Integrons

Domingues, Sara; Silva, Gabriela; Nielsen, Kaare M.

doi:10.4161/mge.22967

Cited by 140 publications

(73 citation statements)

References 151 publications

(214 reference statements)

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“…The second step involved a translocation of part of the new BTA29-BTA6 fusion locus back to the original BTA6 wild-type locus via NAHR. While the translocation and incorporation of DNA circular intermediates has been well characterized in bacterial integron dynamics (Domingues et al, 2012), this is one of the first instances where a similar mechanism was detected in a mammalian species, let alone a complex double-translocation event. The implications of this new allele have extended beyond Brown Swiss and Belgian Blue cattle as White Galloway and White Park cattle were found to carry this allele (Brenig et al, 2013).…”

Section: The Evolutionary and Functional Impacts Of Cnvs In Livestockmentioning

confidence: 83%

The challenges and importance of structural variation detection in livestock

2014

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Recent studies in humans and other model organisms have demonstrated that structural variants (SVs) comprise a substantial proportion of variation among individuals of each species. Many of these variants have been linked to debilitating diseases in humans, thereby cementing the importance of refining methods for their detection. Despite progress in the field, reliable detection of SVs still remains a problem even for human subjects. Many of the underlying problems that make SVs difficult to detect in humans are amplified in livestock species, whose lower quality genome assemblies and incomplete gene annotation can often give rise to false positive SV discoveries. Regardless of the challenges, SV detection is just as important for livestock researchers as it is for human researchers, given that several productive traits and diseases have been linked to copy number variations (CNVs) in cattle, sheep, and pig. Already, there is evidence that many beneficial SVs have been artificially selected in livestock such as a duplication of the agouti signaling protein gene that causes white coat color in sheep. In this review, we will list current SV and CNV discoveries in livestock and discuss the problems that hinder routine discovery and tracking of these polymorphisms. We will also discuss the impacts of selective breeding on CNV and SV frequencies and mention how SV genotyping could be used in the future to improve genetic selection.

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Section: The Evolutionary and Functional Impacts Of Cnvs In Livestockmentioning

confidence: 83%

The challenges and importance of structural variation detection in livestock

2014

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“…4) (187)(188)(189)(190). They are composed of a stable platform into which various gene cassettes that encode accessory functions are integrated.…”

Section: Integronsmentioning

confidence: 99%

“…Mobile integrons are easily transmitted between hosts and are at the origin of the rise of multidrug resistance in some bacteria. Finally, integrons are often associated with other mobile elements (190,206).…”

Section: Fig 3 Schematic Organization Of a Diversity-generating Retromentioning

confidence: 99%

Bacterial Genome Instability

Darmon

Leach

2014

Microbiol Mol Biol Rev

331

285

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SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

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“…Class 1 integrons commonly carry a 5′-conserved segment [5′-CS], which is composed of the integrase gene intI1 , a specific recombination site attI1 located next to intI1 and recognized by intI1 , and a promoter Pc driving the transcription of cassette-borne genes and lying within intI1 (Partridge et al, 2009; Domingues et al, 2012; Gillings, 2014). The bla IMP genes are often found together with other resistance genes in the variable gene cassette arrays of class 1 integrons, and these integrons are further associated with mobile elements such as transposons and plasmids, leading to the easily mobilization of cassette-borne resistance genes across various bacterial species (Gillings et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Sequencing of blaIMP-Carrying IncN2 Plasmids, and Comparative Genomics of IncN2 Plasmids Harboring Class 1 Integrons

Jiang

Yin

et al. 2017

Front. Cell. Infect. Microbiol.

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This work presents the complete nucleotide sequences of p0801-IMP from Klebsiella pneumoniae, p7121-IMP from K. oxytoca, and p17285-IMP from Citrobacter freundii, which are recovered from three different cases of nosocomial infection. These three plasmids represent the first fully sequenced blaIMP-carrying IncN2 plasmids. Further comparative genomics analysis of all the five integron-carrying IncN2 plasmids p0801-IMP, p7121-IMP, p17285-IMP, pJIE137, and p34983-59.134kb indicates that they possess conserved IncN2 backbones with limited genetic variations with respect to gene content and organization. Four class 1 integrons (blaIMP-1-carrying In1223 in p0801-IMP/p7121-IMP, blaIMP-8-carrying In655 in p17285-IMP, In27 in pJIE137, and In1130 in p34983-59.134kb), two insertion sequence-based transposition units (ISEcp1-orfRA1-14 in p17285-IMP, and ISEcp1-blaCTX-M-62-Δorf477-orfRA1-14 in pJIE137), and a novel Tn1696-related transposon Tn6325 carrying In1130 in p34983-59.134kb are indentified in the plasmid accessory regions. In1223 and In655 represent ancestral Tn402-associated integrons, while In27 and In1130 belong to complex class 1 integrons. The relatively small IncN2 backbones are able to integrate different mobile elements which carry various resistance markers, promoting the accumulation and spread of antimicrobial resistance genes among enterobacterial species.

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Integrons

Cited by 140 publications

References 151 publications

The challenges and importance of structural variation detection in livestock

The challenges and importance of structural variation detection in livestock

Bacterial Genome Instability

Sequencing of blaIMP-Carrying IncN2 Plasmids, and Comparative Genomics of IncN2 Plasmids Harboring Class 1 Integrons

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