植物基因组中微型反向重复转座元件研究进展

微型反向重复转座元件(miniature inverted repeat transposable element,MITE)是一类特殊的转座元件,在结构上与有缺失的DNA转座子相似,但具有反转录转座子高拷贝数的特点.MITE时常与基因相伴,对基因调控可能起重要作用,因此,MITE正逐渐成为基因和基因组进化及生物多样性研究的一种重要工具.本文综述了植物基因组MITE的结构、分类、活性及其应用研究进展.     

果蝇转座因子对基因组进化的影响

真核生物基因组织有很多可移动ＤＮＡ片段为称转座因子,果蝇是大量系统研究的最好实验材料之一,其基因组的１０％－１２％是由转座因子组成,在宿主中,ＴＥs也许改变基因表达模型,也许改变ＯＲＦs编码序列,也许对细胞功能产生影响,这此因子遗传的可动性也可能使它们适于建造载体产生转基因生物。因此,对ＴＥs进化的动态研究以及对宿主基因组进化影响的探索将有助于TEs作为载体的细胞工程研究。     

石刁柏EST序列中微卫星分布特征分析

目的:开发新型石刁柏EST - SSR分子标记和开展相关的分子生物学研究.方法:利用EST - trimmer、Repeat Masker、SSRIT等生物信息学分析工具对石刁柏EST数据库中的EST序列进行去除poly A/T尾,载体、重复序列和低质量序列处理,并对EST序列中SSR分布特征进行了分析.结果:在NCBI数据库中下载的8 565条石刁柏EST序列中,重复次数超过5次的SSR共有610个,其中分布于601～ 800bp的EST - SSR标记最多,共464个,占SSR总数的77.33％;主要SSR重复基元类型是二核苷酸,共426个,占SSR总数的69.84％,其次是三核苷酸占SSR总数的29.18％.四核苷酸和五核苷酸的SSR仅各3个.结论:石刁柏EST中存在丰富的SSR信息,其中二核苷酸的AG/TC、GA/CT以及三核苷酸的CTT/GAA是SSR主要的重复单元.     

Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses

Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.     

Steroidal saponins from roots of Asparagus officinalis

Sarsasapogenin M (1) and sarsasapogenin N (2), two new oligospirostanosides with a unique aglycone moiety, (25S)-5beta-spirostan-3beta, 17alpha-diol, along with seven known compounds (25S)-5beta-spirostan-3beta-ol-3-O-beta-d-glucopyranosyl-(1,2)-[beta-d-xylopyranosyl-(1,4)]-beta-d-glucopyranoside (3), (25S)-5beta-spirostan-3beta-ol-3-O-beta-d-glucopyranosyl-(1,2)-beta-d-glucopyranoside (4), (25S)-5beta-spirostan-3beta-ol-3-O-alpha-l-rhamnopyranosyl-(1,2)-[alpha-l-rhamnopyranosyl-(1,4)]-beta-d-glucopyranoside (5), (25S)26-O-beta-d-glucopyranosyl-5beta-furost-20 (22)-ene-3beta,26-diol-3-O-beta-d-glucopyranosyl-(1,2)-beta-d-glucopyranoside (6), yamogenin (7), beta-sitosterol (8), and sitosterol-beta-d-glucoside (9) were isolated from the roots of Asparagus officinalis L. Their structures were determined by spectral analysis, including extensive 1D and 2D NMR experiments.     

高等植物helitron转座子的研究进展

作为重复序列的一种主要类型,转座子在高等植物基因组中具有相当丰富的DNA含量,在改变基因结构、调节基因表达、影响基因组进化,以及创造新基因的过程中扮演着重要的角色。Helitron转座子是DNA转座子的一种,在转座过程中经常捕获基因或基因片段,以及插入到基因附近或基因内部,因此在改变基因组构成、影响基因组的进化过程以及改变基因型和表型等方面起着重要作用。该文对国内外近年来有关植物基因组中helitron转座子的结构特征、鉴定和分类方法、基因组中的含量和在染色体上的分布,以及转座扩增和基因片段的捕获等方面的研究进展进行了综述,并对helitron转座子研究过程中存在的问题进行了讨论,对今后helitron相关的研究进行了展望。     

Two novel hexasaccharides from the roots of Asparagus officinalis

Two non-reducing hexasaccharides isolated from the roots of Asparagus officinalis were identified as 1^F-β-fructofuranosyl-6^G(1-β-fructofuranosyl)₃sucrose and 1^F(1-β-fructofuranosyl)₂-6^G(1-β-fructofuranosyl)₂sucrose by examination of the constituent saccharides, GLC analysis of methyl derivatives, and investigation of partial acid hydrolysates and β-fructofuranosidase-catalysed hydrolysis products.     

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated A. thaliana genes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Potential Role of Transposable Elements in the Rapid Reorganization of the Fusarium oxysporum Genome

The activity of several families of transposable elements (TEs) in the genome of Fusarium oxysporum represents a potential source of karyotypic instability. We investigated transposon-mediated chromosome rearrangements by analyzing the karyotypes of a set of strains in which transposition events had occurred. We uncovered exceptional electrophoretic karyotype (EK) variability, in both number and size of chromosomal bands. We showed that EK differences result from chromosomal translocations, large deletions, and even more complex rearrangements. We also revealed many duplicated chromosomal regions. By following transposition of two elements and analyzing the distribution of different families of TEs on whole chromosomes, we find (i) no evidence of chromosomal breakages induced by transposition, (ii) a clustering of TEs in some regions, and (iii) a correlation between the high level of chromosomal polymorphism and the concentration of TEs. These results suggest that chromosome length polymorphisms likely result from ectopic recombination between TEs that can serve as substrates for these changes.     

Tc1-Like Transposable Elements in the Genome of Lake Trout (Salvelinus namaycush)

This study reports on the DNA sequence of a Tc1-like transposable element Tsn1 from lake trout (Salvelinus namaycush). Tc1-like elements were amplified by PCR using an oligonucleotide primer based on the Tdr1 element of zebrafish. One full-length and two partial-length copies of the transposon were sequenced. In addition, partial Tsn1 elements were recovered from PCR reactions run with primers specific to the 3′ terminus of the 28S rDNA. However, sequence analysis of cloned fragments found that these sequences were not associated with the rDNA cistron. Sequence comparisons indicate that Tsn1 is a type A element common to both salmonid and cyprinid fishes. The consensus sequence of the full-length element (Tsn1) was 1643 nucleotides with long terminal repeats (LTRs) of 225 nucleotides. Tsn1 contains a transposase coding region corresponding to 340 amino acids that includes all of the functional elements of Tc1-like transposons. Southern analysis found a high proportion of the Tsn1 transposons in the lake trout genome to be full-length copies. Received March 7, 1998; accepted July 20, 1998     

An Agrobacterium-transformed cell culture from the monocot Asparagus officinalis

Cultured stem fragments from the monocotyledonous plant Asparagus officinalis infected by the oncogenic bacterium Agrobacterium tumefaciens developed tumorous proliferations. This tissue was propagated in vitro on hormone-free culture medium. The T-DNA-encoded markers nopaline and agrocinopine were unambiguously detected in these tissues. The data demonstrate that stable T-DNA transfer as well as expression of T-DNA genes is possible in at least some monocotyledonous plants. This opens new possibilities for plant genetic engineering using the Ti plasmid as a gene vector.     

Transposable Elements in the Animal Kingdom

Transposable elements (TEs) are commonly thought to be of universal occurrence in eukaryotes. Analysis of complete higher eukaryotic genomes confirms the TE status as substantial genome components and provides insights into their role in shaping the genome structure of extant eukaryotes. This review addresses several recently investigated problems in transposon biology, including the potential roles of promoter organization in transposon function and evolution, the ubiquity of TEs in numerous phyla of the animal kingdom, and the possible connection between transposon content and mode of reproduction.     

Phylogenetic Analysis of Mos1-Like Transposable Elements in the Drosophilidae

We have performed a phylogenetic analysis of 59 mariner elements in 14 Drosophilidae species that are related to the active Drosophila mauritiana Mos1 element. This includes 38 previously described sequences and 21 new sequences amplified by PCR from 10 species. Most of the elements detected are nonfunctional due to several frameshifts and deletions. They have been subdivided into four groups according to specific signatures in the nucleotidic and amino acid sequences. The mean nucleotide diversity is 4.8 ± 0.1% and reflects mainly the divergence of inactive elements over different periods. Although this probably gives rise to occasional homoplasies between distantly related taxa, the elements of each species remain grouped together. Horizontal transfer, reported previously between D. mauritiana and Zaprionus tuberculatus, can be extended to Z. verruca, while the Mos1-like element of Z. indianus belongs to another group. Interpretation of the phylogeny leads to a comparison of the influence of common ancestral sequences and putative horizontal transfers. Received: 31 May 1999 / Accepted: 28 June 1999     

Complete Genome of a Novel Endornavirus Assembled from Next-Generation Sequence Data

Endornaviruses have large double-stranded RNA (dsRNA) genomes that carry a single open reading frame (ORF). Here we report the complete genome of a novel endornavirus, assembled from next-generation sequence data generated from Vitis vinifera-extracted dsRNA. Two different fungal hosts have been identified for this virus, suggesting that horizontal transmission of the virus is possible.     

Steroids from the roots of Asparagus officinalis and their cytotoxic activity

One new (Sarsasapogenin O) and seven known steroids were isolated from the roots of Asparagus officinalis L. Their structures were elucidated on the basis of spectroscopic analysis, including various 2D-NMR techniques, hydrolysis,and by comparison of spectral data of known compounds. These compounds together with nine steroids which were previously isolated from this plant, were tested for cytotoxic activity. Among them, eight compounds displayed significant cytotoxicities against human A2780, HO-8910, Eca-109, MGC-803, CNE, LTEP-a-2, KB and mouse L1210 tumor cells.     

Glider and Vision: Two New Families of Miniature Inverted-Repeat Transposable Elements in Xenopus Laevis Genome

We have characterised from Xenopus laevis two new short interspersed repetitive elements, we have named Glider and Vision, that belong to the family of miniature inverted-repeat transposable elements (MITEs). Glider was first characterised in an intronic region of the α-tropomyosin (α-TM) gene and database search has revealed the presence of this element in 10 other Xenopus laevis genes. Glider elements are about 150 bp long and for some of them, their terminal inverted repeats are flanked by potential target-site duplications. Evidence for the mobility of Glider element has been provided by the presence/absence of one element at corresponding location in duplicated α-TM genes. Vision element has been identified in the promoter region of the cyclin dependant kinase 2 gene (cdk2) where it is boxed in a Glider element. Vision is 284 bp long and is framed by 14-bp terminal inverted repeats that are flanked by 7-bp direct repeats. We have estimated that there are about 20,000 and 300 copies of Glider and Vision respectively scattered throughout the laevis genome. Every MITEs elements but two described in our study are found either in 5′ or in 3′ regulatory regions of genes suggesting a potential role in gene regulation. This revised version was published online in August 2006 with corrections to the Cover Date.