Replication and conjugative mobilization of broad host-range IncQ plasmids

Meyer, Richard J.

doi:10.1016/j.plasmid.2009.05.001

Cited by 148 publications

(157 citation statements)

References 135 publications

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“…Accordingly, MOB F and MOB H relaxosomes are structurally more complex and contain comparably large oriTs (Ͼ300 bp) (2,51,81,92,118). On the other hand, MOB Q1 and certain MOB V relaxosomes are simple, contain short oriTs (Ͻ100 bp), and are promiscuous in their use of different helper T4SSs as mating channels (49,52,100). MOB C1 plasmids are a case apart, since they are mobilizable but code for their own T4CP (22).…”

Section: Mobility Of Genbank Plasmidsmentioning

confidence: 99%

Mobility of Plasmids

Smillie

Garcillán-Barcia

Francia

et al. 2010

Microbiol Mol Biol Rev

986

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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Section: Mobility Of Genbank Plasmidsmentioning

confidence: 99%

Mobility of Plasmids

Smillie

Garcillán-Barcia

Francia

et al. 2010

Microbiol Mol Biol Rev

986

1,054

View full text Add to dashboard Cite

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“…The replication initiation proteins used to retrieve the plasmids and their corresponding reference plasmids were RepA from the IncA/C plasmid pRA1 (34,45), RepA from the IncL/M plasmid pCTX-M3 (52), Rep from the IncP-9 plasmid NAH7 and pWW0 (60,61), RepC from the IncQ plasmid RSF1010 (50,59), and RepB from the IncU plasmid pRA3 (41). The PromA (74) and Ri/Ti (68) plasmids used here were retrieved from the literature and include those representatives whose genome sequences were available in GenBank in July 2009.…”

Section: ϫ5mentioning

confidence: 99%

Predicting Plasmid Promiscuity Based on Genomic Signature

et al. 2010

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Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.Comparative genomics has clearly shown that bacterial evolution occurs not only through genetic changes that are vertically inherited but also by extensive horizontal gene transfer between closely and distantly related bacteria (9). Mobile genetic elements such as plasmids and phages serve as important agents of horizontal gene transfer that can exchange genetic material between chromosomes (26). Plasmids also play a critical role in rapid bacterial adaptation to local environmental changes, as best exemplified by the alarmingly rapid spread of plasmid-encoded multidrug resistance in human pathogens (44,66). In spite of this, very little is understood about the range of bacterial hosts in which these plasmids may have resided and evolved in natural or clinical environments over time, i.e., their potential "evolutionary host range." Understanding the evolutionary history of virulence, catabolic, and other plasmids may help us to reconstruct the plasmid transfer network among microorganisms and track the pathways of gene dissemination.A plasmid's host range can be defined in different ways, but it is typically understood as the range of hosts in which a plasmid can replicate (replication host range, or from here on simply called "host range"). This host range is often narrower than the range of hosts to which the plasmid can transfer by conjugation (tran...

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“…Both subgroups of IncQ family plasmids have similar replicons that consist of three genes that encode a helicase (repA), a primase (repB), a DNA-binding initiator protein (repC), and an oriV region. The oriV region typically contains three complete, identical 22-bp iterons (or 20-bp iterons with 2-bp spacers) that serve as the binding site for RepC proteins (18,22). Although some IncQ family plasmids may possess more than three copies of the iterons, the additional iterons are either partial copies, have sequence variations, or lack the spacer regions (22).…”

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confidence: 99%

Evolutionary Competitiveness of Two Natural Variants of the IncQ-Like Plasmids, pRAS3.1 and pRAS3.2

Loftie-Eaton

Rawlings

2010

J Bacteriol

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Plasmids pRAS3.1 and pRAS3.2 are natural variants of the IncQ-2 plasmid family, that except for two differences, have identical plasmid backbones. Plasmid pRAS3.1 has four 22-bp iterons in its oriV region, while pRAS3.2 has only three 6-bp repeats and pRAS3.1 has five 6-bp repeats in the promoter region of the mobB-mobA/repB genes and pRAS3.2 has only four. In previous work, we showed that the overall effect of these differences was that when the plasmid was in an Escherichia coli host, the copy numbers of pRAS3.1 and pRAS3.2 were approximately 41 and 30, respectively. As pRAS3.1 and pRAS3.2 are likely to have arisen from the same ancestor, we addressed the question of whether one of the variants had an evolutionary advantage over the other. By constructing a set of identical plasmids with the number of 22-bp iterons varying from three to seven, it was found that plasmids with four or five iterons displaced plasmids with three iterons even though they had lower copy numbers. Furthermore, the metabolic load that the plasmids placed on E. coli host cells compared with plasmid-free cells increased with copy number from 10.9% at a copy number of 59 to 2.6% at a copy number of 15. Plasmid pRAS3.1 with four 22-bp iterons was able to displace pRAS3.2 with three iterons when both were coresident in the same host. However, the lower-copy-number pRAS3.2 placed 2.8% less of a metabolic burden on an E. coli host population, and therefore, pRAS3.2 has a competitive advantage over pRAS3.1 at the population level, as pRAS3.2-containing cells would be expected to outgrow pRAS3.1-containing cells.Plasmids of the IncQ family are characterized by their relatively small size (ϳ6 to 15 kb), their ability to replicate in a very wide range of bacterial host cells, and by being readily mobilizable by certain self-transmissible plasmids, in particular the broad-host-range IncP plasmids such as RP4 or RK2 (22). IncQ family plasmids have been subdivided into the IncQ-1 and IncQ-2 groups depending on whether their mobilization genes are of the three-gene IncQ type or the five-gene IncP type. Both subgroups of IncQ family plasmids have similar replicons that consist of three genes that encode a helicase (repA), a primase (repB), a DNA-binding initiator protein (repC), and an oriV region. The oriV region typically contains three complete, identical 22-bp iterons (or 20-bp iterons with 2-bp spacers) that serve as the binding site for RepC proteins (18,22). Although some IncQ family plasmids may possess more than three copies of the iterons, the additional iterons are either partial copies, have sequence variations, or lack the spacer regions (22). It has been shown that even a single-basepair replacement in a single iteron could result in a nonfunctional iteron-containing region and the inability of the IncQ-1 plasmid RSF1010 to replicate (19). Furthermore, in IncQ plasmids, the iterons have been shown to serve as the primary incompatibility determinants with cloned iterons on their own being able to displace the plasmid from which they were ...

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Replication and conjugative mobilization of broad host-range IncQ plasmids

Cited by 148 publications

References 135 publications

Mobility of Plasmids

Mobility of Plasmids

Predicting Plasmid Promiscuity Based on Genomic Signature

Evolutionary Competitiveness of Two Natural Variants of the IncQ-Like Plasmids, pRAS3.1 and pRAS3.2

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