Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem–loop structure

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Abstract
The repABC replicons contain an operon encoding the initiator protein (RepC) and partitioning proteins (RepA and RepB). The latter two proteins negatively regulate the transcription of the operon. In this article we have identified two novel regulatory elements, located within the conserved repB–repC intergenic sequence, which negatively modulate the expression of repC, in plasmid p42d of Rhizobium etli. One of them is a small antisense RNA and the other is a stem–loop structure in the repABC mRNA that occludes the Shine-Dalgarno sequence of repC. According to in vivo and in vitro analyses, the small antisense RNA (57–59 nt) resembles canonical negative regulators of replication because: (i) it is transcribed from a strong constitutive promoter (P2), (ii) the transcript overlaps untranslated region upstream of the RepC coding sequences, (iii) the RNA forms one secondary structure acting as a rho-independent terminator, (iv) the antisense RNA is a strong trans-incompatibility factor and (v) its presence reduces the level of repC expression. Surprisingly, both of these seemingly negative regulators are required for efficient plasmid replication.