The Mu elements of Zea mays

Mutator transposon insertions within maize genes often provide a novel outward reading promoter

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles that result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu-suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5' UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and does not depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlight a strategy for transposons to co-exist with their host.

Does the upstream region possessing MULE-like sequence in rice upregulate PsbS1 gene expression?

The genomic nucleotide sequences of japonica rice (Sasanishiki and Nipponbare) contained about 2.7-kb unique region at the point of 0.4-kb upstream of the OsPsbS1 gene. In this study, we found that japonica rice with a few exceptions possessing such DNA sequences [denoted to OsMULE-japonica specific sequence (JSS)] is distinct by the presence of Mutator-like-element (MULE). Such sequence was absent in most of indica cultivars and Oryza glaberrima. In OsMULE-JSS1, we noted the presence of possible target site duplication (TSD; CTTTTCCAG) and about 80-bp terminal inverted repeat (TIR) near TSD. We also found the enhancement ofOsPsbS1 mRNA accumulation by intensified light, which was not associated with the DNA methylation status in OsMULE/JSS. In addition, O. rufipogon, possible ancestor of modern rice cultivars was found to compose PsbS gene of either japonica (minor) or indica (major) type. Transient gene expression assay showed that the japonica type promoter elevated a reporter gene activity than indica type.

Identification of the maize gravitropism gene lazy plant1 by a transposon-tagging genome resequencing strategy

Since their initial discovery, transposons have been widely used as mutagens for forward and reverse genetic screens in a range of organisms. The problems of high copy number and sequence divergence among related transposons have often limited the efficiency at which tagged genes can be identified. A method was developed to identity the locations of Mutator (Mu) transposons in the Zea mays genome using a simple enrichment method combined with genome resequencing to identify transposon junction fragments. The sequencing library was prepared from genomic DNA by digesting with a restriction enzyme that cuts within a perfectly conserved motif of the Mu terminal inverted repeats (TIR). Paired-end reads containing Mu TIR sequences were computationally identified and chromosomal sequences flanking the transposon were mapped to the maize reference genome. This method has been used to identify Mu insertions in a number of alleles and to isolate the previously unidentified lazy plant1 (la1) gene. The la1 gene is required for the negatively gravitropic response of shoots and mutant plants lack the ability to sense gravity. Using bioinformatic and fluorescence microscopy approaches, we show that the la1 gene encodes a cell membrane and nuclear localized protein. Our Mu-Taq method is readily adaptable to identify the genomic locations of any insertion of a known sequence in any organism using any sequencing platform.

Mu-seq: sequence-based mapping and identification of transposon induced mutations

Mutations tagged by transposon insertions can be readily mapped and identified in organisms with sequenced genomes. Collections of such mutants allow a systematic analysis of gene function, and can be sequence-indexed to build invaluable resources. Here we present Mu-seq (Mutant-seq), a high-throughput NextGen sequencing method for harnessing high-copy transposons. We illustrate the efficacy of Mu-seq by applying it to the Robertson's Mutator system in a large population of maize plants. A single Mu-seq library, for example, constructed from 576 different families (2304 plants), enabled 4, 723 novel, germinal, transposon insertions to be detected, identified, and mapped with single base-pair resolution. In addition to the specificity, efficiency, and reproducibility of Mu-seq, a key feature of this method is its adjustable scale that can accommodate simultaneous profiling of transposons in thousands of individuals. We also describe a Mu-seq bioinformatics framework tailored to high-throughput, genome-wide, and population-wide analysis of transposon insertions.

Regulation of the Mutator system of transposons in maize

The Mutator system has proved to be an invaluable tool for elucidating gene function via insertional mutagenesis. Its high copy number, high transposition frequency, relative lack of insertion specificity, and ease of use has made it the preferred method for gene tagging in maize. Recent advances in high throughput sequencing of insertion sites, combined with the availability of large numbers of pre-mutagenized and sequence-indexed stocks, ensure that this resource will only be more useful in the years ahead. Muk is a locus that can silence Mu-active lines, making it possible to ameliorate the phenotypic effects of high numbers of active Mu transposons and reduce the copy number of these elements during introgressions.

Scarecrow plays a role in establishing Kranz anatomy in maize leaves

More than a quarter of the primary productivity on land, and a large fraction of the food that humans consume, is contributed by plants that fix atmospheric CO(2) by C(4) photosynthesis. It has been estimated that transferring the C(4) pathway to C(3) crops could boost yield by 50% and also increase water use efficiency and reduce the need for fertilizer, particularly in dry, hot environments. The high productivity of maize (Zea mays), sugarcane (Saccharum spp.) and several emerging bioenergy grasses is due largely to C(4) photosynthesis, which is enabled by the orderly arrangement, in concentric rings, of specialized bundle sheath and mesophyll cells in leaves in a pattern known as Kranz anatomy. Here we show that PIN, the auxin efflux protein, is present in the end walls of maize bundle sheath cells, as it is in the endodermis of the root. Since this marker suggests the expression of endodermal genetic programs in bundle sheath cells, we determined whether the transcription factor SCARECROW, which regulates structural differentiation of the root endodermis, also plays a role in the development of Kranz anatomy in maize. Mutations in the Scarecrow gene result in proliferation of bundle sheath cells, abnormal differentiation of bundle sheath chloroplasts, vein disorientation, loss of minor veins and reduction of vein density. Further characterization of this signal transduction pathway should facilitate the transfer of the C(4) trait into C(3) crop species, including rice.

Identification of an active new mutator transposable element in maize

Robertson’s Mutator (Mu) system has been used in large scale mutagenesis in maize, exploiting its high mutation frequency, controllability, preferential insertion in genes, and independence of donor location. Eight Mutator elements have been fully characterized (Mu1, Mu2 /Mu1.7, Mu3, Mu4, Mu5, Mu6/7, Mu8, MuDR), and three are defined by TIR (Mu10, Mu11 and Mu12). The genome sequencing revealed a complex family of Mu-like-elements (MULEs) in the B73 genome. In this article, we report the identification of a new Mu element, named Mu13. Mu13 showed typical Mu characteristics by having a ∼220 bp TIR, creating a 9 bp target site duplication upon insertion, yet the internal sequence is completely different from previously identified Mu elements. Mu13 is not present in the B73 genome or a Zea mays subsp. parviglumis accession, but in W22 and several inbreds that found the Robertson’s Mutator line. Analysis of mutants isolated from the UniformMu mutagenic population indicated that the Mu13 element is active in transposition. Two novel insertions were found in expressed genes. To test other unknown Mu elements, we selected six new Mu elements from the B73 genome. Southern analysis indicated that most of these elements were present in the UniformMu lines. From these results, we conclude that Mu13 is a new and active Mu element that significantly contributed to the mutagenesis in the UniformMu population. The Robertson’s Mutator line may harbor other unknown active Mu elements.

Camouflage patterning in maize leaves results from a defect in porphobilinogen deaminase

Maize leaves are produced from polarized cell divisions that result in clonal cell lineages arrayed along the long axis of the leaf. We utilized this stereotypical division pattern to identify a collection of mutants that form chloroplast pigmentation sectors that violate the clonal cell lineages. Here, we describe the camouflage1 (cf1) mutant, which develops nonclonal, yellow-green sectors in its leaves. We cloned the cf1 gene by transposon tagging and determined that it encodes porphobilinogen deaminase (PBGD), an enzyme that functions early in chlorophyll and heme biosynthesis. While PBGD has been characterized biochemically, no viable mutations in this gene have been reported in plants. To investigate the in vivo function of PBGD, we characterized the cf1 mutant. Histological analyses revealed that cf1 yellow sectors display the novel phenotype of bundle sheath cell-specific death. Light-shift experiments determined that constant light suppressed cf1 sector formation, a dark/light transition is required to induce yellow sectors, and that sectors form only during a limited time of leaf development. Biochemical experiments determined that cf1 mutant leaves have decreased PBGD activity and increased levels of the enzyme substrate in both green and yellow regions. Furthermore, the cf1 yellow regions displayed a reduction in catalase activity. A threshold model is hypothesized to explain the cf1 variegation and incorporates photosynthetic cell differentiation, reactive oxygen species scavenging, and PBGD function.

Mutator transposon in maize and MULEs in the plant genome

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.

Tie-dyed1 encodes a novel, phloem-expressed transmembrane protein that functions in carbohydrate partitioning

Carbon is partitioned between export from the leaf and retention within the leaf, and this process is essential for all aspects of plant growth and development. In most plants, sucrose is loaded into the phloem of carbon-exporting leaves (sources), transported through the veins, and unloaded into carbon-importing tissues (sinks). We have taken a genetic approach to identify genes regulating carbon partitioning in maize (Zea mays). We identified a collection of mutants, called the tie-dyed (tdy) loci, that hyperaccumulate carbohydrates in regions of their leaves. To understand the molecular function of Tdy1, we cloned the gene. Tdy1 encodes a novel transmembrane protein present only in grasses, although two protein domains are conserved across angiosperms. We found that Tdy1 is expressed exclusively in phloem cells of both source and sink tissues, suggesting that Tdy1 may play a role in phloem loading and unloading processes. In addition, Tdy1 RNA accumulates in protophloem cells upon differentiation, suggesting that Tdy1 may function as soon as phloem cells become competent to transport assimilates. Monitoring the movement of a fluorescent, soluble dye showed that tdy1 leaves have retarded phloem loading. However, once the dye entered into the phloem, solute transport appeared equal in wild-type and tdy1 mutant plants, suggesting that tdy1 plants are not defective in phloem unloading. Therefore, even though Tdy1 RNA accumulates in source and sink tissues, we propose that TDY1 functions in carbon partitioning by promoting phloem loading. Possible roles for TDY1 are discussed.

Role of RAD51 in the repair of MuDR-induced double-strand breaks in maize (Zea mays L.)

Rates of Mu transposon insertions and excisions are both high in late somatic cells of maize. In contrast, although high rates of insertions are observed in germinal cells, germinal excisions are recovered only rarely. Plants doubly homozygous for deletion alleles of rad51A1 and rad51A2 do not encode functional RAD51 protein (RAD51-). Approximately 1% of the gametes from RAD51+ plants that carry the MuDR-insertion allele a1-m5216 include at least partial deletions of MuDR and the a1 gene. The structures of these deletions suggest they arise via the repair of MuDR-induced double-strand breaks via nonhomologous end joining. In RAD51- plants these germinal deletions are recovered at rates that are at least 40-fold higher. These rates are not substantially affected by the presence or absence of an a1-containing homolog. Together, these findings indicate that in RAD51+ germinal cells MuDR-induced double-strand breaks (DSBs) are efficiently repaired via RAD51-directed homologous recombination with the sister chromatid. This suggests that RAD51- plants may offer an efficient means to generate deletion alleles for functional genomic studies. Additionally, the high proportion of Mu-active, RAD51- plants that exhibit severe developmental defects suggest that RAD51 plays a critical role in the repair of MuDR-induced DSBs early in vegetative development.

barren inflorescence2 Encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize

Organogenesis in plants is controlled by meristems. Axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. Maize (Zea mays) and rice (Oryza sativa) have additional types of axillary meristems in the inflorescence compared to Arabidopsis (Arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. Previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed that bif2 plays a key role in axillary meristem and lateral primordia initiation in the inflorescence. In this article, we cloned bif2 by transposon tagging. Isolation of bif2-like genes from seven other grasses, along with phylogenetic analysis, showed that bif2 is a co-ortholog of PINOID (PID), which regulates auxin transport in Arabidopsis. Expression analysis showed that bif2 is expressed in all axillary meristems and lateral primordia during inflorescence and vegetative development in maize and rice. Further phenotypic analysis of bif2 mutants in maize illustrates additional roles of bif2 during vegetative development. We propose that bif2/PID sequence and expression are conserved between grasses and Arabidopsis, attesting to the important role they play in development. We provide further support that bif2, and by analogy PID, is required for initiation of both axillary meristems and lateral primordia.

Divergence of duplicated genes in maize: evolution of contrasting targeting information for enzymes in the porphyrin pathway

The divergence of sequence and expression pattern of duplicated genes provides a means for genetic innovation to occur without sacrificing an essential function. The cpx1 and cpx2 genes of maize are a singular example of duplicated genes that have diverged by deletion and creation of protein targeting information. The cpx genes encode coproporphyrinogen III oxidase ('coprogen oxidase'), which catalyzes a step in the synthesis of chlorophyll and heme. In plants, this enzyme has been found exclusively in the plastids. The cpx1 and cpx2 genes encode almost identical, catalytically active enzymes with distinctive N-terminal peptide sequences. The cpx1 gene encodes the expected plastid transit peptide, but this region is deleted from the cpx2 gene. While the 5' regions of both messenger RNAs are highly similar, the cpx2 gene has an open-reading frame that could encode a new targeting signal. GFP fused with CPX1 localized to the plastids. In contrast, the GFP fusion with CPX2 did not target plastids and appeared to localize to mitochondria. Both cpx genes are expressed ubiquitously but, based on mutant phenotype, they seem to have discrete biological roles. Seedlings homozygous for a null mutation in the cpx1 gene completely lack chlorophyll and develop necrotic lesions in the light. However, the mutant seedlings and callus cultures will grow in tissue culture in the dark, implying that they retain a capacity to produce heme. We discuss models for the evolution of the cpx genes and possible roles of mitochondrion-localized coprogen oxidase activity in maize.

Anaconda, a new class of transposon belonging to the Mu superfamily, has diversified by acquiring host genes during rice evolution

A new type of transposon, named Anaconda (Anac) has been found in rice (Oryza sativa). In this paper, we demonstrate that Anaconda elements have diversified by acquisition of host cellular genes, amplification of the elements, and substitution and deletion of short segments. We identified four Anaconda elements in studies of rice alternative oxidase (AOX) genes, and subsequently isolated an additional 23 elements based on the identity of their terminal inverted repeats (TIRs). The Anaconda elements have long TIRs (114-458 bp). They also have direct repeats of 9 or 10 bp in their flanking regions that are thought to have been generated upon transposition. These structural features reveal that the Anaconda elements belong to the Mu superfamily. The most prominent feature of the Anaconda elements is the high frequency with which they have acquired host cellular genes. Of the 27 elements found here, 19 appear to have sequences presumably derived from rice genes, for example, the genes for AOX1c (four elements), cytochrome P450 (five elements), L: -asparaginase (five elements), and PCF8 (two elements). Four elements, AnacA1-A4, have both the AOX1c and P450 genes. One element, AnacB14, involves a gene similar to mudrA of maize MuDR. Database analyses revealed that the loci of 26 of the 27 Anaconda elements in the subspecies japonica are the same as those in the subspecies indica. This suggests that these elements were incorporated before the divergence of these two subspecies.

Genome-wide mutagenesis of Zea mays L. using RescueMu transposons

Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertions and screening of RescueMu plasmid libraries identified plants containing probable germinal insertions. Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants.

Maize-targeted mutagenesis: A knockout resource for maize

We describe an efficient system for site-selected transposon mutagenesis in maize. A total of 43,776 F1 plants were generated by using Robertson's Mutator (Mu) pollen parents and self-pollinated to establish a library of transposon-mutagenized seed. The frequency of new seed mutants was between 10-4 and 10-5 per F1 plant. As a service to the maize community, maize-targeted mutagenesis selects insertions in genes of interest from this library by using the PCR. Pedigree, knockout, sequence, phenotype, and other information is stored in a powerful interactive database (maize-targeted mutagenesis database) that enables analysis of the entire population and the handling of knockout requests. By inhibiting Mu activity in most F1 plants, we sought to reduce somatic insertions that may cause false positives selected from pooled tissue. By monitoring the remaining Mu activity in the F2, however, we demonstrate that seed phenotypes depend on it, and false positives occur in lines that appear to lack it. We conclude that more than half of all mutations arising in this population are suppressed on losing Mu activity. These results have implications for epigenetic models of inbreeding and for functional genomics.

Four loci on abnormal chromosome 10 contribute to meiotic drive in maize

We provide a genetic analysis of the meiotic drive system on maize abnormal chromosome 10 (Ab10) that causes preferential segregation of specific chromosomal regions to the reproductive megaspore. The data indicate that at least four chromosomal regions contribute to meiotic drive, each providing distinct functions that can be differentiated from each other genetically and/or phenotypically. Previous reports established that meiotic drive requires neocentromere activity at specific tandem repeat arrays (knobs) and that two regions on Ab10 are involved in trans-activating neocentromeres. Here we confirm and extend data suggesting that only one of the neocentromere-activating regions is sufficient to move many knobs. We also confirm the localization of a locus/loci on Ab10, thought to be a prerequisite for meiotic drive, which promotes recombination in structural heterozygotes. In addition, we identified two new and independent functions required for meiotic drive. One was identified through the characterization of a deletion derivative of Ab10 [Df(L)] and another as a newly identified meiotic drive mutation (suppressor of meiotic drive 3). In the absence of either function, meiotic drive is abolished but neocentromere activity and the recombination effect typical of Ab10 are unaffected. These results demonstrate that neocentromere activity and increased recombination are not the only events required for meiotic drive.

Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome

Three subfamilies of the En/Spm-type transposable element of carrot, Tdc A, B, and C, were characterized. It was supposed that the Tdc A subfamily may include autonomous elements which can produce transposases. Tdc B elements are defective, but still generate transcripts containing mutant open reading frame (ORF) sequences for transposases. The single member of the Tdc C group recovered seems to be a pseudogene. The sequences of the transposase ORFs of Tdc A and Tdc B elements are more highly conserved than those of the 5; and 3; untranslated regions and introns, as is found in other structural genes that are subject to selection. These observations indicate that the mutations in the nucleotide sequences of the Tdc elements occurred in the host genome. However, the mutations in the 5; and 3; untranslated regions and introns, which may not be sufficient to prevent transposition, accumulated in autonomous elements, which could transpose and produce copies. When the reproduction rate and the rate of disabling mutations reached an equilibrium, that is, when the birth rate of the transposable elements in the genome equalled the death rate, the population of elements achieved a stationary state in the genome, and could thus survive.

Gene enrichment in plant genomic shotgun libraries

The Arabidopsis genome (about 130 Mbp) has been completely sequenced; whereas a draft sequence of the rice genome (about 430 Mbp) is now available and the sequencing of this genome will be completed in the near future. The much larger genomes of several important crop species, such as wheat (about 16,000 Mbp) or maize (about 2500 Mbp), may not be fully sequenced with current technology. Instead, sequencing-analysis strategies are being developed to obtain sequencing and mapping information selectively for the genic fraction (gene space) of complex plant genomes.

Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize

Even in the absence of excisional loss of the associated Mu transposons, some Mu-induced mutant alleles of maize can lose their capacity to condition a mutant phenotype. Three of five Mu-derived rf2a alleles are susceptible to such Mu suppression. The suppressible rf2a-m9437 allele has a novel Mu transposon insertion (Mu10) in its 5' untranslated region (UTR). The suppressible rf2a-m9390 allele has a Mu1 insertion in its 5' UTR. During suppression, alternative transcription initiation sites flanking the Mu1 transposon yield functional transcripts. The suppressible rf2a-m8110 allele has an rcy/Mu7 insertion in its 3' UTR. Suppression of this allele occurs via a previously unreported mechanism; sequences in the terminal inverted repeats of rcy/Mu7 function as alternative polyadenylation sites such that the suppressed rf2a-m8110 allele yields functional rf2a transcripts. No significant differences were observed in the nucleotide compositions of these alternative polyadenylation sites as compared with 94 other polyadenylation sites from maize genes.

Transposon insertions in the promoter of the Zea mays a1 gene differentially affect transcription by the Myb factors P and C1

The understanding of control of gene regulation in higher eukaryotes relies heavily on results derived from non-in vivo studies, but rarely can the significance of these approximations be established in vivo. Here, we investigated the effect of Mutator and Spm insertions on the expression of the flavonoid biosynthetic gene a1, independently regulated by the transcription factors C1 and P. The a1-mum2 and a1-m2 alleles carry Mu1 and Spm insertions, respectively, in a cis-element (ARE) of unknown function located between the P- and C1-binding sites. We show that the insertions of Mu1 and Spm similarly influence the expression of a1 controlled by C1 or P. The P-controlled a1 expression in a1-m2 is Spm dependent, and the mutant phenotype of a1-mum2 is suppressed in the pericarp in the absence of the autonomous MuDR element. Footprints within the ARE affect the regulation of a1 by C1 and P differently, providing evidence that these factors control a1 expression using distinct cis-acting regulatory elements. Together, our findings contribute significantly to one of the best-described plant regulatory systems, while stressing the need to complement with in vivo experiments current approaches used for the study of control of gene expression.

A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing

Both paramutation and Mutator (Mu) transposon inactivation involve heritable changes in gene expression without concomitant changes in DNA sequence. The mechanisms by which these shifts in gene activity are achieved are unknown. Here we present evidence that these two phenomena are linked mechanistically. We show that mutation of a gene, modifier of paramutation 1 (mop1), which prevents paramutation at three different loci in maize, can reverse methylation of Mutator elements reliably. In mop1 mutant backgrounds, methylation of nonautonomous Mu elements can be reversed even in the absence of the regulatory MuDR element. Previously silenced MuDR elements are reactivated sporadically after multiple generations of exposure to mop1 mutations. MuDR methylation is separable from MuDR silencing, because removal of methylation does not cause immediate reactivation. The mop1 mutation does not alter the methylation of certain other transposable elements including those just upstream of a paramutable b1 gene. Our results suggest that the mop1 gene acts on a subset of epigenetically regulated sequences in the maize genome and paramutation and Mu element methylation require a common factor, which we hypothesize influences chromatin structure.

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.

Mutator transposase is widespread in the grasses

Although the Mutator (Mu) system is well characterized in maize (Zea mays), very little is known about this highly mutagenic system of transposons in other grasses. Mutator is regulated by the MuDR class of elements, which encodes two genes, one of which, mudrA, has similarity to a number of bacterial transposases. Experiments in our laboratory, as well as database searches, demonstrate that mudrA sequences are ubiquitous and diverse in the grasses. In several species it is clear that multiple paralogous elements can be present in a single genome. In some species such as wheat (Triticum aestivum) and rice (Oryza sativa), mudrA-similar sequences are represented in cDNA databases, suggesting the presence of active Mu transposon systems in these species. Further, in rice and in sorghum, mudrA-like genes are flanked by long terminal inverted repeats, as well as the short host sequence direct repeats diagnostic of insertion. Thus, there is ample evidence that systems related to Mu in maize are at least potentially active in a wide variety of grasses. However, the mudrB gene, though important for Mu activity in maize, is not necessarily a component of Mu elements in other grasses.

Identification of Mutator insertional mutants of starch-branching enzyme 2a in corn

Starch-branching enzymes (SBE) break the alpha-1,4 linkage of starch, re-attaching the chain to a glucan chain by an alpha-1,6 bond, altering starch structure. SBEs also facilitate starch accumulation by increasing the number of non-reducing ends on the growing chain. In maize (Zea mays), three isoforms of SBE have been identified. To examine the function of the SBEIIa isoform, a reverse genetics polymerase chain reaction-based screen was used to identify a mutant line segregating for a Mutator transposon within Sbe2a. To locate the insertion within the second exon of Sbe2a, the genomic sequence of Sbe2a containing the promoter and 5' end was isolated and sequenced. Plants homozygous for sbe2a::Mu have undetectable levels of Sbe2a transcripts and SBEIIa in their leaves. Characterization of leaf starch from sbe2a::Mu mutants shows reduced branching similar to yet more extreme than that seen in kernels lacking SBEIIb activity. Characterization of endosperm starch from sbe2a::Mu mutants shows branching that is indistinguishable from wild-type controls. These mutant plants have a visible phenotype resembling accelerated senescence, which was correlated with the Mutator insertion within Sbe2a. This correlation suggests a specific role for SBEIIa in leaves, which may be necessary for normal plant development.

Duplication and suppression of chloroplast protein translocation genes in maize

The HCF106 (high chlorophyll fluorescence) gene of maize encodes a chloroplast membrane protein required for translocation of a subset of proteins across the thylakoid membrane. Mutations in HCF106 caused by the insertion of Robertson's Mutator transposable elements have been mapped to chromosome 2S. Here we show that there is a closely related homolog of HCF106 encoded elsewhere in the maize genome (HCF106c) that can partially compensate for these mutations. This homolog maps on chromosome 10L and is part of the most recent set of segmental duplications in the maize genome. Triple mutants that are disrupted in both the HCF106 and Sec-dependent protein translocation pathways provide evidence that they act independently. The HCF106c gene accounts for a previously reported exception to the correlation between epigenetic suppression of hcf106 and methylation of Mutator transposons. We also demonstrate that insertions of Robertson's Mutator elements into either introns or promoters can lead to mutations whose phenotypes are suppressed in the absence of Mu activity, while alleles with insertions in both positions are not suppressed. The implications of these observations are discussed.

FARE, a new family of foldback transposons in Arabidopsis

A new family of transposons, FARE, has been identified in Arabidopsis. The structure of these elements is typical of foldback transposons, a distinct subset of mobile DNA elements found in both plants and animals. The ends of FARE elements are long, conserved inverted repeat sequences typically 550 bp in length. These inverted repeats are modular in organization and are predicted to confer extensive secondary structure to the elements. FARE elements are present in high copy number, are heterogeneous in size, and can be divided into two subgroups. FARE1's average 1.1 kb in length and are composed entirely of the long inverted repeats. FARE2's are larger, up to 16.7 kb in length, and contain a large internal region in addition to the inverted repeat ends. The internal region is predicted to encode three proteins, one of which bears homology to a known transposase. FARE1.1 was isolated as an insertion polymorphism between the ecotypes Columbia and Nossen. This, coupled with the presence of 9-bp target-site duplications, strongly suggests that FARE elements have transposed recently. The termini of FARE elements and other foldback transposons are imperfect palindromic sequences, a unique organization that further distinguishes these elements from other mobile DNAs.

Mutator-like elements in Arabidopsis thaliana. Structure, diversity and evolution

While genome-wide surveys of abundance and diversity of mobile elements have been conducted for some class I transposable element families, little is known about the nature of class II transposable elements on this scale. In this report, we present the results from analysis of the sequence and structural diversity of Mutator-like elements (MULEs) in the genome of Arabidopsis thaliana (Columbia). Sequence similarity searches and subsequent characterization suggest that MULEs exhibit extreme structure, sequence, and size heterogeneity. Multiple alignments at the nucleotide and amino acid levels reveal conserved, potentially transposition-related sequence motifs. While many MULEs share common structural features to Mu elements in maize, some groups lack characteristic long terminal inverted repeats. High sequence similarity and phylogenetic analyses based on nucleotide sequence alignments indicate that many of these elements with diverse structural features may remain transpositionally competent and that multiple MULE lineages may have been evolving independently over long time scales. Finally, there is evidence that MULEs are capable of the acquisition of host DNA segments, which may have implications for adaptive evolution, both at the element and host levels.

Two male-sterile mutants of Zea Mays (Poaceae) with an extra cell division in the anther wall

Two recessive male-sterile mutants of maize with similar patterns of pollen abortion were studied. Genetic studies showed that one of the two mutations was allelic with a previously identified male-sterility locus (ms23) and the other mutation was in a newly identified male-sterility locus (ms32). Cytological characterization of homozygous mutants and fertile heterozygous control siblings was performed using brightfield, fluorescence, and electron microscopy. During normal anther development, the final anther wall periclinal division divides the secondary parietal anther wall layer into the middle layer and tapetum, forming an anther with four wall layers. This is followed by differentiation of the tapetal cells into protoplastic binucleate, secretory tissue. In both the ms23 and ms32 mutants, the prospective tapetal layer divided into two layers, termed t1 and t2, forming an anther with five wall layers. Neither the t1 nor the t2 layers differentiated normally into tapetal layers, as determined by examination of cell walls, nucleus number, and cytoplasmic organization. Pollen mother cells aborted after the onset of prophase I of meiosis, suggesting that an early developmental coordination may exist between tapetum and pollen mother cells.

Mutator-suppressible alleles of rough sheath1 and liguleless3 in maize reveal multiple mechanisms for suppression

Insertions of Mutator transposons into maize genes can generate suppressible alleles. Mu suppression is when, in the absence of Mu activity, the phenotype of a mutant allele reverts to that of its progenitor. Here we present the characterization of five dominant Mu-suppressible alleles of the knox (knotted1-like homeobox) genes liguleless3 and rough sheath1, which exhibit neomorphic phenotypes in the leaves. RNA blot analysis suggests that Mu suppression affects only the neomorphic aspect of the allele, not the wild-type aspect. Additionally, Mu suppression appears to be exerting its effects at the level of transcription or transcript accumulation. We show that truncated transcripts are produced by three alleles, implying a mechanism for Mu suppression of 5' untranslated region insertion alleles distinct from that which has been described previously. Additionally, it is found that Mu suppression can be caused by at least three different types of Mutator elements. Evidence presented here suggests that whether an allele is suppressible or not may depend upon the site of insertion. We cite previous work on the knox gene kn1, and discuss our results in the context of interactions between Mu-encoded products and the inherently negative regulation of neomorphic liguleless3 and rough sheath1 transcription.

Molecular cloning of the maize gene crp1 reveals similarity between regulators of mitochondrial and chloroplast gene expression

The maize nuclear gene crp1 is required for the translation of the chloroplast petA and petD mRNAs and for the processing of the petD mRNA from a polycistronic precursor. In order to understand the biochemical role of the crp1 gene product and the interconnections between chloroplast translation and RNA metabolism, the crp1 gene and cDNA were cloned. The predicted crp1 gene product (CRP1) is related to nuclear genes in fungi that play an analogous role in mitochondrial gene expression, suggesting an underlying mechanistic similarity. Analysis of double mutants that lack both chloroplast ribosomes and crp1 function indicated that CRP1 activates a site-specific endoribonuclease independently of any role it plays in translation. Antibodies prepared to recombinant CRP1 were used to demonstrate that CRP1 is localized to the chloroplast stroma and that it is a component of a multisubunit complex. The CRP1 complex is not associated detectably with either chloroplast membranes or chloroplast ribosomes. Models for CRP1 function and its relationship to other activators of organellar translation are discussed.

Specific expression of the Fusarium transposon Fot1 and effects on target gene transcription

The Fot1 transposon is active in some strains of the plant pathogenic fungus Fusarium oxysporum. In a high-copy-number strain that contains autonomous elements, we have detected a transcript of 1.7 kb hybridizing to Fot1 in very low amounts. Mapping the 3' and 5' termini of this transcript confirms that it corresponds to a Fot1-specific transcript. In this strain, five independent mutants of the transgene (niaD) encoding nitrate reductase have arisen by insertion of Fot1 into the third intron. The analysis of the effect of Fot1 insertion in these mutants shows that, depending on the orientation of Fot1 relative to niaD, different truncated chimeric niaD-Fot1 transcripts are produced. Mapping the 5' and 3' ends of these transcripts reveals (i) premature polyadenylation at sites present in the 5' and 3' untranslated regions of Fot1, and (ii) initiation of some transcripts in the 3' part of the niaD gene at sites located immediately downstream of the Fot1 insertion. Thus, a novel promoter, associated with the end of Fot1, directs transcriptional activity outwards from the element into the coding sequence of the niaD gene. These effects demonstrate that Fot1 insertion provides an additional general mechanism controlling fungal gene expression.

Functional analysis of deletion derivatives of the maize transposon MuDR delineates roles for the MURA and MURB proteins

The regulatory transposon of the Mutator system of transposable elements in maize is MuDR. MuDR elements produce two transcripts, from genes mudrA and mudrB, encoding proteins MURA and MURB, respectively. Like many other transposons, MuDR elements often undergo deletions, usually of internal sequences. Analysis of a deletion that is restricted to the region encoding MURB demonstrates that this gene is not required to cause excisions of a reporter element, although it may be required for transposition or suppression of suppressible alleles. Conversely, a derivative that lacks the region encoding MURA but that produces MURB is nonfunctional for all aspects of Mutator activity. Northern analysis of these derivatives reveals that each of the two transcripts can be independently transcribed, and analysis using an antibody specific for MURB reveals that mudrB transcript can also be successfully translated and its product appropriately localized in the absence of mudrA. A third deletion derivative provides evidence for a source of previously reported antisense transcript.

Regulation of leaf initiation by the terminal ear 1 gene of maize

Higher plants elaborate much of their architecture post-embryonically through development initiated at the tips of shoots. During vegetative growth, leaf primordia arise at predictable sites to give characteristic leaf arrangements, or phyllotaxies. How these sites are determined is a long-standing question that bears on the nature of pattern-formation mechanisms in plants. Fate-mapping studies in several species indicate that each leaf primordium becomes organized from a group of 100-200 cells on the flank of the shoot apex. Although molecular studies indicate that the regulated expression of specific homeobox genes plays some part in this determination process, mechanisms that regulate the timing and position of leaf initiation are less well understood. Here we describe a gene from maize, terminal ear 1. Patterns of expression of this gene in the shoot and phenotypes of mutants indicate a role for terminal ear 1 in regulating leaf initiation. The tel gene product contains conserved RNA-binding motifs, indicating that it may function through an RNA-binding activity.

A SecY homologue is required for the elaboration of the chloroplast thylakoid membrane and for normal chloroplast gene expression

Results of in vitro and genetic studies have provided evidence for four pathways by which proteins are targeted to the chloroplast thylakoid membrane. Although these pathways are initially engaged by distinct substrates and involve some distinct components, an unresolved issue has been whether multiple pathways converge on a common translocation pore in the membrane. A homologue of eubacterial SecY called cpSecY is localized to the thylakoid membrane. Since SecY is a component of a protein-translocating pore in bacteria, cpSecY likely plays an analogous role. To explore the role of cpSecY, we obtained maize mutants with transposon insertions in the corresponding gene. Null cpSecY mutants exhibit a severe loss of thylakoid membrane, differing in this regard from mutants lacking cpSecA. Therefore, cpSecY function is not limited to a translocation step downstream of cpSecA. The phenotype of cpSecY mutants is also much more pleiotropic than that of double mutants in which both the cpSecA- and DeltapH-dependent thylakoid-targeting pathways are disrupted. Therefore, cpSecY function is likely to extend beyond any role it might play in these targeting pathways. CpSecY mutants also exhibit a defect in chloroplast translation, revealing a link between chloroplast membrane biogenesis and chloroplast gene expression.

Functional genomics: probing plant gene function and expression with transposons

Transposable elements provide a convenient and flexible means to disrupt plant genes, so allowing their function to be assessed. By engineering transposons to carry reporter genes and regulatory signals, the expression of target genes can be monitored and to some extent manipulated. Two strategies for using transposons to assess gene function are outlined here: First, the PCR can be used to identify plants that carry insertions into specific genes from among pools of heavily mutagenized individuals (site-selected transposon mutagenesis). This method requires that high copy transposons be used and that a relatively large number of reactions be performed to identify insertions into genes of interest. Second, a large library of plants, each carrying a unique insertion, can be generated. Each insertion site then can be amplified and sequenced systematically. These two methods have been demonstrated in maize, Arabidopsis, and other plant species, and the relative merits of each are discussed in the context of plant genome research.

Mu element-generated gene conversions in maize attenuate the dominant knotted phenotype

The knotted1 gene was first defined by dominant mutations that affect leaf morphology. The original allele, Kn1-O, results from a 17-kb tandem duplication. Mutator (Mu) insertions near the junction of the two repeats suppress the leaf phenotype to different degrees depending on the position of the insertion. The Mu insertions also increase the frequency of recombination at Kn1-O to create derivative alleles in which the Mu element and one copy of the repeat are lost. These derivatives are normal in appearance. Here we describe two derivatives that retained the tandem duplication but gained insertions of 1.7 and 3 kb in length in place of the Mu element. In each case, the inserted DNA is a sequence that normally flanks the distal repeat unit. Thus, each derivative consists of a tandem duplication in which the repeat unit has been extended at its distal end by the length of the new insertion. The 1.7-kb insertion dampens the phenotype, as did the original Mu insertion, whereas the 3-kb insertion completely suppresses the knotted phenotype. We propose that gene conversion, stimulated by the double-strand break of the Mu excision, gave rise to these derivatives.

Characterization of the maize Mutator transposable element MURA transposase as a DNA-binding protein

The autonomous MuDR element of the Mutator (Mu) transposable element family of maize encodes at least two proteins, MURA and MURB. Based on amino acid sequence similarity, previous studies have reported that MURA is likely to be a transposase. The functional characterization of MURA has been hindered by the instability of its cDNA, mudrA, in Escherichia coli. In this study, we report the first successful stabilization and expression of MURA in Saccharomyces cerevisiae. Gel mobility shift assays demonstrate that MURA is a DNA-binding protein that specifically binds to sequences within the highly conserved Mu element terminal inverted repeats (TIRs). DNase I and 1,10-phenanthroline-copper footprinting of MURA-Mu1 TIR complexes indicate that MURA binds to a conserved approximately 32-bp region in the TIR of Mu1. In addition, MURA can bind to the same region in the TIRs of all tested actively transposing Mu elements but binds poorly to the diverged Mu TIRs of inactive elements. Previous studies have reported a correlation between Mu transposon inactivation and methylation of the Mu element TIRs. Gel mobility shift assays demonstrate that MURA can interact differentially with unmethylated, hemimethylated, and homomethylated TIR substrates. The significance of MURA's interaction with the TIRs of Mu elements is discussed in the context of what is known about the regulation and mechanisms of Mutator activities in maize.

The evolution of apical dominance in maize

The domestication of crop plants has often involved an increase in apical dominance (the concentration of resources in the main stem of the plant and a corresponding suppression of axillary branches). A striking example of this phenomenon is seen in maize (Zea mays spp. mays), which exhibits a profound increase in apical dominance compared with its probable wild ancestor, teosinte (Zea mays ssp. parviglumis). Previous research has identified the teosinte branched1 (tb1) gene as a major contributor to this evolutionary change in maize. We have cloned tb1 by transposon tagging and show here that it encodes a protein with homology to the cycloidea gene of snapdragon. The pattern of tb1 expression and the morphology of tb1 mutant plants suggest that tb1 acts both to repress the growth of axillary organs and to enable the formation of female inflorescences. The maize allele of tb1 is expressed at twice the level of the teosinte allele, suggesting that gene regulatory changes underlie the evolutionary divergence of maize from teosinte.

Segmented structure of separate and transposable DNA and RNA elements as suggested by their size distributions

A collection of about 1000 different eukaryotic and prokaryotic DNA mobile and separate elements is compiled from literature-transposons, plasmids, extrachromosomal circular DNA, insertion sequences, as well as viral genomes and separate genome segments. Only small elements are collected, upto 2000 base pairs. Analysis of the sequence length distributions of the elements reveals that certain sizes are clearly preferred, namely those which correspond to multiples of about 345 bp in eukaryotes and multiples of about 210 bp in prokaryotes. This provides additional evidence in support of the theory (1) that segmented structure is characteristic of not only protein-coding sequences (2) but rather of genomes in general. In particular, it confirms the prediction (1) that mobile and separate elements would also be segmented.

Mutator-induced mutations of the rf1 nuclear fertility restorer of T-cytoplasm maize alter the accumulation of T-urf13 mitochondrial transcripts

Dominant alleles of the rf1 and rf2 nuclear-encoded fertility restorer genes are necessary for restoration of pollen fertility in T-cytoplasm maize. To further characterize fertility restoration mediated by the Rf1 allele, 123,500 gametes derived from plants carrying the Mutator transposable element family were screened for rf1-mutant alleles (rf1-m) Four heritable rf1-m alleles were recovered from these populations. Three rf1-m alleles were derived from the progenitor allele Rf1-IA153 and one was derived from Rf1-Ky21. Cosegregation analysis revealed 5.5- and 2.4-kb Mu1-hybridizing EcoRI restriction fragments in all of the male-sterile and none of the male-fertile plants in families segregating for rf1-m3207 and rf1-m3310, respectively. Mitochondrial RNA gel blot analyses indicated that all four rf1-m alleles in male-sterile plants cosegregated with the altered steady-state accumulation of 1.6- and 0.6-kb T-urf13 transcripts, demonstrating that these transcripts are Rf1 dependent. Plants carrying a leaky mutant, rf1-m7323, revealed variable levels of Rf1-associated, T-urf13 transcripts and the degree of pollen fertility. The ability to obtain rf1-m derivatives from Rf1 indicates that Rf1 alleles produce a functional gene product necessary for the accumulation of specific T-urf13 transcripts in T-cytoplasm maize.

Genetic analyses of a putative Mutator-induced deletion involving the blue fluorescent1 (bf1) and brown midrib4 (bm4) loci in maize

A putative Mutator-induced alteration (isolate) involving the blue fluorescent1 (Bf1) and the brown midrib4 (bm4) loci is described. This isolate (Bf1-Mu-044-4) was one of the blue fluorescent1 mutants in a large experiment designed to produce Mutator-induced mutations involving this locus. Evidence is presented supporting the conclusion that this alteration deletes all or part of both the bf1 and bm4 loci. The isolate is infrequently transmitted through the pollen, but is more readily transmitted through the egg, although at less than the expected frequency of 50% for a simple mutation. Heterozygotes of this isolate with the bm4-R allele have brown midribs. These brown midrib plants are shorter than homozygous bm4-R plants and approximately 50% of these Bf1-Mu-044-4/bm4-R heterozygotes do not reach maturity. One putative Mutator-induced bm4 mutation, which occurred in the course of the analysis of the Bf1-Mu-044 isolate, is described. Key words : Mutator, deletion, bf1-bm4 loci.

Ectopic expression of the knox homeo box gene rough sheath1 alters cell fate in the maize leaf

Rough sheath1 (Rs1) is a dominant mutation that alters cell fate and causes unregulated cell division and expansion in the maize leaf. A knox (Kn1 like-homeo box gene) sequence closely linked to the Rs1-O mutation was cloned and shown by transposon mutagenesis to encode the rs1 gene. The deduced amino acid sequence of the RS1 protein is highly similar to KN1 in the homeo domain but contains a unique amino-terminal region. rs1 is expressed in the shoot apical meristem in a circular pattern preceding leaf initiation, but is not detectable in leaf primordia or mature leaves in normal plants. Rings of rs1 expression subtend leaf insertion sites in the shoot, and lateral organ primordia in inflorescence and floral meristems. The timing and position of rs1 expression in meristems suggests a possible role for rs1 in patterning the placement of lateral organs along the axis of the shoot. In contrast to wild type, rs1 is expressed in early leaf primordia of Rs1 mutant plants, suggesting that ectopic expression causes the mutant phenotype. Ectopic expression in Rs1-O plants suggests the ligular [corrected] region is more competent to respond to rs1 than blade or sheath tissues.

Transposon-induced promoter scrambling: a mechanism for the evolution of new alleles

We have studied a germinal revertant of the Mutator (Mu3)-induced mutation (Adh1-3F1124) of the maize alcohol dehydrogenase 1 gene (adh1). Transposon Mu3 was inserted at the TATA box of the promoter. The excision of Mu3 caused a complex, multibreakpoint DNA rearrangement with deletion, inverted duplication, and inversions affecting 430 nucleotides in the promoter region. These changes led to an unusual pattern of adh1 gene expression: increased levels of enzyme activity in one organ, decreased levels in another, and almost unchanged levels in a third organ. The evolutionary impact of transposon-induced promoter scrambling on generation of allelic diversity is discussed. We present a fragmentation model to help explain how transposon excision could induce multiple breakpoint aberrations without involving a homologous chromosome.

Plant transposable elements and the genome

Transposable elements are ubiquitous in the plant kingdom and share many common features, both structural and mechanistic, with mobile elements from other eukaryotes. Transposition of these elements can influence plant genes and genomes in many ways. It is also becoming clear that transposable element derived sequences can be a major component of plant genomes. These sequences are probably, therefore, very significant factors in plant evolution.