The widespread occurrence of <scp>tRNA</scp>‐derived fragments in <i>Saccharomyces cerevisiae</i>

Bąkowska-Żywicka, Kamilla; Mleczko, Anna; Kasprzyk, Marta; Machtel, Piotr; Żywicki, Marek; Twardowski, Tomasz

doi:10.1002/2211-5463.12127

Cited by 25 publications

(20 citation statements)

References 36 publications

(75 reference statements)

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“…Our recent results also show that during amino acid starvation tRNA-His (GTG) is not processed preferentially and the formation of both 5′- and 3′-tRFs does not differ when compared to the optimal growth conditions (Bąkowska-Żywicka et al . 2016 ). In this study, however, the tRFs-His (GTG) possess the highest association with the ribosomes during amino acid stress, meaning that these tRFs might be specifically selected by the ribosomes under certain environmental conditions.…”

Section: Discussionmentioning

confidence: 99%

tRNA-derived short RNAs bind toSaccharomyces cerevisiaeribosomes in a stress-dependent manner and inhibit protein synthesisin vitro

Bąkowska-Żywicka

Kasprzyk

Twardowski

2016

FEMS Yeast Research

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Recently, a number of ribosome-associated non-coding RNAs (rancRNAs) have been discovered in all three domains of life. In our previous studies, we have described several types of rancRNAs in Saccharomyces cerevisiae, derived from many cellular RNAs, including mRNAs, rRNAs, tRNAs and snoRNAs. Here, we present the evidence that the tRNA fragments from simple eukaryotic organism S. cerevisiae directly bind to the ribosomes. Interestingly, rancRNA-tRFs in yeast are derived from both, 5′- and 3′-part of the tRNAs and both types of tRFs associate with the ribosomes in vitro. The location of tRFs within the ribosomes is distinct from classical A- and P-tRNA binding sites. Moreover, 3′-tRFs bind to the distinct site than 5′-tRFs. These interactions are stress dependent and as a consequence, provoke regulation of protein biosynthesis. We observe strong correlation between tRF binding to the ribosomes and inhibition of protein biosynthesis in particular environmental conditions. These results implicate the existence of an ancient and conserved mechanism of translation regulation with the involvement of ribosome-associating tRNA-derived fragments.

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Section: Discussionmentioning

confidence: 99%

tRNA-derived short RNAs bind toSaccharomyces cerevisiaeribosomes in a stress-dependent manner and inhibit protein synthesisin vitro

Bąkowska-Żywicka

Kasprzyk

Twardowski

2016

FEMS Yeast Research

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“…Saccharomyces cerevisiae strain BY4741 was grown in YPD medium with 2% glucose at 30 o C. Environmental stress was induced as previously described 25 in two biological replicates. Briefly, cells were grown to mid-log phase, and stress conditions were applied for 15 min.…”

Section: Strain and Growth Conditionsmentioning

confidence: 99%

Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression

Mleczko

Machtel

Walkowiak

et al. 2019

Preprint

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In recent years, a number of small RNA molecules derived from snoRNAs have been observed. Findings concerning the functions of sdRNAs in cells are limited primarily to their involvement in microRNA pathways. However, similar molecules have been observed in Saccharomyces cerevisiae, which is an organism lacking miRNA machinery. Considering our previous observations, we examined the subcellular localization of sdRNAs in yeast. Our findings reveal that both sdRNAs and their precursors, snoRNAs, are present in the cytoplasm at levels dependent upon stress conditions. Moreover, both sdRNAs and snoRNAs interact with translating ribosomes in a stress-dependent manner. As a consequence of binding to ribosomes, yeast sdRNAs exhibit inhibitory activity on translation. However, observed levels of sdRNAs and snoRNAs in the cytoplasm and their association with ribosomes suggest independent regulation of these molecules by yet unknown factors.

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“…These fragments are relatively long for non-coding RNAs 67 ; although they are longer than miRNAs 68 or piwiRNAs 38 , they have a length similar to other small ncRNAs, such as tRNA fragments (tRFs) 43,46,89 , and snoRNAs. Interestingly, tRNA cleavage into tRFs has often been described as a stress-dependent phenomenon [90][91][92][93][94] , and many authors describe a role for these tRFs in translational regulation [95][96][97][98] . One can thus imagine that a similar phenomenon may occur for the 5.8S rRNA and lead to the production of long and shorter rRFs under stress conditions [99][100] .…”

Section: Fragments Of the 58s Ribosomal Rnamentioning

confidence: 99%

Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

Lambert¹,

Benmoussa²,

P³

2018

Preprint

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The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

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The widespread occurrence of tRNA‐derived fragments in Saccharomyces cerevisiae

Cited by 25 publications

References 36 publications

tRNA-derived short RNAs bind toSaccharomyces cerevisiaeribosomes in a stress-dependent manner and inhibit protein synthesisin vitro

tRNA-derived short RNAs bind toSaccharomyces cerevisiaeribosomes in a stress-dependent manner and inhibit protein synthesisin vitro

Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression

Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

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