Table of Contents

Volume 1, Issue 1

  May/June 2011

  Pages 1 - 87

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 Issue Catalogue (MARC XML)

EDITORIAL

Open Access Article

From ASH to MGE

Adam P. Roberts
Page 1
http://dx.doi.org/10.4161/mge.1.1.15320
Abstract | PDF

Dear Reader,

In April 2010, during the Eyjafjallajökull volcano eruption in Iceland which grounded flights and disrupted the travel plans of thousands of people, the stranded CEO of Landes Bioscience, Ron Landes, and I took the opportunity to meet in London. It was from that meeting that this journal took shape and it is with great pleasure that I am able to introduce the first issue of Mobile Genetic Elements. MGE is a truly international, peer reviewed, multidisciplinary journal focusing on all aspects of mobile genetic elements and horizontal gene transfer throughout life. The scope of the journal is necessarily broad as it is increasingly clear that the consequences of horizontal gene transfer, and the genetic movement mediated by mobile genetic elements, is of fundamental importance to cellular activity, evolution and survival.




RESEARCH PAPERS

Open Access Article

Spread of the group II intron RmInt1 and its insertion sequence target sites in the plant endosymbiont Sinorhizobium meliloti

Emanuele G. Biondi, Nicolás Toro, Marco Bazzicalupo and Francisco Martínez-Abarca
Pages 2 - 7
http://dx.doi.org/10.4161/mge.1.1.15316
Abstract | PDF

RmInt1 is a mobile group II intron from Sinorhizobium meliloti that is exceptionally abundant in this bacterial species. We compared the presence of RmInt1 and two of its insertion sequence homing sites (ISRm2011-2 and ISRm10-2) in two phylogenetic clusters (I and II) identifi ed by AFLP analysis in a collection of S. meliloti fi eld isolates from Italy. Both clusters contained several copies of the ISRm2011-2 element, which is present at high copy number in almost all S. meliloti isolates. By contrast, isolates from cluster I harbored no copies of ISRm10-2 and only a truncated copy of RmInt1, despite the absence of constraints on intron mobility in this genetic background, whereas cluster II strains harbored several copies of this intron. The absence of ISRm10-2 from one of the strains of this cluster suggests that this element was acquired more recently than the other two elements. Furthermore, studies of insertional polymorphisms in cluster II strains revealed the acquisition of ISRm10-2 and subsequent retrohoming of RmInt1 to this homing site. These results highlight the role of intron homing sites (ISs) in facilitating intron dispersal and the dynamic and ongoing nature of the spread of the group II intron RmInt1 in S. meliloti.

Open Access Article

Comprehensive analysis of microRNA genomic loci identifies pervasive repetitive-element origins

Glen M. Borchert and 20 others
Pages 8 - 17
http://dx.doi.org/10.4161/mge.1.1.15766
Abstract | PDF

MicroRNAs (miRs) are small non-coding RNAs that generally function as negative regulators of target messenger RNAs (mRNAs) at the posttranscriptional level. MiRs bind to the 3′UTR of target mRNAs through complementary base pairing, resulting in target mRNA cleavage or translation repression. To date, over 15,000 distinct miRs have been identified in organisms ranging from viruses to man, and interest in miR research continues to intensify. Of note, the most enlightening aspect of miR function – the mRNAs they target – continues to be elusive. Descriptions of the molecular origins of independent miR molecules currently support the hypothesis that miR hairpin generation is based on the adjacent insertion of two related transposable elements (TEs) at one genomic locus. Thus transcription across such TE interfaces establishes many, if not the majority of functional miRs. The implications of these findings are substantial for understanding how TEs confer increased genomic fitness, describing miR transcriptional regulations, and making accurate miR target predictions. In this work, we have performed a comprehensive analysis of the genomic events responsible for the formation of all currently annotated miR loci. We find that the connection between miRs and transposable elements is more significant than previously appreciated, and more broadly, supports an important role for repetitive elements in miR origin, expression and regulatory network formation. Further, we demonstrate the utility of these findings in miR target prediction. Our results greatly expand the existing repertoire of defined miR origins, detailing the formation of 2,392 of 15,176 currently recognized miR genomic loci and supporting a mobile genetic element model for the genomic establishment of functional miRs.

Open Access Article

Identification and characterization of jute LTR retrotransposons: Their abundance, heterogeneity and transcriptional activity

Salim Ahmed, MD Shafiuddin, Muhammad Shafiul Azam, Md. Shahidul Islam, Ajit Ghosh and Haseena Khan
Pages 18 - 28
http://dx.doi.org/10.4161/mge.1.1.16433
Abstract | PDF

Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.


Open Access Article

Independently derived targeting of 28S rDNA by A- and D-clade R2 retrotransposons: Plasticity of integration mechanism

Blaine K. Thompson and Shawn M. Christensen
Pages 29 - 37
http://dx.doi.org/10.4161/mge.1.1.16485
Abstract | PDF

Restriction-like endonuclease (RLE) bearing non-LTR retrotransposons are site-specific elements that integrate into the genome through a target primed reverse transcription mechanism (TPRT). R2 elements have been used as a model system for investigating non-LTR retrotransposon integration. We previously demonstrated that R2 retrotransposons require two subunits of the element-encoded multifunctional protein to integrate—one subunit bound upstream of the insertion site and one bound downstream. R2 elements have been phylogenetically categorized into four clades: R2-A, B, C, and D, that diverged from a common ancestor more than 850 million years ago. All R2 elements target the same sequence within 28S rDNA. The amino-terminal domain of R2Bm, a R2-D clade element, contains a single zinc finger and a Myb motif that are responsible for binding R2 protein downstream of the insertion site. Target site recognition is of interest as it is the first step in the integration reaction and may help elucidate evolutionary history and integration mechanism. The amino-terminal domain of R2-A clade members contains three zinc fingers and a Myb motif. We show here that R2-Lp, an R2-A clade member, uses its amino-terminal DNA binding motifs to bind upstream of the insertion site. Because the R2-A and R2-D clade elements recognize 28S rDNA differently, we conclude the A- and D-clades represent independent targeting events to the 28S site. Our results also indicate a certain plasticity of insertional mechanics exists between the two clades.





REVIEWS

Open Access Article

Tales of conjugation and sex pheromones: A plasmid and enterococcal odyssey

Don B. Clewell
Pages 38 - 54
http://dx.doi.org/10.4161/mge.1.1.15409
Abstract | PDF

This review covers highlights of the author’s experience becoming and working as a plasmid biologist. The account chronicles a progression from studies of ColE1 DNA in Escherichia coli to Gram-positive bacteria with an emphasis on conjugation in enterococci. It deals with gene amplification, conjugative transposons and sex pheromones in the context of bacterial antibiotic resistance.


Open Access Article

The influence of the accessory genome on bacterial pathogen evolution

Robert W. Jackson, Boris Vinatzer, Dawn L. Arnold, Steve Dorus and Jesús Murillo
Pages 55 - 65
http://dx.doi.org/10.4161/mge.1.1.16432
Abstract | PDF

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution.




EXTRA VIEWS

Open Access Article

B1-SINE retrotransposons: Establishing genomic insulatory networks

Angel C. Román, Francisco J. González-Rico and Pedro M. Fernandez-Salguero
Pages 66 - 70
http://dx.doi.org/10.4161/mge.1.1.15455
Abstract | PDF

More than half the size of most mammalian genomes is composed by repetitive sequences. Short Interspersed Nuclear Element (SINE) retrotransposons constitute one of the main components of the genomic repetitive fraction. The abundance and evolutionary conservation of these sequences support their contribution to maintain the stability and proper function of the genome. Several recent studies have unveiled some of these intriguing tasks, which include, but are not limited to the control of transcriptional regulation and the organization of the chromatin. Here, we will comment on our recent report characterizing the insulator/boundary activity of a novel B1 SINE retrotransposon (B1-X35S) widely present in the mouse genome. A remarkable finding was that B1-X35S-dependent insulation required not only the combinatorial binding of transcription factors dioxin receptor (AhR) and Snai2/Slug, but also a molecular switch between RNA Polymerases (Pol) Pol III and Pol II. Moreover, B1-X35S seemingly forms heterochromatic barriers next to gene promoters that bioinformatic analyses revealed to dramatically change from embryonic stem (ES) to fibroblasts cells. The vast presence of B1-X35S in the mouse genome (over 14,000 instances) opens the exciting possibility of a complex network in which retrotransposon-derived insulators convert biological input signals into transcriptional responses by defining gene expression domains. The importance of such mechanism in different cellular and physiological processes will be discussed.

Open Access Article

The tangled past of eukaryotic enzymes involved in anaerobic metabolism

Vladimir Hampl, Courtney W. Stairs and Andrew J. Roger
Pages 71 - 74
http://dx.doi.org/10.4161/mge.1.1.15588
Abstract | PDF

There is little doubt that genes can spread across unrelated prokaryotes, eukaryotes and even between these domains. It is expected that organisms inhabiting a common niche may exchange their genes even more often due to their physical proximity and similar demands. One such niche is anaerobic or microaerophilic environments in some sediments and intestines of animals. Indeed, enzymes advantageous for metabolism in these environments often exhibit an evolutionary history incoherent with the history of their hosts indicating potential transfers. The evolutionary paths of some very basic enzymes for energy metabolism of anaerobic eukaryotes (pyruvate formate lyase, pyruvate:ferredoxin oxidoreductase, [FeFe]hydrogenase and arginine deiminase) seems to be particularly intriguing and although their histories are not identical they share several unexpected features in common. Every enzyme mentioned above is present in groups of eukaryotes that are unrelated to each other. Although the enzyme phylogenies are not always robustly supported, they always suggest that the eukaryotic homologues form one or two clades, in which the relationships are not congruent with the eukaryotic phylogeny. Finally, these eukaryotic enzymes are never specifically related to homologues from α-proteobacteria, ancestors of mitochondria. The most plausible explanation for evolution of this pattern expects one or two interdomain transfers to one or two eukaryotes from prokaryotes, who were not the mitochondrial endosymbiont. Once the genes were introduced into the eukaryotic domain they have spread to other eukaryotic groups exclusively via eukaryote-to-eukaryote transfers. Currently, eukaryote-to-eukaryote gene transfers have been regarded as less common than prokaryote-to-eukaryote transfers. The fact that eukaryotes accepted genes for these enzymes solely from other eukaryotes and not prokaryotes present in the same environment is surprising.




ADDENDA

Open Access Article

Codon bias, tRNA pools, and horizontal gene transfer

Tamir Tuller
Pages 75 - 77
http://dx.doi.org/10.4161/mge.1.1.15400
Abstract | PDF

Horizontal Gene Transfer (HGT) is a major force in bacterial evolution. Bacteria are under a strong selection to optimize their growth rate by improving features related to their codon usage. In a recent study we have shown that these two forces are coupled: 1) the codon bias of transferred genes has a strong influence on the probability that they will become fixed in the new genome, and 2) frequent HGTs may increase the similarity in the tRNA pools of organisms within the same community. Thus, methods for inferring HGTs probably underestimate their number. We believe that that the principles that affect microorganisms may also apply to mobile genetic elements (including plasmids, viruses, and transposons).

Open Access Article

Extraction of tentative mobile introns in fungal histone genes

Hiromi Nishida and Choong-Soo Yun
Pages 78 - 79
http://dx.doi.org/10.4161/mge.1.1.15431
Abstract | PDF

We have identified 305 introns in fungal histone genes. Among the 305 introns, 21 had sequence similarities to introns that have different insertion sites. These 21 introns formed 13 intron-pairs. Nine of the 13 pairs had low similarities (35.3%-47.4%) between the flanking DNA sequences of the introns, suggesting that intron-homing or homologous recombination was rare event in the histone intron distribution. Six of the 9 pairs consisted of the introns in the genes encoding the different histone families. On the other hand, 4 of the 13 pairs had 59.6-76.9% similarities between the flanking DNA sequences and the two intron sizes are similar. These 4 pairs consisted of the introns in the genes encoding the same histone family. Thus, in this analysis, intron-homings were not detected between the fungal genes encoding different histone families.

Open Access Article

Mobilizable bacterial DNA packaged into membrane vesicles induces serial transduction.

Branko Velimirov and Sylvia Hagemann
Pages 80 - 81
http://dx.doi.org/10.4161/mge.1.1.15724
Abstract | PDF

Experiments where the amino acid deficient strain E.coli AB1157 was exposed to a particle fraction harvested from a marine oligotrophic environment, ranging in diameter size between 100-130 nm indicated evidence for horizontal gene transfer resulting in revertant cells with restoration of all genetic deficiencies with frequencies up to 1.94 x 10-5. None of the markers was preferentially transferred indicating that the DNA-transfer is performed by generalized transduction. The highest transfer frequency obtained for single markers was 1.04 x 10-2. All revertant strains were able to produce particles of comparable size that were again infectious, appearing at the beginning of the stationary phase. Ultra structural investigation showed a structural resemblance with membrane vesicles, however, Field Gel Electrophoresis indicated that the DNA content of some of the particles was 370 kbp; much higher than that of the so far known previously described membrane vesicles providing evidence of a new mechanism for horizontal gene transfer.

Open Access Article

How can a dual oriT system contribute to efficient transfer of an integrative and conjugative element?

Ryo Miyazaki and Jan Roelof van der Meer
Pages 82 - 84
http://dx.doi.org/10.4161/mge.1.1.15744
Abstract | PDF

Integrative and conjugative elements (ICEs) are particularly interesting model systems for horizontal gene transfer, because they normally reside in an integrated state in the host chromosome but can excise and self-transfer under particular conditions, typically requiring exquisite regulatory cascades. Despite important advances in our understanding of the transfer mechanisms of a number of ICE, many essential details are lacking. Recently we reported that ICEclc, a 103-kb ICE of Pseudomonas knackmussii B13, has two active origins of transfer (oriTs), which is very much unlike conjugative plasmids that usually employ a single oriT. We discuss here how this dual oriT system could function and how it actually could have presented an evolutionary advantage for ICEclc distribution.

Open Access Article

Neisseria gonorrhoeae and humans perform an evolutionary LINE dance

Mark T. Anderson and H. Steven Seifert
Pages 85 - 87
http://dx.doi.org/10.4161/mge.1.1.15868
Abstract | PDF

Horizontal gene transfer is an important mechanism for generating genetic diversity. As the number of sequenced genomes continues to increase, so do the examples of horizontal genetic exchange between both related and divergent organisms. Here we discuss the recent finding that certain strains of the human pathogen Neisseria gonorrhoeae have incorporated a small fragment of human DNA sequence into their genomes. The horizontally acquired sequence exhibits 98-100% nucleotide identity to a 685-bp portion of the highly repetitive retrotransposable element L1 and its presence in the gonococcal genome has been confirmed by multiple molecular techniques. The possibility of similar L1 horizontal gene transfer events having occurred in other bacteria based on genomic sequence evidence is explored. Potential mechanisms of how N. gonorrhoeae was able to acquire and maintain this human sequence are also discussed in addition to the evolutionary implications of such an event.