Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12

Jung, Daehee; Seo, Jong Seok; Nam, Jayoung; Kim, Jinmi

doi:10.1371/journal.pone.0220137

Cited by 8 publications

(8 citation statements)

References 43 publications

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“…Previous studies have suggested a role for Puf6 in the localization and translational repression of specific mRNAs 28 – 30 . However, in agreement with cell-biological studies 26 , 31 , we found that Puf6-GFP predominantly co-localizes with Gar1-mCherry, an established nucleolar marker (Fig.…”

Section: Resultsmentioning

confidence: 99%

Puf6 primes 60S pre-ribosome nuclear export at low temperature

et al. 2021

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Productive ribosomal RNA (rRNA) compaction during ribosome assembly necessitates establishing correct tertiary contacts between distant secondary structure elements. Here, we quantify the response of the yeast proteome to low temperature (LT), a condition where aberrant mis-paired RNA folding intermediates accumulate. We show that, at LT, yeast cells globally boost production of their ribosome assembly machinery. We find that the LT-induced assembly factor, Puf6, binds to the nascent catalytic RNA-rich subunit interface within the 60S pre-ribosome, at a site that eventually loads the nuclear export apparatus. Ensemble Förster resonance energy transfer studies show that Puf6 mimics the role of Mg2+ to usher a unique long-range tertiary contact to compact rRNA. At LT, puf6 mutants accumulate 60S pre-ribosomes in the nucleus, thus unveiling Puf6-mediated rRNA compaction as a critical temperature-regulated rescue mechanism that counters rRNA misfolding to prime export competence.

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Section: Resultsmentioning

confidence: 99%

Puf6 primes 60S pre-ribosome nuclear export at low temperature

et al. 2021

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“…6 g,h; Additional File 1 : Fig. S6h) motifs were associated with significantly enhanced protein expression, and the Puf6 site (UUGU [ 50 , 51 ]) was associated with a weak but statistically significant increase in expression (beyond the shuffled sequence control) (Fig. 6 i,j; Additional File 1 : Fig.…”

Section: Resultsmentioning

confidence: 99%

“…8 i, blue). These minimal effects may reflect the nature of Puf6 regulation, with known target genes displaying multiple Puf6 binding sites in their 3′ UTRs [ 50 , 51 ].…”

Section: Resultsmentioning

confidence: 99%

Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequences

et al. 2021

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Background The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression through effects on activities such as mRNA stability and translation. Functional elements within this region have largely been identified through analyses of native genes, which contain multiple co-evolved sequence features. Results To explore the effects of 3′ UTR sequence elements outside of native sequence contexts, we analyze hundreds of thousands of random 50-mers inserted into the 3′ UTR of a reporter gene in the yeast Saccharomyces cerevisiae. We determine relative protein expression levels from the fitness of transformants in a growth selection. We find that the consensus 3′ UTR efficiency element significantly boosts expression, independent of sequence context; on the other hand, the consensus positioning element has only a small effect on expression. Some sequence motifs that are binding sites for Puf proteins substantially increase expression in the library, despite these proteins generally being associated with post-transcriptional downregulation of native mRNAs. Our measurements also allow a systematic examination of the effects of point mutations within efficiency element motifs across diverse sequence backgrounds. These mutational scans reveal the relative in vivo importance of individual bases in the efficiency element, which likely reflects their roles in binding the Hrp1 protein involved in cleavage and polyadenylation. Conclusions The regulatory effects of some 3′ UTR sequence features, like the efficiency element, are consistent regardless of sequence context. In contrast, the consequences of other 3′ UTR features appear to be strongly dependent on their evolved context within native genes.

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“…6e,f) and Puf5 (UGUANNNNUA [22,34]) (Fig. 6g,h) motifs were associated with significantly enhanced protein expression, and the Puf6 site (UUGU [36,37]) was associated with a weak increase in expression (beyond the shuffled sequence control) (Fig. 6i,j).…”

Section: Some Puf Protein Binding Sites Increase Protein Expression Imentioning

confidence: 97%

“…8i), and a weak increase in His3 protein expression. These minimal effects may reflect the nature of Puf6 regulation, with known target genes displaying multiple Puf6 binding sites in their 3′ UTRs [36,37].…”

Section: Comparison Of 3′ Utr Sequence Element Effects To Mrna Half-life Measurements Of Native Mrnasmentioning

confidence: 99%

Effects of sequence motifs in the yeast 3′ untranslated region determined from massively-parallel assays of random sequences

Savinov

Brandsen

Angell

et al. 2021

Preprint

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The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression, through effects on activities such as mRNA stability and translation. The underlying functional elements within this region have largely been identified through analyses of the limited number of native genes. To explore the effects of sequence elements when not present in biologically evolved sequence backgrounds, we analyzed hundreds of thousands of random 50-mers inserted into the 3′ UTR of a reporter gene in the yeast Saccharomyces cerevisiae. We determined relative protein expression levels from the fitness of a library of transformants in a growth selection. We find that the consensus 3′ UTR efficiency element significantly boosts expression, independent of sequence context; on the other hand, the consensus positioning element has only a small effect on expression. Some sequence motifs that are binding sites for Puf proteins substantially increase expression in this random library, despite these proteins generally being associated with post-transcriptional downregulation when bound to native mRNAs. Thus, the regulatory effects of 3′ UTR sequence features like the positioning element and Puf binding sites appear to be strongly dependent on their context within native genes, where they exist alongside co-evolved sequence features. Our measurements also allowed a systematic examination of the effects of point mutations within efficiency element motifs across diverse sequence backgrounds. These mutational scans reveal the relative in vivo importance of individual bases in the efficiency element, which likely reflects their roles in binding the Hrp1 protein involved in cleavage and polyadenylation.

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Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12

Cited by 8 publications

References 43 publications

Puf6 primes 60S pre-ribosome nuclear export at low temperature

Puf6 primes 60S pre-ribosome nuclear export at low temperature

Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequences

Effects of sequence motifs in the yeast 3′ untranslated region determined from massively-parallel assays of random sequences

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