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PubMed2006

SmTRC1, a novel Schistosoma mansoni DNA transposon, discloses new families of animal and fungi transposons belonging to the CACTA superfamily.

BACKGROUND: The CACTA (also called En/Spm) superfamily of DNA-only transposons contain the core sequence CACTA in their Terminal Inverted Repeats (TIRs) and so far have only been described in plants. Large transcriptome and genome sequence data have recently become publicly available for Schistosoma mansoni, a digenetic blood fluke that is a major causative agent of schistosomiasis in humans, and have provided a comprehensive repository for the discovery of novel genes and repetitive elements. Despite the extensive description of retroelements in S. mansoni, just a single DNA-only transposon belonging to the Merlin family has so far been reported in this organism. RESULTS: We describe a novel S. mansoni transposon named SmTRC1, for S. mansoni Transposon Related to CACTA 1, an element that shares several characteristics with plant CACTA transposons. Southern blotting indicates approximately 30-300 copies of SmTRC1 in the S. mansoni genome. Using genomic PCR followed by cloning and sequencing, we amplified and characterized a full-length and a truncated copy of this element. RT-PCR using S. mansoni mRNA followed by cloning and sequencing revealed several alternatively spliced transcripts of this transposon, resulting in distinct ORFs coding for different proteins. Interestingly, a survey of complete genomes from animals and fungi revealed several other novel TRC elements, indicating new families of DNA transposons belonging to the CACTA superfamily that have not previously been reported in these kingdoms. The first three bases in the S. mansoni TIR are CCC and they are identical to those in the TIRs of the insects Aedes aegypti and Tribolium castaneum, suggesting that animal TRCs may display a CCC core sequence. CONCLUSION: The DNA-only transposable element SmTRC1 from S. mansoni exhibits various characteristics, such as generation of multiple alternatively-spliced transcripts, the presence of terminal inverted repeats at the extremities of the elements flanked by direct repeats and the presence of a Transposase_21 domain, that suggest a distant relationship to CACTA transposons from Magnoliophyta. Several sequences from other Metazoa and Fungi code for proteins similar to those encoded by SmTRC1, suggesting that such elements have a common ancestry, and indicating inheritance through vertical transmission before separation of the Eumetazoa, Fungi and Plants.

Alternative Splicing↗
PubMed2005

Evidence for apparent gene instability in the rifamycin-producing oligoketide synthase. Implications for combinatorial biosynthesis and heterologous gene expression.

The oligoketide ('polyketide') synthase leading to the formation of proansamycin X in Amycolatopsis mediterranei also prematurely releases a range of acyclic intermediates from the enzyme complex. We intended to study the chemical biology of this ectopic chain release using RifA as a model protein system; however, we were unable to clone the rifA gene in its entirety. Restriction analysis of cosmid clones revealed that rifA is subject to random deletions at high frequency, especially in central regions of the locus. Examination of the gene sequence in this region reveals a high concentration of inverted repeats; we suggest that these sequences are subject to alteration in secondary structure when cloned outside the environment of the A. mediterranei genome, leading to recombination and deletion.

Actinomycetales↗
PubMed2003

Stable transformation of a Mamestra brassicae (lepidoptera) cell line with the lepidopteran-derived transposon piggyBac.

Cabbage moth cells were transfected with the vector pBac[3xP3-EGFPafm] and helper phsp-pBac. Seventeen percent of the transfected cells showed stable EGFP-expression. This indicates successful and stable transformation of M. brassicae cells with a piggyBac-derived vector. Genomic integration of Bac[3xP3-EGFPafm] in stably transformed cells was confirmed by Southern blots and inverse PCR. Since the integrations are stable, and transfection with pBac[3xP3-EGFPafm] alone did not yield in transformations, no cross-reacting transposase activity seems present in M. brassicae cells. Moreover, Southern blotting with a probe for piggyBac transposase indicated the absence of piggyBac-related elements in the genome of Mamestra brassicae. Due to the tissue specificity of the 3xP3-EGFP marker for eye and nervous tissues, it is intriguing that 3xP3-EGFP can successfully be used to identify stably transformed M. brassicae cells of cell line IZD-MB0503, which is hemocyte-derived. Sequence analysis of the insertion sites showed that piggyBac inverted repeats were adjacent to TTAA sequences on both termini in all the clones. The present results are particularly important as they suggest that piggyBac can be used for transgenesis of cabbage moth cells.

Animals↗
PubMed1991

Purification and functional characterization of MerD. A coregulator of the mercury resistance operon in gram-negative bacteria.

Mercury resistance operons (mer) from transposons Tn21, Tn501, and plasmid pDU1358 are highly homologous and inducible with Hg2+. The regulatory gene merR is transcribed from one promoter, which is divergently oriented from the promoter for the other mer genes. MerR, the product of the regulatory gene, negatively regulates its own expression as well as the expression of the other genes. MerR activates transcription of the operon in the presence of inducing concentrations of Hg2+. The most promoter distal gene, merD, which is cotranscribed with the structural genes, down regulates the mer operon. A frame-shift mutation in merD, created by deletion of 3 bp and an insertion of a 16 bp sequence upstream of the major inverted repeats present at the 3' end of the merD sequence, resulted in increased synthesis of the structural gene transcript and higher level of resistance to Hg2+ by a factor of about 2. MerD protein was over-produced using a T7 expression system. The overproduced protein was present in the pellet fraction, when cell lysates were centrifuged at a low speed. Approximately 80% pure MerD protein was recovered from the pellet fraction by extracting with a buffer solution containing 5 M urea. The purified protein migrated as a 13,500 molecular weight protein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the N-terminal amino acid sequence corresponded to that deduced from the DNA sequence of merD. MerD bound specifically with the mer promoter sequence. DNase I footprinting experiments identified a common mer operator sequence for MerR and MerD.

Bacterial Proteins↗
PubMed1995

Differences in DNA sequence recognition by the heat-shock factors of Drosophila melanogaster and the parasitic helminth Schistosoma mansoni.

It was recently shown that schistosome extracts contain heat-shock factor (HSF) activity that correlates with the pattern of hsp70 mRNA levels at different developmental stages of the parasite (Levy-Holtzman and Schechter (1994) Parasitology 108, 35-42). To extend our understanding of the HSF activity revealed in extracts of Schistosoma mansoni (Sm), it was further analyzed by competition experiments and compared with the well characterized HSF of Drosophila melanogaster (Dm). The interactions of HSF in Sm extracts (SmHSF) and HSF of Dm (DmHSF) with 32P-labeled heat shock element (HSE) probes, with and without unlabeled competitor DNA probes (HSE-related oligos), were analyzed by gel retardation assay. The binding and inhibition studies demonstrated that SmHSF and DmHSF differ in HSE sequence recognition: an array of three nGAAn inverted repeats according to the ideal consensus sequence (nGAAnnTTCnnGAAn) is recognized by DmHSF, but not by SmHSF. In the schistosome, binding is attained only when the third pentamer is a variant, composed of nGTAn instead of nGAAn. The presence of this variant in the promoter of the hsp70 gene of the parasite suggests coevolution of the variant sequence together with the SmHSF which interacts efficiently with the variant, but not with the ideal HSE sequence. Further inhibition studies revealed additional differences between SmHSF and DmHSF in recognition of the first and second nGAAn pentamers of HSE. In analogy to other systems of ligand-protein interactions, we propose that the complementarity between the HSE ligand and the HSF protein is higher in SmHSF, as compared to DmHSF.

Animals↗
PubMed2006

DNA topology and geometry in Flp and Cre recombination.

The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the lambda-integrase (Int) family of site-specific recombinases. These recombination systems recognize recombination-target sequences that consist of two 13bp inverted repeats flanking a 6 or 8bp spacer sequence. Recombination reactions involve particular geometric and topological relationships between DNA target sites at synapsis, which we investigate using nicked-circular DNA molecules. Examination of the tertiary structure of synaptic complexes formed on nicked plasmid DNAs by atomic-force microscopy, in conjunction with detailed topological analysis using the mathematics of tangles, shows that only a limited number of recombination-site topologies are consistent with the global structures of plasmids bearing directly and inversely repeated sites. The tangle solutions imply that there is significant distortion of the Holliday-junction intermediate relative to the planar structure of the four-way DNA junction present in the Flp and Cre co-crystal structures. Based on simulations of nucleoprotein structures that connect the two-dimensional tangle solutions with three-dimensional models of the complexes, we propose a recombination mechanism in which the synaptic intermediate is characterized by a non-planar, possibly near-tetrahedral, Holliday-junction intermediate. Only modest conformational changes within this structure are needed to form the symmetric, planar DNA junction, which may be characteristic of shorter-lived intermediates along the recombination pathway.

Base Sequence↗
PubMed1982

Differentiation between alpha promoter and regulator regions of herpes simplex virus 1: the functional domains and sequence of a movable alpha regulator.

The herpes simplex virus genome consists of at least three groups of genes--alpha, beta, and gamma--whose expression is coordinately regulated and sequentially ordered in a cascade fashion. We have established that the elements involved in regulation of alpha genes are a sequence that promotes gene expression and a sequence that confers alpha regulation on the gene by responding to trans-acting regulatory signals. The domains of these sequences were mapped by determining the regulation of thymidine kinase (TK) in L cells converted to TK+ phenotype by chimeric TK indicator genes. The chimeric genes were constructed from appropriate portions of the TK gene fused to donor sequences derived from the 5' nontranscribed and nontranslated leader portions of the viral alpha gene 4. The results were as follows. (i) The natural beta TK indicator extending 5' up to -80 and the chimeric alpha TK extending 5' up to -110 both converted cells to TK+ phenotype but were not regulated. (ii) A segment of the regulator region of the alpha gene 4, extending 5' from position -110, confers inducible alpha-type regulation when fused to the nonregulated but expressible beta TK indicator described above. (iii) The extent of gene induction appears to hinge on the size of the regulatory region inserted into the chimeric gene and correlates with the presence of repeated consensus sequences and G+C-rich inverted repeats in the regulatory region of the alpha gene 4 and other alpha genes.

DNA, Recombinant↗
PubMed1993

Cloning and characterization of a highly conserved satellite DNA sequence specific for the phytoparasitic nematode Bursaphelenchus xylophilus.

The phytoparasitic nematode, Bursaphelenchus xylophilus, contains an unusually abundant satellite DNA which constitutes up to 30% of its genome. It is represented as a tandemly repeated MspI-site-containing sequence with a monomeric unit of 160 bp. Thirteen monomers were cloned and sequenced. The consensus sequence is 62% A+T-rich, with the presence of direct and inverted repeat clusters. Monomers of the sequence are very similar, showing on average 3.9% divergence from the calculated consensus. The results suggest that some homogenizing mechanism is acting to maintain the homogeneity of this satellite DNA despite its abundance and that it is not transcribed.

Animals↗
PubMed1988

IST2: an insertion sequence from Thiobacillus ferrooxidans.

The genome of Thiobacillus ferrooxidans (strain ATCC 19859) contains at least two families of repeated sequences, termed family 1 and 2. The nucleotide sequence of a family 2 member was determined. It is 1408 base pairs long and has structural features similar to those of insertion sequences (IS elements). Terminal inverted repeats 25 base pairs in length are present. These inverted repeats are imperfect and adjacent to target-site duplications 9 base pairs in length. Several open reading frames were detected (the longest was 888 base pairs). We have named this IS element-like sequence IST2. The ends of a second example of IST2 were analyzed and compared to those of the first. The DNA sequences are identical and similarly sized target-site duplications are present.

Base Sequence↗
PubMed1993

Molecular characterization of a mouse Y chromosomal repetitive sequence amplified in distantly related species in the genus Mus.

This report describes a 1.1 kb long mouse Y chromosomal sequence designated 142-4. It has a 42% GC content and is rich in short direct and inverted repeats. 142-4 related sequences are repeated about 200 times in the Mus musculus Y chromosome and their distribution was visualized by in situ hybridization. 142-4 detected a restriction fragment length polymorphism that differentiated between the M. m. musculus type and the M. m. domesticus type Y chromosome. Southern blot analysis of DNAs isolated from a panel of mouse species showed that 142-4 related sequences were amplified in the Y chromosomes of M. minutoides, M. musculus, M. saxicola, M. spicilegus, and M. spretus but not in those of M. caroli, M. cookii, and M. pahari. These results suggest that 142-4 related sequences are evolutionarily unstable and their accumulation patterns do not correlate with the known phylogenetic relationships of mouse species in the genus Mus.

Animals↗
PubMed2003

Making a better RNAi vector for Drosophila: use of intron spacers.

Double-stranded RNA induces sequence-specific inhibition of gene expression at a posttranscriptional level in eukaryotes (RNAi). This natural phenomenon has been developed into a tool for studying gene function in several model organisms, including Drosophila melanogaster. Transgenes bearing inverted repeats are able to exert an RNAi effect in Drosophila, but cloning difficulties and inconsistent silencing complicate the method. We have constructed a transgene containing inverted repeats separated by a functional intron such that mRNA produced by the transgene is predicted to form loopless hairpin RNA following splicing. A single copy of the transgene effectively and uniformly silences expression of a target gene (white) in transgenic flies. We have developed a vector that is designed to produce intron-spliced hairpin RNA corresponding to any Drosophila gene. The vector is under control of the upstream activating sequence (UAS) of the yeast transcriptional activator GAL4. The UAS/GAL4 system allows hairpin RNA to conditionally silence gene expression in Drosophila in a tissue-specific manner. Moreover, the presence of the intron spacer greatly enhances the stability of inverted-repeat sequences in bacteria, facilitating the cloning procedure.

Animals↗
PubMed1989

Analysis of separate isolates of Bordetella pertussis repeated DNA sequences.

Two independent isolates of a Bordetella pertussis repeated DNA unit were sequenced and shown to be an insertion sequence element with five nucleotide differences between the two copies. The sequences were 1053 bp in length with near-perfect terminal inverted repeats of 28 bp, had three open reading frames, and were each flanked by short direct repeats. The two insertion sequences showed considerable homology to two other B. pertussis repeated DNA sequences reported recently: IS481 and a 530 bp repeated DNA unit. The B. pertussis insertion sequence would appear to comprise a group of closely related sequences differing mainly in flanking direct repeats and the terminal inverted repeats. The two isolates reported here, which were from the adenylate cyclase and agglutinogen 2 regions of the genome, were numbered IS48lvl and IS48lv2 respectively.

Base Sequence↗
PubMed1990

Short interspersed repeats from Xenopus that contain multiple octamer motifs are related to known transposable elements.

We have identified in an intron of an X. laevis alpha-tubulin gene a member of a novel family of short (226-431 bp) interspersed repetitive elements. We have isolated other members of this family, which we term Ocr, from ovary cDNA and genome libraries and have identified another two in the published sequences of an H1B histone gene cluster and an actin gene intron. The termini of the Ocr elements are formed by a 19 bp inverted repeat that has clear sequence homologies to those of certain large transposable elements, such as 1723 (Xenopus) and Ac (maize). However, the Ocr elements do not appear to be deletion derivatives of larger transposons. The internal regions of the Ocr elements contain multiple copies of the octamer motif (ATTTGCAT) arranged as divergently-orientated dyads. We have shown by a gel mobility shift assay that these octamer dyads specifically bind what is presumably an OTF-type activator protein in oocyte nuclear extracts. We speculate that short interspersed repetitive families of this type may be generated by a mechanism of replicative transposition that uses a DNA intermediate and involves the interaction of DNA-binding proteins also utilised in other cellular processes.

Animals↗
PubMed1994

A small family of elements with long inverted repeats is located near sites of developmentally regulated DNA rearrangement in Tetrahymena thermophila.

Extensive DNA rearrangement occurs during the development of the somatic macronucleus from the germ line micronucleus in ciliated protozoans. The micronuclear junctions and the macronuclear product of a developmentally regulated DNA rearrangement in Tetrahymena thermophila, Tlr1, have been cloned. The intrachromosomal rearrangement joins sequences that are separated by more than 13 kb in the micronucleus with the elimination of moderately repeated micronucleus-specific DNA sequences. There is a long, 825-bp, inverted repeat near the micronuclear junctions. The inverted repeat contains two different 19-bp tandem repeats. The 19-bp repeats are associated with each other and with DNA rearrangements at seven locations in the micronuclear genome. Southern blot analysis is consistent with the occurrence of the 19-bp repeats within pairs of larger repeated sequences. Another family member was isolated. The 19-mers in that clone are also in close proximity to a rearrangement junction. We propose that the 19-mers define a small family of developmentally regulated DNA rearrangements having elements with long inverted repeats near the junction sites. We discuss the possibility that transposable elements evolve by capture of molecular machinery required for essential cellular functions.

Animals↗
PubMed1991

Nucleotide sequence of Rhizobium meliloti insertion sequence ISRm1: homology to IS2 from Escherichia coli and IS426 from Agrobacterium tumefaciens.

Nucleotide sequencing of Rhizobium meliloti insertion sequence ISRm1 showed that it is 1319 nucleotides long and includes 32/31 nucleotide terminal inverted repeats. Analysis of five different insertion sites using sequencing primers complementary to sequences within the left and right ends demonstrated that ISRm1 generates five bp direct repeats at the sites of insertion. Although ISRm1 has shown a target preference for certain short regions (hot spots), there was no apparent similarity in the DNA sequences near the insertion sites. On one strand ISRm1 contains two contiguous open reading frames (ORFs) spanning most of its length. ISRm1 was found to have over 50% sequence homology to insertion sequences IS2 from Escherichia coli and IS426 from Agrobacterium tumefaciens. Their sizes, the sequences of their inverted repeats, and the characteristics of their insertion sites are also comparable, indicating that ISRm1, IS2 and IS426 belong to a class of related insertion sequences. Comparison of the proteins potentially encoded by these insertion sequences showed that the two ORFs found in ISRm1 are also present in IS2 and IS426, suggesting that they may be functional genes.

Agrobacterium tumefaciens↗
PubMed2004

A method for cloning and sequencing long palindromic DNA junctions.

DNA sequences containing long adjacent inverted repeats (palindromes) are inherently unstable and are associated with many types of chromosomal rearrangements. The instability associated with palindromic sequences also creates difficulties in their molecular analysis: long palindromes (>250 bp/arm) are highly unstable in Escherichia coli, and cannot be directly PCR amplified or sequenced due to their propensity to form intra-strand hairpins. Here, we show that DNA molecules containing long palindromes (>900 bp/arm) can be transformed and stably maintained in Saccharomyces cerevisiae cells lacking a functional SAE2 gene. Treatment of the palindrome-containing DNA with sodium bisulfite at high temperature results in deamination of cytosine, converting it to uracil and thus reducing the propensity to form intra-strand hairpins. The bisulfite-treated DNA can then be PCR amplified, cloned and sequenced, allowing determination of the nucleotide sequence of the junctions. Our data demonstrates that long palindromes with either no spacer (perfect) or a 2 bp spacer can be stably maintained, recovered and sequenced from sae2Delta yeast cells. Since DNA sequences from mammalian cells can be gap repaired by their co-transformation into yeast cells with an appropriate vector, the methods described in this manuscript should provide some of the necessary tools to isolate and characterize palindromic junctions from mammalian cells.

Base Sequence↗
PubMed2001

Androgen-receptor-specific DNA binding to an element in the first exon of the human secretory component gene.

Androgens and glucocorticoids are steroid hormones, which exert their effects in vivo by binding and activating their cognate receptors. These intracellular receptors are transcription factors that can bind specific DNA sequences, called hormone response elements, located near the target genes. Although the androgen receptor (AR) and the glucocorticoid receptor (GR) bind the same consensus DNA sequence, androgen-specific responses can be achieved by non-conventional androgen response elements (AREs). Here we determine the specificity mechanism of such a selective element recently identified in the first exon of the human gene for secretory component (sc ARE). This sc ARE consists of two receptor-binding hexamers separated by three nucleotides. The DNA-binding domains of the AR and GR both bind the sc ARE, but, although the AR fragment dimerizes on the element, the GR fragment does not. Comparing the affinities of the DNA-binding domains for mutant forms of the sc ARE revealed that dimeric GR binding is actively excluded by the left hexamer and more precisely by the presence of a G residue at position -3, relative to the central spacer nucleotide. Inserting a G at this position changed a non-selective element into an androgen-selective one. We postulate that the AR recognizes the sc ARE as a direct repeat of two 5'-TGTTCT-3'-like core sequences instead of the classical inverted repeat. Direct repeat binding is not possible for the GR, thus explaining the selectivity of the sc ARE. This alternative dimerization by the AR on the sc ARE is also indicated by the DNA-binding characteristics of receptor fragments in which the dimerization interfaces were swapped. In addition, the flanking and spacer sequences seem to affect the functionality of the sc ARE.

Animals↗