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PubMed1992

Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA.

Transposable and interspersed repetitive elements (TIREs) are ubiquitous features of both prokaryotic and eukaryotic genomes. However, controversy has arisen as to whether these sequences represent useless 'selfish' DNA elements, with no cellular function, as opposed to useful genetic units. In this review, we selected two insect species, the Dipteran Drosophila and the Lepidopteran Bombyx mori (the silkmoth), in an attempt to resolve this debate. These two species were selected on the basis of the special interest that our laboratory has had over the years in Bombyx with its well known molecular and developmental biology, and the wealth of genetic data that exist for Drosophila. In addition, these two species represent contrasting repetitive element types and patterns of distribution. On one hand, Bombyx exhibits the short interspersion pattern in which Alu-like TIREs predominate while Drosophila possesses the long interspersion pattern in which retroviral-like TIREs are prevalent. In Bombyx, the main TIRE family is Bm-1 while the Drosophila group contains predominantly copia-like elements, non-LTR retroposons, bacterial-type retroposons and fold-back transposable elements sequences. Our analysis of the information revealed highly non-random patterns of both TIRE biology and evolution, more indicative of these sequences acting as genomic symbionts under cellular regulation rather than useless or selfish junk DNA. In addition, we extended our analysis of potential TIRE functionality to what is known from other eukaryotic systems. From this study, it became apparent that these DNA elements may have originated as innocuous or selfish sequences and then adopted functions. The mechanism for this conversion from non-functionality to specific roles is a process of coevolution between the repetitive element and other cellular DNA often times in close physical proximity. The resulting interdependence between repetitive elements and other cellular sequences restrict the number of evolutionarily successful mutational changes for a given function or cistron. This mutual limitation is what we call genome canalization. Well documented examples are discussed to support this hypothesis and a mechanistic model is presented for how such genomic canalization can occur. Also proposed are empirical studies which would support or invalidate aspects of this hypothesis.

Animals↗
PubMed1994

Tad1-1, an active LINE-like element of Neurospora crassa.

Tad is a LINE-like retrotransposon of Neurospora crassa. The element was originally detected and cloned using the am gene as a transposon trap in hybrid strains derived from a cross of Adiopodoume (a wild collected strain) and a laboratory strain devoid of Tad elements. We report the cloning and sequencing of an active Tad element, Tad1-1, which is capable of independent transposition. Transposition was demonstrated by screening for transfer of the element from a donor nucleus that contained the Tad1-1 element as the only active Tad, into a naive nucleus within a forced heterokaryon. We also report here the sequence analysis of Tad1-1, and its comparison with the sequence of another active element, Tad3-2. These elements are approximately 7 kb in length. They contain two long open reading frames (ORFs) encoded on the strand of the same polarity as the full-length transcript. ORF1 encodes a putative protein of 486 amino acids. Homology to the first ORF of other LINE elements is confined to three cysteine-rich motifs, located near the carboxy-terminus, that are thought to be involved in binding nucleic acids. The second ORF is 1156 amino acids in length and shows homology to the reverse transcriptase domains of various retroviruses and retrotransposons. Tad1-1 and Tad3-2 differ in only ten positions over their whole length.

Base Sequence↗
PubMed1995

Male recombination with single and homologous P elements in Drosophila melanogaster.

It has previously been shown that, in the presence of a source of P element transposase, male recombination in Drosophila melanogaster is induced at a rate of about 1% in the region of a single P[CaSpeR] element. This paper shows that recombinant chromosomes retain unaltered P[CaSpeR] elements at the original site in a high proportion of cases. This result is incompatible with a simple model in which recombination occurs by resolution of a Holliday junction following P element excision and repair. It has also previously been shown that homozygous regions containing a P element produce male recombination levels of 10-20%, an order of magnitude higher than that given by a single element. This paper shows that reciprocal recombinant chromosomes retaining P[CaSpeR] elements can be combined to produce similarly high levels of recombination. This result potentially allows for recombinant chromosomes from homologous recombination to be analysed at the molecular level in the region of the inserted element.

Animals↗
PubMed1995

Characterization of a Tc1-like transposable element in zebrafish (Danio rerio).

We have characterized Tdr1, a family of Tc1-like transposable elements found in the genome of zebrafish (Danio rerio). The copy number and distribution of the sequence in the zebrafish genome have been determined, and by these criteria Tdr1 can be classified as a moderately repetitive, interspersed element. Examination of the sequences and structures of several copies of Tdr1 revealed that a particular deletion derivative, 1250 bp long, of the transposon has been amplified to become the dominant form of Tdr1. The deletion in these elements encompasses sequences encoding the N-terminal portion of the putative Tdr1 transposase. Sequences corresponding to the deleted region were also detected, and thus allowed prediction of the nucleotide sequence of a hypothetical full-length element. Well conserved segments of Tc1-like transposons were found in the flanking regions of known fish genes, suggesting that these elements have a long evolutionary history in piscine genomes. Tdr1 elements have long, 208 bp inverted repeats, with a short DNA motif repeated four times at the termini of the inverted repeats. Although different from that of the prototype C. elegans transposon Tc1, this inverted repeat structure is shared by transposable elements from salmonid fish species and two Drosophila species. We propose that these transposons form a subgroup within the Tc1-like family. Comparison of Tc1-like transposons supports the hypothesis that the transposase genes and their flanking sequences have been shaped by independent evolutionary constraints. Although Tc1-like sequences are present in the genomes of several strains of zebrafish and in salmonid fishes, these sequences are not conserved in the genus Danio, thus raising the possibility that these elements can be exploited for gene tagging and genome mapping.

Amino Acid Sequence↗
PubMed1996

Distribution of T1, Q, Pegasus and mariner transposable elements on the polytene chromosomes of PEST, a standard strain of Anopheles gambiae.

The chromosomal locations of four families of transposable elements, T1, Q, Pegasus and mariner, have been determined by in situ hybridization to polytene chromosomes of ovarian nurse cells of the mosquito Anopheles gambiae. As part of this effort, we have developed a vigorous pink-eyed laboratory strain of A. gambiae (PEST), rendered homozygous standard for chromosomal inversions on all autosomes. Ten different individuals of this strain were studied with each transposable element probe. The average number of hybridization sites per genome was 83.9 for T1, 63.4 for Q, 31.5 for Pegasus and 64.7 for mariner, excluding pericentric and centromeric regions. However, some degree of polymorphism was observed within each family such that, considering all ten individuals, 94 different sites were detected for T1, 82 sites for Q, 45 sites for Pegasus and 71 sites for mariner. The mean occupancy per site varied from 0.70 (Pegasus) to 0.91 (mariner), which, while significantly higher than that seen for transposable elements in natural populations of Drosophila melanogaster, is comparable to that seen in established laboratory stocks. In addition, these element families were not randomly distributed. All but Pegasus were concentrated in centromeric heterochromatin and centromere-proximal euchromatin, most showed a deficit of hybridization sites in the distal section of chromosomes, and a significant proportion of sites were coincident between families. These results provide the first detailed examination of the cytogenetic location of transposable elements in a nondrosophilid insect, and, through comparison with the behavior of transposable elements in Drosophila, may provide insight into the interaction between elements and host. The mapped elements are also expected to serve as landmarks useful in integrating the developing physical map of the PEST strain with the chromosomal banding pattern.

Animals↗
PubMed1991

Sequences homologous to Tc(s) transposable elements of Caenorhabditis elegans are widely distributed in the phylum nematoda.

To have a better understanding of the evolutionary history of mobile elements within the nematodes, we examined the distribution and the conservation of homologues to transposable elements from Caenorhabditis elegans (Tc1, Tc2, Tc3, Tc4, Tc5, and FB1) in 19 nematode species belonging to the class Secernentea. Our results show that Tc1 elements display a distribution restricted to the family Rhabditidae with poor conservation. The Tc2 and FB1 homologous elements have the same patchy distribution within the Rhabditidae. They were only found in Caenorhabditis and in Teratorhabditis. The Tc3 element is widely distributed among nematode species. Tc3 homologous elements are present in the majority of the Rhabditidae but also in two genera within the family Panagrolaimidae, and in Bursaphelenchus, which belongs to the order Aphelenchida. Tc4 and Tc5 homologues show the most limited distribution of all tested elements, being strictly limited to C. elegans. These data indicate that in some cases, the distribution of transposable elements in the nematode cannot be explained by strict vertical transmission. The distribution of Tc3, Tc4, and Tc5 suggests that horizontal transmission may have occurred between reproductively isolated species during their evolutionary history.

Animals↗
PubMed1987

Cotransposition of a highly repetitive DNA element with flanking sequences in the genome of the midge Chironomus thummi.

A family of highly repetitive DNA elements, the Cla-elements, is present in the genomes of the two sibling species Chironomus th. thummi and Ch. th. piger. These Cla-elements are organized in large tandem repetitive clusters as well as occurring as interspersed monomeric elements, in both subspecies. The analysis of a monomeric Cla-element and several kilobases of its flanking sequences from Ch. th. piger revealed that the short Cla-elements are cotransposed together with adjacent DNA. We found the same association of Cla-elements with specific flanking DNA in clones obtained from the rDNA of Ch. th. thummi and from nonribosomal Cla-DNA of Ch. th. piger. The Cla-element-flanking DNA is clearly also repetitive, but mainly of interspersed organization.

Animals↗
PubMed1993

Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.).

Copia-like retrotransposable elements were identified in allotetraploid cotton, Gossypium hirsutum, and two species representing its diploid progenitors, G. herbaceum and G. raimondii. These elements are present in high copy number in all three species. Because the two diploid genomic groups have been isolated on opposite sides of the world for 6-11 million years, horizontal transfer of elements between these species is highly unlikely. Elements were intensively sampled to generate a model of copia-like retrotransposable element evolution in systems where vertical transmission is the sole probable means of descent. Copia-like retrotransposon diversity is equally great in all three Gossypium species. Despite this high heterogeneity, analysis of 89 partial reverse transcriptase sequences resulted in the recognition of nine sharply differentiated retrotransposon lineages, each containing elements that share high sequence similarity. No evidence of horizontal transfer from other taxa was obtained. Phylogenetic analyses demonstrate that element topologies are incongruent with Gossypium phylogeny. Consideration of processes that obscure phylogenetic reconstruction of multigene families (including sampling error, variable degrees of orthology and paralogy, differential lineage age and lineage loss and/or proliferation) demonstrates that incongruence between organismal and retrotransposon trees is expected under conditions in which vertical processes are the sole means of transmission. Identification of closely related elements between species allowed rates of copia-like retrotransposon sequence evolution to be estimated as approximately 10(-9) nucleotide substitutions/site/year. These rates are consistent with the interpretation that these retrotransposons have been evolving under functional constraints for most of the time frame bracketed by the species studied. Extrapolation of these results to previous studies that sampled from more highly divergent taxa indicates that horizontal transfer need not be invoked to explain observed phylogenetic patterns.

Amino Acid Sequence↗
PubMed1999

Concentrations of trace elements in sera of newborns, young infants, and adults.

Concentrations of trace elements in newborns, infants, and adults may be significantly different from each other. Serum trace element reference ranges for different age groups are of value for diagnostic purposes. Inductively coupled plasma-mass spectrometry was applied to the determination of the 21 trace elements Ba, Be, Bi, Ca, Cd, Co, Cs, Cu, La, Li, Hg, Mg, Mn, Mo, Pb, Rb, Sb, Sn, Sr, TI, and Zn in a total of 117 sera of individuals representing different age groups. After microwave-assisted acid digestion with high-purity reagents, 20 umbilical cord sera, 5 sera of fully breast-fed infants, 6 sera of formula-fed infants, 66 sera of patients suffering internal diseases, and 20 sera of healthy blood donors were analyzed for trace elements. One serum and two whole-blood reference materials were analyzed for quality control. Experimental concentrations were in good agreement with certified values. Umbilical cord serum concentrations of the essential elements Ca, Co, Cu, and Mg and of the nonessential and toxic elements Ba, Be, Li, Pb, and Sb were elevated compared to the elemental concentrations in the sera of infants and adults. Serum levels of Ba, Ca, Co, Mn, Pb, and Sb of infants were much higher and serum Cu was significantly lower than in adults. Serum Cu increased significantly with age (newborns: 353 microg/L; infants: 755 microg/L; healthy adults: 810 microg/L), whereas for other trace elements no age-dependence could be established.

Adult↗
PubMed1994

An elemental correlation study in cancerous and normal breast tissue with successive clinical stages by neutron activation analysis.

Influence of trace elements in body metabolism and their physiological importance in various diseases have motivated their accurate and quantitative determination in biological tissues and fluids. Instrumental Neutron Activation Analysis (INAA) using short and long term irradiation has been employed to determine five minor elements (Cl, K, Na, Mg, P) and 15 trace elements (As, Br, Co, Cr, Cs, Cu, Fe, Hg, Mn, Rb, Sb, Se, Sc, Sr, and Zn) in cancerous and normal breast tissue from 30 patients of four clinical stages. Several elements show enhancement in cancerous breast tissue. Selenium shows maximum enhancement of 94.7% followed by K (81.6%), Sc (66.7%), Cu (58.2%) Na (48.5%), P (44.4%), and Zn (39.2%). Some elements, such as Fe, Cr, and Mn, are depressed by 30.8, 30.1, and 12.8%, respectively. These elements compete for binding sites in the cell, change its enzymatic activity and exert direct or indirect action on the carcinogenic process accelerating the growth of tumors. This is further evidenced by histopathological examination of cancerous cells showing poor cytological differentiation. An attempt has been made to correlate trace element concentrations of Se, Cu, Zn, Rb, Br, Hg, As, Co, Fe, Cr, and Mn and the ratios of Se/Zn, K/P, Cu/Zn, Na/K, and Se/Fe with the clinical stages of cancer. Inhibition of enzymatic activity caused by variation in trace element concentrations results in immunological breakdown of the body system.

Adult↗
PubMed1988

Mineral- and trace element concentrations in human breast milk, placenta, maternal blood, and the blood of the newborn.

The concentrations of the essential trace elements Cu, Fe, and Zn, and of the mineral elements Ca, K, Mg, and P during the perinatal period in human placenta and in the blood of the mother and the newborn (cord blood) were determined. Breast milk (colostrum and transitory milk) was also included to permit correlations between the different compartments. No correlations were found. The uptake by nutrition and the body-pools of the mother and their mobilization for these elements seem to be sufficiently high for an adequate supply of the fetus and the milk in the geographical region of Munich (Bavaria, FRG) under these investigations. Differences in the mineral-and trace element concentrations of colostrum and transitory milk for the elements P and Zn and to a lesser extent for Ca and Mg were observed. Additionally, breast milk samples from different geographical regions in Bavaria were investigated. Results for the heavy metals Cd, Hg, and Pb, and for the essential trace element Se are also presented for these samples, and can be seen as a reflection of the overall environmental and dietary influences during pregnancy in these geographical regions. ICP (Inductively Coupled Plasma)-emission spectrometry was used for the determination of the elements Cu, Fe, Zn, Ca, K, Mg, and P. For the additionally given elements in the milk-samples anodic stripping voltammetry (DPASV) (Cd, Pb), hydride atomic absorption spectrometry (AAS) (Se), and cold vapor AAS (Hg) were applied.

Female↗
PubMed1997

Concentration, distribution, and comparison of selected trace elements in bed sediment and fish tissue in the South Platte River Basin, USA, 1992-1993.

During August-November 1992 and August 1993, bed sediment and fish liver were sampled in the South Platte River Basin and analyzed for 45 elements in bed sediment and 19 elements in fish liver. The results for aluminum, arsenic, cadmium, chromium, copper, iron, lead,manganese, selenium, silver, uranium, and zinc are presented here. All 12 trace elements were detected in bed sediment, but not all were detected in fish liver or in all species of fish. A background concentration of trace elements in bed sediment was calculated using the cumulative frequency curves of trace element concentrations at all sites. Arsenic, cadmium, copper, lead, manganese, silver, uranium, and zinc concentrations were greater than background concentrations at sites in mining areas or at sites that have natural sources of these elements. Trace element concentrations in fish liver generally did not follow the same patterns as concentrations in bed sediment, although concentrations of aluminum and cadmium were higher in fish liver collected at mountain sites that had been disturbed by mining. Concentrations of aluminum, arsenic, cadmium, chromium, copper, iron, lead, silver, and zinc increased in bed sediments in urban areas. Iron, silver, and zinc concentrations in fish liver also increased in urban areas. Concentrations of cadmium, copper, silver, and zinc in fish liver increased in the agricultural areas of the basin. Downstream changes in trace element concentrations may be the result of geological changes in addition to changes in land use along the river.

Animals↗
PubMed2001

The transposon Tip100 from the common morning glory is an autonomous element that can transpose in tobacco plants.

The mutable flaked or a (flaked) (a(f)) line of the common morning glory (Ipomoea purpurea) displays white flowers with colored flakes, and the a(f) mutation is caused by the insertion of a transposable element named Tip100 into the CHS-D gene for anthocyanin biosynthesis. The 3.9-kb Tip100 element belongs to the Ac/Ds family and contains an ORF encoding a polypeptide of 808 amino acids. The frequency and timing of flower variegation vary in different a(f) lines, and a genetic element termed Modulator has been postulated to affect the variegation pattern. Since the pattern of flower variegation is determined by the frequency and timing of excision of Tip100 from the CHS-D gene, we wished to determine whether Tip100 is an autonomous element that is itself capable of transposition in a heterologous host. To do this, we introduced the element into the genome of tobacco plants by Agrobacterium-mediated transformation. The intact Tip100 element was able to excise from its original position in the chromosome and reinsert into new sites in the tobacco genome, whereas an internal deletion derivative was not. Based on these results, we conclude that Tip100 is an autonomous element. We also discuss the nature of the putative Modulator element affecting flower and leaf variegation in various mutable lines of the morning glory.

Alleles↗
PubMed2003

Tourist C transposable elements are closely associated with genes expressed in flowers of rice (Oryza sativa).

Tourist elements comprise a group of transposable elements in plants. One of these elements, Tourist-OsaCatA(a Tourist C element), has been found in the 5; flanking region of a catalase gene, CatA, in rice (Oryza sativa). Using reverse transcriptase-PCR (RT-PCR) analyses of leaves, roots, flowers and developing seeds of rice, we assessed the transcription levels of ten known genes containing Tourist C elements, and of three additional putative genes for which expressed sequence tags (ESTs) including Tourist C elements have been isolated. We found that nine of the ten known genes and two of the three represented by ESTs were expressed in at least one of the organs we analyzed, and all of the genes detected were expressed in flowers, usually in stamens or pistils. We also assessed the expression of the 29 Tourist C-containing hypothetical coding sequences (CDSs) obtained so far by high-throughput genomic sequencing. We found that CDSs of all 11 genes whose transcripts were detectable by RT-PCR were expressed in flowers, especially in stamens or pistils. In contrast, RT-PCR analyses of genes or CDSs associated with other miniature inverted-repeat transposable elements (MITEs), such as Tourist D, Gaijin, Explorer, and Castaway, showed that some of them were expressed only minimally or not at all in flowers. Therefore, compared with other MITEs, Tourist C elements seem to show a strong association with genes that are expressed in the flowers of rice.

DNA Transposable Elements↗
PubMed2003

Survival of Tdc transposable elements of the En/Spm superfamily in the carrot genome.

Three subfamilies of the En/Spm-type transposable element of carrot, Tdc A, B, and C, were characterized. It was supposed that the Tdc A subfamily may include autonomous elements which can produce transposases. Tdc B elements are defective, but still generate transcripts containing mutant open reading frame (ORF) sequences for transposases. The single member of the Tdc C group recovered seems to be a pseudogene. The sequences of the transposase ORFs of Tdc A and Tdc B elements are more highly conserved than those of the 5; and 3; untranslated regions and introns, as is found in other structural genes that are subject to selection. These observations indicate that the mutations in the nucleotide sequences of the Tdc elements occurred in the host genome. However, the mutations in the 5; and 3; untranslated regions and introns, which may not be sufficient to prevent transposition, accumulated in autonomous elements, which could transpose and produce copies. When the reproduction rate and the rate of disabling mutations reached an equilibrium, that is, when the birth rate of the transposable elements in the genome equalled the death rate, the population of elements achieved a stationary state in the genome, and could thus survive.

Amino Acid Sequence↗
PubMed2006

Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.).

Members of a novel Master family of class II transposons were identified in the carrot genome. Two elements, 2.5 kb long DcMaster1 and 4.4 kb long DcMaster-a, are characterized by 22 bp imperfect terminal inverted repeats and by 3 bp target site duplications. GenBank search revealed that related elements are also present in Medicago truncatula, including a 5.1 kb element MtMaster-a. Both DcMaster-a and MtMaster-a contain open reading frames encoding for putative transposases with the complete DDE domain typical for plant class II transposable elements belonging to PIF/Harbinger superfamily, where the Master elements form a distinct group. Less than 10 copies of the DcMaster element containing the DDE domain are present in genomes of carrot and other Apiaceae, but more copies with internal deletions or insertions may occur. DcMaster elements were associated with putative coding regions in 8 of 14 identified insertion sites. PCR amplification of carrot genomic DNA using a primer complementary to TIRs of DcMaster gave products < 400 bp in size. We speculate that these may all represent a MITE-like family of transposable elements that we named Krak, present in the carrot genome in at least 3,600 copies.

Amino Acid Sequence↗
PubMed1996

The transposable element Tan1 of Aspergillus niger var. awamori, a new member of the Fot1 family.

Aspergillus niger var. awamori has transposable elements that we refer to as Vader and Tan1 (transposon A. niger). Vader was identified by screening unstable nitrate reductase (niaD) mutants for insertions. Four of the isolated niaD mutants were shown to contain a small insertion element. This 437 bp insertion element, Vader, is flanked by 44 bp inverted repeats (IR) and is present in approximately 15 copies in the genomes of two A. niger strains examined. A synthetic 44 bp oligomer of the inverted repeat of Vader has now been used to clone, via the polymerase chain reaction, a 2.3 kb Tan1 element. The Tan1 element has also been isolated from a partial genomic library. Tan1 is present as a single copy in A. niger var. awamori. The Tan1 element has a unique organization: IR-ORF-IR-IR-Vader-IR. The single open reading frame (ORF) (1668 bp) encodes a putative transposase homologous to Fusarium oxysporum Fot1 and Magnaporthe grisea Pot2. Immediately 3' to the second inverted repeat, which bounds the transposase, is a copy of the AT-rich Vader element. We hypothesize that at some stage the independent Vader element, although inactive by itself, arose from Tan1, resulting in current strains with only one copy of Tan1 providing transposase activity and numerous mobile copies of Vader dispersed in the genome.

Amino Acid Sequence↗
PubMed1998

P element sequences can compensate for a deletion of the yellow regulatory region in Drosophila melanogaster.

The effects of interactions between P element and yellow regulatory sequences on the control of yellow expression were studied. The y mutations used in the analysis lack a segment of upstream sequence that extends from position -146 bp to -70 bp, relative to the transcription start site of the yellow gene. This sequence has been found to be necessary for the function of the yellow promoter. The insertion of one or two P element copies at position -69 bp compensates for the deletion in the regulatory region and restores yellow expression. After mobilization of the P element, new phenotypes were selected and molecularly characterized. Two regions in the 5' part of the P element, from 23 bp to 71 bp and from 82 bp to 108 bp, can each partially compensate for the yellow deletion. In addition, deletion derivatives of the P element were themselves able to activate yellow transcription. All such P elements retain at least 108 bp of sequence at the 5' end and 15-17 bp at the 3' end. Thus, the region of the P element from 23 bp to 108 bp contains cis-regulatory elements that can influence the transcription of neighboring genes.

Animals↗