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At least 469 records · Page 26Linked to original sources
PubMed2001

Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses.

We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources provides surprising insights into the evolution of eukaryotic retrotransposons. First, it indicates that the lineage of elements leading to vertebrate retroviruses acquired a new RNH domain either from non-LTR retrotransposons or from a eukaryotic host genome. The preexisting retroviral RNH domain degenerated to become the tether (connection) domain of the reverse transcriptase (RT)-RNH complex. Second, it indicates that all LTR retrotransposons arose in eukaryotes well after the origin of the non-LTR retrotransposons. Because of the younger age of the LTR retrotransposons, their complex structure, and the absence of any prokaryotic precursors, we propose that the LTR retrotransposons originated as a fusion between a DNA-mediated transposon and a non-LTR retrotransposon. The resulting two-step mechanism of LTR retrotransposition, in which RNA is reverse transcribed away from the chromosomal target site, rather than directly onto the target site, was probably an adaptation to the uncoupling of transcription and translation in eukaryotic cells.

Amino Acid Motifs↗
PubMed2000

The complete genomic sequence of a BLV strain from a Holstein cow from Argentina.

DNA was extracted from the peripheral blood of a seropositive, PCR-positive, BLV-infected Holstein cow (No. 38) from Argentina. The DNA was amplified via PCR with a series of overlapping primers encompassing the entire BLV proviral DNA. The amplified BLV ARG 38 DNA was cloned, sequenced, and compared phylogenetically to three other full-length BLV sequences. Characterization of its deduced proteins and its relationship to other members of the PTLV/BLV genus of retroviruses are discussed.

Amino Acid Sequence↗
PubMed2002

The novel early region 3 protein E3/49K is specifically expressed by adenoviruses of subgenus D: implications for epidemic keratoconjunctivitis and adenovirus evolution.

The early transcription unit 3 (E3) of adenoviruses (Ads) encodes immunomodulatory functions. We previously described a novel gene of 49K within the E3 region of Ad19a, an Ad of subgenus D that is similar to Ad8 and Ad37 causes epidemic keratoconjunctivitis (EKC). Interestingly, 49K was reported not to be present in Ad9 and Ad17, other subgenus D Ads not causing EKC. Therefore, we investigated whether 49K is selectively expressed in EKC-causing Ads. Using specific DNA probes, we detect 49K-homologous genes in all subgenus D Ads tested. Moreover, 49K-specific antibodies recognize a high molecular weight protein in cells infected with all subgenus D serotypes irrespective of their ability to cause EKC. Sequencing of several 49K genes reveals a high homology without a distinct feature recognizable for those of EKC-associated Ad strains. Thus, E3/49K is a subgenus D specific E3 protein whose expression does not correlate with the EKC-causing phenotype and thus may rather be implicated in illnesses commonly caused by this subgenus. Interestingly, the 49K sequences of Ad19a and Ad37 are identical. To estimate the extent of the sequence identity between these two viruses, we initially sequenced the right ITR and the hexon. This analysis revealed that the right ITR of Ad19a is identical to Ad37, while the hexon sequence is Ad19p-like. This suggested that the region of identity is much larger and that Ad19a arose by recombination of Ad37 with an Ad19p-like Ad. Further sequencing mapped the crossover within the DNA binding protein. Thus, Ad19a contains a large sequence block ( approximately 13 kb), from the 100K gene to the right ITR, identical to Ad37. The implications of these findings in light of the temporal appearance of the EKC-causing Ad strains are discussed.

Adenovirus E3 Proteins↗
PubMed2001

Vertebrate LTR retrotransposons of the Tf1/sushi group.

LTR retrotransposons of the Tf1/sushi group from a diversity of vertebrates, including fish, amphibians, and mammals (humans, mice, and others), are described as full-length or partial elements. These elements are compared, and the mechanisms involved in self-priming of reverse transcriptase and programmed phase shifting are inferred. Evidence is presented that in mammals these elements are still transcriptionally active and are represented as proteins. This suggests that members of the Tf1/sushi group are present as functional elements (or incorporated as partial elements into host genes) in diverse vertebrate lineages.

Amino Acid Sequence↗
PubMed2000

Identification and characterization of the promoter for the gene encoding the human myeloid IgA Fc receptor (FcalphaR, CD89).

The Fc receptor for IgA (FcalphaR, CD89), a transmembrane glycoprotein, is expressed exclusively on human phagocytic cells including monocytes, macrophages, eosinophils, and neutrophils, and is capable of triggering various effector functions. In the present study, we identified and characterized, for the first time, the FcalphaR promoter. A 929-bp fragment of FcalphaR 5'-flanking sequence directed expression of a reporter gene specifically in monocytic cell line U937. Deletion analyses localized element(s) directing tissue-specific reporter gene expression to the 259 bp proximal to the translation initiation site. Within the region, the sequence between 59 and 197 bp downstream of the major transcription start site was shown to be essential for promoter activity. This sequence contains multiple potential binding sites for transcription factors which have been reported to function in myeloid-specific gene expression, including three CCAAT enhancer-binding protein (C/EBP)-binding sites, an NF-kappaB-binding site, an Spl site, an Ets family protein consensus-binding site, and a Myb-binding site. In addition, we identified two polymorphisms (C-->T transition) at the positions 114 bp upstream and 56 bp downstream of the major transcription start site, and demonstrated that the FcalphaR promoter region carrying both the -114T and +56T alleles had significantly lower promoter activity than that harboring the C alleles at both sites. Characterization of this promoter will facilitate further analyses of activation stimuli and transcription factors involved in FcalphaR-mediated immune system, and provide new insights into the mechanism(s) underlying altered FcalphaR expression associated with diseases such as allergic diseaes and IgA nephropathy.

Antigens, CD↗
PubMed2005

Complete mitochondrial genomes of the three brown algae (Heterokonta: Phaeophyceae) Dictyota dichotoma, Fucus vesiculosus and Desmarestia viridis.

We report the complete mitochondrial sequences of three brown algae (Dictyota dichotoma, Fucus vesiculosus and Desmarestia viridis) belonging to three phaeophycean lineages. They have circular mapping organization and contain almost the same set of mitochondrial genes, despite their size differences (31,617, 36,392 and 39,049 bp, respectively). These include the genes for three rRNAs (23S, 16S and 5S), 25-26 tRNAs, 35 known mitochondrial proteins and 3-4 ORFs. This gene set complements two previously studied brown algal mtDNAs, Pylaiella littoralis and Laminaria digitata. Exceptions to the very similar overall organization include the displacement of orfs, tRNA genes and four protein-coding genes found at different locations in the D. dichotoma mitochondrial genome. We present a phylogenetic analysis based on ten concatenated genes (7,479 nucleotides) and 29 taxa. Stramenopiles were always monophyletic with heterotrophic species at the base. Results support both multiple primary and multiple secondary acquisitions of plastids.

Base Sequence↗
PubMed2005

A 0.3-kb fragment containing the R-U5-5' leader sequence is essential for the induction of spongiform neurodegeneration by A8 murine leukemia virus.

Friend murine leukemia virus (Fr-MLV) clone A8 causes spongiform neurodegeneration in the rat brain. The A8-env gene is a primary determinant of neuropathogenicity, and the 1.5-kb ClaI-HindIII fragment containing the LTR and 5' leader from A8 are additionally required for spongiosis. After replacement of the A8 enhancer region of the neuropathogenic chimera with the enhancer region of non-neuropathogenic 57, viral titer in the brain was reduced by two orders of magnitude. However, the A8 enhancer region was not responsible for the induction of spongiosis. The region responsible for neuropathogenesis was located in the 0.3-kb KpnI-AatII fragment of A8 containing the R-U5-5' leader. The chimeric virus possessing this 0.3-kb fragment of A8 and the A8-env in the 57 background induced a high rate of spongiform neurodegeneration within 7 weeks (9/9 of infected rats). Studies using cultured cells suggest that the 0.3-kb fragment influences the expression of Env protein. Furthermore, these neuropathogenic chimerae, despite low viral replication in the brain, exhibited a stronger expression of Env protein compared with that of non-neuropathogenic viruses.

5' Untranslated Regions↗
PubMed2003

Enhancement of equine infectious anemia virus virulence by identification and removal of suboptimal nucleotides.

Pathogenicity was reportedly restored to an avirulent molecular clone of equine infectious anemia virus (EIAV) by substitution of 3' sequences from the pathogenic variant strain (EIAV(PV)). However, the incidence of disease in horses/ponies was found to be significantly lower (P = 0.016) with the chimeric clone (EIAV(UK)) than with EIAV(PV). This was attributable to 3' rather than 5' regions of the proviral genome, where EIAV(UK) differs from the consensus EIAV(PV) sequence by having a 68-bp duplication in the 3' LTR and arginine (R(103)) rather than tryptophan (W(103)) at position 103 in the second exon of rev. In EIAV(UK) recipients the duplication was rapidly eliminated and R(103) replaced by W(103) in the viral population. Furthermore, removal of the 3' variant sequences from EIAV(UK) (EIAV(UK3)) resulted in an equivalent (P = 0.013) disease potential in Equus caballus to EIAV(PV). The 68-bp duplication and/or R(103) may limit peak viral RNA accumulation during acute infection.

Amino Acid Sequence↗
PubMed2003

A co-opted gypsy-type LTR-retrotransposon is conserved in the genomes of humans, sheep, mice, and rats.

One subset of sequences present within mammalian genomes is the retroelements, which include endogenous retroviruses and retrotransposons. While there are typically thousands of copies of endogenous retroviruses within mammalian hosts, almost no LTR-retrotransposon-like sequences have been identified. Here, we report the presence of a remarkably intact and conserved gypsy-type LTR-retrotransposon sequence within the genomes of several mammals, including humans and mice. Each host probably contains a single orthologous element, indicating that the original, ancestral gypsy LTR-retrotransposon first integrated into mammals over 70 million years ago. It is thus the first described example of a near-intact orthologous retroelement within humans and mice and is one of the most ancient retroelement sequences described to date. Despite their extreme age, the orthologs within each species examined contain a large ORF, between 4.0 and 5.2 kb in length, encoding proteins with sequence similarity to LTR-retrotransposon-derived Capsid (CA), Protease (PR), Reverse Transcriptase (RT), RibonucleaseH (RNaseH), and Integrase (IN). Calculation of nonsynonymous and synonymous nucleotide substitution frequencies indicated that the encoded proteins are under purifying selection, suggesting that these elements have, in fact, been co-opted by their hosts. A possible function for these elements, involving gypsy LTR-retrotransposon restriction in mammals, is discussed.

Amino Acid Sequence↗
PubMed2000

Genome organization and phylogenetic distribution of a novel family of ancient murine endogenous proviruses with evidence for transposition-mediated proliferation.

A new family of murine endogenous proviruses (VL6.0) is described here. The intact provirus is near 6 kb in length and shows a genomic organization of 5' LTR, gag, pol, env, and 3' LTR. The primer binding site (PBS) is that of a tRNA(gly). The lack of functional open reading frames and occurrence of significant gaps in most, if not all, members of this group show it to be ancient. Our estimate of copy number per haploid genome is 30+. Members of this group have been isolated from Mus musculus domesticus, M. m. casteneus, M. m. hortulanus, M. caroli, and M. spretus. The occurrence of these sequences throughout such diverse members of the genus Mus may indicate that the date of the original infection predated the divergence of the extant Mus lineages at around 2.5 million years ago. Analysis of gap (deletion/insertion) patterns indicates that these sequences may have proliferated within the Mus genome by a mechanism of reverse transcriptase-mediated transposition. As yet, there are no closely related murine retroviruses described. The closest mammalian retrovirus based on sequence similarity is from the miniature swine (Sus scrofa).

Amino Acid Sequence↗
PubMed1998

RNA expression from a site-specific non-LTR retrotransposon microinjected into Xenopus oocytes.

Tx1L is a site-specific non-LTR retrotransposon (NLR) that has been identified in the genome of Xenopus laevis. Using microinjection into Xenopus oocytes, several aspects of RNA expression by these elements were investigated. With constructs carrying various parts of the element we saw no evidence of promoter activity, unlike what has been shown for several other elements of this class. Tx1L transcription was induced by linking a whole element to a promoter that is active in oocytes. Among the RNAs produced, about half had 3' ends located near the end of the element, suggesting that instruction for 3' end formation are encoded in the element or its target. Deletion of the 3' UTR of Tx1L and of surrounding target sequences indicated that these regions are not required for termination or processing of the RNA. PolyA or very A-rich sequences were added at these 3' ends, despite the absence of canonical polyA addition signals. A significant proportion of non-A residues was found in the 3' untemplated tails, and this is reminiscent of non-templated insertions often found at the 3' junction of new genomic copies of some NLRs.

3' Untranslated Regions↗
PubMed2002

MMTV-associated transcription factor binding sites increase nm23-H1 metastasis suppressor gene expression in human breast carcinoma cell lines.

We hypothesize that elevation of nm23-HI metastasis suppressor gene expression in micrometastatic tumor cells may reduce their subsequent colonization and invasion, and induce differentiation, with a clinical benefit. This report presents the first analysis of the nm23-HI promoter to identify sites which can increase its transcription. Deletion mapping of a 2.1 kb nm23-H1 promoter fragment tethered to a reporter gene identified three regions involved in its differential expression levels among a panel of human breast carcinoma cell lines: a 195 bp NheI-XbaI fragment responsible for basal expression levels, a 248 bp AvrII-Nhel fragment which contributed to the elevated nm23-H1 expression observed in the high expressing cell lines, and a 544 bp AvrII fragment containing an inhibitory element. Examination of the 248 bp AvrII-NheI fragment revealed the unexpected presence of three transcription factor binding sites (MAF/Ets, CTF/NF1 half site and ACAAAG enhancer) previously identified in the MMTV-LTR, and in WAP and milk gene promoters, proposed to mediate mammary-specific gene expression. Mutation of the three sites, individually or together, resulted in two-fold reductions in reporter gene expression. As controls, the same panel of mutations caused a different pattern of reporter gene expression in a non-mammary cell line, and mutation of another nearby site was without effect on nm23-HI. Our data identify a complex regulatory pattern for nm23-H1 transcription, and suggest that a mammary-specific cassette of transcription factors contribute to its elevated expression

Binding Sites↗
PubMed2000

HERV-IP-T47D, a novel type C-related human endogenous retroviral sequence derived from T47D particles.

A new type C retrovirus-related endogenous pol sequence (ERV-FTD) found to be occasionally copackaged in retrovirus-like particles released by the human mammary carcinoma cell line T47D was used to screen a human genomic library (Seifarth W, Skladny H, Krieg-Schneider F, Reichert A, Hehlmann R, and Leib-Mösch C: J Virol 1995;69:6408-6416). The DNA sequence of one full-length clone now reveals a human endogenous proviral sequence (HERV) of 4190 bp in length comprising a 5' LTR (489 bp) and regions with 37 and 74% overall amino acid homology to RTVL-Ia gag and pol genes, respectively. About 35 related elements were found to be distributed on all human chromosomes except 16, 17, and Y. Sequence comparisons with Mo-MuLV and various type C-related HERVs suggest that despite a proline primer-binding site this novel HERV element, now named HERV-IP-T47D, can be assigned to one family together with known HERV-I elements. Phylogenetic analyses of 5 proviral and 25 solitary LTR sequences confirmed the existence of two distinct but closely related subgroups of the HERV-IP superfamily in the primate genome. In contrast to most known HERV-families, the evolutionary age of HERV-IP elements dates back prior to the divergence of New and Old World monkeys. Despite their old age, members of the HERV-IP family are still transcriptionally active and were found to be highly expressed in specific human tissues such as liver and kidney.

Amino Acid Sequence↗
PubMed1999

High rate of human T lymphotropic virus type IIa infection in HIV type 1-infected intravenous drug abusers in Ireland.

Serological and molecular analyses of a cohort of HIV-1-infected intravenous drug abusers (IVDAs) (n = 103) in Dublin, Ireland have demonstrated that 15 of 103 (14.6%) were infected with HTLV-II, which is the highest infection rate yet recorded for any European country. Restriction fragment length polymorphism (RFLP) analysis of the env region of the provirus demonstrated that the infection involved only the HTLV-IIa subtype; the HTLV-IIb subtype was not detected. Phylogenetic analysis of the nucleotide sequences of the long terminal repeat (LTR) confirmed infection with the HTLV-IIa subtype, and demonstrated that the viruses clustered closely with HTLV-IIa isolates from North American IVDAs. Previous observations that IVDAs in southern Europe, specifically Spain and Italy, appear to be infected predominantly with the HTLV-IIb subtype, along with the present report and evidence that IVDAs in Sweden are infected with the HTLV-IIa subtype, suggest different origins of HTLV-II infection in Europe.

Adult↗
PubMed2006

Distribution of human T cell lymphotropic virus type 1 (HTLV-1) subtypes in Brazil: genetic characterization of LTR and tax region.

We report the molecular and epidemiological characterization of 128 human T cell lymphotropic virus type 1 (HTLV-1) isolates from Brazilian patients with different clinical manifestations of the infection. Thirty-two percent of the patients were asymptomatic, 44% had HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), and 23% had adult T cell leukemia/lymphoma (ATLL). Phylogenetic analysis performed using part of the LTR region of the viral genome revealed that all Brazilian isolates belonged to the Cosmopolitan subtype, with the following distribution within the Transcontinental subgroup: 81.6% within the Latin American cluster and 15.8% outside the Latin American cluster. Two isolates belonged to the Japanese subgroup. Molecular analysis of the tax region showed a high nucleotide similarity ( approximately 99%) with 41 prototype sequences, including the ATK-1 isolate. The mean number of nucleotide substitutions ranged from 1 to 8. Five specific nucleotide substitutions, C7401T, T7914C, C7920T, C7982T, and G8231A, were highly conserved among the Brazilian isolates (79.6%), with a frequency ranging from 81.6% to 100% in the sample group and from 18.4% to 24.1% in the prototypes used, suggesting the existence of a molecular signature. These changes were not correlated with a specific clinical status of the patients and could be a molecular characteristic of the HTLV-1 strains that circulate in Brazil.

Adolescent↗
PubMed1999

Hormone-dependent regulation of intercellular adhesion molecule-1 gene expression: cloning and analysis of 5'-regulatory region of rat intercellular adhesion molecule-1 gene in FRTL-5 rat thyroid cells.

Intercellular adhesion molecule-1 (ICAM-1) has been suggested to play an important role in the perpetuation of autoimmune thyroid disease. To clarify the regulation of ICAM-1 gene in thyroid cells, we investigated ICAM-1 expression in the FRTL-5 thyroid cell model and defined several elements in the 5'-regulatory region that are important for transcriptional regulation of the rat ICAM-1 gene. Cells maintained in medium with 5% serum but without hydrocortisone, insulin, and thyrotropin (TSH) express the highest levels of ICAM-1 RNA. TSH/forskolin downregulate ICAM-1 RNA levels independent of the presence or absence of hydrocortisone or insulin. Moreover, TSH/forskolin decrease ICAM-1 RNA levels that are maximally induced by two cytokines: 100 ng/mL tumor necrosis factor-alpha (TNF-alpha) or 100 U/ml interferon-gamma (IFN-gamma). The effect of TSH/forskolin, as well as TNF-alpha and IFN-gamma, on ICAM-1 RNA levels is transcriptional. Thus, we cloned a 1.8-kb fragment of the 5'-flanking region of the rat ICAM-1 gene, upstream of the translational start site, and showed that TNF-alpha or IFN-gamma caused a 3.5- and greater than 12-fold increase respectively, in its promoter activity, when linked to a luciferase reporter gene and stably transfected into FRTL-5 cells. TSH or forskolin, in contrast, halved the activity of the full length chimera within 24 hours and significantly suppressed the TNF-alpha and IFN-gamma-induced increase (>50%; p < 0.02). Using 5'-deletion mutants, we located the element important for the TNF-alpha effect between -431 and -175 bp; we additionally show that deletion of a NF-kappaB core element within this region, TTGGAAATTC (-240 to -230 bp), causes the loss of TNF-alpha inducibility. The effect of IFN-gamma could be localized between -175 bp and -97 bp from the start of translation. This region contains 2 regulatory elements known to be involved in IFN-gamma action in other eukaryotic cells, an IFN-gamma activated site (GAS), -138 to -128 bp, and Spl site, -112 to -108 bp. Deletion of the 10 bp GAS sequence resulted in the complete loss of IFN-gamma induction of pCAM-175 promoter activity. TSH and forskolin action was also mapped between -175 bp and -97 bp from the start of translation. The mutant construct, pCAM-175delGAS mutl, which has no GAS sequence, exhibited no TSH-mediated suppression of promoter activity. We thus show that TSH/cAMP can downregulate ICAM-1 gene expression and inhibit the activity of cytokines (TNF-alpha and IFN-gamma) to increase ICAM-1 gene expression in FRTL-5 thyroid cells. We also localized elements on the 5'-flanking region of ICAM-1 important for these actions. We propose that this TSH/cyclic adenosine monophosphate (cAMP) action is a component of the mechanism to preserve self-tolerance of the thyroid during hormone-induced growth and function of the gland, and it may attenuate cytokine action during inflammatory reactions.

Animals↗
PubMed2002

Complete nucleotide sequence of the M RNA segment of Andes virus and analysis of the variability of the termini of the virus S, M and L RNA segments.

Hantavirus pulmonary syndrome (HPS) has been recognized increasingly as a significant public health problem in South America since Andes virus was first discovered in Argentina. Here, the isolation of Andes virus is reported from an infected rodent captured in Argentina in close vicinity to the place of the first HPS case, AH1. The complete nucleotide sequences of the virus M segment, partial L segment and the termini of the S, M and L segment genome RNAs were determined. The Andes virus M RNA segment is 3671 nt in length and is predicted to encode a glycoprotein precursor 1138 aa in length; it generally resembles the other HPS-associated hantaviruses in its organization. Relative to the G1 glycoprotein of other HPS-associated hantaviruses, an additional potential glycosylation site was found but this is located in the predicted cytoplasmic domain and is therefore unlikely to be glycosylated. In phylogenetic analyses, Andes virus, together with the more related hantaviruses, represented a monophyletic lineage. The S-terminal nucleotides were conserved relative to other New World hantaviruses. The M and L segment RNA termini had short deletions in the region believed to contain the sequence and structural features necessary for initiation of virus RNA replication and transcription. Clinical manifestations of Andes virus infections range from fulminant respiratory disease with high lethality to mild course without sequelae. Andes virus has also been associated with person-to-person transmission. Accumulation of Andes virus genetic data will be essential for understanding the factors that regulate virus replication and transmission and to determine the pathogenesis of HPS.

Animals↗
PubMed2000

Molecular characterization of the Abp1 5'-flanking region in maize and the teosintes.

Auxin-binding protein 1 subsp. mays (ABP1) has been suggested as a receptor mediating auxin-induced cell expansion and differentiation. In maize (Zea mays), ABP1 is encoded by a single gene, Abp1. The TATA and CAAT promoter elements as well as the transcriptional start site were previously identified and all were found to be located within a transposable element (TE), Tourist-Zm11. In this study we report the cloning and characterization of the Abp1 5'-flanking region in maize and its wild relatives, the teosintes. We provide evidence for insertion polymorphism corresponding to Tourist-Zm11 and two novel TEs, Batuta and Pilgrim. Despite this polymorphic structure, the Abp1 core promoter in maize and the teosintes is conserved, is located downstream of the TE insertions in the 5'-flanking region, and is TATA-less. We discuss the potential evolutionary impact of these TEs on the regulation of Abp1 gene expression.

Blotting, Northern↗