Genome-wide transcript profiling of endosperm without paternal contribution identifies parent-of-origin-dependent regulation of AGAMOUS-LIKE36

Seed development in angiosperms is dependent on the interplay among different transcriptional programs operating in the embryo, the endosperm, and the maternally-derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, analyses of mutants in the cell-cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) have revealed the importance of a paternal genome for the effective development of the endosperm and ultimately the seed. Here we have exploited cdka;1 fertilization as a novel tool for the identification of seed regulators and factors involved in parent-of-origin–specific regulation during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds and identified approximately 600 genes that are downregulated in the absence of a paternal genome. Among those, AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors were significantly overrepresented. Here, AGL36 was chosen for an in-depth study and shown to be imprinted. We demonstrate that AGL36 parent-of-origin–dependent expression is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2), revealing a new type of dual epigenetic regulation in seeds.

Seeds of flowering plants consist of three different organisms that develop in parallel. In contrast to animals, a double fertilization event takes place in plants, producing two fertilization products, the embryo and the endosperm. Imprinting, the parent-of-origin–specific expression of genes, typically takes place in the mammalian placenta and in the plant endosperm. A prevailing hypothesis predicts that a parental tug-of-war on the allocation of available recourses to the developing progeny has led to the evolution of imprinting systems where genes expressed from the mother dampen growth whereas genes expressed from the father are growth enhancers. The number of imprinted genes identified in plants is low compared to mammals, and this precludes the elucidation of the epigenetic mechanisms responsible for this specialized expression system. Here, we have used genome-wide transcript profiling of endosperm without paternal contribution to identify seed regulators and, among these, imprinted genes. We identified a cluster of downregulated MADS-box transcription factors, including AGL36, that was subsequently shown to be imprinted by an epigenetic mechanism involving the DNA methylase MET1 and the glycosylase DME. In addition, the expression of the active AGL36 allele was dampened by the FIS Polycomb Repressive Complex, identifying a novel mode of regulation of imprinted genes.

The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis

Background

SET-domain proteins are histone lysine (K) methyltransferases (HMTase) implicated in defining transcriptionally permissive or repressive chromatin. The Arabidopsis ASH1 HOMOLOG 2 (ASHH2) protein (also called SDG8, EFS and CCR1) has been suggested to methylate H3K4 and/or H3K36 and is similar to Drosophila ASH1, a positive maintainer of gene expression, and yeast Set2, a H3K36 HMTase. Mutation of the ASHH2 gene has pleiotropic developmental effects. Here we focus on the role of ASHH2 in plant reproduction.

Methodology/Principal Findings

A slightly reduced transmission of the ashh2 allele in reciprocal crosses implied involvement in gametogenesis or gamete function. However, the main requirement of ASHH2 is sporophytic. On the female side, close to 80% of mature ovules lack embryo sac. On the male side, anthers frequently develop without pollen sacs or with specific defects in the tapetum layer, resulting in reduction in the number of functional pollen per anther by up to ∼90%. In consistence with the phenotypic findings, an ASHH2 promoter-reporter gene was expressed at the site of megaspore mother cell formation as well as tapetum layers and pollen. ashh2 mutations also result in homeotic changes in floral organ identity. Transcriptional profiling identified more than 300 up-regulated and 600 down-regulated genes in ashh2 mutant inflorescences, whereof the latter included genes involved in determination of floral organ identity, embryo sac and anther/pollen development. This was confirmed by real-time PCR. In the chromatin of such genes (AP1, AtDMC1 and MYB99) we observed a reduction of H3K36 trimethylation (me3), but not H3K4me3 or H3K36me2.

Conclusions/Significance

The severe distortion of reproductive organ development in ashh2 mutants, argues that ASHH2 is required for the correct expression of genes essential to reproductive development. The reduction in the ashh2 mutant of H3K36me3 on down-regulated genes relevant to the observed defects, implicates ASHH2 in regulation of gene expression via H3K36 trimethylation in chromatin of Arabidopsis inflorescences.

AtMBD8 is involved in control of flowering time in the C24 ecotype of Arabidopsis thaliana

The Arabidopsis thaliana accession C24 is a vernalization-responsive, moderately late flowering ecotype. We report that a mutation in AtMBD8, which encodes a protein with a putative Methyl-CpG-Binding Domain (MBD), in C24 background, results in a delay in flowering time during both long and short days. The atmbd8-1 mutant responded to vernalization as wild type (wt) plants. Consistent with a role in modulation of flowering time, an AtMBD8::GUS-reporter construct was expressed in the shoot meristem region and developing leaves. Full-genome transcriptional profiling revealed very few changes in gene expression between atmbd8-1 and wt plants. The expression level of FLC, the major repressor of transition to flowering, was unchanged in atmbd8-1, and in accordance with that, genes upstream of FLC were unaffected by the mutation. The expression level of CONSTANS, involved in photoperiodic control of flowering, was very similar in atmbd8-1 and wt plants. In contrast, the major promoters of flowering, FT and SOC1, were both downregulated. As FT is a regulator of SOC1, we conclude that AtMBD8 is a novel promoter of flowering that acts upstream of FT in the C24 accession. In contrast to atmbd8-1, the Colombia (Col) SALK T-DNA insertion line, atmbd8-2, did not display a delayed transition to flowering. Transcriptional profiling revealed that a substantial number of genes were differentially expressed between C24 and Col wt seedlings. Several of these genes are also differentially expressed in late flowering mutants. We suggest that these differences contribute to the contrasting effect of a mutation in AtMBD8 in the two ecotypes.

Plant peptides in signalling: looking for new partners

A novel candidate ligand-receptor system, INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and the related receptor-like kinases (RLKs) HAESA (HAE) and HAESA-LIKE (HSL)2, has been shown to control floral abscission in Arabidopsis thaliana. Furthermore, several IDA-LIKE (IDL) proteins, which contain a conserved C-terminal domain resembling that of the CLAVATA (CLV)3-ENDOSPERM SURROUNDING REGION (ESR)-RELATED (CLE) protein family, have been shown to be partially redundant with IDA. Here, we use the genetic similarities between the IDA and CLV3 signalling systems to hypothesize that closely related peptide ligands are likely to interact with families of closely related RLKs. Guided by this hypothesis and with the aid of genetics and novel methods, ligand-receptor systems can be identified to improve our understanding of developmental processes in plants.

The EPIP peptide of INFLORESCENCE DEFICIENT IN ABSCISSION is sufficient to induce abscission in arabidopsis through the receptor-like kinases HAESA and HAESA-LIKE2

In Arabidopsis thaliana, the final step of floral organ abscission is regulated by INFLORESCENCE DEFICIENT IN ABSCISSION (IDA): ida mutants fail to abscise floral organs, and plants overexpressing IDA display earlier abscission. We show that five IDA-LIKE (IDL) genes are expressed in different tissues, but plants overexpressing these genes have phenotypes similar to IDA-overexpressing plants, suggesting functional redundancy. IDA/IDL proteins have N-terminal signal peptides and a C-terminal conserved motif (extended PIP [EPIP]) at the C terminus (EPIP-C). IDA can, similar to CLAVATA3, be processed by an activity from cauliflower meristems. The EPIP-C of IDA and IDL1 replaced IDA function in vivo, when the signal peptide was present. In addition, synthetic IDA and IDL1 EPIP peptides rescued ida and induced early floral abscission in wild-type flowers. The EPIP-C of the other IDL proteins could partially substitute for IDA function. Similarly to ida, a double mutant between the receptor-like kinases (RLKs) HAESA (HAE) and HAESA-LIKE2 (HSL2) displays nonabscising flowers. Neither overexpression of IDA nor synthetic EPIP or EPIP-C peptides could rescue the hae hsl2 abscission deficiency. We propose that IDA and the IDL proteins constitute a family of putative ligands that act through RLKs to regulate different events during plant development.

The BLADE-ON-PETIOLE genes are essential for abscission zone formation in Arabidopsis

The Arabidopsis BLADE-ON-PETIOLE 1 (BOP1) and BOP2 genes encode redundant transcription factors that promote morphological asymmetry during leaf and floral development. Loss-of-function bop1 bop2 mutants display a range of developmental defects, including a loss of floral organ abscission. Abscission occurs along specialised cell files, called abscission zones (AZs) that develop at the junction between the leaving organ and main plant body. We have characterized the bop1 bop2 abscission phenotype to determine how BOP1 and BOP2 contribute to the known abscission developmental framework. Histological analysis and petal breakstrength measurements of bop1 bop2 flowers show no differentiation of floral AZs. Furthermore, vestigial cauline leaf AZs are also undifferentiated in bop1 bop2 mutants, suggesting that BOP proteins are essential to establish AZ cells in different tissues. In support of this hypothesis, BOP1/BOP2 activity is required for both premature floral organ abscission and the ectopic abscission of cauline leaves promoted by the INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) gene under the control of the constitutive CaMV 35S promoter. Expression of several abscission-related marker genes, including IDA, is relatively unperturbed in bop1 bop2 mutants, indicating that these AZ genes respond to positional cues that are independent of BOP1/BOP2 activity. We also show that BOP1 and BOP2 promote growth of nectary glands, which normally develop at the receptacle adjacent to developing AZs. Taken together, these data suggest that BOP1/BOP2 activity is required for multiple cell differentiation events in the proximal regions of inflorescence lateral organs.

The Arabidopsis SET-domain protein ASHR3 is involved in stamen development and interacts with the bHLH transcription factor ABORTED MICROSPORES (AMS)

The Arabidopsis thaliana genome contains more than 30 genes encoding SET-domain proteins that are thought to be epigenetic regulators of gene expression and chromatin structure. SET-domain proteins can be divided into subgroups, and members of the Polycomb group (PcG) and trithorax group (trxG) have been shown to be important regulators of development. Both in animals and plants some of these proteins are components of multimeric protein complexes. Here, we have analyzed the Arabidopsis trxG protein ASHR3 which has a SET domain and pre- and post-SET domains similar to that of Ash1 in Drosophila. In addition to the SET domain, a divergent PHD finger is found in the N-terminus of the ASHR3 protein. As expected from SET-domain proteins involved in transcriptional activation, ASHR3 (coupled to GFP) localizes to euchromatin. A yeast two-hybrid screening revealed that the ASHR3 protein interacts with the putative basic helix-loop-helix (bHLH) transcription factor ABORTED MICROSPORES (AMS), which is involved in anther and stamen development in Arabidopsis. Deletion mapping indicated that both the PHD finger and the SET domain mediate the interaction between the two proteins. Overexpression of ASHR3 led in general to growth arrest, and specifically to degenerated anthers and male sterility. Expression analyses demonstrated that ASHR3 like AMS is expressed in the anther and in stamen filaments. We therefore propose that AMS can target ASHR3 to chromatin and regulate genes involved in stamen development and function.

Drosophila dSet2 functions in H3-K36 methylation and is required for development

Lysine methylation has important functions in biological processes that range from heterochromatin formation to transcription regulation. Here, we demonstrate that Drosophila dSet2 encodes a developmentally essential histone H3 lysine 36 (K36) methyltransferase. Larvae subjected to RNA interference-mediated (RNAi) suppression of dSet2 lack dSet2 expression and H3-K36 methylation, indicating that dSet2 is the sole enzyme responsible for this modification in Drosophila melanogaster. dSet2 RNAi blocks puparium formation and adult development, and causes partial (blister) separation of the dorsal and ventral wing epithelia, defects suggesting a failure of the ecdysone-controlled genetic program. A transheterozygous EcR null mutation/dSet2 RNAi combination produces a complete (balloon) separation of the wing surfaces, revealing a genetic interaction between EcR and dSet2. Using immunoprecipitation, we demonstrate that dSet2 associates with the hyperphosphorylated form of RNA polymerase II (RNAPII).

Peroxiredoxin antioxidants in seed physiology

Peroxiredoxins are thiol–requiring antioxidants found in organisms ranging from bacteria to humans. They can be divided into two subgroups with either one or two conserved cysteine residues. In plants, 1–Cys peroxiredoxins have been identified in a number of grasses and cereals, and in the dicotyledonous speciesArabidopsis thaliana. In contrast to other antioxidants, the 1–Cys peroxiredoxin genes are expressed solely in seeds, and only in the parts of the seeds surviving desiccation, i.e. the embryo and the aleurone layer. The expression pattern is characteristic of late embryogenesis–abundant genes. The PER1 protein of barley is present in high concentrations in the nucleus at the onset of desiccation. 1–Cys genes are expressed in a dormancy–related manner in mature seeds, in that transcript levels are high in imbibed dormant seeds, but disappear upon germination of their non–dormant counterparts. 1–Cys transcript levels can be up–regulated by ABA and osmotic stresses and suppressed by gibberellic acid. Two hypotheses have been put forward on the function of 1–Cys peroxiredoxins in seed physiology. First, these proteins might protect macromolecules of embryo and aleurone cells against damaging reactive oxygen species during seed desiccation and early imbibition. And second, seed peroxiredoxins might play a role in the maintenance of dormancy. These hypotheses are discussed, taking into account present knowledge of the biochemistry and molecular biology of peroxiredoxins.

The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9

Proteins containing the evolutionarily conserved SET domain are involved in regulation of eukaryotic gene expression and chromatin structure through their histone lysine methyltransferase (HMTase) activity. The Drosophila SU(VAR)3-9 protein and related proteins of other organisms have been associated with gene repression and heterochromatinization. In Arabidopsis there are 10 SUVH and 5 SUVR genes encoding proteins similar to SU(VAR)3-9, and 4 SUVH proteins have been shown to control heterochromatic silencing by its HMTase activity and by directing DNA methylation. The SUVR proteins differ from the SUVH proteins in their domain structure, and we show that the closely related SUVR1, SUVR2 and SUVR4 proteins contain a novel domain at their N-terminus, and a SUVR specific region preceding the SET domain. Green fluorescent protein (GFP)-fusions of these SUVR proteins preferably localize to the nucleolus, suggesting involvement in regulation of rRNA expression, in contrast to other SET-domain proteins studied so far. A novel HMTase specificity was demonstrated for SUVR4, in that monomethylated histone H3K9 is its preferred substrate in vitro.

Ethylene-dependent and -independent pathways controlling floral abscission are revealed to converge using promoter::reporter gene constructs in the ida abscission mutant

The process of floral organ abscission in Arabidopsis thaliana can be modulated by ethylene and involves numerous genes contributing to cell separation. One gene that is absolutely required for abscission is INFLORESCENCE DEFICIENT IN ABSCISSION, IDA, as the ida mutant is completely blocked in abscission. To elucidate the genetic pathways regulating floral abscission, molecular markers expressed in the floral abscission zone have been studied in an ida mutant background. Using plants with promoter-reporter gene constructs including promoters of a novel FLORAL ABSCISSION ASSOCIATED gene (FAA) encoding a putative single-stranded binding protein (BASIL), chitinase (CHIT::GUS) and cellulase (BAC::GUS), it is shown that IDA acts in the last steps of the abscission process. These markers, as well as HAESA, encoding a receptor-like kinase, were unaffected in their temporal expression patterns in ida compared with wild-type plants; thus showing that different regulatory pathways are active in the abscission process. In contrast to BASIL, CHIT::GUS and BAC::GUS showed, however, much weaker induction of expression in an ida background, consistent with a reduction in pathogen-associated responses and a lack of total dissolution of cell walls in the mutant. IDA, encoding a putative secreted peptide ligand, and HAESA appeared to have identical patterns of expression in floral abscission zones. Lastly, to address the role of ethylene, IDA::GUS expression in the wild type and the ethylene-insensitive mutant etr1-1 was compared. Similar temporal patterns, yet restricted spatial expression patterns were observed in etr1-1, suggesting that the pathways regulated by IDA and by ethylene act in parallel, but are, to some degree, interdependent.

The Drosophila SET domain encoding gene dEset is essential for proper development

We have identified dEset, the fly homolog of human SETDB1 and mouse ESET histone lysine methyltransferases (HKMTases) that methylates the lysine 9 residue of histone 3 (H3-K9) and negatively regulates transcription of target genes. By using spatio-temporal RNA interference we show that dEset is required at several stages of development coinciding with ecdysone pulses, possibly as a repressor of transcription of target genes. Several interacting partners, for example USP, spire, and cut up were identified in a yeast two-hybrid screen. The spatio-temporal expression profiles of dEset and its potential partners suggest that they may act together or even in a larger complex.

The Drosophila G9a gene encodes a multi-catalytic histone methyltransferase required for normal development

Mammalian G9a is a histone H3 Lys-9 (H3–K9) methyltransferase localized in euchromatin and acts as a co-regulator for specific transcription factors. G9a is required for proper development in mammals as g9a⁻/g9a⁻ mice show growth retardation and early lethality. Here we describe the cloning, the biochemical and genetical analyses of the Drosophila homolog dG9a. We show that dG9a shares the structural organization of mammalian G9a, and that it is a multi-catalytic histone methyltransferase with specificity not only for lysines 9 and 27 on H3 but also for H4. Surprisingly, it is not the H4–K20 residue that is the target for this methylation. Spatiotemporal expression analyses reveal that dG9a is abundantly expressed in the gonads of both sexes, with no detectable expression in gonadectomized adults. In addition we find a low but clearly observable level of dG9a transcript in developing embryos, larvae and pupae. Genetic and RNAi experiments reveal that dG9a is involved in ecdysone regulatory pathways.

An inverted repeat transgene with a structure that cannot generate double-stranded RNA, suffers silencing independent of DNA methylation

Transgene silencing in plants is most often dependent on homologous sequences, e.g. tandemly repeated T-DNAs. We have identified an Arabidopsis line (ex2-4 line 4) displaying silencing of the T-DNA-born nptII gene. This line contains a truncated copy of the T-DNA encompassing the nptII gene with its nos promoter adjacent to an intact T-DNA copy. The orientation of the intact and the truncated copies preclude the generation of a double-stranded nptII transcript. Therefore, we have investigated the genomic landscape surrounding T-DNA insertion in the silenced ex2-4 line 4 and five single-copy ex2-4 lines without silencing in search of features that might explain the silencing phenomenon. GC content, putative matrix-attachment regions and transcriptional interference from neighbouring genes could all be ruled out as major causes of silencing. Bisulphite sequencing revealed de novo methylation of the nos promoter both in non-silenced and silenced plants of this line, thus silencing was not correlated to DNA methylation level. Also, the methylation pattern deviated from that characteristic for RNA-mediated DNA methylation and silencing. Our data therefore suggest that ex2-4 line 4 represents a case where silencing is due to DNA-DNA pairing, i.e. pairing between the intact T-DNA and the adjacent truncated, inverted T-DNA copy.

Overexpression of INFLORESCENCE DEFICIENT IN ABSCISSION activates cell separation in vestigial abscission zones in Arabidopsis

Plants may shed organs when they have been injured or served their purpose. The differential pattern of organ abscission in different species is most likely the result of evolutionary adaptation to a variety of life styles and environments. The final step of abscission-related cell separation in floral organs of wild-type Arabidopsis thaliana, which only abscises sepals, petals, and stamens, is controlled by INFLORESCENCE DEFICIENT IN ABSCISSION (IDA). Here, we demonstrate that Arabidopsis 35S:IDA lines constitutively overexpressing IDA exhibit earlier abscission of floral organs, showing that the abscission zones are responsive to IDA soon after the opening of the flowers. In addition, ectopic abscission was observed at the bases of the pedicel, branches of the inflorescence, and cauline leaves. The silique valves also dehisced prematurely. Scanning electron microscopy indicated a spread of middle lamella degradation from preformed abscission zone cells to neighboring cells. A transcript encoding an arabinogalactan protein (AGP) was upregulated in the 35S:IDA lines, and large amounts of AGP were secreted at the sites of abscission. AGP was shown to be a constituent of wild-type floral abscission zones during and soon after cell separation had been completed. We suggest that the restricted expression pattern of IDA precludes abscission of nonfloral organs in Arabidopsis.

Transgene silencing may be mediated by aberrant sense promoter sequence transcripts generated from cryptic promoters

To investigate whether silencing of a T-DNA-carried nptII gene in five single-copy transgenic Arabidopsis lines might be due to position effects, genomic DNA flanking the insertions was analysed for gene density, GC content, presence of short repeats and transposable elements, i.e. factors suggested to promote silencing. No single, common factor could explain the observed silencing. However, in two lines, a transcript covering the nos promoter driving the nptII gene was detected. In sibling sublines with approximately 100% silencing, the nos promoter was heavily methylated. In silico analysis suggested the presence of cryptic core promoters upstream of the nos promoter, in one case in the plant DNA and in the other in a short inverted TDNA region. These fragments were able to drive reporter gene expression in transgenic Arabidopsis plants. Our results indicate that methylation and silencing of transgenic promoters may be mediated by aberrant RNA transcribed from cryptic promoters at the transgene insertion site.

Molecular analysis of Arabidopsis endosperm and embryo promoter trap lines: reporter-gene expression can result from T-DNA insertions in antisense orientation, in introns and in intergenic regions, in addition to sense insertion at the 5' end of genes

Random insertions of promoterless reporter genes in genomes are a common tool for identifying marker lines with tissue-specific expression patterns. Such lines are assumed to reflect the activity of endogenous promoters and should facilitate the cloning of genes expressed in the corresponding tissues. To identify genes active in seed organs, plant DNA flanking T-DNA insertions (T-DNAs) have been cloned in 16 Arabidopsis thaliana GUS-reporter lines. T-DNAs were found in proximal promoter regions, 5' UTR or intron with GUS in the same (sense) orientation as the tagged gene, but contrary to expectations also in inverted orientation in the 5' end of genes or in intergenic regions. RT-PCR, northern analysis, and data on expression patterns of tagged genes, compared with the expression pattern of the reporter lines, suggest that the expression pattern of a reporter gene will reflect the pattern of a tagged gene when inserted in sense orientation in the 5' UTR or intron. When inserted in the promoter region, the reporter-gene expression patterns may be restricted compared with the endogenous gene. Among the trapped genes, the previously described nitrate transporter gene AtNRT1.1, the cyclophilin gene ROC3, and the histone deacetylase gene AtHD2C were found. Reporter-gene expression when positioned in antisense orientation, for example, in the SLEEPY1 gene, is indicative of antisense expression of the tagged gene. For T-DNAs found in intergenic regions, it is suggested that the reporter gene is transcribed from cryptic promoters or promoters of as yet unannotated genes.

ABI3 mediates expression of the peroxiredoxin antioxidant AtPER1 gene and induction by oxidative stress

The peroxiredoxin antioxidant gene AtPER1 has been considered to be specifically expressed in the embryo and aleurone layer during maturation and desiccation stages of development, and in the mature seed, typically for late embryogenesis-abundant (lea) transcripts. In the abscisic acid-insensitive abi3-1 mutant, the AtPER1 transcript level is strongly reduced, suggesting ABI3 to be a prime regulator of AtPER1. We have studied the expression pattern and regulation of AtPER1 with a series of nine promoter::GUS constructs with deletions and/or mutations in putative regulatory elements. Arabidopsis lines harbouring these constructs revealed AtPER1 promoter activity in the endosperm, especially the chalazal cyst, already when the embryo is in the late globular stage, in the embryo from the late torpedo stage, and in distinct cells of unfertilized and fertilized ovules. Early expression seems to be dependent on a putative antioxidant-responsive promoter element (ARE), while from the bent cotyledon stage endosperm and embryo expression is dependent on an ABA-responsive element (ABRE) likely to bind ABI5. The shortest promoter fragment (113 bp), devoid of ARE, ABRE and without an intact RY/Sph element thought to bind ABI3 did not drive GUS expression. The AtPER1::GUS construct also revealed expression in cotyledons, meristems and stem branching points. In general, seed and vegetative expression coincided with the expression pattern of ABI3. In plants ectopically expressing ABI3, AtPER1::GUS expression was found in true leaves, and AtPER1 could be induced by exogenous ABA and oxidative stress (H2O2 and hydroquinone). ABI3-mediated oxidative stress induction was dependent on the presence of an intact ARE element.

Seed 1-cysteine peroxiredoxin antioxidants are not involved in dormancy, but contribute to inhibition of germination during stress

Peroxiredoxins (Prx) are thiol-dependent antioxidants containing one (1-cysteine [-Cys]) or two (2-Cys) conserved Cys residues that protect lipids, enzymes, and DNA against reactive oxygen species. In plants, the 1-Cys Prxs are highly expressed during late seed development, and the expression pattern is dormancy related in mature seeds. We have expressed the Arabidopsis 1-Cys Prx AtPER1 in Escherichia coli and show that this protein has antioxidant activity in vitro and protects E. coli in vivo against the toxic oxidant cumene hydroperoxide. Although some 1-Cys Prxs are targeted to the nucleus, a green fluorescent protein-AtPER1 fusion protein was also localized to the cytoplasm in an onion epidermis subcellular localization assay. It has been proposed that seed Prxs are involved in maintenance of dormancy and/or protect the embryo and aleurone layer surviving desiccation against damage caused by reactive oxygen species. These hypotheses were tested using transgenic Arabidopsis lines overexpressing the barley (Hordeum vulgare) 1-Cys PER1 protein and lines with reduced levels of AtPER1 due to antisensing or RNA interference. We found no correlation between Prx levels and the duration of the after-ripening period required before germination. Thus, Prxs are unlikely to contribute to maintenance of dormancy. RNA interference lines almost devoid of AtPER1 protein developed and germinated normally under standard growth room conditions. However, seeds from lines overexpressing PER1 were less inclined to germinate than wild-type seeds in the presence of NaCl, mannitol, and methyl viologen, suggesting that Prx can sense harsh environmental surroundings and play a part in the inhibition of germination under unfavorable conditions.

Inflorescence deficient in abscission controls floral organ abscission in Arabidopsis and identifies a novel family of putative ligands in plants

Abscission is an active process that enables plants to shed unwanted organs. Because the purpose of the flower is to facilitate pollination, it often is abscised after fertilization. We have identified an Arabidopsis ethylene-sensitive mutant, inflorescence deficient in abscission (ida), in which floral organs remain attached to the plant body after the shedding of mature seeds, even though a floral abscission zone develops. The IDA gene, positioned in the genomic DNA flanking the single T-DNA present in the ida line, was identified by complementation. The gene encodes a small protein with an N-terminal signal peptide, suggesting that the IDA protein is the ligand of an unknown receptor involved in the developmental control of floral abscission. We have identified Arabidopsis genes, and cDNAs from a variety of plant species, that encode similar proteins, which are distinct from known ligands. IDA and the IDA-like proteins may represent a new class of ligands in plants.

Ten members of the Arabidopsis gene family encoding methyl-CpG-binding domain proteins are transcriptionally active and at least one, AtMBD11, is crucial for normal development

Animal proteins that contain a methyl-CpG-binding domain (MBD) are suggested to provide a link between DNA methylation, chromatin remodelling and gene silencing. However, some MBD proteins reside in chromatin remodelling complexes, but do not have specific affinity for methylated DNA. It has recently been shown that the Arabidopsis genome contains 12 putative genes encoding proteins with domains similar to MBD, of which at least three bind symmetrically methylated DNA. Using a bioinformatics approach, we have identified additional domains in a number of these proteins and, on this basis and extended sequence similarity, divided the proteins into subgroups. Using RT-PCR we show that 10 of the AtMBD genes are active and differentially expressed in diverse tissues. To investigate the biological significance of AtMBD proteins, we have transformed Arabidopsis with a construct aimed at RNA interference with expression of the AtMBD11 gene, normally active in most tissues. The resulting 35S::AtMBD11-RNAi plants displayed a variety of phenotypic effects, including aerial rosettes, serrated leaves, abnormal position of flowers, fertility problems and late flowering. Arabidopsis lines with reduced expression of genes involved in chromatin remodelling and transgene silencing show similar phenotypes. Our results suggest an important role for AtMBD proteins in plant development.

Isolation of GUS marker lines for genes expressed in Arabidopsis endosperm, embryo and maternal tissues

In order to identify marker lines expressing GUS in various endosperm compartments and at different developmental stages, a collection of Arabidopsis thaliana (L.) Heynh. promoter trap lines were screened. The screen identified 16 lines displaying GUS-reporter gene expression in the endosperm, embryo and other seed organs. The distinctive patterns of GUS expression in these lines provide molecular markers for most cell compartments in the endosperm of Arabidopsis seeds at all developmental stages, and represent a valuable research tool for characterizing present and future Arabidopsis seed mutants. GUS expression patterns of these 16 lines are presented here. One line showed chalazal endosperm-specific GUS activity at the heart stage of embryo development. In six lines embryo-specific GUS activity was detected. Six lines exhibited GUS activity predominantly in the endosperm and embryo while two lines showed strong GUS activity in all seed organs. In one line GUS activity was detected in integuments and syncytial endosperm, while the GUS activity at the cotyledonary stage of the embryo was seed coat-specific. In addition, two funiculus markers and two silique markers expressed in the abscission zone and the guard cells are also presented.

Analyses of single-copy Arabidopsis T-DNA-transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing

In genetically transformed plants, transgene silencing has been correlated with multiple and complex insertions of foreign DNA, e.g. T-DNA and vector backbone sequences. Occasionally, single-copy transgenes also suffer transgene silencing. We have compared integration patterns and T-DNA/plant DNA junctions in a collection of 37 single-copy T-DNA-transformed Arabidopsis lines, of which 13 displayed silencing. Vector sequences were found integrated in five lines, but only one of these displayed silencing. Truncated T-DNA copies, positioned in inverse orientation to an intact T-DNA copy, were discovered in three lines. The whole nptII gene with pnos promoter was present in the truncated copy of one such line in which heavy silencing has been observed. In the two other lines no silencing has been observed over five generations. Thus, vector sequences and short additional T-DNA sequences are not sufficient or necessary to induce transgene silencing. DNA methylation of selected restriction endonuclease sites could not be correlated with silencing. Our collection of T-DNA/plant DNA junctions has also been used to evaluate current models of T-DNA integration. Data for some of our lines are compatible with T-DNA integration in double-strand breaks, while for others initial invasion of plant DNA by the left or by the right T-DNA end seem important.

A human CpG island randomly inserted into a plant genome is protected from methylation

In vertebrate genomes the dinucleotide CpG is heavily methylated, except in CpG islands, which are normally unmethylated. It is not clear why the CpG islands are such poor substrates for DNA methyltransferase. Plant genomes display methylation, but otherwise the genomes of plants and animals represent two very divergent evolutionary lines. To gain a further understanding of the resistance of CpG islands to methylation, we introduced a human CpG island from the proteasome-like subunit I gene into the genome of the plant Arabidopsis thaliana. Our results show that prevention of methylation is an intrinsic property of CpG islands, recognized even if a human CpG island is transferred to a plant genome. Two different parts of the human CpG island - the promoter region/ first exon and exon 2-4 - both displayed resistance against methylation, but the promoter/ exon1 construct seemed to be most resistant. In contrast, certain sites in a plant CpG-rich region used as a control transgene were always methylated. The frequency of silencing of the adjacent nptII (KmR) gene in the human CpG constructs was lower than observed for the plant CpG-rich region. These results have implications for understanding DNA methylation, and for construction of vectors that will reduce transgene silencing.