sequence alignments have permitted the identification and
the characterization of several new PRMTs in different biological systems (5, 20, 26, 46, 83, 95). Although there are inherent
dangers in characterizing homologous proteins based solely on
sequence alignments, such analyses are useful for the development of experimental validation to test for methyltransferase
activity and function. This can lead to the potential identification of novel PRMT-like proteins in unicellular eukaryotes.
In addition to PRMT1, PRMT3, and PRMT5, other arginine
methyltransferase-encoding genes can be identified in the genomes of certain unicellular eukaryotes. In both of the protozoans Leishmania major and Trypanosoma brucei, three genes
(LmjF16.0030, LmjF06.0870, and LmjF03.0600 in Leishmania
and Tb927.5.3960, Tb927.7.5490, and Tb10.70.3860 in Trypanosoma) encode putative PRMTs that demonstrate low sequence
similarity to human PRMT6, PRMT7, and PRMT8, respectively.
The genome of the soil-living amoeba Dictyostelium discoideum
also contains two predicted protein arginine methyltransferaseencoding genes (DDB0219438 and DDB0217760) in addition to
the genes for its PRMT1 and PRMT5 homologs (Table 1). Interestingly, the amino-terminal domains of the putative PRMTs
encoded by the Trypanosoma Tb10.70.3860 and the Dictyostelium
DDB0217760 genes are predicted to contain a signal peptide
sequence and a transmembrane helix, respectively. Because human PRMT8 is targeted to the plasma membrane via N-terminal myristoylation (46), it appears that the Trypanosoma
Tb10.70.3860, the Dictyostelium DDB0217760, and human
PRMT8 genes have evolved different mechanisms for membrane
localization. Predicted methyltransferases showing 31% and 26%
amino acid sequence identity to human PRMT4 can also be
found in the genomes of Cryptococcus neoformans and Toxoplasma gondii, respectively. Future studies with these predicted
PRMTs will undoubtedly provide significant insights into the evolution of arginine methyltransferases and the roles performed by
these enzymes in the biology of unicellular eukaryotes.
895
896
5.
6.
7.
8.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
lation of ribosome biosynthesis by a translational response in fission yeast.
Mol. Cell. Biol. 26:1731–1742.
Bachand, F., and P. A. Silver. 2004. PRMT3 is a ribosomal protein methyltransferase that affects the cellular levels of ribosomal subunits. EMBO J.
23:2641–2650.
Bao, S., Y. Qyang, P. Yang, H. Kim, H. Du, G. Bartholomeusz, J. Henkel,
R. Pimental, F. Verde, and S. Marcus. 2001. The highly conserved protein
methyltransferase, Skb1, is a mediator of hyperosmotic stress response in
the fission yeast Schizosaccharomyces pombe. J. Biol. Chem. 276:14549–
14552.
Bedford, M. T., and S. Richard. 2005. Arginine methylation an emerging
regulator of protein function. Mol. Cell 18:263–272.
Bienen, E. J., E. Hammadi, and G. C. Hill. 1981. Trypanosoma brucei:
biochemical and morphological changes during in vitro transformation of
bloodstream- to procyclic-trypomastigotes. Exp. Parasitol. 51:408–417.
Bienen, E. J., G. C. Hill, and K. O. Shin. 1983. Elaboration of mitochondrial
function during Trypanosoma brucei differentiation. Mol. Biochem. Parasitol. 7:75–86.
Boisvert, F. M., J. Cote, M. C. Boulanger, P. Cleroux, F. Bachand, C.
Autexier, and S. Richard. 2002. Symmetrical dimethylarginine methylation
is required for the localization of SMN in Cajal bodies and pre-mRNA
splicing. J. Cell Biol. 159:957–969.
Boisvert, F. M., J. Cote, M. C. Boulanger, and S. Richard. 2003. A proteomic analysis of arginine-methylated protein complexes. Mol. Cell. Proteomics 2:1319–1330.
Boisvert, F. M., U. Dery, J. Y. Masson, and S. Richard. 2005. Arginine
methylation of MRE11 by PRMT1 is required for DNA damage checkpoint
control. Genes Dev. 19:671–676.
Byvoet, P., G. R. Shepherd, J. M. Hardin, and B. J. Noland. 1972. The
distribution and turnover of labeled methyl groups in histone fractions of
cultured mammalian cells. Arch. Biochem. Biophys. 148:558–567.
Chang, F. N., I. J. Navickas, C. Au, and C. Budzilowicz. 1978. Identification
of the methylated ribosomal proteins in HeLa cells and the fluctuation of
methylation during the cell cycle. Biochim. Biophys. Acta 518:89–94.
Chang, F. N., I. J. Navickas, C. N. Chang, and B. M. Dancis. 1976. Methylation of ribosomal proteins in HeLa cells. Arch. Biochem. Biophys. 172:
627–633.
Chern, M. K., K. N. Chang, L. F. Liu, T. C. Tam, Y. C. Liu, Y. L. Liang, and
M. F. Tam. 2002. Yeast ribosomal protein L12 is a substrate of proteinarginine methyltransferase 2. J. Biol. Chem. 277:15345–15353.
Cid, V. J., M. J. Shulewitz, K. L. McDonald, and J. Thorner. 2001. Dynamic
localization of the Swe1 regulator Hsl7 during the Saccharomyces cerevisiae cell cycle. Mol. Biol. Cell 12:1645–1669.
Cimato, T. R., J. Tang, Y. Xu, C. Guarnaccia, H. R. Herschman, S. Pongor,
and J. M. Aletta. 2002. Nerve growth factor-mediated increases in protein
methylation occur predominantly at type I arginine methylation sites and
involve protein arginine methyltransferase 1. J. Neurosci. Res. 67:435–442.
Clotet, J., X. Escote, M. A. Adrover, G. Yaakov, E. Gari, M. Aldea, E. de
Nadal, and F. Posas. 2006. Phosphorylation of Hsl1 by Hog1 leads to a G2
arrest essential for cell survival at high osmolarity. EMBO J. 25:2338–2346.
Cook, J. R., J. H. Lee, Z. H. Yang, C. D. Krause, N. Herth, R. Hoffmann,
and S. Pestka. 2006. FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues. Biochem. Biophys.
Res. Commun. 342:472–481.
Cote, J., F. M. Boisvert, M. C. Boulanger, M. T. Bedford, and S. Richard.
2003. Sam68 RNA binding protein is an in vivo substrate for protein
arginine N-methyltransferase 1. Mol. Biol. Cell 14:274–287.
Cuthbert, G. L., S. Daujat, A. W. Snowden, H. Erdjument-Bromage, T.
Hagiwara, M. Yamada, R. Schneider, P. D. Gregory, P. Tempst, A. J.
Bannister, and T. Kouzarides. 2004. Histone deimination antagonizes
arginine methylation. Cell 118:545–553.
Daniel, J. A., M. G. Pray-Grant, and P. A. Grant. 2005. Effector proteins for
methylated histones: an expanding family. Cell Cycle 4:919–926.
Duerre, J. A., and C. T. Lee. 1974. In vivo methylation and turnover of rat
brain histones. J. Neurochem. 23:541–547.
Frankel, A., and S. Clarke. 2000. PRMT3 is a distinct member of the
protein arginine N-methyltransferase family. Conferral of substrate specificity by a zinc-finger domain. J. Biol. Chem. 275:32974–32982.
Frankel, A., N. Yadav, J. Lee, T. L. Branscombe, S. Clarke, and M. T.
Bedford. 2002. The novel human protein arginine N-methyltransferase
PRMT6 is a nuclear enzyme displaying unique substrate specificity. J. Biol.
Chem. 277:3537–3543.
Friesen, W. J., S. Paushkin, A. Wyce, S. Massenet, G. S. Pesiridis, G. Van
Duyne, J. Rappsilber, M. Mann, and G. Dreyfuss. 2001. The methylosome,
a 20S complex containing JBP1 and pICln, produces dimethylargininemodified Sm proteins. Mol. Cell. Biol. 21:8289–8300.
Gary, J. D., and S. Clarke. 1998. RNA and protein interactions modulated
by protein arginine methylation. Prog. Nucleic Acid Res. Mol. Biol. 61:65–
131.
Gary, J. D., W. J. Lin, M. C. Yang, H. R. Herschman, and S. Clarke. 1996.
The predominant protein-arginine methyltransferase from Saccharomyces
cerevisiae. J. Biol. Chem. 271:12585–12594.
EUKARYOT. CELL
30. Ghaemmaghami, S., W. K. Huh, K. Bower, R. W. Howson, A. Belle, N.
Dephoure, E. K. O’Shea, and J. S. Weissman. 2003. Global analysis of
protein expression in yeast. Nature 425:737–741.
31. Gilbreth, M., P. Yang, G. Bartholomeusz, R. A. Pimental, S. Kansra, R.
Gadiraju, and S. Marcus. 1998. Negative regulation of mitosis in fission
yeast by the shk1 interacting protein skb1 and its human homolog, Skb1Hs.
Proc. Natl. Acad. Sci. USA 95:14781–14786.
32. Gilbreth, M., P. Yang, D. Wang, J. Frost, A. Polverino, M. H. Cobb, and S.
Marcus. 1996. The highly conserved skb1 gene encodes a protein that
interacts with Shk1, a fission yeast Ste20/PAK homolog. Proc. Natl. Acad.
Sci. USA 93:13802–13807.
33. Goulah, C. C., M. Pelletier, and L. K. Read. 2006. Arginine methylation
regulates mitochondrial gene expression in Trypanosoma brucei through
multiple effector proteins. RNA 12:1545–1555.
34. Green, D. M., K. A. Marfatia, E. B. Crafton, X. Zhang, X. Cheng, and A. H.
Corbett. 2002. Nab2p is required for poly(A) RNA export in Saccharomyces cerevisiae and is regulated by arginine methylation via Hmt1p. J. Biol.
Chem. 277:7752–7760.
35. Hagiwara, T., K. Nakashima, H. Hirano, T. Senshu, and M. Yamada. 2002.
Deimination of arginine residues in nucleophosmin/B23 and histones in
HL-60 granulocytes. Biochem. Biophys. Res. Commun. 290:979–983.
36. Hebert, M. D., K. B. Shpargel, J. K. Ospina, K. E. Tucker, and A. G.
Matera. 2002. Coilin methylation regulates nuclear body formation. Dev.
Cell 3:329–337.
37. Henry, M. F., and P. A. Silver. 1996. A novel methyltransferase (Hmt1p)
modifies poly(A)⫹-RNA-binding proteins. Mol. Cell. Biol. 16:3668–3678.
38. Herrmann, F., J. Lee, M. T. Bedford, and F. O. Fackelmayer. 2005. Dynamics of human protein arginine methyltransferase 1(PRMT1) in vivo.
J. Biol. Chem. 280:38005–38010.
39. Hidaka, Y., T. Hagiwara, and M. Yamada. 2005. Methylation of the guanidino group of arginine residues prevents citrullination by peptidylarginine
deiminase IV. FEBS Lett. 579:4088–4092.
40. Inoue, K., T. Mizuno, K. Wada, and M. Hagiwara. 2000. Novel RING finger
proteins, Air1p and Air2p, interact with Hmt1p and inhibit the arginine
methylation of Npl3p. J. Biol. Chem. 275:32793–32799.
41. Jenuwein, T., and C. D. Allis. 2001. Translating the histone code. Science
293:1074–1080.
42. Kaiser, P., R. A. Sia, E. G. Bardes, D. J. Lew, and S. I. Reed. 1998. Cdc34
and the F-box protein Met30 are required for degradation of the Cdkinhibitory kinase Swe1. Genes Dev. 12:2587–2597.
43. Kearney, P. L., M. Bhatia, N. G. Jones, L. Yuan, M. C. Glascock, K. L.
Catchings, M. Yamada, and P. R. Thompson. 2005. Kinetic characterization of protein arginine deiminase 4: a transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis. Biochemistry
44:10570–10582.
44. Kruiswijk, T., A. Kunst, R. J. Planta, and W. H. Mager. 1978. Modification
of yeast ribosomal proteins. Methylation. Biochem. J. 175:221–225.
45. Lacoste, N., R. T. Utley, J. M. Hunter, G. G. Poirier, and J. Cote. 2002.
Disruptor of telomeric silencing-1 is a chromatin-specific histone H3 methyltransferase. J. Biol. Chem. 277:30421–30424.
46. Lee, J., J. Sayegh, J. Daniel, S. Clarke, and M. T. Bedford. 2005. PRMT8,
a new membrane-bound tissue-specific member of the protein arginine
methyltransferase family. J. Biol. Chem. 280:32890–32896.
47. Lee, J. H., J. R. Cook, B. P. Pollack, T. G. Kinzy, D. Norris, and S. Pestka.
2000. Hsl7p, the yeast homologue of human JBP1, is a protein methyltransferase. Biochem. Biophys. Res. Commun. 274:105–111.
48. Lee, K. S., S. Asano, J. E. Park, K. Sakchaisri, and R. L. Erikson. 2005.
Monitoring the cell cycle by multi-kinase-dependent regulation of Swe1/
Wee1 in budding yeast. Cell Cycle 4:1346–1349.
49. Lee, M. S., M. Henry, and P. A. Silver. 1996. A protein that shuttles
between the nucleus and the cytoplasm is an important mediator of RNA
export. Genes Dev. 10:1233–1246.
50. Lee, S. W., S. J. Berger, S. Martinovic, L. Pasa-Tolic, G. A. Anderson, Y.
Shen, R. Zhao, and R. D. Smith. 2002. Direct mass spectrometric analysis
of intact proteins of the yeast large ribosomal subunit using capillary LC/
FTICR. Proc. Natl. Acad. Sci. USA 99:5942–5947.
51. Lhoest, J., Y. Lobet, E. Costers, and C. Colson. 1984. Methylated proteins
and amino acids in the ribosomes of Saccharomyces cerevisiae. Eur. J. Biochem. 141:585–590.
52. Liang, G., R. J. Klose, K. E. Gardner, and Y. Zhang. 2007. Yeast Jhd2p is a
histone H3 Lys4 trimethyl demethylase. Nat. Struct. Mol. Biol. 14:243–245.
53. Lin, C. H., H. M. Huang, M. Hsieh, K. M. Pollard, and C. Li. 2002.
Arginine methylation of recombinant murine fibrillarin by protein arginine
methyltransferase. J. Protein Chem. 21:447–453.
54. Lin, W. J., J. D. Gary, M. C. Yang, S. Clarke, and H. R. Herschman. 1996.
The mammalian immediate-early TIS21 protein and the leukemia-associated BTG1 protein interact with a protein-arginine N-methyltransferase.
J. Biol. Chem. 271:15034–15044.
55. Longtine, M. S., C. L. Theesfeld, J. N. McMillan, E. Weaver, J. R. Pringle,
and D. J. Lew. 2000. Septin-dependent assembly of a cell cycle-regulatory
module in Saccharomyces cerevisiae. Mol. Cell. Biol. 20:4049–4061.
56. Louie, D. F., K. A. Resing, T. S. Lewis, and N. G. Ahn. 1996. Mass spec-
Downloaded from http://ec.asm.org/ on February 23, 2013 by PENN STATE UNIV
9.
MINIREVIEW
VOL. 6, 2007
57.
58.
59.
61.
62.
63.
64.
65.
66.
67.
68.
69.
70.
71.
72.
73.
74.
75.
76.
77.
78.
79.
80.
897
81. Sakchaisri, K., S. Asano, L. R. Yu, M. J. Shulewitz, C. J. Park, J. E. Park,
Y. W. Cho, T. D. Veenstra, J. Thorner, and K. S. Lee. 2004. Coupling
morphogenesis to mitotic entry. Proc. Natl. Acad. Sci. USA 101:4124–4129.
82. Schulze, A. 2003. Creatine deficiency syndromes. Mol. Cell Biochem. 244:
143–150.
83. Scott, H. S., S. E. Antonarakis, M. D. Lalioti, C. Rossier, P. A. Silver, and
M. F. Henry. 1998. Identification and characterization of two putative
human arginine methyltransferases (HRMT1L1 and HRMT1L2). Genomics 48:330–340.
84. Seward, D. J., G. Cubberley, S. Kim, M. Schonewald, L. Zhang, B. Tripet,
and D. L. Bentley. 2007. Demethylation of trimethylated histone H3 Lys4 in
vivo by JARID1 JmjC proteins. Nat. Struct. Mol. Biol. 14:240–242.
85. Shen, E. C., M. F. Henry, V. H. Weiss, S. R. Valentini, P. A. Silver, and
M. S. Lee. 1998. Arginine methylation facilitates the nuclear export of
hnRNP proteins. Genes Dev. 12:679–691.
86. Shi, Y., F. Lan, C. Matson, P. Mulligan, J. R. Whetstine, P. A. Cole, and
R. A. Casero. 2004. Histone demethylation mediated by the nuclear amine
oxidase homolog LSD1. Cell 119:941–953.
87. Shulewitz, M. J., C. J. Inouye, and J. Thorner. 1999. Hsl7 localizes to a
septin ring and serves as an adapter in a regulatory pathway that relieves
tyrosine phosphorylation of Cdc28 protein kinase in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:7123–7137.
88. Smith, J. J., K. P. Rucknagel, A. Schierhorn, J. Tang, A. Nemeth, M.
Linder, H. R. Herschman, and E. Wahle. 1999. Unusual sites of arginine
methylation in poly(A)-binding protein II and in vitro methylation by protein arginine methyltransferases PRMT1 and PRMT3. J. Biol. Chem. 274:
13229–13234.
89. Smith, W. A., B. T. Schurter, F. Wong-Staal, and M. David. 2004. Arginine
methylation of RNA helicase a determines its subcellular localization.
J. Biol. Chem. 279:22795–22798.
90. Subramaniam, C., P. Veazey, S. Redmond, J. Hayes-Sinclair, E. Chambers,
M. Carrington, K. Gull, K. Matthews, D. Horn, and M. C. Field. 2006.
Chromosome-wide analysis of gene function by RNA interference in the
African trypanosome. Eukaryot. Cell 5:1539–1549.
91. Swiercz, R., M. D. Person, and M. T. Bedford. 2005. Ribosomal protein S2
is a substrate for mammalian PRMT3 (protein arginine methyltransferase
3). Biochem. J. 386:85–91.
92. Tan, C. P., and S. Nakielny. 2006. Control of the DNA methylation system
component MBD2 by protein arginine methylation. Mol. Cell. Biol. 26:
7224–7235.
93. Tang, J., J. D. Gary, S. Clarke, and H. R. Herschman. 1998. PRMT 3, a type
I protein arginine N-methyltransferase that differs from PRMT1 in its
oligomerization, subcellular localization, substrate specificity, and regulation. J. Biol. Chem. 273:16935–16945.
94. Theesfeld, C. L., T. R. Zyla, E. G. Bardes, and D. J. Lew. 2003. A monitor
for bud emergence in the yeast morphogenesis checkpoint. Mol. Biol. Cell
14:3280–3291.
95. Trojer, P., M. Dangl, I. Bauer, S. Graessle, P. Loidl, and G. Brosch. 2004.
Histone methyltransferases in Aspergillus nidulans: evidence for a novel
enzyme with a unique substrate specificity. Biochemistry 43:10834–10843.
96. Umeyama, T., A. Kaneko, Y. Nagai, N. Hanaoka, K. Tanabe, Y. Takano, M.
Niimi, and Y. Uehara. 2005. Candida albicans protein kinase CaHsl1p
regulates cell elongation and virulence. Mol. Microbiol. 55:381–395.
97. Vossenaar, E. R., A. J. Zendman, W. J. van Venrooij, and G. J. Pruijn. 2003.
PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. Bioessays 25:1106–1118.
98. Wang, Y., J. Wysocka, J. Sayegh, Y. H. Lee, J. R. Perlin, L. Leonelli, L. S.
Sonbuchner, C. H. McDonald, R. G. Cook, Y. Dou, R. G. Roeder, S. Clarke,
M. R. Stallcup, C. D. Allis, and S. A. Coonrod. 2004. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science
306:279–283.
99. Weiss, V. H., A. E. McBride, M. A. Soriano, D. J. Filman, P. A. Silver, and
J. M. Hogle. 2000. The structure and oligomerization of the yeast arginine
methyltransferase, Hmt1. Nat. Struct. Biol. 7:1165–1171.
100. Xu, C., and M. F. Henry. 2004. Nuclear export of hnRNP Hrp1p and
nuclear export of hnRNP Npl3p are linked and influenced by the methylation state of Npl3p. Mol. Cell. Biol. 24:10742–10756.
101. Xu, C., P. A. Henry, A. Setya, and M. F. Henry. 2003. In vivo analysis of
nucleolar proteins modified by the yeast arginine methyltransferase Hmt1/
Rmt1p. RNA 9:746–759.
102. Yamada, A., B. Duffy, J. A. Perry, and S. Kornbluth. 2004. DNA replication
checkpoint control of Wee1 stability by vertebrate Hsl7. J. Cell Biol. 167:
841–849.
103. Yarlett, N., A. Quamina, and C. J. Bacchi. 1991. Protein methylases in
Trypanosoma brucei brucei: activities and response to DL-alpha-difluoromethylornithine. J. Gen. Microbiol. 137:717–724.
104. Yu, M. C., F. Bachand, A. E. McBride, S. Komili, J. M. Casolari, and P. A.
Silver. 2004. Arginine methyltransferase affects interactions and recruitment of mRNA processing and export factors. Genes Dev. 18:2024–2035.
105. Yu, M. C., D. W. Lamming, J. A. Eskin, D. A. Sinclair, and P. A. Silver.
2006. The role of protein arginine methylation in the formation of silent
chromatin. Genes Dev. 20:3249–3254.
Downloaded from http://ec.asm.org/ on February 23, 2013 by PENN STATE UNIV
60.
trometric analysis of 40 S ribosomal proteins from Rat-1 fibroblasts. J. Biol.
Chem. 271:28189–28198.
Ma, X. J., Q. Lu, and M. Grunstein. 1996. A search for proteins that
interact genetically with histone H3 and H4 amino termini uncovers novel
regulators of the Swe1 kinase in Saccharomyces cerevisiae. Genes Dev.
10:1327–1340.
Marcus, S., A. Polverino, E. Chang, D. Robbins, M. H. Cobb, and M. H.
Wigler. 1995. Shk1, a homolog of the Saccharomyces cerevisiae Ste20 and
mammalian p65PAK protein kinases, is a component of a Ras/Cdc42 signaling module in the fission yeast Schizosaccharomyces pombe. Proc. Natl.
Acad. Sci. USA 92:6180–6184.
McBride, A. E., J. T. Cook, E. A. Stemmler, K. L. Rutledge, K. A. McGrath,
and J. A. Rubens. 2005. Arginine methylation of yeast mRNA-binding
protein Npl3 directly affects its function, nuclear export, and intranuclear
protein interactions. J. Biol. Chem. 280:30888–30898.
McBride, A. E., and P. A. Silver. 2001. State of the arg: protein methylation
at arginine comes of age. Cell 106:5–8.
McMillan, J. N., M. S. Longtine, R. A. Sia, C. L. Theesfeld, E. S. Bardes,
J. R. Pringle, and D. J. Lew. 1999. The morphogenesis checkpoint in
Saccharomyces cerevisiae: cell cycle control of Swe1p degradation by Hsl1p
and Hsl7p. Mol. Cell. Biol. 19:6929–6939.
McMillan, J. N., C. L. Theesfeld, J. C. Harrison, E. S. Bardes, and D. J.
Lew. 2002. Determinants of Swe1p degradation in Saccharomyces cerevisiae. Mol. Biol. Cell 13:3560–3575.
Meister, G., C. Eggert, D. Buhler, H. Brahms, C. Kambach, and U. Fischer.
2001. Methylation of Sm proteins by a complex containing PRMT5 and the
putative U snRNP assembly factor pICln. Curr. Biol. 11:1990–1994.
Miranda, T. B., J. Sayegh, A. Frankel, J. E. Katz, M. Miranda, and S.
Clarke. 2006. Yeast Hsl7 (histone synthetic lethal 7) catalyses the in vitro
formation of omega-N(G)-monomethylarginine in calf thymus histone
H2A. Biochem. J. 395:563–570.
Nakashima, K., T. Hagiwara, and M. Yamada. 2002. Nuclear localization of
peptidylarginine deiminase V and histone deimination in granulocytes.
J. Biol. Chem. 277:49562–49568.
Nichols, R. C., X. W. Wang, J. Tang, B. J. Hamilton, F. A. High, H. R.
Herschman, and W. F. Rigby. 2000. The RGG domain in hnRNP A2 affects
subcellular localization. Exp. Cell Res. 256:522–532.
Niewmierzycka, A., and S. Clarke. 1999. S-Adenosylmethionine-dependent
methylation in Saccharomyces cerevisiae. Identification of a novel protein
arginine methyltransferase. J. Biol. Chem. 274:814–824.
Olsson, I., J. Berrez, A. Leipus, C. Ostlund, and A. Mutvei. 2007. The
arginine methyltransferase Rmt2 is enriched in the nucleus and co-purifies
with the nuclear porins Nup49, Nup57 and Nup100. Exp. Cell Res. 313:
1778–1789.
Paik, W. K., and S. Kim. 1967. Enzymatic methylation of protein fractions
from calf thymus nuclei. Biochem. Biophys. Res. Commun. 29:14–20.
Pal, S., S. N. Vishwanath, H. Erdjument-Bromage, P. Tempst, and S. Sif.
2004. Human SWI/SNF-associated PRMT5 methylates histone H3 arginine
8 and negatively regulates expression of ST7 and NM23 tumor suppressor
genes. Mol. Cell. Biol. 24:9630–9645.
Paolantonacci, P., F. Lawrence, F. Lederer, and M. Robert-Gero. 1986.
Protein methylation and protein methylases in Leishmania donovani and
Leishmania tropica promastigotes. Mol. Biochem. Parasitol. 21:47–54.
Pawlak, M. R., C. A. Scherer, J. Chen, M. J. Roshon, and H. E. Ruley. 2000.
Arginine N-methyltransferase 1 is required for early postimplantation
mouse development, but cells deficient in the enzyme are viable. Mol. Cell.
Biol. 20:4859–4869.
Pelletier, M., D. A. Pasternack, and L. K. Read. 2005. In vitro and in vivo
analysis of the major type I protein arginine methyltransferase from
Trypanosoma brucei. Mol. Biochem. Parasitol. 144:206–217.
Perreault, A., C. Lemieux, and F. Bachand. 2007. Regulation of the nuclear
poly(A)-binding protein by arginine methylation in fission yeast. J. Biol.
Chem. 282:7552–7562.
Porras-Yakushi, T. R., J. P. Whitelegge, and S. Clarke. 2006. A novel SET
domain methyltransferase in yeast: Rkm2-dependent trimethylation of ribosomal protein L12ab at lysine 10. J. Biol. Chem. 281:35835–35845.
Porras-Yakushi, T. R., J. P. Whitelegge, T. B. Miranda, and S. Clarke.
2005. A novel SET domain methyltransferase modifies ribosomal protein
Rpl23ab in yeast. J. Biol. Chem. 280:34590–34598.
Raijmakers, R., A. J. Zendman, W. V. Egberts, E. R. Vossenaar, J. Raats, C.
Soede-Huijbregts, F. P. Rutjes, P. A. van Veelen, J. W. Drijfhout, and G. J.
Pruijn. 2007. Methylation of arginine residues interferes with citrullination by
peptidylarginine deiminases in vitro. J. Mol. Biol. 367:1118–1129.
Ramagopal, S. 1991. Covalent modifications of ribosomal proteins in growing and aggregation-competent Dictyostelium discoideum: phosphorylation
and methylation. Biochem. Cell Biol. 69:263–268.
Ruault, M., and L. Pillus. 2006. Chromatin-modifying enzymes are essential when the Saccharomyces cerevisiae morphogenesis checkpoint is constitutively activated. Genetics 174:1135–1149.
Rusche, L. N., A. L. Kirchmaier, and J. Rine. 2003. The establishment,
inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu. Rev. Biochem. 72:481–516.
MINIREVIEW
898
MINIREVIEW
106. Yu, Y., H. Ji, J. A. Doudna, and J. A. Leary. 2005. Mass spectrometric
analysis of the human 40S ribosomal subunit: native and HCV IRES-bound
complexes. Protein Sci. 14:1438–1446.
107. Zhang, X., and X. Cheng. 2003. Structure of the predominant protein
arginine methyltransferase PRMT1 and analysis of its binding to substrate
peptides. Structure (Cambridge) 11:509–520.
EUKARYOT. CELL
108. Zhang, X., L. Zhou, and X. Cheng. 2000. Crystal structure of the conserved
core of protein arginine methyltransferase PRMT3. EMBO J. 19:3509–
3519.
109. Zobel-Thropp, P., J. D. Gary, and S. Clarke. 1998. Delta-N-methylarginine
is a novel posttranslational modification of arginine residues in yeast proteins. J. Biol. Chem. 273:29283–29286.
Downloaded from http://ec.asm.org/ on February 23, 2013 by PENN STATE UNIV