Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

Young, David J.; Guydosh, Nicholas R.; Zhang, Fan; Hinnebusch, Alan G.; Green, Rachel

doi:10.1016/j.cell.2015.07.041

Cited by 189 publications

(238 citation statements)

References 39 publications

(62 reference statements)

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“…Experiments without CHX, on the other hand, report positive correlations of varying magnitude (Fig 1D, 0x Gerashchenko NAR points and purple labels). Experiments by Pop [36], Lareau [26], Nedialkova [29], Guydosh [35] and Gardin [33] produce weak to moderate correlations, but experiments by Gerashchenko [34], Jan [41], Williams [42], Weinberg [38], and Young [37] produce fairly strong and highly statistically significant correlations.…”

Section: Pretreatment With Cycloheximide Consistently Changes Enrichmmentioning

confidence: 99%

“…An alternative experimental protocol uses an optimized harvesting and flash-freezing process that allows CHX pretreatment to be omitted [15,17,26,29,[33][34][35][36][37][38]. Experiments performed with this protocol have revealed that treatment with CHX affects several high-level characteristics of footprinting data, including the distribution of lengths of nuclease-protected fragments in mammalian cells [39] and the amount of enrichment in ribosome density at the 5' end of coding sequences in yeast [34].…”

Section: Introductionmentioning

confidence: 99%

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Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

Hussmann

Patchett

Johnson

et al. 2015

Preprint

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Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX) to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in all such experiments, codons decoded by less abundant tRNAs were in fact being translated more slowly before the addition of CHX disrupted these dynamics. Author SummaryRibosome profiling measures the precise locations of millions of actively translating ribosomes on mRNAs. In theory, the frequency with which ribosomes are observed positioned over each type of codon can be used to quantify the speed with which each codon is translated. In practice, ribosome profiling experiments in yeast that use translation inhibitors to arrest translation before measuring the positions of ribosomes report very different Data Availability Statement: Sequencing data has been deposited to the SRA with accession number SRP060588.Funding: This work was supported by NIH grant R01-GM-093086 to SS and NIH grant GM053655 to AJ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Competing Interests: The authors have declared that no competing interests exist.apparent translation speeds for each codon than experiments that do not use inhibitors.To explain this inconsistency, we show that a previously unappreciated mechanism causes experiments using translation inhibitors to not measure ribosomes at each position on mRNAs in proportion to the actual amount of time spent there in vivo. Understanding this mechanism reveals that experiments without inhibitors more accurately measure translation dynamics and provides guidance for the design and interpretation of future ribosome profiling experiments.

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Section: Pretreatment With Cycloheximide Consistently Changes Enrichmmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

Hussmann

Patchett

Johnson

et al. 2015

Preprint

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“…ATP hydrolysis by Rli1 promotes release of the 60S subunit (Shoemaker and Green 2011). Depletion of Rli1 leads to aberrant reinitiation near the stop codon, leading to translation of 39 UTR sequences (Young et al 2015). In mammals, the protein Ligatin, or the complex of MCT-1 and DENR, promote release of mRNA and deacylated tRNA from the 40S subunit in the final step of recycling (Skabkin et al 2010).…”

Section: Termination and Recyclingmentioning

confidence: 99%

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

2016

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In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae. The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.

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“…26,95 To get further insight into the involvement of ABCE1 in cell proliferation, we considered its potential role in the synthesis of proteins essential for cell cycle progression. The translation of certain transcripts is highly dependent on the initiation step, which is determined by both the activity of initiation factors and the 5 0 -UTR structure of mRNA.…”

Section: Discussionmentioning

confidence: 99%

“…[23][24][25] Moreover, ABCE1 recycling activity may control non-canonical 3 0 -UTR translation on stalled ribosomes during stress. 26 The function of ABCE1 in ribosome recycling is conserved in archaea, in contrast to the initiation stage lacking the eukaryotic homologues of eIF3 and eIF5. 27 Thus, ABCE1 role in translation could be considered as a link between termination, recycling and initiation.…”

Section: Introductionmentioning

confidence: 99%

ABCE1 is essential for S phase progression in human cells

et al. 2016

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ABCE1 is a highly conserved protein universally present in eukaryotes and archaea, which is crucial for the viability of different organisms. First identified as RNase L inhibitor, ABCE1 is currently recognized as an essential translation factor involved in several stages of eukaryotic translation and ribosome biogenesis. The nature of vital functions of ABCE1, however, remains unexplained. Here, we study the role of ABCE1 in human cell proliferation and its possible connection to translation. We show that ABCE1 depletion by siRNA results in a decreased rate of cell growth due to accumulation of cells in S phase, which is accompanied by inefficient DNA synthesis and reduced histone mRNA and protein levels. We infer that in addition to the role in general translation, ABCE1 is involved in histone biosynthesis and DNA replication and therefore is essential for normal S phase progression. In addition, we analyze whether ABCE1 is implicated in transcript-specific translation via its association with the eIF3 complex subunits known to control the synthesis of cell proliferation-related proteins. The expression levels of a few such targets regulated by eIF3A, however, were not consistently affected by ABCE1 depletion.

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Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3′UTRs In Vivo

Cited by 189 publications

References 39 publications

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

Understanding biases in ribosome profiling experiments reveals signatures of translation dynamics in yeast

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

ABCE1 is essential for S phase progression in human cells

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