Question

“Antisense RNA molecules serve a wide range of regulatory functions in bacteria”. Discuss. Illustrate your answer with specific examples of bacterial cell antisense RNA mechanism

Answer 1

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.

In 1981, Tomizawa and colleagues showed that the ~108 nucleotide RNAI RNA controls the copy number of plasmid ColE1 by preventing RNAII processing to generate replication primers (105, 106). That same year, Nordström and colleagues identified the ~90 nucleotide CopA RNA, which controls the copy number of plasmid R1 by regulating the translation of the RepA replication initiator protein (99). A few years later, the 70 nucleotide RNA-OUT of the transposon Tn10 was found to affect transposition by repressing transposase synthesis (95). In addition, the ~ 70 nucleotide Sar RNA of bacteriophage P22

Annual review of genetics
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Bacterial antisense RNAs: How many are there and what are they doing?
Maureen Kiley Thomason and Gisela Storz

Additional article information

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.

Keywords: small RNA, gene regulation, transcription interference, mRNA stability
INTRODUCTION
In the past ten years there has been an explosion in the identification of small, regulatory RNAs (sRNAs) encoded on bacterial chromosomes. While some of these regulatory RNAs act by binding to and modulating protein activity, the majority of characterized sRNAs act by base pairing with target mRNAs. These base pairing sRNAs fall into two categories: trans-encoded and cis-encoded. The trans-encoded sRNAs are encoded at genomic locations distant from the mRNAs they regulate, and thus generally only share limited complimentarity with their targets. In part due to the ability to act via limited complimentary, many of these trans-encoded sRNAs have multiple mRNA targets. In a number of bacteria, this type of base pairing requires the RNA chaperone protein Hfq. Thus far the trans-encoded sRNAs are the most extensively characterized sRNAs and are discussed in a number of recent reviews (71, 118). In general, there has been less focus on cis-encoded sRNAs. These RNAs are transcribed from the DNA strand opposite another gene on bacterial chromosomes and thus have perfect complimentarity with this target. As we describe here, increasing numbers of bacterial cis-encoded RNAs of various sizes, which we denote antisense RNAs, are being reported and many are being characterized, raising questions about their physiological roles and mechanisms of action.

Ironically, antisense RNAs encoded on plasmids, phage and transposons were among the first regulatory sRNAs to be studied. In 1981, Tomizawa and colleagues showed that the ~108 nucleotide RNAI RNA controls the copy number of plasmid ColE1 by preventing RNAII processing to generate replication primers. That same year, Nordström and colleagues identified the ~90 nucleotide CopA RNA, which controls the copy number of plasmid R1 by regulating the translation of the RepA replication initiator protein. A few years later, the 70 nucleotide RNA-OUT of the transposon Tn10 was found to affect transposition by repressing transposase synthesis. In addition, the ~ 70 nucleotide Sar RNA of bacteriophage P22 and the 77 nucleotide OOP RNA of bacteriophage λ were reported to repress synthesis of the Ant and cII phage proteins, respectively. Another type of plasmid antisense RNA discovered early on was the ~70 nucleotide Sok RNA of plasmid R1, which represses synthesis of the toxic Hok protein responsible for postsegregational killing of cells when the R1 plasmid is lost.