Measurement of Ribosomal RNA Turnover In Vivo by Use of Deuterium-Labeled Glucose

Defoiche, Julien; Zhang, Yan; Lagneaux, Laurence; Pettengell, Ruth; Hegedus, Andrea M.; Willems, Luc; Macallan, Derek C.

doi:10.1373/clinchem.2008.119446

Cited by 36 publications

(36 citation statements)

References 28 publications

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“…Might defects in rRNA processing contribute to reduced translation in Mtr4-deficient cells? We consider this unlikely for several reasons: First, since mature rRNAs are abundant and very stable, with half-lives that are days long (Yi et al 1999;Defoiche et al 2009), it would be unlikely that mature rRNA levels decrease sufficiently to affect ribosome levels and perturb translation. Our finding that the amount of unprocessed pre-rRNA that accumulated following Mtr4 knockdown was extremely small and that levels of 5.8S and 18S rRNAs were Figure 7.…”

Section: Discussionmentioning

confidence: 99%

An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression

et al. 2017

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Many long noncoding RNAs (lncRNAs) are unstable and rapidly degraded in the nucleus by the nuclear exosome. An exosome adaptor complex called NEXT (nuclear exosome targeting) functions to facilitate turnover of some of these lncRNAs. Here we show that knockdown of one NEXT subunit, Mtr4, but neither of the other two subunits, resulted in accumulation of two types of lncRNAs: prematurely terminated RNAs (ptRNAs) and upstream antisense RNAs (uaRNAs). This suggested a NEXT-independent Mtr4 function, and, consistent with this, we isolated a distinct complex containing Mtr4 and the zinc finger protein ZFC3H1. Strikingly, knockdown of either protein not only increased pt/uaRNA levels but also led to their accumulation in the cytoplasm. Furthermore, all pt/uaRNAs examined associated with active ribosomes, but, paradoxically, this correlated with a global reduction in heavy polysomes and overall repression of translation. Our findings highlight a critical role for Mtr4/ZFC3H1 in nuclear surveillance of naturally unstable lncRNAs to prevent their accumulation, transport to the cytoplasm, and resultant disruption of protein synthesis.

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Section: Discussionmentioning

confidence: 99%

An Mtr4/ZFC3H1 complex facilitates turnover of unstable nuclear RNAs to prevent their cytoplasmic transport and global translational repression

et al. 2017

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“…The half-life of ribosomes in vivo might be up to several days (43). To focus only on the free form and not yet incorporated Rpl23 proteins, we used ultracentrifugation to separate the newly synthesized Rpl23 (Fig.…”

Section: Figure 2 the Function Of Bcp1 Is Tightly Connected With Manmentioning

confidence: 99%

Bcp1 Is the Nuclear Chaperone of Rpl23 in Saccharomyces cerevisiae

Ting

Johnson

et al. 2017

Journal of Biological Chemistry

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Edited by Linda SpremulliEukaryotic ribosomes are composed of rRNAs and ribosomal proteins. Ribosomal proteins are translated in the cytoplasm and imported into the nucleus for assembly with the rRNAs. It has been shown that chaperones or karyopherins responsible for import can maintain the stability of ribosomal proteins by neutralizing unfavorable positive charges and thus facilitate their transports. Among 79 ribosomal proteins in yeast, only a few are identified with specific chaperones. Besides the classic role in maintaining protein stability, chaperones have additional roles in transport, chaperoning the assembly site, and dissociation of ribosomal proteins from karyopherins. Bcp1 has been shown to be necessary for the export of Mss4, a phosphatidylinositol 4-phosphate 5-kinase, and required for ribosome biogenesis. However, its specific function in ribosome biogenesis has not been described. Here, we show that Bcp1 dissociates Rpl23 from the karyopherins and associates with Rpl23 afterward. Loss of Bcp1 causes instability of Rpl23 and deficiency of 60S subunits. In summary, Bcp1 is a novel 60S biogenesis factor via chaperoning Rpl23 in the nucleus.The ribosome is a large macromolecular complex responsible for decoding cellular genetic information into proteins. There are two ribosomal subunits; in the eukaryotes, they are the (60S) large subunit and the small (40S) subunit, each composed of both rRNAs and ribosomal proteins. In eukaryotic cells, the assembly of ribosomes occurs in the nucleolus, a subcompartment of the nucleus devoted to ribosome biogenesis. rRNAs are transcribed by RNA polymerase I and III, and the initial assembly and processing events occur co-transcriptionally. The mRNAs of ribosomal proteins are transcribed in the nucleus by RNA polymerase II and translated in the cytoplasm. Consequently, the ribosomal proteins must be imported into the nucleus for assembly with the rRNAs. After ribosome assemblies have achieved a certain stage of maturation, export factors are loaded to direct these huge complexes to cross the nuclear membrane through the nuclear pore complexes (1-6). In the cytoplasm, ribosomes undergo additional steps in the maturation process; the trans-acting factors that are exported with nascent ribosomal subunits need to be stripped off, additional ribosomal proteins are added, and in the case of the 40S subunit, the final rRNA processing occurs (7,8). The synthesis of ribosomes requires the coordination of many non-ribosomal trans-acting factors at different stages for this pathway to be completed. About 200 trans-acting factors are involved in rRNA processing, rRNA folding, protein loading, and export. To date, more trans-acting factors have continued to be identified (7, 9, 10).BCP1 is an essential gene involved in the export of Mss4 (11), a phosphatidylinositol (PI) 2 4-phosphate 5-kinase that catalyzes the phosphorylation of PI4-phosphate and acts with the PI4-kinase, Stt4p, at the plasma membrane to generate PI4,5P 2 (12, 13). Phosphoinositols are critical small signal...

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“…18 With half lives of hours to days, tRNAs are more robust than mRNAs, which merely persist for minutes to hours. 19 Folding and stability of tRNA molecules is further controlled by numerous post-transcriptional modifications that cluster primarily in the anticodonstem loop, the D-and T-stems. 20 Since structural and functional integrity of tRNA molecules is so crucial for proper cellular functioning, many control pathways evolved, which recognize and degrade misfolded or hypomodified tRNA molecules rapidly (reviewed in ref.…”

Section: Functions Of Genuine Trnamentioning

confidence: 99%