Concomitant regulation of Mu1 transposition and Mutator activity in maize

Rejuvenation by shoot apex culture recapitulates the developmental increase of methylation at the maize gene Pl-Blotched

Cytosine methylation provides an attractive epigenetic modification for the global maintenance of phases in plant development; however, there are few known examples of specific genes whose methylation status changes in a developmentally regulated manner. Pl-Blotched, an allele of purple plant1 (pl1), which encodes a myb-like transcription factor that regulates anthocyanin production in maize, is one such gene: certain cytosines at the 3' end of this allele are hypomethylated in seedlings, become hypermethylated in organs formed in the adult phase, and are hypomethylated again in the next generation. We tested whether this developmental pattern of low juvenile cytosine methylation followed by higher methylation in adult tissues could also be observed in plants "rejuvenated" via shoot apex culture. We found that cytosine methylation patterns at Pl-Blotched were indeed recapitulated in culture-rejuvenated plants, showing hypomethylation in leaves with juvenile patterns of differentiation (even though they were made by an old meristem) followed by hypermethylation in later-formed leaves. Our results show that methylation status at that locus is determined by the developmental phase of the shoot, rather than by the age of the meristem forming it. These results support the hypothesis that DNA methylation is employed by the plant to maintain an epigenetic state.

Maize Mu transposons are targeted to the 5' untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome

The widespread use of the maize Mutator (Mu) system to generate mutants exploits the preference of Mu transposons to insert into genic regions. However, little is known about the specificity of Mu insertions within genes. Analysis of 79 independently isolated Mu-induced alleles at the gl8 locus established that at least 75 contain Mu insertions. Analysis of the terminal inverted repeats (TIRs) of the inserted transposons defined three new Mu transposons: Mu10, Mu 11, and Mu12. A large percentage (>80%) of the insertions are located in the 5' untranslated region (UTR) of the gl8 gene. Ten positions within the 5' UTR experienced multiple independent Mu insertions. Analyses of the nucleotide composition of the 9-bp TSD and the sequences directly flanking the TSD reveals that the nucleotide composition of Mu insertion sites differs dramatically from that of random DNA. In particular, the frequencies at which C's and G's are observed at positions -2 and +2 (relative to the TSD) are substantially higher than expected. Insertion sites of 315 RescueMu insertions displayed the same nonrandom nucleotide composition observed for the gl8-Mu alleles. Hence, this study provides strong evidence for the involvement of sequences flanking the TSD in Mu insertion-site selection.

Characterization of the germinal and somatic activity of the Arabidopsis transposable element Tag1

Tag1 is an autonomous transposon of Arabidopsis thaliana. The excision behavior of Tag1 during reproductive and vegetative development was examined using CaMV 35STag1-GUS constructs. Germinal reversion frequencies varied from 0 to 27% and correlated with Tag1 copy number. Southern blot and somatic sector analyses indicated that each revertant was derived from an independent excision event, and approximately 75% of the revertants had new Tag1 insertions. Revertants were obtained with similar frequencies from the male and female parents. In flowers, small somatic sectors were observed in siliques, carpels, petals and sepals while stemlike organs (filaments and pedicels) had larger sectors. No sectors encompassing entire flowers or inflorescences were observed, however, indicating that excision occurs late in flower development and rarely in inflorescence meristems. Late excision was also observed during vegetative development with 99.8% of leaves showing small sectors encompassing no more than 20 cells. Roots and cotyledons, however, showed larger sectors that included entire lateral roots and cotyledons. These results indicate that Tag1 can excise in the embryo and all the organs of the plant with the timing of excision being restricted to late stages of vegetative and reproductive development in the shoot.

Amplification of Ac in tomato is correlated with high Ac transposition activity

We have assayed the transposition activity of the maize transposable element Ac in transgenic tomato plants that had a single copy of Ac. We found that Ac elements were in either a high or low activity state and that an Ac insertion could cycle from low to high activity within a generation. The different transposition activities were not simply due to the chromosomal position of the element, because the same Ac insertion had different levels of activity in sibling plants. Transposition activity was measured by two methods, one genetic and one physical; both assays gave similar results for each plant studied. Notably, plants with active Ac elements had progeny with amplified Ac copy number, while no amplification was detected in lines containing Ac in a low activity state. Analysis of lines with amplified elements revealed that the elements could be either clustered or dispersed. Our results were consistent with amplification being the result of transposition.

Ds read-out transcription in transgenic tomato plants

To select for Ds transposition in transgenic tomato plants a phenotypic excision assay, based on restoration of hygromycin phosphotransferase (HPT II) gene expression, was employed. Some tomato plants, however, expressed the marker gene even though the Ds had not excised. Read-out transcriptional activity of the Ds element is responsible for the expression of the HPT II gene. Transcription initiation was mapped to multiple positions spanning about 300 bp in the subterminal part of the Ds element. In this respect Ds in tomato resembles the maize element Mu1, which also promotes transcription outward from the element. Transposon read-out transcription might thus supply an additional general mechanism for controlling plant gene expression.

The generation of Mutator transposable element subfamilies in maize

The mobile DNAs of the Mutator system of maize (Zea mays) are exceptional both in structure and diversity. So far, six subfamilies of Mu elements have been discovered; all Mu elements share highly conserved terminal inverted repeats (TIRs), but each sub-family is defined by internal sequences that are apparently unrelated to the internal sequences of any other Mu subfamily. The Mu1/Mu2 subfamily of elements was created by the acquisition of a portion of a standard maize gene (termed MRS-A) within two Mu TIRs. Beside the unusually long (185-359 bp) and diverse TIRs found on all of these elements, other direct and inverted repeats are often found either within the central portion of a Mu element or within a TIR.Our computer analyses have shown that sequence duplications (mostly short direct repeats interrupted by a few base pairs) are common in non-autonomous members of the Mutator, Ac/Ds, and Spm(En) systems. These duplications are often tightly associated with the element-internal end of the TIRs. Comparisons of Mu element sequences have indicated that they share more terminal components than previously reported; all subfamilies have at least the most terminal 215 bp, at one end or the other, of the 359-bp Mu5 TIR. These data suggest that many Mu element subfamilies were generated from a parental element that had termini like those of Mu5. With the Mu5 TIRs as a standard, it was possible to determine that elements like Mu4 could have had their unusual TIRs created through a three-step process involving (1) addition of sequences to interrupt one TIR, (2) formation of a stem-loop structure by one strand of the element, and (3) a subsequent DNA repair/gene conversion event that duplicated the insertion(s) within the other TIR. A similar repair/conversion extending from a TIR stem into loop DNA could explain the additional inverted repeat sequences added to the internal ends of the Mu4 and Mu7 TIRs. This same basic mechanism was found to be capable of generating new Mu element subfamilies. After endonucleolytic attack of the loop within the stem-loop structure, repair/conversion of the gap could occur as an intermolecular event to generate novel internal sequences and, therefore, a new Mu element subfamily. Evidence supporting and expanding this model of new Mu element subfamily creation was identified in the sequence of MRS-A.

Identification of a defective transposable element in tobacco

A putative defective transposable element has been identified in tobacco. This element has been found and characterised in two separate parts of the tobacco genome, specifically within the 3rd intron of the pollen-specific polygalacturonase gene (Npg1) and upstream of the endochitinase gene (Chn50). The element is ca. 0.4 kb in length and is bounded by conserved inverted repeats and putative target site duplications. It appears to fall into the category of non-autonomous transposable elements.

Molecular analysis of the loss of somatic instability in the bz2::mu1 allele of maize

Multiple genetic and epigenetic changes were detected within one plant generation at the bz2::mu1 mutable allele in a population of 118 plants. Loss of somatic instability in bz2::mu1 was usually correlated with methylation of the Mu1 transposable element; in 6 plants, somatic instability was lost as a result of mutations in bz2::mu1. This is a surprisingly high frequency of mutation per allele (2.5%) for the Mutator family, for which germinal revertants occur at a frequency of about 10(-4) per gamete. One germinal excision event was found that contained an 8 bp deletion, frameshift mutation in Bronze-2. The three other mutants described occurred as a result of abortive transposition, in which 75-77 bp deletions were generated at the junction between Bronze-2 and Mu1. We discuss the possible mechanisms, and the role of host factors in abortive transposition in maize.

Binding sites for maize nuclear proteins in the terminal inverted repeats of the Mu1 transposable element

Nuclear protein extracts from Mu-active, Mu-inactive and non-Mutator lines of maize were used to identify the binding sites for maize nuclear proteins in the terminal inverted repeats (TIR) of the Mu1 transposable element. We found binding activities of nuclear proteins that specifically interact with both TIRs of the Mu1 element. DNase I footprinting was performed to localize the binding sites. We found that the nuclear proteins from Mu-active lines and non-Mu lines bound to the Mu1 TIR at two different sites, i.e. a 13 bp sequence (CGGGAACGGTAAA, designated as site I) and another 8 bp sequence (CGGCGTCT, designated as site II). However, the nuclear proteins from Mu-inactive lines bound only one of these sites, i.e. site I. Mobility shift assays with synthetic oligonucleotides containing site I and II respectively confirmed the specificities of these binding activities. Site I was shown to be an imperfect direct repeat of a hexamer binding site (CGGGAACGGTAA). Oligonucleotides containing either of the hexamers showed specific binding activity to nuclear protein from both Mu-active and Mu-inactive lines. The possible role of these proteins in Mu transposition is discussed.

The Mu1 transposable element of maize contains two promoter signals recognized by the Escherichia coli RNA polymerase

The galactokinase (GalK) expression plasmid vector system pKO-1 has been used to screen for promoter elements in the maize transposable element Mu1 that function in Escherichia coli. Two transcriptional start points, named S1 and S2, were identified, which are located in the two direct repeats of the transposable element. This paper demonstrates that sequence elements exist in a plant transposable element which function as prokaryotic promotors.

Somatically heritable switches in the DNA modification of Mu transposable elements monitored with a suppressible mutant in maize

Many transposable elements in maize alternate between active and inactive phases associated with the modification of their DNA. Elements in an inactive phase lose their ability to transpose, their ability to excise from reporter alleles and, in some cases, their ability to enhance or suppress mutant phenotypes caused by their insertion. The maize mutant hcf106 is a recessive pale green seedling lethal caused by the insertion of the transposable element Mu1. We show that the hcf106 mutant phenotype is suppressed in lines that have lost Mu activity. That is, homozygous hcf106 seedlings are dark green and viable when transposable elements belonging to the Robertson's Mutator family are modified in their terminal inverted repeats, a diagnostic feature of inactive lines. This property of the mutant phenotype has been used to follow clonal leaf sectors containing modified Mu elements that arise from single somatic cells during plant development. The distribution of these sectors indicates that epigenetic switches involving Mu DNA modification occur progressively as the meristem ages.

Characterization of bz1 mutants isolated from mutator stocks with high and low numbers of Mu1 elements

The high frequency of mutations in Mutator stocks of maize is the result of transposition of Mu elements. Nine different Mu elements that share the 220 bp Mu terminal inverted repeats have been described. Mu1 elements have been found inserted into most of the molecularly characterized mutant alleles isolated from Mutator stocks, and most Mutator stocks contain a high number of Mu1 elements (10-60). However, it is clear that additional Mu elements, which share the Mu1 termini but have unrelated internal sequences, can also transpose in Mutator stocks. We were interested in comparing the mutation frequency and type of elements that inserted into a particular locus when Mutator stocks with differing numbers of Mu1 elements were utilized. Furthermore, previous studies with Mu-induced mutations have demonstrated that the element that inserted most frequently was Mu1. Therefore, to try to obtain Mu elements different from Mu1 we utilized a stock that had a low number (3-6) of Mu1 elements as well as a Mutator stock with a more typical number of Mu1 elements (20-60). Utilizing both stocks, we isolated numerous mutants at one gene, Bronze 1 (Bz1), and compared the type of elements inserted. In this paper we report that both the high and low Mu1 stocks produced bz1 mutants at frequencies characteristic of Mutator stocks, 6.6 and 4.3 x 10(-5), respectively. We describe the isolation of 20 bz1 mutations, and the initial molecular characterization of eight unstable mutations: two from the high Mu1 stock and six from the low Mu1 stock. The six alleles isolated from the low Mu1 stock appear to contain deleted Mu1 elements, and the two alleles isolated from the high Mu1 stock contain elements very similar to Mu1. When the mutants from the low Mu1 stocks were examined, it was found that the Mu1-related elements increased from 3-6 copies to 9-20 copies in one generation. The high number of Mu1-related elements was maintained in subsequent outcrosses. This spontaneous activation and amplification of Mu1-related elements occurred in at least 1% of the low Mu1 plants.

Transposon mutagenesis of nuclear photosynthetic genes in Zea mays

The discovery of a new maize (Zea mays L.) transposon system, Mutator, and the cloning of the 1.4 kilobase transposon, Mul, have made feasible the isolation of nuclear photosynthetic genes which are recognized only by their mutant phenotype. Mutant maize plants which express a high chlorophyll fluorescent (hcf) phenotype due to a defect in the electron transport or photophosphorylation apparatus have been isolated following mutagenesis with an active Mutator stock. The affected genes and their products in these mutants are inaccessible to classical methods of analysis. However, mutagenesis with the Mutator transposon makes it possible to isolate these genes.Although the PSII-deficient mutant hcf3 has been thoroughly studied by classical photo-biological methods, the nature of the lesion which results in the observed phenotype has not been established. A Mutator-induced allele of hcf3 has been isolated. A fragment of genomic DNA has been identified which is homologous to Mul and co-segregates with the mutant phenotype. This fragment is expected to contain a portion of the hcf3 locus which will be used to clone the normal gene. Direct study of the gene can provide insight into the nature and function of its polypeptide product.This approach can be used to study any photosynthetic gene which has been interrupted by a transposon. The isolation of more than 100 different chemically-induced hcf mutants, most of which can not be fully characterized using classical means, indicates the wealth of information which can be obtained using a transposon tagging technique.

Regulation of mutator activities in maize

We discuss the properties of the Mutator (Mu) transposable element family of maize. We report the cloning of bz2-mu1, a mutable allele containing a 1.4-kb Mu element, using a combination of transposon tagging and tests for differential hybridization to northern and Southern blots. We report the sequence of this allele and the Mu element insertion, and propose a model for the structure of the Bz2 locus. We discuss the relationship between increased DNA modification of Mu elements and loss of somatic instability at bz2-mu1. To further explore this aspect of regulation of Mutator, we have used gene-specific probes to determine the level of modification at this locus in active and inactive Mutator lines. We have also utilized CsCl density gradients to estimate the overall level of DNA modification in active and inactive lines; we find that Mu elements in active lines are hypomethylated relative to other maize nuclear DNAs examined, and that in inactive lines the level of modification in Mu elements is similar to the genome as a whole. Utilizing gamma-irradiation, we have demonstrated that inactive lines can be reactivated; this reactivation is first noted as restitution of the spotted kernel phenotype characteristic of bz2-mu1 in active Mutator lines. Hybridization analysis of DNA from reactivated plants demonstrates that the Mu elements in general, and specifically the Mu element at bz2-mu1, have the lower level of DNA modification characteristic of active lines. These results are discussed in terms of the role and timing of DNA modification in regulating Mutator activities.