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1.  The role of horizontal gene transfer in kleptoplastidy and the establishment of photosynthesis in the eukaryotes 
Mobile Genetic Elements  2013;3(2):e24773.
Found in different eukaryotic lineages, kleptoplastidy is the ability to sequester chloroplasts from algal preys that are ingested and partially digested. While most of the genetic information required for the activity and maintenance of the kleptoplastids disappeared with the digestion of the algal nuclei, the photosynthetic organelles remain active during extended period of time. Many different hypotheses have been proposed to explain the longevity of the kleptoplastids within their host. The most popular one involves Horizontal Gene Transfer (HGT) from the algal genome to the host nucleus. In order to test this hypothesis, transcriptome-based analyses have been performed on different kleptoplastidic organisms during the past few years. However, the variability of the results obtained does not allow drawing a convincing conclusion regarding the precise role of HGT in kleptoplastidy. Understanding the mechanism that allow persistence of the plastids is crucial, not only for the characterization of kleptoplastidy, but also for important evolutionary questions surrounding endosymbiotic events and the emergence and spread of photosynthesis in the eukaryotes. Here, I discuss alternative theories that could explain the longevity of sequestered plastids in their host, with special focus on the simplest chloroplast stability hypothesis.
PMCID: PMC3681741  PMID: 23914312
photosynthesis; endosymbiosis; photosymbiosis; kleptoplastidy; horizontal gene transfer; foraminifera; diatom; EST; plastid
2.  Composition of the DNA-uptake complex of Vibrio cholerae 
Mobile Genetic Elements  2014;4(1):e28142.
Natural competence for transformation is a developmental program that allows certain bacteria to take up free extracellular DNA from the environment and integrate this DNA into their genome. Thereby, natural transformation acts as mode of horizontal gene transfer and impacts bacterial evolution. The number of genes induced upon competence induction varies significantly between organisms. However, all of the naturally competent bacteria possess competence genes that encode so-called DNA-uptake machineries. Some components of these multi-protein complexes resemble subunits of type IV pili and type II secretion systems. However, knowledge on the mechanistic aspects of such DNA-uptake complexes is still very limited. Here, we discuss some new findings regarding the DNA-uptake machinery of the naturally transformable human pathogen Vibrio cholerae. The potential of this organism to initiate the competence program was discovered less than a decade ago. However, recent studies have provided new insight into both the regulatory pathways of competence induction and into the DNA uptake dynamics.
PMCID: PMC3919817  PMID: 24558639
horizontal gene transfer; V. cholerae; DNA uptake machinery; type IV pilus; natural transformation
3.  Quadruplex-forming DNA sequences spread by retrotransposons may serve as genome regulators 
Mobile Genetic Elements  2014;4(1):e28084.
Transposable elements (TEs) are ubiquitous genome inhabitants in eukaryotes. Increasing evidence shows that TEs are involved in regulatory networks of eukaryotic cells and contribute to genome evolution. Recently, we reported that many plant long-terminal repeat (LTR) retrotransposons contain DNA quadruplex-forming sequences at precise positions inside their LTRs and that quadruplexes are better preserved in evolutionary younger elements. As quadruplexes can modulate molecular processes, quadruplexes found at specific distances upstream and downstream from the endogenous TE promoter can affect transcription of the element. Moreover, quadruplexes found in solo LTRs, as well as in 3′ ends of 5′-truncated copies of LINE-1 elements, can affect expression of neighboring genes. Here, we propose that this way retrotransposons can serve as vehicles for spread of DNA quadruplexes. Quadruplexes can thus fulfill a dual regulatory role—to influence both the retrotransposons carrying them and the neighboring host genes, e.g., by direct effect on transcription or by modifying the local chromatin state. Additionally, four-stranded DNA structures may serve as hotspots for recombination-based genome rearrangements.
PMCID: PMC3933402  PMID: 24616836
LTR retrotransposons; DNA quadruplexes; TE transcription
4.  Does ectopic cell death cause somatic mutations in the neighboring cells by activating transposons? 
Mobile Genetic Elements  2014;4(1):e28040.
Ectopic cell death in Drosophila produces a nonautonomous inhibition of RNA interference (RNAi) in neighboring normal cells. The expression of transposable elements (TE) is increased due to this reduction in the silencing mechanism. New insertions of TE have been documented in mutants for RNAi functions. These observations raise the possibility that persistent environmental insults that produce cell death might increase the frequency of somatic mutations, which might trigger somatic genetic disease.
PMCID: PMC3926873  PMID: 24567848
RNAi; cell death; transposons; signaling; somatic mutation
5.  Insertion sequence distribution bias in Archaea 
Mobile Genetic Elements  2014;4(1):e27829.
Insertion sequences (IS) are common transposable elements in Archaea. Intergenic IS elements are usually less harmful than intragenic ISs, simply because they are less likely to disrupt host gene function. However, because regulatory sequences are intergenic and upstream of genes, we hypothesized that not all intergenic regions are selectively equivalent for IS insertion. We tested this hypothesis by analyzing the distributions of intergenic IS elements within 155 fully sequenced archaeal genomes. Of the 22 genomes with enough IS elements for statistical analysis, five have significantly fewer ISs between divergently oriented neighboring genes than expected by chance, and seven have significantly more ISs between convergently oriented genes. Furthermore, of the 85 genomes with at least one expected IS within each of the three possible neighboring gene orientations (i.e., divergent, convergent, and tandem), 73 genomes have fewer ISs between divergently oriented genes than expected, and 60 have more ISs between convergently oriented genes than expected (both values deviate significantly from binomial probabilities of random distribution). We suspect that these non-random IS distributions are molded by natural selection resulting from differential disruption of neighboring gene regulation, and that this selective pressure has affected transposable element distributions in prokaryotes for billions of years.
PMCID: PMC3912053  PMID: 24558638
DNA transposon; transposable element; IS element; natural selection
6.  Continuing analysis of microRNA origins 
Mobile Genetic Elements  2014;3(6):e27755.
MicroRNAs (miRs) are small noncoding RNAs that typically act as regulators of gene expression by base pairing with the 3′ UTR of messenger RNAs (mRNAs) and either repressing their translation or initiating degradation. As of this writing over 24,500 distinct miRs have been identified, but the functions of the vast majority of these remain undescribed. This paper represents a summary of our in depth analysis of the genomic origins of miR loci, detailing the formation of 1,213 of the 7,321 recently identified miRs and thereby bringing the total number of miR loci with defined molecular origin to 3,605. Interestingly, our analyses also identify evidence for a second, novel mechanism of miR locus generation through describing the formation of 273 miR loci from mutations to other forms of noncoding RNAs. Importantly, several independent investigations of the genomic origins of miR loci have now supported the hypothesis that miR hairpins are formed by the adjacent genomic insertion of two complementary transposable elements (TEs) into opposing strands. While our results agree that subsequent transcription over such TE interfaces leads to the formation of the majority of functional miR loci, we now also find evidence suggesting that a subset of miR loci were actually formed by an alternative mechanism—point mutations in other structurally complex, noncoding RNAs (e.g., tRNAs and snoRNAs).
PMCID: PMC3891635  PMID: 24475369
LINE; microRNA; miR; miRNA; noncoding RNA; repetitive; retrotransposon; SINE; transposable; transposon
7.  Analysis of horizontal genetic transfer in red algae in the post-genomics age 
Mobile Genetic Elements  2014;3(6):e27669.
The recently published genome of the unicellular red alga Porphyridium purpureum revealed a gene-rich, intron-poor species, which is surprising for a free-living mesophile. Of the 8,355 predicted protein-coding regions, up to 773 (9.3%) were implicated in horizontal genetic transfer (HGT) events involving other prokaryote and eukaryote lineages. A much smaller number, up to 174 (2.1%) showed unambiguous evidence of vertical inheritance. Together with other red algal genomes, nearly all published in 2013, these data provide an excellent platform for studying diverse aspects of algal biology and evolution. This novel information will help investigators test existing hypotheses about the impact of endosymbiosis and HGT on algal evolution and enable comparative analysis within a more-refined, hypothesis-driven framework that extends beyond HGT. Here we explore the impacts of this infusion of red algal genome data on addressing questions regarding the complex nature of algal evolution and highlight the need for scalable phylogenomic approaches to handle the forthcoming deluge of sequence information.
PMCID: PMC3891758  PMID: 24475368
red algae; phylogenomics; horizontal genetic transfer; endosymbiosis; algal evolution
8.  Mobile Genetic Elements evolves 
Mobile Genetic Elements  2014;4(1):e27706.
PMCID: PMC3891760  PMID: 24475370
9.  Lost in translation 
Mobile Genetic Elements  2013;3(6):e27525.
“Young” APE-type non-LTR retrotransposons (non-LTRs) typically encode two open reading frames (ORFs 1 and 2). The shorter ORF1 translation product (ORF1p) comprises an RNA binding activity, thought to bind to non-LTR transcript RNA, protect against nuclease degradation and specify nuclear import of the ribonuclear protein complex (RNP). ORF2 encodes a multifunctional protein (ORF2p) comprising apurinic/apyrimidinic endonuclease (APE) and reverse-transcriptase (RT) activities, responsible for genome replication and re-integration into chromosomal DNA. However, some clades of APE-type non-LTRs only encode a single ORF—corresponding to the multifunctional ORF2p outlined above (and for simplicity referred-to as ORF2 below). The absence of an ORF1 correlates with the acquisition of a 2A oligopeptide translational recoding element (some 18–30 amino acids) into the N-terminal region of ORF2p. In the case of non-LTRs encoding two ORFs, the presence of ORF1 would necessarily downregulate the translation of ORF2. We argue that in the absence of an ORF1, 2A could provide the corresponding translational downregulation of ORF2. While multiple molecules of ORF1p are required to decorate the non-LTR transcript RNA in the cytoplasm, conceivably only a single molecule of ORF2p is required for target-primed reverse transcription/integration in the nucleus. Why would the translation of ORF2 need to be controlled by such mechanisms? An “excess” of ORF2p could result in disadvantageous levels of genome instability by, for example, enhancing short, interspersed, element (SINE) retrotransposition and the generation of processed pseudogenes. If so, the acquisition of mechanisms—such as 2A—to control ORF2p biogenesis would be advantageous.
PMCID: PMC3894237  PMID: 24475367
non-LTR retrotransposons; retrotransposition; 2A oligopeptide; translational recoding
10.  MuB gives a new twist to target DNA selection 
Mobile Genetic Elements  2013;3(5):e27515.
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.
PMCID: PMC3894238  PMID: 24478936
phage Mu; AAA+ ATPase; nucleoprotein filament; symmetry mismatch; helical filament; DNA transposition
11.  Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome 
Mobile Genetic Elements  2013;3(6):e27460.
The family Anostomidae is an interesting model for studies of repetitive elements, mainly because of the presence of high numbers of heterochromatic segments related to a peculiar system of female heterogamety, which is restricted to a few species of Leporinus genus. Thus, cytogenetic mapping of the retrotransposable elements Rex1, Rex3, and Rex6 was performed in six Leporinus species, to elucidate the genomic organization of this genus. The sequencing of the Rex1 and Rex3 elements detected different base pair compositions in these elements among species, whereas the Rex6 element was not identified in the genomes of these species. FISH analysis using Rex1 detected different distribution patterns, L. elongatus, L. macrocephalus, and L. obtusidens had clusters in the terminal regions, whereas the signals were dispersed throughout all of the chromosomes with some signals in the terminal position in other species. The Rex3 signals were found mainly in the terminal positions in all the chromosomes of all species. The W chromosomes of L. elongatus, L. macrocephalus, and L. obtusidens contained the Rex1 and Rex3 signal in an interstitial position. These results suggest the emergence of different activity levels for these elements during the evolution of the species analyzed. Despite the conserved karyotype macrostructure species Leporinus often discussed, our results show some variation in hybridization patterns, particularly between the species with specific patterns in their sex chromosomes and species without this differentiated system.
PMCID: PMC3881107  PMID: 24404417
transposable elements; mobile DNA; repetitive sequences; sex chromosome; FISH
12.  Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms 
Mobile Genetic Elements  2013;3(5):e27313.
Diatoms are highly successful marine and freshwater algae that contribute up to 20% of global carbon fixation. These species are leading candidates for biofuel production owing to ease of culturing and high fatty acid content. To assist in strain improvement and downstream applications for potential use as a biofuel, it is important to understand the evolution of lipid biosynthesis in diatoms. The evolutionary history of diatoms is however complicated by likely multiple endosymbioses involving the capture of foreign cells and horizontal gene transfer into the host genome. Using a phylogenomic approach, we assessed the evolutionary history of 12 diatom genes putatively encoding functions related to lipid biosynthesis. We found evidence of gene transfer likely from a green algal source for seven of these genes, with the remaining showing either vertical inheritance or evolutionary histories too complicated to interpret given current genome data. The functions of horizontally transferred genes encompass all aspects of lipid biosynthesis (initiation, biosynthesis, and desaturation of fatty acids) as well as fatty acid elongation, and are not restricted to plastid-targeted proteins. Our findings demonstrate that the transfer, duplication, and subfunctionalization of genes were key steps in the evolution of lipid biosynthesis in diatoms and other photosynthetic eukaryotes. This target pathway for biofuel research is highly chimeric and surprisingly, our results suggest that research done on related genes in green algae may have application to diatom models.
PMCID: PMC3881603  PMID: 24404416
diatoms; fatty acid biosynthesis; horizontal gene transfer; lipid metabolism; phylogenomics; endosymbiosis
13.  Toxin–antitoxin systems 
Mobile Genetic Elements  2013;3(5):e26219.
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.
PMCID: PMC3827094  PMID: 24251069
toxin; antitoxin; RNA interferase; translation; cloning; protein expression
14.  The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome 
Mobile Genetic Elements  2013;3(4):e25845.
Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed.
PMCID: PMC3812789  PMID: 24195014
Bacteroidetes; Ceratium; dinoflagellates; endosymbiotic gene transfer; genome; horizontal gene transfer; minicircle; peridinin plastid; Pyrocystis
15.  Chromosomal location of retrotransposable REX 1 in the genomes in five Prochilodus (Teleostei 
Mobile Genetic Elements  2013;3(4):e25846.
Transposable elements are repetitive DNA sequences comprising a group of segments able to move and carry sequences within the genome. Studies involving comparative genomics have revealed that most vertebrates have different populations of transposable elements with significant differences among species of the same lineage. Few studies have been conducted in fish, the most diverse group of vertebrates, with the objective to locate different types of transposable elements. Therefore, this study proposed to map the retrotransposable element Rex1 applying Fluorescent in situ Hybridization (FISH) in five species of the genus Prochilodus (Prochilodus argenteus, Prochilodus brevis, Prochilodus costatus, Prochilodus lineatus and Prochilodus nigricans). After the application of the Rex1 probe, scattered markings were found throughout the genome of analyzed species, and also the presence of small clusters located in the centromeric and telomeric regions coincident with the heterochromatin distribution pattern. This was the first description of the retrotransposable element Rex1 in Prochilodus genome seeking for a better understanding of the distribution pattern of these retrotransposons in the genome of teleost fish.
PMCID: PMC3812791  PMID: 24195015
heterochromatic; genome; dispersed elements; conserved karyotypic; fish
16.  Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations? 
Mobile Genetic Elements  2013;3(4):e25847.
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.
PMCID: PMC3812792  PMID: 24195016
bacteriophages; transduction; lysogeny; horizontal gene transfer; antibiotic resistance
17.  Non-LTR retrotransposons and microsatellites 
Mobile Genetic Elements  2013;3(4):e25674.
The human genome is laden with both non-LTR (long-terminal repeat) retrotransposons and microsatellite repeats. Both types of sequences are able to, either actively or passively, mutagenize the genomes of human individuals and are therefore poised to dynamically alter the human genomic landscape across generations. Non-LTR retrotransposons, such as L1 and Alu, are a major source of new microsatellites, which are born both concurrently and subsequently to L1 and Alu integration into the genome. Likewise, the mutation dynamics of microsatellite repeats have a direct impact on the fitness of their non-LTR retrotransposon parent owing to microsatellite expansion and contraction. This review explores the interactions and dynamics between non-LTR retrotransposons and microsatellites in the context of genomic variation and evolution.
PMCID: PMC3812793  PMID: 24195012
Alu; genomic instability; genomic variation; LINE-1; microsatellite; mononucleotide repeat; mutation rate; poly(A); retrotransposition; retrotransposon
18.  Identification and characterization of MGEs and their insertion sites in the gorilla genome 
Mobile Genetic Elements  2013;3(4):e25675.
Recently published gorilla genome has offered an opportunity to study human evolution through variety of approaches. Mobile genetic elements (MGEs) insert non randomly in genome through mechanisms such as retrotransposition and may cause gene inactivation, transduction, regulation of gene expression and genome expansion. Here we report that majority of gorilla genome is occupied with MGEs (> 36%) with presence of LTRs and Non-LTRs such as Alus and L1s. Other types of MGEs such as MIRs, retrovirus like elements ERVs and DNA transposons are also found using repeatmasker and ELAN pipeline. The distribution is similar to Humans and Macaca genome. Using DNA Scanner we also scanned preinsertion loci for number of different properties such as DNA denaturation, energy measures, potential for protein interactions and sequence based features. We also predicted preinsertion loci with > 70% accuracy using a machine learning tool called insertion site finder (ISF) based upon support vector machines.
PMCID: PMC3812790  PMID: 24195013
mobile genetic elements; primates; LINEs; SINEs; Alu; L1; truncation points; physiochemical properties
19.  Insertion sequence AS5 (ISAS5) is involved in the genomic plasticity of Aeromonas salmonicida 
Mobile Genetic Elements  2013;3(3):e25640.
The genome of the fish pathogen Aeromonas salmonicida subsp salmonicida harbors a large number of insertion sequences (ISs), many of which are located on plasmids. In the present study, we analyzed the small plasmid profile of A. salmonicida strains to identify evidences of plasmid alterations. Ten out of 78 strains analyzed displayed an unconventional plasmid profile. However the HER1104 strain was unique, having a positive PCR signal for pAsal1 plasmid despite not carrying this plasmid. Instead, HER1104 was bearing a plasmid at higher molecular weight than pAsal1. We characterized this new larger plasmid, which we called pAsal1B since it is a derivative of pAsal1 containing one more complete IS (ISAS5) than the parental plasmid. An additional 96 bp relic of ISAS5 was also present in pAsal1B. These results propose that ISAS5 is another active mobile genetic element in A. salmonicida subsp salmonicida and provided further proof of the genomic plasticity of this bacterium.
PMCID: PMC3742599  PMID: 23956951
furunculosis; Aeromonas salmonicida; plasmid; DNA rearrangement; insertion sequence
20.  The DpnI/DpnII pneumococcal system, defense against foreign attack without compromising genetic exchange 
Mobile Genetic Elements  2013;3(4):e25582.
Natural genetic transformation and restriction-modification (R–M) systems play potentially antagonistic roles in bacteria. R–M systems, degrading foreign DNA to protect the cell from bacteriophage, can interfere with transformation, which relies on foreign DNA to promote genetic diversity. Here we describe how the human pathogen Streptococcus pneumoniae, which is naturally transformable, yet possesses either of two R–M systems, DpnI or DpnII, accommodates these conflicting processes. In addition to the classic restrictase and double-stranded DNA methylase, the DpnII system possesses an unusual single-stranded (ss) DNA methylase, DpnA, which is specifically induced during competence for genetic transformation. We provide further insight into our recent discovery that DpnA, which protects transforming foreign ssDNA from restriction, is crucial for acquisition of pathogenicity islands.
PMCID: PMC3812788  PMID: 24195011
Streptococcus pneumoniae; DpnA ssDNA methylase; capsule switch; competence; genetic transformation; heterologous DNA transfer; pathogenicity island transfer; restriction–modification
21.  First report on class 1 integrons and Trimethoprim-resistance genes from dfrA group in uropathogenic E. coli (UPEC) from the Aleppo area in Syria 
Mobile Genetic Elements  2013;3(3):e25204.
Horizontal gene transfer (HGT) introduces advantageous genetic elements into pathogenic bacteria using tools such as class1 integrons. This study aimed at investigating the distribution of these integrons among uropathogenic E. coli (UPEC) isolated from patients in Aleppo, Syria. It also set to uncover the frequencies of the clinically relevant DfrA1 and DfrA17,7, as well as various associations leading to reduced susceptibility. This study involved 75 Trimethoprim-resistant E. coli isolates from in- and outpatients with urinary tract infections (UTIs) from 3 major hospitals in Aleppo. Bacterial identification, resistance and extended-spectrum-β-lactamase (ESBL) production testing were performed according to Clinical Laboratory Standards Institute guidelines. Detection of integrons and DfrA genes was done using PCR and statistical significance was inferred through χ2 (Fisher’s) test. Class1 integrons were detected in 54.6% of isolates while DfrA1 and DfrA17,7 were found in 16% and 70.6% of tested samples respectively. Furthermore, only DfrA17,7 were strongly associated with class1 integrons, as were reduced susceptibility to the majority of individual antibiotics, multidrug resistance and ESBL production. This study demonstrated the high prevalence of class1 integrons among UPEC strains in Aleppo, Syria, as well as their significant associations with MDR. This data give information for local healthcare provision using antibiotic chemotherapy.
PMCID: PMC3742597  PMID: 23956949
DfrA17,7; DfrA1; antibiotic resistance; urinary tract infections
22.  Pitfalls encountered while investigating genetic elements by PCR 
Mobile Genetic Elements  2013;3(3):e25255.
The unprecedented wealth of databases that have become available in the era of next-generation sequencing has considerably increased our knowledge of bacterial genetic elements (GEs). At the same time, the advent of single-cell based approaches has brought realization that unsuspected heterogeneity may occur in the bacterial population from a single colony. The increasing use of PCR-based techniques to study new GEs requires careful consideration of the possible different PCR targets associated with different subpopulations if incorrect or incomplete interpretations are to be avoided. In this commentary, confining ourselves to our direct experience, we illustrate some examples of PCR pitfalls that may be encountered while investigating GEs.
PMCID: PMC3742598  PMID: 23956950
genetic elements; PCR mapping; PCR pitfalls; single-cell based approaches; Intra-colony heterogeneity
23.  Transpositional transgenesis with piggyBac 
Mobile Genetic Elements  2013;3(3):e25167.
Transposons are mobile genetic elements that are capable of self-directed excision and subsequent reintegration within the host genome. Transposase such as piggyBac, Sleeping Beauty and Tol2 catalyze these reactions and have shown potential as tools for the stable integration of transgenes when used in the binary plasmid mode. Recent modifications to the transposase and/or the terminal repeats of the transposon have increased their integration efficiency and/or specificity. We recently described the development of a piggyBac transposase system, the helper independent, single construct self-inactivating plasmid called GENIE. Here we describe the structure, safety and function of these transpositional vectors and their use in animal transgenesis and cell transfection.
PMCID: PMC3742596  PMID: 23956948
transposon; transposase; transgenesis; transgene; piggyBac; cell transfections
24.  piggyBac 
Mobile Genetic Elements  2013;3(2):e24417.
In addition to their natural role in eukaryotic genome evolution, transposons can be powerful tools for functional genomics in diverse taxa. The piggyBac transposon has been applied as such in eukaryotic parasites, both protozoa and helminths, and in several important vector mosquitoes. piggyBac is advantageous for functional genomics because of its ability to transduce a wide range of taxa, its capacity to integrate large DNA ‘cargoes’ relative to other mobile genetic elements, its propensity to target transcriptional units and its ability to re-mobilize without leaving a pattern of non-excised sequences or ‘footprint’ in the genome. We recently demonstrated that piggyBac can integrate transgenes into the genome of the parasitic nematode Strongyloides ratti, an important model for parasitic nematode biology and a close relative of the significant human pathogen S. stercoralis. Unlike transgenes encoded in conventional plasmid vectors, which we assume are assembled into multi-copy episomal arrays as they are in Caenorhabditis elegans, transgenes integrated via piggyBac are not only stably inherited in S. ratti, they are also continuously expressed. This has allowed derivation of the first stable transgene expressing lines in any parasitic nematode, a significant advance in the development of functional genomic tools for these important pathogens.
PMCID: PMC3681738  PMID: 23914309
transposon; piggyBac; transgenesis; parasitic nematode; Strongyloides; chromosomal integration; gene silencing
25.  What happens when Penelope comes? 
Mobile Genetic Elements  2013;3(2):e24542.
Transposable elements (TEs) are ubiquitous residents in eukaryotic genomes. They can cause dramatic changes in gene expression and lead to gross rearrangements of chromosome structure, providing the basis for rapid evolution. The virilis species group of Drosophila contains certain species that can be crossed under experimental conditions and their phylogeny is thoroughly investigated. We have shown that Drosophila virilis, the most primitive karyotypically and probably the ancestral species of the group, is in the process of colonization by a very unusual retroelement Penelope which apparently repeatedly invaded the species of the group in the past. However, the molecular mechanisms and evolutionary consequences of such invasions are poorly understood. In this commentary, we discuss the implications of our recent investigation into the response of the RNA silencing system to Penelope invasion of a new host genome which can be achieved in different ways.
PMCID: PMC3681739  PMID: 23914310
Drosophila; Penelope retroelement; evolution; invasion; small RNAs

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