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。     

水稻逆转录转座子RIRE10拷贝数与LTR区转录活性的鉴定

在水稻第四号染色体的长臂上鉴定了一个结构完整的Ty3型逆转录转座子RIRE10。RIRE10两LTR间的中间区域在gag pol的上游还包含另一个开放阅读框。通过RT PCR与Northern印迹杂交检测到来自LTR区的转录产物 ;根据点杂交结果 ,鉴定出包含中间区域的RIRE10成员的个数以及LTR区的拷贝数。除了 6 5个完整的逆转录转座子所具备的两个LTR外 ,水稻基因组还含有近 90 0个RIRE10的solo LTR。LTR区的转录以及导致solo LTR产生的同源重组可能影响了RIRE10成员在水稻基因组中的转座活性     

植物基因组中的非LTR反转录转座子SINEs和LINEs

反转录转座子是基因组进化的推动者之一。分为LTR和非LTR两种类型。前者是真核基因组的主要组分,结构和转座方式与逆转录病毒类似。后者是最初发现于动物基因组新近发现在植物基因组中也广泛存在的新型重复序列,包括LINEs(long interspersed nuclear elements)和SINEs(short interspersed nuclear elements)两个亚型。它们大多因自身或受宿主基因组的调控而失去转座活性。其转座机理目前还不十分清楚,推测LINEs可以自主转座,SINEs依赖其他转座子被动转座。种系分析认为LINEs可能是最古老的反转录转座子,SINEs的起源未知。文章对以上内容进行了归纳和讨论。     

细菌中介导多重耐药的Tn7转座子研究进展

转座子是介导细菌耐药性传播的重要可移动遗传元件。Tn7转座子与细菌耐药密切相关,其携带转座模块和Ⅱ类整合子系统。Tn7编码转座相关蛋白TnsABCDE进行“剪切-粘贴”机制转座,转座核心TnsABC也可与三链DNA或Cas-RNA复合物结合实现转座。近年来新发现了多种介导多重耐药的Tn7转座子,其在介导细菌抗生素、消毒剂和重金属抗性基因的获得、传播扩散等方面发挥了重要作用。本文综述了细菌中Tn7转座子的遗传结构、转座机制、流行以及新发现的介导多重耐药的Tn7转座子,以期为细菌中Tn7转座子的深入研究提供参考。     

植物活性长末端重复序列反转录转座子研究进展

长末端重复序列(Long terminal repeat,LTR)反转录转座子是真核生物基因组中普遍存在的一类可移动的DNA序列,它们以RNA为媒介,通过"复制粘贴"机制在基因组中不断自我复制。在高等植物中,许多活性的LTR反转录转座子已被详尽研究并应用于分子标记技术、基因标签、插入型突变及基因功能等分析。本文对植物活性LTR反转录转座子进行全面的调查,并对其结构、拷贝数和分布以及转座特性进行系统的归纳,分析了植物活性LTR反转录转座子的gag(种属特异抗原)和pol(聚合酶)序列特征,以及LTR序列中顺式调控元件的分布。研究发现自主有活性的LTR反转录转座子必须具备LTR区域以及编码Gag、Pr、Int、Rt和Rh蛋白的基因区。其中两端LTR区域具有高度同源性且富含顺式调控元件;Rt蛋白必备RVT结构域;Rh蛋白必备RNase_H1_RT结构域。这些结果为后续植物活性LTR反转录转座子的鉴定和功能分析奠定了重要基础。     

水稻MITEs类转座子mPing研究进展

Miniature Ping(mPing)是小型反向重复转座子(Miniature Inverted-Repeat Transposable Elements,MITEs)类转座子Tourist-like超家族重要成员,是水稻基因组内检测到的第一个活跃的MITEs,是MITEs大家族中少数低拷贝且可以在自然状态下维持转座活性的成员之一,因此,mPing是转座子相关领域研究的良好素材。该文综合阐述了近年来国内外有关mPing的结构、转座酶供体、激活特性以及对基因组的影响等方面的研究进展,为进一步深入探究MITEs的转座机制以及mPing转座子的开发利用提供资料。     

植物反转录转座子及其在功能基因组学中的应用

高等植物中的反转录转座子是构成植物基因组的重要成分之一.它分病毒家族和非病毒家族两类,病毒家族包括反转录病毒和类似于反转录病毒的非病毒转座子,病毒家族中的反转录转座子可再细分为Ty3-gypsy类和Ty1-copia类;非病毒家族可细分为LINE类和SINE类.正常情况下大部分反转录转座子不具有活性,某些生物或非生物因素胁迫可激活部分反转录转座子转座.反转录转座子自身编码反转录酶进行转录,以"拷贝-粘贴"的转座模式导致基因组扩增和进化.具有活性的反转录转座子通过插入产生新的突变,可作为一种基因标签技术,应用于功能基因组学研究,并成为研究植物基因功能和表达的重要技术平台.本文综述了近几年来在植物反转录转座子方面的研究进展,主要包括植物反转录转座子的结构、特征、活性及其对基因组的影响和它们在功能基因组学中的应用.     

植物LTR类反转录转座子序列分析识别方法

LTR类反转录转座子(Long terminal repeat retrotransponson)是真核生物中的一类重要转座元件,具有分布广泛、异质性高等特点,在真核生物基因组进化中起着重要作用,现广泛应用于植物的基因功能分析和遗传多样性研究等方面。LTR类反转录转座子的序列识别是其应用的前提条件,因此对LTR类反转录转座子的序列鉴定和分析方法的研究具有重要的理论意义和实际应用价值。LTR类反转录转座子序列的生物信息学分析软件按原理可大致分为序列比对分析和相关序列保守区域识别鉴定两类。比对软件如BLAST、DNAstar等,是一种序列相似性搜索程序,通过与已知的反转录转座子序列比对后的序列相似性来判断未知序列是否是反转录转座子序列,但这类软件不能直接获得具体的LTR等特征序列的相关信息,不能对反转录转座子序列的全长进行识别。识别鉴定软件按原理可分为从头算起法、比较基因组法、同源搜索法和结构基础法4种,如LTR-Finder等基于从头算起法的识别鉴定软件,可对LTR类反转录转座子全序列进行较准确地预测和注释,RepeatMasker等基于同源搜索法的软件,通过与数据库中的序列的相似性比对后发现可能存在的LTR类反转录转座子。文章对不同的LTR类反转录转座子预测方法进行了比较和分析,在此基础上归纳总结出一套分析LTR类反转录转座子序列的操作流程,旨在为LTR类反转录转座子序列的分析提供参考。     

酵母转座子—Ty因子及其对基因表达的影响

酵母转座子Ty因子是酵母基因组中的一组中度重复顺序,其平均长度为6kb,两端为短的同向重复序列(δ-序列),在一级结构上与反转录病毒的原病毒形式非常相似。Ty因子自身还可以编码三个蛋白产物,其结构与功能分别和反转录病毒的gag、rev、int基因产物相关联。因此,很可能它们之间在起源上有着某种联系。Ty因子在基因组中可以用同源重组的方式或非同源重组的方式(即转座)发生位置和数目的变动。在移动的同时,它们也明显地影响着酵母基因的表达,有时,Ty因子可以用增强子的方式来大大提高某个酵母基因的表达水平。     

Identification of novel LTR retrotransposons in the genome of Aedes aegypti

We have detected seventy-six novel LTR retrotransposons in the genome of the mosquito Aedes aegypti by a genome wide analysis using the LTR_STRUC program. We have performed a phylogenetic classification of these novel elements and a distribution analysis in the genome of A. aegypti. These mobile elements belong either to the Ty3/gypsy or to the Bel family of retrotransposons and were not annotated in the mosquito LTR retrotransposon database (TEfam). We have found that  1.8% of the genome is occupied by these newly detected retrotransposons that are distributed predominantly in intergenic genomic sequences and introns. The potential role of retrotransposon insertions linked to host genes is described and discussed. We show that a retrotransposon family belonging to the Osvaldo lineage has peculiar structural features, and its presence is likely to be restricted to the A. aegypti and to the Culex pipiens quinquefasciatus genomes. Furthermore we show that the ninja-like group of elements lacks the Primer Binding Site (PBS) sequence necessary for the replication of retrotransposons. These results integrate the knowledge on the complicate genomic structure of an important disease vector.     

Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data

Background  

Long terminal repeat (LTR) retrotransposons are a class of mobile genetic element capable of autonomous transposition via an RNA intermediate. Their large size and proliferative ability make them important contributors to genome size evolution, especially in plants, where they can reach exceptionally high copy numbers and contribute substantially to variation in genome size even among closely related taxa. Using a phylogenetic approach, we characterize dynamics of proliferation events of Ty3/gypsy-like LTR retrotransposons that led to massive genomic expansion in three Helianthus (sunflower) species of ancient hybrid origin. The three hybrid species are independently derived from the same two parental species, offering a unique opportunity to explore patterns of retrotransposon proliferation in light of reticulate evolutionary events in this species group.     

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.     

Ty1-copia group retrotransposons and the evolution of retroelements in the eukaryotes

Ty1-copia group retrotransposons are among the best studied transposable elements in the eukaryotes. This review discusses the extent of these transposons in the eukaryote kingdoms and compares models for the evolution of these genetic elements in the light of recent phylogenetic data. These data show that the Ty1-copia group is widespread among invertebrate eukaryotes, especially in the higher plant kingdom, where these genetic elements are unusually common and heterogeneous in their sequence. The phylogenetic data also suggest that the present day spectrum of Ty1-copia group retrotransposons has been influenced both by divergence during vertical transmission down evolving lineages and by horizontal transmission between distantly related species. Lastly, the factors affecting Ty1-copia group retrotransposon copy number and sequence heterogeneity in eukaryotic genomes and the effects of transpositional quiescence and defective retrotransposons upon evolution of Ty1-copia group retrotransposons are discussed.     

Evidence for the Role of Recombination in the Regulatory Evolution of Saccharomyces cerevisiae Ty Elements

The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons residing within a single genome. In this article we report the results of such an analysis of two closely related families of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon evolution. Received: 30 September 1997 / Accepted: 3 February 1998