R391: a Conjugative Integrating Mosaic Comprised of Phage, Plasmid, and Transposon Elements

Abstract

The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.Horizontal gene transfer, the intraspecies and interspecies exchange of genetic information, plays an important role in the evolution of bacteria (10,24,26,39,65). Three major mechanisms, transformation, transduction, and conjugation (9), provide bacterial populations with access to a "horizontal gene pool," enabling them to rapidly respond to environmental challenges (16, 34).The most important contributor to horizontal gene transfer is the heterogeneous group of mobile genetic elements that includes plasmids, insertion (IS) elements, transposons, integrons, phages, and genomic islands (10, 17). They are "selfish" elements that promote their own maintenance and distribution and, in addition, can function as vectors for accessory DNA elements. These accessory elements commonly consist of genes that are nonessential for survival but confer a phenotype, which is advantageous under particular environmental conditions. Prominent examples of such traits are antibiotic and heavy metal resistances, degradation of xenobiotic compounds, symbiosis and virulence determinants, resistance to radiation, and increased mutation frequency (15).A group of related conjugative DNA elements has been identified as carriers of antibiotic resistance genes in members of the ␥-Proteobacteria from dispersed global locations. R391, the archetype of this group, was originally detected in a South African Providencia rettgeri isolate (8); for many years, it was believed to be a plasmid and was assigned to a new incompatibility group, IncJ. Subsequently, other IncJ elements, conferring the same phenotype as that conferred by R391 (19, 20) (32), and Shewanella putrefaciens (pMERPH; mercury resistance) from the United Kingdom (48). Previous studies have exa...

Identification of the Origin of Transfer (oriT) and a New Gene Required for Mobilization of the SXT/R391 Family of Integrating Conjugative Elements

“…piscicida (AJ870986). orf35 and orf1755 code for hypothetical proteins of unknown functions (6,40). Our analysis did not reveal any domain or molecular arrangement typical of oriTs in VchoM_02001241, orf35, orf1755, or the hypothetical ORF in ICEPdaSpa1.…”

“…Beaber et al (4) mapped the oriT locus of SXT MO10 (oriT SXT ) to a 550-bp intergenic region between traD and traJ. While no open reading frame (ORF) between traD and traJ in SXT MO10 has been annotated (4), orf35, a putative ORF that encodes a protein of unknown function, has been annotated to occur at the same locus in R391, with no evidence for the presence of an oriT locus (6). The presence of an ORF in this region of R391 led us to question whether oriT SXT had been properly assigned.…”

“…R391 is an ICE derived from a clinical isolate of Providencia rettgeri from South Africa (16), conferring kanamycin and mercury resistance (41). Both genetic studies and DNA sequence analyses revealed that R391 and SXT MO10 are functionally and genetically related (4,6,26). They share a highly conserved genetic backbone, coding for their regulation, excision/integration, and conjugative transfer (3).…”

An inducible tellurite-resistance operon in Proteus mirabilis

“…Furthermore, the ter operon was not located on large IncJ or IncT plasmids found in some strains of P. vulgaris and Providencia spp. (Boltner et al, 2002;Murata et al, 2002). A phylogenetic analysis of Te r proteins suggests a rather recent dissemination among the enteric bacteria, most likely accelerated by transmissible plasmids (Taylor et al, 2002).…”

Genetic and Structural Analysis of the Bacteroides Conjugative Transposon CTn341

“…For example, in gram-positive organisms Tn916 encodes tetracycline resistance and Tn1546 carries vancomycin resistance determinants (9). In gram-negative bacteria there is the IncJ family of integrating elements and the related element SXT that carry resistance to multiple antibiotics in enteric organisms and Vibrio cholerae (3,6).…”