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J Biol Chem, Vol. 273, Issue 21, 13255-13263, May 22, 1998
From the Department of Microbiology and Immunology, University of
Rochester School of Medicine and Dentistry,
Rochester, New York 14618
The eukaryotic 25 S, 18 S, and 5.8 S rRNAs are
synthesized as a single transcript with two internal transcribed
spacers (ITS1 and ITS2), which are removed by endo- and
exoribonucleolytic steps to produce mature rRNA. Genetic selection for
suppressors of a polyadenylation defect yielded two cold-sensitive
alleles of a gene that we named RRP6 (ribosomal
RNA processing). Molecular cloning of
RRP6 revealed its homology to a 100-kDa human, nucleolar PM-Scl autoantigen and to Escherichia coli RNase D, a
3'-5' exoribonuclease. Recessive mutations in rrp6 result
in the accumulation of a novel 5.8 S rRNA processing intermediate,
called 5.8 S*, which has normal 5' ends, but retains ~30 nucleotides
of ITS2. Pulse-chase analysis of 5.8 S rRNA processing in an
rrp6- strain revealed a precursor-product relationship
between 5.8 S* and 5.8 S rRNAs, suggesting that Rrp6p plays a role in
the removal of the last 30 nucleotides of ITS2 from 5.8 S precursors. A
portion of 5.8 S* rRNA assembles into 60 S ribosomes which form
polyribosomes, suggesting that they function in protein synthesis.
These findings indicate that Rrp6p plays a role in 5.8 S rRNA 3' end
formation, and they identify a functional intermediate in the rRNA
processing pathway.
The maturation of the three major classes of eukaryotic RNA
(mRNA, rRNA, and tRNA) requires extensive processing events,
including endonucleolytic and exonucleolytic cleavages, intron removal, and exon splicing, as well as nucleotide additions and removals exemplified by polyadenylation and editing. Three of the four eukaryotic rRNAs are synthesized as a single precursor RNA and must
undergo a complex series of processing events to produce mature 18 S,
5.8 S, and 25 S rRNAs. Central to this process is the removal of the
two internal transcribed spacers
(ITS)1 that separate 18 S
from 5.8 S (ITS1) and 5.8 S from 25 S (ITS2) (Fig.
1). In the yeast Saccharomyces
cerevisiae, the removal of ITS1, which is coupled to the removal
of the 5' external transcribed spacer, features a series of cleavage
events requiring proteins, small nucleolar RNAs and the
ribonucleoprotein RNase MRP (reviewed in Refs. 1 and 2). Cleavage
within ITS1 separates 20 S RNA from 27 S RNA. 20 S RNA is processed in
the cytoplasm to form mature 18 S rRNA, while 27 S RNA is processed by
two alternative pathways. Some 15% of 27 S undergoes cleavage at a
site that appears to correspond to the 5' end of the long form of 5.8 S
rRNA, while RNase MRP, in conjunction with Rrp5p cleaves the remaining
27 S molecules, which then undergo 5'-3' exonucleolytic processing to
generate the 5' end of the short form of 5.8 S (3-6).
Rrp6p, the Yeast Homologue of the Human PM-Scl 100-kDa
Autoantigen, Is Essential for Efficient 5.8 S rRNA 3' End
Formation*
ABSTRACT
Top
Abstract
Introduction
Procedures
Results
Discussion
References
INTRODUCTION
Top
Abstract
Introduction
Procedures
Results
Discussion
References
View larger version (18K):
[in a new window]
Fig. 1.
Diagram of the major processing events
involved in removal of ITS1 and ITS2 from pre-rRNA.
The events required for processing of ITS2 remain less well characterized than those for ITS1. After processing by alternative pathways during the latter stages of ITS1 removal, both types of 27 S rRNAs undergo cleavages within ITS2 that separate 25 S molecules, with either mature or extended 5' ends, from 5.8 S precursors (7 SL and 7 SS) with 3' extensions. These 3' extensions must be removed to produce mature 5.8 SL and 5.8 SS rRNAs. Recessive mutations in the S. cerevisiae RRP4 gene result in the accumulation of 3' extended forms of 5.8 S rRNA suggesting a role for Rrp4p in 5.8 S rRNA 3' end processing. Indeed, immunoprecipitates of Rrp4p demonstrated 3'-5' riboexonuclease activity in vitro (7). More extensive analysis of Rrp4p immunoprecipitates revealed the existence of Rrp4p in a multisubunit complex, called the exosome (8). In addition to Rrp4p, the exosome contains three 3'-5' riboexonucleases required for efficient maturation of 5.8 S rRNA 3' ends. Each of these enzymes show strong homology to 3'-5' riboexonucleases found in Escherichia coli.
In this report, we present the identification and characterization of RRP6, the product of which plays a role in the proper 3' end processing of 5.8 S rRNA. Mutations in RRP6 result in the accumulation of 3' extended 5.8 S rRNAs. RRP6 encodes a protein highly homologous to the human PM-Scl 100-kDa autoantigen, as well as proteins of unknown function from Caenorhabditis elegans and Schizosaccharomyces pombe. Each of these eukaryotic proteins share homology in their central domains with the E. coli 3'-5' exoribonuclease RNase D, suggesting the conservation of some RNase D function from bacteria to humans.
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EXPERIMENTAL PROCEDURES |
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Abstract
Introduction
Procedures
Results
Discussion
References
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Strains, Media, and Genetic Techniques-- The experiments reported here were performed using the yeast strains described in Table I. The suppressor isolation has been described by Briggs and Butler (9).
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was used for all
recombinant DNA manipulations.
Plasmids and Oligonucleotides--
The plasmids and
deoxyoligonucleotides utilized in this study are described in Table
II. Restriction enzymes were purchased from Life Technologies, Inc., Promega, or New England Biolabs, and
digestions were performed as per manufacturers' instructions. Double-stranded DNA probe templates were prepared by diethylaminoethyl paper purification from 1% agarose gels and radiolabeled by random hexamer priming with 5'-[-32P]deoxyCTP (NEN Life
Science Products, 3000 Ci/mmol) and the Klenow fragment of DNA
polymerase (Boehringer Mannheim), according to the manufacturer's
instructions. Deoxyoligonucleotide probes (25 pmol; Oligos Etc., Inc.)
were radiolabeled by incubation for 60 min at 37 °C in 15-µl
reactions containing 50 mM Tris-Cl, pH 7.5, 10 mM MgCl2, 5 mM dithiothreitol with
1 unit of T4 polynucleotide kinase (Life Technologies, Inc.) and 50 µCi of 5'-[
-32P]ATP (NEN Life Science Products, 6000 Ci/mmol). Unincorporated nucleotides were removed from probes by
chromatography on Sephadex G-25.
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Molecular Cloning of RRP6--
Twenty µg of library DNA (9)
were transformed into strain 1BC1 (Table I), and transformants were
selected on URA
plates at 25 °C for 36 h, after
which the plates were incubated at 14 °C until putative
RRP6-containing complementing plasmid-bearing strains grew
above background levels. One colony out of approximately 100,000 transformants displayed reproducible complementation of the
cold-sensitive phenotype after rescue of the plasmid from yeast cells
and retransformation into 1BC1. The apparent low number of
RRP6 transformants is likely due to its tight centromere
linkage, since E. coli colony blot hybridization experiments
indicate that its representation in the library is similar to other
genes (9). A 3.5-kilobase RRP6-specific
XbaI/EcoRI fragment was cloned into the same
sites in YIplac211 (13) to produce pUNC9. CEN15 was removed
from pUNC9 by digestion with XbaI and BglII,
filling in the 5' overhangs with the Klenow fragment DNA polymerase and
ligation of the plasmid with T4 DNA ligase to produce p10dXB. Analysis of the linkage between rrp6-1 and UNC733 was
carried out by transformation of ABC1-2D with p10dXB linearized with
BamHI.
RNA Analyses-- Total RNA was prepared and Northern analysis carried out as described previously (14). Levels of specific RNAs were quantitated by storage PhosphorImager analysis (Molecular Dynamics) and normalized to 5 S rRNA levels, which were quantitated by FluorImager analysis (Molecular Dynamics) of ethidium bromide-stained gels or by storage PhosphorImager analysis after hybridization of 5'-32P-labeled deoxyoligonucleotide probes to 5.8 S rRNA or to the RNA polymerase III-transcribed ScR1 (Table II).
For analyses of small rRNA transcripts, 3 µg of total RNA were separated on a 12% polyacrylamide, 8 M urea gel, and RNAs were transferred to GeneScreen membranes (DuPont) by electroblotting at 10 V for 16 h at 4 °C. Hybridizations were performed at 42 °C as described previously (14) except that formamide was omitted when oligonucleotide probes were used. Length determinations of 5.8 S* rRNA were made by linear regression from a semilog plot of the mobilities of 7 S, 5.8 S, and 5 S rRNA as a function of their known lengths. Primer extension analysis of 5.8 S rRNA was performed as described (15). Polyribosomes were prepared and analyzed as described (16).DNA Sequence Analyses-- The accession numbers of the nucleotide and protein sequences analyzed in this study are as follows: Rrp6p, Z74909; Homo sapiens, Q01780; S. pombe, Q10146; C. elegans, P34607; E. coli, P09155; Haemophilus influenza, P44442. Sequence data derived from complementing plasmid pC114 were compared with the yeast genome sequence data base using the BLAST program at the National Center for Biotechnology Information2 and the Stanford Genome Resource Data Base.3 Pairwise comparisons of Rrp6p and proteins from other species were made using BESTFIT, and the protein sequences were aligned using Pileup and MSAShade. Putative nuclear localization signals were determined using the Psort program.
Construction and Analysis of a rrp6 Null Allele--
The
URA3 portion of pUNC9 was deleted by digestion with
AatII and NarI, followed by filling the
overhanging ends with the Klenow fragment of DNA polymerase and
subsequent ligation to produce pUN9d4. URA3 was removed from
pJJ244 (17) with BamHI and PvuII and inserted
into BamHI/EcoRV-digested pBR322 to produce
pBRU2. The internal BglII fragment of RRP6 in
pUN9d4 was replaced with the BamHI fragment containing
URA3 from pBRU2 to produce pdRRP6F. Disruption of
chromosomal RRP6 was carried out by digestion of pdRRP6F
with BamHI and PvuII to liberate
rrp6::URA3 followed by transformation of the
digestion mixture into a diploid made by crossing T481 and T581 (Table
I). Disruptants were selected on synthetic complete URA
plates at 30 °C. Disruption of RRP6 was verified by PCR
using primers flanking the RRP6 BglII sites (Table II, Fig.
6).
Pulse-Chase Analysis of 5.8 S rRNA Processing-- Cultures of BPO2 and BPO2-12F (Table I) were grown at 30 °C in synthetic complete glucose medium supplemented with uracil (20 mg/ml) to an A600 of 1.7. Cells were harvested by centrifugation, resuspended in 5 ml of fresh medium lacking uracil and labeled for 3 min by the addition of 50 µCi of [5,6-3H] uracil/ml (NEN Life Science Products, 39 Ci/mmol). Following the initial pulse labeling, the radioactive precursor was chased for up to 1 h by the addition of unlabeled uracil at a final concentration of 300 µg/ml. At various times, samples were taken, the cells collected by centrifugation and frozen in dry ice. Total RNA was isolated from yeast cells as described (14). Small RNAs were separated by electrophoresis on 6% polyacrylamide gels containing 7.5 M urea in 50 mM Tris borate (pH 8.3). Gels were fixed in 30% methanol, 10% acetic acid for 1 h, incubated in EN3HANCE (NEN Life Science Products) for 1 h and washed with water for 20 min. The gels were then dried and subjected to autoradiography. Quantitation of the amount of [5,6-3H]uracil incorporated into specific RNAs was determined by cutting the appropriate bands from the dried gels and determining the amount of radioactivity present by scintillation counting.
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RESULTS |
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Top
Abstract
Introduction
Procedures
Results
Discussion
References
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Isolation of rrp6 Mutations as Suppressors of a Polyadenylation Defect-- Pseudoreversion analysis of the pap1-1 temperature sensitive mutation in S. cerevisiae was carried out to identify gene products that play roles in the mechanism or function of polyadenylation (9). We isolated five independent suppressors that exhibited a cold-sensitive growth phenotype at 14 °C from an initial population of about 5,000 spontaneously arising pseudorevertants that allowed growth of a pap1-1 strain at the restrictive temperature of 30 °C (Table III). Two of the five cold-sensitive suppressor strains isolated represented alleles of the RRP6 complementation group (previously named PDS1) (9). Tetrad analysis after sporulation of a diploid homozygous for pap1-1 and rrp6-1 demonstrated independent, 2:2 segregation of both the cold-sensitive and suppressor phenotypes indicating that the rrp6-1 mutation occurred in a single-copy nuclear gene, extragenic to pap1-1. Normal growth at low temperature of a diploid heterozygous for rrp6-1 or rrp6-2 indicated that these mutations are recessive, suggesting loss of function mutations. Delineation of the mechanism of suppression of pap1-1 by alleles of rrp6 will be presented elsewhere.
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Molecular Cloning and Sequence Analysis of RRP6--
The
recessivity of the rrp6-1 cold-sensitive phenotype allowed
us to clone the wild-type gene by complementation. We transformed an
rrp6-1 strain with a yeast centromere-based genomic library (9), and isolated one plasmid that conferred wild-type growth at
14 °C (pC114, Fig. 2). Plasmid rescue
and retransformation confirmed plasmid linkage to complementation.
Sequence determination of the ends of the pC114 insert and comparison
with the European Molecular Biology Laboratory (EMBL) data base mapped
the insert to chromosome XV. We performed a number of deletions to
isolate the complementing open reading frame and found that
complementation required the presence of a previously uncharacterized
open reading frame, UNC733 (SCYOR001W, GenBankTM accession
no. Z74909). For linkage analysis of rrp6-1 and
UNC733, we targeted integration of an UNC733,URA3
plasmid (p10dXB; Fig. 2) into the chromosomal UNC733 locus
in an rrp6-1,ura3-52 strain. This strain was crossed to an
RRP6,ura3-52 strain, the resultant diploid was sporulated, and the progeny were analyzed. All cold-sensitive progeny were URA+ (36/36) and all URA spores were
cold-resistant (25/25), thus demonstrating tight linkage of
rrp6-1 to the UNC733,URA3 plasmid. Furthermore,
we constructed a strain with YIpRRP6 integrated at RRP6,
which lost the integrated plasmid spontaneously in the absence of
selection, probably due to the presence of CEN15 on the
plasmid. Half of the resultant URA isolates demonstrated
normal growth at 14 °C, suggesting that homologous recombination
between the chromosomal rrp6-1 and the plasmid-borne
UNC733 had removed the chromosomal lesion. Taken together,
these data indicate that the previously cloned, but hitherto
uncharacterized gene UNC733 is allelic to rrp6-1
and will hereafter be referred to as RRP6.
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The rrp6-1 Mutation Causes the Accumulation of a 3' Extended 5.8 S rRNA Processing Intermediate-- In light of the striking homology between Rrp6p and a known nucleolar protein, we reasoned that rrp6-1 might cause a defect in some aspect of rRNA processing or ribosome biogenesis. Northern analysis of total cellular RNA from normal, rrp6-1, and rrp6-1 cells harboring the complementing plasmid YCpRRP6 revealed no obvious defects in the processing of the large rRNA precursors (data not shown). However, Northern blot analysis of total RNA separated on a polyacrylamide gel, using an oligonucleotide probe complementary to an internal portion of 5.8 S rRNA (o5.8S in Table II), revealed the accumulation of a novel 5.8 S rRNA intermediate in rrp6-1 strains (Fig. 4A). This intermediate (labeled 5.8S* in Fig. 4) is a doublet ~30 nucleotides longer than mature 5.8 S rRNA, and accounts for half of the 5.8 S rRNA in rrp6-1 strains. As expected, the presence of the complementing plasmid, YCpRRP6, reduces the accumulation of 5.8 S* by 95%, suggesting semidominance of rrp6-1 over RRP6. To determine if 5.8 S* represents a 5' or 3' extension of mature 5.8 S rRNA, we probed the same Northern blot with random-primed probes complementary to portions of ITS1 or ITS2 (Fig. 4, B and C, respectively). The ITS2 probe, but not the ITS1 probe, hybridized to 5.8 S*, suggesting that this molecule carries an extension at its 3' end.
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HindIII markers. C, Northern blot detection of
5.8 S rRNAs in normal and rrp6-1 strains compared with
those from the ascospore progeny analyzed in B.
Rrp6p Defects Block the Major Pathway of 5.8 S rRNA Processing-- The results presented above cannot distinguish between a role for Rrp6p in normal 5.8 S 3' end formation, or a role in destroying 5.8 S rRNA molecules with improperly processed 3' ends. The former model predicts that 5.8 S* rRNA should appear before 5.8 S rRNA, thereby slowing its rate of formation compared with that in normal cells. To test this, we analyzed 5.8 S rRNA processing by pulse-chase labeling with [3H]uracil in normal and rrp6::URA3 cells. The results, shown in Fig. 7, illustrate two interesting aspects of 5.8 S rRNA processing in mutant cells. First, the rate and extent of formation of total 5.8 S (5.8 S + 5.8 S*) is similar in normal and rrp6::URA3 cells. Second, the rates of formation of 5.8 S and 5.8 S* are vastly different in the two strains. In rrp6::URA3 cells, 5.8 S rRNA appears at one-twentieth the rate in normal cells. Importantly, 5.8 S* formation precedes that of 5.8 S rRNA in rrp6::URA3 cells and 5.8 S* levels fall as 5.8 S levels begin to rise. These findings suggest that 5.8 S* rRNA is an intermediate in the major pathway leading to the production of mature 5.8 S rRNA.
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Assembly of 5.8 S* rRNA into Active 60 S Ribosomes-- The viability and incomplete loss of 5.8 S rRNA 3' end formation displayed by the rrp6::URA3 disruptant could result from partial Rrp6p function or from activity produced from a duplicate copy of Rrp6p. However, a search of the open reading frames in the S. cerevisiae genome data base revealed no significant matches to the Rrp6p amino acid sequence other than Rrp6p itself. Partial Rrp6p activity from the rrp6::URA3 disruptant seems unlikely since it would result from a polypeptide with only 39 amino acids of Rrp6p. Finally, rrp6::URA3 cells grow surprisingly well considering that they produce mature 5.8 S rRNA 20-fold more slowly than normal cells. This led us to consider whether 5.8 S* rRNA may function in ribosomes, thereby accounting for the viability of rrp6::URA3 cells. Accordingly, we assessed the ability of 5.8 S* to assemble into 60 S ribosomal subunits and polyribosomes. Total RNA samples prepared from fractions of rrp6-1 and rrp6-1,YCpRRP6 polyribosomal gradients were analyzed by Northern blotting. Hybridization of o5.8S to samples derived from rrp6-1 cells revealed a distribution of 5.8 S* rRNA across the polyribosomal gradient identical to that for normal 5.8 S rRNA (Fig. 8). On the other hand, 7 S pre-5.8 S rRNA assembles into 60 S ribosomes, but does not form polyribosomes, consistent with previous findings (28). These results suggest that some portion of 5.8 S* rRNA assembles into active 60 S subunits and may account in part for the ability of rrp6- strains to survive despite slow production of mature 5.8 S rRNA.
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DISCUSSION |
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Top
Abstract
Introduction
Procedures
Results
Discussion
References
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The experiments described here provide evidence that RRP6 encodes a protein essential for efficient 3' end formation of 5.8 S rRNA. Recessive mutations in this gene cause a block in 5.8 S rRNA processing, resulting in the accumulation of 5.8 S molecules with normal 5' ends but with ~30-nucleotide extensions at their 3' ends. The homologies among Rrp6p, the human nucleolar PM-Scl 100 kDa autoantigen, and the E. coli 3'-5' exoribonuclease RNase D suggest that RRP6 may encode a nuclear and/or nucleolar exoribonuclease that plays a direct role in 5.8 S 3' end formation. Moreover, RNase D shows greater similarity to Rrp6p, PM-Scl 100 kDa, and predicted proteins from C. elegans and S. pombe than it does to any of the other four E. coli exoribonucleases, suggesting conservation of a specific RNase D function from bacteria to humans.
RNase D exhibits a non-processive 3'-5' exoribonuclease activity in vitro and may play a role in 3' end processing of tRNAs in E. coli (29, 30). Considering the similarity between Rrp6p and RNase D, we looked in rrp6 mutants for evidence of defects in tRNA processing, but observed no changes in the pattern of tRNATyr nor tRNALeu3 precursors (data not shown). These results indicate that rrp6 defects differ from those caused by a mutation in the RNA component of RNase P, which results in the accumulation of a similarly 3' extended form of 5.8 S rRNA, but which also causes defects in tRNA processing (31).
Loss of Rrp6p activity causes a 20-fold decrease in the rate of production of mature 5.8 S rRNA (Fig. 7B), suggesting that it plays an important role in the major pathway of 5.8 S rRNA 3' end processing. Recently, Mitchell et al. (8) identified and characterized a complex named the exosome, containing three or possibly four 3'-5' riboexonucleases required for efficient 5.8 S 3' end processing activity (8). Rrp6p is distinct from the proteins found in the exosome, yet our findings suggest that full 5.8 S rRNA processing activity by the exosome may require Rrp6p activity. Whether Rrp6p exists in a complex distinct from the exosome, or is a weakly associated subunit remains to be determined. Each of the exosomal riboexonucleases are required for cell growth, while Rrp6p is only required for growth at elevated temperature. The viability of rrp6 strains may result from the accumulation of 5.8 S* and its apparent ability to assemble into functional 60 S subunits.
Rrp6p shows strong similarity to PM-Scl 100 kDa, a protein to which autoantibodies are found in patients suffering from polymyositis, scleroderma, and an overlap of these two diseases (18, 32, 33). Immunofluorescence studies using autoantibodies to PM-Scl 100 kDa indicated that the human protein resides mostly in the nucleolus, with the remainder spread throughout the rest of the nucleus (34, 35). Immunoprecipitation experiments indicated that PM-Scl 100 kDa exists in large complexes containing 11-16 other proteins, but no small RNAs (35, 36). The cold-sensitive phenotype of rrp6-1 cells, as well as its semidominance over RRP6 is consistent with function of Rrp6p in a multisubunit complex. Whether Rrp6p acts alone, in concert with the exosome, or as part of a separate complex is currently under investigation.
We embarked on these studies in an effort to shed light on poly(A)
function in yeast. The observation that mutations producing specialized
ribosomes can suppress a polyadenylation defect is reminiscent of the
effects of ski and mak mutations on the stability and translation of poly(A) killer RNAs, as well as the
ability of dcp1, mrt, xrn1 and
spb mutations to suppress poly(A)-binding protein defects
(37-42). However, we have found that loss of function mutations in
XRN1, as well as in genes such as SPB2(RPL46) and
RPL16B that increase the ratio of 40 S to 60 S
ribosomes, do not suppress pap1-1
(43).4 Instead, our
unpublished results suggest that RRP6 may act at an early
step in mRNA biogenesis by limiting the levels of slowly, or
improperly processed precursor mRNAs.
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ACKNOWLEDGEMENTS |
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We thank Lasse Lindahl for providing plasmids and for helpful discussions, and Terry Platt and the members of our laboratory for comments on the manuscript.
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FOOTNOTES |
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* This work was supported by United States Public Health Service Predoctoral Training Grant 5-T32-AI070362 (to M. W. B.) and National Science Foundation Grants MCB-931664 and MCB-9603893 (to J. S. B.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
The nucleotide sequence(s) reported in this paper has been submitted to the GenBankTM/EMBL Data Bank with accession number(s) Z74909.
To whom correspondence should be addressed: Dept. of Microbiology
and Immunology, University of Rochester School of Medicine and
Dentistry, 601 Elmwood Ave., Box 672, Rochester, NY 14618. Tel.:
716-275-7921; Fax: 716-473-9573; E-mail:
btlr{at}uhura.cc.rochester.edu.
1 The abbreviations used are: ITS, internal transcribed spacer; PCR, polymerase chain reaction.
2 The BLAST program is available via the World Wide Web (http://www.ncbi.nlm.nih.gov/Recipon/bs_seq.html).
3 The Stanford Genome Resource Data Base is available via the World Wide Web (http://genome-www.stanford.edu).
4 M. W. Briggs, K. T. D. Burkard, and J. S. Butler, unpublished results.
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