Download Mutator Transposon in Maize and MULEs in the Plant Genome

遗 传 学 报
Acta Genetica Sinica, June 2006,
ISSN 0379-4172
33 (6)：477–487
Mutator Transposon in Maize and MULEs in the Plant Genome
DIAO Xian-Min1,①, Damon Lisch2
1. National Millet Improvement Center of China, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences，
Shijiazhuang 050031, China;
2. University of California at Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, CA 94720, USA
Abstract: Mutator (Mu) is by far the most mutagenic plant transposon. The high frequency of transposition and the tendency to
insert into low copy sequences for such transposon have made it the primary means by which genes are mutagenized in maize (Zea
mays L.). Mus like elements (MULEs) are widespread among angiosperms and multiple-diverged functional variants can be present
in a single genome. MULEs often capture genetic sequences. These Pack-MuLEs can mobilize thousands of gene fragments, which
may have had a significant impact on host genome evolution. There is also evidence that MULEs can move between reproductively
isolated species. Here we present an overview of the discovery, features and utility of Mu transposon. Classification of Mu elements
and future directions of related research are also discussed. Understanding Mu will help us elucidate the dynamic genome.
Key words: Mutator; transposon; genome evolution; MULE; Pack-MuLE
Transposons or “controlling elements” were discovered by Barbara McClintock in maize (Zea mays L.)
in the early 1950s, but the theory of transposition was
not widely accepted until 1970s. Transposable elements of one type or another have been found in all
organisms, including all plants that have been investigated. Transposons make up over 50% DNA of the
genome in many species with large genomes. Transposon can rearrange genomes and alter individual gene
structure and expression as a consequence of transposition, insertion, excision and chromosome breakage.
Many transposon system have been studied in China,
such as Ac/Ds, Spm/dSpm, Tourist, Stowaway in maize,
Mariner in soybean (Glycine max L.) and Tam in
Snapdragon[1,2]. However, little is known about Mutator (simplified as Mu), which is the hot point of transposon research in America. Mutator transposon was
discovered by Robertson in 1978 from a maize line
that yielded diverse mutations at a frequency much
higher than the spontaneous mutation frequency [3, 4]. It
was found that these mutations were caused by the
insertion of Mu transposons. Mu elements have be-
come the major tool of gene discovery in maize functional genome research and other related fields. Here
we review the discovery, properties, genetic application of Mu transposon and its role in plant gene and
genome evolution.
1
The Discovery of Mu Transposon
A maize line, known as Mutator, was sent to D.
S. Robertson of Iowa State University from the University of Wisconsin for detailed analysis of its frequent mutations. Genetic experiment by Robertson
demonstrated that not only the heritable mutation
frequency of this line was very high, but a great deal
of somatic variation was also observed. Further research showed that these mutations were not caused
by the previously discovered transposons such as
Ac/Ds and Spm/dSpm. In Ac/Ds and Spm/dSpm lines,
only a few autonomous elements are present and they
segregate as a Mendelian element. Transpositions of
these elements, when they occurred, could be detected as changes in the segregation ratios of activity.
Received: 2005-09-21; Accepted: 2005-10-08
This work was supported by the National Natural Science Foundation of China (No.30370766).
① Corresponding author. E-mail: [email protected]; Tel: +86-311-8767 0697
478
In contrast, 90% of the progeny of an outcross of a
Mutator line carried active transposons and were consistent with a very high duplication rate. Those
progenies that did lose activity appeared to do so due
to epigenetic silencing, rather than the segregation of
an autonomous, or controlling element. This was
confirmed in many later experiments [5,6]. The complexity and epigenetic regulation features of this putative transposon system delayed the discovery of the
means by which the system was regulated.
In the 1980s, using this Mutator line as mutagen
for gene tagging became popular. A new kind of
transposon inserted into an allele of alcohol dehydrogenase1 and was cloned by Bennetzen et al [7]. Now we
know that this transposon is a nonautonomous member
of the Mu transposon family, which was named Mu1.
Characterization of Mu1 and using it as a probe not
only identified a new kind of transposon but also
opened a new era of efficient maize functional genome
research. This new transposon was named Mutator
because it came from Mutator maize line. Schnable et
al. [8] identified a Cy/rcy transposon system from an
independent maize line with similar transposion and
genetic properties of Mu system, which was later
demonstrated to be Mu7 of the Mu family. In the early
1990s, a minimal version of the Mutator line was used
to isolate the regulatory transposon for the Mutator
system. This regulator, which was isolated independently in three different laboratories, was designated as
MuDR, in honor of Don Robertson. The isolation of
the autonomous two-element, MuDR [9, 10], the creation
of a minimal Mutator line [11] and an engineered rescue-Mu element [12] have made it possible for a systematically elucidation of this super transposon family.
2
The Components and Gene Structure of
MuDR and Mu Transposon Family
All maize Mu-transposable elements are regulated
by MuDR, which is the autonomous element; MuDR
carries two genes, mudrA and mudrB (Fig. 1). The
mudrA transcript encodes a 120 kDa protein, MURA,
which is the transposase of the family. MURA contains
a domain with high similarity to several bacterial
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transposase, which was used as evidence for its very
early origin [13]. The mudrB major transcript encodes a
23 kDa protein (MURB) that is not similar to any sequences in public database outside maize and its close
relatives. Although the precise function of MURB remains enigmatic, both deletion derivatives and transgenic experiments suggest that MURB is required for
Mu insertions, especially germinally transmitted insertions [14]. Only two maize lines with active MuDR elements have been identified so far, but all maize lines
carry MuDR elements derivatives, or homologous
MuDR sequences (hMuDRs), whose coding sequences
are 80%–99% identical to those of MuDR. Surprisingly,
these hMuDRs can be expressed at the transcription
level though they are not associated with Mutator activity and they might play an as-yet-unknown function
in Mutator regulation [5].
Unlike Ac/Ds and Spm/dSpm transpson systems,
which mostly comprise of the autonomous element
and its deletion derivatives, the Mu transposon system
contains complex family elements, including
autonomous MuDR, homologous MuDR elements and
many variants with similar TIRs. All Mu transposon
elements share similar -170-220 bp TIRs; the length
of direct repeat sequence flanking the inserted elements is 9 bp. Many Mu elements contain additional
direct or inverted repeat sequences. Although deletion
derivatives are the most common source of Ds element from Ac and of dSpm elements from Spm, most
Mu elements internal sequences are unrelated to the
tranposase-coding sequence of MuDR, or to each
other (Fig. 1). In most cases, the internal sequences of
Mu elements are part of a host gene and it seems that
Mu TIRs can capture host functional sequence by so
far unknown mechanism. These kinds of elements are
called Pack-MuLEs [15]. In some species, such as rice
(Oryza sativa L.), there can be thousands of independently derived Pack-MuLEs.
Jittery is a newly isolated and characterized
member of Mu element, whose transposase-coding
sequence is only a 3.9 kb gene with high identity to
mudrA but not to mudrB. The length of direct host
sequence duplication flanking the Jittery insertions is
also 9 bp, but its 177 bp TIRs are unrelated to that of
DIAO Xian-Min et al.: Mutator Transposon in Maize and MULEs in the Plant Genome
479
Fig. 1 The Mutator transposon family in maize and the engineered RescueMu
All classes of Mu elements share similar terminal inverted repeats (TIRs; Black ends), but each class has a unique internal sequence
that shares similarity to various host functional protein coding sequences, as indicated in the figure. Mu1 is similar to MRS-A
(Mu-related sequence A). Mu3 is similar to an Arabidopsis protein and Mago nashi protein. Mu4 includes a sequence 95% identical
to a maize expressed sequence, accession No. BG466445. Mu7 is similar to Arabidopsis protein accession No. NP-192120. Mu8
contains a sequence with similarity to pgp1 protein from Arabidopsis. RescueMu is an engineered element based on Mu1 used as a
gene-tagging tool, into which unique tag sequence, pBluescript and selectable maker were inserted. For MuDR, the position of mudrA
and mudrB are indicated. The figure is a modified version from Lisch (2002) [17].
MuDR. Despite limited investigation has been done
on the transposition activity of Jittery, the results so
far obtained demonstrated that it is an autonomous
transposable element. Jittery, like MuDR causes a
high frequency of late somatic reversion, but like deletion derivatives that lack mudrB, it is not associated
with new insertions [16].
In addition to the members of Mu elements found
in maize, many Mu-like elements (MULEs) have been
identified in both dicots and monocots. Mu transposon
family is characterized by the presence of many diversified and potentially functional variants, and it’s very
high levels of activity in maize, which complicated
analysis of its origin and evolution.
3
Transposition Activity of Mu
Data related to Mu transposition activity are
largely a product of investigations on maize, although
MULEs in Arabidopsis had been confirmed to be active in DDM1 mutant background [18]. Two main types
of transpositions occur with maize Mu elements. One
is somatic excision, or excision and insertion late during development in somatic cells and tissues, the other
one is insertions occurring in germinal cells, which is
the source of heritable new mutations in Mutator lines.
Mu excisions have been investigated extensively with
anthocyanin reporter alleles, such as a1-mum2, because pigmented spots can easily be visualized and
quantified. Most somatic excisions occur in the late
development stage, within the last two or three cell
divisions of a given lineage, though early excisions
can occasionally occur. The most visible result of somatic excision is revertant sectors, resulting from the
excision of the inserted transposon and restoration of
the a1 pigmentation function. Two kinds of somatic
excision have been documented for Mu elements, the
cut-only and the cut-and-paste. The excised transposons of the cut-only form were failed in inserting
into other sites of the host genome. Cut-and-paste
transposition is the typical mode of transposition of
DNA transposons and is often associated with reinsertion elsewhere in the genome. But excision of Ac/Ds
and Spm/dSpm elements typically result in minor
changes to the host sequence duplication created on
transposon insertion. In contrast, Mu element excision
create deletions and additions of the host gene[19, 20].
In contrast to high frequency of somatic revertant
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mutations, germinally transmitted revertants are extremely rare in Mutator lines, which suggest that excisions are prevented by some kind of mechanism in
cells that give rise to gametes[21]. In minimal Mutator
lines with just one copy of Mu1 initially inserted into
the a1-mum2 allele and one copy of MuDR, from
10%–20% of progeny contain more than one copy
of Mu1 or MuDR[11] and many experiments conformed that the existing Mu insertion segregate in a
Mendelian fasion. These experiments reveal that new
germinal insertions must happen without the loss of
the existing Mu insertion; in another word, some kind
of duplicative or replicative MuDR transposition happens during the process of development[5, 18]. Though
germinal duplicative insertion can occur throughout
the development, which mostly begins late in sporophyte cell divisions, where transposition events create
small clusters of gametes carrying the same mutations.
Germinal transposition continue through meiosis to
the last mitotic divisions of the gametophytes, and the
after meiosis insertion generates sperm with different
mutations [3,22]. The frequency of germinally transmitted insertions depends on the Mutator line used, but
there are clear position effects on both cis and trans
activity of individual MuDR elements [17].
Many Mu-induced mutations are suppressible.
The mutant phenotype in these cases arises only in the
presence of active MuDR elements, probably due to
steric effects introduced by the presence of the transposase bound to the transposon TIRs. Consistent with
this model, many suppressible Mu insertions are in
promoter regions. However, Mu insertion into introns
can also be suppressible [23], and it is likely that Mu
suppression will turn out to be more complex than a
simple model of steric hindrance would suggest.
Many investigations have demonstrated that Mu
transposons generally insert into single copy or
low-copy-number regions of the genome [24], which
makes it a powerful tool for maize functional gene tagging. By analyzing the sequences that flanking the 88
RescueMu insertions, Dietrich and co-authors demonstrated that 69% of these sequences were genes and only
4% were repetitive retrotransposons[25]. A much recent
experiment also with RescueMu shows that the rate of
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single copy insertion is about 66%, which is consistent
with the previous result [26]. Both Ac/Ds and Spm/dSpm
tend to transpose to genetically linked sites. In contrast,
Mutator transposes to unlinked sites, an advantage for
whole genome mutagenesis applications. However,
Hardeman and Chandler[27] found that certain classes of
Mu elements predominantly targeted certain genes,
which implies that some Mu elements may have insertion affinities. The 5′UTR region or the promoter region
of gl8 gene showed a strong preference for Mu element
insertion, 62 of 75 insertions of gl8 gene targeted in this
region, suggesting that 5′UTR targeting might be a feature of Mu insertion. But introns and other regions of
genes are also often targeted by Mu elements[25]. Analysis of 339 target site duplications (TSDs) created by Mu
insertions also showed some degree of sequence preference, the weak consensus for Mu insertion was
CTCB(G/C)(A/C)(G/A)(A/G)C.
Furthermore,
sequences immediately linked to TSDs also showed conservation; the consensus sequence of 5′ of the TSD is
CCT and that of the 3′ of the TSD is AGG. Mu-targeted
sequences were found to be GC rich relative to the rest
of the maize genome [25]. However, many Mu insertion
sites do not have the consensus sequence.
Four types of assays are usually used to demonstrate
Mutator system activity, including examination of somatic
instability of reporter alleles (such as sectored leaves,
kernels or anthers), special enzymes to detect methylation
of diagnostic restriction sites in the TIRs (HinfⅠfor Mu1
and SacⅠfor MuDR), the detection of new insertions in
progeny plants, and an elevated forward mutation frequency resulting from new germinal insertions[5]. Which
method should be used depends on needs of the user.
Early observations of Mutator suggested that the loss of
activity was due to epigenetic silencing, rather than simple segregation of a regulatory transposon. Two models
for silencing had been proposed: ectopic paring between
homologous TIRs and posttranscriptional RNA-based
silencing [5,28]. Until recently, the detailed initiation and
process of Mu family silencing still remains enigmatic. A
dominant locus that can initiate Mutator silencing, Mu
killer (Muk), was cloned. This locus was demonstrated to
be an inverted duplication of a partially deleted autonomous MuDR element. Muk produces a mudrA hairpin
DIAO Xian-Min et al.: Mutator Transposon in Maize and MULEs in the Plant Genome
transcript that is processed into small RNAs that targets
mudrA for silencing. This, in turn, results in transcriptional silencing of mudrA, and subsequently mudrB. Muk
provides the first example of a natural occurrence of derivative that is able to initiate heritable silencing of an
active transposon family [29, 30]. This discovery not only
clarified our understanding of Mu epigenetic silencing,
but also gave us new tools for investigation of both
transcriptional and posttranscriptional regulation of
gene expression.
It is suggested that the initial silencing of Mu activity is followed by detectable TIRs methylation[5].
Indeed, 5′-methylation of cytosines within TIRs is a
diagnostic feature of Mu transposons silencing state.
In typical Mutator lines or complex lines, both MuDR
and nonautonomous element, such as Mu1, can be
methylated gradually in the progeny of a linage or at
different development stage of an individual plant.
The methylation of MuDR is accompanied by transcriptional silencing and loss of activity [5,31]. In
minimal lines with single copy of MuDR, both MuDR
and the nonautonomous elements are unmethylated.
Methylation of nonautonomous elements occurs if
MuDR element is lost due to genetic segregation. In
such cases that MuDR is restored genetically, the methylation of nonautonomous elements is lost, suggesting that it represents a default state that occurs in
the absence of the transposase[17, 32]. This default methylation is dependent on at least two mutations that
were discovered due to their effects on paramutation.
In mop1 (mediator of paramutation) mutants, paramutatable alleles of several color genes are epigenetically activated and nonautonomous Mu elements
481
are hypomethylated. MuDR elements that had been
silenced by Mu killer are also hypomethylated in a
mop1 mutant background. If this element is maintained in a mutant background for multiple generations, one of the two genes encoded by MuDR, the
transposase mudrA becomes reactivated. Further, the
second gene, mudrB, remains methylated and silenced, suggesting that, although the two genes had
both been silenced by Muk, maintenance of that silenced state is mediated by different factors[33]. Silenced Mu elements in typical lines can also be reactivated by gamma and UV radiation of seeds and pollen, and radiation treatments are more efficient on
lines within one or two generations of silencing than
those lines that had kept many generations of silence
state[5]. Singer et al. [18] found that Mutator-like elements (MULEs) in Arabidopsis genome become demethylated and active in the chromatin-remodeling
mutant ddm1 (Decrease in DNA Methylation), which
leads to loss of heterochromatic DNA methylation.
4
Genetic Application of Mu Transposon
Transposon tagging is one of the main methods
used in functional genome research. Ac/Ds tagging
system has not only been successfully used in maize
but also in rice and Arabidopsis [34]. The advantages of
Mu tagging are that it moves to any chromosome, it
causes a very high mutation rate, insertions tend to be
into or near genes, and most loci appear to be potential targets. Using this transposon system, many maize
genes have been cloned and characterized, some of
which are listed in Table 1.
Table 1 List of some Mu tagging cloned maize functional genes
No.
Gene or allele
Possible function
Database code
Reference
1
Su1
Kernel development related
AY290402
[35]
2
Rough sheath1
Leaf sheath development related
L44133
[36]
3
APETALA2
Spikelet development related
AF048900
[37]
4
Ligueless3
Architecture of ligule
AF457125
[38]
5
Knotted1
Leaf development
AY312169
[39]
6
Viviparous1
Induction of embryo development
AJ001635
[40]
7
Adh1
Oxygen starvation response
X04049
[7]
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Targeted mutagenesis was the initial application
in typical Mutator lines, because it is relatively easy
for scientists to recover mutations in well-studied
genes that confer visible phenotypes [5]. For loci with
a recessive loss-of-function allele, wild-type plant with
active Mu were crossed to the homozygous recessive
tester stock, mutant individuals in the F1 progeny
would be expected to carry a Mu-tagged allele from
the Mu-active parent. For loci with dominant
gain-of-function alleles, Mu-active lines homozygous
for the dominant allele need to be established first, and
then crossed to a normal test line. Normal individuals
of the F1 most likely contained a Mu-inserted disruption of the dominant allele. Because Mu causes a high
mutation rate, large populations of Mu active lines
have been screened to find new phenotypes of interest.
Three big project of Mu-tagging maize functional genome research had been carried out in the
United States. The Trait Utility System for Corn
(TUSC) was implemented by Pioneer Hi-Bred, Inc.,
which was based on DNA samples of ~45 000
Mu-active individual plants and the available of
maize EST sequences. Using a primer running out
from the Mu TIR sequence and a primer designed on
the basis of an EST of interest, population screening
can be used to find individuals with a Mu insertion
into or near the gene of interest. Progeny analysis can
then be used to determine which plants transmitted a
heritable mutant allele. Maize-Targeted Mutagenesis
(MTM) is a US National Science Foundation funded
project for public maize research service. With the
same strategy to TUSC, MTM uses PCR to screen
from a population of ~46 000 Mu active plants and
provide users with seed for phenotypic characterization. RescueMu was another project carried out by
joint co-operation of Stanford University, UC Berkeley and other institutes, which involves screening
progeny of RescueMu transformed maize plants. This
approach has the virtue of combining genomic sequencing and functional genomics into a single step,
in which RescueMu insertions provide not only a
mutation but also a cloned allele for sequencing.
Since Mu transposon had been effectively used
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in maize functional genome research, it would be
advantageous if we use this system in other plant
species for gene tagging as well. The most direct way
to do this is to create a heterologous Mu transposon
tagging in other species. Unfortunately, although
mudrA and mudrB have been successfully transformed into rice, and the transformed genes can be
inherited for a few generations, transcription of
mudrA and mudrB was not detected (unpublished
data). So we need more knowledge about Mu epigenetic regulation and transferring gene silencing.
Transposition active MULEs have been observed in
Arabidopsis DDM1 mutant [18] and a fungal species
Fusarium oxysporum [41], suggesting that transpositionally active Mu elements do exist in organisms in
addition to maize. Thus, screening for active and
mutagenic MULEs may be another option for Mu
tagging in species such as rice.
5
Occurrence and Classification of Mu
Elements in Other Plant Genomes
It has been demonstrated that homologs of
mudrA exist in many plant genomes, but homologs
of mudrB have only been observed in Z. luxurians,
Z. diploperennis and a few other species closely related to maize[42]. Mu-like elements are generically
referred to as MULEs[15]. Autonomous MULEs show
varying degrees of similarity with mudrA in maize.
So far intact element of MULEs, including TIRs and
TSDs, had been cloned and characterized from
Arabidopsis, Brassic napus, rice, sorghum (Sorghum
bicolor L.), sugar cane (Saccharum officinarum L.),
wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), foxtail millet (Setaria italica L.) and a few
bamboo species (Bambuseae) species[5, 42-44]. Lisch et
al.[42] cloned and characterized mudrA sequences
from 28 plant species. Cluster analysis based on the
unclear tide identity of the cloned fragments showed
a discrepancy in the relationship between phylogeny
of the sample species and the evolution phylogeny of
those MULEs. Eisen et al. [13] found that the sequence
of transposase mudrA was similar to transposase of
some insertion sequence (IS) in a group of bacteria
DIAO Xian-Min et al.: Mutator Transposon in Maize and MULEs in the Plant Genome
species such as Mycobacterium bovis. These suggest
that the Mu transposon family might have had a very
early origin. The genomes of fungus do have MULEs
and even a transpositional active one was characterized
[41]
. To date no MULEs have been reported in animals.
Not only do we know that MULEs are ubiquitous in plant genomes so far tested, but analysis of
public EST data demonstrate that MULEs in many
plants, including rice, wheat, sugar cane and barley
are transcripted. Thus, transcriptional active MULEs
maybe a common property of plant genomes[42]. Most
MULEs contain mudrA genes that are well diverged
from that in maize, but many of those MULEs have
good open-reading frames with evidence for selection
at the amino acid level, consistent with continued
functionality. Conservation of TIR sequences with
each other and targeted side duplication (TSD) is also
constant with continued transposition activity. Many
duplicated copies of one kind MULEs were found in
the sequenced rice genome (unpublished observation),
and we found several MULEs of Setaria viridis were
highly polymorphic among different genotypes of the
same species by Southern blot (unpublished data),
suggesting activity in this species. Database search
using the protein sequence of MURA reveals that
proteins with high similarity to MURA exist in
Arabodopsis, potato (Salanum tuberosum L.), tomato
(Lycopersicon esculentum M.) and many other plant
species [42]. Yoshida [45] found a rice MULE expressed
in callus subcultured with praline and even found a
transcriptionally active MULE in rice somaclonal
lines. Three instances of transpositionally active
MULEs have been reported, including Jittery in
maize, AtMu1 in Arabidopsis DDM mutant and Hop1
in the fungus Fusarium oxysporum. Jittery resembles
Mutator in the length of the element’s TIRs, the size
of the target site duplication, and the makeup of its
transposase, but differs from MuDR in that it encodes
a single MURA-like protein. Jittery also differs from
Mutator elements in the high frequency with which it
excises to produce germinal revertants and in its low
copy number in most maize lines and maize relatives
examined. However, Jittery cannot be considered as a
bona fide transposon in its present host line, because
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it does not reinsert in the genome [16]. Together, these
data suggest that MULEs may be transpositionally
active now or in the near past in many plant genomes.
Thus, it is quite likely that active Mu systems in other
plant species may be as useful as Mutator does in
maize.
MULEs can be widely diverged from each other
even they come from the same genome. Jittery, which
is an active MULE in maize, is more similar to MULEs
in rice and Arabidopsis than it is to MuDR
[16]
. Re-
markably, two of MULEs in Arabidopsis with high
similarity to Jittery appear to be host functional genes
rather than transposons; mutations in those genes cause
defects in the far-red-light response pathway
[46-48]
. In
this case, it appears that the transposase has been recruited by the host to perform a novel function.
The distribution of any given group of MULEs in
the grasses is patchy, suggesting the possibility of
horizontal gene transfer. Diao and colleagues[49] found
a MULE from Setaria with high similarity to a MULE
from rice; the nucleotide identity between the two
elements is as high as 90% including corresponding
intron sequences. Given the 50–60 million years of
evolution divergence that separate Setaria and rice[50],
the high degree of similarity of non-coding sequences
can only be explained by horizontal transfer[49]. This is
the first well-documented example of horizontal transfer of any nuclear-encoded genes between higher
plants. It is clear that the evolution of Mu super family
is markedly different from their hosts.
MULEs form a highly complex and broadly diversified family of transposon. All Mu-related elements so
far found in plant genomes can be classified into four
groups: the first includes MuDR and hMuDRs as stated
in the second part of the review. Many of these elements
contain point mutations but are transcriptionally expressed and may play a role in the epigenetic regulation
of the family [5]. The second group includes elements
that have mudrA homologs and long distinct TIRs from
MuDR, such as Jittery in maize and Sf4 in Setaria. The
third group of Mu super family includes those elements
that share similar TIRs with a MULE encoding mudrA
but that carry internal sequences that are unrelated to the
484
transposase. Examples of these include some of the
nonautonmous elements in maize. Their internal sequences are captured fragments of host genes. These
elements are known as Pack-MULEs, and they can be
present in large numbers in any given genome [15, 51, 52].
The fourth group includes transposons that carry
mudrA-like genes but lack long TIRs. Individual instances of this class of elements may represent coopted
mudrA genes, genes such as Far1 in Arabidopsis [46, 47].
6
Mu Elements in Plant Genome and Gene
Evolution
The genome of all plant species is in a state of dynamic equilibrium between evolution and stability, but
of course stability is always temporary. The diverse activity of transposons has been demonstrated to be an
important factor affecting on the evolution of genes and
genomes [1,53,54]. Transposon can induce gene silencing
or reactivation, gene or genome restructuring including
deletion, duplication, reversion and translocation. The
accumulation of such changes undoubtedly has had a
profound impact on genome evolution.
Mu transposons are the most active, most complex and most ubiquitous DNA transposable element in
plant genomes, suggesting a special role in gene and
genome evolution. Unlike Ac/Ds and Spm/dSpm,
whose activity result in relatively minor changes to the
host sequence, Mu activity can result in a wide range
of changes[12]. It has demonstrated that MuDR elements in different loci can show distinct frequencies of
transposition, suggesting that this class of elements is
particularly sensitive to their local environment. It is
clear that Mu elements can evolve a novel function,
such as in the case of the Arabidopsis Far1 gene [46, 47].
The most recent discovery of the impact of Mu elements on plant genome evolution is Pack-MULEs,
which contain fragments of genes. With systematic and
careful analysis, Jiang et al.[55, 56] fund more than 3 000
Pack-MULEs in the rice genome, and Pack-MULEs
also had been seen in maize and Arabidopsis. The
large number of Pack-MULEs and their presence in
multiple genomes suggest that they may be a major
component of most or all flowering plant genomes.
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Gene fragments from different rice genes were found
together in -23% of Pack-MULEs in rice, suggesting a
means by which hybrid genes could be created due to
the activity of a transposon. At least 5% of
Pack-MULEs were found to be expressed, as evidenced by full-length cDNAs, with an identical DNA
sequence match. Hence, by the criterion of expression
at the RNA level, many of these Pack-MULEs are already new genes. The ability of Pack-MULEs to capture gene fragments combined with the possibility of
horizontal transfer as documented by Diao et al.[49]
also suggest a means by which gene fragments could
be moved between species.
Although we have made some progress in understanding of the MuDR/Mu superfamily, many interesting
puzzles remains to be explored for future research. The
most intriguing questions include the detail mechanism of
Mu transposition and the epigenetic regulation of Mu
silencing and reactivation. The solution for such questions
will help us establish Mu tagging system in other plants
than maize and widening its application in plant genetics.
The frequent transposition and interaction with host genomes make the evolution study of transposons difficult,
but analysis of this fascinating super family of elements
and a clear understanding of their evolution will certainly
help us understand the dynamics of gene and genome
evolution. Pack-MULE structure is ubiquitous in plant
genomes and predicted to be a mechansism for the creation of novel genes[51, 52], but we know nothing about the
mechanism of fragments acquisition and so far no instances of newly created genes in this way have been
reported. As stated by Shapiro of Chicago University[54]
“transposable elements are the key to a 21st century
view of evolution”, advances in our understanding of
the MULE super family will for certainly help us to illuminate both transposon and genome evolution.
Acknowledgement: We thank Hui Zhi of National
Millet Improvement Center of China for figure
preparation.
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487
Mutator 转座子及 MULE 在植物基因与基因组进化中的作用
刁现民 1，Damon Lisch2
1. 河北省农林科学院谷子研究所 国家谷子改良中心，石家庄 050031；
2. 美国伯克力加州大学植物与微生物学系，伯克力 CA 94720，美国
摘 要：Mutator（Mu）转座子是植物中已发现的转座最活跃的转座子，其高的转座频率及趋向于单拷贝功能基因转座的特
性，使该转座子成为玉米功能基因克隆的主要方法。Mu 转座子的同源类似因子广泛存在于被子植物基因组中，而且同一
基因组中往往具有多种变异类型。它不仅具有其他 DNA 转座子在基因和基因组进化中的普遍作用，而且具有能够承载基
因组内功能基因和基因片段的载体功能，这种载体 Mu 转座子（Pack-MuLEs）能够在基因组内移动众多的基因片段，从而
对基因和基因组进化产生作用。Mu 转座子的同源序列发生在水稻与狗尾草之间的水平转移提供了高等植物核基因水平转
移的首个例证。对 Mu 转座子的了解促进了我们对动态基因组概念的认识。文章对 Mutator 转座子的发现、转座特征、基
因标签应用等的研究进展进行了综述，对 Mu 转座子家族的同源序列进行了分类，讨论了该转座子在基因组进化中的作用，
分析了应加强研究的问题。
关键词：Mutator 转座子；基因组进化；MuLE；载体 Mu 转座子
作者简介：刁现民（1963-），男，河北南和县人，理学博士。研究方向：作物遗传育种与分子生物学