Development of an efficient two-element transposon tagging system in Arabidopsis thaliana

Probing the effects of streptomycin on Brassica napus germination and assessing its molecular interactions using extensive molecular dynamics (MD) simulations

Antibiotics are chemical compounds that are used to treat and prevent disease in humans and animals. They have been used in animal feed for over 60 years and are widely used in industrial farming. Antibiotics can have negative environmental impacts, including the potential to contribute to the development of antibiotic-resistant organisms. They can enter the environment through various pathways, including the manufacturing process, the direct application of antibiotic-laden manure to fields, and through grazing animals. Antibiotics that are given to animals can be excreted from where they can enter soil and groundwater which enable their entry in plants. Streptomycin is an antibiotic that is used against a range of gram-positive and gram-negative bacteria, but its use has led to the development of antibiotic resistance in some pathogens. It has also been shown to have negative impacts on a range of plant species, including tobacco, tomato, and wheat. Although, the major effect of streptomycin on plant physiology have been studied, the molecular mechanisms at play are barely understood in plant body. In current study, we examined the impact of streptomycin on germination of Brassica napus and then using docking, MM-GBBSA and MD simulations identified key proteins that interact with streptomycin by performing rigorous computational screening of 106 different proteins. Our finding suggest that streptomycin might be interacting with acyl-CoA oxidases, protochlorophyllide reductase B and leucoanthocyanidin dioxygenase based on simulation and docking analysis.

Jack of all trades versus master of one: how generalist versus specialist strategies of transposable elements relate to their horizontal transfer between lineages

Transposable elements (TEs) are obligate genomic parasites, relying on host germline cells to ensure their replication and passage to future generations. While some TEs exhibit high fidelity to their host genome, being passed from parent to offspring through vertical transmission for millions of years, others frequently invade new and distantly related hosts through horizontal transfer. In this review, I highlight how the complexity of interactions between TE and host required for transposition may be an important determinant of horizontal transfer: with TEs with more complex regulatory requirements being less able to invade new host genomes.

DEFECTIVELY ORGANIZED TRIBUTARIES 5 is not required for leaf venation patterning in Arabidopsis thaliana

The search for genetic regulators of leaf venation patterning started over 30 years ago, primarily focused on mutant screens in the eudicotyledon Arabidopsis thaliana. Developmental perturbations in either cotyledons or true leaves led to the identification of transcription factors required to elaborate the characteristic reticulated vein network. An ortholog of one of these, the C2H2 zinc finger protein DEFECTIVELY ORGANIZED TRIBUTARIES 5 (AtDOT5), was recently identified through transcriptomics as a candidate regulator of parallel venation in maize (Zea mays) leaves. To elucidate how AtDOT5 regulates vein patterning, we generated three independent loss-of-function mutations by gene editing in Arabidopsis. Surprisingly, none of them exhibited any obvious phenotypic perturbations. To reconcile our findings with earlier reports, we re-evaluated the original Atdot5-1 and Atdot5-2 alleles. By genome sequencing, we show that reported mutations at the Atdot5-1 locus are actually polymorphisms between Landsberg erecta and Columbia ecotypes, and that other mutations present in the background most likely cause the pleiotropic mutant phenotype observed. We further show that a T-DNA insertion in the Atdot5-2 locus has no impact on leaf venation patterns when segregated from other T-DNA insertions present in the original line. We thus conclude that AtDOT5 plays no role in leaf venation patterning in Arabidopsis.

Mapping of T-DNA and Ac/Ds by TAIL-PCR to Analyze Chromosomal Rearrangements

Insertion mutagenesis using known DNA sequences such as T-DNA and transposons is an important tool for studies on gene function in plant sciences. The transposons Activator (Ac)/Dissociation (Ds) have been systematically used to manipulate plant chromosomes. For both of these applications, the recovery of genomic DNA sequences flanking the insertions is required to estimate the sizes and/or scales of the reconstituted chromosomes. In this chapter, we describe the protocols for thermal asymmetric interlaced PCR (TAIL-PCR) for isolation of genomic sequences flanking DNA inserts in plant genomes.

50 years of Arabidopsis research: highlights and future directions

922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.

Genome-wide approach in Arabidopsis thaliana to assess the toxicity of cadmium sulfide quantum dots

Cadmium sulfide quantum dots (CdS QDs) are used in the manufacture of a number of electronics products. Their small size allows their ready entry into living cells, but as yet no attempt has been made to assess their toxicity. Our aim was to exploit two Ds transposition-induced mutant lines of Arabidopsis thaliana which tolerated exposure to CdS QDs to identify the genetic basis of their tolerance. Both a genome-wide top-down (from mutant to genes) and a bottom-up (from gene expression to phenotype) approach were applied. The differential responses of the mutants compared to the wild type showed that sensitivity to CdS QDs was unrelated to sensitivity to Cd(2+) ions. A transcriptomic analysis identified a number of genes whose transcript abundance was correlated with the tolerance. The phenotype of one of the mutants was correlated with the overexpression of ELM2, an MYB containing gene visited by a Ds transposon. Segregation analysis showed that the genetic basis of CdS QDs tolerance in both mutants was monogenic. The phenotype of the other mutant could be explained by the mutation of HCF101, a gene involved in photosynthesis.

Molecular biology of maize Ac/Ds elements: an overview

Maize Activator (Ac) is one of the prototype transposable elements of the hAT transposon superfamily, members of which were identified in plants, fungi, and animals. The autonomous Ac and nonautonomous Dissociation (Ds) elements are mobilized by the single transposase protein encoded by Ac. To date Ac/Ds transposons were shown to be functional in approximately 20 plant species and have become the most widely used transposable elements for gene tagging and functional genomics approaches in plants. In this chapter we review the biology, regulation, and transposition mechanism of Ac/Ds elements in maize and heterologous plants. We discuss the parameters that are known to influence the functionality and transposition efficiency of Ac/Ds transposons and need to be considered when designing Ac transposase expression constructs and Ds elements for application in heterologous plant species.

Survey of natural and transgenic gene markers used to monitor transposon activity

Marker genes have played a critical role in the discovery of plant transposable elements, our understanding of transposon biology, and the utility of transposable elements as tools in functional genomics. Marker traits in model plants have been useful to detect transposable elements and to study the dynamics of transposition. Transposon-induced changes in the sequence of marker genes and consequently their expression have contributed to our understanding of molecular mechanisms of transposition and associated genome rearrangements. Further, marker genes that have been cloned and are compatible in heterologous systems have found versatile utility in the design of DNA constructs that have enabled us to understand the finer details of transposition mechanisms, and also allowed the use of transposon-based tools for functional genomics. This chapter traces the role of marker traits and marker genes (endogenous and transgenic) in various plant systems, and their contributions to the advancement of transposon biology over the past several decades.

Transposable elements as catalysts for chromosome rearrangements

Barbara McClintock first showed that transposable elements in maize can induce major chromosomal rearrangements, including duplications, deletions, inversions, and translocations. More recently, researchers have made significant progress in elucidating the mechanisms by which transposons can induce genome rearrangements. For the Ac/Ds transposable element system, rearrangements are generated when the termini of different elements are used as substrates for transposition. The resulting alternative transposition reaction directly generates a variety of rearrangements. The size and type of rearrangements produced depend on the location and orientation of transposon insertion. A single locus containing a pair of alternative transposition-competent elements can produce a virtually unlimited number of genome rearrangements. With a basic understanding of the mechanisms involved, researchers are beginning to utilize both naturally occurring and in vitro-generated configurations of transposable elements in order to manipulate chromosome structure.

The role of plastidial glucose-6-phosphate/phosphate translocators in vegetative tissues of Arabidopsis thaliana mutants impaired in starch biosynthesis

Arabidopsis thaliana mutants impaired in starch biosynthesis due to defects in either ADP glucose pyrophosphorylase (adg1-1), plastidic phosphoglucose mutase (pgm) or a new allele of plastidic phosphoglucose isomerase (pgi1-2) exhibit substantial activity of glucose-6-phosphate (Glc6P) transport in leaves that is mediated by a Glc6P/phosphate translocator (GPT) of the inner plastid envelope membrane. In contrast to the wild type, GPT2, one of two functional GPT genes of A. thaliana, is strongly induced in these mutants during the light period. The proposed function of the GPT in plastids of non-green tissues is the provision of Glc6P for starch biosynthesis and/or the oxidative pentose phosphate pathway. The function of GPT in photosynthetic tissues, however, remains obscure. The adg1-1 and pgi1-2 mutants were crossed with the gpt2-1 mutant defective in GPT2. Whereas adg1-1/gpt2-1 was starch-free, residual starch could be detected in pgi1-2/gpt2-1 and was confined to stomatal guard cells, bundle sheath cells and root tips, which parallels the reported spatial expression profile of AtGPT1. Glucose content in the cytosolic heteroglycan increased substantially in adg1-1 but decreased in pgi1-2, suggesting that the plastidic Glc6P pool contributes to its biosynthesis. The abundance of GPT2 mRNA correlates with increased levels of soluble sugars, in particular of glucose in leaves, suggesting induction by the sugar-sensing pathway. The possible function of GPT2 in starch-free mutants is discussed in the background of carbon requirement in leaves during the light-dark cycle.

Genetic screens to identify plant stress genes

A powerful means to learn about gene functions in a developmental or physiological context in an organism is to isolate the corresponding mutants with altered phenotypes. Diverse mutagenic agents, including chemical and biological, have been widely employed, and each comes with its own advantages and inconveniences. For Arabidopsis thaliana, whose genome sequence is publicly available, the reliance of reverse genetics to understand the relevant roles of genes particularly those coding for proteins in growth and development is now a common practice. Identifying multiple alleles at each locus is important because they can potentially reveal epistatic relationship in a signaling pathway or components belonging to a common signaling complex by their synergistic or even allele-specific enhancement of the phenotypic severity. In this article, we describe mutagenesis by using ethyl methanesulfonate (EMS) and transfer (T)-DNA-mediated insertion or activation tagging as applied to the most widely used genetic plant model A. thaliana. Also, we demonstrate the utility of several genetic screening approaches to dissect adaptive responses to various abiotic stresses.

Genetic technologies for the identification of plant genes controlling environmental stress responses

Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.

Vein patterning screens and the defectively organized tributaries mutants in Arabidopsis thaliana

Leaf veins form a closed network that transports essential photosynthates, water and signaling molecules to the developing plant. The formation of the patterns of these networks during leaf ontogeny is an active subject of modeling and computer simulation. To investigate the vein patterning process, we performed screens for defects in juvenile leaf vein patterning in Arabidopsis thaliana lines subjected to mutagenesis via diepoxybutane, activation tagging or the Dissociation/Activator transposon. We identified over 40 vein pattern defective lines, providing a phenotypic resource for the testing of vein patterning models. In addition, we report the chromosomal linkage for 13 of these, eight of which were successfully cloned. We further describe the phenotypes of five of these mutants, which we call the defectively organized tributaries (dot) mutants, and their corresponding molecular identities. The diversity of the individual genes affected in this collection of pattern mutants suggests that vein pattern is highly sensitive to perturbations in many cellular processes. Despite this diversity of causes, the resulting pattern defects fall into a limited number of classes, including parallel, spurred, misaligned, open, midvein gap and irregularly spaced. These classes may represent sensitivities to cellular processes associated with the DOT genes. The ontogeny of common defective patterns should be accommodated into any robust model for the ontogeny and evolution of pattern.

Activation tagging in plants—generation of novel, gain-of-function mutations

Activation tagging is a mutagenesis strategy that generates dominant, gain-of-function mutations as a consequence of gene over-expression. These mutations cause a class of mutant previously unobtainable by conventional mutagenesis. Unlike most mutant phenotypes, which are generally a consequence of gene inactivation, activation tagged phenotypes arise from excess functional gene product. Gene over-expression mutations are obtained by randomly inserting regulatory sequences throughout the genome, using either high-throughput plant transformation or mobile transposable elements to distribute these regulatory elements. Since the sequence of the regulatory element vector is known, it acts as a molecular tag, making isolation of the over-expressed gene a relatively straightforward process using standard molecular biological techniques. Activation tagged phenotypes have been generated by the over-expression of genes encoding a diverse range of protein and RNA products that are involved in all aspects of plant biogenesis. This mutation approach has been used extensively in Arabidopsis and to a lesser extent in several other species. In this review we summarise activation tagging in plants and suggest that the development of this mutagenesis strategy in more plants of agronomic significance is highly desirable.

Use of the transposable element Ac/Ds in conjunction with Spm/dSpm for gene tagging allows extensive genome coverage with a limited number of starter lines: functional analysis of a four-element system in Arabidopsis thaliana

We have developed a novel four-element based gene tagging system in Arabidopsis to minimize the number of starter lines required to generate genome-wide insertions for saturation mutagenesis. In this system, the non-autonomous cassette, Ds(dSpm), comprises of both Ds and dSpm elements cloned one within the other along with appropriate selection markers to allow efficient monitoring of excision and re-integration of the transposons. Trans-activation of the outer borders (Ds) and selection against the negative selection marker (iaaH) linked to the cassette ensures unlinked spread of the Ds(dSpm) cassette from the initial site of integration of the T-DNA. This creates several launch pads within the genome from where the internal element (dSpm) can be subsequently mobilized to generate secondary insertions. In this study, starting from a single T-DNA integration we could spread the Ds(dSpm) cassette to 11 different locations over all the five chromosomes of Arabidopsis. The frequency of unlinked Ds transpositions in the F2 generation varied between 0.05 and 3.35%. Three of these lines were then deployed to trans-activate the internal dSpm element which led to the selection of 29 dSpm insertions. The study conclusively shows the feasibility of deploying Ds and the dSpm elements in a single construct for insertional mutagenesis.

The HY2 gene as an efficient marker for transposon excision in Arabidopsis

Transposable elements can generate germinal and somatic mutations, and hence represent a powerful tool for the analysis of gene function. Transposons from maize have been adapted to mutagenise the genomes of diverse species. The efficiency of these systems partly relies on the ease with which germinal (i.e. germinally transmitted) or somatic excisions can be detected. Here we describe the use of HY2, a gene that codes for an enzyme involved in the biosynthesis of the phytochrome chromophore, to monitor the excision of a Ds gene-trap element in Arabidopsis thaliana. Taking advantage of the altered germination and de-etiolation behaviour of a Ds -tagged hy2 mutant, we have designed an efficient protocol for the recovery of germinal revertants, making HY2 the most precocious excision marker available, to the best of our knowledge. In addition, HY2 is also useful for generating visible sectors in photosynthetic tissues, thanks to the somatic instability of this mutable hy2 allele.

Gene trapping of the Arabidopsis genome with a firefly luciferase reporter

Experiments with gene-trap vectors containing the firefly luciferase (LUC) reporter genes were carried out with the aim of analyzing functions of the Arabidopsis genome. Studies with protein fusion-type trap vectors as well as an internal ribosome entry site (IRES)-assisted non-fusion-type vector revealed that both types of vectors were suitable for gene trapping in Arabidopsis, although there were some differences in trapping efficiencies. The established trap lines were subjected to analyses for light responses, demonstrating the powerful and unique applications of a LUC-trapping system. A systematic survey of the insertion sites of the T-DNAs in LUC-expressing lines revealed 12-41% gene-trapping efficiencies depending on the vector. We demonstrate that the LUC-trapping system provides a unique system with which to monitor temporal expression of plant genes.

A resource of mapped dissociation launch pads for targeted insertional mutagenesis in the Arabidopsis genome

We describe a new resource for targeted insertional mutagenesis in Arabidopsis using a maize (Zea mays) Activator/Dissociation (Ds) two-element system. The two components of the system, T-DNA vectors carrying a Ds launch pad and a stable Activator transposase source, were designed to simplify selection of transposition events and maximize their usefulness. Because Ds elements preferentially transpose to nearby genomic sites, they can be used in targeted mutagenesis of linked genes. To efficiently target all genes throughout the genome, we generated a large population of transgenic Arabidopsis plants containing the Ds launch pad construct, identified lines containing single Ds launch pad inserts, and mapped the positions of Ds launch pads in 89 lines. The integration sites of the Ds launch pads were relatively evenly distributed on all five chromosomes, except for a region of chromosomes 2 and 4 and the centromeric regions. This resource therefore provides access to the majority of the Arabidopsis genome for targeted tagging.

Proliferating Floral Organs (Pfo), a Lotus japonicus gene required for specifying floral meristem determinacy and organ identity, encodes an F-box protein

To study flower development in the model legume Lotus japonicus, a population of transgenic plants containing a maize transposable element (Ac) in their genome was screened for floral mutants. One mutation named proliferating floral organs (pfo) causes plants to produce a large number of sepal-like organs instead of normal flowers. It segregates as a single recessive Mendelian locus, and causes sterility. Scanning electron microscopy revealed that pfo affects the identity, number and arrangement of floral organs. Sepal-like organs form in the first whorl, and secondary floral meristems are produced in the next whorl. These in turn produce sepal-like organs in the first whorl and floral meristems in the second whorl, and the process is reiterated. Petals and stamens are absent while carpels are either absent or reduced. The pfo phenotype was correlated with the presence of an Ac insertion yielding a 1.6-kb HindIII restriction fragment on Southern blots. Both the mutant phenotype and this Ac element are unstable. Using the transposon as a tag, the Pfo gene was isolated. Conceptual translation of Pfo predicts a protein containing an F-box, with high overall similarity to the Antirrhinum FIMBRIATA, Arabidopsis UNUSUAL FLORAL ORGANS and Pisum sativum Stamina pistilloida proteins. This suggests that Pfo may regulate floral organ identity and meristem determinacy by targeting proteins for ubiquitination.

Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes

To assist in the analysis of plant gene functions we have generated a new Arabidopsis insertion mutant collection of 90 000 lines that carry the T-DNA of Agrobacterium gene fusion vector pPCV6NFHyg. Segregation analysis indicates that the average frequency of insertion sites is 1.29 per line, predicting about 116 100 independent tagged loci in the collection. The average T-DNA copy number estimated by Southern DNA hybridization is 2.4, as over 50% of the insertion loci contain tandem T-DNA copies. The collection is pooled in two arrays providing 40 PCR templates, each containing DNA from either 4000 or 5000 individual plants. A rapid and sensitive PCR technique using high-quality template DNA accelerates the identification of T-DNA tagged genes without DNA hybridization. The PCR screening is performed by agarose gel electrophoresis followed by isolation and direct sequencing of DNA fragments of amplified T-DNA insert junctions. To estimate the mutation recovery rate, 39 700 lines have been screened for T-DNA tags in 154 genes yielding 87 confirmed mutations in 73 target genes. Screening the whole collection with both T-DNA border primers requires 170 PCR reactions that are expected to detect a mutation in a gene with at least twofold redundancy and an estimated probability of 77%. Using this technique, an M2 family segregating a characterized gene mutation can be identified within 4 weeks.

A transgenic perspective on plant functional genomics

Transgenic crops are very much in the news due to the increasing public debate on their acceptance. In the scientific community though, transgenic plants are proving to be powerful tools to study various aspects of plant sciences. The emerging scientific revolution sparked by genomics based technologies is producing enormous amounts of DNA sequence information that, together with plant transformation methodology, is opening up new experimental opportunities for functional genomics analysis. An overview is provided here on the use of transgenic technology for the functional analysis of plant genes in model plants and a link made to their utilization in transgenic crops. In transgenic plants, insertional mutagenesis using heterologous maize transposons or Agrobacterium mediated T-DNA insertions, have been valuable tools for the identification and isolation of genes that display a mutant phenotype. To discover functions of genes that do not display phenotypes when mutated, insertion sequences have been engineered to monitor or change the expression pattern of adjacent genes. These gene detector insertions can detect adjacent promoters, enhancers or gene exons and precisely reflect the expression pattern of the tagged gene. Activation tag insertions can mis-express the adjacent gene and confer dominant phenotypes that help bridge the phenotype gap. Employment of various forms of gene silencing technology broadens the scope of recovering knockout phenotypes for genes with redundant function. All these transgenic strategies describing gene-phenotype relationships can be addressed by high throughput reverse genetics methods that will help provide functions to the genes discovered by genome sequencing. The gene functions discovered by insertional mutagenesis and silencing strategies along with expression pattern analysis will provide an integrated functional genomics perspective and offer unique applications in transgenic crops.

KOJAK encodes a cellulose synthase-like protein required for root hair cell morphogenesis in Arabidopsis

The cell wall is an important determinant of plant cell form. Here we define a class of Arabidopsis root hair mutants with defective cell walls. Plants homozygous for kojak (kjk) mutations initiate root hairs that rupture at their tip soon after initiation. The KJK gene was isolated by positional cloning, and its identity was confirmed by the molecular complementation of the Kjk(-) phenotype and the sequence of three kjk mutant alleles. KOJAK encodes a cellulose synthase-like protein, AtCSLD3. KOJAK/AtCSLD3 is the first member of this subfamily of proteins to be shown to have a function in cell growth. Subcellular localization of the KOJAK/AtCSLD3 protein using a GFP fusion shows that KOJAK/AtCSLD3 is located on the endoplasmic reticulum, indicating that KOJAK/AtCSLD3 is required for the synthesis of a noncellulosic wall polysaccharide. Consistent with the cell specific defect in the roots of kjk mutants, KOJAK/AtCSDL3 is preferentially expressed in hair cells of the epidermis. The Kjk(-) phenotype and the pattern of KOJAK/AtCSLD3 expression suggest that this gene acts early in the process of root hair outgrowth. These results suggest that KOJAK/AtCSLD3 is involved in the biosynthesis of beta-glucan-containing polysaccharides that are required during root hair elongation.

Recovery of Mutants Impaired in Pathogenicity After Transposition of Impala in Fusarium oxysporum f. sp. melonis

ABSTRACT The ability of transposon impala to inactivate genes involved in pathogenicity was tested in Fusarium oxysporum f. sp. melonis. Somatic excision of an impala copy inserted in the nitrate reductase-encoding niaD gene was positively selected through a phenotypic assay based on the restoration of nitrate reductase activity. Independent excision events were analyzed molecularly and shown to carry reinsertedimpala in more than 70% of the cases. Mapping of reinserted impala elements on large NotI-restriction fragments showed that impala transposes randomly. By screening 746 revertants on plants, a high proportion (3.5%) of mutants impaired in their pathogenic potential was recovered. According to the kinetics of wilt symptom development, the strains that were impaired in pathogenicity were clustered in three classes: class 1 grouped two strains that never induced Fusarium wilt symptoms on the host plant; class 2 and class 3 grouped 15 and 9 revertants which caused symptoms more than 50 and 30 days after inoculation, respectively. The first results demonstrate the efficiency of transposition in generating mutants affected in pathogenicity, which are usually difficult to obtain by classical mutagenesis, and open the possibility to clone the altered genes with impala as a tag.

Efficient insertion mutagenesis of Arabidopsis by tissue culture-induced activation of the tobacco retrotransposon Tto1

The tobacco retrotransposon Tto1 is one of a few active retrotransposons in plants. Its transposition is activated by tissue culture and is primarily regulated at the transcriptional level. Here we demonstrate that Tto1 introduced in Arabidopsis is also activated by tissue culture. Transcription of Tto1 was induced by tissue culture and driven by its LTR promoter. Transposed copies of Tto1 were observed in almost all of the plants regenerated from the explants cultured for only 1 week. A total of 255 independent regenerated lines have been produced, and the average copy number of transposed Tto1 in these lines is estimated to be 3.2. Sequences flanking Tto1 were amplified by thermal asymmetric interlaced (TAIL)-PCR. Of 165 independent amplified products, 123 showed significant homology to known genes or hypothetical protein genes. The insertion sites of Tto1 are spread over all chromosomes and the target site sequence shows moderate consensus. Taken together, these results indicate that Tto1 can be used as a tool for efficient insertion mutagenesis of Arabidopsis which is especially suitable as a reverse genetics system.

Analysis of extrachromosomal Ac/Ds transposable elements

The mechanism of transposition of the maize Ac/Ds elements is not well understood. The true transposition intermediates are not known and it has not been possible to distinguish between excision models involving 8-bp staggered cuts or 1-bp staggered cuts followed by hairpin formation. In this work, we have analyzed extrachromosomal excision products to gain insight into the excision mechanism. Plasmid rescue was used to demonstrate that Ds excision is associated with the formation of circular molecules. In addition, we present evidence for the formation of linear extrachromosomal species during Ds excision. Sequences found at the termini of circular and linear elements showed a broad range of nucleotide additions or deletions, suggesting that these species are not true intermediates. Additional nucleotides adjacent to the termini in extrachromosomal elements were compared to the sequence of the original donor site. This analysis showed that: (1) the first nucleotide adjacent to the transposon end was significantly more similar to the first nucleotide flanking the element in the donor site than to a random sequence and (2) the second and farther nucleotides did not resemble the donor site. The implications of these findings for excision models are discussed.

A four-element based transposon system for allele specific tagging in plants--theoretical considerations

The two-element transposon constructs, utilizing either Ac/Ds or Spm/dSpm, allow random tagging of genes in heterologous model species, but are inadequate for directed tagging of specific alleles of agronomic importance. We propose the use of Ac/Ds in conjunction with Spm/dSpm to develop a four-element system for directed tagging of crop-specific alleles. The four-element based construct would include both Ds and dSpm along with relevant marker genes and would function in two steps. In the first step dSpm(Ds) stocks (a minimum of two) would be crossed to a line containing transposases of Spm and unlinked integrations would be selected from segregating population by the use of a negative selection marker to develop stocks representing integration of dSpm(Ds) at a large number of locations in the genome. Selections would be made for a line in which dSpm(Ds) shows partial or complete linkage to the allele of interest. In the second step selected line would be crossed to a line containing Ac transposase to induce transpositions of Ds element to linked sites thereby exploiting the natural tendency of Ds element to jump to linked sites. Unlinked jumps of dSpm(Ds) and linked jumps of Ds could be monitored by appropriate marker genes. The proposed model would allow tagging of allele of interest in chromosome addition lines and also help in the efficient use of genic male sterility systems for hybrid seed production by tightly marking the fertility restorer gene with a negative selection marker.

FIDDLEHEAD, a gene required to suppress epidermal cell interactions in Arabidopsis, encodes a putative lipid biosynthetic enzyme

In plants, the outer epidermal cell wall and cuticle presents a semipermeable barrier that maintains the external integrity of the plant and regulates the passage of various classes of molecules into and out of the organism. During vegetative development, the epidermal cells remain relatively inert, failing to respond to wounding or grafting. During reproductive development and fertilization, however, the epidermis is developmentally more labile and participates in two types of contact-mediated cell interactions: organ fusion and pollen hydration. Here we describe the isolation and characterization of one gene whose product normally functions in blocking both types of epidermal cell interactions during vegetative development: the FIDDLEHEAD gene. As suggested by previous biochemical analyses, the gene encodes a protein that is probably involved in the synthesis of long-chain lipids found in the cuticle and shows similarity to a large class of genes encoding proteins related to beta-ketoacyl-CoA synthases and chalcone synthases. In situ hybridization reveals an epidermal pattern of expression consistent with a role for this protein in the synthesis of lipid components that are thought to localize extracellularly and probably modify the properties of the cuticle.

Photosynthesis, sugars and the regulation of gene expression

Sugar-mediated regulation of gene expression is a mechanism controlling the expression of many different plant genes. In this review, a compilation of the genes encoding photosynthetic proteins, subject to this mode of regulation, is presented. Several groups have devised different screening strategies to obtain Arabidopsis mutants in sugar sensing and signalling. An overview of these strategies has been included. Sugar-mediated regulation of gene expression is thought to require the hexokinase (HXK) protein. It has previously been shown that one such sugar, mannose, is capable of blocking germination in Arabidopsis. This inhibition is also mediated by HXK and occurs in the low millimolar concentration range. Here, the use of germination on mannose as an effective screening strategy for putative sugar sensing and signalling mutants is reported. T-DNA- and EMS-mutagenized collections were used to isolate 31 mannose-insensitive germination (mig) mutants. With the use of these mutants, a comparison between this screen and other existing sugar-sensing screens is presented.

Genetic analysis of salt-tolerant mutants in Arabidopsis thaliana

Stress caused by the increased salinity of irrigated fields impairs plant growth and is one of the major constraints that limits crop productivity in many important agricultural areas. As a contribution to solving such agronomic problems, we have carried out a large-scale screening for Arabidopsis thaliana mutants induced on different genetic backgrounds by EMS treatment, fast neutron bombardment, or T-DNA insertions. From the 675,500 seeds we screened, 17 mutant lines were isolated, all but one of which yielded 25-70% germination levels on 250 mm NaCl medium, a condition in which their ancestor ecotypes are unable to germinate. Monogenic recessive inheritance of NaCl-tolerant germination was displayed with incomplete penetrance by all the selected mutants, which fell into five complementation groups. These were named SALOBRENO (SAN) and mapped relative to polymorphic microsatellites, the map positions of three of them suggesting that they are novel genes. Strains carrying mutations in the SAN1-SAN4 genes display similar responses to both ionic effects and osmotic pressure, their germination being NaCl and mannitol tolerant but KCl and Na(2)SO(4) sensitive. In addition, NaCl-, KCl-, and mannitol-tolerant as well as abscisic-acid-insensitive germination was displayed by sañ5, whose genetic and molecular characterization indicates that it carries an extremely hypomorphic or null allele of the ABI4 gene, its deduced protein product lacking the APETALA2 DNA binding domain.

Transposition of the autonomous Fot1 element in the filamentous fungus Fusarium oxysporum

Autonomous mobility of different copies of the Fot1 element was determined for several strains of the fungal plant pathogen Fusarium oxysporum to develop a transposon tagging system. Two Fot1 copies inserted into the third intron of the nitrate reductase structural gene (niaD) were separately introduced into two genetic backgrounds devoid of endogenous Fot1 elements. Mobility of these copies was observed through a phenotypic assay for excision based on the restoration of nitrate reductase activity. Inactivation of the Fot1 transposase open reading frame (frameshift, deletion, or disruption) prevented excision in strains free of Fot1 elements. Molecular analysis of the Nia+ revertant strains showed that the Fot1 element reintegrated frequently into new genomic sites after excision and that it can transpose from the introduced niaD gene into a different chromosome. Sequence analysis of several Fot1 excision sites revealed the so-called footprint left by this transposable element. Three reinserted Fot1 elements were cloned and the DNA sequences flanking the transposon were determined using inverse polymerase chain reaction. In all cases, the transposon was inserted into a TA dinucleotide and created the characteristic TA target site duplication. The availability of autonomous Fot1 copies will now permit the development of an efficient two-component transposon tagging system comprising a trans-activator element supplying transposase and a cis-responsive marked element.

Members of the Arabidopsis actin gene family are widely dispersed in the genome

Plant genomes are subjected to a variety of DNA turnover mechanisms that are thought to result in rapid expansion and presumable contraction of gene copy number. The evolutionary history of the 10 actin genes in Arabidopsis thaliana is well characterized and can be traced to the origin of vascular plant genomes. Knowledge about the genomic position of each actin gene may be the key to tracing landmark genomic duplication events that define plant families or genera and facilitate further mutant isolation. All 10 actin genes were mapped by following the segregation of cleaved amplified polymorphisms between two ecotypes and identifying actin gene locations among yeast artificial chromosomes. The Arabidopsis actin genes are widely dispersed on four different chromosomes (1, 2, 3, and 5). Even the members of three closely related and recently duplicated pairs of actin genes are unlinked. Several other cytoskeletal genes (profilins, tubulins) that might have evolved in concert with actins were also mapped, but showed few patterns consistent with that evolutionary history. Thus, the events that gave rise to the actin gene family have been obscured either by the duplication of very small genic fragments or by extensive rearrangement of the genome.

HORMONE-INDUCED SIGNALING DURING MOSS DEVELOPMENT

Understanding how a cell responds to hormonal signals with a new program of cellular differentiation and organization is an important focus of research in developmental biology. In Funaria hygrometrica and Physcomitrella patens, two related species of moss, cytokinin induces the development of a bud during the transition from filamentous to meristematic growth. Within hours of cytokinin perception, a single-celled initial responds with changes in patterns of cell expansion, elongation, and division to begin the process of bud assembly. Bud assembly in moss provides an excellent model for the study of hormone-induced organogenesis because it is a relatively simple, well-defined process. Since buds form in a nonrandom pattern on cells that are not embedded in other tissues, it is possible to predict which cells will respond and where the ensuing changes will take place. In addition, bud assembly is amenable to biochemical, cellular, and molecular biological analyses. This review examines our current understanding of cytokinin-induced bud assembly and the potential underlying mechanisms, reviews the state of genetic analyses in moss, and sets goals for future research with this organism.

Systematic gain-of-function genetics in Drosophila

A modular misexpression system was used to carry out systematic gain-of-function genetic screens in Drosophila. The system is based on inducible expression of genes tagged by insertion of a P-element vector carrying a GAL4-regulated promoter oriented to transcribe flanking genomic sequences. To identify genes involved in eye and wing development, the 2300 independent lines were screened for dominant phenotypes. Among many novel genes, the screen identified known genes, including hedgehog and decapentaplegic, implicated in these processes. A genetic interaction screen for suppressors of a cell migration defect in a hypomorphic slow border cells mutant identified known genes with likely roles in tyrosine kinase signaling and control of actin cytoskeleton, among many novel genes. These studies demonstrate the ability of the modular misexpression system to identify developmentally important genes and suggest that it will be generally useful for genetic interaction screens.

Repetitive elements and their genetic applications in zebrafish

Repetitive elements provide important clues about chromosome dynamics, evolutionary forces, and mechanisms for exchange of genetic information between organisms. Repetitive sequences, especially the mobile elements, have many potential applications in genetic research. DNA transposons and retroposons are routinely used for insertional mutagenesis, gene mapping, gene tagging, and gene transfer in several model systems. Once they are developed for the zebrafish, they will greatly facilitate the identification, mapping, and isolation of genes involved in development as well as the investigation of the evolutionary processes that have been shaping eukaryotic genomes. In this review repetitive elements are characterized in terms of their lengths and other physical properties, copy numbers, modes of amplification, and mobilities within a single genome and between genomes. Examples of how they can be used to screen genomes for species and individual strain differences are presented. This review does not cover repetitive gene families that encode well-studied products such as rRNAs, tRNAs, and the like.

Novel GUS expression patterns following transposition of an enhancer trap Ds element in Arabidopsis

Enhancer trap derivatives of the maize Dissociation (Ds) transposon were introduced into Arabidopsis thaliana. The enhancer trap Ds was so designed that upon transposition to sites containing regulatory sequences in adjacent genomic DNA, transcription of a Ds-borne beta-glucuronidase (GUS) gene would be activated. Sixty percent of all transposition events were associated with GUS expression patterns including one linked to a mutant phenotype. Patterns of GUS expression were found in various organs and were stably inheritable in the F4 and F5 progenies. These results demonstrate the potential value of the technique as a means for detection of developmentally regulated genes and analysis of their function. The enhancer trap construct used in our experiments, as well as the seeds of primary transformants are publicly available.

Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements

The crucifer Arabidopsis thaliana has been used widely as a model organism for the study of plant development. We describe here the development of an efficient insertional mutagenesis system in Arabidopsis that permits identification of genes by their patterns of expression during development. Transposable elements of the Ac/Ds system carrying the GUS reporter gene have been designed to act as enhancer traps or gene traps. A novel selection scheme maximizes recovery of unlinked transposition events. In this study 491 plants carrying independent transposon insertions were generated and screened for expression patterns. One-half of the enhancer trap insertions and one-quarter of the gene trap insertions displayed GUS expression in seedlings or flowers, including expression patterns specific to organs, tissues, cell types, or developmental stages. The patterns identify genes that act during organogenesis, pattern formation, or cell differentiation. Transposon insertion lines with specific GUS expression patterns provide valuable markers for studies of Arabidopsis development and identify new cell types or subtypes in plants. The diversity of gene expression patterns generated suggests that the identification and cloning of Arabidopsis genes expressed in any developmental process is feasible using this system.

Ac/Ds transposon mutagenesis in Arabidopsis thaliana: mutant spectrum and frequency of Ds insertion mutants

Using a two-component Ac/Ds system consisting of a stabilized Ac element (Acc1) and a non-autonomous element (DsA), 650 families of plants carrying independent germinal DsA excisions/transpositions were isolated. Progenies of 559 of these Acc1/DsA families, together with 43 families of plants selected for excision/transposition of wild-type (wt) Ac, were subjected to a broad screening program for mutants exhibiting visible alterations. This resulted in the identification of 48 mutants showing a wide variety of mutant phenotypes, including embryo lethality (24 mutants), chlorophyll defects (5 mutants), defective seedlings (2 mutants), reduced fertility (5 mutants), reduced size (3 mutants), altered leaf morphology (2 mutants), dark green, unexpanded rosette leaves (3 mutants), and aberrant flower or shoot morphology (4 mutants). To whether these mutants were due to transposon insertions, a series of Southern blot experiments was performed on 28 families, comparing in each case several mutant plants with others showing the wild-type phenotype. A preliminary analysis revealed in 4 of the 28 families analyzed a common, novel DsA fragment in all mutant plants, which was present only in heterozygous plants with wt phenotype, as expected for DsA insertion mutations. These four mutants included two showing embryo lethality, one with dark green, unexpanded rosette leaves and stunted inflorescences, and one with curly growth of stems, leaves and siliques. Further evidence for DsA insertion mutations was obtained for one embryo lethal mutant and for the stunted mutant, while in case of the second embryo lethal mutant, the DsA insertion could be separated from the mutant locus by genetic recombination.

Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis

Gene trap transposon mutagenesis can identify essential genes whose functions in later development are obscured by an early lethal phenotype. In higher plants, many genes are required for haploid gametophyte viability, so that the phenotypic effects of their disruption cannot be readily observed in the diploid plant body. The PROLIFERA (PRL) gene, identified by gene trap transposon mutagenesis in Arabidopsis, is required for megaga-metophyte and embryo development. Reporter gene expression patterns revealed that PRL was expressed in dividing cells throughout the plant. PRL is related to the MCM2-3-5 family of yeast genes that are required for the initiation of DNA replication.

The maize transposable element Ac is mobile in the legume Lotus japonicus

To evaluate the prospects for transposon mutagenesis in the autogamous diploid legume Lotus japonicus, the behaviour of the maize transposable element Ac was analysed in the progeny of 38 independent transgenic plants. The conditions for monitoring donor site excision using histochemical localization of beta-glucuronidase activity or the alternative spectinomycin resistance assay were established, and used to follow Ac mobility through two generations. Somatic excision was monitored as variegated cotyledons in the T2 generation and germinal excision events were scored in segregating T3 families as complete beta-glucuronidase-mediated staining of cotyledons or as a fully green spectinomycin-resistant phenotype. Using these assays an average germinal excision frequency of 12% was estimated in the T3 offspring from variegated plants. The fidelity of the excision assays was ascertained by comparing the frequency of germinal excision to the frequency of Ac reinsertion at new positions of the genome. Transposition of Ac in 42% of the plants and detection of the characteristic Ac insertion/excision footprints suggests that insertion mutagenesis with the autonomous maize Activator element is feasible in Lotus japonicus. Parameters influencing Ac behaviour, such as dosage, position effects and modification of the element itself, were also investigated comparing homozygous and hemizygous plants from the same family and by analysing different transformants.

Modification of the 5' untranslated leader region of the maize Activator element leads to increased activity in Arabidopsis

In contrast to its behavior in tobacco and tomato, the maize transposable element Ac is relatively inactive in Arabidopsis. We show here that removal of 537 bp within a CpG-rich region of the Ac 5' untranslated leader region significantly increases the excision frequency of the element in Arabidopsis. This increase did not appear to be correlated with the removal of sequences that are methylated in inactive Ac elements in maize, as these sites were not methylated in Ac elements in Arabidopsis transformants. The deletion within the 5' untranslated leader did not increase Ac activity by increasing levels of steady-state transposase mRNA, as assayed by RNase protection experiments. Moreover, there was no correlation between the levels of steady-state transposase mRNA and Ac element activity. This suggests that post-transcriptional regulation of Ac activity occurs in Arabidopsis.

Tansley Review No. 75 Arabidopsis- its use in the genetic and molecular analysis of plant morphogenesis

In the last decade, the weed Arabidopsis thaliana has come to prominence as a major new model system for investigating genetic and molecular aspects of developmental plant morphology. Extensive genetic and molecular information about the Arabidopsis genome, facilitated by international collaborations and the production of novel mutagenic systems, has enabled a vast array of mutants to be identified, most of which reveal nuclear genes that control different aspects of plant developmental processes. An ever increasing number of these newly identified genes have been isolated and within the next few years an overall view of the molecular control of plant development is likely to emerge. Particularly prevalent amongst these Arabidopsis mutants are those which alter morphogenic processes cither by changes in differentiation patterns of specific cell types, homeotic conversion of entire structures or abnormal patterns of cell division. Mutants in the control of morphogenesis of most parts of the Arabidopsis plant have been identified and characterized. The most abundant classes are in embryogenesis including seedling pattern formation, root morphogenesis, floral morphology (including pollen and anther formation) and mutunts affecting shoot apical inenstern morphology. The first genes to be isolated from morphological mutants have been identified as transcription factors capable of controlling expression of other gene classes as part of a hierarchy of gene control. The relative ease with which many interesting and potentially important genes in morphogenesis have been revealed by identificatic.n of mutants makes it highly likely that with the aid of Arabidopsis thatiana, an understanding of the extremely complex molecular basis of plant morphogenesis may at last be Hirbin reach. Contents Summary 19 I. Introduction 19 II. Why Arabidopsis? 20 III. The developing seed 22 IV. The root 25 V. The shoot apex 27 VI. The Leaf 28 VII. Whole plant morphology 30 VIII. Floral development 31 IX. Sub-cellular tnorphology 32 X. Discussion and future possihihties 32 XI. Acknowledgements 32 XII. References 34.

Analysis of the chromosomal distribution of transposon-carrying T-DNAs in tomato using the inverse polymerase chain reaction

We are developing a system for isolating tomato genes by transposon mutagenesis. In maize and tobacco, the transposon Activator (Ac) transposes preferentially to genetically linked sites. To identify transposons linked to various target genes, we have determined the RFLP map locations of Ac- and Dissociation (Ds)-carrying T-DNAs in a number of transformants. T-DNA flanking sequences were isolated using the inverse polymerase chain reaction (IPCR) and located on the RFLP map of tomato. The authenticity of IPCR reaction products was tested by several criteria including nested primer amplification, DNA sequence analysis and PCR amplification of the corresponding insertion target sequences. We report the RFLP map locations of 37 transposon-carrying T-DNAs. We also report the map locations of nine transposed Ds elements. T-DNAs were identified on all chromosomes except chromosome 6. Our data revealed no apparent chromosomal preference for T-DNA integration events. Lines carrying transposons at known map locations have been established which should prove a useful resource for isolating tomato genes by transposon mutagenesis.

Analysis of the frequency of inheritance of transposed Ds elements in Arabidopsis after activation by a CaMV 35S promoter fusion to the Ac transposase gene

The Ac/Ds transposon system of maize shows low activity in Arabidopsis. However, fusion of the CaMV 35S promoter to the transposase gene (35S::TPase) increases the abundance of the single Ac mRNA encoded by Ac and increases the frequency of Ds excision. In the experiments reported here it is examined whether this high excision frequency is associated with efficient re-insertion of the transposon. This was measured by using a Ds that carried a hygromycin resistance gene (HPT) and was inserted within a streptomycin resistance gene (SPT). Excision of Ds therefore gives rise to streptomycin resistance, while hygromycin resistance is associated with the presence of a transposed Ds or with retention of the element at its original location. Self-fertilisation of most individuals heterozygous for Ds and 35S::TPase produced many streptomycin-resistant (strep(r)) progeny, but in many of these families a small proportion of strep(r) seedlings were also resistant to hygromycin (hyg(r)). Nevertheless, 70% of families tested did give rise to at least one strep(r), hyg(r) seedling, and over 90% of these individuals carried a transposed Ds. In contrast, the Ac promoter fusion to the transposase gene (Ac::TPase) produced fewer strep(r)hyg(r) progeny, and only 53% of these carried a transposed Ds. However, a higher proportion of the strep(r) seedlings were also hyg(r) than after activation by 35S::TPase. We also examined the genotype of strep(r), hyg(r) seedlings and demonstrated that after activation by 35S::TPase many of these were homozygous for the transposed Ds, while this did not occur after activation by Ac::TPase. From these and other data we conclude that excisions driven by 35S::TPase usually occur prior to floral development, and that although a low proportion of strep(r) progeny plants inherit a transposed Ds, those that do can be efficiently selected with an antibiotic resistance gene contained within the element. Our data have important implications for transposon tagging strategies in transgenic plants and these are discussed.