Cis-encoded antisense RNAs (asRNAs) are regulatory non-coding transcripts encoded at the same locus of their target gene, but on the opposite DNA strand. The short asRNAs transcripts have a perfect complementarity with the cis-encoded mRNA molecules and use base-pairing to modulate the stability and/or the translational rate of the target mRNA.
In bacteria, asRNAs play a key role in the control of the biological functions of diverse mobile genetic elements, such as plasmids, transposons and bacteriophages. In the temperate phage λ of Escherichia coli, the OOP asRNA is encoded on the opposite strand of the cII gene and overlaps with the 3’ end of the cII mRNA coding sequence. OOP interacts by base-pairing to facilitate the degradation of the λ CII-repressor mRNA and reduce the level of the CII protein, which is pivotal regulator of the “lysis vs. lysogeny” decision of λ in E. coli.
In the enteropathogenic bacterium Salmonella Typhimurium strain 4/74, we used RNA-seq technology to reveal the high expression of STnc1390, an asRNA encoded within the Gifsy-1 lambdoid prophage. Similarly to OOP, STnc1390 is encoded tail-to-tail to cII and head-to-head to gpO, which encodes for the Gifsy-1 O replication protein. Unlike OOP, the STnc1390 antisense transcription does not overlap with the 3’ coding region of the cII mRNA, suggesting that the asRNA performs a different role in the biology of Gifsy-1.
In our study, we examined the role of STnc1390 during the infection of Salmonella by Gifsy-1 and discovered that over-expression of this asRNA in naive bacteria prevents the proliferation of the phage. The role of STnc1390 in the control of the Gifsy-1 phage replication and in the control of the synthesis of the O replication protein will be discussed.