Identification of a megaplasmid centromere reveals genetic structural diversity within the repABC family of basic replicons.
The basic replication unit of many plasmids and second chromosomes in the alpha-proteobacteria consists of a repABC locus that encodes the trans- and cis-acting components required for both semiautonomous replication and replicon maintenance in a cell population. In terms of physical genetic organization and at the nucleotide sequence level, repABC loci are well conserved across various genera. As with all repABC-type replicons that have been genetically characterized, the 1.4 Mb pSymA and 1.7 Mb pSymB megaplasmids from the plant endosymbiont Sinorhizobium meliloti encode strong incompatibility (inc) determinants. We have identified a novel inc sequence upstream of the repA2 gene in pSymA that is not present on pSymB and not reported in other repABC plasmids that have been characterized. This region, in concert with the repA and repB genes, stabilizes a test plasmid indicating that it constitutes a partitioning (par) system for the megaplasmid. Purified RepB binds to this sequence and binding may be enhanced by RepA. We have isolated 19 point mutations that eliminate incompatibility, reduce RepB binding or the stabilization phenotype associated with this sequence and all of these map to a 16-nucleotide palindromic sequence centred 330 bp upstream of the repA2 gene. An additional five near-perfect repeats of this palindrome are located further upstream of the repA2 gene and we show that they share some conservation with known RepB binding sites in different locations on other repABC plasmids and to two sequences found on the tumour inducing plasmid of Agrobacterium tumefaciens. These additional palindromes also bind RepB but one of them does not display obvious incompatibility effects. A heterogenic distribution of par sequences demonstrates unexpected diversity in the structural genetic organization of repABC loci, despite their obvious levels of similarity.
MacLellan
Shawn R
SR
Centre for Environmental Genomics, Department of Biology, McMaster University, Hamilton, Ontario, Canada.
Zaheer
Rahat
R
Sartor
Andrea L
AL
MacLean
Allyson M
AM
Finan
Turlough M
TM
D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D002503:Centromere / Q000235:genetics*; D004265:DNA Helicases / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D014644:Genetic Variation; D010957:Plasmids / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012093:Replicon / Q000235:genetics*; D016962:Sinorhizobium meliloti / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C048817:RepB protein, Bacteria; C043650:RepC protein, Staphylococcus aureus; D015534:Trans-Activators; C045264:replication initiator protein; D004265:DNA Helicases