Functional characterization of the<i>Drosophila MRP</i>(mitochondrial RNA processing) RNA gene

Schneider, Mary D; Bains, Anupinder K.; Rajendra, T. K.; Domiński, Zbigniew; Matera, A. Gregory; Simmonds, Andrew

doi:10.1261/rna.2227710

Cited by 9 publications

(11 citation statements)

References 43 publications

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“…In contrast, among the transcripts with a lower abundance on the ribosome, only about 40% coded for proteins and the others annotated as noncoding transcripts, including, e.g., the RNase MRP RNA (Ϫ5.09 log 2 -fold change). The RNA component of RNase MRP is a polymerase III transcript with a nucleolar localization in Drosophila (75). Thus, MRP RNA is a good substrate for RNA ligation but is expected to be present at a much lower abundance in the ribosome pulldown, which also demonstrates the specificity of the method.…”

Section: Resultsmentioning

confidence: 99%

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

Antic

Wolfinger

Skucha

et al. 2015

Molecular and Cellular Biology

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The translation and degradation of mRNAs are two key steps in gene expression that are highly regulated and targeted by many factors, including microRNAs (miRNAs). While it is well established that translation and mRNA degradation are tightly coupled, it is still not entirely clear where in the cell mRNA degradation takes place. In this study, we investigated the possibility of mRNA degradation on the ribosome in Drosophila cells. Using polysome profiles and ribosome affinity purification, we could demonstrate the copurification of various deadenylation and decapping factors with ribosome complexes. Also, AGO1 and GW182, two key factors in the miRNA-mediated mRNA degradation pathway, were associated with ribosome complexes. Their copurification was dependent on intact mRNAs, suggesting the association of these factors with the mRNA rather than the ribosome itself. Furthermore, we isolated decapped mRNA degradation intermediates from ribosome complexes and performed high-throughput sequencing analysis. Interestingly, 93% of the decapped mRNA fragments (approximately 12,000) could be detected at the same relative abundance on ribosome complexes and in cell lysates. In summary, our findings strongly indicate the association of the majority of bulk mRNAs as well as mRNAs targeted by miRNAs with the ribosome during their degradation.

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Section: Resultsmentioning

confidence: 99%

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

Antic

Wolfinger

Skucha

et al. 2015

Molecular and Cellular Biology

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“…The identification of potential ''specificity factors'' (whether they are novel factors transiently associated with RNase MRP in vivo or bona fide RNase MRP components) would be interesting, especially in light of recent data indicating that the involvement of RNase MRP in the processing of pre-rRNA may go beyond the known cleavage at the A3 site (Lindahl et al 2009;Schneider et al 2010).…”

Section: Esakova Et Almentioning

confidence: 99%

Substrate recognition by ribonucleoprotein ribonuclease MRP

Esakova

Perederina²,

Quan

et al. 2010

RNA

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The ribonucleoprotein complex ribonuclease (RNase) MRP is a site-specific endoribonuclease essential for the survival of the eukaryotic cell. RNase MRP closely resembles RNase P (a universal endoribonuclease responsible for the maturation of the 59 ends of tRNA) but recognizes distinct substrates including pre-rRNA and mRNA. Here we report the results of an in vitro selection of Saccharomyces cerevisiae RNase MRP substrates starting from a pool of random sequences. The results indicate that RNase MRP cleaves single-stranded RNA and is sensitive to sequences in the immediate vicinity of the cleavage site requiring a cytosine at the position +4 relative to the cleavage site. Structural implications of the differences in substrate recognition by RNases P and MRP are discussed.

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“…Outside the mitochondria, RNase MRP was shown to participate in the maturation of the 59 end of 5.8S rRNA (Schmitt and Clayton 1993;Chu et al 1994;Lygerou et al 1996a); recent data indicate that RNase MRP may be involved in other steps of rRNA maturation (Lindahl et al 2009;Schneider et al 2010). In addition, RNase MRP was shown to be involved in the regulation of the cell cycle in yeast by cleaving the 59 UTR of Cyclin B2 mRNA (Cai et al 2002;Gill et al 2004Gill et al , 2006.…”

Section: Introductionmentioning

confidence: 99%

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

Khanova¹,

Esakova²,

Perederina³

et al. 2012

RNA

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Eukaryotic ribonuclease (RNase) P and RNase MRP are closely related ribonucleoprotein complexes involved in the metabolism of various RNA molecules including tRNA, rRNA, and some mRNAs. While evolutionarily related to bacterial RNase P, eukaryotic enzymes of the RNase P/MRP family are much more complex. Saccharomyces cerevisiae RNase P consists of a catalytic RNA component and nine essential proteins; yeast RNase MRP has an RNA component resembling that in RNase P and 10 essential proteins, most of which are shared with RNase P. The structural organizations of eukaryotic RNases P/MRP are not clear. Here we present the results of RNA-protein UV crosslinking studies performed on RNase P and RNase MRP holoenzymes isolated from yeast. The results indicate locations of specific protein-binding sites in the RNA components of RNase P and RNase MRP and shed light on the structural organizations of these large ribonucleoprotein complexes.

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Functional characterization of theDrosophila MRP(mitochondrial RNA processing) RNA gene

Cited by 9 publications

References 43 publications

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

General and MicroRNA-Mediated mRNA Degradation Occurs on Ribosome Complexes in Drosophila Cells

Substrate recognition by ribonucleoprotein ribonuclease MRP

Structural organizations of yeast RNase P and RNase MRP holoenzymes as revealed by UV-crosslinking studies of RNA–protein interactions

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