Search results for "Mobile genetic element"

The Gypsy Database (GyDB) of mobile genetic elements.

2007

In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by t…

2021

Antibiotic resistance genes of important Gram-negative bacterial pathogens are residing in mobile genetic elements such as conjugative plasmids. These elements rapidly disperse between cells when antibiotics are present and hence our continuous use of antimicrobials selects for elements that often harbor multiple resistance genes. Plasmid-dependent (or male-specific or, in some cases, pilus-dependent) bacteriophages are bacterial viruses that infect specifically bacteria that carry certain plasmids. The introduction of these specialized phages into a plasmid-abundant bacterial community has many beneficial effects from an anthropocentric viewpoint: the majority of the plasmids are lost whil…

Evolutionary rescue of bacteria via horizontal gene transfer under a lethal β-lactam concentration

2013

β-Lactams are a commonly used class of bactericidal antibiotics. The number of β-lactam-resistant pathogens is constantly increasing in hospitals around the world. Interestingly, most of the β-lactam-resistant bacteria carry mobile genetic elements, such as conjugative plasmids, that render the pathogen resistant. These elements mediate their own transfer from one bacterium to another, producing new resistant strains via horizontal gene transfer. Here we investigated whether it is possible that transfer of the resistance element from another bacterium may evolutionarily rescue a susceptible bacterium exposed to a lethal concentration of the β-lactam ampicillin. Indeed, the rescuing occurs e…

Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracell…

2014

Particularly interesting cases of mutualistic endosymbioses come from the establishment of co-obligate associations of more than one species of endosymbiotic bacteria. Throughout symbiotic accommodation from a free-living bacterium, passing through a facultative stage and ending as an obligate intracellular one, the symbiont experiences massive genomic losses and phenotypic adjustments. Here, we scrutinized the changes in the coevolution of Serratia symbiotica and Buchnera aphidicola endosymbionts in aphids, paying particular attention to the transformations undergone by S. symbiotica to become an obligate endosymbiont. Although it is already known that S. symbiotica is facultative in Acyrt…

Rapid differentiation between livestock-associated and livestock-independent Staphylococcus aureus CC398 clades.

2013

Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet (M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clade…

GyDB mobilomics: LTR retroelements and integrase-related transposons of the pea aphid Acyrthosiphon pisum genome

2011

[EN] The Gypsy Database concerning Mobile Genetic Elements (release 2.0) is a wiki-style project devoted to the phylogenetic classification of LTR retroelements and their viral and host gene relatives characterized from distinct organisms. Furthermore, GyDB 2.0 is concerned with studying mobile elements within genomes. Therefore, an in-progress repository was created for databases with annotations of mobile genetic elements from particular genomes. This repository is called Mobilomics and the first uploaded database contains 549 LTR retroelements and related transposases which have been annotated from the genome of the Pea aphid Acyrthosiphon pisum. Mobilomics is accessible from the GyDB 2.…

Structure and expression of clustered P element homologues in Drosophila subobscura and Drosophila guanche

1995

Abstract Sequence relationships and functional aspects were analysed in the P element homologues of Drosophila subobscura (Ds) and D. guanche (Dg) . In both species, the P homologues are clustered at a single genomic position. They lack the characteristic terminal structures of actively transposing P elements, but they have the coding capacity for a 66-kDa ‘repressor-like’ protein. Two different types of cluster units (G-type and A-type) can be distinguished. The A-type unit, which is present in multiple copies, is transcribed in adult flies. In contrast, the G-type unit has a much lower copy number and is apparently not expressed. In Dg , the isolated G-type sequence carries a 420-bp inser…

Core and Accessory Genome Analysis of Vibrio mimicus

2021

© 2021 by the authors.

Mobile genetic element proliferation and gene inactivation impact over the genome structure and metabolic capabilities of Sodalis glossinidius, the s…

2010

Abstract Background Genome reduction is a common evolutionary process in symbiotic and pathogenic bacteria. This process has been extensively characterized in bacterial endosymbionts of insects, where primary mutualistic bacteria represent the most extreme cases of genome reduction consequence of a massive process of gene inactivation and loss during their evolution from free-living ancestors. Sodalis glossinidius, the secondary endosymbiont of tsetse flies, contains one of the few complete genomes of bacteria at the very beginning of the symbiotic association, allowing to evaluate the relative impact of mobile genetic element proliferation and gene inactivation over the structure and funct…