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Characterisation of mobile genetic elements in Mycoplasma hominis with the description of ICEHo-II, a variant mycoplasma integrative and conjugative element. 人支原体中移动遗传元件的特征与ICEHo-II的描述,一个变体支原体整合和共轭元件。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-11-07 DOI: 10.1186/s13100-020-00225-9
Birgit Henrich, Stephanie Hammerlage, Sebastian Scharf, Diana Haberhausen, Ursula Fürnkranz, Karl Köhrer, Lena Peitzmann, Pier Luigi Fiori, Joachim Spergser, Klaus Pfeffer, Alexander T Dilthey

Background: Mobile genetic elements are found in genomes throughout the microbial world, mediating genome plasticity and important prokaryotic phenotypes. Even the cell wall-less mycoplasmas, which are known to harbour a minimal set of genes, seem to accumulate mobile genetic elements. In Mycoplasma hominis, a facultative pathogen of the human urogenital tract and an inherently very heterogeneous species, four different MGE-classes had been detected until now: insertion sequence ISMhom-1, prophage MHoV-1, a tetracycline resistance mediating transposon, and ICEHo, a species-specific variant of a mycoplasma integrative and conjugative element encoding a T4SS secretion system (termed MICE).

Results: To characterize the prevalence of these MGEs, genomes of 23 M. hominis isolates were assembled using whole genome sequencing and bioinformatically analysed for the presence of mobile genetic elements. In addition to the previously described MGEs, a new ICEHo variant was found, which we designate ICEHo-II. Of 15 ICEHo-II genes, five are common MICE genes; eight are unique to ICEHo-II; and two represent a duplication of a gene also present in ICEHo-I. In 150 M. hominis isolates and based on a screening PCR, prevalence of ICEHo-I was 40.7%; of ICEHo-II, 28.7%; and of both elements, 15.3%. Activity of ICEHo-I and -II was demonstrated by detection of circularized extrachromosomal forms of the elements through PCR and subsequent Sanger sequencing.

Conclusions: Nanopore sequencing enabled the identification of mobile genetic elements and of ICEHo-II, a novel MICE element of M. hominis, whose phenotypic impact and potential impact on pathogenicity can now be elucidated.

背景:在整个微生物世界的基因组中都发现了可移动的遗传元件,介导基因组可塑性和重要的原核表型。即使是没有细胞壁的支原体,虽然已知它拥有最少的基因,似乎也会积累可移动的遗传元素。人支原体是一种人类泌尿生殖道的兼性病原体,是一种本质上非常异质性的物种,迄今为止已经检测到四种不同的mge类:插入序列ismhom1,噬菌体MHoV-1,四环素抗性介导转座子,以及ICEHo,一种编码T4SS分泌系统(称为MICE)的支原体整合和共轭元件的物种特异性变体。结果:为了表征这些MGEs的流行程度,我们对23个MGEs的基因组进行了分析。利用全基因组测序对古人类分离株进行组装,并对其移动遗传元件的存在进行生物信息学分析。除了先前描述的MGEs外,还发现了一个新的ICEHo变体,我们将其命名为ICEHo- ii。在15个ICEHo-II基因中,有5个是常见的MICE基因;8个是ICEHo-II独有的;两个代表了iceho - 1中也存在的基因的重复。在150米。基于PCR筛选,iceho - 1的患病率为40.7%;ICEHo-II为28.7%;这两种元素都是15.3%通过PCR和随后的Sanger测序检测到这些元件的环状染色体外形式,证实了iceho - 1和-II的活性。结论:纳米孔测序能够鉴定出人类支原体的可移动遗传元件和ICEHo-II,这是一种新的小鼠元件,现在可以阐明其表型影响和对致病性的潜在影响。
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引用次数: 4
Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains. 全面的基因组分析揭示了内源性逆转录病毒编码逆转录病毒样蛋白结构域的动态进化。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-09-17 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00224-w
Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi Imanishi, So Nakagawa

Background: Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes.

Results: We investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (~ 0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences showed bimodal distributions, suggesting that a large proportion of ERV-ORFs either recently, or anciently, inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify candidates for ERV-derived genes, we estimated the ratio of non-synonymous to synonymous substitution rates (dN/dS) for ERV-ORFs in human and non-human mammalian pairs, and found that approximately 42% of the ERV-ORFs showed dN/dS < 1. Further, using functional genomics data including transcriptome sequencing, we determined that approximately 9.7% of these selected ERV-ORFs exhibited transcriptional potential.

Conclusions: These results suggest that purifying selection operates on a certain portion of ERV-ORFs, some of which may correspond to uncharacterized functional genes hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

背景:内源性逆转录病毒(ERVs)是哺乳动物生殖系细胞古代逆转录病毒感染的残余。大部分erv失去了它们的开放阅读框(orf),而其他erv保留了它们并被宿主物种所期待。然而,目前尚不清楚有多少比例的erv拥有orf (erv - orf),被转录,并作为增选基因的候选者。结果:我们研究了19种哺乳动物基因组中含有逆转录病毒样蛋白结构域(gag、pro、pol和env)的176,401个erv - orf的特征。具有orf的erv的比例总体上很小(约0.15%),尽管它们因结构域类型和物种而有所不同。观察到的ERV-ORF与一致序列的差异表现为双峰分布,这表明大部分ERV-ORF要么是最近的,要么是古代的,插入到哺乳动物基因组中。另外,很少有缺乏orf的erv被发现表现出类似的发散模式。为了确定erv衍生基因的候选基因,我们估计了人类和非人类哺乳动物对erv - orf的非同义与同义替代率(dN/dS)的比率,发现大约42%的erv - orf显示dN/dS。结论:这些结果表明纯化选择作用于一定部分的erv - orf,其中一些可能对应于隐藏在哺乳动物基因组中的未表征的功能基因。总之,我们的分析表明,可能有比我们目前所知的更多的erv - orf以特定于宿主物种的方式被增选,这可能有助于哺乳动物的进化和多样化。
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引用次数: 14
The Dfam community resource of transposable element families, sequence models, and genome annotations 转座子家族的Dfam群落资源、序列模型和基因组注释
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-09-17 DOI: 10.21203/rs.3.rs-76062/v1
Jessica M. Storer, R. Hubley, Jeb Rosen, T. Wheeler, A. Smit
Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.
Dfam是一个包含重复DNA家族、序列模型和基因组注释的开放式数据库。Dfam(https://dfam.org)代表了从模式生物中转座元件家族的原理验证集合到广泛物种的群落资源的进化,以及策划和未策划的数据集。此外,自Dfam 3.0以来的发布提供了辅助的一致序列模型、转座元件-蛋白质比对和正式的分类系统,以支持资源中代表的生物体的日益多样性。最新发布的包括EBI贡献的336个物种中的266740个新的从头产生的转座元件家族。这一扩展展示了Dfam的许多新功能的实用性,并为改进从头生成的转座元件数据集提供了长期挑战。
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引用次数: 187
Twenty years of transposable element analysis in the Arabidopsis thaliana genome. 拟南芥基因组转座因子分析二十年。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-07-27 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00223-x
Hadi Quesneville

Transposable elements (TEs) are mobile repetitive DNA sequences shown to be major drivers of genome evolution. As the first plant to have its genome sequenced and analyzed at the genomic scale, Arabidopsis thaliana has largely contributed to our TE knowledge. The present report describes 20 years of accumulated TE knowledge gained through the study of the Arabidopsis genome and covers the known TE families, their relative abundance, and their genomic distribution. It presents our knowledge of the different TE family activities, mobility, population and long-term evolutionary dynamics. Finally, the role of TE as substrates for new genes and their impact on gene expression is illustrated through a few selected demonstrative cases. Promising future directions for TE studies in this species conclude the review.

转座因子(te)是可移动的重复DNA序列,是基因组进化的主要驱动力。作为第一个在基因组尺度上进行基因组测序和分析的植物,拟南芥对我们的TE知识做出了很大的贡献。本报告描述了20年来通过研究拟南芥基因组积累的TE知识,涵盖了已知的TE家族、它们的相对丰度和基因组分布。它展示了我们对不同TE家族活动、流动性、人口和长期进化动态的了解。最后,TE作为新基因的底物的作用及其对基因表达的影响通过几个选定的示范案例来说明。展望了该物种TE研究的未来方向。
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引用次数: 62
Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. pogo,一个独立的IS630-Tc1-马里纳转座子超家族的进化,揭示了脊椎动物中反复发生的驯化事件。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-07-22 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00220-0
Bo Gao, Yali Wang, Mohamed Diaby, Wencheng Zong, Dan Shen, Saisai Wang, Cai Chen, Xiaoyan Wang, Chengyi Song

Background: Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood.

Results: Here, phylogenetic analysis show that pogo transposases, together with Tc1/mariner, DD34E/Gambol, and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover, and Fot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals-even mammals-and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix-turn-helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2-7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29-56D) were observed for pogo transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains.

Conclusions: This is the first report to systematically reveal the evolutionary profiles of the pogo transposons, suggesting that pogo and Tc1/Mariner are two separate superfamilies of ITm group, and demonstrating the repeated domestications of pogo in vertebrates. These data indicate that pogo transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of pogo transposons and updates the classification of ITm group.

背景:Tc1/mariner和Zator作为IS630-Tc1-mariner(ITm)组的两个超家族,已被明确定义。然而,曾经被指定为Tc1/水手超家族重要家族的pogo转座子的分子进化和驯化仍然知之甚少。结果:系统发育分析表明,pogo转座酶与Tc1/mariner、DD34E/Gambol和Zator转座酶一起形成了四个具有高度bootstrap支持的不同单系分支(> = 74%),表明它们是ITm组的独立超家族。pogo超家族具有高度多样性,有六个不同的家族(Passer、Tigger、pogoR、Lemi、Mover和Fot/Fot-like),分布广泛,扩展范围遍及真核生物的所有王国。它在动物和真菌中广泛存在,但在陆地植物中的分类分布受到限制。它已经入侵了几乎所有动物谱系,甚至哺乳动物,并在脊椎动物中被反复驯化,具有12个基因,包括着丝粒相关蛋白B(CENPB)、CENPB DNA结合结构域含1(CENPBD1)、Jrk螺旋-转螺旋蛋白(Jrk)、Jrk样蛋白(JRKL)、源自KRAB结构域的pogo转座子(POGK)和ZNF结构域(POGZ),和Tigger转座元件衍生自2至7(TIGD2-7),推断为源自该超家族。其中两个(JRKL和TIGD2)似乎是共同驯化的,其他代表了独立的驯化事件。四个基因(TIGD3、TIGD4、TIGD5和POGZ)往往代表脊椎动物的古老驯化,而其他基因只出现在哺乳动物中,似乎是最近驯化的。观察到pogo转座子的显著结构变化,包括靶位点重复(TSD)类型和DDE三联体特征(DD29-56D)。大多数驯化基因来源于完整的转座酶基因;但是CENPB、POGK和POGZ是与附加功能结构域融合的嵌合基因。结论:这是第一份系统揭示pogo转座子进化特征的报告,表明pogo和Tc1/Mariner是ITm群中两个独立的超家族,并证明了pogo在脊椎动物中的重复驯化。这些数据表明,pogo转座子在真菌和动物的基因组和基因进化中发挥了重要作用。本研究扩展了我们对pogo转座子多样性的理解,并更新了ITm组的分类。
{"title":"Evolution of <i>pogo</i>, a separate superfamily of <i>IS630-Tc1-mariner</i> transposons, revealing recurrent domestication events in vertebrates.","authors":"Bo Gao,&nbsp;Yali Wang,&nbsp;Mohamed Diaby,&nbsp;Wencheng Zong,&nbsp;Dan Shen,&nbsp;Saisai Wang,&nbsp;Cai Chen,&nbsp;Xiaoyan Wang,&nbsp;Chengyi Song","doi":"10.1186/s13100-020-00220-0","DOIUrl":"10.1186/s13100-020-00220-0","url":null,"abstract":"<p><strong>Background: </strong><i>Tc1/mariner</i> and <i>Zator</i>, as two superfamilies of <i>IS630-Tc1</i>-<i>mariner</i> (<i>ITm</i>) group, have been well-defined. However, the molecular evolution and domestication of <i>pogo</i> transposons, once designated as an important family of the <i>Tc1/mariner</i> superfamily, are still poorly understood.</p><p><strong>Results: </strong>Here, phylogenetic analysis show that <i>pogo</i> transposases, together with <i>Tc1/mariner</i>, DD34E/<i>Gambol</i>, and <i>Zator</i> transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of <i>ITm</i> group. The <i>pogo</i> superfamily represents high diversity with six distinct families (<i>Passer</i>, <i>Tigger</i>, <i>pogoR</i>, <i>Lemi</i>, <i>Mover</i>, and <i>Fot/Fot-like</i>) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals-even mammals-and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix-turn-helix protein (JRK), JRK like (JRKL), <i>pogo</i> transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and <i>Tigger</i> transposable element-derived 2 to 7 (TIGD2-7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. Four genes (TIGD3, TIGD4, TIGD5, and POGZ) tend to represent ancient domestications in vertebrates, while the others only emerge in mammals and seem to be domesticated recently. Significant structural variations including target site duplication (TSD) types and the DDE triad signatures (DD29-56D) were observed for <i>pogo</i> transposons. Most domesticated genes are derived from the complete transposase genes; but CENPB, POGK, and POGZ are chimeric genes fused with additional functional domains.</p><p><strong>Conclusions: </strong>This is the first report to systematically reveal the evolutionary profiles of the <i>pogo</i> transposons, suggesting that <i>pogo</i> and <i>Tc1/Mariner</i> are two separate superfamilies of <i>ITm</i> group, and demonstrating the repeated domestications of <i>pogo</i> in vertebrates. These data indicate that <i>pogo</i> transposons have played important roles in shaping the genome and gene evolution of fungi and animals. This study expands our understanding of the diversity of <i>pogo</i> transposons and updates the classification of <i>ITm</i> group.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"25"},"PeriodicalIF":4.9,"publicationDate":"2020-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00220-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38218735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 42
LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA. LINE-1 ORF1p不决定人类/猩猩SVA和长猿LAVA的底物偏好。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-07-11 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00222-y
Annette Damert

Background: Non-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons - SVA (SINE-R-VNTR-Alu) and LAVA (L1-Alu-VNTR-Alu) - are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbon. Both SVA and LAVA have been shown to be mobilized by the autonomous LINE-1 (L1)-encoded protein machinery in a cell-based assay in trans. The efficiency of human SVA retrotransposition in vitro has, however, been considerably lower than would be expected based on recent pedigree-based in vivo estimates. The VNTR composite elements across hominoids - gibbon LAVA, orangutan SVA_A descendants and hominine SVA_D descendants - display characteristic structures of the 5' Alu-like domain and the VNTR. Different partner L1 subfamilies are currently active in each of the lineages. The possibility that the lineage-specific types of VNTR composites evolved in response to evolutionary changes in their autonomous partners, particularly in the nucleic acid binding L1 ORF1-encoded protein, has not been addressed.

Results: Here I report the identification and functional characterization of a highly active human SVA element using an improved mneo retrotransposition reporter cassette. The modified cassette (mneoM) minimizes splicing between the VNTR of human SVAs and the neomycin phosphotransferase stop codon. SVA deletion analysis provides evidence that key elements determining its mobilization efficiency reside in the VNTR and 5' hexameric repeats. Simultaneous removal of the 5' hexameric repeats and part of the VNTR has an additive negative effect on mobilization rates. Taking advantage of the modified reporter cassette that facilitates robust cross-species comparison of SVA/LAVA retrotransposition, I show that the ORF1-encoded proteins of the L1 subfamilies currently active in gibbon, orangutan and human do not display substrate preference for gibbon LAVA versus orangutan SVA versus human SVA. Finally, I demonstrate that an orangutan-derived ORF1p supports only limited retrotransposition of SVA/LAVA in trans, despite being fully functional in L1 mobilization in cis.

Conclusions: Overall, the analysis confirms SVA as a highly active human retrotransposon and preferred substrate of the L1-encoded protein machinery. Based on the results obtained in human cells coevolution of L1 ORF1p and VNTR composites does not appear very likely. The changes in orangutan L1 ORF1p that markedly reduce its mobilization capacity in trans might explain the different SVA insertion rates in the orangutan and hominine lineages, respectively.

背景:非自主VNTR(可变数目串联重复)复合反转录转座子- SVA (sin - r -VNTR- alu)和LAVA (L1-Alu-VNTR-Alu)是类人猿特有的。类人猿的SVA扩展,长臂猿的LAVA扩展。在一项基于细胞的反式实验中,SVA和LAVA都被自主的LINE-1 (L1)编码的蛋白质机制所动员。然而,人类SVA在体外逆转录转位的效率远远低于最近基于家系的体内估计。类人猿(长臂猿LAVA、猩猩SVA_A后代和人猿SVA_D后代)的VNTR复合元素显示出5′Alu-like结构域和VNTR的特征结构。不同的伴侣L1亚家族目前在每个谱系中都很活跃。谱系特异性VNTR复合物的进化可能是对其自主伴侣的进化变化的反应,特别是在核酸结合L1 orf1编码蛋白中,尚未得到解决。结果:在这里,我报告了一个高活性的人类SVA元件的鉴定和功能表征,使用改进的mneo逆转录报告盒。修饰盒(mneoM)最大限度地减少了人类SVAs VNTR与新霉素磷酸转移酶停止密码子之间的剪接。SVA缺失分析提供证据表明,决定其动员效率的关键因素存在于VNTR和5'六聚体重复序列中。同时去除5'六聚体重复序列和部分VNTR对动员率有附加的负面影响。利用改进的报告磁带,促进了对SVA/LAVA反转录转位的强大的跨物种比较,我表明,目前在长臂猿、猩猩和人类中活跃的L1亚家族的orf1编码蛋白对长臂猿LAVA、猩猩SVA和人类SVA并没有表现出底物偏好。最后,我证明了猩猩衍生的ORF1p在反式中仅支持有限的SVA/LAVA反转位,尽管在顺式中L1动员中具有完全功能。结论:总的来说,分析证实了SVA是一个高活性的人类反转录转座子和l1编码蛋白机制的首选底物。基于在人类细胞中获得的结果,L1、ORF1p和VNTR复合物的共同进化不太可能出现。猩猩L1 ORF1p基因的变化显著降低了其转运能力,这可能解释了猩猩和人猿谱系中SVA插入率的不同。
{"title":"LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA.","authors":"Annette Damert","doi":"10.1186/s13100-020-00222-y","DOIUrl":"https://doi.org/10.1186/s13100-020-00222-y","url":null,"abstract":"<p><strong>Background: </strong>Non-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons - SVA (SINE-R-VNTR-<i>Alu</i>) and LAVA (L1-<i>Alu</i>-VNTR-<i>Alu</i>) - are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbon. Both SVA and LAVA have been shown to be mobilized by the autonomous LINE-1 (L1)-encoded protein machinery in a cell-based assay in <i>trans</i>. The efficiency of human SVA retrotransposition in vitro has, however, been considerably lower than would be expected based on recent pedigree-based in vivo estimates. The VNTR composite elements across hominoids - gibbon LAVA, orangutan SVA_A descendants and hominine SVA_D descendants - display characteristic structures of the 5' <i>Alu</i>-like domain and the VNTR. Different partner L1 subfamilies are currently active in each of the lineages. The possibility that the lineage-specific types of VNTR composites evolved in response to evolutionary changes in their autonomous partners, particularly in the nucleic acid binding L1 ORF1-encoded protein, has not been addressed.</p><p><strong>Results: </strong>Here I report the identification and functional characterization of a highly active human SVA element using an improved <i>mneo</i> retrotransposition reporter cassette. The modified cassette (<i>mneoM</i>) minimizes splicing between the VNTR of human SVAs and the neomycin phosphotransferase stop codon. SVA deletion analysis provides evidence that key elements determining its mobilization efficiency reside in the VNTR and 5' hexameric repeats. Simultaneous removal of the 5' hexameric repeats and part of the VNTR has an additive negative effect on mobilization rates. Taking advantage of the modified reporter cassette that facilitates robust cross-species comparison of SVA/LAVA retrotransposition, I show that the ORF1-encoded proteins of the L1 subfamilies currently active in gibbon, orangutan and human do not display substrate preference for gibbon LAVA versus orangutan SVA versus human SVA. Finally, I demonstrate that an orangutan-derived ORF1p supports only limited retrotransposition of SVA/LAVA in <i>trans</i>, despite being fully functional in L1 mobilization in <i>cis</i>.</p><p><strong>Conclusions: </strong>Overall, the analysis confirms SVA as a highly active human retrotransposon and preferred substrate of the L1-encoded protein machinery. Based on the results obtained in human cells coevolution of L1 ORF1p and VNTR composites does not appear very likely. The changes in orangutan L1 ORF1p that markedly reduce its mobilization capacity in <i>trans</i> might explain the different SVA insertion rates in the orangutan and hominine lineages, respectively.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"27"},"PeriodicalIF":4.9,"publicationDate":"2020-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00222-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38169547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of E. coli. 深度测序揭示了MuB在转位免疫和靶标捕获中的新作用,并重新定义了大肠杆菌的岛状Ter区域。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-07-09 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00217-9
David M Walker, Rasika M Harshey

Background: The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the E. coli genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (cis-immunity) as well as the entire ~ 37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for cis-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo.

Results: We tracked Mu transposition from six different starting locations on the E. coli genome, in the presence and absence of MuB. The data reveal that Mu's ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for cis-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the E. coli genome.

Conclusions: The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.

背景:靶捕获蛋白MuB负责大肠杆菌基因组中噬菌体Mu的高效转位。然而,一些靶点是禁止的,如Mu末端外的区域(顺式免疫)和整个~ 37kb的Mu基因组(Mu基因组免疫)。矛盾的是,MuB负责顺式免疫,也与Mu基因组免疫有关,但通过不同的机制。本研究旨在剖析MuB在体内靶标选择中的作用。结果:我们在存在和不存在MuB的情况下,从大肠杆菌基因组的六个不同起始位置跟踪了Mu转位。这些数据表明,Mu在克隆群体中的单次跳跃中对整个基因组进行采样的能力独立于MuB, MuB负责顺式免疫,在Mu基因组免疫中起次要作用,并促进插入到转录活性区域。出乎意料的是,在没有MuB的情况下,转位模式有助于扩展大肠杆菌基因组的岛状Ter片段的边界。结论:本研究的结果明确地证明了两种不同的Mu靶免疫机制的运作,其中只有一种完全依赖于MuB。该研究还揭示了体内Mu靶点选择的几个有趣且迄今未知的方面,特别是MuB在促进启动子和翻译起始位点靶点捕获方面的作用,可能是通过取代参与基因表达的大分子复合物。同样,MuB促进转位到基因组受限的Ter区域。
{"title":"Deep sequencing reveals new roles for MuB in transposition immunity and target-capture, and redefines the insular Ter region of <i>E. coli</i>.","authors":"David M Walker,&nbsp;Rasika M Harshey","doi":"10.1186/s13100-020-00217-9","DOIUrl":"https://doi.org/10.1186/s13100-020-00217-9","url":null,"abstract":"<p><strong>Background: </strong>The target capture protein MuB is responsible for the high efficiency of phage Mu transposition within the <i>E. coli</i> genome. However, some targets are off-limits, such as regions immediately outside the Mu ends (<i>cis</i>-immunity) as well as the entire ~ 37 kb genome of Mu (Mu genome immunity). Paradoxically, MuB is responsible for <i>cis</i>-immunity and is also implicated in Mu genome immunity, but via different mechanisms. This study was undertaken to dissect the role of MuB in target choice in vivo.</p><p><strong>Results: </strong>We tracked Mu transposition from six different starting locations on the <i>E. coli</i> genome, in the presence and absence of MuB. The data reveal that Mu's ability to sample the entire genome during a single hop in a clonal population is independent of MuB, and that MuB is responsible for <i>cis</i>-immunity, plays a minor role in Mu genome immunity, and facilitates insertions into transcriptionally active regions. Unexpectedly, transposition patterns in the absence of MuB have helped extend the boundaries of the insular Ter segment of the <i>E. coli</i> genome.</p><p><strong>Conclusions: </strong>The results in this study demonstrate unambiguously the operation of two distinct mechanisms of Mu target immunity, only one of which is wholly dependent on MuB. The study also reveals several interesting and hitherto unknown aspects of Mu target choice in vivo, particularly the role of MuB in facilitating the capture of promoter and translation start site targets, likely by displacing macromolecular complexes engaged in gene expression. So also, MuB facilitates transposition into the restricted Ter region of the genome.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"11 ","pages":"26"},"PeriodicalIF":4.9,"publicationDate":"2020-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13100-020-00217-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38159010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
IS982 and kin: new insights into an old IS family. IS982 和亲属:对一个古老的 IS 家族的新认识。
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-07-04 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00221-z
Nancy Fayad, Mireille Kallassy Awad, Jacques Mahillon

Insertion sequences (IS) are ubiquitous transposable elements with a very simple organization: two inverted repeats flanking a transposase coding gene. IS982 is one of 26 insertion sequence families known so far. With 70 registered members in the ISFinder database, this family remains somewhat unexplored, despite the association of many of its members with important features such as antibiotic resistance. IS982 has a fairly simple organization with a mean length of ca. 1 Kb, two inverted repeats with conserved 5' AC 3' ends flanking a transposase coding gene and direct repeats of variable lengths. Its transposase has a RNAse-H like chemistry with an atypical DDE motif. In this study, we first highlight the current knowledge on the IS982 family by dissecting its registered members and their characteristics. Secondly, we bring new insights into this old, yet uncharted IS family, by exploring its registered elements, as well as the genomic and proteomic databases of bacterial and archaeal strains. This probing showed that the presence and distribution of this family goes far beyond the clear-cut registry of ISFinder database.

插入序列(IS)是一种无处不在的转座元件,其组织结构非常简单:两个倒置重复序列位于一个转座酶编码基因的侧翼。IS982 是目前已知的 26 个插入序列家族之一。ISFinder 数据库中有 70 个注册成员,尽管该家族的许多成员与抗生素耐药性等重要特征有关,但该家族在某种程度上仍未被探索。IS982 的组织结构相当简单,平均长度约为 1 Kb,两个具有保守的 5' AC 3' 端的倒位重复序列位于一个转座酶编码基因和长度可变的直接重复序列的侧翼。它的转座酶具有类似 RNAse-H 的化学性质和非典型的 DDE 主题。在本研究中,我们首先通过剖析 IS982 家族的注册成员及其特征,强调了目前对 IS982 家族的了解。其次,我们通过探索其注册元素以及细菌和古菌株的基因组和蛋白质组数据库,为这个古老而未知的 IS 家族带来了新的见解。这种探索表明,这个家族的存在和分布远远超出了 ISFinder 数据库的明确登记范围。
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引用次数: 0
Transposable elements in Drosophila. 果蝇中的可转座元件
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-07-03 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00213-z
Vincent Mérel, Matthieu Boulesteix, Marie Fablet, Cristina Vieira

Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.

多年来,人们一直把果蝇作为生物学模型进行研究,生物学的许多发现都依赖于这一物种。对转座元件(TE)的研究也不例外。果蝇为我们了解转座及其调控机制做出了巨大贡献,但最重要的是,它是最早对种群进行遗传和基因组研究的生物之一。在这篇综述文章中,我们将以一种非常宽泛的方式,从历史的角度以及该领域的最新发现来探讨果蝇的TEs。
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引用次数: 0
Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data. 鸡全基因组测序数据中内源性禽白血病病毒E亚群(ALVE)插入的鉴定和特征
IF 4.9 2区 生物学 Q1 GENETICS & HEREDITY Pub Date : 2020-06-30 eCollection Date: 2020-01-01 DOI: 10.1186/s13100-020-00216-w
Andrew S Mason, Ashlee R Lund, Paul M Hocking, Janet E Fulton, David W Burt

Background: Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants.

Results: We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes.

Conclusions: obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations.

背景:内源性逆转录病毒(ERVs)是逆转录病毒感染的残余,可引起宿主机体长时间的基因组和免疫应激。在鸡中,内源性禽白血病病毒E亚群(ALVE)的表达与肌肉生长速度和产蛋量的降低有关,并为新型重组病毒的产生提供了可能。然而,由于ALVEs不完整的鉴定和与理想性状(如ALVE21和缓慢的羽毛)的关联,ALVEs可以留在商业种群中。全基因组测序(WGS)数据的可用性促进了这些逆转录病毒残留物的高通量鉴定和表征。结果:我们开发了一种新的生物信息学ERV鉴定管道obsERVer,可以在WGS数据中鉴定ALVEs,而无需进一步测序。通过这个管道,从hyline International的8个精英层系中鉴定了20个ALVEs,其中包括4个新的整合和一个快速羽毛表型逆转基因的特征,其中仍然含有ALVE21。这些生物信息学检测到的位点随后使用新的高通量KASP测定法进行验证,结果表明obsERVer高度精确,并且显示0%的错误发现率。进一步分析了57个不同的鸡WGS数据集的ALVE含量,确定了总共322个整合位点,其中80%以上是新的。与外源ALV一样,ALVEs表现出对接近蛋白质编码基因的位点偏好,但也表现出对基因内有害整合的选择迹象。结论:obsERVer是一个高度精确且广泛适用于识别WGS数据中逆转录病毒整合的管道。商业层的ALVE鉴定有助于开发高通量诊断分析,这将有助于ALVE管理,目的是最终从高性能生产线中根除ALVE。利用obsERVer对非商业鸡数据集的分析揭示了广泛的ALVE多样性,并有助于研究这些erv在野生和家养种群中的生物学效应。
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引用次数: 9
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Mobile DNA
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