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PubMed2000

Tn5044, a novel Tn3 family transposon coding for temperature-sensitive mercury resistance.

We report the discovery and characterization of the mercury resistance transposon, Tn5044, from a Xanthomonas strain from the Kamchatka peninsula. In addition to the standard set of merRTPCAD genes, the mer operon of Tn5044 contains a gene named sigY that encodes the RNA polymerase sigma factor-like protein. Mercury resistance determined by Tn5044 is expressed at low (30 degrees C) but not at elevated temperatures (37 degrees C). None of the mer operon genes downstream of merA is responsible for the temperature-sensitive mercury resistance. The transposition module of Tn5044 is closely related to those of Tn1412 isolated from medical sources and to Tn5563 and ISXc5 from environmental sources. However, Tn5044 differs from these transposons in that it has unusually long terminal inverted repeats. Sequence analysis of the transposase (tnpA) genes places Tn5044 and its close relatives into the Tn3 subgroup of the Tn3 family. However, the orientation of their resolvase and transposase genes is unusual for the Tn3 family: tnpR is proximal to the end of the transposon, while divergently transcribed tnpA is oriented inwardly. The region between tnpA and tnpR genes is unusually large and contains two short conserved open reading frames. In addition to the complete set of sequence motifs common to true resolvases, the resolvase of Tn5044 and its close relatives possesses a C-terminal extension showing no homology to known proteins. Despite this peculiarity, Tn5044 resolvase can resolve cointegrates formed during Tn5044 transposition controlled by tnpA. Genetic data suggest that the extension is essential for TnpR functioning.

Amino Acid Sequence↗
PubMed1982

Human DNA sequence homologous to the transforming gene (mos) of Moloney murine sarcoma virus.

We describe the molecular cloning of a 9-kilo-base-pair BamHI fragment from human placental DNA containing a sequence homologous to the transforming gene (v-mos) of Moloney murine sarcoma virus. The DNA sequence of the homologous region of human DNA (termed humos) was resolved and compared to that of the mouse cellular homolog of v-mos (termed mumos) [Van Beveren, C., van Straaten, F., Galleshaw, J.A. & Verma, I.M. (1981) Cell 27, 97-108]. The humos gene contained an open reading frame of 346 codons that was aligned with the equivalent mumos DNA sequence by the introduction of two gaps of 15 and 3 bases into the mumos DNA and a single gap of 9 bases into the humos DNA. The aligned coding sequences were 77% homologous and terminated at equivalent opal codons. The humos open reading frame initiated at an ATG found internally in the mumos coding sequence. The polypeptides predicted from the DNA sequence to be encoded by humos and mumos also were found to be extensively homologous, and 253 of 337 amino acids were shared between the two polypeptides. The first five NH2-terminal and last two COOH-terminal amino acids of the humos gene product were in common with those of mumos. In addition, near the middle of the polypeptide chains, four regions ranging from 19 to 26 consecutive amino acids were conserved. However, we have not been able to transform mouse cells with transfected humos DNA fragments or with hybrid DNA recombinants containing humos and retroviral long terminal repeat (LTR) sequences.

Animals↗
PubMed1992

Regulation of HIV-1 gene expression by cellular transcription factors.

The human CD4+ T lymphocytes in the peripheral blood represent a major target for HIV-1 infection in vivo. In the quiescent state T lymphocytes are nonpermissive for the propagation of HIV-1. Antigenic or mitogenic stimulation of T lymphocytes triggers a cascade of biochemical events that lead to cellular proliferation and activation of transcription and replication of HIV-1. Transcription of HIV-1 provirus in infected T cells is regulated by the interaction of both viral proteins and cellular transcription factors with the viral long terminal repeat (LTR) sequences. HIV-1 LTR has been shown to contain recognition sequences for many cellular transcription factors. These include both positive and negative regulatory factors. Interplay of cellular proteins involve both the upstream and downstream regions of the viral LTR. Our full understanding of the transcriptional regulation of HIV-1 provirus will require isolation and characterization of each of these cellular factors which bind to the HIV-1 LTR. Mutational analyses of HIV-1 LTR indicate that not all these various cellular factors are absolutely essential for the regulation of LTR-mediated viral gene expression, but their presence or absence may determine the course of HIV-1 replication in the infected cells. A balance between the inhibitory host transcription factors and the stimulatory cellular and/or viral protein factors possibly determine the final consequence of HIV-1 replication and pathogenesis.

Gene Expression Regulation, Viral↗
PubMed2001

The p38 SAPK pathway regulates the expression of the MMP-9 collagenase via AP-1-dependent promoter activation.

The invasive phenotype of cancers critically depends on the expression of proteases such as the M(R) 92,000 type IV collagenase (MMP-9). Several growth factors and oncogenes were found to increase promoter activity and as a consequence protease expression. This frequently requires the activation of the transcription factor AP-1 by signal transduction cascades such as the ERK and JNK pathways. We have previously demonstrated that the tumor promoter TPA can induce MMP-9 expression via a third signaling cascade, the p38 pathway. Considering that TPA is a potent activator of AP-1, we hypothesized that this transcription factor might also be required for p38 pathway-dependent MMP-9 regulation. While dominant negative p38 and MKK-6 mutants reduced MMP-9 promoter activity in CAT assays, a construct encoding an activating mutation in the MKK-6 protein potently stimulated it. This was mediated via 144 bp of the 5'flanking region of the wild-type promoter, which contains an AP-1 site at -79. Both point mutations in this motif and the expression of a c-jun protein lacking its transactivation domain and therefore acting as a dominant negative AP-1 mutant abrogated MKK-6-dependent promoter stimulation. Finally SB 203580, a specific p38 pathway inhibitor, reduced MMP-9 expression/secretion and in vitro invasion of cancer cells. Thus, our results provide evidence that also the third SAPK/MAPK signaling cascade, the p38 signal transduction pathway, stimulates MMP-9 expression in an AP-1-dependent fashion.

Base Sequence↗
PubMed1998

Exchange of viral promoter/enhancer elements with heterologous regulatory sequences generates targeted hybrid long terminal repeat vectors for gene therapy of melanoma.

To generate transcriptionally targeted vectors, tissue-specific elements of the human tyrosinase promoter were exchanged with corresponding viral elements in the Moloney murine leukemia virus long terminal repeat (LTR). From these experiments, a vesicular stomatitis virus type G pseudotyped, hybrid LTR vector that contained three tyrosinase enhancer elements and gave high-level, tightly tissue-specific expression at high titers (3 x 10(7) CFU/ml) was constructed.

Animals↗
PubMed2002

AR possesses an intrinsic hormone-independent transcriptional activity.

Recent research has highlighted the functional importance of chromatin structure in transcriptional regulation. We have used Xenopus oocytes as a model system to investigate the action of AR in the context of chromatin. By manipulating the levels of AR expression, we have observed both agonist-dependent and -independent activation by AR. Expression of AR at relatively low levels resulted in strong agonist-dependent activation, whereas high levels of AR also led to hormone-independent activation. By using gel mobility shift and deoxyribonuclease I footprinting assays, we demonstrate that AR expressed in Xenopus oocytes binds to a consensus androgen response element in vitro in a ligand-independent manner. Expression of the coactivators steroid receptor coactivator-1, receptor-associated coactivator-3, and p300 stimulated both agonist-dependent and -independent activation by AR. Furthermore, this hormone-independent activity of AR is also observed in mammalian cells. Antagonists such as casodex can inhibit hormone-independent activity of AR, and this inhibition appears to correlate with the enhanced association with corepressor silencing mediator of retinoid and thyroid hormone receptors. Altogether, our studies reveal that AR has a capacity to activate transcription in a ligand-independent manner.

Acetyltransferases↗
PubMed2005

The evolution of transposons in Schizosaccharomyces pombe.

Recent studies of the LTR-retrotransposons of Schizosaccharomyces pombe have shed considerable light on their evolution and function. The sequencing of the S. pombe genome allowed analysis of its transposon content. This analysis provides information about the maintenance and loss of transposons in the genome. The results of transposition assays and biochemical analyses demonstrate that the N-terminal protein of Tf1 is functionally equivalent to the Gag proteins of retroviruses and retrotransposons. Despite this conservation of function, the N-terminal protein of Tf1 lacks any sequence similarity to other known Gag proteins. Sequence analysis and experimental data also indicate that the Tf1 transposons of S. pombe target their integration into specific sites in the host genome. Transposition events resulting from the expression of Tf1 reveal a strong preference for intergenic regions, specifically at pol II promoters in a window 100-400 bp upstream of open reading frames. The complete and partial copies of Tf transposons in the sequenced genome of S. pombe show the same association of integration with promoter regions. This body of work explores how the transposon interacts with the host, the balance between the transposons propagation and loss, and how different families of transposons evolve.

DNA Polymerase II↗
PubMed1991

Activation of a diphtheria toxin A gene by expression of human immunodeficiency virus-1 Tat and Rev proteins in transfected cells.

Expression of a gene encoding the diphtheria toxin A (DT-A) fragment, controlled by tissue specific regulatory elements, has previously been used to kill selected cell populations. Here, we have examined the feasibility of controlling DT-A expression using regulatory systems from the human immunodeficiency virus (HIV-1) genome. Plasmids were constructed which express either DT-A or, as a model system, the luciferase (luc) reporter gene, under control of HIV-1 long terminal repeat (LTR) sequences (-167 to +80). While trans-activation by expression of the viral protein Tat was demonstrated, significant basal expression was observed. To reduce basal expression, cis-acting negative regulatory elements from the env region of the HIV-1 genome were inserted in the 3' untranslated region of both the luc and DT-A constructs. This dramatically reduced basal expression from the HIV LTR, and now both viral regulatory proteins Tat and Rev were required for maximal trans-activation. Such regulation of DT-A expression might be therapeutically applied to selectively kill HIV-infected cells in acquired immunodeficiency syndrome (AIDS) and AIDS-related complex (ARC).

Diphtheria Toxin↗
PubMed1991

Characterization of products of TY1-mediated reverse transcription in Saccharomyces cerevisiae.

Transposition of the yeast transposable element, Ty, has been shown to require a reverse transcription process. By analysing the extrachromosomal Ty-specific nucleic acid molecules associated with overproduced Ty virus-like particles (Ty-VLPs), we identified several reverse transcribed cDNA strands. Most of them resemble the characteristic intermediates of the reverse transcription process described for authentic retroviruses: a (-) strong-stop DNA strand covalently bound to an RNA primer, two elongated (-) strands with one or two long terminal repeat (LTR) sequences and a (+) strong-stop DNA. Surprisingly, complete (+) strands and full-length linear duplex Ty DNA could not be detected. The structural features of two additional (+) strands may indicate some differences between the mechanisms of (+) strand synthesis in Ty and other retrotransposons or retroviruses.

Base Sequence↗
PubMed2000

A novel approach for inducing enhanced and selective transgene expression in hepatocellular-carcinoma cells.

Utility of the alpha-fetoprotein (afp) promoter for gene therapy against hepatocellular carcinoma (HCC) is limited because of the weak promoter activity. To circumvent this, the 5.1-kb 5;-flanking sequence of the human afp gene including the entire enhancer and silencer regions as well as the promoter region was employed for achieving strong, HCC-selective transgene expression. To thoroughly inhibit the promoter activity of the 5;-flanking sequence of the human afp gene, the afp 5;-flanking region was inserted downstream of the human interleukin-2 (il-2) gene controlled by the simian-virus-40 (SV40) early promoter. il-2-production ability of HCC cells transduced with the construct was significantly enhanced compared with that transduced with the same construct lacking the afp 5;-flanking region. Importantly, il-2 production of non-HCC cells was substantially inhibited by the addition of the afp 5;-flanking region to the construct. When the afp 5;-flanking region was inserted downstream of the human tumor-necrosis-factor-alpha (tnf-alpha) gene controlled by the retrovirus long-terminal-repeat (LTR) enhancer/promoter, tnf-alpha production ability of HCC cells was significantly enhanced and that of non-HCC cells was significantly suppressed compared with that transduced with the same construct lacking the afp 5;-flanking region. Our results indicated that the afp 5;-flanking region gave the enhanced HCC-selective activity to the non-tissue specific SV40 early promoter and LTR enhancer/promoter. It is essential for successful gene therapy to induce strong, target-cell-selective transgene expression. This novel strategy, therefore, may contribute to the establishment of HCC-selective cancer gene therapy.

3T3 Cells↗
PubMed1994

Analysis of the complete genome of smallpox variola major virus strain Bangladesh-1975.

We analyzed the 186,102 base pairs (bp) that constitute the entire DNA genome of a highly virulent variola virus isolated from Bangladesh in 1975. The linear, double-stranded molecule has relatively small (725 bp) inverted terminal repeat (ITR) sequences containing three 69-bp direct repeat elements, a 54-bp partial repeat element, and a 105-base telomeric end-loop that can be maximally base-paired to contain 17 mismatches. Proximal to the right-end ITR sequences are another seven 69-bp elements and a 53- and a 27-bp partial element. Sequence analysis showed 187 closely spaced open reading frames specifying putative major proteins containing > or = 65 amino acids. Most of the virus proteins correspond to proteins in current databases, including 150 proteins that have > 90% identity to major gene products encoded by vaccinia virus, the smallpox vaccine. Variola virus has a group of proteins that are truncated compared with vaccinia virus counterparts and a smaller group of proteins that are elongated. The terminal regions encode several novel proteins and variants of other poxvirus proteins that potentially augment variola virus transmissibility and virulence for its only natural host, humans.

Animals↗
PubMed2002

Expression of the Idefix retrotransposon in early follicle cells in the germarium of Drosophila melanogaster is determined by its LTR sequences and a specific genomic context.

Retrotransposons are transcriptionally activated in different tissues and cell types by a variety of genomic and environmental factors. Transcription of LTR retrotransposons is controlled by cis-acting regulatory sequences in the 5' LTR. Mobilization of two LTR retroelements, Idefix and ZAM, occurs in the unstable RevI line of Drosophila melanogaster, in which their copy numbers are high, while they are low in all other stocks tested. Here we show that both a full-length and a subgenomic Idefix transcript that are necessary for its mobilization are present in the Rev1 line, but not in the other lines. Studies on transgenic strains demonstrate that the 5' LTR of Idefix contains sequences that direct the tissue-specific expression of the retroelement in testes and ovaries of adult flies. In ovaries, expression occurs in the early follicle and in other somatic cells of the germarium, and is strictly associated with the unstable genetic context conferred by the RevI line. Control of tissue-specific Idefix expression by interactions between cis-acting sequences of its LTR and trans-acting genomic factors provides an opportunity to use this retroelement as a tool for the study of the early follicle cell lineage in the germarium.

Alternative Splicing↗
PubMed2006

Screening for and genetic analysis on T-DNA-inserted mutant pool in rice.

T-DNA tagging technique has provided a powerful strategy for identifying new functional genes in plants, and the key for success is the discovery of T-DNA-inserted mutants with changed phenotype. In this study, we screened 4,416 rice T1 tagged lines generated by enhancer trap system integrated with GLL4/VP16-UAS elements from two transformed parents, ZH11 and ZH15. We found many lines showed obvious morphological mutations, including two types--fake-homozygous mutation and separating mutation. The mutation phenotype was related to 14 kinds of trait such as plant height, heading date, leaf shape, leaf color, tiller number, panicle shape, spikelet number, grain shape, disease-like mutation, male sterility, awn, and so on. Among them, plant height, heading date, leaf color and male sterility had a comparatively high mutation frequency (over 1%). The mutation frequency of plant height and leaf color had no significant change between different years or transformed parents, but the frequency of heading date and male sterility varied greatly, suggesting that environment had a great effect on the expression of latter two traits. By conducting continuously co-segregating analyses in T1 and T2 generation, we identified 3 T-DNA-inserted mutants with malformed panicle or spikelets, which would provide a base for cloning correlative functional genes. At the same time, we selected randomly 42 lines with mutation phenotype and obtained 40 flanking sequences from 39 tagged lines by plasmid rescue or TAIL-PCR, of which, 26 were vector backbone sequence, 14 had good identity to rice genome sequence. The BlastN result showed the T-DNA preferentially integrated into protein-coding region in plants.

DNA, Bacterial↗
PubMedDate not supplied

[In vitro and in vivo inhibition of HIV1 replication by retroviral transfer of interferon alpha, beta, or gamma genes: application to gene therapy of AIDS].

Somatic gene therapy is defined as the transfer of a heterologous gene into an organism for the purpose of correcting a genetic defect or providing a new therapeutic function to the target cell and thus inducing a cure or improving associated symptoms. While encouraging results have been generated by recent clinical evaluation of combination of anti-viral drugs, Aids still constitute an obvious candidate among the infectious diseases which might be treated by gene therapy. We have therefore chosen to develop and evaluate a gene therapy strategy based on the transfer into human target cells of HIV1-inducible interferon (IFN) alpha, beta or gamma genes. In a preliminary study, myeloïd U937 cell lines transfected with expression vectors containing the IFN alpha, beta or gamma genes under the control of the long terminal repeat (LTR) sequences of HIV1 were shown to be strongly resistant against an in vitro and in vivo (in HIV1 challenged SCID mice model) HIV1 infection. This cellular resistance was correlated with a strong induction of transgenic IFN synthesis and for IFN gamma, with a defect of HIV particles maturation. Secondly, construction and production of high titer retroviral vectors containing Tat-inducible IFN genes allowed efficient transduction of lymphoïd cell lines and human primary lymphocytes. These transduced cells were shown to be highly resistant against laboratory and primary HIV isolates. Taken together, our in vitro and in vivo results suggest that HIV1 inducible IFN gene therapy can be beneficial to HIV-infected individuals provided the fact that methods are developed that allow the efficient transduction of human hematopoïetic stem cells.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Plant transposable elements: where genetics meets genomics.

Transposable elements are the single largest component of the genetic material of most eukaryotes. The recent availability of large quantities of genomic sequence has led to a shift from the genetic characterization of single elements to genome-wide analysis of enormous transposable-element populations. Nowhere is this shift more evident than in plants, in which transposable elements were first discovered and where they are still actively reshaping genomes.

DNA Methylation↗
PubMed1988

The long terminal repeat of feline endogenous RD-114 retroviral DNAs: analysis of transcription regulatory activity and nucleotide sequence.

Six cloned 5' long terminal repeat (LTR) and adjoining cellular DNA regions of partially deleted feline endogenous RD-114 proviral loci were linked to the chloramphenicol acetyltransferase (CAT) gene and assayed for their ability to promote transient CAT expression. One endogenous LTR (clone CRL-3) and the LTR from an infectious RD-114 provirus, EX-LTR, were capable of actively expressing the CAT gene. DNA sequence comparison of these LTRs with an inactive endogenous LTR (CR-1) revealed extensive homology in all regions except in the 5' half of U3. The homologous portion contained transcriptional regulatory sequences including CAT, TATA, polyadenylation signal boxes and an octamer enhancer, which is rarely seen in retroviruses. Variations in the 5' half of U3 were primarily due to insertions and deletions. A major difference was in number of copies and integrity of tandemly repeated sequences. EX-LTR contained two pairs of tandem direct repeats, while the two endogenous LTRs contained different deletions of repeated sequences. DNA sequence data also revealed that the primer binding site for RD-114 loci was complementary to a glycine tRNA isotype, the use of which is distinct from any other known retrovirus. An analysis of the steady state RNA levels in T-lymphoid cell lines showed that at least three different incomplete proviral transcripts and their spliced products made up the majority of expressed RD-114 mRNA, and further demonstrated that partially deleted proviral loci have the potential to be transcriptionally vigorous in certain feline cell types.

Acetyltransferases↗
PubMed2001

Detection of MMTV-like LTR and LTR-env gene sequences in human breast cancer.

We have previously reported, using the polymerase chain reaction (PCR), the presence of a 660 bp sequence homologous to the env gene of MMTV in 38% of the human breast cancers studied, but not in normal breasts nor in other tumors or tissues. We have now investigated the presence of MMTV-like LTR sequences in human breast cancer and normal breast tissue. Primers were selected to amplify a 630 bp sequence homologous to MMTV, but not to the endogenous retrovirus HERV-K10. This sequence was detected in 41.5% of the breast cancers and none of the normal breasts. A larger 1.2 kb LTR fragment was also amplified with high homology to MMTV. Finally, a 1.6 kb fragment containing env and LTR sequences was amplified, cloned and sequenced from breast cancer DNA. The human LTRs were highly homologous to MMTV contain enhancer and promoter elements, the glucocorticoid responsive element (GRE) and the superantigen (Sag) sequences. Presence of functional sequences implies involvement in transcriptional regulation, whereas presence of an env-LTR sequence indicates contiguity within the genome of a potential provirus. Their presence in breast cancer DNA, but not in normal tissue, suggest an exogenous origin.

Animals↗
PubMed2005

PILER: identification and classification of genomic repeats.

SUMMARY: Repeated elements such as satellites and transposons are ubiquitous in eukaryotic genomes. De novo computational identification and classification of such elements is a challenging problem. Therefore, repeat annotation of sequenced genomes has historically largely relied on sequence similarity to hand-curated libraries of known repeat families. We present a new approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster. AVAILABILITY: The PILER software is freely available at http://www.drive5.com/piler.

Algorithms↗