Physiological roles of antisense RNAs in prokaryotes

Abstract

Prokaryotes encounter constant and often brutal modifications to their environment. In order to survive, they need to maintain fitness, which includes adapting their protein expression patterns. Many factors control gene expression but this review focuses on just one, namely antisense RNAs (asRNAs), a class of non-coding RNAs (ncRNAs) characterized by their location in cis and their perfect complementarity with their targets. asRNAs were considered for a long time to be trivial and only to be found on mobile genetic elements. However, recent advances in methodology have revealed that their abundance and potential activities have been underestimated. This review aims to illustrate the role of asRNA in various physiologically crucial functions in both archaea and bacteria, which can be regrouped in three categories: cell maintenance, horizontal gene transfer and virulence. A literature survey of asRNAs demonstrates the difficulties to characterize and assign a role to asRNAs. With the aim of facilitating this task, we describe recent technological advances that could be of interest to identify new asRNAs and to discover their function.

Are Antisense Proteins in Prokaryotes Functional?

“…Antisense transcription has been widely disregarded as noise (Raghavan et al, 2012;Lloréns-Rico et al, 2016). However, despite these generalizations, these elements have recently been found to at least sometimes have physiological roles (Wade and Grainger, 2014;Lejars et al, 2019). Functional RNAs which are not yet well understood include structured noncoding RNAs such as riboswitches (Hücker et al, 2017b;Stav et al, 2019).…”

“…Their functions, if any, are poorly understood in most cases. The characteristics of antisense RNAs range widely in terms for instance of length, location in relation to the sense gene, and mechanisms of regulation (Lejars et al, 2019). In studies so far they are usually associated with reducing transcription of the sense gene, but they can also increase it, for instance by changing the structure of the sense transcript -various mechanisms are known in each case (Lasa et al, 2012).…”

“…They can influence single genes, or have global effects for instance through a target involved in general translation. Other known effects relate to functions including virulence, motility, various mechanisms of gene transfer, and biofilm formation (Lejars et al, 2019). The numerous examples of antisense transcription which have been investigated do not just include short antisense RNAs, though these are well-known; the many longer examples include a 1200 nucleotide antisense RNA in Salmonella enterica, AmgR (Courtney and Chatterjee, 2014).…”

Are Antisense Proteins in Prokaryotes Functional?

“…Their functions, if any, are poorly understood in most cases. The characteristics of antisense RNAs range widely in terms for instance of length, location in relation to the sense gene, and mechanisms of regulation (Lejars et al, 2019). In studies so far they are usually associated with reducing transcription of the sense gene, but they can also increase it, for instance by changing the structure of the sense transcript.…”

Improving Bacterial Ribosome Profiling Data Quality

“…Some studies have claimed that ORFs antisense to annotated genes, detectable by increasing the read depth, mostly result from transcription initiation or termination inaccuracy and therefore are presumably non-functional sequences [54,[75][76][77]. A number of other researchers have proposed that many antisense RNA sequences are in fact functional [78][79][80]. We additionally propose the stronger claim that many antisense ORFs with reads mapping to them include undetected protein-coding ORFs.…”