Genomic islands and the evolution of catabolic pathways in bacteria

Self Cite

106

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.

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

Self Cite

106

“…H orizontal gene transfer and mobile genetic elements play a significant role in bacterial evolution (1)(2)(3)(4). Conjugative transposons (5,6), also known as integrative and conjugative elements (ICEs) (4,7), are mobile genetic elements that are normally integrated into the chromosome.…”

mentioning

confidence: 99%

“…Conjugative transposons (5,6), also known as integrative and conjugative elements (ICEs) (4,7), are mobile genetic elements that are normally integrated into the chromosome. They can excise and transfer to recipients through conjugation (mating) and integrate into the chromosome of the recipient (5,6).…”

mentioning

confidence: 99%

“…They can excise and transfer to recipients through conjugation (mating) and integrate into the chromosome of the recipient (5,6). ICEs encode proteins required for conjugal transfer and can also encode proteins involved in resistance to antibiotics (5,6), metabolism of alternative carbon sources (4,8), symbiosis (9), and other processes (10). ICEs and putative ICEs have been found in many bacteria (10) and are important agents of horizontal gene transfer because they are capable of moving themselves and other DNA to recipients (6,(11)(12)(13).…”

mentioning

confidence: 99%

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Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response

Auchtung

Lee

Monson

et al. 2005

239

523

Horizontal gene transfer contributes to the evolution of bacterial species. Mobile genetic elements play an important role in horizontal gene transfer, and characterization of the regulation of these elements should provide insight into conditions that influence bacterial evolution. We characterized a mobile genetic element, ICEBs1, in the Gram-positive bacterium Bacillus subtilis and found that it is a functional integrative and conjugative element (ICE) capable of transferring to Bacillus and Listeria species. We identified two conditions that promote ICEBs1 transfer: conditions that induce the global DNA damage response and crowding by potential recipients that lack ICEBs1. Transfer of ICEBs1 into cells that already contain the element is inhibited by an intercellular signaling peptide encoded by ICEBs1. The dual regulation of ICEBs1 allows for passive propagation in the host cell until either the potential mating partners lacking ICEBs1 are present or the host cell is in distress.conjugation ͉ horizontal gene transfer ͉ quorum sensing ͉ peptide signaling ͉ DNA microarrays

“…Plasmids isolated thus far from different ecological niches encode a versatile array of accessory functions, ranging from antibiotic resistance to nitrogen fixation. These functions may confer an advantage to their host in its ecological niche, making the burden of carrying the plasmid worthwhile (3,(6)(7)(8)(9)(10). Therefore, accessory functions carried by plasmids in a specific ecological niche may be enriched by requirements that are relevant for that niche.…”

mentioning

confidence: 99%

Insights into the bovine rumen plasmidome

Kav

Sasson

Jami

et al. 2012

136

115

Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.