Abstract
The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been discovered. These rancRNAs have proven to be efficient players in the regulation of translation as a first wave of stress adaptation by directly targeting the ribosome, the central enzyme of protein production. This underlying principle appears to be highly conserved, since rancRNAs are present in all three domains of life. Here, we review the major findings and mechanistic peculiarities of rancRNAs, a class of transcripts that is providing new and broader perspectives on the complexity of the ribosome and translation regulation.
Highlights
The term gene expression invokes, in the classical view, the process by which the information encoded in DNA is transcribed into a messenger RNA, which is subsequently used as a template for the synthesis of proteins during the translation process
Over the past decade, mounting evidence has confirmed ribosome-associated ncRNAs to be involved in translation modulation, representing a molecular strategy conserved in all three domains of life
RancRNAs can originate from intergenic regions of the genome or represent processing products of functional coding and noncoding precursor transcripts. This heterogeneity applies to the effect that rancRNAs have on protein production, being able to act as global regulators of protein synthesis, and capable of affecting the entire proteome, or to directly modulate the expression of individual mRNAs
Summary
With the implementation of avant-garde technologies and experimental strategies, recent research has revealed an expanding universe of non-coding RNAs (ncRNAs). RancRNAs constitute a very heterogeneous group of regulatory RNA molecules; they show a vast diversity in their origin, length, and mechanism of action Some of these ncRNAs have been found to modulate protein biosynthesis on a global scale, while others affect the translation of specific mRNAs, such as, for example, the well described bacterial transfer-messenger RNA (tmRNA) and the almost universally conserved signal recognition particle (SRP) RNA [23,24]. Given the fact that the production of proteins by ribosomes is a highly energy-demanding process, it is subjected to stringent control, which allows gene expression to rapidly change in response to various stresses [28,29] This immediate reprogramming of protein biosynthesis is crucial for cellular adaptation and survival under conditions of physiological changes [30–32]. Troucei [15 circumvent this problem, novel computational pipelines were developed to identify and and STqAuaRnPtifAy st(asbtlaebfulencRtioNnaAl RpNrAopcreoscseisnsigngpprroodduuctcstanadnnaolvyezlenrc)R,NdAetsriagnnsceridptsfofrromanthaelyses in richia cooblita[in3e5d].RNUAlt-iSmeqareteadlys.,Stohmee exxapmrpelsessinocnlu,drei:bAoPsAoRmT (eauatosmsoacteidatpiiopenli,naenfodr afnuanlycsitsionality predictoefdRNraAntrcaRnsNcrAiptsc)a, unsdedidtoaatneasl,ywzehcDicNhAilnibcrlauridesefrnomovSeaclchnacroRmNycAes cserpeveicsiiaee,sHoarlofperraxocessin volcanii, and Trypanosoma brucei [15–20,34], and STARPA (stable RNA processing product ucts dearniavlyezderf),rdoemsigndeidvfeorrsaenaplyrsiems ianrEyscRheNricAhiasc,oalil[w35a].yUsltihmaavteely,tothebeexperxespseiorni,mribeonsotamlely verif for exaamssopclieat,ionno, arnthdefurnnctbiolnoatlitoyrofqtRheTp-rPedCicRtedanraanlcyRsNisA, caannddidatpesp, rwohaicchhiensclutedsetnionvgelthe eff ribosomnceRNfuAnscpteicoiensaolritpyro.cessing products derived from diverse primary RNAs, always have to be experimentally verified via, for example, northern blot or qRT-PCR analysis, and approaches testing the effects on ribosome functionality
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