Mutator-like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains

Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation

BACKGROUND

Despite its conserved role on gene expression and transposable element (TE) silencing, genome-wide CG methylation differs substantially between wild Arabidopsis thaliana accessions.

RESULTS

To test our hypothesis that global reduction of CG methylation would reduce epigenomic, transcriptomic, and phenotypic diversity in A. thaliana accessions, we knock out MET1, which is required for CG methylation, in 18 early-flowering accessions. Homozygous met1 mutants in all accessions suffer from common developmental defects such as dwarfism and delayed flowering, in addition to accession-specific abnormalities in rosette leaf architecture, silique morphology, and fertility. Integrated analysis of genome-wide methylation, chromatin accessibility, and transcriptomes confirms that MET1 inactivation greatly reduces CG methylation and alters chromatin accessibility at thousands of loci. While the effects on TE activation are similarly drastic in all accessions, the quantitative effects on non-TE genes vary greatly. The global expression profiles of accessions become considerably more divergent from each other after genome-wide removal of CG methylation, although a few genes with diverse expression profiles across wild-type accessions tend to become more similar in mutants. Most differentially expressed genes do not exhibit altered chromatin accessibility or CG methylation in cis, suggesting that absence of MET1 can have profound indirect effects on gene expression and that these effects vary substantially between accessions.

CONCLUSIONS

Systematic analysis of MET1 requirement in different A. thaliana accessions reveals a dual role for CG methylation: for many genes, CG methylation appears to canalize expression levels, with methylation masking regulatory divergence. However, for a smaller subset of genes, CG methylation increases expression diversity beyond genetically encoded differences.

Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids

MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application of the Mutator system in other organisms. To harness less constrained systems as alternatives, we attempted to clone TED and Jittery, two recently isolated autonomous Mutator-like elements (MULEs) from maize, respectively. Their full-length transcripts and genomic copies are successfully cloned when the incubation time for bacteria to recover from heat shock is extended appropriately prior to plating. However, during their proliferation in E. coli, TED transformed plasmids are unstable, as evidenced by derivatives from which frameshift, deletion mutations, or IS transposon insertions are readily detected. Our results suggest that neither leaky expression of the transposase nor the presence of terminal inverse repeats (TIRs) are responsible for the cloning barriers, which were once ascribed to the presence of the Shine–Dalgarno-like sequence. Instead, the internal sequence of TED (from 1250 to 2845 bp), especially the exons in this region, was the most likely causer. The findings provide novel insights into the property and function of the Mutator superfamily and shed light on the dissection of toxic effects on cloning from MULEs.

Fast co-evolution of anti-silencing systems shapes the invasiveness of Mu-like DNA transposons in eudicots

Transposable elements (TEs) constitute a major threat to genome stability and are therefore typically silenced by epigenetic mechanisms. In response, some TEs have evolved counteracting systems to suppress epigenetic silencing. In the model plant Arabidopsis thaliana, two such anti-silencing systems have been identified and found to be mediated by the VANC DNA-binding proteins encoded by VANDAL transposons. Here, we show that anti-silencing systems have rapidly diversified since their origin in eudicots by gaining and losing VANC-containing domains, such as DUF1985, DUF287, and Ulp1, as well as target sequence motifs. We further demonstrate that these motifs determine anti-silencing specificity by sequence, density, and helical periodicity. Moreover, such rapid diversification yielded at least 10 distinct VANC-induced anti-silencing systems in Arabidopsis. Strikingly, anti-silencing of non-autonomous VANDALs, which can act as reservoirs of 24-nt small RNAs, is critical to prevent the demise of cognate autonomous TEs and to ensure their propagation. Our findings illustrate how complex co-evolutionary dynamics between TEs and host suppression pathways have shaped the emergence of new epigenetic control mechanisms.

The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato

Cucurbit downy mildew (DM), caused by the obligate biotroph Pseudoperonospora cubensis, is a destructive disease in cucumber. A valuable source of DM resistance is the Indian cucumber accession PI 197088, which harbours several quantitative trait loci (QTLs) contributing to quantitatively inherited DM resistance. With a combination of fine-mapping and transcriptomics, we identified Amino Acid Permease 2A (CsAAP2A) as a candidate gene for QTL DM4.1.3. Whole-genome and Sanger sequencing revealed the insertion of a Cucumis Mu-like element (CUMULE) transposon in the allele of the resistant near-isogenic line DM4.1.3. To confirm whether loss of CsAAP2A contributes to partial DM resistance, we performed targeting induced local lesions in genomes on a DM-susceptible cucumber genotype to identify an additional csaap2a mutant, which indeed was partially DM resistant. In view of the loss of the putative function as amino acid transporter, we measured amino acids in leaves. We found that DM-inoculated leaves of line DM4.1.3 (with the csaap2a mutation) contained significantly fewer amino acids than wild-type cucumber. The decreased flow of amino acids towards infected leaves in csaap2a plants compared to the wild type might explain the resistant phenotype of the mutant, as this would limit the available nutrients for the pathogen and thereby its fitness. To examine whether AAP genes play a conserved role as susceptibility factors in plant-oomycete interactions, we made targeted mutations in two AAP genes from tomato and studied the effect on susceptibility to Phytophthora infestans. We conclude that not only CsAAP2A but also SlAAP5A/SlAAP5B are susceptibility genes for oomycete pathogens.

CsMYB60 is a key regulator of flavonols and proanthocyanidans that determine the colour of fruit spines in cucumber

Spine colour is an important fruit quality trait that influences the commercial value of cucumber (Cucumis sativus). However, little is known about the metabolites and the regulatory mechanisms of their biosynthesis in black spine varieties. In this study, we determined that the pigments of black spines are flavonoids, including flavonols and proanthocyanidins (PAs). We identified CsMYB60 as the best candidate for the previously identified B (Black spine) locus. Expression levels of CsMYB60 and the key genes involved in flavonoid biosynthesis were higher in black-spine inbred lines than that in white-spine lines at different developmental stages. The insertion of a Mutator-like element (CsMULE) in the second intron of CsMYB60 decreased its expression in a white-spine line. Transient overexpression assays indicated that CsMYB60 is a key regulatory gene and Cs4CL is a key structural gene in the pigmentation of black spines. In addition, the DNA methylation level in the CsMYB60 promoter was much lower in the black-spine line compared with white-spine line. The CsMULE insert may decrease the expression level of CsMYB60, causing hindered synthesis of flavonols and PAs in cucumber fruit spines.

Rpp1 Encodes a ULP1-NBS-LRR Protein That Controls Immunity to Phakopsora pachyrhizi in Soybean

Phakopsora pachyrhizi is the causal agent of Asian soybean rust. Susceptible soybean plants infected by virulent isolates of P. pachyrhizi are characterized by tan-colored lesions and erumpent uredinia on the leaf surface. Germplasm screening and genetic analyses have led to the identification of seven loci, Rpp1 to Rpp7, that provide varying degrees of resistance to P. pachyrhizi (Rpp). Two genes, Rpp1 and Rpp1b, map to the same region on soybean chromosome 18. Rpp1 is unique among the Rpp genes in that it confers an immune response (IR) to avirulent P. pachyrhizi isolates. The IR is characterized by a lack of visible symptoms, whereas resistance provided by Rpp1b to Rpp7 results in red-brown foliar lesions. Rpp1 maps to a region spanning approximately 150 kb on chromosome 18 between markers Sct_187 and Sat_064 in L85-2378 (Rpp1), an isoline developed from Williams 82 and PI 200492 (Rpp1). To identify Rpp1, we constructed a bacterial artificial chromosome library from soybean accession PI 200492. Sequencing of the Rpp1 locus identified three homologous nucleotide binding site-leucine rich repeat (NBS-LRR) candidate resistance genes between Sct_187 and Sat_064. Each candidate gene is also predicted to encode an N-terminal ubiquitin-like protease 1 (ULP1) domain. Cosilencing of the Rpp1 candidates abrogated the immune response in the Rpp1 resistant soybean accession PI 200492, indicating that Rpp1 is a ULP1-NBS-LRR protein and plays a key role in the IR.

Histone modifications at the grapevine VvOMT3 locus, which encodes an enzyme responsible for methoxypyrazine production in the berry

Some herbaceous characters in wine are attributed to the presence of aroma compounds collectively known as methoxypyrazines (MPs). In grape berries their formation has been hypothesised to start from a reaction of two amino acids or an amino acid and an unknown 1,2-dicarbonyl compound, leading to the formation of hydroxypyrazine, which is then enzymatically methylated to form a MP. The enzyme responsible of the formation of 3-isobutyl-2-methoxypyrazine has been recently identified as VvOMT3 whose regulation is still not understood. The concentration of MPs in grapes is known to be influenced by development, environmental stimuli and most importantly grape variety. In order to investigate the chromatin arrangement of that region a chromatin immunoprecipitation analysis has been performed and putative differences in epigenetic regulation of VvOMT3 spatially between the skin and flesh tissues and also temporally during fruit development have been detected. There are also allelic differences in VvOMT3 histone modifications which are maintained in subsequent generations. This study provides evidence of histone tail modification of the VvOMT3 locus in grapevine, which may play a role in the spatial and developmental regulation of the expression of this gene.

Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes

BACKGROUND

Cucurbitaceae species contain a significantly lower number of genes coding for proteins with similarity to plant resistance genes belonging to the NBS-LRR family than other plant species of similar genome size. A large proportion of these genes are organized in clusters that appear to be hotspots of variability. The genomes of the Cucurbitaceae species measured until now are intermediate in size (between 350 and 450 Mb) and they apparently have not undergone any genome duplications beside those at the origin of eudicots. The cluster containing the largest number of NBS-LRR genes has previously been analyzed in melon and related species and showed a high degree of interspecific and intraspecific variability. It was of interest to study whether similar behavior occurred in other cluster of the same family of genes.

RESULTS

The cluster of NBS-LRR genes located in melon chromosome 9 was analyzed and compared with the syntenic regions in other cucurbit genomes. This is the second cluster in number within this species and it contains nine sequences with a NBS-LRR annotation including two genes, Fom1 and Prv, providing resistance against Fusarium and Ppapaya ring-spot virus (PRSV). The variability within the melon species appears to consist essentially of single nucleotide polymorphisms. Clusters of similar genes are present in the syntenic regions of the two species of Cucurbitaceae that were sequenced, cucumber and watermelon. Most of the genes in the syntenic clusters can be aligned between species and a hypothesis of generation of the cluster is proposed. The number of genes in the watermelon cluster is similar to that in melon while a higher number of genes (12) is present in cucumber, a species with a smaller genome than melon. After comparing genome resequencing data of 115 cucumber varieties, deletion of a group of genes is observed in a group of varieties of Indian origin.

CONCLUSIONS

Clusters of genes coding for NBS-LRR proteins in cucurbits appear to have specific variability in different regions of the genome and between different species. This observation is in favour of considering that the adaptation of plant species to changing environments is based upon the variability that may occur at any location in the genome and that has been produced by specific mechanisms of sequence variation acting on plant genomes. This information could be useful both to understand the evolution of species and for plant breeding.

Phylogenetic and Genomic Analyses Resolve the Origin of Important Plant Genes Derived from Transposable Elements

Once perceived as merely selfish, transposable elements (TEs) are now recognized as potent agents of adaptation. One way TEs contribute to evolution is through TE exaptation, a process whereby TEs, which persist by replicating in the genome, transform into novel host genes, which persist by conferring phenotypic benefits. Known exapted TEs (ETEs) contribute diverse and vital functions, and may facilitate punctuated equilibrium, yet little is known about this process. To better understand TE exaptation, we designed an approach to resolve the phylogenetic context and timing of exaptation events and subsequent patterns of ETE diversification. Starting with known ETEs, we search in diverse genomes for basal ETEs and closely related TEs, carefully curate the numerous candidate sequences, and infer detailed phylogenies. To distinguish TEs from ETEs, we also weigh several key genomic characteristics including repetitiveness, terminal repeats, pseudogenic features, and conserved domains. Applying this approach to the well-characterized plant ETEs MUG and FHY3, we show that each group is paraphyletic and we argue that this pattern demonstrates that each originated in not one but multiple exaptation events. These exaptations and subsequent ETE diversification occurred throughout angiosperm evolution including the crown group expansion, the angiosperm radiation, and the primitive evolution of angiosperms. In addition, we detect evidence of several putative novel ETE families. Our findings support the hypothesis that TE exaptation generates novel genes more frequently than is currently thought, often coinciding with key periods of evolution.

Mutator and MULE Transposons

The Mutator system of transposable elements (TEs) is a highly mutagenic family of transposons in maize. Because they transpose at high rates and target genic regions, these transposons can rapidly generate large numbers of new mutants, which has made the Mutator system a favored tool for both forward and reverse mutagenesis in maize. Low copy number versions of this system have also proved to be excellent models for understanding the regulation and behavior of Class II transposons in plants. Notably, the availability of a naturally occurring locus that can heritably silence autonomous Mutator elements has provided insights into the means by which otherwise active transposons are recognized and silenced. This chapter will provide a review of the biology, regulation, evolution and uses of this remarkable transposon system, with an emphasis on recent developments in our understanding of the ways in which this TE system is recognized and epigenetically silenced as well as recent evidence that Mu-like elements (MULEs) have had a significant impact on the evolution of plant genomes.

What makes up plant genomes: The vanishing line between transposable elements and genes

The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.

Computational methods for identification of DNA transposons

The initial identification of transposable elements (TEs) was attributed to the activity of DNA transposable elements, which are prevalent in plants. Unlike RNA elements, which accumulate in the gene-poor heterochromatic regions, most DNA elements are located in the gene rich regions and many of them carry genes or gene fragments. As such, DNA elements have a more intimate relationship with genes and may have an immediate impact on gene expression and gene function. DNA elements are structurally distinct from RNA elements and most of them have terminal inverted repeats (TIRs). Such structural features have been used to identify the relevant elements from genomic sequences. Among the DNA elements in plants, the most abundant type is the miniature inverted repeat transposable elements (MITEs). This chapter discusses the methods to identify MITEs, Helitrons, and other DNA transposable elements.

Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts

Over the past several years, there has been an explosion in our understanding of the mechanisms by which plant transposable elements (TEs) are epigenetically silenced and maintained in an inactive state over long periods of time. This highly efficient process results in vast numbers of inactive TEs; indeed, the majority of many plant genomes are composed of these quiescent elements. This observation has led to the rather static view that TEs represent an essentially inert portion of plant genomes. However, recent work has demonstrated that TE silencing is a highly dynamic process that often involves transcription of TEs at particular times and places during plant development. Plants appear to use transcripts from silenced TEs as an ongoing source of information concerning the mobile portion of the genome. In contrast to our understanding of silencing pathways, we know relatively little about the ways in which TEs evade silencing. However, vast differences in TE content between even closely related plant species suggest that they are often wildly successful at doing so. Here, we discuss TE activity in plants as the result of a constantly shifting balance between host strategies for TE silencing and TE strategies for escape and amplification.

Phantom, a new subclass of Mutator DNA transposons found in insect viruses and widely distributed in animals

Transposons of the Mutator (Mu) superfamily have been shown to play a critical role in the evolution of plant genomes. However, the identification of Mutator transposons in other eukaryotes has been quite limited. Here we describe a previously uncharacterized group of DNA transposons designated Phantom identified in the genomes of a wide range of eukaryotic taxa, including many animals, and provide evidence for its inclusion within the Mutator superfamily. Interestingly three Phantom proteins were also identified in two insect viruses and phylogenetic analysis suggests horizontal movement from insect to virus, providing a new line of evidence for the role of viruses in the horizontal transfer of DNA transposons in animals. Many of the Phantom transposases are predicted to harbor a FLYWCH domain in the amino terminus, which displays a WRKY-GCM1 fold characteristic of the DNA binding domain (DBD) of Mutator transposases and of several transcription factors. While some Phantom elements have terminal inverted repeats similar in length and structure to Mutator elements, some display subterminal inverted repeats (sub-TIRs) and others have more complex termini reminiscent of so-called Foldback (FB) transposons. The structural plasticity of Phantom and the distant relationship of its encoded protein to known transposases may have impeded the discovery of this group of transposons and it suggests that structure in itself is not a reliable character for transposon classification.

GIN transposons: genetic elements linking retrotransposons and genes

In a previous work, we characterized a gene, called Gypsy Integrase 1 (GIN1), which encodes a protein very similar to the integrase domains present in Gypsy/Ty3 retrotransposons. I describe here a paralog of GIN1 and GIN2 and show that both genes are present in multiple vertebrates and that a likely homolog is found in urochordates. Surprisingly, phylogenetic and structural analyses support the counterintuitive idea that the GIN genes did not directly derive from retrotransposons but from a novel type of animal-specific DNA transposons, the GIN elements. These elements, described for the first time in this study, are characterized by containing a gene that encodes a protein that is also very similar to Gypsy/Ty3 integrases. It turns out that the sequences of the integrases encoded by GIN1 and GIN2 are more similar to those found in GIN elements than to those detected in retrotransposons. Moreover, several introns are in the same positions in the integrase-encoding genes of some GIN elements, GIN1 and GIN2. The simplest explanation for these results is that GIN elements appeared early in animal evolution by co-option of the integrase of a retrotransposon, they later expanded in multiple animal lineages, and, eventually, gave rise to the GIN genes. In summary, GIN transposons may be the "missing link" that explain how GIN genes evolved from retrotransposons. GIN1 and GIN2 may have contributed to control the expansion of GIN elements and Gypsy/Ty3 retrotransposons in chordates.

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

Background

In eukaryotes, long terminal repeat (LTR) retrotransposons such as Copia, BEL and Gypsy integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The Gypsy INT-like transposase is also conserved in the Polinton/Maverick self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as TDD-4 and TDD-5. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS3, IS481, IS30 and IS630 families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons.

Results

A new diverse eukaryotic superfamily of DNA transposons, named Ginger (for 'Gypsy INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS3 and IS481 bacterial transposons, the Ginger termini resemble those of the Gypsy LTR retrotransposons. Currently, Ginger transposons can be divided into two distinct groups named Ginger1 and Ginger2/Tdd. Elements from the Ginger1 group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The Ginger1-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire Gypsy-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of Gypsy and endogenous retrovirus (ERV) integrases. Ginger1 transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the Gypsy integrases, apparently have evolved from the Ginger1 transposase genes. We also introduce a second Ginger group, designated Ginger2/Tdd, which includes the previously reported DNA transposon TDD-4.

Conclusions

The Ginger superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons. Ginger elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.

Molecular characterization of the Arginine decarboxylase gene family in rice

Arginine decarboxylase (ADC) is a key enzyme in plants that converts arginine into putrescine, an important mediator of abiotic stress tolerance. Adc genes have been isolated from a number of dicotyledonous plants but the oat and rice Adc genes are the only representatives of monocotyledonous species described thus far. Rice has a small family of Adc genes, and OsAdc1 expression has been shown to fluctuate under drought and chilling stress. We identified and characterized a second rice Adc gene (OsAdc2) which encodes a 629-amino-acid protein with a predicted molecular mass of 67 kDa. An unusual feature of the OsAdc2 gene is the presence of an intron and a short upstream open reading frame in the 5'-UTR. Sequence comparisons showed that OsAdc2 is more closely related to the oat Adc gene than to OsAdc1 or to its dicot homologs, and mRNA analysis showed that the two rice genes are also differently regulated. Whereas OsAdc1 is expressed in leaf, root and stem, OsAdc2 expression is restricted to stem tissue. Protein expression was investigated with specific antibodies against ADC1 and ADC2, corroborating the mRNA data. We discuss the expression profiles of OsAdc1 and OsAdc2 and potential functions for the two corresponding proteins.

Genome-wide analysis of the "cut-and-paste" transposons of grapevine

Background

The grapevine is a widely cultivated crop and a high number of different varieties have been selected since its domestication in the Neolithic period. Although sexual crossing has been a major driver of grapevine evolution, its vegetative propagation enhanced the impact of somatic mutations and has been important for grapevine diversity. Transposable elements are known to be major contributors to genome variability and, in particular, to somatic mutations. Thus, transposable elements have probably played a major role in grapevine domestication and evolution. The recent publication of the complete grapevine genome opens the possibility for an in deep analysis of its transposon content.

Principal Findings

We present here a detailed analysis of the “cut-and-paste” class II transposons present in the genome of grapevine. We characterized 1160 potentially complete grapevine transposons as well as 2086 defective copies. We report on the structure of each element, their potentiality to encode a functional transposase, and the existence of matching ESTs that could suggest their transcription.

Conclusions

Our results show that these elements have transduplicated and amplified cellular sequences and some of them have been domesticated and probably fulfill cellular functions. In addition, we provide evidences that the mobility of these elements has contributed to the genomic variability of this species.

Give-and-take: interactions between DNA transposons and their host plant genomes

Recent genome sequencing efforts have revealed how extensively transposable elements (TEs) have contributed to the shaping of present day plant genomes. DNA transposons associate preferentially with the euchromatic or genic component of plant genomes and have had the opportunity to interact intimately with the genes of the plant host. These interactions have resulted in TEs acquiring host sequences, forming chimeric genes through exon shuffling, replacing regulatory sequences, mobilizing genes around the genome, and contributing genes to the host. The close interaction of transposons with genes has also led to the evolution of intricate cellular mechanisms for silencing transposon activity. Transposons have thus become important subjects of study in understanding epigenetic regulation and, in cases where transposons have amplified to high numbers, how to escape that regulation.