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At least 757 records · Page 42Linked to original sources
PubMed2001

The diversification of Citrus clementina Hort. ex Tan., a vegetatively propagated crop species.

Clementines, due to their high quality, are one of the most important cultivated citrus mandarins. As in the case of sweet orange and satsuma mandarins, genetic variability within this species is minimal when analyzed by molecular markers, because the existing varieties have not been obtained through hybridization, but through the selection of spontaneous mutations affecting traits of agronomic interest. This would explain, at least in part, the greater diversity for agronomic traits when compared to the variability for molecular markers. Another possible (nonexclusive) reason is that the types of molecular marker used are not focused on the kind of molecular change mainly involved in the origination of new clementine cultivars; i.e., are all sources of variation equally involved in the diversification of these plants? To answer this question, different kinds of markers based on primers of random sequence, simple sequence repeats, and retrotransposon sequences that may reveal point mutations, and somatic recombination and transposon activity, respectively, were used to compare the level of variability among 24 clementine varieties. Their ISSR, RAPD, and AFLP analysis provided only two polymorphic bands, distinguishing just two varieties. No variability was found by SSRs, i.e., no new allele arising through somatic recombination was detected. Instead, the amplification of sequences adjacent to retrotransposons yielded a higher number of polymorphisms (14.6 vs 2.4% for the previous mentioned marker types). Two geographical distant groups, one from North Africa and the other from Spain, have evolved in agreement with polymorphisms based on IRAP markers anchored to, at least, two different Copia-like retrotransposon sequences. Therefore, this study suggests that the DNA of this type of mobile elements is evolving faster than the DNA of other markers in this clonal lineage.

Alleles↗
PubMed1995

Analysis of a retron EC86 and EC67 insertion site in Escherichia coli.

The Escherichia coli clinical strain 49 contains the integration sites for the retrons EC86 and EC67 but not the retrons themselves. To compare the chromosomal structures before and after retron integration, the DNA sequence of the integration site in strain 49 was determined and compared to the corresponding sequences in strains containing EC86 and EC67. The results suggested that when these retrons inserted into the E. coli chromosome they replaced a 3.5-kb fragment of chromosomal DNA. It is proposed that the replacement of preexisting DNA by a retron may be a general mechanism for retron integration, since in the three examples in which the integration sites are known, the retrons appear to have integrated into the chromosome by replacing a preexisting DNA segment.

Amino Acid Sequence↗
PubMed1996

Functional comparison of conjugative transposons Tn916 and Tn925.

During interspecies matings between Bacillus subtilis and Bacillus thuringiensis subsp. israelensis, transfer of conjugative transposon Tn916 was detected at a frequency of 1.1 x 10(-4) transconjugants per donor. Tn916-dependent transfer of plasmids pC194 and pE194 was detected at frequencies of 1.4 x 10(-5) and 3.2 x 10(-7) transconjugants per donor, respectively. Similar frequencies were obtained during parallel matings with otherwise isogenic strains that contain Tn925 instead of Tn916. Tn916- or Tn925-dependent transfer of plasmids pC194 or pUB110 from the recipient to the donor (retrotransfer) was not observed during inter- or intraspecies matings. Transposon-mediated plasmid transfer by Tn916 and Tn925 is a Rec independent event. Thus, the data from studies in which otherwise isogenic donor and recipient strains were used indicated that Tn916 and Tn925 are, from a functional point of view, much more similar than previously suggested.

Bacillus subtilis↗
PubMed1997

Ty3/gypsy-like retrotransposon sequences in tomato.

Polymerase chain reactions (PCRs) were carried out with DNAs of eight tomato species using primers directed at the reverse transcriptase domain of Ty3/gypsy-like LTR retrotransposons. All DNAs gave PCR products of the expected size which, after cloning and sequencing, were confirmed as representing Ty3/gypsy-like elements. The sequences were heterogeneous, only 3 of the 16 being identical and the most diverse showing 124/426 pairwise nucleotide differences. Multiple alignment and construction of neighbor joining trees divided the sequences into six groups, three comprising five, three, and five sequences respectively, and the other three containing a single sequence each.

Amino Acid Sequence↗
PubMed2000

A broad-host-range plasmid for isolating mobile genetic elements in gram-negative bacteria.

Plasmid pGBG1 was constructed to isolate mobile genetic elements in a wide variety of gram-negative bacteria. The mutation target, carried on a broad-host-range vector, allows positive selection for tetracycline resistance. In tests using several gram-negative bacteria we could detect transposition events of either insertion sequences or transposons. A new insertion sequence (IS) element was identified in Ralstonia eutropha.

Agrobacterium tumefaciens↗
PubMed1995

An immunological analysis of Ty1 virus-like particle structure.

We present an immunological characterization of the Ty1 virus-like particle (VLP). A panel of monoclonal and polyclonal antibodies were raised against the TYA particle-forming protein. Using these antibodies in epitope availability assays two N-terminal regions of the TYA protein were mapped projecting from or at the surface of the proteinaceous shell of the VLP. Two different C-termini of the TYA protein, corresponding to the C-terminus of the full-length and truncated forms, were seen to be buried within the particle core and not available for antibody binding. RNase accessibility studies demonstrated a difference in the porosity of the protein shell surrounding the Ty1 nucleic acid between different particle types, suggesting differences in subunit organization.

Amino Acid Sequence↗
PubMed1995

Analysis of TYA protein regions necessary for formation of the Ty1 virus-like particle structure.

The yeast retrotransposon, Ty1, produces a macromolecular structure known as a virus-like particle (VLP) as an essential part of its replication cycle. The Ty1 Gag-like structural protein TYA, p1-440, alone is capable of directing assembly of the VLP. In order to determine the TYA sequences required for assembly, we have produced a series of truncated and deleted TYA forms and assessed their ability to assemble into particles. Removal of 100 amino acids from the C-terminus renders the TYA protein, p1-340, incapable of particle assembly; however, p1-363 with 77 residues missing from the C-terminus is capable of assembly. Removal of 40 amino acids from the N-terminus (p41-440 and p41-381) does not affect particle formation but more severely N-truncated forms, p71-381 and p100-381, are present as large aggregates within the cells and are therefore either incapable of or unavailable for VLP formation. Analysis of an internally deleted TYA, p1-381 delta 62-114, has identified this as a possible region of the TYA protein important for subunit:subunit interactions during the particle assembly.

Fungal Proteins↗
PubMed1996

The Escherichia coli retrons Ec67 and Ec86 replace DNA between the cos site and a transcription terminator of a 186-related prophage.

Retrons are unusual, reverse transcriptase-encoding elements found in bacteria. Although there are a number of indications that retrons are mobile elements, their transposition has not been observed. The Escherichia coli retrons Ec67 and Ec86 are different retrons inserted at the same site and we have further characterized this site in search of clues to the mechanism of retron transposition. We confirm, by extending previous sequence analysis, that Ec67 and Ec86 are inserted into prophages related to coliphage 186. Comparison with the recently published sequence of the 186 96-2% region indicates that the retrons have replaced approximately 180 bp of DNA between the phage cohesive end site (cos) and the transcription terminator of a phage DNA-packaging gene. These features--DNA replacement at the insertion site and the location of retron junctions near transcription terminators or DNA cleavage sites--are shared with other retrons and suggest ways in which retron transposition might have occurred.

Amino Acid Sequence↗
PubMed2001

A C-terminal deletion mutant of pokeweed antiviral protein inhibits programmed +1 ribosomal frameshifting and Ty1 retrotransposition without depurinating the sarcin/ricin loop of rRNA.

Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein characterized by its ability to depurinate the sarcin/ricin (S/R) loop of the large rRNA of prokaryotic and eukaryotic ribosomes. Here, a series of PAP mutants were used to examine the relationship between depurination of the S/R loop and inhibition of +1 programmed ribosomal frameshifting (PRF) and to define PAP sequences critical for inhibition of +1 PRF and Ty1 retrotransposition in the yeast Saccharomyces cerevisiae. Using three different classes of mutants we present evidence that strong binding of a C-terminal PAP mutant (PAPc) to ribosomes is sufficient to inhibit +1 PRF and Ty1 retrotransposition in the absence of S/R loop depurination. PAPc did not affect the totivirus ScV-L-A and HIV-1-directed -1 PRF efficiencies or the ability of cells to maintain the M(1)-dependent killer phenotype, demonstrating the specificity of the effect of PAPc on +1 PRF.

Cell Line↗
PubMed2001

Enhanced expression of the early retrotransposon in C3H mouse-derived myeloid leukemia cells.

Cells of acute myeloid leukemia (AML) from C3H/He mice express an increased amount of RNA for an endogenous retrovirus-like retrotransposon, intracisternal A-particle element. We analyzed the transcription of other mouse retrotransposons in C3H-derived tumor cells and found that all the AML lines from different mice overexpress early-transposon (ETn) RNA. In contrast, only faint levels of ETn were detected in the cells from other tumors, including hepatoma and lymphoma. The polyadenylation sites of the ETn RNA in the AML cells varied. We also determined the binding site for the nuclear extract of the AML cells in the long terminal repeat sequence of ETn. The overexpression of ETn as a common phenotype of AML cells suggests that myeloid cells with this phenotype are the origin of all the AML cells or that the phenotype is acquired during leukemogenesis.

Animals↗
PubMed2001

Ty1 retrotransposition and programmed +1 ribosomal frameshifting require the integrity of the protein synthetic translocation step.

Programmed ribosomal frameshifting is utilized by a number of RNA viruses to ensure the correct ratio of viral structural to enzymatic proteins for viral particle assembly. Altering frameshifting efficiencies upsets this ratio, inhibiting virus propagation. Two yeast viruses that induce host cell ribosomes to shift translational reading frame were used as tools to explore the interactions between viruses and host cellular protein synthetic machinery. Previous studies showed that the ribosome-inactivating protein pokeweed antiviral protein specifically inhibited propagation of the Ty1 retrotransposable element of yeast as a consequence of inhibition of programmed +1 ribosomal frameshifting. Here, complementary genetic and pharmacological approaches were employed to test whether inhibition of Ty1 retrotransposition is a general feature of alterations in the translocation step of elongation and +1 frameshifting. The results demonstrate that cells harboring a variety of mutant alleles of two host-encoded proteins that are involved in translocation, eukaryotic elongation factor-2 and the ribosome-associated protein RPP0, have Ty1 propagation defects. We also show that sordarin, a fungus-specific inhibitor of eEF-2 function, specifically inhibits programmed +1 ribosomal frameshifting and Ty1 retrotransposition. These findings serve to link inhibition of Ty1 retrotransposition and +1 frameshifting to changes in the translocation step of elongation.

Frameshifting, Ribosomal↗
PubMed2002

Potential multiple endonuclease functions and a ribonuclease H encoded in retroposon genomes.

Among the retroposons, the source of the endonuclease activity is known to be variable and can be provided as either a retroviral-like integrase or a protein similar to the cellular apurinic-apyrimidinic endonuclease. It has also been reported that other retroposon and retrointron sequences have limited similarity to various eubacterial endonucleases. We investigated whether any retroposon genomes possibly encode multiple endonuclease functions. Amino acid alignments were generated and analyzed for the presence of the characterized ordered-series-of-motifs (OSM) representative of four different endonuclease functions. The results indicate that SLACS, CZAR, CRE1, CRE2, and some Trypanosoma brucei retroposon sequences encode multiple putative endonuclease functions. Interestingly, one of the endonuclease functions is embedded within the potential ribonuclease H sequence found in SLACS, CZAR, CRE1, CRE2, and R2BM retroposons.

Amino Acid Sequence↗
PubMed1995

Genital-associated lymphoid tissue in female non-human primates.

We investigated genital-associated lymphoid tissue (GENALT) in non-human primates (macaques), by augmenting vaginal with oral immunization. The vaccine was a recombinant particulate SIV antigen (p27:Ty-VLP), linked to CT-B, and administered into the vagina by a paediatric naso-gastric tube and into the stomach by a gastric tube. Oro-vaginal or vagino-oral sequence of immunization elicited specific CD4+ T cell proliferative responses to p27 antigen in the genital lymph nodes and the spleen but not in unrelated lymph nodes. CD4+ T cells reconstituted with B cells and macrophages from the genital lymph nodes induced specific IgA and to a lesser extent IgG anti-p27 antibodies. However, the corresponding splenic cells induced greater IgG than IgA antibody synthesis. Intramuscular immunization primed splenic but not genital lymph node cells, and induced CD4+ T cell proliferative responses and predominantly B cell IgG antibody synthesis. Finding primed B and T cells in the genital lymph nodes after augmenting vaginal by oral immunization provides experimental evidence for GENALT in non-human primates. This primate model of vaginal immunization suggests 3 levels of specific immunity: (1) secretory IgA (and IgG) in the cervico-vaginal mucosal epithelium; (2) primed CD4+ T cells and B cells in the genital lymph nodes and the spleen; and (3) circulating CD4+ T cells, B cells and IgG and IgA antibodies specific to the immunizing antigen.

Administration, Intravaginal↗
PubMed1995

Autoimmunity, apoptosis defects and retroviruses.

Autoimmunity and AIDS both share the common feature of increased expression of retroviral protein products and abnormal apoptosis of immune cells (81). This leads to a more global immunomodulatory defect (82-84). The challenge in the future will be to devise compounds that can either regulate the effect of the retroviral products on apoptosis, or that can inhibit apoptosis pathways in order to restore normal immune system function.

Amino Acid Sequence↗
PubMed2003

The replication strategy of foamy viruses.

The replication strategy of foamy viruses diverges in many aspects from what is commonly accepted as the rules of retroviral replication. Although many questions on the details of the replication pathway are still unanswered, it appears that foamy viruses have adopted a strategy which functionally bridges the retroviral and the hepadnaviral replication pathways. A number of experimental findings in favour of the view that foamy viruses are reverse transcribing DNA viruses which integrate into the host cell genome are discussed.

Animals↗