Putative Transposable Element Research Articles

Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides

The trichloroethene reductive dehalogenase gene (tceA) of Dehalococcoides spp. was detected in 12 of 21 trichloroethene-to-ethene dechlorinating enrichment cultures established from aquifer and sediment samples collected from diverse geographic locations in the USA. Analysis of the tceA chromosomal regions indicated that the tceA genes shared greater than 95% sequence identity, and all shared identical tceAB spacer sequences and tceB genes downstream of tceA. A putative transposable element (PTE) was present 1077 bp downstream of the tceB stop codon in three of eight chromosomal regions analyzed. Sequence identity was interrupted downstream of tceB and upstream or downstream of the PTE, suggesting that intrachromosomal or interchromosomal transfer of tceAB had occurred.

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

The transposon Mutator was first identified in maize, and is one of the most active mobile elements in plants. The Arabidopsis thaliana genome contains at least 200 Mutator-like elements (MULEs), which contain the Mutator-like transposase gene, and often additional genes. We have detected a novel type of MULEs in melon (CUMULE), which, besides the transposase, contains two ubiquitin-like specific protease-like sequences (ULP1). This element is not present in the observed location in some melon cultivars. Multiple copies of this element exist in the Cucumis melo genome, and it has been detected in other Cucurbitaceae species. Analysis of the A. thaliana genome revealed more than 90 CUMULE-like elements, containing one or two Ulp1-like sequences, although no evidence of mobility exists for these elements. We detected various putative transposable elements containing ULP1-like sequences in rice. The discovery of these MULEs in melon and Arabidopsis, and the existence of similar elements in rice and maize, suggest that a proteolytic function may be important for this subset of the MULE transposable elements.

Three new satellite sequences and a mobile element found inside HSP70 introns of the Mediterranean mussel (Mytilus galloprovincialis)

We report the characterization of 3 new repetitive sequences from the bivalve mollusc Mytilus galloprovincialis, designated Mg1, Mg2, and Mg3, with monomer lengths of 169, 260, and 70 bp, respectively. The 3 repeats together constitute approximately 7.8% of the M. galloprovincialis genome and were found, together with ApaI-type 2 repeats, inside the introns of 2 genes of the HSP70 family, hsc70 and hsc71. Both the monomer length and the genomic content of the repeats indicate satellite sequences. The Mg1 repetitive region and its flanking sequences exhibit significant homology to CvE, a member of the Pearl family of mobile elements found in the eastern oyster (Crassostrea virginica). Thus, the whole homologous region is designated MgE, the first putative transposable element characterized in M. galloprovincialis. The ApaI, Mg2, and Mg3 repeats are continuously arranged inside the introns of both the hsc70 and hsc71 genes. The presence of perfect inverted repeats flanking the ApaI-Mg2-Mg3 repetitive region, as well as a sequence analysis of the repeats, indicates a transposition-like insertion of this region. The genes of the HSP70 family are highly conserved, and the presence of repetitive DNA or of mobile elements inside their introns is reported here for the first time.

Structural and Genomic Properties of the Hyperthermophilic Archaeal Virus ATV with an Extracellular Stage of the Reproductive Cycle

A novel virus, ATV, of the hyperthermophilic archaeal genus Acidianus has the unique property of undergoing a major morphological development outside of, and independently of, the host cell. Virions are extruded from host cells as lemon-shaped tail-less particles, after which they develop long tails at each pointed end, at temperatures close to that of the natural habitat, 85 °C. The extracellularly developed tails constitute tubes, which terminate in an anchor-like structure that is not observed in the tail-less particles. A thin filament is located within the tube, which exhibits a periodic structure. Tail development produces a one half reduction in the volume of the virion, concurrent with a slight expansion of the virion surface. The circular, double-stranded DNA genome contains 62,730 bp and is exceptional for a crenarchaeal virus in that it carries four putative transposable elements as well as genes, which previously have been associated only with archaeal self-transmissable plasmids. In total, it encodes 72 predicted proteins, including 11 structural proteins with molecular masses in the range of 12 to 90 kDa. Several of the larger proteins are rich in coiled coil and/or low complexity sequence domains, which are unusual for archaea. One protein, in particular P800, resembles an intermediate filament protein in its structural properties. It is modified in the two-tailed, but not in the tail-less, virion particles and it may contribute to viral tail development. Exceptionally for a crenarchaeal virus, infection with ATV results either in viral replication and subsequent cell lysis or in conversion of the infected cell to a lysogen. The lysogenic cycle involves integration of the viral genome into the host chromosome, probably facilitated by the virus-encoded integrase and this process can be interrupted by different stress factors.

Variability in the Region Downstream of the bla CMY-2 β-Lactamase Gene in Escherichia coli and Salmonella enterica Plasmids

We used sequencing and PCR mapping to investigate the regions flanking the blaCMY-2 beta-lactamase gene carried by plasmids from Escherichia coli and Salmonella enterica. Results revealed genetic heterogeneity in the region downstream from blaCMY-2 and identified a putative transposable element bearing blaCMY-2.

AT-rich sequences from the arbuscular mycorrhizal fungus Gigaspora rosea exhibit ARS function in the yeast Saccharomyces cerevisiae

Autonomous replicating sequences are DNA elements that trigger DNA replication and are widely used in the development of episomal transformation vectors for fungi. In this paper, a genomic library from the mycorrhizal fungus Gigaspora rosea was constructed in the integrative plasmid YIp5 and screened in the budding yeast Saccharomyces cerevisiae for sequences that act as ARS and trigger plasmid replication. Two genetic elements ( GrARS2, GrARS6) promoted high-rates of yeast transformation. Sequence analysis of these elements shows them to be AT-rich (72–80%) and to contain multiple near-matches to the yeast autonomous consensus sequences ACS and EACS. GrARS2 contained a putative miniature inverted-repeat transposable element (MITE) delimited by 28-bp terminal inverted repeats (TIRs). Disruption of this element and removal of one TIR increased plasmid stability several fold. The potential for palindromes to affect DNA replication is discussed.

Chompy: An infestation of MITE-like repetitive elements in the crocodilian genome

Interspersed repeats are a major component of most eukaryotic genomes and have an impact on genome size and stability, but the repetitive element landscape of crocodilian genomes has not yet been fully investigated. In this report, we provide the first detailed characterization of an interspersed repeat element in any crocodilian genome. Chompy is a putative miniature inverted-repeat transposable element (MITE) family initially recovered from the genome of Alligator mississippiensis (American alligator) but also present in the genomes of Crocodylus moreletii (Morelet's crocodile) and Gavialis gangeticus (Indian gharial). The element has all of the hallmarks of MITEs including terminal inverted repeats, possible target site duplications, and a tendency to form secondary structures. We estimate the copy number in the alligator genome to be ∼46,000 copies. As a result of their size and unique properties, Chompy elements may provide a useful source of genomic variation for crocodilian comparative genomics.

Reverse transcriptional profiling: non-correspondence of transcript level variation and proximal promoter polymorphism

BackgroundVariation in gene expression between two Drosophila melanogaster strains, as revealed by transcriptional profiling, seldom corresponded to variation in proximal promoter sequence for 34 genes analyzed. Two sets of protein-coding genes were selected from pre-existing microarray data: (1) those whose expression varied significantly and reproducibly between strains, and (2) those whose transcript levels did not vary. Only genes whose regulation of expression was uncharacterized were chosen. At least one kB of the proximal promoters of 15–19 genes in each set was sequenced and compared between strains (Oregon R and Russian 2b).ResultsOf the many promoter polymorphisms, 89.6% were SNPs and 10.4% were indels, including homopolymer tracts, microsatellite repeats, and putative transposable element footprints. More than half of the SNPs were changes within a nucleotide class. Hypothetically, genes differing in expression between the two strains should have more proximal promoter polymorphisms than those whose expression is similar. The number, frequency, and type of polymorphism, however, were the same in both sets of genes. In fact, the promoters of six genes with significantly different mRNA expression were identical in sequence.ConclusionFor these genes, sequences external to the proximal promoter, such as enhancers or in trans, must play a greater role than the proximal promoter in transcriptomic variation between D. melanogaster strains.

Sequence analysis of the plasmid genome of the probiotic strain Lactobacillus paracasei NFBC338 which includes the plasmids pCD01 and pCD02

Lactobacillus paracasei NFBC338 is a probiotic strain that was isolated from the human gastrointestinal tract (GIT) and contains a plasmid genome of ⩾80 kb. Using a shotgun sequencing approach, two of the plasmids, pCD01 (19,882 bp) and pCD02 (8554 bp) have been completely sequenced, and four contiguous sequences (Contigs) have been assembled. Bioinformatic analysis of pCD01 revealed that it contains 23 putative open reading frames (ORFs) and that it contains regions characterised by potential replication functions and multidrug resistance (MDR). In contrast, the content of pCD02 is mainly cryptic, although, it does contain two insertion sequence (IS) elements. Indeed, up to 17% of the entire plasmid genome encodes putative transposable elements. In addition, there are a number of interesting ORFs distributed over the four Contigs that show significant homology to genes such as those involved in adherence and biotin metabolism, which may prove beneficial to Lb. paracasei NFBC338 under certain environmental conditions. This study provides a novel insight into the rich plasmid complement of this probiotic Lactobacillus strain, which may potentially be exploited as the basis for development of improved genetic tools for probiotic lactobacilli.

Molecular comparisons of the Culex pipiens (L.) complex esterase gene amplicons

The amplification of carboxylesterase genes is a mechanism of organophosphate resistance in Culex mosquitoes. Amplified carboxylesterase genes from an insecticide resistant Culex pipiens strain collected in Cyprus were analysed and compared to other Culex amplified carboxylesterase alleles. A 12 kb section of genomic DNA containing two gene loci coding for carboxylesterase alleles A5 and B5 was cloned and sequenced. A comparison between this amplicon and one from a strain with co-amplified carboxylesterase alleles A2 and B2 revealed a number of differences. The intergenic spacer was 3.7 kb in length in the A5–B5 amplicon (2.7 kb in A2–B2) and contained putative Juan and transposable elements upstream of B5. A fragment of a gene with high homology to aldehyde oxidase was also present immediately downstream of A5. The comparison revealed no differences that would explain the successful spread of the A2–B2 amplicon worldwide whilst the A5–B5 amplicon is restricted to the Mediterranean.

Relationship Between Avirulence Gene (avrA) Diversity in Ralstonia solanacearum and Bacterial Wilt Incidence

Bacterial wilt, caused by Ralstonia solanacearum, is a serious disease of tobacco in North and South Carolina. In contrast, the disease rarely occurs on tobacco in Georgia and Florida, although bacterial wilt is a common problem on tomato. We investigated whether this difference in disease incidence could be explained by qualitative characteristics of avirulence gene avrA in the R. solanacearum population in the southeastern United States. Sequence analysis established that wild-type avrA has a 792-bp open reading frame. Polymerase chain reaction (PCR) amplification of avrA from 139 R. solanacearum strains generated either 792-bp or approximately 960-bp DNA fragments. Strains that elicited a hypersensitive reaction (HR) on tobacco contained the 792-bp allele, and were pathogenic on tomato and avirulent on tobacco. All HR-negative strains generated a approximately 960-bp DNA fragment, and wilted both tomato and tobacco. The DNA sequence of avrA in six HR-negative strains revealed the presence of one of two putative miniature inverted-repeat transposable elements (MITEs): a 152-bp MITE between nucleotides 542 and 543, or a 170-bp MITE between nucleotides 461 and 462 or 574 and 575. Southern analysis suggested that the 170-bp MITE is unique to strains from the southeastern United States and the Caribbean. Mutated avrA alleles were present in strains from 96 and 75% of North and South Carolina sites, respectively, and only in 13 and 0% of the sites in Georgia and Florida, respectively. Introduction of the wildtype allele on a plasmid into four HR-negative strains reduced their virulence on both tobacco and tomato. Inactivation of avrA in an HR-positive, avirulent strain, resulted in a mutant that was weakly virulent on tobacco. Thus, the incidence of bacterial wilt of tobacco in the southeastern United States is partially explained by which avrA allele dominates the local R. solanacearum population.

Pearl, a novel family of putative transposable elements in bivalve mollusks.

While genome sequencing projects have discovered numerous types of transposable elements in diverse eukaryotes, there are many taxa of ecological and evolutionary significance that have received little attention, such as the molluscan class Bivalvia. Examination of a 0.7-MB genomic sequence database from the cupped oyster Crassostrea virginica revealed the presence of a common interspersed element, CvA. CvA possesses subterminal inverted repeats, a tandemly repeated core element, a tetranucleotide microsatellite region, and the ability to form stable secondary structures. Three other less abundant repetitive elements with a similar structure but little sequence similarity were also found in C. virginica. Ana-1, a repetitive element with similar features, was discovered in the blood ark Anadara trapezia by probing a genomic library with a dimeric repeat element contained in intron 2 of a minor globin gene in that species. All of these elements are flanked by the dinucleotide AA, a putative target-site duplication. They exhibit structural similarity to the sea urchin Tsp family and Drosophila SGM insertion sequences; in addition, they possess regions of sequence similarity to satellite DNA from several bivalve species. We suggest that the Crassostrea repetitive elements and Ana-1 are members of a new MITE-like family of nonautonomous transposable elements, named pearl. Pearl is the first putative nonautonomous DNA transposon to be identified in the phylum Mollusca.

CTX-M-1, CTX-M-3, and CTX-M-14 beta-lactamases from Enterobacteriaceae isolated in France.

Six clinical CTX-M-producing isolates of the family Enterobacteriaceae were detected between 1999 and 2000 in different French hospitals. Two strains produced CTX-M-1 and CTX-M-3 and four strains produced CTX-M-14, a mutant Ala-231-->Val of CTX-M-9. A putative transposable element, ISEcp-1, was located 43 bp upstream of all the bla(CTX-M) genes. Two CTX-M-14-encoding plasmids exhibited similar restriction patterns. The CTX-M-1- and CTX-M-3-encoding plasmids were related to the CTX-M-1- and CTX-M-3-encoding plasmids previously reported in 1990 in France and in 1998 in Poland, respectively.

DNA Fingerprint Probe from Mycosphaerella graminicola Identifies an Active Transposable Element

ABSTRACT DNA fingerprinting has been used extensively to characterize populations of Mycosphaerella graminicola, the Septoria tritici blotch pathogen of wheat. The highly polymorphic DNA fingerprints of Mycosphaerella graminicola were assumed to reflect the action of transposable elements. However, there was no direct evidence to support that conclusion. To test the transposable element hypothesis, the DNA fingerprint probe pSTL70 was sequenced, along with three other clones from a subgenomic library that hybridized with pSTL70. Analysis of these sequences revealed that pSTL70 contains the 3' end of a reverse transcriptase sequence plus 29- and 79-bp direct repeats. These are characteristics of transposable elements identified in other organisms. Southern analyses indicated that either the direct-repeat or reverse-transcriptase sequences by themselves essentially duplicated the original DNA fingerprint pattern, but other portions of pSTL70 contained single-copy DNA. Analysis of 60 progeny from a sexual cross between two Dutch isolates of Mycosphaerella graminicola identified several new bands that were not present in the parents. Thus, the putative transposable element probably is active during meiosis. Tests of single-spore isolates revealed gains or losses of one or more DNA fingerprint bands in 4 out of 10 asexual lines derived from isolate IPO94269. Therefore, DNA fingerprint patterns produced by the putative transposable element were capable of changes during asexual reproduction of this isolate. Probe pSTL70 did not hybridize at high stringency to genomic DNAs from other fungi related to Septoria and Mycosphaerella. These results indicate that the DNA fingerprint probe pSTL70 most likely identifies a transposable element in Mycosphaerella graminicola that may have been acquired recently, and appears to be active during both sexual and asexual reproduction.

Genomic Exploration of the Hemiascomycetous Yeasts: 14. Debaryomyces hansenii var. hansenii

By analyzing 2830 random sequence tags (RSTs), totalling 2.7 Mb, we explored the genome of the marine, osmo- and halotolerant yeast, Debaryomyces hansenii. A contig 29 kb in length harbors the entire mitochondrial genome. The genes encoding Cox1, Cox2, Cox3, Cob, Atp6, Atp8, Atp9, several subunits of the NADH dehydrogenase complex 1 and 11 tRNAs were unambiguously identified. An equivalent number of putative transposable elements compared to Saccharomyces cerevisiae were detected, the majority of which are more related to higher eukaryote copia elements. BLASTX comparisons of RSTs with databases revealed at least 1119 putative open reading frames with homology to S. cerevisiae and 49 to other genomes. Specific functions, including transport of metabolites, are clearly over-represented in D. hansenii compared to S. cerevisiae, consistent with the observed difference in physiology of the two species. The sequences have been deposited with EMBL under the accession numbers AL436045– AL438874.

Genetic analyses of two independent chlorophyll-deficient mutants identified among the progeny of a single chimeric foliage soybean plant

Chimeric (variegated) foliage plants are frequently observed in many species. In soybean [Glycine max(L.) Merr.], progeny of chimeric plants are a source of nuclear and cytoplasmically inherited mutants. Self-pollinated progeny of a single chimeric plant derived from tissue culture of PI 427099 (Jilin 3) included plants with green foliage, chimeric foliage, yellow foliage (viable), and yellow foliage (lethal). Our objectives were to determine (1) inheritance, linkage, and allelism of the lethal-yellow mutant with known chlorophyll-deficient mutants; (2) inheritance, linkage, and allelism of the viable-yellow mutant with known chlorophyll-deficient mutants; (3) allelism of the lethal-yellow mutant with the viable-yellow mutant; and (4) male and female gamete transmission of the viable-yellow mutant trait. The viable-yellow mutant was allelic to T323, y20 y20 (Ames 2) Mdh1-n Mdh1-n (Ames 2) and was assigned genetic type collection number T361 and gene symbol y20 y20 (Ames 24) Mdh1-n Mdh1-n (Ames 22). The lethal-yellow mutant was allelic to T225H (Y18 y18) and was assigned genetic type collection number T362H and gene symbol Y18 y18 (Ames 2). T225H became Y18 y18 (Ames 1). The two chlorophyll-deficient mutants were not linked to each other. There was no significant difference in F(1) male or female gamete transmission of the viable-yellow mutant. However, many cross-combinations gave significant deviations from the expected 3 green plants:1 viable-yellow plant in the F(2) generation. The allelism of these two chlorophyll-deficient mutants with mutants T225H and T323, derived from putative transposable element systems, is intriguing. An explanation of this phenomenon awaits molecular experimentation.

Structure and location of a ferritin gene of the yellow fever mosquito Aedes aegypti.

We have isolated and sequenced a genomic clone encoding the 24- and 26-kDa ferritin subunits in the mosquito Aedes aegypti (Rockefeller strain). The A. aegypti gene differs from other known ferritin genes in that it possesses an additional intron and an unusually large second intron. The additional intron is located within the 5' untranslated region, between the CAP site and the start codon. The second intron contains numerous putative transposable elements. In addition, unlike the human and rat ferritin genes, the A. aegypti ferritin gene is a single copy gene, located at 88.3% FLpter on the q-arm of chromosome 1. Primer extension analysis indicates that the A. aegypti ferritin gene has multiple transcriptional start sites. A differential usage of these sites is observed with varied cellular iron concentrations.

Gene structure and polymorphism of an invertebrate nitric oxide synthase gene.

Nitric oxide synthases (NOSs) are ubiquitous in living organisms. However, little is known about the evolution of this large gene family. The first inducible NOS to be described from an invertebrate regulates malaria parasite (Plasmodium spp.) development in the mosquito Anopheles stephensi. This single copy gene shows the highest homology to the vertebrate neuronal isoforms, followed by decreasing homology to endothelial and inducible isoforms. The open reading frame of 1247 amino acids is encoded by 19 exons, which span approximately 33 kilobases. More than 50% of the mosquito exons, distributed around the putative heme, calmodulin, and FAD/NADPH cofactor-binding domains, are conserved with those of the three human genes. Repetitive elements identified within the larger introns include a polymorphic dinucleotide repeat, two tandem repeats, and a putative miniature inverted repeat transposable element. Sequence analysis and primer extension indicate that the upstream promoter is 'TATA-less' with multiple transcription start sites within approximately 250 base pairs of the initiation methionine. Transcription factor binding sites in the 5'-flanking sequence demonstrate a bipartite distribution of lipopolysaccharide- and inflammatory cytokine-responsive elements that is strikingly similar to that described for vertebrate inducible NOS gene promoters.

A sequence similar to bacterial transposable IS elements present in the 5' untranslated region of the bovine butanediol dehydrogenase cDNA.

A sequence similar to prokaryotic transposable elements was identified in the long 5' untranslated region (5'UTR) of the butanediol dehydrogenase cDNA isolated from a bovine brain lambda gt11 library. Several observations suggested that this sequence could be related to bacterial IS elements: (a) 58% nucleotide sequence identity, (b) 56% amino acid sequence identity, and (c) the presence of inverted terminal repeats. However, nucleotide sequence analyses of the 5'UTR bovine cDNA showed the presence of chain-terminating nucleotide substitutions that would render it incapable of encoding a functional transposase. Finally, it was observed that different vertebrate genomes have sequences related to this putative transposable element.

Characterization of nonautonomous Tc1-like transposable elements of channel catfish (Ictalurus punctatus)

Putative nonautonomous transposable elements from channel catfish (Ictalurus punctatus) were identified. They were named Tipnon elements for Tc1-like transposable elements from channel catfish that are nonautonomous. These elements were defined by their terminal repeats that share identity to members of the known Tc1/mariner transposon superfamily. They show structural similarities to Tc1-like elements, but share little sequence identity beyond the terminal inverted repeats. They do not harbor any amino acid blocks that show similarities to the Tc1-like or other transposases and thus may represent truly nonautonomous transposons in channel catfish. They are abundant in the channel catfish genome with a copy number of 32 000, having 500 base pair per copy, this family of nonautonomous transposon-like elements account for 1.6% of the channel catfish genomic DNA. Their high abundance and transposon-like terminal repeats indicate that they may play important roles in gene evolution and in genomic architecture of catfish. Similarity search for potential coding capacity of the Tipnon elements revealed that they contain sequence blocks that can potentially encode amino acid blocks similar to the para-type sodium channel proteins in cockroaches or house flies, proteins that function in the central nervous system as voltage-gated sodium transporters. Sequences surrounding the terminal inverted repeats are divergent from those used by the reconstructed Sleeping Beauty fish transposase.