Comparative analysis of the replicon regions of eleven ColE2-related plasmids

Hiraga, Shin‐ichiro; Sugiyama, Tomohiko; Itoh, Tateo

doi:10.1128/jb.176.23.7233-7243.1994

Cited by 66 publications

(77 citation statements)

References 77 publications

(66 reference statements)

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“…The second determinant (IncB) was contained in a 2 kb EcoRI-PstI fragment that spans the minimal fragment with capacity to replicate. In ColE2-related plasmids, the incompatibility displayed by the minimal replicating fragment was due to either the origin of replication, a sequence of around 30 bp, or to a small regulatory antisense RNA (Hiraga et al, 1994). In this case, we were unable to locate IncB more precisely since pAori31 only showed a partial incompatibility, whilst pAoril9 did not lead to the curing of pPT23A in any of the eight transformants analysed.…”

Section: Identification Of Two Putative Maintenance Determinants In Tmentioning

confidence: 79%

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Replication regions from plant-pathogenic Pseudomonas syringae plasmids are similar to ColE2-related replicons

et al. 1999

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Many strains of the phytopathogen Pseudomonas syringae contain mutually compatible plasmids that share extensive regions of sequence homology and essential replication determinants. The replication regions of two compatible large plasmids involved in virulence or pathogenicity, pPT23A from P. syringae pv. tomato strain PT23 and pAV505 from P. syringae pv. phaseolicola strain HR11302A, were isolated. DNA sequencing of the origins of replication revealed homologous ORFs, designated ORF-Pto and ORF-Pph, respectively. Both ORFs are 1311 bp long and encode peptides of 437 amino acids with predicted molecular masses of 48259 (Pto) and 48334 (Pph) Da. Expression of the two ORFs in Escherichia coli produced peptides of 50 kDa (Pto) and 56 kDa (Pph). The predicted peptides showed an overall identity of 897 %, being highly conserved from residues 1 to 373, but showing considerable variation in their C-terminal regions (50% identity over the last 64 aa). The two ORFs had significant similarity with the putative replication protein from plasmid pTiKl2 of Thiobacillus intermedius and other ColE2-related plasmids. However, both peptides were 100 residues longer than any of the known ColE2-related rep sequences. Subcloning of fragments from the replication region of pPT23A revealed the presence of a t least three incompatibility determinants, designated IncA, lncB and IncC. Partial sequencing of the region downstream of ORF-Pto revealed homology to the rulAB genes, involved in UV resistance, from plasmid pPSR1. It is proposed that the replication origin of pPT23A serves as the prototype of a family of related plasmids.

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Section: Identification Of Two Putative Maintenance Determinants In Tmentioning

confidence: 79%

“…phaseolicola HRll302A; ColE2-P9 from Shigella sp. and ColE3-CA38 from E. coli (Hiraga et a/., 1994); pAL5000 from Mycobacterium fortuitum (Rauzier et a/., 1988); pRBLl (Ankri e t a/., 1996) and pBL-A8 (V. Leret, accession no. Y 1 1902) from Brevibacterium linens.…”

Section: Orf-pto and Orf-pph Are Similar To Other Replication Proteinsmentioning

confidence: 99%

Replication regions from plant-pathogenic Pseudomonas syringae plasmids are similar to ColE2-related replicons

et al. 1999

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“…Furthermore, some conservation of this loop sequence is seen across a range of other antisense-controlled replicons. This is most notable in ColE2 replicons (CCGCCAA), but also to some extent in the RNA I molecules of ColE1 (CUACCAA) and pT181 (UGACCAA) (Hiraga et al, 1994), suggesting that this sequence and consequently the replication control regions themselves may have a common evolutionary origin.…”

Section: Discussionmentioning

confidence: 95%

“…Chi-related sequences have been similarly implicated in recombination events in the formation of mosaic RepFIB-related repA genes in plasmids from natural populations of E. coli (Boyd et al, 1996). Mosaic regions have also been identified in the ColE2 family of antisense-control-regulated replicons, with one breakpoint between segments again found between the inc and rep regions (Hiraga et al, 1994). However, no Chi sites could be identified in this region, excluding the possibility of Chi-mediated hom- The existence of mosaic replicons causes additional complications for the classification of bacterial plasmids and for attempts to assess the evolutionary relationships between plasmids and their replicons.…”

Section: Discussionmentioning

confidence: 99%

Mosaic plasmids and mosaic replicons: evolutionary lessons from the analysis of genetic diversity in IncFII-related replicons The EMBL accession numbers for the sequences reported in this paper are AJ009980 (pGSH500 alpha replicon) and AJ009981 (pLV1402 alpha replicon).

et al. 2000

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The alpha replicons of the multi-replicon plasmids pGSH500 and pLV1402 have been characterized by DNA sequence analysis. Analysis of the DNA sequence of a 3672 bp HindIII fragment from pFDT100, which contains the pGSH500 alpha replicon, revealed similarity to a number of replicons belonging to, or related to, those of the IncFII family. The replicon region contains copA, tapA, repA and oriR, and replication initiation and termination sites are related to those from the IncFII replicon of R1. A copB gene was found to lie upstream of the HindIII site in the parental plasmid pGSH500. Downstream of oriR, a 707 bp region shows 726 % identity to a region of the Escherichia coli chromosome at 433', suggesting this region of pGSH500 may have been incorporated into the plasmid during a past chromosomal recombination event. Oligonucleotide primers homologous to consensus regions in the copB and repA genes, and the oriR regions from a number of IncFII-related replicons were used to amplify replication regions from pLV1402. Analysis of the amplified regions has shown the presence of copB, copA, tapA and repA genes. Phylogenetic analysis of Rep protein sequences from the RepFIIA family of antisense-control-regulated replicons revealed the presence of three distinct subgroups of Rep proteins. Comparative analysis of DNA and protein sequences from members of the RepFIIA family provides evidence supporting the roles of both non-selective divergence in co-integrate (multi-replicon) plasmids and Chi-mediatedrecombination in replicon evolution, and in particular, that such processes may have been widespread in the evolution of the RepFIIA family.

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“…This type of regulation involving the A component is frequently found in the soplpar partitioning systems (Williams & Thomas, 1992;Hiraga, 1992). plasmids is included (Hiraga et a/., 1994) and the primer RNA (5' ppApGpA) for leading strand synthesis (arrow) is marked (***) . Positions where the 15 bp consensus sequence matches the ColE2 ori sequence are marked (+).…”

Section: P I E L E a Y S I Q G I K K M V T T I A Q -K N A K L Q F L Gmentioning

confidence: 99%

Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors

et al. 1997

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The complete nucleotide sequence of the 5936 bp cryptic plasmid pFAJ2600 from Rhodococcus erythropolis N186/21 was determined. Based on the characteristics of its putative replication genes, mpA and mpB, pFAJ2600 was assigned to the family of pAL50OO-relatd small replicons identified in Mycobacterium (pAL5000), CorynebaCterium (pXZ10142), Brevibacterium (pRBLI), Bifidobacterium (pMB1) and Neisseria (pJD1). The replication systems of these plasmids show striking similarities to the ones used by the ColE2 family of plasmids from Enterobacteria with respect to both trans-acting factors and ori sequences. Two possible plasmid stabilization systems are encoded on pFAJ2600: a site-specific recombinase (PmrA) related to the Escherichia coli Xer proteins for plasmid multimer resolution and an ATPase (ParA) related to the A-type of proteins in soplpar partitioning systems. The proposed replication termination region of pFAJ2600 has features in common with the Ter loci of Bacillus subtilis. Chimeras composed of a pUC18-Cmr derivative inserted in the parA-repA intergenic region of vector pFAJ2600 produced vectors that could be shuttled between Escherichia coli and several Rhodococcus species (R. erythropolis, R. fascians, R. rhodochrous, R. fuber). The pFAJ2600-based shuttle vector pFAJ2574 was stably maintained in R. erythropolis and R. fascians growing under nonlrelective conditions. Department Of

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Comparative analysis of the replicon regions of eleven ColE2-related plasmids

Abstract: The incA gene product of ColE2-P9 and ColE3-CA38 plasmids is an antisense RNA that regulates the production of the plasmid-coded Rep

Cited by 66 publications

References 77 publications

Replication regions from plant-pathogenic Pseudomonas syringae plasmids are similar to ColE2-related replicons

Replication regions from plant-pathogenic Pseudomonas syringae plasmids are similar to ColE2-related replicons

Mosaic plasmids and mosaic replicons: evolutionary lessons from the analysis of genetic diversity in IncFII-related replicons The EMBL accession numbers for the sequences reported in this paper are AJ009980 (pGSH500 alpha replicon) and AJ009981 (pLV1402 alpha replicon).

Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors

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