Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication

Ruiz-Masó, José A.; Espinosa, Manuel; Solar, Gloria del

doi:10.1093/nar/gkl1099

Cited by 35 publications

(43 citation statements)

References 45 publications

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“…RepB specifically recognizes its cognate origin by binding to the bind locus of the pMV158 dso (del Solar et al , 1993). The bind locus consists of a triple 11‐bp direct repeat and can be assumed to be a B‐DNA duplex that severely bends on binding of RepB (Ruiz‐Masó et al , 2007). Our studies show that RepB 6 binds to a single dsDNA containing the triple direct repeat (Figure 5B and C) and that RepB 1 , RepB 2 and RepB 6 are the predominant species in vivo (Supplementary Figure S3).…”

Section: Discussionmentioning

confidence: 99%

Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

Boer

Ruiz-Masó

López‐Blanco

et al. 2009

EMBO J

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RepB initiates plasmid rolling-circle replication by binding to a triple 11-bp direct repeat (bind locus) and cleaving the DNA at a specific distant site located in a hairpin loop within the nic locus of the origin. The structure of native full-length RepB reveals a hexameric ring molecule, where each protomer has two domains. The origin-binding and catalytic domains show a three-layer a-b-a sandwich fold. The active site is positioned at one of the faces of the b-sheet and coordinates a Mn 2 þ ion at short distance from the essential nucleophilic Y99. The oligomerization domains (ODs), each consisting of four a-helices, together define a compact ring with a central channel, a feature found in ring helicases. The toroidal arrangement of RepB suggests that, similar to ring helicases, it encircles one of the DNA strands during replication to confer processivity to the replisome complex. The catalytic domains appear to be highly mobile with respect to ODs. This mobility may account for the adaptation of the protein to two distinct DNA recognition sites.

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Section: Discussionmentioning

confidence: 99%

Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

Boer

Ruiz-Masó

López‐Blanco

et al. 2009

EMBO J

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“…Proteins having a Rep-3 domain also perform strand-transfer reactions generally seen during rolling circle (RC) replication (Moscoso et al 1995; Ruiz-Maso et al 2007). RC replication is also seen during horizontal transfer of indigenous plasmids.…”

Section: Resultsmentioning

confidence: 99%

Multiple Mechanisms Contribute to Lateral Transfer of an Organophosphate Degradation (opd) Island in Sphingobium fuliginis ATCC 27551

Paul

Longkumer

Chakka

et al. 2012

G3 Genes|Genomes|Genetics

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The complete sequence of pPDL2 (37,317 bp), an indigenous plasmid of Sphingobium fuliginis ATCC 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attP, typically seen in integrative mobilizable elements (IME). In agreement with this sequence information, site-specific recombination was observed between pPDL2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attB site at the 3′ end of the seryl tRNA gene of Sphingobium japonicum. The opd gene cluster on pPDL2 was found to be part of an active catabolic transposon with mobile elements y4qE and Tn3 at its flanking ends. Besides the previously reported opd cluster, this transposon contains genes coding for protocatechuate dioxygenase and for two transport proteins from the major facilitator family that are predicted to be involved in transport and metabolism of aromatic compounds. A pPDL2 derivative, pPDL2-K, was horizontally transferred into Escherichia coli and Acinetobacter strains, suggesting that the oriT identified in pPDL2 is functional. A well-defined replicative origin (oriV), repA was identified along with a plasmid addiction module relB/relE that would support stable maintenance of pPDL2 in Sphingobium fuliginis ATCC 27551. However, if pPDL2 is laterally transferred into hosts that do not support its replication, the opd cluster appears to integrate into the host chromosome, either through transposition or through site-specific integration. The data presented in this study help to explain the existence of identical opd genes among soil bacteria.

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“…This seems to be the case in pMV158, where the extrusion frequency of the cruciform involving IR-I is very low at the growth temperature of the plasmid host (37°C) (69). In vitro footprinting experiments performed with supercoiled pMV158 DNA showed that binding of RepB to the nic locus promotes the extrusion of the IR-I cruciform, which in turn indicates that initiation of replication would take place only when specific binding of RepB occurs (64). Genetic analysis of the pC194 dso pointed to the existence of a hairpin located downstream of the nick site (70) that was shown to be important for replication of the plasmid (71).…”

Section: The Double-strand Originmentioning

confidence: 97%

“…Interestingly, the existence of distant DRs has not been elucidated in some plasmids of this subfamily (unpublished observation). The role of the different regions of the pMV158-dso in the interaction with the plasmid-encoded RepB initiator protein has been addressed in a systematic study (35,(61)(62)(63)(64). RepB binds with high affinity to the bind locus, which is made up of three 11-bp tandem DRs located 84 bp downstream from the nick site.…”

Section: The Double-strand Originmentioning

confidence: 99%

“…A second RepB binding site is located in a region around the nick site, within the nic locus. Characterization of the relative affinity of RepB for the bind and nic loci revealed that the three DRs of the bind locus constitute the primary binding site, whereas the weaker binding of RepB to the nic locus could be involved in recognition of the nick site during initiation of replication (64). In plasmids of the pT181 and pC194 families, the DNA sequences of the bind (IRIII) and nic (IRII) loci are located in contiguous inverted repeats (IR) (Fig.…”

Section: The Double-strand Originmentioning

confidence: 99%

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Plasmid Rolling-Circle Replication

et al. 2015

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Plasmids are DNA entities that undergo controlled replication independent of the chromosomal DNA, a crucial step that guarantees the prevalence of the plasmid in its host. DNA replication has to cope with the incapacity of the DNA polymerases to start de novo DNA synthesis, and different replication mechanisms offer diverse solutions to this problem. Rolling-circle replication (RCR) is a mechanism adopted by certain plasmids, among other genetic elements, that represents one of the simplest initiation strategies, that is, the nicking by a replication initiator protein on one parental strand to generate the primer for leading-strand initiation and a single priming site for lagging-strand synthesis. All RCR plasmid genomes consist of a number of basic elements: leading strand initiation and control, lagging strand origin, phenotypic determinants, and mobilization, generally in that order of frequency. RCR has been mainly characterized in Gram-positive bacterial plasmids, although it has also been described in Gram-negative bacterial or archaeal plasmids. Here we aim to provide an overview of the RCR plasmids' lifestyle, with emphasis on their characteristic traits, promiscuity, stability, utility as vectors, etc. While RCR is one of the best-characterized plasmid replication mechanisms, there are still many questions left unanswered, which will be pointed out along the way in this review.

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Interactions between the RepB initiator protein of plasmid pMV158 and two distant DNA regions within the origin of replication

Cited by 35 publications

References 45 publications

Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

Multiple Mechanisms Contribute to Lateral Transfer of an Organophosphate Degradation (opd) Island in Sphingobium fuliginis ATCC 27551

Plasmid Rolling-Circle Replication

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