Nezha, a novel active miniature inverted-repeat transposable element in cyanobacteria

Miniature inverted-repeat transposable elements (MITEs) were first identified in plants and exerted extensive proliferations throughout eukaryotic and archaeal genomes. But very few MITEs have been characterized in bacteria. We identified a novel MITE, called Nezha, in cyanobacteria Anabaena variabilis ATCC 29413 and Nostoc sp. PCC 7120. Nezha, like most previously known MITEs in other organisms, is small in size, non-coding, carrying TIR and DR signals, and of potential to form a stable RNA secondary structure, and it tends to insert into A+T-rich regions. Recent transpositions of Nezha were observed in A. variabilis ATCC 29413 and Nostoc sp. PCC 7120, respectively. Nezha might have proliferated recently with aid from the transposase encoded by ISNpu3-like elements. A possible horizontal transfer event of Nezha from cyanobacteria to Polaromonas JS666 is also observed.     

MiteFinderII: a novel tool to identify miniature inverted-repeat transposable elements hidden in eukaryotic genomes

Background

Miniature inverted-repeat transposable element (MITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. There is an urgent need to develop bioinformatics tools to effectively identify MITEs on a whole genome-wide scale. However, most of currently existing tools suffer from low ability to deal with large eukaryotic genomes.

Methods

In this paper, we proposed a novel tool MiteFinderII, which was adapted from our previous algorithm MiteFinder, to efficiently detect MITEs from genomics sequences. It has six major steps: (1) build K-mer Index and search for inverted repeats; (2) filtration of inverted repeats with low complexity; (3) merger of inverted repeats; (4) filtration of candidates with low score; (5) selection of final MITE sequences; (6) selection of representative sequences.

Results

To test the performance, MiteFinderII and three other existing algorithms were applied to identify MITEs on the whole genome of oryza sativa. Results suggest that MiteFinderII outperforms existing popular tools in terms of both specificity and recall. Additionally, it is much faster and more memory-efficient than other tools in the detection.

Conclusion

MiteFinderII is an accurate and effective tool to detect MITEs hidden in eukaryotic genomes. The source code is freely accessible at the website: https://github.com/screamer/miteFinder.

     

植物中活性MITEs转座子研究进展

MITEs(Miniature inverted-repeat transposable elements)转座子是一种特殊的转座子,其既有DNA转座子的转座特性——"剪切-粘贴"转座方式,又有RNA转座子的高拷贝特性。目前已被报道的MITEs种类和数量虽然很多,但是关于有转座活性的MITEs的报道却甚少。本文总结了近几年来有关活性MITEs的相关报道,发现具有转座活性的MITEs种类大都分布在Tourist家族,分别是m Ping、m Ging、Ph Tourist1、Tmi1和Ph Tst-3,另外还有Stowaway-like家族的d Tstu1和MITE-39以及Mutator家族的Ah MITE1。文中还分析了这些活性MITEs的结构(TIR和TSD)、拷贝数、进化模式以及转座特性等,为鉴定其他活性MITEs以及MITEs转座和扩增机制的研究奠定了基础。     

Transposition of a fungal miniature inverted-repeat transposable element through the action of a Tc1-like transposase

The mimp1 element previously identified in the ascomycete fungus Fusarium oxysporum has hallmarks of miniature inverted-repeat transposable elements (MITEs): short size, terminal inverted repeats (TIRs), structural homogeneity, and a stable secondary structure. Since mimp1 has no coding capacity, its mobilization requires a transposase-encoding element. On the basis of the similarity of TIRs and target-site preference with the autonomous Tc1-like element impala, together with a correlated distribution of both elements among the Fusarium genus, we investigated the ability of mimp1 to jump upon expression of the impala transposase provided in trans. Under these conditions, we present evidence that mimp1 transposes by a cut-and-paste mechanism into TA dinucleotides, which are duplicated upon insertion. Our results also show that mimp1 reinserts very frequently in genic regions for at least one-third of the cases. We also show that the mimp1/impala double-component system is fully functional in the heterologous species F. graminearum, allowing the development of a highly efficient tool for gene tagging in filamentous fungi.     

Spring: a novel family of miniature inverted-repeat transposable elements is associated with genes in apple

The apple, Malusxdomestica Borkh., belongs to the family Rosaceae and subfamily Maloideae and has a genome size of approximately 750 Mb. In this study, a novel family of transposable elements, designated Spring, has been identified in the apple genome. The four Spring elements, Spring-1 to Spring-4, share all the classic features of miniature inverted-repeat transposable elements (MITEs), including small size (approximately 148 bp), no coding potential, A/T richness, insertion bias toward noncoding regions, terminal inverted repeats (TIRs), target site duplications, and potential for forming secondary structures. Evidence of previous mobility of Spring-4 is demonstrated by sequence alignment of genes encoding 1-aminocyclopropane-1-carboxylic acid synthase from both apple and a related member of the Maloideae subfamily, pear. The Spring elements are flanked by either 8- or 9-bp direct repeats, and they differ significantly in size compared to other previously reported MITEs in plants. The TIRs of these Spring elements are not found in any other previously reported plant genes or transposons, except for apple. The possible role of Spring elements in the apple genome is discussed.     

Identification and characterisation of five novel miniature inverted-repeat transposable elements (MITEs) in amphioxus (Branchiostoma floridae)

As the sister group to vertebrates, amphioxus is consistently used as a model of genome evolution for understanding the invertebrate/vertebrate transition. The amphioxus genome has not undergone massive duplications like those in the vertebrates or disruptive rearrangements like in the genome of Ciona, a urochordate, making it an ideal evolutionary model. Transposable elements have been linked to many genomic evolutionary changes including increased genome size, modified gene expression, massive gene rearrangements, and possibly intron evolution. Despite their importance in genome evolution, few previous examples of transposable elements have been identified in amphioxus. We report five novel Miniature Inverted-repeat Transposable Elements (MITEs) identified by an analysis of amphioxus DNA sequence, which we have named LanceleTn-1, LanceleTn-2, LanceleTn-3a, LanceleTn-3b and LanceleTn-4. Several of the LanceleTn elements were identified in the amphioxus ParaHox cluster, and we suggest these have had important implications for the evolution of this highly conserved gene cluster. The estimated high copy numbers of these elements implies that MITEs are probably the most abundant type of mobile element in amphioxus, and are thus likely to have been of fundamental importance in shaping the evolution of the amphioxus genome.     

A recently active miniature inverted-repeat transposable element, Chunjie, inserted into an operon without disturbing the operon structure in Geobacter uraniireducens Rf4

Miniature inverted-repeat transposable elements (MITEs) are short DNA transposons with terminal inverted repeat (TIR) signals and have been extensively studied in plants and other eukaryotes. But little is known about them in eubacteria. We identified a novel and recently active MITE, Chunjie, when studying the recent duplication of an operon consisting of ABC transporters and a phosphate uptake regulator in the chromosome of Geobacter uraniireducens Rf4. Chunjie resembles the other known MITEs in many aspects, e.g., having TIR signals and direct repeats, small in size, noncoding, able to fold into a stable secondary structure, and typically inserted into A + T-rich regions. At least one case of recent transposition was observed, i.e., the insertion of Chunjie into one copy of the aforementioned operon. As far as we know, this is the first report that the insertion of a MITE does not disrupt the operon structure.     

A single-base deletion in soybean flavonol synthase gene is associated with magenta flower color

The Wm locus of soybean [Glycine max (L.) Merr.] controls flower color. Dominant Wm and recessive wm allele of the locus produce purple and magenta flower, respectively. A putative full-length cDNA of flavonol synthase (FLS), gmfls1 was isolated by 5′ RACE and end-to-end PCR from a cultivar Harosoy with purple flower (WmWm). Sequence analysis revealed that gmfls1 consisted of 1,208 nucleotides encoding 334 amino acids. It had 59–72% homology with FLS proteins of other plant species. Conserved dioxygenase domains A and B were found in the deduced polypeptide. Sequence comparison between Harosoy and Harosoy-wm (magenta flower mutant of Harosoy; wmwm) revealed that they differed by a single G deletion in the coding region of Harosoy-wm. The deletion changed the subsequent reading frame resulting in a truncated polypeptide consisting of 37 amino acids that lacked the dioxygenase domains A and B. Extracts of E. coli cells expressing gmfls1 of Harosoy catalyzed the formation of quercetin from dihydroquercetin, whereas cell extracts expressing gmfls1 of Harosoy-wm had no FLS activity. Genomic Southern analysis suggested the existence of three to four copies of the FLS gene in the soybean genome. CAPS analysis was performed to detect the single-base deletion. Harosoy and Clark (WmWm) exhibited longer fragments, while Harosoy-wm had shorter fragments due to the single-base deletion. The CAPS marker co-segregated with genotypes at Wm locus in a F₂ population segregating for the locus. Linkage mapping using SSR markers revealed that the Wm and gmfls1 were mapped at similar position in the molecular linkage group F. The above results strongly suggest that gmfls1 represents the Wm gene and that the single-base deletion may be responsible for magenta flower color.

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A tiger mouse and relatives. Variants caused by an activated transposable element?

In a laboratory-bred population of wild Peruvian house mice, one male had an excessive rate of non-pairing of the X and Y chromosomes. After crossing him with laboratory stock mice, a mouse of very unusual phenotype appeared from a yellow (AyA) mother. He was yellow with black dorsal stripes; hence Tiger. He was mated to many females, and inbred F2 and F3 generations were raised. There were no more tiger phenotypes, but his F1 contained an excess of black-and-tans over yellows, showing him to be a gonosomic mosaic Ayat/atat; the homozygous cell line probably arose from the heterozygous one. The mitotic karyotype was normal. Some of Tiger's mates were of known allozyme types and their progeny were scored. The allozyme segregations were normal, except at the Es-3 locus (esterase-3), for which Tiger was typed as homozygous. Several unusual events among Tiger's close relatives included a mutation to an unstable pattern mutant, three probable translocations, and several cases of somatic defect. All unusual mice derived from Tiger's yellow mother, whose genome was one-quarter Peruvian. Yellow is associated with an ecotropic murine leukemia virus. The Peru genome is characterized by a high occurrence of mutation and aberrant karyotypes. It is suggested that something from the Peru genome in Tiger's mother caused instability of the DNA sequence associated with yellow, with related disturbance at different locations thereafter. The nature of this instability, and of the Peru genome, is discussed.     

Eye color pigment granules in Drosophila mauritiana: mosaics produced by excision of a transposable element

Compound eyes of the white-peach (wpch) mutant strain of Drosophila mauritiana have some pigment and receptor cells with wild-type eye color pigmentation. These eyes are mosaic, because excision of a transposable element reverts wpch to wild type during the development of somatic cells. Wild-type patches have three types of pigment granule residing in three respective cell types: primary pigment cells, secondary pigment cells, and retinula (visual receptor) cells. Most aspects of these granules, as well as all other aspects of compound eye ultrastructure, are exactly as in the better studied sibling species D. melanogaster. In the wpch parts of the eye, small and giant unpigmented "pigment granules" reside in secondary pigment cells. These white granules are just like the corresponding granules of w mutant D. melanogaster. Small vs. large patches of pigmented cells likely represent excision events occurring late vs. early respectively during development. Mosaics of eye color markers have been important in developmental analyses; the ease of constructing mosaics of D. mauritiana gives this preparation advantages for mosaic analyses.     

A novel single-base deletion mutation of the RUNX2 gene in a Chinese family with cleidocranial dysplasia

We identified a disease-causing mutation of the RUNX2 gene in a four-generation Chinese family affected with cleidocranial dysplasia (CCD). For mutation analysis, the coding region of RUNX2 was sequenced with DNA from two patients and three unaffected family members. The RUNX2 mutation was investigated in 50 normal controls by denaturing high pressure liquid chromatography. A heterozygous single-base deletion (c.549delC) of RUNX2, which predicts a termination site at the 185th codon and leads to a stop in the runt domain of RUNX2 protein, was detected in both patients but not in the three unaffected members of the family. This mutation was also not found in 50 controls and has not been reported previously. We demonstrated that a novel mutation (c.549delC) of RUNX2 is associated with CCD in a Chinese family, adding to the repertoire of RUNX2 mutations related to CCD.     

A moso bamboo (<Emphasis Type="Italic">Phyllostachys edulis</Emphasis>) miniature inverted-repeat transposable element (MITE): the possible role of a suppressor

Transposable elements (transposons) are fragments of DNA sequences which can move within host genome. Miniature inverted-repeat transposable elements (MITEs) are widespread and high-copy transposable elements in eukaryotic genomes. Tourist-like MITEs are especially abundant in plant kingdom. Earlier genome-wide analysis has shown that MITEs are widely distributed in the moso bamboo genome and preferentially inserted into gene regions. In the present study, in order to examine the potential influence of MITEs on the moso bamboo gene expressions, a highly conserved Tourist-like MITE family, which distributed near genes, was selected as research focus and named PhTst-3 (Phyllostachys edulis Tourist-like element 3). The MITEs’ insertion sites were tested in moso bamboo half-sib seedlings by real-time fluorescence quantitative PCR. Amplification polymorphisms were found in a copy of PhTst-3 (PhTst-3-55) which was located in the intron of PH01002699G0010. This inserted PhTst-3-55 had a significant impact on the gene expression revealed by the real-time fluorescence quantitative PCR. The gene expression levels were four times higher in the absence of PhTst-3-55 than those in the presence of it. This finding suggests that the PhTst-3 located in the intron is involved in the regulation of the gene. In order to examine the impact of PhTst-3-55 on the near genes, the PhTst-3-55 was inserted into a promoter analysis vector, pxk7S2D, between the two promoter sequences. The Agrobacterium-mediated transient expression showed that PhTst-3-55 insertion decreases the expression level of upstream GUS gene and downstream GFP gene. So, PhTst-3-55 can have a silencing role by bidirectionally inhibiting gene expression.     

Melanoma loss-of-function mutants in Xiphophorus caused by Xmrk-oncogene deletion and gene disruption by a transposable element.

The overexpression of the Xmrk oncogene (ONC-Xmrk) in pigment cells of certain Xiphophorus hybrids has been found to be the primary change that results in the formation of malignant melanoma. Spontaneous mutant stocks have been isolated that have lost the ability to induce tumor formation when crossed with Xiphophorus helleri. Two of these loss-of-function mutants were analyzed for genetic defects in ONC-Xmrk's. In the lof-1 mutant a novel transposable element, TX-1, has jumped into ONC-Xmrk, leading to a disruption of the gene and a truncated protein product lacking the carboxyterminal domain of the receptor tyrosine kinase. TX-1 is obviously an active LTR-containing retrotransposon in Xiphophorus that was not found in other fish species outside the family Poeciliidae. Surprisingly, it does not encode any protein, suggesting the existence of a helper function for this retroelement. In the lof-2 mutant the entire ONC-Xmrk gene was found to be deleted. These data show that ONC-Xmrk is indeed the tumor-inducing gene of Xiphophorus and thus the critical constituent of the tumor (Tu) locus.     

A novel nemaline myopathy in the Amish caused by a mutation in troponin T1

The nemaline myopathies are characterized by weakness and eosinophilic, rodlike (nemaline) inclusions in muscle fibers. Amish nemaline myopathy is a form of nemaline myopathy common among the Old Order Amish. In the first months of life, affected infants have tremors with hypotonia and mild contractures of the shoulders and hips. Progressive worsening of the proximal contractures, weakness, and a pectus carinatum deformity develop before the children die of respiratory insufficiency, usually in the second year. The disorder has an incidence of approximately 1 in 500 among the Amish, and it is inherited in an autosomal recessive pattern. Using a genealogy database, automated pedigree software, and linkage analysis of DNA samples from four sibships, we identified an approximately 2-cM interval on chromosome 19q13.4 that was homozygous in all affected individuals. The gene for the sarcomeric thin-filament protein, slow skeletal muscle troponin T (TNNT1), maps to this interval and was sequenced. We identified a stop codon in exon 11, predicted to truncate the protein at amino acid 179, which segregates with the disease. We conclude that Amish nemaline myopathy is a distinct, heritable, myopathic disorder caused by a mutation in TNNT1.     

Molecular and evolutionary analysis of two divergent subfamilies of a novel miniature inverted repeat transposable element in the yellow fever mosquito, Aedes aegypti

A novel family of miniature inverted repeat transposable elements (MITEs) named Pony was discovered in the yellow fever mosquito, Aedes aegypti. It has all the characteristics of MITEs, including terminal inverted repeats, no coding potential, A+T richness, small size, and the potential to form stable secondary structures. Past mobility of PONY: was indicated by the identification of two Pony insertions which resulted in the duplication of the TA dinucleotide targets. Two highly divergent subfamilies, A and B, were identified in A. aegypti based on sequence comparison and phylogenetic analysis of 38 elements. These subfamilies showed less than 62% sequence similarity. However, within each subfamily, most elements were highly conserved, and multiple subgroups could be identified, indicating recent amplifications from different source genes. Different scenarios are presented to explain the evolutionary history of these subfamilies. Both subfamilies share conserved terminal inverted repeats similar to those of the Tc2 DNA transposons in Caenorhabditis elegans, indicating that Pony may have been borrowing the transposition machinery from a Tc2-like transposon in mosquitoes. In addition to the terminal inverted repeats, full-length and partial subterminal repeats of a sequence motif TTGATTCAWATTCCGRACA represent the majority of the conservation between the two subfamilies, indicating that they may be important structural and/or functional components of the Pony elements. In contrast to known autonomous DNA transposons, both subfamilies of PONY: are highly reiterated in the A. aegypti genome (8,400 and 9, 900 copies, respectively). Together, they constitute approximately 1. 1% of the entire genome. Pony elements were frequently found near other transposable elements or in the noncoding regions of genes. The relative abundance of MITEs varies in eukaryotic genomes, which may have in part contributed to the different organizations of the genomes and reflect different types of interactions between the hosts and these widespread transposable elements.     

A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies

To reveal the genome-wide aspects of Xenopus T2 family miniature inverted-repeat transposable elements (MITEs), we performed a systematic search and classification of MITEs by a newly developed procedure. A terminal sequence motif (T2-motif: TTAAAGGRR) was retrieved from the Xenopus tropicalis genome database. We then selected 51- to 1,000-bp MITE candidates framed by an inverted pair of 2 T2-motifs. The 34,398 candidates were classified into possible clusters by a novel terminal sequence (TS)-clustering method on the basis of differences in their short terminal sequences. Finally, 19,242 MITEs were classified into 16 major MITE subfamilies (TS subfamilies), 10 of which showed apparent homologies to known T2 MITE subfamilies, and the rest were novel TS subfamilies. Intra- and inter-subfamily similarities or differences were investigated by analyses of diversity in GC content, total length, and sequence alignments. Furthermore, genome-wide conservation of the inverted pair structure of subfamily-specific TS stretches and their target site sequence (TTAA) were analyzed. The results suggested that some TS subfamilies might include active or at least recently active MITEs for transposition and/or amplification, but some others might have lost such activities a long time ago. The present methodology was efficient in identifying and classifying MITEs, thereby providing information on the evolutionary dynamics of MITEs.     

<Emphasis Type="Italic"> Zaba</Emphasis>: a novel miniature transposable element present in genomes of legume plants

A novel family of miniature transposable elements, named Zaba, was identified in pea (Pisum sativum) and subsequently also in other legume species using computer analysis of their DNA sequences. Zaba elements are 141–190 bp long, generate 10-bp target site duplications, and their terminal inverted repeats make up most of the sequence. Zaba elements thus resemble class 3 foldback transposons. The elements are only moderately repetitive in pea (tens to hundreds copies per haploid genome), but they are present in up to thousands of copies in the genomes of several Medicago and Vicia species. More detailed analysis of the elements from pea, including isolation of new sequences from a genomic library, revealed that a fraction of these elements are truncated, and that their last transposition probably did not occur recently. A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions.Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material.Communicated by M.-A. Grandbastien