Characterization of endogenous retroviruses in sheep

Endogenous retrovirus (ERV) sequences have been found in all mammals. In vitro and in vivo experiments revealed ERV activation and cross-species infection in several species. Sheep (Ovis aries) are used for various biotechnological purposes; however, they have not yet been comprehensively screened for ERV sequences. Therefore, the aim of the study was to classify the ERV sequences in the ovine genome (OERV) by analyzing the retroviral pro-pol sequences. Three OERV beta families and nine OERV gamma families were revealed. Novel open reading frames (ORF) in the amplified proviral fragment were found in one OERV beta family and two OERV gamma families. Hybrid OERV produced by putative recombination events were not detected. Quantitative analysis of the OERV sequences in the ovine genome revealed no relevant variations in the endogenous retroviral loads of different breeds. Expression analysis of different tissues from fetal and pregnant sheep detected mRNA from both gammaretrovirus families, showing ORF fragments. Thus, the release of retroviruses from sheep cells cannot be excluded.     

Characterization of the bovine endogenous retrovirus beta3 genome

We recently used degenerate PCR and locus-specific PCR methods to identify the endogenous retroviruses (ERV) in the bovine genome. Using the ovine ERV classification system, the bovine ERVs (BERVs) could be classified into four families. Here, we searched the most recently released bovine genome database with the partial nucleotide sequence of the pro/pol region of the BERV beta3 family. This allowed us to obtain and analyze the complete genome of BERV beta3. The BERV beta3 genome is 7666 nucleotides long and has the typical retroviral organization, namely, 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3'. The deduced open reading frames for gag, pro, pol and env of BERV Beta en- code 507, 271, 879 and 603 amino acids, respectively. BERV beta3 showed little amino acid similarity to other betaretroviruses. Phylogenetic analysis showed that it clusters with HERV-K. This is the first report describing the genetic structure and sequence of an entire BERV.     

Structural characterization of the genome of BERV gamma4, the most abundant endogenous retrovirus family in cattle

The genome of replication-competent BERV gamma4 provirus, which is the most abundant ERV family in the bovine genome, was characterized in detail. The BERV gamma4 genome showed that BERV gamma4 harbors 8576 nucleotides and has the typical 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3' retroviral organization with a long leader region positioned before the gag open reading frame. Multiple sequences analysis showed that the nucleotide difference between 5' and 3' LTRs was 4.2% (mean value 0.042) in average, suggesting that the provirus formed at most 13.3 million years ago. Gag separated by a stop codon from pro-pol in the same reading frame, while env resides in another reading frame lacking of a functional surface domain. According to the current bovine genome sequence assembly, the full-length BERV gamma4 provirus sequences were only found in the chromosomes 1, 2, 6, 10, 15, 23, 26, 28, X, and unassigned, although the partial sequences almost evenly distributed in the entire bovine genome. This is the first detailed study describing the genome structure of BERV gamma4, the most abundant ERV family present in bovine genome. Combined with our recent reports on characterization of ERVs in bovine, this study will contribute to illuminate ERVs in the cattle of which no information was previously available.     

Multiple groups of novel retroviral genomes in pigs and related species

In view of the concern over potential infection hazards in the use of porcine tissues and organs for xenotransplantation to humans, we investigated the diversity of porcine endogenous retrovirus (PERV) genomes in the DNA of domestic pigs and related species. In addition to the three known envelope subgroups of infectious gamma retroviruses (PERV-A, -B, and -C), classed together here as PERV group gamma 1, four novel groups of gamma retrovirus (gamma 2 to gamma 5) and four novel groups of beta retrovirus (beta 1 to beta 4) genomes were detected in pig DNA using generic and specific PCR primers. PCR quantification indicated that the retroviral genome copy number in the Landrace x Duroc F(1) hybrid pig ranged from 2 (beta 2 and gamma 5) to approximately 50 (gamma 1). The gamma 1, gamma 2, and beta 4 genomes were transcribed into RNA in adult kidney tissue. Apart from gamma 1, the retroviral genomes are not known to be infectious, and sequencing of a small number of amplified genome fragments revealed stop codons in putative open reading frames in several cases. Analysis of DNA from wild boar and other species of Old World pigs (Suidae) and New World peccaries (Tayassuidae) showed that one retrovirus group, beta 2, was common to all species tested, while the others were present among all Old World species but absent from New World species. The PERV-C subgroup of gamma1 genomes segregated among domestic pigs and were absent from two African species (red river hog and warthog). Thus domestic swine and their phylogenetic relatives harbor multiple groups of hitherto undescribed PERV genomes.     

Characterization of porcine endogenous retrovirus gamma pro-pol nucleotide sequences

Endogenous retroviral sequences in the pig genome (PERV) represent a potential infectious risk in xenotransplantation. All known infectious PERV have been asssigned to the PERV gamma1 family, consisting of the subfamilies A, B, and C. The aim of the study was the concise examination of PERV gamma by the analysis of the retroviral pro-pol sequences. The analysis of 52 pro-pol clones amplified in this study revealed eight PERV gamma families. In addition to four already-described families (gamma1, gamma4, gamma5, gamma6), four novel families (gamma7, gamma8, gamma9, gamma10) were identified. Quantitative analysis of the novel PERV gamma sequences in selected breeds revealed variations in the endogenous retroviral load. Open reading frames (ORF) in the amplified proviral fragment were only found for PERV gamma1. In addition, novel ORF-containing PERV gamma1 clones consisting of hybrid sequences were revealed. Sequence comparison from published full-length PERV gamma1 clones of the PERV subfamilies A, B, and C resulted in a lack of strict correlation of the classification of pro-pol and env. The results indicated the occurrence of causative recombination events between retroviral genomes. Thus, our study on PERV gamma provides new data for the evaluation and selection of pigs intended to be used in xenotransplantation.     

Paleogenomic record of the extinction of human endogenous retrovirus ERV9

An outstanding question of genome evolution is what stops the invasion of a host genome by transposable elements (TEs). The human genome, harboring the remnants of many extinct TE families, offers an extraordinary opportunity to investigate this problem. ERV9 is an endogenous retrovirus repeatedly mobilized during primate evolution, 15 to 6 million years ago (MYA), which left a trace of over a hundred provirus-like copies and at least 4,000 solitary long terminal repeats (LTRs) in the human genome. Then, its proliferation ceased for unknown reasons, and the family went extinct. We have made a detailed reconstruction of its last active subfamily, ERV9_XII, by examining 115 solitary LTRs from it. These insertions were grouped into 11 sets according to shared nucleotide variants, which could be placed in a sequential order of 10 to 6 MYA. At least 75% of the subfamily was produced 8 to 6 MYA, during a stage of intense proliferation. With new analytical tools, we show that the youngest and most prolific sets may have been produced by effectively instantaneous expansions of corresponding single-sequence variants. The extinction of this family apparently was not a consequence of its slow gradual degeneration, but the outcome of the fixation of specific restrictive alleles in the human-chimpanzee ancestral population. Three species-specific insertions (two in humans and one in chimpanzees) were identified, further supporting that extinction took place when these two species were beginning to diverge. These are the only fixed differences of this kind so far observed between humans and chimpanzees, apart from those belonging to the human endogenous retrovirus K family.     

Footprint of APOBEC3 on the Genome of Human Retroelements

Almost half of the human genome is composed of transposable elements. The genomic structures and life cycles of some of these elements suggest they are a result of waves of retroviral infection and transposition over millions of years. The reduction of retrotransposition activity in primates compared to that in nonprimates, such as mice, has been attributed to the positive selection of several antiretroviral factors, such as apolipoprotein B mRNA editing enzymes. Among these, APOBEC3G is known to mutate G to A within the context of GG in the genome of endogenous as well as several exogenous retroelements (the underlining marks the G that is mutated). On the other hand, APOBEC3F and to a lesser extent other APOBEC3 members induce G-to-A changes within the nucleotide GA. It is known that these enzymes can induce deleterious mutations in the genome of retroviral sequences, but the evolution and/or inactivation of retroelements as a result of mutation by these proteins is not clear. Here, we analyze the mutation signatures of these proteins on large populations of long interspersed nuclear element (LINE), short interspersed nuclear element (SINE), and endogenous retrovirus (ERV) families in the human genome to infer possible evolutionary pressure and/or hypermutation events. Sequence context dependency of mutation by APOBEC3 allows investigation of the changes in the genome of retroelements by inspecting the depletion of G and enrichment of A within the APOBEC3 target and product motifs, respectively. Analysis of approximately 22,000 LINE-1 (L1), 24,000 SINE Alu, and 3,000 ERV sequences showed a footprint of GG→AG mutation by APOBEC3G and GA→AA mutation by other members of the APOBEC3 family (e.g., APOBEC3F) on the genome of ERV-K and ERV-1 elements but not on those of ERV-L, LINE, or SINE.     

A speedy method to detect inserted DNA fragment in cell lines transfected with retroviral vectors

Cells transfected by retroviral vectors are brought in agene of particular interest and are very useful in avariety of experiments. It is essential to testify that theDNA fragment was successfully introduced into the cellstogether with the retroviral vectors. Polymerase chainreaction is believed to be a fast and convenient method forthis purpose when using primers flanking the cloning siteof the inserted DNA. Unfortunately, a single PCR reactionoften fails to amplify the targeted fragment because of theexistence of endogenous virus DNA in cell genome. However,in this study we conducted a procedure for a single PCR,using vector-specific primers as well as a nested PCR, andsuccessfully detected the DNA fragments cloned in MFGretroviral vectors in 22 transfected cell lines. We alsoproved that real time quantitative PCR in combination withMFG-specific primer is useful to determine copy number ofthe retroviral vector in murine producer cell lines.     

绿豆Ty1／Copia类反转录转座子逆转录酶序列的克隆和分析

利用Ty1/copia类反转录转座子的保守位点设计简并引物,从绿豆(Vignaradiata(L.)Wilczek)基因组中扩增得到了反转录转座子的逆转录酶序列。对扩增得到的约270bp的片段进行分离和克隆,并随机挑选了40个克隆进行测序,结果得到了36个单独的核酸序列,其中18个含有移码突变或终止子。根据序列比对,这些克隆可分为9组以及单个的9种。这40个克隆中,核酸序列相似性从8%到100%,显示出其核酸序列的高度异质性。将这些克隆的核酸序列与来自其他种植物的相应序列进行谱系分析,发现有些克隆与来自其他种植物的相应序列的亲缘关系比这些克隆之间更为接近。斑点杂交显示Ty1/copia反转录转座子约占绿豆基因组的9.3%。     

Isolation and Characterization of Ty1/copia-like Reverse Transcriptase Sequences from Mung Bean (Vigna radiata)

Ty1/copia-like sequences were amplified from mung bean (Vigna radiata (L.) Wilczek) genomic DNA, by PCR with degenerate oligonucleotide primers corresponding to highly conserved domains in the Ty1/copia-like retrotransposons. PCR fragments of roughly 270 bp were isolated and cloned, and forty clones were sequenced. Thirty-six of the forty clones had unique nucleotide sequences, and eighteen clones had a frameshift, a stop codon, or both. Alignment of the nucleotide sequences indicated that these clones, denoted Tvr, fell into nine subgroups and nine ungrouped sequences. The nucleotide sequence similarity between these elements ranged from 8% to 100%, which indicates high level of sequence heterogeneity among these clones. A phylogenetic analysis comparing these clones with corresponding sequences from other plant species showed that some of the Tvr clones are more closely related to Ty1/copia-like retrotransposons from other species than to other Tvr clones. Dot blot analysis revealed that Ty1/copia-like retrotransposons comprise about 9.3% of the mung bean genome.     

逆转录病毒介导的人血小板生成素(TPO)在骨髓基质细胞中的表达

为探讨逆转录病毒介导的TPO基因在人骨髓基质细胞系HFCL中的表达,利用脂质体法将含TPO基因的逆转录病毒载体导入HF-CL细胞中,RT-PCR和基因组DNAPCR分析证实mRNA水平有表达,基因组中整合有Neo基因和TPO基因。TPO依赖细胞株TD-3检测生物学活性表明转染的骨髓基质细胞分泌TPO。上述结果为进一步研究转基因骨髓基质细胞对造血细胞的调控作用提供了必要的基础资料。