PREM-1, a putative maize retroelement has LTR (long terminal repeat) sequences that are preferentially transcribed in pollen

A family of highly dispersed repetitive elements, designated PREM-1, which are transcribed primarily during pollen development, has been identified in maize. Sequence data from six PREM-1-containing genomic clones suggest that the PREM-1 sequences are the LTRs of a family of putative retroelements. PREM-1 LTRs are estimated to be present in about 10 000 to 40 000 copies in the maize genome. Although related sequences have been detected in sorghum and crab grass, highly homologous sequences appear to be specific to the genus Zea (maize and teosinte). A diverse group of RNAs that contain portions of the PREM-1 sequence at their 3 ends are transcribed in pollen; highest levels appear in early uninucleate microspores. The PREM-1-containing cDNAs do not appear to code for protein products since stop codons are present in all three reading frames. The possible significance of expression of retroelements in the male gametophyte, in terms of transposition of DNA, is discussed.     

Major repeat components covering one‐third of the ginseng (Panax ginseng C.A. Meyer) genome and evidence for allotetraploidy

Ginseng (Panax ginseng) is a famous medicinal herb, but the composition and structure of its genome are largely unknown. Here we characterized the major repeat components and inspected their distribution in the ginseng genome. By analyzing three repeat‐rich bacterial artificial chromosome (BAC) sequences from ginseng, we identified complex insertion patterns of 34 long terminal repeat retrotransposons (LTR‐RTs) and 11 LTR‐RT derivatives accounting for more than 80% of the BAC sequences. The LTR‐RTs were classified into three Ty3/gypsy (PgDel, PgTat and PgAthila) and two Ty1/Copia (PgTork and PgOryco) families. Mapping of 30‐Gbp Illumina whole‐genome shotgun reads to the BAC sequences revealed that these five LTR‐RT families occupy at least 34% of the ginseng genome. The Ty3/Gypsy families were predominant, comprising 74 and 33% of the BAC sequences and the genome, respectively. In particular, the PgDel family accounted for 29% of the genome and presumably played major roles in enlargement of the size of the ginseng genome. Fluorescence in situ hybridization (FISH) revealed that the PgDel1 elements are distributed throughout the chromosomes along dispersed heterochromatic regions except for ribosomal DNA blocks. The intensity of the PgDel2 FISH signals was biased toward 24 out of 48 chromosomes. Unique gene probes showed two pairs of signals with different locations, one pair in subtelomeric regions on PgDel2‐rich chromosomes and the other in interstitial regions on PgDel2‐poor chromosomes, demonstrating allotetraploidy in ginseng. Our findings promote understanding of the evolution of the ginseng genome and of that of related species in the Araliaceae.     

A repetitive DNA sequence in the salmonid fishes similar to a retroviral long terminal repeat

Summary We describe the characteristics of a repetitive DNA sequence from the rainbow trout and related salmonid fishes that is similar to a retroviral long terminal repeat (LTR). The repeat is 160 bp long and contains a region of homology to the LTR of the avian sarcoma virus. Two clones with this repeat from the chum salmon also have a polypurine tract and tRNA binding site, respectively, and these clones may represent the two LTRs of a retrovirus or retroviral-like repetitive element. Copies of the repeat are also adjacent to rainbow trout and chum salmon protamine genes. These repeats may be solo LTRs. There appears to be some polymorphism in restriction sites between individual rainbow trout and considerable differences between salmonid fish species when the repeat is used as a probe.     

Evolution of the large genome in Capsicum annuum occurred through accumulation of single-type long terminal repeat retrotransposons and their derivatives

Although plant genome sizes are extremely diverse, the mechanism underlying the expansion of huge genomes that did not experience whole‐genome duplication has not been elucidated. The pepper, Capsicum annuum, is an excellent model for studies of genome expansion due to its large genome size (2700 Mb) and the absence of whole genome duplication. As most of the pepper genome structure has been identified as constitutive heterochromatin, we investigated the evolution of this region in detail. Our findings show that the constitutive heterochromatin in pepper was actively expanded 20.0–7.5 million years ago through a massive accumulation of single‐type Ty3/Gypsy‐like elements that belong to the Del subgroup. Interestingly, derivatives of the Del elements, such as non‐autonomous long terminal repeat retrotransposons and long‐unit tandem repeats, played important roles in the expansion of constitutive heterochromatic regions. This expansion occurred not only in the existing heterochromatic regions but also into the euchromatic regions. Furthermore, our results revealed a repeat of unit length 18–24 kb. This repeat was found not only in the pepper genome but also in the other solanaceous species, such as potato and tomato. These results represent a characteristic mechanism for large genome evolution in plants.     

Nucleotide sequence of terminal repeats of 412 transposable elements of Drosophila melanogaster: A similarity to proviral long terminal repeats and its implications for the mechanism of transposition

We have sequenced the long terminal direct repeats (and adjacent DNA) of two members of the 412 family of transposable elements of Drosophila melanogaster cloned on fragments of DNA from strain Oregon R. The repeats of the first element are identical and 481 base-pairs long; the repeats of the second are also identical but are 571 base-pairs long. The first 482 base-pairs of the 571 base-pair sequence correspond to the 481 base-pair repeat differing by five base substitutions and one addition/deletion. The 571 base-pair repeats are rare. Each of these 412 elements is flanked by a four base-pair direct repeat, suggesting that insertion of a 412 element is associated with duplication of four base-pairs. Analysis of the “empty site” from strain Canton S corresponding to one of these elements supports this conclusion. The sequence of 481 base-pair repeats and of 412 DNA immediately adjacent to them show striking similarities to corresponding regions of vertebrate proviruses and we discuss the implications this may have for the mechanism of transposition.     

Z-DNA–Containing Long Terminal Repeats of Human Endogenous Retrovirus Families Provide Alternative Promoters for Human Functional Genes

Transposable elements (TEs) account for approximately 45% of the human genome. TEs have proliferated randomly and integrated into functional genes during hominoid radiation. They appear as right-handed B-DNA double helices and slightly elongated left-handed Z-DNAs. Human endogenous retrovirus (HERV) families are widely distributed in human chromosomes at a ratio of 8%. They contain a 5′-long terminal repeat (LTR)-gag-pol-env-3′-LTR structure. LTRs contain the U3 enhancer and promoter region, transcribed R region, and U5 region. LTRs can influence host gene expression by acting as regulatory elements. In this review, we describe the alternative promoters derived from LTR elements that overlap Z-DNA by comparing Z-hunt and DeepZ data for human functional genes. We also present evidence showing the regulatory activity of LTR elements containing Z-DNA in GSDML. Taken together, the regulatory activity of LTR elements with Z-DNA allows us to understand gene function in relation to various human diseases.     

Synthesis of (±)-8,16,26,34-Tetrahydroxy-6,10,14,18,24,28,32,36-octaoxohentetracontane as a Potent Synthetic Analog of Race T Toxin Produced by Helminthosporium maydis

A stereoisomeric mixture of (±)-8,16,26,34-tetrahydroxy-6,10,14,18,24,28,32,36-octaoxo-hentetracontane (C₄₁) was synthesized together with (±)-8,16-dihydroxy-6,10,14,18-tetraoxotri-cosane (C₂₃), utilizing bis addition of pentyl-l,5-dimagnesiumbromide to two moles of a C₁₈-alde-hyde.     

BB染色体组野生种花生LTR反转录转座子RT基因的多样性分析

利用简并PCR技术从野生花生种(Arachis ipaensis Krapov. et W. C. Greg.)的基因组中扩增分离Ty1-copia类(1类)和Ty3-gypsy类(2类)反转录转座子RT基因,并对其序列特征、多样性、系统进化关系及转录活性进行分析。结果显示:对于1和2类RT基因,目的条带分别约为260和430 bp;分离获得了23和32条序列,长度范围分别为262～266、395～435 bp;AT所占比例分别为61.60%～69.17%和55.79%～61.34%;核苷酸序列间相似性分别为52.5%～98.9%和45.0%～98.8%,氨基酸序列间相似性分别为39.8%～100%和9.0%～97.2%。其中2类基因的异质性高于1类;1类和2类基因分别有3条和15条发生了无义突变,2类的无义突变发生率远高于1类。1类基因的保守基序保守性较高,2类的保守基序呈一定程度的变异。代表序列的蛋白质三级结构基本类似。聚类分析结果显示,1类和2类基因可被分为5个和6个家族。1类和2类基因都有部分序列与其他物种的RT基因序列亲缘关系较近,表明它们之间可能存在两类反转录转座子的横向传...     

SIV of stump-tailed macaque (SIVstm) is a divergent Asian isolate.

Analysis of molecularly cloned DNAs of SIVs isolated from Asian rhesus macaque (Macaca mulatta; SIVmac) and pig-tailed macaque (Macaca nemestrina; SIVmne) has indicated a high degree of sequence homology between these viruses. Thus SIVmac and SIVmne might have originated from the same or very closely related viruses. We have cloned and sequenced a PCR-amplified segment containing the LTR sequences of SIV originating from a stump-tailed macaque (Macaca arctoides; SIVstm). Comparative sequence analysis indicates that SIVstm belongs to the SIV/HIV-2 group; however, it is genetically distinct from the other members.     

Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza

Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27,000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.     

MiR-217 is involved in Tat-induced HIV-1 long terminal repeat (LTR) transactivation by down-regulation of SIRT1

MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and may contribute to the development and progression of many infective diseases including human immunodeficiency virus 1 (HIV-1) infection. The Tat protein is fundamental to viral gene expression. In this study, our goal was to investigate the regulation of a specific miRNA (known as miR-217) in multinuclear activation of galactosidase indicator (MAGI) cells and explore the mechanisms by which miR-217 influenced Tat-induced HIV-1 transactivation through down-regulation of SIRT1 expression. We showed that miR-217 was up-regulated when Tat was expressed in multinuclear activation of galactosidase indicator cells. Forced expression of "miR-217 mimics" increased Tat-induced LTR transactivation. In addition, miR-217 significantly inhibited SIRT1 protein expression by acting on the 3'-UTR of the SIRT1 mRNA. In turn, the decrease in SIRT1 protein abundance provoked by miR-217 affected two important types of downstream signaling molecules that were regulated by Tat. Lower expression of SIRT1 caused by miR-217 enhanced Tat-induced phosphorylation of IKK and p65-NFkB and also exacerbated the loss of AMPK phosphorylation triggered by Tat. Our results uncover previously unknown links between Tat and a specific host cell miRNA that targets SIRT1. We also demonstrate that this regulatory mechanism impinges on p65-NFkB and AMPK signaling: two important host cell pathways that influence HIV-1 pathogenesis. Our results also suggest that strategies to augment SIRT1 protein expression by down-regulation of miR-217 may have therapeutic benefits to prevent HIV-1 replication.