Mobile genetic elements最新文献_第10页

Novel strategies for gene trapping and insertional mutagenesis mediated by Sleeping Beauty transposon. 睡美人转座子介导的基因诱捕和插入突变新策略。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-10-02 DOI: 10.4161/mge.26499

Guili Song, Zongbin Cui

{"title":"Novel strategies for gene trapping and insertional mutagenesis mediated by Sleeping Beauty transposon.","authors":"Guili Song, Zongbin Cui","doi":"10.4161/mge.26499","DOIUrl":"https://doi.org/10.4161/mge.26499","url":null,"abstract":"Gene and poly(A) trappings are high-throughput approaches to capture and interrupt the expression of endogenous genes within a target genome. Although a number of trapping vectors have been developed for investigation of gene functions in cells and vertebrate models, there is still room for the improvement of their efficiency and sensitivity. Recently, two novel trapping vectors mediated by Sleeping Beauty (SB) transposon have been generated by the combination of three functional cassettes that are required for finding endogenous genes, disrupting the expression of trapped genes, and inducing the excision of integrated traps from their original insertion sites and then inserting into another gene. In addition, several other strategies are utilized to improve the activities of two trapping vectors. First, activities of all components were examined in vitro before the generation of two vectors. Second, the inducible promoter from the tilapia Hsp70 gene was used to drive the expression of SB gene, which can mediate the excision of integrated transposons upon induction at 37 °C. Third, the Cre/LoxP system was introduced to delete the SB expression cassette for stabilization of gene interruption and bio-safety. Fourth, three stop codons in different reading frames were introduced downstream of a strong splice acceptor (SA) in the gene trapping vector to effectively terminate the translation of trapped endogenous genes. Fifth, the strong splicing donor (SD) and AU-rich RNA-destabilizing element exhibited no obvious insertion bias and markedly reduced SD read-through events, and the combination of an enhanced SA, a poly(A) signal and a transcript terminator in the poly(A) trapping vector efficiently disrupted the transcription of trapped genes. Thus, these two trapping vectors are alternative and effective tools for large-scale identification and disruption of endogenous genes in vertebrate cells and animals.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e26499"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.26499","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31881530","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}

引用次数: 5

MuB gives a new twist to target DNA selection. MuB给目标DNA选择带来了新的变化。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-12-12 DOI: 10.4161/mge.27515

Marija Dramićanin, Santiago Ramón-Maiques

{"title":"MuB gives a new twist to target DNA selection.","authors":"Marija Dramićanin, Santiago Ramón-Maiques","doi":"10.4161/mge.27515","DOIUrl":"https://doi.org/10.4161/mge.27515","url":null,"abstract":"Transposition target immunity is a phenomenon observed in some DNA transposons that are able to distinguish the host chromosome from their own DNA sequence, thus avoiding self-destructive insertions. The first molecular insight into target selection and immunity mechanisms came from the study of phage Mu transposition, which uses the protein MuB as a barrier to self-insertion. MuB is an ATP-dependent non-specific DNA binding protein that regulates the activity of the MuA transposase and captures target DNA for transposition. However, a detailed mechanistic understanding of MuB functioning was hindered by the poor solubility of the MuB-ATP complexes. Here we comment on the recent discovery that MuB is an AAA+ ATPase that upon ATP binding assembles into helical filaments that coat the DNA. Remarkably, the helical parameters of the MuB filament do not match those of the bound DNA. This intriguing mismatch symmetry led us to propose a model on how MuB targets DNA for transposition, favoring DNA bending and recognition by the transposase at the filament edge. We also speculate on a different protective role of MuB during immunity, where filament stickiness could favor the condensation of the DNA into a compact state that occludes it from the transposase.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e27515"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.27515","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32076350","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}

引用次数: 3

Domesticated transposable element gene products in human cancer. 人类癌症中驯化的转座因子基因产物。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-10-14 DOI: 10.4161/mge.26693

Jesse D Riordan, Adam J Dupuy

引用次数: 14

Toxin-antitoxin systems: Biology, identification, and application. 毒素-抗毒素系统：生物学、鉴定和应用。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-08-20 DOI: 10.4161/mge.26219

Simon J Unterholzner, Brigitte Poppenberger, Wilfried Rozhon

{"title":"Toxin-antitoxin systems: Biology, identification, and application.","authors":"Simon J Unterholzner, Brigitte Poppenberger, Wilfried Rozhon","doi":"10.4161/mge.26219","DOIUrl":"10.4161/mge.26219","url":null,"abstract":"Toxin-antitoxin (TA) systems are small genetic elements composed of a toxin gene and its cognate antitoxin. The toxins of all known TA systems are proteins while the antitoxins are either proteins or non-coding RNAs. Based on the molecular nature of the antitoxin and its mode of interaction with the toxin the TA modules are currently grouped into five classes. In general, the toxin is more stable than the antitoxin but the latter is expressed to a higher level. If supply of the antitoxin stops, for instance under special growth conditions or by plasmid loss in case of plasmid encoded TA systems, the antitoxin is rapidly degraded and can no longer counteract the toxin. Consequently, the toxin becomes activated and can act on its cellular targets. Typically, TA toxins act on crucial cellular processes including translation, replication, cytoskeleton formation, membrane integrity, and cell wall biosynthesis. TA systems and their components are also versatile tools for a multitude of purposes in basic research and biotechnology. Currently, TA systems are frequently used for selection in cloning and for single protein expression in living bacterial cells. Since several TA toxins exhibit activity in yeast and mammalian cells they may be useful for applications in eukaryotic systems. TA modules are also considered as promising targets for the development of antibacterial drugs and their potential to combat viral infection may aid in controlling infectious diseases.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e26219"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f3/67/mge-3-e26219.PMC3827094.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31881529","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}

引用次数: 0

Genome variation in the hyperthermophilic archaeon Aeropyrum. 嗜热古菌Aeropyrum的基因组变异。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-10-25 DOI: 10.4161/mge.26833

Takashi Daifuku, Takashi Yoshida, Yoshihiko Sako

{"title":"Genome variation in the hyperthermophilic archaeon Aeropyrum.","authors":"Takashi Daifuku, Takashi Yoshida, Yoshihiko Sako","doi":"10.4161/mge.26833","DOIUrl":"https://doi.org/10.4161/mge.26833","url":null,"abstract":"Aeropyrum spp are aerobic, heterotrophic, and hyperthermophilic marine archaea. There are two closely related Aeropyrum species, Aeropyrum camini and Aeropyrum pernix, which are isolated from geographically distinct locations. Recently, we compared their genome sequences to determine their genomic variation. They possess highly conserved small genomes, reflecting their close relationship. The entire genome similarity may result from their survival strategies in adapting to extreme environmental conditions. Meanwhile, synteny disruptions were observed in some regions including clustered regularly interspaced short palindromic repeats elements. Further, the largest portion of their non-orthologous genes were genes in the two proviral regions of A. pernix (Aeropyrum pernix spindle-shaped virus 1 and Aeropyrum pernix ovoid virus 1) or ORFans considered to be derived from viruses. Our data shows that genomic diversification of Aeropyrum spp may be substantially induced by viruses. This suggests that Aeropyrum spp may have a large pan-genome that can be extended by viruses, while each of the species shares a highly conserved small genome specializing for extreme environments.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e26833"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.26833","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31881534","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}

引用次数: 0

Enzyme evolution beyond gene duplication: A model for incorporating horizontal gene transfer. 超越基因复制的酶进化:一个整合水平基因转移的模型。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-10-02 DOI: 10.4161/mge.26439

Lianet Noda-García, Francisco Barona-Gómez

{"title":"Enzyme evolution beyond gene duplication: A model for incorporating horizontal gene transfer.","authors":"Lianet Noda-García, Francisco Barona-Gómez","doi":"10.4161/mge.26439","DOIUrl":"https://doi.org/10.4161/mge.26439","url":null,"abstract":"Understanding the evolution of enzyme function after gene duplication has been a major goal of molecular biologists, biochemists and evolutionary biologists alike, for almost half a century. In contrast, the impact that horizontal gene transfer (HGT) has had on the evolution of enzyme specialization and the assembly of metabolic networks has just started to being investigated. Traditionally, evolutionary studies of enzymes have been limited to either the function of enzymes in vitro, or to sequence variability at the population level, where in almost all cases the starting conceptual framework embraces gene duplication as the mechanism responsible for the appearance of genetic redundancy. Very recently, we merged comparative phylogenomics, detection of selection signals, enzyme kinetics, X-ray crystallography and computational molecular dynamics, to characterize the sub-functionalization process of an amino acid biosynthetic enzyme prompted by an episode of HGT in bacteria. Some of the evolutionary implications of these functional studies, including a proposed model of enzyme specialization independent of gene duplication, are developed in this commentary.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e26439"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/mge.26439","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31880965","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}

引用次数: 13

Horizontal transfer of potential mobile units in phytoplasmas. 植物原体中潜在可移动单位的水平转移。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-08-20 DOI: 10.4161/mge.26145

Chuan Ku, Wen-Sui Lo, Chih-Horng Kuo

引用次数: 23

Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria. CRISPR-Cas 系统的染色体靶向可促进细菌基因组的可塑性。

Mobile genetic elements Pub Date : 2013-09-01 Epub Date: 2013-10-25 DOI: 10.4161/mge.26831

Ron L Dy, Andrew R Pitman, Peter C Fineran

{"title":"Chromosomal targeting by CRISPR-Cas systems can contribute to genome plasticity in bacteria.","authors":"Ron L Dy, Andrew R Pitman, Peter C Fineran","doi":"10.4161/mge.26831","DOIUrl":"10.4161/mge.26831","url":null,"abstract":"The clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins form adaptive immune systems in bacteria to combat phage and other foreign genetic elements. Typically, short spacer sequences are acquired from the invader DNA and incorporated into CRISPR arrays in the bacterial genome. Small RNAs are generated that contain these spacer sequences and enable sequence-specific destruction of the foreign nucleic acids. Occasionally, spacers are acquired from the chromosome, which instead leads to targeting of the host genome. Chromosomal targeting is highly toxic to the bacterium, providing a strong selective pressure for a variety of evolutionary routes that enable host cell survival. Mutations that inactivate the CRISPR-Cas functionality, such as within the cas genes, CRISPR repeat, protospacer adjacent motifs (PAM), and target sequence, mediate escape from toxicity. This self-targeting might provide some explanation for the incomplete distribution of CRISPR-Cas systems in less than half of sequenced bacterial genomes. More importantly, self-genome targeting can cause large-scale genomic alterations, including remodeling or deletion of pathogenicity islands and other non-mobile chromosomal regions. While control of horizontal gene transfer is perceived as their main function, our recent work illuminates an alternative role of CRISPR-Cas systems in causing host genomic changes and influencing bacterial evolution.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 5","pages":"e26831"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827097/pdf/mge-3-e26831.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31881532","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}

引用次数: 0

Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations? 噬菌体能否将环境细菌中的抗生素耐药性基因转移到与人体相关的细菌群中？

Mobile genetic elements Pub Date : 2013-07-01 Epub Date: 2013-08-02 DOI: 10.4161/mge.25847

Maite Muniesa, Marta Colomer-Lluch, Juan Jofre

{"title":"Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations?","authors":"Maite Muniesa, Marta Colomer-Lluch, Juan Jofre","doi":"10.4161/mge.25847","DOIUrl":"10.4161/mge.25847","url":null,"abstract":"Environments without any contact with anthropogenic antibiotics show a great abundance of antibiotic resistance genes that use to be chromosomal and are part of the core genes of the species that harbor them. Some of these genes are shared with human pathogens where they appear in mobile genetic elements. Diversity of antibiotic resistance genes in non-contaminated environments is much greater than in human and animal pathogens, and in environments contaminated with antibiotic from anthropogenic activities. This suggests the existence of some bottleneck effect for the mobilization of antibiotic resistance genes among different biomes. Bacteriophages have characteristics that make them suitable vectors between different biomes, and as well for transferring genes from biome to biome. Recent metagenomic studies and detection of bacterial genes by genomic techniques in the bacteriophage fraction of different microbiota provide indirect evidences that the mobilization of genes mediated by phages, including antibiotic resistance genes, is far more relevant than previously thought. Our hypothesis is that bacteriophages might be of critical importance for evading one of the bottlenecks, the lack of ecological connectivity that modulates the pass of antibiotic resistance genes from natural environments such as waters and soils, to animal and human microbiomes. This commentary concentrates on the potential importance of bacteriophages in transferring resistance genes from the environment to human and animal body microbiomes, but there is no doubt that transduction occurs also in body microbiomes.","PeriodicalId":89441,"journal":{"name":"Mobile genetic elements","volume":"3 4","pages":"e25847"},"PeriodicalIF":0.0,"publicationDate":"2013-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a1/b5/mge-3-e25847.PMC3812792.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31837429","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}

引用次数: 0

Non-LTR retrotransposons and microsatellites: Partners in genomic variation. 非ltr反转录转座子和微卫星:基因组变异的伙伴。

Mobile genetic elements Pub Date : 2013-07-01 Epub Date: 2013-07-11 DOI: 10.4161/mge.25674

Fiorella C Grandi, Wenfeng An

引用次数: 15