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PubMed2005

What transposable elements tell us about genome organization and evolution: the case of Drosophila.

Transposable elements (TEs) have been identified in every organism in which they have been looked for. The sequencing of large genomes, such as the human genome and those of Drosophila, Arabidopsis, Caenorhabditis, has also shown that they are a major constituent of these genomes, accounting for 15% of the genome of Drosophila, 45% of the human genome, and more than 70% in some plants and amphibians. Compared with the 1% of genomic DNA dedicated to protein-coding sequences in the human genome, this has prompted various researchers to suggest that the TEs and the other repetitive sequences that constitute the so-called "noncoding DNA", are where the most stimulating discoveries will be made in the future (Bromham, 2002). We are therefore getting further and further from the original idea that this DNA was simply "junk DNA", that owed its presence in the genome entirely to its capacity for selfish transposition. Our understanding of the structures of TEs, their distribution along the genomes, their sequence and insertion polymorphisms within genomes, and within and between populations and species, their impact on genes and on the regulatory mechanisms of genetic expression, their effects on exon shuffling and other phenomena that reshape the genome, and their impact on genome size has increased dramatically in recent years. This leads to a more general picture of the impact of TEs on genomes, though many copies are still mainly selfish or junk DNA. In this review we focus mainly on discoveries made in Drosophila, but we also use information about other genomes when this helps to elucidate the general processes involved in the organization, plasticity, and evolution of genomes.

Animals↗
PubMed1998

A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation.

In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa, a methylated 5S rRNA pseudogene, Psi63, was identified. We characterized the Psi63 region to better understand the control and function of DNA methylation. The 120-bp 5S rRNA-like region of Psi63 is interrupted by a 1.9-kb insertion that has characteristics of sequences that have been modified by repeat-induced point mutation (RIP). We found sequences related to this insertion in wild-type strains of N. crassa and other Neurospora species. Most showed evidence of RIP; but one, isolated from the N. crassa host of Psi63, showed no evidence of RIP. A deletion from near the center of this sequence apparently rendered it incapable of participating in RIP with the related full-length copies. The Psi63 insertion and the related sequences have features of transposons and are related to the Fot1 class of fungal transposable elements. Apparently Psi63 was generated by insertion of a previously unrecognized Neurospora transposable element into a 5S rRNA gene, followed by RIP. We name the resulting inactivated Neurospora transposon PuntRIP1 and the related sequence showing no evidence of RIP, but harboring a deletion that presumably rendered it defective for transposition, dPunt.

Amino Acid Sequence↗
PubMed2000

Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize.

A 314-bp DNA element called Heartbreaker-hm1 (Hbr-hm1) was previously identified in the 3' untranslated region of a mutant allele of the maize disease resistance gene HM1. This element has structural features of miniature inverted-repeat transposable elements (MITEs) and is a member of a large family of approximately 4,000 copies in the maize genome. Unlike previously described MITEs, most members of the Hbr family display over 90% sequence identity. This, coupled with the insertion of an Hbr element into an allele of the HM1 gene, suggested that this family might have spread recently throughout the genome. Consistent with this view is the finding that Hbr insertion sites are remarkably polymorphic. Ten of ten loci containing Hbr elements were found to be polymorphic for the presence or absence of Hbr among a collection of maize inbred lines and teosinte strains. Despite the fact that over 80% of the maize genome contain moderate to highly repetitive DNA, we find that randomly chosen Hbr elements are predominantly in single or low copy regions. Furthermore, when used to query both the public and private databases of plant genes, over 50% of the sequences flanking these Hbr elements resulted in significant "hits." Taken together, these data indicate that the presence or absence of Hbr elements is a significant contributory factor to the high level of polymorphism associated with maize genic regions.

Base Sequence↗
PubMed2006

[Characterization of macrolide-resistance mediated by transposable elements Tn1545 and Tn917 in clinical Isolates of Streptococcus pneumoniae].

OBJECTIVE: To investigate the characterization of ermB gene expression and dissemination in macrolide-resistant Streptococcus pneumoniae (Sp) in Shanghai. METHODS: Eighty-six erythromycin-resistant isolates of Sp were isolated from 3 hospitals in Shanghai. E-test or K-B disk diffusion test were used to determine the susceptibility to 12 antibiotics according to the National Committee for Clinical Laboratory Standards. Macrolide resistant genes ermB and mefE, and transposable elements Tn1545 and Tn917 were amplified by PCR. The isolates were divided into Tn1545 and Tn917 groups according to the transposable elements thereof. Double disc test with erythromycin and clindamycin discs divided the isolates into 2 macrolide resistant phenotypes: cMLS(B) (inducible) phenotype and M phenotype (resistant to erythromycin and sensitive to clindamycin). BOX-PCR was used to analyze the homology of the S. pneumoniae. RESULTS: (1) Of the 86 erythromycin-resistant isolates, the positive rates of ermB, mefE, Tn1545, and Tn917 were 94%, 46%, 87% and 7% respectively. Tn1545 and Tn917 were not detected in 5 ermB-mdfE + strains. (2) Most strains in the Tn1545 and Tn917 groups were highly resistant to erythromycin with a MIC50 of 256 microg/ml. The Tn917 group had a lower MIC to beta-lactam antibiotics and lower resistance to tetracycline, levofloxacin, and compound sulfonamide in comparison with the Tn1545 group. (3) The most common macrolide resistance phenotype of the Tn1545 group was cMLS(B) phenotype. Three strains in the Tn917 group had a 194 bp deletion in the promoter region of ermB and an insertion of TAAA motif in the N end of leader peptide, resulting in the change of the ermB gene from inducible to constitutive expression. (4) BOX-PCR showed that Tn1545 and Tn917 might spread horizontally. CONCLUSION: In Shanghai ermB-mediated cMLS(B) is the most prevalent phenotype in macrolide-resistant Streptococcus pneumoniae isolates. Primarily, the ermB gene was carried and spread horizontally by Tn1545.

Anti-Bacterial Agents↗
PubMed2003

Transposable elements and vertebrate protein diversity.

Interspersed repetitive sequences are major components of eukaryotic genomes. Repetitive elements comprise about 50% of the mammalian genome. They interact with the whole genome and influence its evolution. Repetitive elements may serve as recombination hot spots or acquire specific cellular functions such as RNA transcription control or become part of protein coding regions. The latter is a subject of presented analysis. We searched all currently available vertebrate protein sequences, including human proteome complement for the presence of transposable elements. It appears that insertion of TE-cassettes into open reading frames is a general phenomena. They can be found in all vertebrate lineages and originate in all types of transposable elements. It seems that genomes use those cassettes as 'ready to use' motifs in their evolutionary experiments. Most of TE-cassettes are used to create alternative forms of a message and usually the other form, without TE-cassette, is expressed in a cell. Tables listing vertebrate messages with TE-cassettes are available at http://warta.bio.psu.edu/ScrapYard/.

Animals↗
PubMed2004

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.

Among the genus Ipomoea, three morning glories, I. nil (the Japanese morning glory), I. purpurea (the common morning glory), and I. tricolor, were domesticated well for floricultural plants, and many spontaneous mutants displaying various flower pigmentation patterns were isolated. Most of these spontaneous mutations were found to be caused by the insertion of DNA transposable elements in the genes for the anthocyanin pigmentation in flowers, and many of them exhibited variegated flowers, such as white flowers with pigmented spots and sectors. Here, we describe the historical background of the mutants displaying variegated flowers and review the genetic and epigenetic regulation in flower pigmentation associated with transposable elements of these morning glories. The flecked, speckled, r-1, and purple mutations in I. nil were caused by insertions of Tpn1 and its relatives in the En/Spm superfamily, Tpn2, Tpn3, and Tpn4, into the genes for anthocyanin coloration in flowers, i.e., DFR-B, CHI, CHS-D, and InNHX1, respectively. Similarly, the flaked and pink mutants of I. purpurea have distantly related elements, Tip100 and Tip201, in the Ac/Ds superfamily inserted into the CHS-D and F3'H genes, respectively. The flower variegation patterns can be determined by the frequency and timing of the excision of these transposons, and their stable insertions produce plain color flowers without generating pigmented spots or sectors; furthermore, both genetic and epigenetic regulation appeared to play important roles in determining the frequency and timing of the excision of the transposons. However, flower variegation is not always associated with the excision of an integrated DNA transposon from one of the genes for anthocyanin pigmentation. The mutant Flying Saucers of I. tricolor displaying variegated flowers was found to have the transposon ItMULE1 inserted into the DFR-B promoter region, but no excision of ItMULE1 from the DFR-B could be detected in the variegated flower lines. The instable pearly-vrg allele in cv. Flying Saucers is likely to be an epiallele because the DNA methylation in the DFR-B promoter appeared to be associated with flower pigmentation.

Alleles↗
PubMed1998

Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrant family of elements.

Although the genome of Arabidopsis thaliana has a small amount of repetitive DNA, it contains representatives of most classes of mobile elements. However, to date, no miniature inverted-repeat transposable element (MITE) has been described in this plant. Here, we describe a new family of repeated sequences that we have named Emigrant, which are dispersed in the genome of Arabidopsis and fulfil all the requirements of MITEs. These sequences are short, AT-rich, have terminal inverted repeats (TIRs), and do not seem to have any coding capacity. Evidence for the mobility of Emigrant elements has been obtained from the absence of one of these elements in a specific Arabidopsis ecotype. Emigrant is also present in the genome of different Brassicae and its TIRs are 74% identical to those of Wujin elements, a recently described family of MITEs from the yellow fever mosquito Aedes aegypti.

Arabidopsis↗
PubMed1995

The transposable element impala, a fungal member of the Tc1-mariner superfamily.

A new transposable element has been isolated from an unstable niaD mutant of the fungus Fusarium oxysporum. This element, called impala, is 1280 nucleotides long and has inverted repeats of 27 bp. Impala inserts into a TA site and leaves behind a "foot-print" when it excises. The inserted element, impala-160, is cis-active, but is probably trans-defective owing to several stop codons and frameshifts. Similarities exist between the inverted repeats of impala and those of transposons belonging to the widely dispersed mariner and Tc1 families. Moreover, translation of the open reading frame revealed three regions showing high similarities with Tc1 from Caenorhabditis elegans and with the mariner element of Drosophila mauritiana. The overall comparison shows that impala occupies an intermediate position between the mariner and Tc1-like elements, suggesting that all these elements belong to the same superfamily. The degree of relatedness observed between these elements, described in different kingdoms, raises the question of their origin and evolution.

Amino Acid Sequence↗
PubMed2000

Recent amplification of miniature inverted-repeat transposable elements in the vector mosquito Culex pipiens: characterization of the Mimo family.

We describe a new family of repetitive elements, named Mimo, from the mosquito Culex pipiens. Structural characteristics of these elements fit well with those of miniature inverted-repeat transposable elements (MITEs), which are ubiquitous and highly abundant in plant genomes. The occurrence of Mimo in C. pipiens provides new evidence that MITEs are not restricted to plant genomes, but may be widespread in arthropods as well. The copy number of Mimo elements in C. pipiens ( approximately 1000 copies in a 540Mb genome) supports the hypothesis that there is a positive correlation between genome size and the magnitude of MITE proliferation. In contrast to most MITE families described so far, members of the Mimo family share a high sequence conservation, which may reflect a recent amplification history in this species. In addition, we found that Mimo elements are a frequent nest for other MITE-like elements, suggesting that multiple and successive MITE transposition events have occurred very recently in the C. pipiens genome. Despite evidence for recent mobility of these MITEs, no element has been found to encode a protein; therefore, we do not know how they have transposed and have spread in the genome. However, some sequence similarities in terminal inverted-repeats suggest a possible filiation of some of these mosquito MITEs with pogo-like DNA transposons.

Animals↗
PubMed2006

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium.

The DNA content of eukaryotic nuclei (C-value) varies approximately 200,000-fold, but there is only a approximately 20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the repetitive fraction, although little is known about the evolutionary dynamics of the specific components that lead to genome size variation. To understand the modes and mechanisms that underlie variation in genome composition, we generated sequence data from whole genome shotgun (WGS) libraries for three representative diploid (n = 13) members of Gossypium that vary in genome size from 880 to 2460 Mb (1C) and from a phylogenetic outgroup, Gossypioides kirkii, with an estimated genome size of 588 Mb. Copy number estimates including all dispersed repetitive sequences indicate that 40%-65% of each genome is composed of transposable elements. Inspection of individual sequence types revealed differential, lineage-specific expansion of various families of transposable elements among the different plant lineages. Copia-like retrotransposable element sequences have differentially accumulated in the Gossypium species with the smallest genome, G. raimondii, while gypsy-like sequences have proliferated in the lineages with larger genomes. Phylogenetic analyses demonstrated a pattern of lineage-specific amplification of particular subfamilies of retrotransposons within each species studied. One particular group of gypsy-like retrotransposon sequences, Gorge3 (Gossypium retrotransposable gypsy-like element), appears to have undergone a massive proliferation in two plant lineages, accounting for a major fraction of genome-size change. Like maize, Gossypium has undergone a threefold increase in genome size due to the accumulation of LTR retrotransposons over the 5-10 Myr since its origin.

Base Sequence↗
PubMed1997

Tag1 is an autonomous transposable element that shows somatic excision in both Arabidopsis and tobacco.

Tag1 is a transposable element first identified as an insertion in the CHL1 gene of Arabidopsis. The chl1::Tag1 mutant originated from a plant (ecotype Landsberg erecta) that had been transformed with the maize transposon Activator (Ac), which is distantly related to Tag1. Genomic analysis of untransformed Landsberg erecta plants demonstrated that two identical Tag1 elements are present in the Landsberg erecta genome. To determine what provides transposase function for Tag1 transposition, we examined Tag1 excision in different genetic backgrounds. First, the chl1::Tag1 mutant was backcrossed to untransformed wild-type Arabidopsis plants to remove the Ac element(s) from the genome. F2 progeny that had no Ac elements but still retained Tag1 in the CHL1 gene were identified. Tag1 still excised in these Ac-minus progeny producing CHL1 revertants; therefore, Ac is not required for Tag1 excision. Next, Tag1 was inserted between a cauliflower mosaic virus 35S promoter and a beta-glucuronidase (GUS) marker gene and transformed into tobacco. Transformants showed blue-staining sectors indicative of Tag1 excision. Transgenic tobacco containing a defective Tag1 element, which was constructed in vitro by deleting an internal 1.4-kb EcoRI fragment, did not show blue-staining sectors. We conclude that Tag1 is an autonomous element capable of independent excision. The 35S-GUS::Tag1 construct was then introduced into Arabidopsis. Blue-staining sectors were found in cotyledons, leaves, and roots, showing that Tag1 undergoes somatic excision during vegetative development in its native host.

Arabidopsis↗
PubMed1994

Genome and stresses: reactions against aggressions, behavior of transposable elements.

The action of stresses on the genome can be considered as responses of cells or organisms to external aggressions. Stress factors are of environmental origin (climatic or trophic) or of genomic nature (introduction of foreign genetic material, for example). In both cases, important perturbations can occur and modify hereditary potentialities, creating new combinations compatible with survival; such a situation may increase the variability of the genome, and allow evolutive processes to take place. The behavior of transposable elements under stress conditions is thus of particular interest, since these sequences are sources of mutations and therefore of genetic variability; they may play an important role in population adaptation. The survey of the available experimental results suggest that, although some examples of mutations and transposable elements movements induced by external factors are clearly described, environmental injuries or introduction of foreign material into a genome are not systematically followed by drastic genomic changes.

Adaptation, Physiological↗
PubMed1991

hobo transposable elements in Drosophila melanogaster and D. simulans.

Genomic patterns of occurrence of the transposable element hobo are polymorphic in the sibling species Drosophila melanogaster and D. simulans. Most tested strains of both species have apparently complete (3.0 kb) and smaller hobo elements (H lines), but in both species some strains completely lack such canonical hobo elements (E lines). The occurrence of H and E lines in D. simulans as well as in D. melanogaster implies that an hypothesis of recent introduction in the latter species is inadequate to explain the phylogenetic occurrence of hobo. Particular internally deleted elements, the approximately 1.5 kb Th1 and Th2 elements, are abundant in many lines of D. melanogaster, and an analogous 1.1 kb internally deleted element, h del sim, is abundant in most lines of D. simulans. Besides the canonical hobo sequences, both species (and their sibling species D. sechellia and D. mauritiana) have many hobo-hybridizing sequences per genome that do not appear to be closely related to the canonical hobo sequence.

Animals↗
PubMed1991

Identification of an unusual structure in the Drosophila melanogaster transposable element copia: evidence for copia transposition through an RNA intermediate.

The Drosophila melanogaster transposable element copia is usually 5 kb long with long terminal repeats (LTRs), and its major transcripts are a full-length 5-kb RNA and a 2-kb RNA. We have previously shown that the 2-kb RNA is generated through splicing. Here, we have cloned a genomic intronless copia using an oligodeoxyribonucleotide probe which is specific for the junction of the two exons. The unusual copia is bounded by two LTRs and lacks precisely the intron of the 2-kb copia RNA. Identification of genomic intronless copia strongly suggests that copia transposes through an RNA intermediate. Moreover, we have found that copia virus-like particles (VLPs), in which reverse transcription of copia RNA seems likely to occur, packages the spliced copia RNA much less efficiently than the full-length copia RNA. This result leads to the suggestion that much lower copy number of genomic intronless copia, as compared with that of 'normal' copia, may be responsible for the inefficient packaging of the spliced copia RNA into the VLP.

Animals↗
PubMed2005

Insertion and excision of a transposable element governs the red floral phenotype in commercial petunias.

Commercial cultivars of Petunia hybrida with red flowers (red petunias) accumulate cyanidin 3-glucoside as a main floral anthocyanin pigment. The conversion of anthocyanidin 3-glucosides to anthocyanidin 3-rutinosides is catalyzed by a UDP-rhamnose: anthocyanidin 3-glucoside-rhamnosyltransferase (RT). In red petunias, the RT gene is known to be disrupted by the insertion of a transposable element (dTph3). We have cloned the dTph3-like element (called dTph3-C) from a red petunia. Unlike dTph3, dTph3-C harbored a perfect terminal inverted repeat. In addition, an excision product (so-called "footprint") of dTph3/dTph3-C was found in another red petunia. The RT transcripts harboring this footprint could not produce the RT enzyme because a stop codon was created in the footprint sequence. The genotypes of the 42 commercial petunias which exhibit different anthocyanin pigmentation were determined by multiplex PCR. In this technique, the amplified products from normal, dTph3/dTph3-C-inserted, and footprint-retaining RT genes can be separated from one another. Our results indicate that the red-floral phenotype of commercial petunias is governed by insertion and excision events of a transposable element in the coding region of the RT gene.

Anthocyanins↗
PubMed1995

Somatic movement of the mariner transposable element and lifespan of Drosophila species.

The effect of somatic movement of the mariner transposable element on lifespan was measured in Drosophila simulans and Drosophila melanogaster males at 25 degrees C. In D. simulans this movement significantly decreased lifespan, whereas in D. melanogaster no correlation between transposon movement and lifespan was found. The results in D. simulans support the hypothesis that somatic genetic damage induced by DNA element movement can reduce lifespan.

Aging↗
PubMed2003

Molecular paleontology of transposable elements in the Drosophila melanogaster genome.

We report here a superfamily of "cut and paste" DNA transposons called Transib. These transposons populate the Drosophila melanogaster and Anopheles gambiae genomes, use a transposase that is not similar to any known proteins, and are characterized by 5-bp target site duplications. We found that the fly genome, which was thought to be colonized by the P element <100 years ago, harbors approximately 5 million year (Myr)-old fossils of ProtoP, an ancient ancestor of the P element. We also show that Hoppel, a previously reported transposable element (TE), is a nonautonomous derivate of ProtoP. We found that the "rolling-circle" Helitron transposons identified previously in plants and worms populate also insect genomes. Our results indicate that Helitrons were horizontally transferred into the fly or/and mosquito genomes. We have also identified a most abundant TE in the fly genome, DNAREP1_DM, which is an approximately 10-Myr-old footprint of a Penelope-like retrotransposon. We estimated that TEs are three times more abundant than reported previously, making up approximately 22% of the whole genome. The chromosomal and age distributions of TEs in D. melanogaster are very similar to those in Arabidopsis thaliana. Both genomes contain only relatively young TEs (<20 Myr old), constituting a main component of paracentromeric regions.

Amino Acid Sequence↗
PubMed1984

Chromatin structure at the 44D larval cuticle gene locus in Drosophila: the effect of a transposable element insertion.

The chromatin structure of the larval cuticle gene cluster at 44D was characterized in embryos from wild-type (Oregon R) and a variant line (2/3) of Drosophila melanogaster. A major DNase I hypersensitive (DH) site was found between genes II and III in the chromatin, in a position 5' to the transcriptional start of the genes in the cluster. The introduction of a 7.3 kilobase transposable element into the cluster in the 2/3 variant enhanced the sensitivity of the major site in 2/3 chromatin but had no other effect upon the pattern of DH sites associated with the wild-type sequences. The wild-type sequences were packaged into an ordered nucleosome-like array in embryos, as revealed by digestion with the chemical cleavage reagent (methidiumpropyl-EDTA) iron (II) [MPE . Fe(II)]. Nucleolytic cleavage within the transposable element chromatin shows it to be organized in an ordered array punctuated by several DH sites. While the patterns of DNase I hypersensitivity are similar in the vicinity of the direct terminal repeats, the patterns revealed by micrococcal nuclease and MPE . Fe(II) are not, indicating a different chromatin organization of these two identical sequences.

Animals↗