Shaping bacterial genomes with integrative and conjugative elements

Burrus, Vincent; Waldor, Matthew K.

doi:10.1016/j.resmic.2004.01.012

Cited by 395 publications

(353 citation statements)

References 78 publications

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“…Interestingly, Actinobacterial ICE systems typically use conjugation apparatus belonging to the SpoIIE/FtsK family, which allows transfer of double-stranded DNA (te Poele et al, 2008;Bordeleau et al, 2012). However, the conjugation machinery here is more reminiscent of gram-negative and Firmicute systems of single-stranded transfer (Burrus and Waldor, 2004).…”

Section: Iron Acquisition Hgtmentioning

confidence: 99%

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Bonham

Wolfe

Dutton

2016

Preprint

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Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

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Section: Iron Acquisition Hgtmentioning

confidence: 99%

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Bonham

Wolfe

Dutton

2016

Preprint

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“…We therefore hypothesize that PAPI-1 transfer resembles the movement of integrative and conjugative elements (ICEs), a group of self-transmissible mobile genetic elements that distribute widely in bacteria and contribute greatly to lateral gene flow in prokaryotes (25). In the genus of Pseudomonas, the clc element of Pseudomonas sp.…”

Section: Fmentioning

confidence: 99%

Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa

Qiu

Gurkar

Lory

2006

Proc. Natl. Acad. Sci. U.S.A.

109

150

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The large Pseudomonas aeruginosa pathogenicity island PAPI-1 of strain PA14 is a cluster of 108 genes that encode a number of virulence features. We demonstrate that, in a subpopulation of cells, PAPI-1 can exist in an extrachromosomal circular form after precise excision from its integration site within the 3 terminus of the tRNA Lys gene. Circular PAPI-1 can reintegrate into either of the two tRNA Lys genes, including the one that was used for integration of small pathogenicity island PAPI-2 in strain PA14. The excision requires PAPI-1-encoded integrase, a member of the tyrosine recombinase family. PAPI-1 Soj contains the conserved domains of proteins that are related to chromosome and plasmid partition. soj plays a role in maintaining PAPI-1 and mutations in soj result in the loss of PAPI-1 from P. aeruginosa. We further demonstrate that, during coculture, the PAPI-1-containing strains are able to transfer it into P. aeruginosa recipient strains that do not harbor this island naturally. After transfer, PAPI-1 integrates into either of the two tRNA Lys genes. PAPI-1 encompasses many features of mobile elements, including mobilization and maintenance modules. Together with the virulence determinants, PAPI-1 plays an important role in the evolution of P. aeruginosa, by expanding its natural habitat from soil and water to animal and human infections.evolution ͉ horizontal gene transfer ͉ integration

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“…Integrative and conjugative elements (ICEs) are frequently detected mobile genome inhabitants. They can contribute to host adaptation by dispersing dozens to hundreds of genes in a single transfer event (4)(5)(6). It has been estimated that conjugative systems of ICEs are more abundant among bacteria than those of plasmids (7), yet we know far less about ICE behavior because they are difficult to follow and isolate.…”

mentioning

confidence: 99%

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

Delavat

Mitri

Pelet

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

106

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Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using timelapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer.

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Shaping bacterial genomes with integrative and conjugative elements

Cited by 395 publications

References 78 publications

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa

Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

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