Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors

Fang, Feng; Phillips, Seasson N.; Butler, J. Scott

doi:10.1261/rna.2900205

Cited by 62 publications

(76 citation statements)

References 30 publications

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“…As shown here and elsewhere (Fig. 2, 6, and 7) (16,43,48), rai1 mutations affect rRNA maturation at both ends of 5.8S rRNA. At the 5= end, Rai1 inactivation tips the scales in favor of the L form of 5.8S rRNA, in agreement with its function as a cofactor of Rat1.…”

Section: Discussionsupporting

confidence: 82%

The Evolutionarily Conserved Protein LAS1 Is Required for Pre-rRNA Processing at Both Ends of ITS2

Schillewaert

Wacheul

Lhommé³

et al. 2012

Molecular and Cellular Biology

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Ribosome synthesis entails the formation of mature rRNAs from long precursor molecules, following a complex pre-rRNA processing pathway. Why the generation of mature rRNA ends is so complicated is unclear. Nor is it understood how pre-rRNA processing is coordinated at distant sites on pre-rRNA molecules. Here we characterized, in budding yeast and human cells, the evolutionarily conserved protein Las1. We found that, in both species, Las1 is required to process ITS2, which separates the 5.8S and 25S/28S rRNAs. In yeast, Las1 is required for pre-rRNA processing at both ends of ITS2. It is required for Rrp6-dependent formation of the 5.8S rRNA 3= end and for Rat1-dependent formation of the 25S rRNA 5= end. We further show that the Rat1-Rai1 5=-3= exoribonuclease (exoRNase) complex functionally connects processing at both ends of the 5.8S rRNA. We suggest that prerRNA processing is coordinated at both ends of 5.8S rRNA and both ends of ITS2, which are brought together by pre-rRNA folding, by an RNA processing complex. Consistently, we note the conspicuous presence of ϳ7-or 8-nucleotide extensions on both ends of 5.8S rRNA precursors and at the 5= end of pre-25S RNAs suggestive of a protected spacer fragment of similar length. Ribosomes are essential to all life forms. Ribogenesis is a major metabolic activity requiring the coordinated expression of the core RNA and protein components of the small and large subunits and also of a myriad of trans-acting protein and RNA factors, their maturation, packaging, and transport (reviewed in references 21, 29, and 42). Despite this great complexity, ribogenesis is an extremely robust process. Quality control and fail-safe mechanisms are available at all steps along the assembly pathway to ensure that a sufficient amount of functional ribosomes is provided at all times (reviewed in references 24 and 30).In eukaryotes, ribogenesis is initiated in the nucleolus. There, at the interface between the cortical side of fibrillar centers (FCs) and the surrounding dense fibrillar components (DFCs), RNA polymerase I is recruited and threaded along the ribosomal DNA (rDNA), producing pre-rRNA transcripts that extend into the DFC, where pre-rRNAs undergo cotranscriptional modification. In fast-growing budding yeast cells, up to 50 to 70% of pre-rRNA molecules are also subjected to cotranscriptional cleavage (3,23,28,36). Cotranscriptional cleavage occurs in internal transcribed spacer 1 (ITS1), separating the precursors destined to mature into the small and large ribosome subunit rRNAs, i.e., the 18S and 5.8S-25S rRNAs, respectively (28,36,47). This strategy, involving the cosynthesis of three of the four mature rRNAs from a single long transcript, contributes to coordinating the synthesis of the various components of the translational machinery. This strategy has been extensively conserved throughout evolution and predates the eukaryotes, since the Bacteria and Archaea also synthesize their rRNAs from polycistronic precursors (reviewed in reference 31).The synthesis of mature rRNAs relie...

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Section: Discussionsupporting

confidence: 82%

The Evolutionarily Conserved Protein LAS1 Is Required for Pre-rRNA Processing at Both Ends of ITS2

Schillewaert

Wacheul

Lhommé³

et al. 2012

Molecular and Cellular Biology

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“…However, Rrp6 has functions distinct from those of other exosome subunits, in 5.8S rRNA processing (Briggs et al, 1998;Allmang et al, 1999a,b). Most, if not all, studies related to nuclear mRNA surveillance in yeast have been shown to require Rrp6 but, importantly, core exosome subunits have neither been tested nor shown to contribute to this function (e.g., Hilleren et al, 2001;Libri et al, 2002;Zenklusen et al, 2002;Das et al, 2003;Thomsen et al, 2003;Hieronymus et al, 2004;Fang et al, 2005;Kuai et al, 2005;Roth et al, 2005;Davis and Ares, 2006;Vodala et al, 2008). Finally, and consistent with our findings here, recent data have shown that yeast Rrp6 has RNA processing functions independent of the core exosome (Callahan and Butler, 2008).…”

Section: Rrp6 Function Independent Of the Nuclear Exosomesupporting

confidence: 84%

“…Nonetheless, based on its initial purification in the yeast nuclear exosome, most if not all subsequent phenotypes associated with loss of Rrp6 have been equated with perturbation of the nuclear exosome. Remarkably, despite its numerous roles in ribonucleometabolic pathways (Briggs et al, 1998;Bousquet-Antonelli et al, 2000;Burkard and Butler, 2000;Hilleren et al, 2001;Jensen et al, 2001;Dichtl et al, 2002;Libri et al, 2002;Zenklusen et al, 2002;Das et al, 2003;Thomsen et al, 2003;Hieronymus et al, 2004;Fang et al, 2005;Kuai et al, 2005;Roth et al, 2005;Reis and Campbell, 2007), it is not essential for viability in yeast (Briggs et al, 1998). Thus, whether these nuclear functions are specific to Rrp6 and/or are occurring in the context of an exosome complex is unclear.…”

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confidence: 99%

Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression

Graham

Kiss²,

Andrulis

2009

MBoC

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Exosome complexes are 3 to 5 exoribonucleases composed of subunits that are critical for numerous distinct RNA metabolic (ribonucleometabolic) pathways. Several studies have implicated the exosome subunits Rrp6 and Dis3 in chromosome segregation and cell division but the functional relevance of these findings remains unclear. Here, we report that, in Drosophila melanogaster S2 tissue culture cells, dRrp6 is required for cell proliferation and error-free mitosis, but the core exosome subunit Rrp40 is not. Micorarray analysis of dRrp6-depleted cell reveals increased levels of cell cycleand mitosis-related transcripts. Depletion of dRrp6 elicits a decrease in the frequency of mitotic cells and in the mitotic marker phospho-histone H3 (pH3), with a concomitant increase in defects in chromosome congression, separation, and segregation. Endogenous dRrp6 dynamically redistributes during mitosis, accumulating predominantly but not exclusively on the condensed chromosomes. In contrast, core subunits localize predominantly to MTs throughout cell division. Finally, dRrp6-depleted cells treated with microtubule poisons exhibit normal kinetochore recruitment of the spindle assembly checkpoint protein BubR1 without restoring pH3 levels, suggesting that these cells undergo premature chromosome condensation. Collectively, these data support the idea that dRrp6 has a core exosome-independent role in cell cycle and mitotic progression. INTRODUCTIONExosome complexes are critical players in the processing and degradation of many RNA species (Houseley et al., 2006). Found in both archaebacteria and eukaryotes, these complexes are composed of a "core" set of subunits. With respect to the yeast and human core complexes, they consist of six RNase PH domain-containing proteins (Rrp41, Rrp42, Rrp43, Rrp45, Rrp46, and Mtr3) and three S1 domain-containing proteins (Rrp4, Rrp40, and Csl4). Our understanding of exosome complex form and function has advanced greatly though the report of the crystal structures of archaebacterial (Buttner et al., 2005; and eukaryotic exosome core (Liu et al., 2006) complexes. The RNase PH subunits assemble into a hexameric ring upon which the S1 domain subunits reside. It has been proposed that the cylindrical shape and central channel of exosome complexes have evolved as a means to tightly regulate RNA recognition and subsequent decay (Lorentzen and Conti, 2006).Eukaryotes have compartment-specific exosome subunits and cofactors in addition to the core subunits. Although the eubacterial RNase R homolog Dis3 (also referred to as Rrp44) interacts with the yeast core (Mitchell et al., 1997;Allmang et al., 1999b;Dziembowski et al., 2007), it does not associate with either the human or trypanosome core (Chen et al., 2001;Estevez et al., 2003). Moreover, many archaebacteria lack an RNase R-like protein (Koonin et al., 2001). Thus, strictly speaking, Dis3 is not a core exosome component. Another exosome subunit missing in archaebacteria but present in eukaryotes is Rrp6, an RNase D homolog. Rrp6 associates specifical...

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“…Its exonuclease activity is similar to that of Xrn1p, but Rat1p/Xrn2p is present at only one-tenth of the abundance of Xrn1p (Poole and Stevens 1995). Rat1 mutants show defects in the 59 processing of 5.8s rRNA (Amberg et al 1992;Fang et al 2005) and of snoRNAs (Lee et al 2003), and in degradation of pre-mRNAs (Bousquet-Antonelli et al 2000). The N-terminal 765 amino acids of Rat1p correspond to residues 1-671 of Xrn1p; the most important difference within this region is the insertion of a bipartite nuclear localization signal in Rat1p.…”

Section: Introductionmentioning

confidence: 99%

Roles of aTrypanosoma brucei5′→3′ exoribonuclease homolog in mRNA degradation

Irmer²,

Gudjonsdottir-Planck³

et al. 2006

RNA

100

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The genome of the kinetoplastid parasite Trypanosoma brucei encodes four homologs of the Saccharomyces cerevisiae 59/39 exoribonucleases Xrn1p and Xrn2p/Rat1p, XRNA, XRNB, XRNC, and XRND. In S. cerevisiae, Xrn1p is a cytosolic enzyme involved in degradation of mRNA, whereas Xrn2p is involved in RNA processing in the nucleus. Trypanosome XRND was found in the nucleus, XRNB and XRNC were found in the cytoplasm, and XRNA appeared to be in both compartments. XRND and XRNA were essential for parasite growth. Depletion of XRNA increased the abundances of highly unstable developmentally regulated mRNAs, perhaps by delaying a deadenylation-independent decay pathway. Degradation of more stable or unregulated mRNAs was not affected by XRNA depletion although a slight decrease in average poly(A) tail length was observed. We conclude that in trypanosomes 59/39 exonuclease activity is important in degradation of highly unstable, regulated mRNAs, but that for other mRNAs another step is more important in determining the decay rate.

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Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors

Cited by 62 publications

References 30 publications

The Evolutionarily Conserved Protein LAS1 Is Required for Pre-rRNA Processing at Both Ends of ITS2

The Evolutionarily Conserved Protein LAS1 Is Required for Pre-rRNA Processing at Both Ends of ITS2

Core Exosome-independent Roles for Rrp6 in Cell Cycle Progression

Roles of aTrypanosoma brucei5′→3′ exoribonuclease homolog in mRNA degradation

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