Bacterial antisense RNAs: how many are there, and what are they doing?

Abstract

Antisense RNAs encoded on the DNA strand opposite another gene have the potential to form extensive base-pairing interactions with the corresponding sense RNA. Unlike other smaller regulatory RNAs in bacteria, antisense RNAs range in size from tens to thousands of nucleotides. The numbers of antisense RNAs reported for different bacteria vary extensively, but hundreds have been suggested in some species. If all of these reported antisense RNAs are expressed at levels sufficient to regulate the genes encoded opposite them, antisense RNAs could significantly impact gene expression in bacteria. Here, we review the evidence for these RNA regulators and describe what is known about the functions and mechanisms of action for some of these RNAs. Important considerations for future research as well as potential applications are also discussed.

Figure 1

Length and overlap of selected antisense RNAs with their sense transcripts. (A) RNAs antisense to transposase and toxic protein mRNAs. The ~85 nucleotide antisense RNA STnc490 of S. enterica completely overlaps the 5′-end of the IS200 transposase mRNA tnpA-1 (96), while the ~84 nucleotide CC2739-CC2740 antisense RNA of C. crescentus overlaps the IS1111A transposase mRNA CC2740 by 32 nucleotides at the 5′-end (52). In E. coli, the 77 nucleotide SymR antisense RNA completely overlaps the 5′-end of the mRNA for the SymE toxin (41). (B) RNAs antisense to mRNAs encoding transcription regulators. The 109 nucleotide GadY antisense RNA of E. coli overlaps the intergenic region of the dicistronic gadXW mRNA which encodes two transcription regulators (69, 108). The long ~2,200 nucleotide alr1690-α-furA antisense RNA of Anabaena encompasses the entire alr1690 coding region and extends through the gene encoding the FurA transcriptional regulator into its promoter and regulator regions (33). The ~131 nucleotide ArnA transcript of C. glutamicum overlaps ~ 99 nucleotides at 5′-end of the cg1935 mRNA encoding a putative transcription regulator (122). (C) RNAs antisense to genes encoding metabolic and virulence proteins. The ~177 nucleotide IsrR antisense RNA of Synechocystis overlaps the central portion of the isiA gene, which encodes a protein important under conditions of iron deficiency (13). A series of four antisense S-box RNAs ranging in length from 264 to 1,000 nucleotides in C acetobutylicum are transcribed from a promoter located downstream in the opposite orientation from the ubiG-mccBA operon encoding proteins important for SAM recycling. These S-box antisense transcripts can overlap the mccA gene by ~700 nucleotides (2). The ~1,200 nucleotide AmgR antisense RNA of S. enterica overlaps the entire first gene of the mgtCBR operon extending ~360 nucleotides into the mgtC 5′ UTR and promoter region (53). Sense RNAs are dark blue and antisense RNAs are light blue. The protein-coding regions of both classes of RNAs are indicated by thicker lines.

Figure 2

Mechanisms by which antisense RNAs act. Antisense RNAs can induce transcription interference (A), where transcription from one promoter blocks transcription from a second promoter by preventing RNA polymerase from either binding or extending a transcript encoded on the opposite strand. Transcription interference does not involve basepairing and does not occur when the antisense RNA is provided in trans. In transcription attenuation (B), base pairing of the antisense RNA to the target RNA causes changes in the target RNA structure ultimately affecting transcription termination. Antisense RNAs can also affect target RNA degradation by endonucleases (C) and exonucleases (D). In these cases, base pairing between the sense and antisense RNAs can directly either generate or block a ribonuclease target site. Antisense RNAs can also indirectly affect the binding of the ribonuclease at a distance from the site of base pairing. Finally, antisense RNAs can directly block ribosome binding (E) or indirectly positively or negatively impact ribosome binding by affecting the target mRNA structure (F). The sense RNAs are indicated in dark blue while the antisense RNA are shown in light blue.