The repABC plasmid family

Abstract

repABC plasmids are widely distributed among α-proteobacteria. They are especially common in Rhizobiales. Some strains of this bacterial order can contain multiple repABC replicons indicating that this plasmid family includes several incompatibility groups. The replication and stable maintenance of these replicons depend on the presence of a repABC operon. The repABC operons sequenced to date share some general characteristics. All of them contain at least three protein-encoding genes: repA, repB and repC. The first two genes encode proteins involved in plasmid segregation, whereas repC encodes a protein crucial for replication. The origin of replication maps within the repC gene. In contrast, the centromere-like sequence (parS) can be located at various positions in the operon. In this review we will summarize current knowledge about this plasmid family, with special emphasis on their structural diversity and their complex genetic regulation. Finally, we will examine some ideas about their evolutionary origin and trends.

Introduction

Bacteria belonging to Agrobacterium or Rhizobium genera can establish close relationships with plants. The consequences of such interactions are very diverse: most Agrobacterium species are plant–pathogens, whereas members of the genus Rhizobium are nitrogen-fixing legume symbionts. In the late 1960s and early 1970s it became clear that Agrobacterium and Rhizobium possess large plasmids of low copy-number and that most of the genes involved in plant–microbe interaction were carried on such plasmids (Higashi, 1967, Escobar and Dandekar, 2003).

The first molecular description of the replication and partitioning of one of these plasmids was a paper by Nishiguchi and co-workers in 1987; they reported the locus responsible for the replication and stable maintenance of pRiA4b, a plasmid in Agrobacterium rhizogenes A4. This locus consists of an operon of three genes: repA is the first gene to be transcribed and repC the last. Similar operons have subsequently been found in many plasmids and secondary chromosomes in at least 19 α-proteobacteria genera (Table 1). Interestingly, some bacterial strains contain several plasmids, each carrying one repABC operon. Moreover, replicons harboring two functional repABC operons have also been found. The most evident cases of this peculiarity are in Rhizobium etli CFN42 and Rhizobium leguminosarum 3841, each of which has six plasmids all belonging to the repABC family. Two replicons in R. etli CFN42 and one in R. leguminosarum 3841 contain two repABC operons. This suggests, different repABC plasmids belong to different incompatibility groups (Young et al., 2006, González et al., 2006).

The repABC operons have several characteristics in common: the three genes are always in the same relative order: repA is upstream from repB, with repC as the downstream gene of the operon. The large intergenic sequence between repB and repC genes contains a gene encoding a small antisense RNA. RepA and RepB have sequence similarities with proteins involved in active segregation of plasmids and chromosomes, and RepC is a replication initiator protein (Bartosik et al., 1998, Ramirez-Romero et al., 2001, Pappas and Winans, 2003b). The small RNA, as we will show, plays an essential role in the control of plasmid replication (Venkova-Canova et al., 2004, Chai and Winans, 2005a, MacLellan et al., 2005). In addition to sequence diversity among repABC operons, there are other differences. Some possess elements not found in any other repABC operons or in only a few members of the family. These differences can be broadly classified into three categories: (i) differences involving transcriptional regulatory elements, (ii) differences related to the number and position of par-sites (centromere-like sequences, formally parS), and (iii) the presence of peptide-encoding minigenes within the repABC operon (Fig. 1).

In this paper, only replicons containing a repABC operon will be considered to belong to the repABC plasmid family. This review addresses only repABC replication-partitioning systems and not the gene content of the members of this plasmid family. We will discuss current knowledge about the elements constituting the replication-partitioning system of this plasmid family. We will consider, specifically, their complex genetic regulation, and then the origin and evolution of this family of plasmids.