Complete genome sequence of the incompatibility group I1 plasmid R64

Sampei, G.; Furuya, Nobuhisa; Tachibana, Keiko; Saitou, Yasuhiro; Suzuki, Takuji; Mizobuchi, Kiyoshi; Komano, Teruya

doi:10.1016/j.plasmid.2010.05.005

Cited by 94 publications

(108 citation statements)

References 58 publications

Supporting

Mentioning

104

Contrasting

Unclassified

Order By: Relevance

“…This region contains the genes pilL to pilV from the type 4b pilin system (T4Pb) (53). This system is similar to the previously described of R64 plasmid system involved in liquid and surface mating (54,55) and the pilin genes found in the PAPI-1 selftransmission genome island in many Pseudomonas genomes (56,57). These genes show, on average, more than 55% divergence from the corresponding orthologs in P. aeruginosa PA07 and P. protegens Pf-5 genomes (see Table S8 in the supplemental material).…”

Section: Sequencing and Assemblymentioning

confidence: 83%

The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment

et al. 2013

View full text Add to dashboard Cite

dMicrobial adaptation to environmental conditions is a complex process, including acquisition of positive traits through horizontal gene transfer or the modification of existing genes through duplication and/or mutation. In this study, we examined the adaptation of a Pseudomonas fluorescens isolate (R124) from the nutrient-limited mineral environment of a silica cave in comparison with P. fluorescens isolates from surface soil and the rhizosphere. Examination of metal homeostasis gene pathways demonstrated a high degree of conservation, suggesting that such systems remain functionally similar across chemical environments. The examination of genomic islands unique to our strain revealed the presence of genes involved in carbohydrate metabolism, aromatic carbon metabolism, and carbon turnover, confirmed through phenotypic assays, suggesting the acquisition of potentially novel mechanisms for energy metabolism in this strain. We also identified a twitching motility phenotype active at low-nutrient concentrations that may allow alternative exploratory mechanisms for this organism in a geochemical environment. Two sets of candidate twitching motility genes are present within the genome, one on the chromosome and one on a plasmid; however, a plasmid knockout identified the functional gene as being present on the chromosome. This work highlights the plasticity of the Pseudomonas genome, allowing the acquisition of novel nutrient-scavenging pathways across diverse geochemical environments while maintaining a core of functional stress response genes. Genomics has revolutionized the way we study microorganisms in the environment; in the postgenomic era, it is possible to describe the enzymatic pathway corresponding to metabolic pathways that are only hypothesized (1) or to predict the environmental function of uncultivated bacterial phyla based on singlecell isolation and genomic amplification (2, 3). The result has been a profound change in our understanding of microbial interactions and processes; however, not all environments have benefited from this revolution. At the intersection of microbiology and geology, comparative genomics has yet to examine how the interaction between microbes and minerals leads to genomic adaptation (4). As a result, numerous fundamental questions remain to be answered, such as what is the role of microorganisms in mineral precipitation and weathering (5, 6).In this study we examined the genome of an organism isolated from a predominantly mineral environment, using a cave-isolated Pseudomonas strain as a model. Due to their ubiquitous distribution in terrestrial environments and association with opportunistic infections, pseudomonads have been studied for many years, and a large number of representative genomes exist: 37 completed projects within the genus Pseudomonas. Among the hundreds of bacterial species we have isolated from cave environments, we decided to examine the genomic adaptations of Pseudomonas fluorescens to this mineral environment. P. fluorescens is an advantageous organism f...

show abstract

Section: Sequencing and Assemblymentioning

confidence: 83%

The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment

et al. 2013

View full text Add to dashboard Cite

show abstract

“…2A). P2 shows homology to R-64 and ColIb-P9-type conjugative plasmids of the IncI1 incompatibility group, a family of plasmids also encoding multiple antibiotic resistances (29)(30)(31) (Fig. 2B).…”

Section: Resultsmentioning

confidence: 99%

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

Stecher

Denzler

Maier

et al. 2012

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

432

399

View full text Add to dashboard Cite

The mammalian gut harbors a dense microbial community interacting in multiple ways, including horizontal gene transfer (HGT). Pangenome analyses established particularly high levels of genetic flux between Gram-negative Enterobacteriaceae. However, the mechanisms fostering intraenterobacterial HGT are incompletely understood. Using a mouse colitis model, we found that Salmonella-inflicted enteropathy elicits parallel blooms of the pathogen and of resident commensal Escherichia coli. These blooms boosted conjugative HGT of the colicin-plasmid p2 from Salmonella enterica serovar Typhimurium to E. coli. Transconjugation efficiencies of ∼100% in vivo were attributable to high intrinsic p2-transfer rates. Plasmid-encoded fitness benefits contributed little. Under normal conditions, HGT was blocked by the commensal microbiota inhibiting contact-dependent conjugation between Enterobacteriaceae. Our data show that pathogen-driven inflammatory responses in the gut can generate transient enterobacterial blooms in which conjugative transfer occurs at unprecedented rates. These blooms may favor reassortment of plasmid-encoded genes between pathogens and commensals fostering the spread of fitness-, virulence-, and antibiotic-resistance determinants.bacterial evolution | hospital-acquired infection | mucosal immune response | plasmid spread

show abstract

“…The sequence coverage of the de novo assemblies was on average over 100, with a minimum (for some 454-sequenced plasmids) of 60 sequence reads of coverage per assembled base. High-coverage scaffolds of the genomes were reconstructed by scaffolding the contigs against the closely related IncI1 reference R64 (15). Putative open reading frames (ORFs) were identified by GeneMarkHMMp version 2.6p (24).…”

Section: Methodsmentioning

confidence: 99%

“…Complete nucleotide sequences of a number of IncI1-I␥ plasmids are available in the GenBank database. All IncI1-I␥ plasmids characterized contained a set of highly conserved core genes involved in essential functions, such as replication, maintenance, stability, and transfer as well as some unique accessory elements (15).…”

mentioning

confidence: 99%

Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans

Smith

Bossers

Harders

et al. 2015

Antimicrob Agents Chemother

View full text Add to dashboard Cite

The aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-I␥ plasmids obtained from Escherichia coli and Salmonella enterica isolates from animal and human reservoirs. For this, 251 IncI1-I␥ plasmids carrying various extended-spectrum ␤-lactamase (ESBL) or AmpC ␤-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-I␥ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation in traY and excA genes found in IncI1-I␥ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology.

show abstract

Complete genome sequence of the incompatibility group I1 plasmid R64

Cited by 94 publications

References 58 publications

The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment

The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans

Contact Info

Product

Resources

About