Mobile DNA最新文献_第10页

A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition. Ty1整合酶伙伴的蛋白质组学筛选鉴定蛋白激酶CK2是Ty1反转录转位的调节因子。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-11-18 DOI: 10.1186/s13100-022-00284-0

Anastasia Barkova, Indranil Adhya, Christine Conesa, Amna Asif-Laidin, Amandine Bonnet, Elise Rabut, Carine Chagneau, Pascale Lesage, Joël Acker

{"title":"A proteomic screen of Ty1 integrase partners identifies the protein kinase CK2 as a regulator of Ty1 retrotransposition.","authors":"Anastasia Barkova, Indranil Adhya, Christine Conesa, Amna Asif-Laidin, Amandine Bonnet, Elise Rabut, Carine Chagneau, Pascale Lesage, Joël Acker","doi":"10.1186/s13100-022-00284-0","DOIUrl":"https://doi.org/10.1186/s13100-022-00284-0","url":null,"abstract":"Background: Transposable elements are ubiquitous and play a fundamental role in shaping genomes during evolution. Since excessive transposition can be mutagenic, mechanisms exist in the cells to keep these mobile elements under control. Although many cellular factors regulating the mobility of the retrovirus-like transposon Ty1 in Saccharomyces cerevisiae have been identified in genetic screens, only very few of them interact physically with Ty1 integrase (IN).Results: Here, we perform a proteomic screen to establish Ty1 IN interactome. Among the 265 potential interacting partners, we focus our study on the conserved CK2 kinase. We confirm the interaction between IN and CK2, demonstrate that IN is a substrate of CK2 in vitro and identify the modified residues. We find that Ty1 IN is phosphorylated in vivo and that these modifications are dependent in part on CK2. No significant change in Ty1 retromobility could be observed when we introduce phospho-ablative mutations that prevent IN phosphorylation by CK2 in vitro. However, the absence of CK2 holoenzyme results in a strong stimulation of Ty1 retrotransposition, characterized by an increase in Ty1 mRNA and protein levels and a high accumulation of cDNA.Conclusion: Our study shows that Ty1 IN is phosphorylated, as observed for retroviral INs and highlights an important role of CK2 in the regulation of Ty1 retrotransposition. In addition, the proteomic approach enabled the identification of many new Ty1 IN interacting partners, whose potential role in the control of Ty1 mobility will be interesting to study.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"26"},"PeriodicalIF":4.9,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9673352/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40501290","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: 0

A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease. 一种独特的真核生物复合样DNA转座子谱系，编码DDD/E转座酶和His-Me指归巢酶。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-10-22 DOI: 10.1186/s13100-022-00281-3

Kenji K Kojima, Weidong Bao

{"title":"A unique eukaryotic lineage of composite-like DNA transposons encoding a DDD/E transposase and a His-Me finger homing endonuclease.","authors":"Kenji K Kojima, Weidong Bao","doi":"10.1186/s13100-022-00281-3","DOIUrl":"https://doi.org/10.1186/s13100-022-00281-3","url":null,"abstract":"Background: DNA transposons are ubiquitous components of eukaryotic genomes. A major group of them encode a DDD/E transposase and contain terminal inverted repeats (TIRs) of varying lengths. The Kolobok superfamily of DNA transposons has been found in a wide spectrum of organisms.Results: Here we report a new Kolobok lineage, designated KolobokP. They were identified in 7 animal phyla (Mollusca, Phoronida, Annelida, Nemertea, Bryozoa, Chordata, and Echinodermata), and are especially rich in bivalves. Unlike other Kolobok families, KolobokP adopts a composite-like architecture: an internal region (INT) flanked by two long terminal direct repeats (LTDRs), which exhibit their own short terminal inverted repeats ranging up to 18 bps. The excision of LTDRs was strongly suggested. The LTDR lengths seem to be constrained to be either around 450-bp or around 660-bp. The internal region encodes a DDD/E transposase and a small His-Me finger nuclease, which likely originated from the homing endonuclease encoded by a group I intron from a eukaryotic species. The architecture of KolobokP resembles composite DNA transposons, usually observed in bacterial genomes, and long terminal repeat (LTR) retrotransposons. In addition to this monomeric LTDR-INT-LTDR structure, plenty of solo LTDRs and multimers represented as (LTDR-INT)n-LTDR are also observed. Our structural and phylogenetic analysis supported the birth of KolobokP in the late stage of the Kolobok evolution. We propose KolobokP families propagate themselves in two ways: the canonical transposition catalyzed by their transposase and the sequence-specific cleavage by their endonuclease followed by the multimerization through the unequal crossover.Conclusions: The presence of homing endonuclease and long terminal direct repeats of KolobokP families suggest their unique dual replication mechanisms: transposition and induced unequal crossover.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"24"},"PeriodicalIF":4.9,"publicationDate":"2022-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9587614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40566318","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: 0

Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns. 核rDNA位置L2066上的移动I组内含子携带有义和反义归巢的内切酶基因，受到剪接体内含子的干扰。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-10-08 DOI: 10.1186/s13100-022-00280-4

Kjersti Lian, Betty M N Furulund, Anders A Tveita, Peik Haugen, Steinar D Johansen

{"title":"Mobile group I introns at nuclear rDNA position L2066 harbor sense and antisense homing endonuclease genes intervened by spliceosomal introns.","authors":"Kjersti Lian, Betty M N Furulund, Anders A Tveita, Peik Haugen, Steinar D Johansen","doi":"10.1186/s13100-022-00280-4","DOIUrl":"https://doi.org/10.1186/s13100-022-00280-4","url":null,"abstract":"Background: Mobile group I introns encode homing endonucleases that confer intron mobility initiated by a double-strand break in the intron-lacking allele at the site of insertion. Nuclear ribosomal DNA of some fungi and protists contain mobile group I introns harboring His-Cys homing endonuclease genes (HEGs). An intriguing question is how protein-coding genes embedded in nuclear ribosomal DNA become expressed. To address this gap of knowledge we analyzed nuclear L2066 group I introns from myxomycetes and ascomycetes.Results: A total of 34 introns were investigated, including two identified mobile-type introns in myxomycetes with HEGs oriented in sense or antisense directions. Intriguingly, both HEGs are interrupted by spliceosomal introns. The intron in Didymium squamulosum, which harbors an antisense oriented HEG, was investigated in more detail. The group I intron RNA self-splices in vitro, thus generating ligated exons and full-length intron circles. The intron HEG is expressed in vivo in Didymium cells, which involves removal of a 47-nt spliceosomal intron (I-47) and 3' polyadenylation of the mRNA. The D. squamulosum HEG (lacking the I-47 intron) was over-expressed in E. coli, and the corresponding protein was purified and shown to confer endonuclease activity. The homing endonuclease was shown to cleave an intron-lacking DNA and to produce a pentanucleotide 3' overhang at the intron insertion site.Conclusions: The L2066 family of nuclear group I introns all belong to the group IE subclass. The D. squamulosum L2066 intron contains major hallmarks of a true mobile group I intron by encoding a His-Cys homing endonuclease that generates a double-strand break at the DNA insertion site. We propose a potential model to explain how an antisense HEG becomes expressed from a nuclear ribosomal DNA locus.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"23"},"PeriodicalIF":4.9,"publicationDate":"2022-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9548176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33495189","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: 0

Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells. 转座因子在I型IFN细胞应答中的转录动力学。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-09-06 DOI: 10.1186/s13100-022-00277-z

Giulia Irene Maria Pasquesi, Conor J Kelly, Andrea D Ordonez, Edward B Chuong

{"title":"Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells.","authors":"Giulia Irene Maria Pasquesi, Conor J Kelly, Andrea D Ordonez, Edward B Chuong","doi":"10.1186/s13100-022-00277-z","DOIUrl":"https://doi.org/10.1186/s13100-022-00277-z","url":null,"abstract":"Background: Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN.Results: We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN.Conclusion: Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"22"},"PeriodicalIF":4.9,"publicationDate":"2022-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9446614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40354677","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

Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp. 与寄生蜂相关的Helitron转座子的多重水平转移。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-08-19 DOI: 10.1186/s13100-022-00278-y

Pedro Heringer, Gustavo C S Kuhn

{"title":"Multiple horizontal transfers of a Helitron transposon associated with a parasitoid wasp.","authors":"Pedro Heringer, Gustavo C S Kuhn","doi":"10.1186/s13100-022-00278-y","DOIUrl":"https://doi.org/10.1186/s13100-022-00278-y","url":null,"abstract":"In a previous study we described a Helitron transposon that apparently became one of the segments in the symbiotic Cotesia vestalis bracovirus (CvBV) from the parasitoid wasp C. vestalis. We presented evidence that this Helitron, named Hel_c35, invaded the C. vestalis genome through a horizontal transfer (HT) event from a dipteran and was later transferred horizontally from C. vestalis to a lepidopteran species. Based on the phylogeny of Hel_c35, we suggested that both HTs occurred in East Asia. We have also anticipated that, as more sequenced genomes from new species become available, more HTs involving Hel_c35 would be detected. Although the inclusion of Hel_c35 as a CvBV segment turned out to be a methodological artifact, the fact that Hel_c35 copies are present in the genomes of C. vestalis and other arthropods still remains. Here, we investigated the evolution of Hel_c35 in arthropods using an updated data set to reassess our previous findings. Most species (95%) included in the present work had their genomes sequenced after our initial study was published, thus representing new descriptions of taxa harboring Hel_c35. Our results expand considerably the number of putative HTs involving Hel_c35, with up to dozens of previously undescribed events, and suggest that the most recent HTs associated with C. vestalis took place in Europe. Considering the phylogenetic distribution of Hel_c35, and the evidence that its DNA sequences are present in the calyx fluid of C. vestalis and tissues from its parasitized host, we argue that many HT events were favored by the behavior of this wasp.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"20"},"PeriodicalIF":4.9,"publicationDate":"2022-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9389653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40623759","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: 4

Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria. 基因组分析揭示了整合和接合元件在植物致病菌中的作用。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-08-12 DOI: 10.1186/s13100-022-00275-1

Jéssica Catarine Silva de Assis, Osiel Silva Gonçalves, Alexia Suellen Fernandes, Marisa Vieira de Queiroz, Denise Mara Soares Bazzolli, Mateus Ferreira Santana

{"title":"Genomic analysis reveals the role of integrative and conjugative elements in plant pathogenic bacteria.","authors":"Jéssica Catarine Silva de Assis, Osiel Silva Gonçalves, Alexia Suellen Fernandes, Marisa Vieira de Queiroz, Denise Mara Soares Bazzolli, Mateus Ferreira Santana","doi":"10.1186/s13100-022-00275-1","DOIUrl":"https://doi.org/10.1186/s13100-022-00275-1","url":null,"abstract":"Background: ICEs are mobile genetic elements found integrated into bacterial chromosomes that can excise and be transferred to a new cell. They play an important role in horizontal gene transmission and carry accessory genes that may provide interesting phenotypes for the bacteria. Here, we seek to research the presence and the role of ICEs in 300 genomes of phytopathogenic bacteria with the greatest scientific and economic impact.Results: Seventy-eight ICEs (45 distinct elements) were identified and characterized in chromosomes of Agrobacterium tumefaciens, Dickeya dadantii, and D. solani, Pectobacterium carotovorum and P. atrosepticum, Pseudomonas syringae, Ralstonia solanacearum Species Complex, and Xanthomonas campestris. Intriguingly, the co-occurrence of four ICEs was observed in some P. syringae strains. Moreover, we identified 31 novel elements, carrying 396 accessory genes with potential influence on virulence and fitness, such as genes coding for functions related to T3SS, cell wall degradation and resistance to heavy metals. We also present the analysis of previously reported data on the expression of cargo genes related to the virulence of P. atrosepticum ICEs, which evidences the role of these genes in the infection process of tobacco plants.Conclusions: Altogether, this paper has highlighted the potential of ICEs to affect the pathogenicity and lifestyle of these phytopathogens and direct the spread of significant putative virulence genes in phytopathogenic bacteria.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"19"},"PeriodicalIF":4.9,"publicationDate":"2022-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9373382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40610167","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

Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin 染色体外线性dna LTRs扩增(ALE-seq)鉴定了两个活性Oryco LTR反转录转座子

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-06-13 DOI: 10.1186/s13100-022-00274-2

Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, Yang, Tae-Jin

{"title":"Amplification of LTRs of extrachromosomal linear DNAs (ALE-seq) identifies two active Oryco LTR retrotransposons in the rice cultivar Dongjin","authors":"Koo, Hyunjin, Kim, Soomin, Park, Hyun-Seung, Lee, Sang-Ji, Paek, Nam-Chon, Cho, Jungnam, Yang, Tae-Jin","doi":"10.1186/s13100-022-00274-2","DOIUrl":"https://doi.org/10.1186/s13100-022-00274-2","url":null,"abstract":"Long terminal repeat retrotransposons (LTR-RTs) make up a considerable portion of plant genomes. New insertions of these active LTR-RTs modify gene structures and functions and play an important role in genome evolution. Therefore, identifying active forms of LTR-RTs could uncover the effects of these elements in plants. Extrachromosomal linear DNA (eclDNA) forms during LTR-RT replication; therefore, amplification LTRs of eclDNAs followed by sequencing (ALE-seq) uncover the current transpositional potential of the LTR-RTs. The ALE-seq protocol was validated by identification of Tos17 in callus of Nipponbare cultivar. Here, we identified two active LTR-RTs belonging to the Oryco family on chromosomes 6 and 9 in rice cultivar Dongjin callus based on the ALE-seq technology. Each Oryco family member has paired LTRs with identical sequences and internal domain regions. Comparison of the two LTR-RTs revealed 97% sequence identity in their internal domains and 65% sequence identity in their LTRs. These two putatively active Oryco LTR-RT family members could be used to expand our knowledge of retrotransposition mechanisms and the effects of LTR-RTs on the rice genome.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"29 1","pages":""},"PeriodicalIF":4.9,"publicationDate":"2022-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138518116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction: Characterization of transposable elements within the Bemisia tabaci species complex 更正：烟粉虱物种复合体中转座元件的特征

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-06-08 DOI: 10.1186/s13100-022-00273-3

Juan Paolo A. Sicat, Paul Visendi, Steven O. Sewe, S. Bouvaine, S. Seal

引用次数: 0

Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants 综合分析克隆和种子繁殖模式物种的长读和短读转录组，揭示了植物自主和非自主转座子转录激活的先决条件

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-05-12 DOI: 10.1186/s13100-022-00271-5

Ting Chen, C. Winefield

引用次数: 0

On Turedo Hierarchies and Intrinsic Universality 论社会层次与内在普遍性

IF 4.9 2区生物学

Mobile DNA Pub Date : 2022-05-09 DOI: 10.48550/arXiv.2205.04103

Samuel Nalin, Guillaume Theyssier

{"title":"On Turedo Hierarchies and Intrinsic Universality","authors":"Samuel Nalin, Guillaume Theyssier","doi":"10.48550/arXiv.2205.04103","DOIUrl":"https://doi.org/10.48550/arXiv.2205.04103","url":null,"abstract":"This paper is about turedos, which are Turing machine whose head can move in the plane (or in a higher-dimensional space) but only in a selfavoiding way, by putting marks (letters) on visited positions and moving only to unmarked, therefore unvisited, positions. The key parameter of turedos is their lookup radius: the distance up to which the head can look around in order to make its decision of where to move to and what mark to write. In this paper we study the hierarchy of turedos according to their lookup radius and the dimension of space using notions of simulation up to spatio-temporal rescaling (a standard approach in cellular automata or self-assembly systems). We establish that there is a rich interplay between the turedo parameters and the notion of simulation considered. We show in particular, for the most liberal simulations, the existence of 3D turedos of radius 1 that are intrinsically universal for all radii, but that this is impossible in dimension 2, where some radius 2 turedo are impossible to simulate at radius 1. Using stricter notions of simulation, intrinsic universality becomes impossible, even in dimension 3, and there is a strict radius hierarchy. Finally, when restricting to radius 1, universality is again possible in dimension 3, but not in dimension 2, where we show however that a radius 3 turedo can simulate all radius 1 turedos.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"26 1 1","pages":"6:1-6:18"},"PeriodicalIF":4.9,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86102084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2