Replication and Control of Circular Bacterial Plasmids

G del Solar

R Giraldo

María Ruiz-Echevarría

M Espinosa

Ramón Díaz-Orejas

Centro de Investigaciones Biológicas, CSIC, E-28006 Madrid, Spain

^{Corresponding author. Mailing address: Centro de Investigaciones Biológicas, C.S.I.C., Velázquez 144, E-28006 Madrid, Spain. Phone: 34-91-5611800. Fax: 34-91-5627518. E-mail:}se.cisc.onserf.@391dbic.

Abstract

An essential feature of bacterial plasmids is their ability to replicate as autonomous genetic elements in a controlled way within the host. Therefore, they can be used to explore the mechanisms involved in DNA replication and to analyze the different strategies that couple DNA replication to other critical events in the cell cycle. In this review, we focus on replication and its control in circular plasmids. Plasmid replication can be conveniently divided into three stages: initiation, elongation, and termination. The inability of DNA polymerases to initiate de novo replication makes necessary the independent generation of a primer. This is solved, in circular plasmids, by two main strategies: (i) opening of the strands followed by RNA priming (theta and strand displacement replication) or (ii) cleavage of one of the DNA strands to generate a 3′-OH end (rolling-circle replication). Initiation is catalyzed most frequently by one or a few plasmid-encoded initiation proteins that recognize plasmid-specific DNA sequences and determine the point from which replication starts (the origin of replication). In some cases, these proteins also participate directly in the generation of the primer. These initiators can also play the role of pilot proteins that guide the assembly of the host replisome at the plasmid origin. Elongation of plasmid replication is carried out basically by DNA polymerase III holoenzyme (and, in some cases, by DNA polymerase I at an early stage), with the participation of other host proteins that form the replisome. Termination of replication has specific requirements and implications for reinitiation, studies of which have started. The initiation stage plays an additional role: it is the stage at which mechanisms controlling replication operate. The objective of this control is to maintain a fixed concentration of plasmid molecules in a growing bacterial population (duplication of the plasmid pool paced with duplication of the bacterial population). The molecules involved directly in this control can be (i) RNA (antisense RNA), (ii) DNA sequences (iterons), or (iii) antisense RNA and proteins acting in concert. The control elements maintain an average frequency of one plasmid replication per plasmid copy per cell cycle and can “sense” and correct deviations from this average. Most of the current knowledge on plasmid replication and its control is based on the results of analyses performed with pure cultures under steady-state growth conditions. This knowledge sets important parameters needed to understand the maintenance of these genetic elements in mixed populations and under environmental conditions.

Abstract

Plasmids are extrachromosomal DNA elements with characteristic copy numbers within the host. These replicons have been found in species from the three representatives of the living world, namely, the domains Archaea, Bacteria, and Eukarya (318). Plasmids may constitute a substantial amount of the total genetic content of an organism, representing more than 25% of the genetic material of the cell in some members of the Archaea (127, 331). They can incorporate and deliver genes by recombination or transposition, thus favoring genetic exchanges in bacterial populations. Since plasmids can be introduced into new hosts by a variety of mechanisms, they can be considered to be a pool of extrachromosomal DNA which is shared among populations. The wealth of genetic information carried by plasmids, their impact in the microbial communities, and the potential of these elements to act as natural cloning vectors have stimulated research into plasmids not only from the fundamental but also from the clinical, biotechnological, and environmental points of view. Three main factors have contributed to the development of plasmid research: (i) the genetic organization of these elements is apparently simple, (ii) they can be easily isolated and manipulated in vitro, and (iii) since plasmids are dispensable, their manipulation does not appear, in principle, to have adverse consequences to the hosts.

The feature that better defines plasmids is that they replicate in an autonomous and self-controlled way. The analysis of plasmid replication and its control has led to milestone discoveries, such as the existence of antisense RNAs, and has contributed to the unraveling of mechanisms of DNA replication, macromolecular interactions, and control of gene expression. The ability of some plasmids to pass across the so-called genetic barriers among different living organisms has posed questions about general mechanisms governing replication and about the communication between plasmid replication components and the host machinery involved in DNA replication. This plasmid-host communication has attracted the attention of researchers working in environmental and in evolutionary fields. Plasmid host range studies also have clear implications in clinical microbiology and in biotechnology. Despite their autonomous replication, plasmids extensively use the replication machinery of the host, and therefore plasmid replication studies facilitate the exploration of the mechanisms involved in chromosome replication.

ACKNOWLEDGMENTS

We are indebted to Deepak Bastia, Dhruba Chattoraj, Don Helinski, and Martine Couturier for critical reading of the manuscript and many useful comments and to Saleem Khan for many interesting discussions. We thank all the colleagues who provided us with unpublished information, and we apologize to those colleagues who feel that their work is insufficiently cited. Thanks are due also to our past and present collaborators.

During the writing of this review, our labs were financed by Comisión Interministerial de Ciencia y Tecnología, grants PB94-0127 and PB96-0917 (to R.D.) and grant BIO97-0347 (to M.E.).

ACKNOWLEDGMENTS

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