A Ty1-copia group retrotransposon sequence in a vertebrate.

Summary We have used the polymerase chain reaction (PCR) to isolate a sequence characteristic of aTy1-copia group retrotransposon from the genome of the herring (Clupea harengus). This is the firstTy1-copia group retrotransposon sequence described in a vertebrate. Phylogenetic comparison of this sequence with other members of this group of retrotransposons shows that it resembles more closely some Tyl-copia group members fromDrosophila melanogaster than other group members in plants and fungi. These observations provide further evidence that theTy1-copia group LTR retrotransposons span many of the major eukaryote species boundaries, suggesting that horizontal transmission between different species has played a role in the evolution of this retrotransposon group.     

Structural and evolutionary analyses of the Ty3/gypsy group of LTR retrotransposons in the genome of Anopheles gambiae

The recent availability of the genome of Anopheles gambiae offers an extraordinary opportunity for comparative studies of the diversity of transposable elements (TEs) and their evolutionary dynamics between two related species, taking advantage of the existing information from Drosophila melanogaster. To this goal, we screened the genome of A. gambiae for elements belonging to the Ty3/gypsy group of long-terminal repeat (LTR) retrotransposons. The A. gambiae genome displays a rich diversity of LTR retrotransposons, clearly greater than D. melanogaster. We have characterized in detail 63 families, belonging to five of the nine main lineages of the Ty3/gypsy group. The Mag lineage is the most diverse and abundant, with more than 30 families. In sharp contrast with this finding, a single family belonging to this lineage has been found in D. melanogaster, here reported for the first time in the literature, most probably consisting of old inactive elements. The CsRn1 lineage is also abundant in A. gambiae but almost absent from D. melanogaster. Conversely, the Osvaldo lineage has been detected in Drosophila but not in Anopheles. Comparison of structural characteristics of different families led to the identification of several lineage-specific features such as the primer-binding site (PBS), the gag-pol translational recoding signal (TRS), which is extraordinarily diverse within the Ty3/gypsy retrotransposons of A. gambiae, or the presence/absence of specific amino acid motifs. Interestingly, some of these characteristics, although in general well conserved within lineages, may have evolved independently in particular branches of the phylogenetic tree. We also show evidence of recent activity for around 75% of the families. Nevertheless, almost all families contain a high proportion of degenerate members and solitary LTRs (solo LTRs), indicative of a lower turnover rate of retrotransposons belonging to the Ty3/gypsy group in A. gambiae than in D. melanogaster. Finally, we have detected significant overrepresentations of insertions on the X chromosome versus autosomes and of putatively active insertions on euchromatin versus heterochromatin.     

裸燕麦Ty1-copia类反转录转座子反转录酶序列的分离、鉴定与分析

本研究根据Ty1-copia类反转录转座子反转录酶的保守区设计简并引物,通过PCR扩增,从裸燕麦(Avena nuda L.)品种‘品燕1号’基因组中分离获得23条Ty1-copia类反转录转座子序列,并对序列特征、系统发育关系及其转录活性进行分析。结果显示,23条Ty1-copia类反转录转座子存在较高的异质性,序列间的一致性为45%～98%,存在插入、移码和终止密码突变,但频率不高;系统发育分析结果表明,燕麦Ty1-copia类反转录转座子在进化过程中主要为垂直传递。本研究通过检索燕麦基因表达数据库,发现了5个有转录活性的Ty1-copia类反转录转座子。     

Ty1 Gag Enhances the Stability and Nuclear Export of Ty1 mRNA

Retrotransposon and retroviral RNA delivery to particle assembly sites is essential for their replication. mRNA and Gag from the Ty1 retrotransposon colocalize in cytoplasmic foci, which are required for transposition and may be the sites for virus‐like particle (VLP) assembly. To determine which Ty1 components are required to form mRNA/Gag foci, localization studies were performed in a Ty1‐less strain expressing galactose‐inducible Ty1 plasmids (pGTy1) containing mutations in GAG or POL. Ty1 mRNA/Gag foci remained unaltered in mutants defective in Ty1 protease (PR) or deleted for POL. However, Ty1 mRNA containing a frameshift mutation (Ty1fs) that prevents the synthesis of all proteins accumulated in the nucleus. Ty1fs RNA showed a decrease in stability that was mediated by the cytoplasmic exosome, nonsense‐mediated decay (NMD) and the processing body. Localization of Ty1fs RNA remained unchanged in an nmd2Δ mutant. When Gag and Ty1fs mRNA were expressed independently, Gag provided in trans increased Ty1fs RNA level and restored localization of Ty1fs RNA in cytoplasmic foci. Endogenously expressed Gag also localized to the nuclear periphery independent of RNA export. These results suggest that Gag is required for Ty1 mRNA stability, efficient nuclear export and localization into cytoplasmic foci.     

Isolation and characterization of two novel retrotransposons of the Ty1-copia group in oat genomes

Two repetitive sequences, As32 and As22, of 826 and 742 bp, respectively, were isolated from Avena strigosa (As genome). Databank searches revealed their high homology to different segments of the family of Ty1-copia retrotransposons. Southern hybridization showed them to be present in diploid and polyploid oat species. Polymerase chain reaction with primers designed to amplify the segment between them showed that As32 and As22 sequences are composed of two different Ty1-copia retrotransposons. The segment amplified from the pAs32 insert was 2,264 bp long and contained the entire GAG and AP domains, and more than half of the IN domain. This new element has been designated TAS-1 (transposon, A. strigosa, 1) and appears to contain a long open reading frame that encodes a polypeptide of 625 amino acids. Slot-blot and fluorescence in situ hybridization analyses revealed it to be a component of both A- and D-genome chromosomes. Further, the chromosomes involved in one C-A intergenomic translocation in A. murphyi (AC genomes), one C-D intergenomic translocation in A. byzantina cv. Kanota (ACD genomes), and two C-D intergenomic translocations in A. sativa cv. Extra Klock, were identified. Based on its physical distribution and Southern hybridization pattern, a parental retro-transposon represented by TAS-1 appears to have been active at least twice during the evolution of the genomes in species of Avena.     

Structural features of the mdg1 lineage of the Ty3/gypsy group of LTR retrotransposons inferred from the phylogenetic analyses of its open reading frames

The increasing amount of data generated in recent years has opened the way to exhaustive studies of the relationships among different members of the Ty3/gypsy group of LTR retrotransposons, a widespread group of eukaryotic transposable elements. Former research led to the identification of several independent lineages within this group. One of the worse represented of them is that of mdg1, integrated so far only by the Drosophila retrotransposons mdg1 and 412. Our exhaustive database searches indicate the existence of three other Drosophila members of this lineage. Two of them correspond to elements already known, namely, Stalker and blood, but the third one is a new element, which we have called Pilgrim. This element is well represented within the D. melanogaster genome, as revealed by our Southern blot analysis of different strains. The case of Stalker is particularly remarkable, since its phylogenetic relationships clearly point to the mosaic origin of its genome. Finally, our analysis of the evolution of a small ORF preserved within the 5′ leader region of these elements indicates different evolutionary rates, presumably as a result of distinct selective constraints. Received: 16 October 2000 / Accepted: 6 April 2001