Persistence Mechanisms of Conjugative Plasmids

Bahl, Martin Iain; Hansen, Lars Hestbjerg; Sørensen, Søren J.

doi:10.1007/978-1-60327-853-9_5

Cited by 42 publications

(36 citation statements)

References 139 publications

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“…In contrast to phages, plasmids exist independently of the host chromosome and are generally non-lethal [29]. When the phenotypic features of the plasmid are not required for bacterial survival, the plasmid will exist only in a small minority of the total microbial population [30]. In this way the forces of selective pressure are reduced compared to the host chromosome.…”

Section: Discussionmentioning

confidence: 99%

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Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

et al. 2012

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BackgroundWe sought to assess whether the concept of relative entropy (information capacity), could aid our understanding of the process of horizontal gene transfer in microbes. We analyzed the differences in information capacity between prokaryotic chromosomes, genomic islands (GI), phages, and plasmids. Relative entropy was estimated using the Kullback-Leibler measure.ResultsRelative entropy was highest in bacterial chromosomes and had the sequence chromosomes > GI > phage > plasmid. There was an association between relative entropy and AT content in chromosomes, phages, plasmids and GIs with the strongest association being in phages. Relative entropy was also found to be lower in the obligate intracellular Mycobacterium leprae than in the related M. tuberculosis when measured on a shared set of highly conserved genes.ConclusionsWe argue that relative entropy differences reflect how plasmids, phages and GIs interact with microbial host chromosomes and that all these biological entities are, or have been, subjected to different selective pressures. The rate at which amelioration of horizontally acquired DNA occurs within the chromosome is likely to account for the small differences between chromosomes and stably incorporated GIs compared to the transient or independent replicons such as phages and plasmids.

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Section: Discussionmentioning

confidence: 99%

“…In this way the forces of selective pressure are reduced compared to the host chromosome. Phages also exist independently of bacterial chromosomes but rely on the bacterial machinery for replication [29,30]. However, those phages that are lytic will be under greater selective pressure than plasmids.…”

Section: Discussionmentioning

confidence: 99%

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

et al. 2012

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“…Plasmids are regarded as selfish genetic elements because they can spread and survive without necessarily increasing their host fitness (7,113). In this light, how can one interpret the existence of so many nontransmissible plasmids?…”

Section: How Mobile Are Nonmobilizable Plasmids?mentioning

confidence: 99%

Mobility of Plasmids

Smillie

Garcillán-Barcia

Francia

et al. 2010

Microbiol Mol Biol Rev

960

1,054

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International audiencePlasmids are key vectors of horizontal gene transfer and essential genetic engineering tools. They code for genes involved in many aspects of microbial biology, including detoxication, virulence, ecological interactions, and antibiotic resistance. While many studies have decorticated the mechanisms of mobility in model plasmids, the identification and characterization of plasmid mobility from genome data are unexplored. By reviewing the available data and literature, we established a computational protocol to identify and classify conjugation and mobilization genetic modules in 1,730 plasmids. This allowed the accurate classification of proteobacterial conjugative or mobilizable systems in a combination of four mating pair formation and six relaxase families. The available evidence suggests that half of the plasmids are nonmobilizable and that half of the remaining plasmids are conjugative. Some conjugative systems are much more abundant than others and preferably associated with some clades or plasmid sizes. Most very large plasmids are nonmobilizable, with evidence of ongoing domestication into secondary chromosomes. The evolution of conjugation elements shows ancient divergence between mobility systems, with relaxases and type IV coupling proteins (T4CPs) often following separate paths from type IV secretion systems. Phylogenetic patterns of mobility proteins are consistent with the phylogeny of the host prokaryotes, suggesting that plasmid mobility is in general circumscribed within large clades. Our survey suggests the existence of unsuspected new relaxases in archaea and new conjugation systems in cyanobacteria and actinobacteria. Few genes, e.g., T4CPs, relaxases, and VirB4, are at the core of plasmid conjugation, and together with accessory genes, they have evolved into specific systems adapted to specific physiological and ecological contexts

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“…In addition, the impact of a particular HGT event may depend on environmental parameters, 4 , 10 - 12 such as the presence or absence of antibiotics, toxic metal ions and nutrients. Upon a change in environment, previously beneficial DNA may no longer provide a selective advantage, and instead can reduce host fitness 13 . In addition to DNA uptake mechanisms, bacteria therefore require systems that either block the entry of alien DNA or can remove such DNA from the cell.…”

Section: Introductionmentioning

confidence: 99%

CRISPR-Cas systems preferentially target the leading regions of MOB_Fconjugative plasmids

Westra¹,

Staals²,

Gort³

et al. 2013

RNA Biology

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Most prokaryotes contain CRISPR-Cas immune systems that provide protection against mobile genetic elements. We have focused on the ability of CRISPR-Cas to block plasmid conjugation, and analyzed the position of target sequences (protospacers) on conjugative plasmids. The analysis reveals that protospacers are non-uniformly distributed over plasmid regions in a pattern that is determined by the plasmid’s mobilization type (MOB). While MOBP plasmids are most frequently targeted in the region entering the recipient cell last (lagging region), MOBF plasmids are mostly targeted in the region entering the recipient cell first (leading region). To explain this protospacer distribution bias, we propose two mutually non-exclusive hypotheses: (1) spacers are acquired more frequently from either the leading or lagging region depending on the MOB type (2) CRISPR-interference is more efficient when spacers target these preferred regions. To test the latter hypothesis, we analyzed Type I-E CRISPR-interference against MOBF prototype plasmid F in Escherichia coli. Our results show that plasmid conjugation is effectively inhibited, but the level of immunity is not affected by targeting the plasmid in the leading or lagging region. Moreover, CRISPR-immunity levels do not depend on whether the incoming single-stranded plasmid DNA, or the DNA strand synthesized in the recipient is targeted. Our findings indicate that single-stranded DNA may not be a target for Type I-E CRISPR-Cas systems, and suggest that the protospacer distribution bias might be due to spacer acquisition preferences.

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Persistence Mechanisms of Conjugative Plasmids

Cited by 42 publications

References 139 publications

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Mobility of Plasmids

CRISPR-Cas systems preferentially target the leading regions of MOB_Fconjugative plasmids

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Persistence Mechanisms of Conjugative Plasmids

Cited by 42 publications

References 139 publications

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Mobility of Plasmids

CRISPR-Cas systems preferentially target the leading regions of MOBFconjugative plasmids

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CRISPR-Cas systems preferentially target the leading regions of MOB_Fconjugative plasmids