Nucleotide sequence of the maize transposable element Mul

Bronze-2 gene of maize: reconstruction of a wild-type allele and analysis of transcription and splicing

The maize Bronze-2 (Bz2) gene, whose product acts late in the anthocyanin biosynthetic pathway, has been cloned and its transcript has been mapped. We have developed a general procedure for reconstructing wild-type alleles from transposable element-induced mutants. An existing transposon-containing clone, bz2::mu1 [McLaughlin, M., and Walbot, V. (1987). Genetics 117, 771-776], was modified by replacing the region of bz2::mu1 containing the transposon with the corresponding polymerase chain reaction-amplified sequence from the progenitor allele that has no Mu insertion. Particle gun delivery of the reconstructed Bz2 gene to embryonic scutellar tissue lacking a functional Bz2 gene complemented the bz2 mutant phenotype, as demonstrated by the production of purple spots. Having cloned the wild-type allele, we then analyzed the Bz2 transcript, whose features include an 82-nucleotide 5'-untranslated leader, one small intron (78 base pairs) within the coding region, and multiple polyadenylation sites. Four Mutator transposon insertions that eliminate gene function were mapped within the 850-nucleotide transcription unit. We found that variable levels of unspliced Bz2 RNA are present in purple husk tissue; this finding may indicate that the expression of Bz2 is regulated in part at the level of transcript processing.

Cloning of the y1 Locus of Maize, a Gene Involved in the Biosynthesis of Carotenoids

The y1 gene is one of the genes responsible for the production of [beta]-carotene in the endosperm and leaves of maize. We have cloned a Robertson's Mutator-tagged allele of the y1 gene (y1-mum) by using a Mu3 element as a hybridization probe. We substantiate that the cloned sequence is a portion of the y1 gene by molecular analyses of a revertant of a putative Mutator-induced y1 allele and the incidence of insertions within the cloned y1 sequence from several independently derived Mutator-induced y1 mutant stocks. The y1-mum sequence was used to isolate the standard Y1 allele, which conditions the presence of [beta]-carotene in the endosperm of the maize kernel.

A tandem duplication causes the Kn1-O allele of Knotted, a dominant morphological mutant of maize

Molecular and genetic techniques are used to define Kn1-O, a mutation which interferes with the normal differentiation of vascular tissue in leaves. Sequences associated with a previously cloned allele, Kn1-2F11, were used as hybridization probes in a Southern analysis of Kn1-O. By this analysis, Kn1-O lacks the Ds2 transposable element that causes Kn1-2F11 but instead is associated with a sequence duplication. Sequence and restriction analysis of genomic clones show that the duplication consists of a tandem array of two 17-kb repeats. Analysis of Kn1-O derivatives indicates that the duplication itself conditions the mutant phenotype; a severely knotted line, Kn1-Ox, has gained a repeat unit to form a triplication, whereas normal derivatives have either lost a repeat unit or sustained insertions that disrupt the tandem duplication. These insertions map near the central junction of the tandem duplication, suggesting that the mutant phenotype results from the novel juxtaposition of sequences. We discuss models that relate the tandem duplication of sequences to altered gene expression.

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.

The Mu1 maize transposable element induces tissue-specific aberrant splicing and polyadenylation in two Adh1 mutants

Insertions of the maize transposable element Robertson's Mutator (Mu) into intron 1 of the Adh1 gene have produced a number of mutant alleles altered in quantitative expression. It has previously been shown that transcription and mRNA accumulation are reduced for two of these alleles, Adh1-S3034 and Adh1-S4477. In this report, we describe the presence of Mu1-hybridizing polyadenylated transcripts in roots of anaerobically induced seedlings of these same mutants. Sequence analysis of Mu1-hybridizing clones from a cDNA library of S3034 RNA indicated that these transcripts originated from the Adh1 locus and were produced by alternative processing of S3034 pre-mRNA. Approximately half of the cDNAs represented transcripts that had not undergone excision of the intron containing the 1.4-kilobase Mu1 insertion but were processed in response to signals present in the transposable element. Mu1 contains a donor splice site in the 5'-terminal inverted repeat that can be joined to the Adh1 exon 2 acceptor, resulting in removal of most of the Mu1 sequences from the pre-mRNA; alternatively this donor can be spliced to an acceptor within Mu1, removing an 89-nucleotide intron. Mu1 also contains polyadenylation signals that are used to produce truncated transcripts. These Mu1 transcripts produced by aberrant splicing and polyadenylation were not detected in RNA isolated from developing kernels.

The Mu1 maize transposable element induces tissue-specific aberrant splicing and polyadenylation in two Adh1 mutants

Insertions of the maize transposable element Robertson's Mutator (Mu) into intron 1 of the Adh1 gene have produced a number of mutant alleles altered in quantitative expression. It has previously been shown that transcription and mRNA accumulation are reduced for two of these alleles, Adh1-S3034 and Adh1-S4477. In this report, we describe the presence of Mu1-hybridizing polyadenylated transcripts in roots of anaerobically induced seedlings of these same mutants. Sequence analysis of Mu1-hybridizing clones from a cDNA library of S3034 RNA indicated that these transcripts originated from the Adh1 locus and were produced by alternative processing of S3034 pre-mRNA. Approximately half of the cDNAs represented transcripts that had not undergone excision of the intron containing the 1.4-kilobase Mu1 insertion but were processed in response to signals present in the transposable element. Mu1 contains a donor splice site in the 5'-terminal inverted repeat that can be joined to the Adh1 exon 2 acceptor, resulting in removal of most of the Mu1 sequences from the pre-mRNA; alternatively this donor can be spliced to an acceptor within Mu1, removing an 89-nucleotide intron. Mu1 also contains polyadenylation signals that are used to produce truncated transcripts. These Mu1 transcripts produced by aberrant splicing and polyadenylation were not detected in RNA isolated from developing kernels.

Isolation and sequence analysis of Caenorhabditis briggsae repetitive elements related to the Caenorhabditis elegans transposon Tc1

We have identified two repetitive element families in the genome of the nematode Caenorhabditis briggsae with extensive sequence identity to the Caenorhabditis elegans transposable element Tc1. Five members each of the TCb1 (previously known as Barney) and TCb2 families were isolated by hybridization to a Tc1 probe. Tc1-hybridizing repetitive elements were grouped into either the TCb1 or TCb2 family based on cross-hybridization intensities among the C. briggsae elements. The genomic copy number of the TCb1 family is 15 and the TCb2 family copy number is 33 in the C. briggsae strain G16. The two transposable element families show numerous genomic hybridization pattern differences between two C. briggsae strains, suggestive of transpositional activity. Two members of the TCb1 family, TCb1#5 and TCb1#10, were sequenced. Each of these two elements had suffered an independent single large deletion. TCb1#5 had a 627-bp internal deletion and TCb1#10 had lost 316 bp of one end. The two sequenced TCb1 elements were highly conserved over the sequences they shared. A 1616-bp composite TCb1 element was constructed from TCb1#5 and TCb1#10. The composite TCb1 element has 80-bp terminal inverted repeats with three nucleotide mismatches and two open reading frames (ORFs) on opposite strands. TCb1 and the 1610-bp Tc1 share 58% overall nucleotide sequence identity, and the greatest similarity occurs in their ORF1 and inverted repeat termini.

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.

The effect of insertion of the maize transposable element mutator is dependent on genetic background

A secondary mutant, derived from an allele of maize alcohol dehydrogenase 1 (Adh1) carrying a Mutator transposable element (Mu1) in its first intron, was reported to exhibit a threefold decrease in ADH enzymatic activity and steady-state RNA levels compared to the original mutant. The original mutant, Adh1-S3034 (abbreviated S3034), was previously characterized at the molecular level. The derivative, abbreviated S3034b, has now been cloned; at the DNA sequence level the insertion and surrounding Adh1 sequences are indistinguishable from S3034. Furthermore, in our lines there is no difference in relative ADH activities between products of the two putative alleles. A comparison of gene expression in heterozygotes obtained by crossing to different tester lines reveals a correlation between the measured decrease in levels of ADH polypeptide produced by the mutant allele and the background in which it is measured; this effect is distinct from any background-related variation in the expression of the progenitor allele. It does not appear to be attributable to alternative patterns of DNA modification. It appears to reflect a background-associated difference in the level of normal Adh1-RNA produced. Thus the previously reported distinction between S3034 and S3034b may be due to differences in the extent to which the mutant allele and a given genetic background interact to produce functional Adh1-RNA.

Molecular and genetic characterization of Mu transposable elements in Zea mays: behavior in callus culture and regenerated plants

Active Mutator lines of maize (Zea mays L.) have a high mutation rate and contain multiple hypomethylated 1.4-kb and 1.7-kb Mu transposable elements. Correlated with the inactivation of the Mutator system, these Mu elements cease to transpose and become more methylated. To determine whether the shock of tissue culture can affect Mutator activities, F1 progenies of outcrosses between active or inactive Mutator stocks and inbred line A188 were used to initiate embryogenic callus cultures. HinfI restriction digestion of genomic DNA isolated from 3-5-month-old cultures demonstrated that there is a very good correlation between the modification state of Mu elements in the cultures and the Mutator parent. Despite the dedifferentiation and rapid proliferation characteristic of tissue culture, the Mutator activity state is relatively stable during an extended tissue culture period. Cultures established from inactive Mutator lines were not reactivated; cultures established from active lines maintained a high Mu copy number, and most Mu elements remained unmodified. In contrast, weakly active Mutator parents gave rise to cultures in which Mu element modification could switch between low and high methylation during the culture period. Evidence for transposition was investigated with EcoRI digestion of genomic DNA isolated at different times during culture. The appearance of novel Mu-hybridizing fragments and a strong background hybridization are interpreted as evidence that transposition events occur during culture. Plants regenerated from such active cultures transmitted Mutator activity to their progeny.

Composite transposable elements in the Xenopus laevis genome

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

Composite transposable elements in the Xenopus laevis genome

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

Mu transposable elements are structurally diverse and distributed throughout the genus Zea

The Robertson's Mutator stock of maize exhibits a high mutation rate due to the transposition of the Mu family of transposable elements. All characterized Mu elements contain similar approximately 200-bp terminal inverted repeats, yet the internal sequences of the elements may be completely unrelated. Non-Mutator stocks of maize have a 20-100-fold lower mutation rate relative to Mutator stocks, yet they contain multiple sequences that hybridize to the Mu terminal inverted repeats. Most of these sequences do not cohybridize to internal regions of previously cloned Mu elements. We have cloned two such sequences from the maize line B37, a non-Mutator inbred line. These sequences, termed Mu4 and Mu5, have an organization characteristic of transposable elements and possess approximately 200-bp Mu terminal inverted repeats that flank internal DNA, which is unrelated to other cloned Mu elements. Mu4 and Mu5 are both flanked by 9-bp direct repeats as has been observed for other Mu elements. However, we have no direct evidence that they have recently transposed because they have not been found in known genes. Although the internal regions of Mu4 and Mu5 are not related by sequence similarity, both elements share an unusual structural feature: the terminal inverted repeats extend more than 100 bp internally from Mu-similar termini. The distribution of these elements in maize lines and related species suggests that Mu elements are an ancient component of the maize genome. Moreover, the structure of the Mu termini and the fact that Mu termini are found flanking different internal sequences leads us to speculate that Mu termini once may have been capable of transposing as independent entities.

The bz-rcy allele of the Cy transposable element system of Zea mays contains a Mu-like element insertion

The receptive component of the Cy transposable element system (rcy:Mu7) at the Bz locus of Zea mays L. is 2.2 kb and has long terminal inverted repeats. The insertion is flanked by a 9 bp duplication. In the presence of an autonomous Cy element in the genome, rcy:Mu7 is excised from bz-rcy in a manner consistent with a model suggested previously. The termini of rcy:Mu7 have 85% sequence similarity with the Mu1 element of Z. mays. This is consistent with the observation that Mu1 can behave genetically like a receptive component of the Cy system.

Molecular Analysis of viviparous-1: An Abscisic Acid-Insensitive Mutant of Maize

The viviparous-1 (vp1) gene in maize controls multiple developmental responses associated with the maturation phase of seed formation. Most notably, mutant embryos have reduced sensitivity to the hormone abscisic acid, resulting in precocious germination, and blocked anthocyanin synthesis in aleurone and embryo tissues. The Vp1 locus was cloned by transposon tagging, using the Robertson's Mutator element present in the vp1-mum1 mutant allele. Detection of DNA rearrangements in several spontaneous and transposable element-induced mutant vp1 alleles, including a partial deletion of the locus, confirmed the identity of the clone. The Vp1 gene encodes a 2500-nucleotide mRNA that is expressed specifically in embryo and endosperm tissues of the developing seed. This transcript is absent in seed tissues of vp1 mutant stocks. Expression of C1, a regulatory gene for the anthocyanin pathway, is selectively blocked at the mRNA level in vp1 mutant seed tissues, indicating the Vp1 may control the anthocyanin pathway by regulating C1. We suggest that the Vp1 gene product functions to potentiate multiple signal transduction pathways in specific seed tissues.

Molecular Analysis of viviparous-1: An Abscisic Acid-Insensitive Mutant of Maize

The viviparous-1 (vp1) gene in maize controls multiple developmental responses associated with the maturation phase of seed formation. Most notably, mutant embryos have reduced sensitivity to the hormone abscisic acid, resulting in precocious germination, and blocked anthocyanin synthesis in aleurone and embryo tissues. The Vp1 locus was cloned by transposon tagging, using the Robertson's Mutator element present in the vp1-mum1 mutant allele. Detection of DNA rearrangements in several spontaneous and transposable element-induced mutant vp1 alleles, including a partial deletion of the locus, confirmed the identity of the clone. The Vp1 gene encodes a 2500-nucleotide mRNA that is expressed specifically in embryo and endosperm tissues of the developing seed. This transcript is absent in seed tissues of vp1 mutant stocks. Expression of C1, a regulatory gene for the anthocyanin pathway, is selectively blocked at the mRNA level in vp1 mutant seed tissues, indicating the Vp1 may control the anthocyanin pathway by regulating C1. We suggest that the Vp1 gene product functions to potentiate multiple signal transduction pathways in specific seed tissues.

Molecular characterization of Mutator systems in maize embryogenic callus cultures indicates Mu element activity in vitro

Active Mutator lines of maize (Zea mays L.) are characterized by their ability to generate new mutants at a high rate and by somatic instability at Mutator-induced mutant alleles. Mutagenically active lines with fewer than ten Mu elements per diploid genome have not been observed. Alteration of Mutator activity has been shown to correlate with the state of modification of Hinfl restiction sites that lie within inverted terminal repeats of Mu elements. To determine whether active Mutator systems can be established and maintained in culture, copy number and modification state of Mu elements were investigated in embryogenic callus lines derived from F1S of crosses of active Mutator stock with the inbred lines A188 and H99. All callus lines studied maintain high Mu-element copy numbers, and more than half show a continued lack of modification at the Mu element Hinfl sites; thus, parameters associated with mutagenic activity in planta are present in some, but not all, callus lines. Mutator activity was then tested directly by restriction fragment analysis of subclonal populations from A188/Mu (2) and H99/Mu (2) embryonic cultures. Novel Mu-homologous restriction fragments occurred in 38% of the subpopulations which contained unmodified Mu elements, but not in control cultures containing modified, genetically inactive Mu elements. We conclude that Mu elements from active Mutator parents can remain transpositionally active in embryogenic cell culture. Active Mutator cell lines may be useful for the production of mutations in vitro.

Cloning and structural analysis of the snap-back DNA of Pharbitis nil

We isolated and cloned DNA fragments that exist as inverted-repeat structures in the genome of Pharbitis nil. The method used exploited the fact that if inverted repeat DNA is present in the DNA fragment, intramolecular double-stranded structures can be partly formed within single-stranded DNA molecules after denaturation and rapid renaturation of the fragment. The rapidly renaturing DNA fragments (termed snap-back DNA) were isolated by hybroxylapatite column chromatography and treatment with mungbean nuclease and were cloned into the pUC9 vector. Four snap-back DNA members out of thousands of independent clones obtained were characterized with respect to the reiteration frequency and the nucleotide sequences. When used as probes in Southern hybridization experiments, some of the members identified restriction fragment length polymorphism among the cultivars, suggesting that these sequences might be fluid in the genome. One of the four clones has regions of nucleotide sequence homology to those of inverted-repeat regions in the transposon Taml of Antirrhinum majus.

The Tc3 family of transposable genetic elements in Caenorhabditis elegans

We describe genetic and molecular properties of Tc3, a family of transposable elements in Caenorhabditis elegans. About 15 Tc3 elements are present in the genomes of several different wild-type varieties of C. elegans, but Tc3 transposition and excision are not detected in these strains. Tc3 transposition and excision occur at high frequencies, however, in strain TR679, a mutant identified because of its highly active Tc1 elements. In TR679, Tc3 is responsible for several spontaneous mutations affecting the unc-22 gene. Tc3-induced mutations are unstable, and revertants result from precise or nearly precise excision of Tc3. Although Tc3 is very active in TR679, it is not detectably active in several other mutator mutants, all of which exhibit high levels of Tc1 activity. Tc3 is 2.5 kilobases long, and except for sequences near its inverted repeat termini, it is unrelated to Tc1. The termini of Tc3 are inverted repeats of at least 70 base pairs; the terminal 8 nucleotides of Tc3 are identical to 8 of the terminal 9 nucleotides of Tc1.

Mu1-induced mutant alleles of maize exhibit background-dependent changes in expression and RNA processing

We have examined effects of mutations created by transposition of the Mu1 element of maize into genes coding for Adh 1 and Sh 1, by means of allozyme measurements, DNA and RNA hybridization, cloning, and sequencing. From our analysis of mutant alleles we conclude that the element acts both to reduce steady-state levels of RNA and to induce aberrant processing of primary transcripts. We also conclude that genetic background can exert considerable influence in determining the degree to which Mu1 affects these aspects of gene expression.

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.

Insertion of Mu into the Shrunken 1 gene of maize affects transcriptional and post-transcriptional regulation of Sh1 RNA

Insertion of a Mu transposable element at the Shrunken 1 (Sh1) locus of maize has resulted in kernels with the typical collapsed appearance of sh mutants. Molecular analysis of the mutant gene has revealed the presence of a 1.4 kb insertion immediately upstream from the normal transcriptional start site. Mu insertion has brought about a series of changes in gene expression: the mRNA cap site has been shifted downstream so that it now lies inside the Mu element; transcription is reduced approximately sixfold, and the sh mRNA steady-state level is less than 4% of that found in the nonmutant. This disparity reflects a mutational defect in post-transcriptional regulation which is manifested as a decrease in Sh RNA abundance.

Sequence, genomic distribution and DNA modification of a Mu1 element from non-mutator maize stocks

The increased mutation rate of Mutator stocks of maize has been shown to be the result of transposition of Mu elements. One element, Mu1, is present in 10-60 copies in Mutator stocks and approximately 0-3 copies in non-Mutator stocks. The sequence, structure and genomic distribution of an intact Mu1 element cloned from the non-Mutator inbred line B37 has been determined. The sequence of this element, termed Mu1.4-B37, is identical to Mu1 and it is flanked by 9-bp direct repeats indicative of a target site duplication. Mu1.4-B37 is not in the same genomic location in all stocks, which further suggests that it transposed into its genomic location in B37. We previously reported that in genomic DNA this element is modified such that certain methylation-sensitive restriction enzymes will not cut sites within the element. This is similar to that observed for Mu elements in Mutator stocks that have lost activity. We report herein that the Mu1.4-B37 element loses its modification and becomes accessible to digestion when placed in an active Mutator stock by genetic crosses. This suggests that factors conditioning unmodified elements are dominant in the initial cross between Mutator and non-Mutator stocks. In F2 individuals that have subsequently lost Mutator activity the Mu1.4-B37 element again becomes modified as do most of the Mu elements in the stock. Thus, the modification state of the Mu1.4-B37 element and the other Mu1-like elements correlates with Mutator activity. We hypothesize that factor(s) within an active Mutator stock may inhibit the modification of Mu elements, and that this activity is missing in non-Mutator stocks and may become limiting in certain Mutator stocks resulting in DNA modification.

Sequence identity between an inverted repeat family of transposable elements in Drosophila and Caenorhabditis

The Tc1-like transposable elements, originally described in Caenorhabditis elegans, have a much wider phylogenetic distribution than previously thought. In this paper, we demonstrate that Tc1 shares sequence identity in its open reading frame and terminal repeats with a new transposable element Barney (also known as TCb1-Transposon Caenorhabditis briggsae 1). Barney was detected and isolated by Tc1 hybridization from the closely related nematode species, Caenorhabditis briggsae. The conserved open reading frames of Tc1 and Barney share identity with a structurally similar family of elements named HB found in Drosophila melanogaster, after the introduction of 3 small centrally located deletions in HB1. These reading frames would code for proteins with 30% amino acid identity (42% when conservative changes are included). Tc1, Barney and HB1 contain highly conserved blocks of amino acids which are likely to be in the functional domains of the putative transposase.

An embryogenic cell line of maize from A188 (Minnesota) contains Mu1-like elements

The maize inbred line A188 is popularly used for the production of embryogenic cell lines. A188, maintained at the University of Minnesota, was found upon molecular analysis to contain 2 to 4 copies of a DNA sequence very similar in structure to transposable Mu1 elements, which have been implicated in Robertson's Mutator system. These Mu1-like elements are in the same chromosomal locations in sibling plants and in A188 cell cultures derived from them. This suggests that the elements are in an inactive state and do not undergo transposition. However, we have observed that they are not modified at the target sites for certain restriction endonucleases. Possible causes for the apparent lack of transposition of these Mu1-like elements in these A188 lines are discussed. Inasmuch as the elements do not transpose, they must be maintained in this line as homozygous Mendelian elements by self-pollination.

An RFLP adjacent to the maize waxy gene has the structure of a transposable element

Two maize inbred lines harbor non-mutant waxy (Wx) genes that display restriction fragment length polymorphism (RFLP) upstream from the start of Wx transcription. Sequencing of this region in the two strains revealed a DNA insertion with the structural features of a transposable element. The insertion is 316 bp in length, has 15 bp imperfect inverted repeats and is flanked by a 5 bp direct repeat generated upon insertion. Sequences homologous to this insertion are present in multiple copies in maize and its relatives teosinte and Tripsacum but not in the more distantly related dicot tobacco. Finally, this element is not homologous with any previously described maize DNA insertion.

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.

Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system

In the progeny of an active Mutator plant, the number of Mu elements increases on self-pollination and maintains the average parental Mu content on outcrossing to a non-Mutator line; both patterns of transmission require an increase in the absolute number of Mu elements from one generation to the next. The same average copy number of Mu elements is transmitted through the male and female, but there is wide variation in the absolute copy number among the progeny. In inactive Mutator plants-defined both by the loss of somatic instability at a reporter gene (bronze2-mu1) and by modification of the HinfI sites in the terminal inverted repeat sequences of Mu elements - the absolute copy number of Mu elements is fixed in the parent. Thus, in outcrosses Mu element number is halved, and on self-pollination Mu copy number is constant. Reactivation of somatic mutability at cryptic bz2-mu1 alleles in inactive individuals by crossing to an active line seems not to involve an increase in Mu element copy number transmitted by the inactive individual. These and other results suggest that increases in Mu copy number occur late in plant development or in the gametophyte rather than after fertilization.

Isolation and characterization of a 1.7-kb transposable element from a mutator line of maize

We have cloned and sequenced a 1.7-kb Mu element from a Mutator line of maize and compared its structure to Mu1, a 1.4-kb element. With the exception of a 385-bp block of DNA present in the 1.7-kb element, these transposable elements are structurally similar, sharing terminally inverted and internal direct repeated sequences. Derivation of 1.4-kb elements from the 1.7-kb class via deletion of internal sequence is suggested by the finding that a portion of the extra DNA in Mu1.7 is part of a truncated direct repeat sequence in the 1.4-kb element. An abundant poly(A)+ RNA homologous to a portion of this extra DNA is present in several tissues of both Mutator and non-Mutator lines. Analysis of transcripts from an unstable mutant bronze 1 (bz) allele containing a Mu1.7 element inserted in an exon of the gene detects three species of poly(A)+ RNA that hybridize to a Bz1 (Bronze) gene probe: the largest contains the entire Mu1.7 element in the Bz1 gene transcript; another appears to be a spliced, chimeric transcript; the smallest is normal size Bz1 mRNA. The latter is most likely encoded by the normal-size alleles detected by Southern analysis of tissue expressing purple pigment, suggesting that normal gene function is restored by excision of the Mu1.7 element.

Organ-specific expression of maize Adh1 is altered after a Mu transposon insertion

A new, unstable, organ-specific Adh1 mutant was isolated from a Robertson's mutator line by germinating kernels under partial anaerobic conditions. Families of kernels which showed segregation of a conditional anaerobic lethal phenotype were identified. One mutant, Adh1-3F1124, was shown to express approximately 6% normal levels of ADH1 in seed and anaerobically treated seedlings but expresses normal levels of ADH1 in pollen, the male gametophyte. The ADH1 polypeptide encoded by the mutant allele was found to be indistinguishable from that encoded by the Adh1-3F progenitor but its message levels were lower in seed and seedlings. Robertson's mutator lines are known to carry Mu transposons that cause increased mutation rates. Genomic Southern analysis of Adh1-3F1124 and Adh1-3F showed the presence of a 1.85 kbp insertion at the 5' region of Adh1. Comparison of the DNA sequences revealed that a Mu 1-like element was inserted 31 bp 5' from the transcriptional start site of Adh1-3F1124 gene. The insertion of the Mu element creates an additional TATA box by duplicating the 9 bp genomic sequence--ATATAAATC--at the site of insertion. Consequently, there are two potentially functional TATA sequences, separated by the 1.85 kbp Mu element, 5' to the transcriptional start site. It is not yet understood how such an arrangement alters the organ-specific expression of Adh1.

An extrachromosomal form of the Mu transposons of maize

Maize lines known as Robertson's Mutator (Mu) lines generate unstable recessive mutations at high frequencies. These lines carry actively transposing copies of the transposons (Tn) Mu1 and Mu1.7. TnMu1 and TnMu1.7 are approximately 1400 and 1700 base pairs long, respectively, and they have 210-base-pair terminal inverted repeats. We report here extrachromosomal forms of TnMu1 and TnMu1.7. The extrachromosomal Mu1 and Mu1.7 molecules are resistant to alkaline denaturation and to proteinase treatment and have circular restriction maps; therefore, they are probably covalently closed circular DNA. Further, we show that their occurrence is correlated with Mu activity, so they are probably generated during Mu transposition as transposition intermediates or as products of Mu excision. When the total extrachromosomal supercoiled DNA from immature male flowers of a Mu line was examined by electron microscopy, the Mu transposons appeared to constitute a significant fraction of the extrachromosomal DNA circles in Mu lines.

Nucleotide sequence analysis of alpha-amylase and thiol protease genes that are hormonally regulated in barley aleurone cells

We have determined the nucleotide sequences of Amy32b, a type A alpha-amylase gene, and of the gene for aleurain, a thiol protease closely related to mammalian cathepsin H. Both are expressed in barley aleurone cells under control of the plant hormones gibberellic acid and abscisic acid, but only aleurain is expressed at high levels in other barley tissues. Sequence analysis indicates that the 5' end of the aleurain gene, comprising 3 exons and 2 introns, may have become associated with the remainder of the gene, encoding the protease domain of the protein, by some sort of recombination event. This 5' domain of the gene is very G + C-rich and is flanked by inverted repetitive sequences. We found two different groups of homologous sequence elements. The first group consists of four blocks of sequences conserved in the same spatial arrangement in both genes; these are arranged at similar intervals upstream from the Amy32b TATA box and from a TATA box present in intron 3 of aleurain, outside of the 5' domain and upstream from the protease domain. A part of two of these conserved sequences is similar to the core sequence of certain enhancer elements characterized from mammalian cells. The second group of homologous elements is present in the upstream region of both genes. We speculate that these conserved sets of sequences may have some role in either the tissue specificity of expression of the genes or in some part of the hormonal regulation imposed on them.

Sequences from sea urchin TU transposons are conserved among multiple eucaryotic species, including humans

Sequences homologous to various structural domains of the Strongylocentrotus purpuratus TU family of transposons are present in sea urchin species closely related to S. purpuratus and were found in close proximity to each other in linkage patterns that differed for different species. Sequence homologs of the inverted repeat outer domain (IVR-OD) segment were, in addition, present in a sea urchin related only distantly to S. purpuratus and in all other eucaryotic organisms surveyed. In humans, a polymorphic hybridization pattern was seen for genomic DNA obtained from different individuals. Sequence comparisons revealed that repeated sequence motifs similar to those making up the 15-base-pair direct repeat unit of the IVR-OD domain of the TU elements exist in the IVRs of transposons identified in Drosophila melanogaster and maize and in the transcription control regions of certain eucaryotic viral and cellular genes. The remarkable evolutionary conservation of IVR-OD homologs may reflect a biological role for these sequences in DNA transposition, the regulation of gene expression, or both.

Inheritance of mutator activity in Zea mays as assayed by somatic instability of the bz2-mu1 allele

Mutator lines of maize were originally defined by their high forward mutation rate, now known to be caused by the transposition of numerous Mu elements. A high frequency of somatic instability, seen as a fine purple spotting pattern on the aleurone tissue, is characteristic of Mu-induced mutable alleles of genes of the anthocyanin pathway. Loss of such somatic instability has been correlated with the de novo, specific modification of Mu element DNA. In this report the presence or loss of somatic instability at the bz2-mu1 allele has been monitored to investigate the inheritance of the Mutator phenomenon. The active state is labile and may become weakly active (low fraction of spotted kernel progeny) or totally inactive (no spotted kernel progeny) during either outcrossing to non-Mutator lines or on self-pollination. In contrast, the inactive state is relatively permanent with rare reactivation in subsequent crosses to non-Mutator lines. Cryptic bz2-mu1 alleles in weakly active lines can be efficiently reactivated to somatic instability when crossed with an active line. However, in reciprocal crosses of active and totally inactive individuals, strong maternal effects were observed on the inactivation of a somatically unstable bz2-mu1 allele and on the reactivation of cryptic bz2-mu1 alleles. In general, the activity state of the female parent determines the mutability of the progeny.

Stable non-mutator stocks of maize have sequences homologous to the Mu1 transposable element

Mutator stocks of maize produce mutants at many loci at rates 20- to 50-fold above spontaneous levels. Current evidence suggests that this high mutation rate is mediated by an active transposable element system, Mu. Members of this transposable element family are found in approximately 10-60 copies in Mutator stocks. We report here an initial characterization of previously undetected sequences homologous to Mu elements in eight non-Mutator inbred lines and varieties of maize that have a normal low mutation rate. All stocks have approximately 40 copies of sequences homologous only to the terminal repeat and show weak homology to an internal probe. In addition, several of the stocks contain an intact Mu element. One intact Mu element and two terminal-specific clones have been isolated from one non-Mutator line, B37. The cloned sequences have been used to demonstrate that in genomic DNA the intact element, termed Mu1.4B37, is modified, such that restriction sites in its termini are not accessible to cleavage by the HinfI restriction enzyme. This modification is similar to that observed in Mutator lines that have lost activity. We hypothesize that the DNA modification of the Mu-like element may contribute to the lack of Mutator activity in B37.

Insertion of the Mu1 transposable element into the first intron of maize Adh1 interferes with transcript elongation but does not disrupt chromatin structure

The presence of the Mu1 transposable element within the first intervening sequence of the maize Adh1 gene interfered with transcription through that gene. Insertion of the element did not have an apparent effect on transcription initiation or chromatin structure. In nuclei isolated from anaerobically induced roots, in which Adh1 is transcriptionally active, a subset of the Adh1 chromatin is arranged in a unique conformation characterized by a generalized sensitivity to nucleases, specific DNAase I sensitive sites and a nucleosome array distinct from the inactive configuration present in leaf nuclei. The chromatin organization of the Mu1-induced mutant alleles is indistinguishable from that of the progenitor Adh1-S allele and a point mutant allele that is null for ADH1 activity. The initiation of transcription also proved to be unaffected in these mutants. Nuclear runoff experiments indicated that Adh1 sequences upstream from the point of Mu1 insertion were transcribed normally, but sequences downstream to the insertion were drastically reduced relative to a reference gene expressed in anaerobic root nuclei. Thus, it was concluded that the defect in these Mu1-induced mutants does not reside at the level of gene accessibility or transcript initiation. Rather, Mu1 presents an impediment to the progress of the polymerase II complex during transcript elongation.

DNA modification of a maize transposable element correlates with loss of activity

An unstable allele of the bronze 2 (bz2) locus was isolated from a Robertson's Mutator Zea mays line containing a family of active transposable Mu elements. This mutation is somatically unstable, resulting in numerous revertant purple sectors on a bronze kernel. By following the variegated kernel phenotype through two generations, several lineages have been identified that have a distorted transmission of the mutant phenotype (fewer variegated kernels are produced than expected). Southern blot analysis of Mu elements in these plants demonstrates a correlation between an inhibition of digestion of Mu elements by certain restriction enzymes and the loss of somatic reversion at the mutant allele. The DNA modification can occur in all the Mu elements in a plant within one generation; however, plants have been identified that contain both modified and unmodified elements, suggesting that the modification can occur in a progressive manner. We hypothesize that the DNA modification results in nonfunctional elements.