Mobile genetic elements最新文献

{"title":"The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?","authors":"Peter Arensburger, B. Piégu, Y. Bigot","doi":"10.1080/2159256X.2016.1256852","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1256852","url":null,"abstract":"ABSTRACT Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1256852","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60154405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conjugative transmission of antibiotic-resistance from stream water Escherichia coli as related to number of sulfamethoxazole but not class 1 and 2 integrase genes","authors":"S. Suhartono, M. Savin","doi":"10.1080/2159256X.2016.1256851","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1256851","url":null,"abstract":"ABSTRACT A conjugation assay was used to determine the effects of phenotypic resistance to one to up to 5 antibiotics, sampling site of origin, presence or absence of class 1 and/or class 2 integrase (intI) genes (intI1 and intI2), and the number of sulfamethoxazole resistance (sul) and trimethoprim resistance (dfr) genes on the transfer frequencies of plasmids from environmental, antibiotic-resistant Escherichia coli. Of 51 sulfamethoxazole and trimethoprim-resistant E. coli isolates conferring at least one mob gene (mobP51, mobF11, mobF12, mobQ11, mobQ12, or mobQu), 38 produced transconjugants with an overall mean frequency of 1.60 × 10−3 transconjugants/ donors (T/D) or 5.89 × 10−3 transconjugants/recipients (T/R). The presence or absence of intI1 and intI2 and the presence or absence of different targeted dfr genes (dfrA1, dfrA8, dfrA12, dfrA14, dfrA17, and/or dfrB3) were not statistically related to plasmid transfer frequencies as determined by ANOVA (P ≥ 0.05). However, E. coli isolates recovered 2 km downstream of wastewater treatment plant effluent input, and those possessing resistance to 3 antibiotics had significantly greater plasmid transfer frequency than their counterparts when calculated as T/D (ANOVA followed by Fisher's least significant difference means comparison, P < 0.05). Greater plasmid transfer frequency calculated as T/D was also measured for E. coli possessing 3 compared to a single sul gene. The in-vitro frequency suggests that horizontal gene transfer of conjugative mediated-antibiotic (sul) resistance genes may be significant among resistant, stream bacteria.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1256851","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60154319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome wide occurrence and insertion preferences of INGI/RIME and SLACS CRE transposable elements in Trypanosoma brucei","authors":"M. F. Khan, Kush Shrivastava, Rebeka Sinha, Virendra Kumar, A. K. Jaitly","doi":"10.1080/2159256X.2016.1240747","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1240747","url":null,"abstract":"ABSTRACT Retrotransposons play significant role in genome remodelling of T. brucei and about 5% of its genome consists of retrotransposons including INGI/RIME elements. INGI is one of the dispersed repetitive elements in T. brucei genome which is found distributed throughout all the chromosomes. SLACS (Spliced Leader Associated Conserved Sequence) however, is more conserved in its nature and lacks the typical poly-distributional pattern of LINE like transposons. We have found total 589 copies of these TEs with only 17.06 % (104 copies out of 589) copies with both ends intact thus showing a majority of truncated copies. Complete SLACS CRE were found only on chromosome 9, whereas, complete INGI/RIME were more ubiquitously distributed. The 50 – 70 bp upstream flanking sequence of these elements shows suitable nucleotide biophysical properties to favor transposition.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":"821"},"PeriodicalIF":0.0,"publicationDate":"2016-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1240747","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60154203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposable elements and circular DNAs","authors":"T. Mourier","doi":"10.1080/2159256X.2016.1240748","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1240748","url":null,"abstract":"ABSTRACT Circular DNAs are extra-chromosomal fragments that become circularized by genomic recombination events. We have recently shown that yeast LTR elements generate circular DNAs through recombination events between their flanking long terminal repeats (LTRs). Similarly, circular DNAs can be generated by recombination between LTRs residing at different genomic loci, in which case the circular DNA will contain the intervening sequence. In yeast, this can result in gene copy number variations when circles contain genes and origins of replication. Here, I speculate on the potential and implications of circular DNAs generated through recombination between human transposable elements.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"8 1","pages":"453 - 62"},"PeriodicalIF":0.0,"publicationDate":"2016-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1240748","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LTRclassifier: A website for fast structural LTR retrotransposons classification in plants","authors":"Cécile Monat, Ndomassi Tando, Christine Tranchant-Dubreuil, F. Sabot","doi":"10.1080/2159256X.2016.1241050","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1241050","url":null,"abstract":"ABSTRACT Automatic classification of LTR retrotransposons is a big challenge in the area of massive genomics. Many tools were developed to detect them but automatic classification is somehow challenging. Here we propose a simple approach, LTRclassifier, based on HMM recognition followed by BLAST analyses (i) to classify plant LTR retrotransposons in their respective superfamily, and (ii) to provide automatically a basic functional annotation of these elements. The method was tested on various TE databases, and shown to be robust and fast. This tool is available as a web service implemented at IRD bioinformatics facility, http://LTRclassifier.ird.fr/.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1241050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60154148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposon for protein engineering","authors":"Vandan Shah, J. Kim","doi":"10.1080/2159256X.2016.1239601","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1239601","url":null,"abstract":"ABSTRACT Protein insertional fusion and circular permutation are 2 promising protein engineering techniques for creating integrated functionalities and sequence diversity of a protein, respectively. Finding insertion locations for protein insertional fusion and new termini for circular permutation through a rational approach is not always straightforward, especially, for proteins without detailed structural knowledge. On the contrary, a combinatorial approach facilitates a comprehensive search to evaluate all potential insertion sites and new termini locations. Conventional methods used to create random insertional fusion libraries generate sub-optimal inter-domain linker length and composition between fused proteins. There are also methods available for construction of random circular permutation libraries. However, these methods too, impose many drawbacks, such as significant sequence modification at the new termini of circular permutants and additionally, require re-design of transposons for tailored expression of circular permutants. Furthermore, these conventional methods employ relatively inefficient blunt-end ligation during library construction. In this commentary, we present a concise overview and key findings of engineered Mu transposons, which have recently been developed in our group as a facile and efficient tool to alleviate limitations realized from conventional methods and to construct high quality libraries for random insertional fusion and random circular permutation.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":"02"},"PeriodicalIF":0.0,"publicationDate":"2016-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1239601","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60154029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heavy metal and junk DNA","authors":"A. M. Roy-Engel","doi":"10.1080/2159256X.2016.1234428","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1234428","url":null,"abstract":"","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1234428","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"60153889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulation of long interspersed nuclear element-1 in the mouse hippocampus during maturation.","authors":"Mikako Ueno,&nbsp;Tadashi Okamura,&nbsp;Masayoshi Mishina,&nbsp;Yukihito Ishizaka","doi":"10.1080/2159256X.2016.1211980","DOIUrl":"https://doi.org/10.1080/2159256X.2016.1211980","url":null,"abstract":"<p><strong>Background: </strong>Retrotransposition of long interspersed nuclear element-1 (L1-RTP) is proposed to contribute to central nervous system (CNS) plasticity by inducing mosaicism of neuronal cells. Clinical studies have identified increased L1 copy numbers in the brains of patients with psychiatric disorders. These observations implicate that L1-RTP is important for neurogenesis and that its deregulation represents a risk factor for mental disorders. However, no supportive evidence is available for understanding the importance of L1-RTP in CNS function.</p><p><strong>Findings: </strong>To explore the physiological role of L1-RTP in CNS, we examined the L1 copy number during maturation. Interestingly, the L1 copy number increased after birth in the mouse hippocampus, but not the frontal lobe, with maximal copy numbers found in 8-week-old mice. This age-dependent L1 increase was abolished by administration of a reverse-transcriptase inhibitor, stavudine (d4T), which showed no toxic effects. Notably, the age-dependent L1 increase was attenuated by post-weaning social isolation (SI) stress, a well-known intervention for inducing psychiatric disorders in mice, or deletion of the NR2A gene that encodes a subunit of the glutamate receptor. Moreover, the negative effects of SI stress on L1-RTP were partially restored by environmental enrichment with voluntary running, but not by fluoxetine, a commonly used anti-psychiatric drug. Finally, behavioral experiments revealed that learning memory was defective in d4T-treated mice, which was similarly observed in mice raised under SI stress.</p><p><strong>Conclusion: </strong>We detected the modulation of L1-RTP in the hippocampus during maturation of the CNS. In a recent study, we demonstrated that stimulants such as methamphetamine and cocaine were active in the induction of L1-RTP in neuronal cells, and previous studies have shown that NR2A-deficient mice are susceptible to mental abnormality. Herein, our data support the notion that the age-dependent modulation of L1-RTP is involved in genome differentiation in the hippocampus, and that modulation defects are linked to the development of psychiatric disorders.</p>","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 4","pages":"e1211980"},"PeriodicalIF":0.0,"publicationDate":"2016-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/2159256X.2016.1211980","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34408026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An updated view of plasmid conjugation and mobilization in Staphylococcus.","authors":"Joshua P Ramsay, Stephen M Kwong, Riley J T Murphy, Karina Yui Eto, Karina J Price, Quang T Nguyen, Frances G O'Brien, Warren B Grubb, Geoffrey W Coombs, Neville Firth","doi":"10.1080/2159256X.2016.1208317","DOIUrl":"10.1080/2159256X.2016.1208317","url":null,"abstract":"<p><p>The horizontal gene transfer facilitated by mobile genetic elements impacts almost all areas of bacterial evolution, including the accretion and dissemination of antimicrobial-resistance genes in the human and animal pathogen Staphylococcus aureus. Genome surveys of staphylococcal plasmids have revealed an unexpected paucity of conjugation and mobilization loci, perhaps suggesting that conjugation plays only a minor role in the evolution of this genus. In this letter we present the DNA sequences of historically documented staphylococcal conjugative plasmids and highlight that at least 3 distinct and widely distributed families of conjugative plasmids currently contribute to the dissemination of antimicrobial resistance in Staphylococcus. We also review the recently documented \"relaxase-in trans\" mechanism of conjugative mobilization facilitated by conjugative plasmids pWBG749 and pSK41, and discuss how this may facilitate the horizontal transmission of around 90% of plasmids that were previously considered non-mobilizable. Finally, we enumerate unique sequenced S. aureus plasmids with a potential mechanism of mobilization and predict that at least 80% of all non-conjugative S. aureus plasmids are mobilizable by at least one mechanism. We suggest that a greater research focus on the molecular biology of conjugation is essential if we are to recognize gene-transfer mechanisms from our increasingly in silico analyses. </p>","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 4","pages":"e1208317"},"PeriodicalIF":0.0,"publicationDate":"2016-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7b/3c/kmge-06-04-1208317.PMC4993578.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34408025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The importance of L1 ORF2p cryptic sequence to ORF2p fragment-mediated cytotoxicity.","authors":"Claiborne M Christian, Kristine J Kines, Victoria P Belancio","doi":"10.1080/2159256X.2016.1198300","DOIUrl":"10.1080/2159256X.2016.1198300","url":null,"abstract":"<p><p>The Long Interspersed Element 1 (LINE1 or L1) ORF2 protein (ORF2p) can cause DNA damage through the activity of its endonuclease domain (EN). The DNA double-strand breaks (DSB) introduced by the ORF2p EN have the potential to be mutagenic. Previously, our lab has shown that ORF2p fragments containing the EN domain could be expressed in mammalian cells and have variable cytotoxicity. Inclusion of the ORF2p sequence C-terminal to the EN domain in these fragments both reduced the cytotoxicity of these fragments and increased their presence in the nucleus as detected by Western blot analysis. Here, we identify the amino acids (aa 270-274) in the newly-identified ORF2p Cryptic region (Cry) that may be important to the subcellular localization and cytotoxic potential of these EN-containing ORF2p fragments. </p>","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"6 4","pages":"e1198300"},"PeriodicalIF":0.0,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8e/bc/kmge-06-04-1198300.PMC4993571.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34711987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}