Suppressors of a U4 Snrna Mutation Define a Novel U6 Snrnp Protein with RNA-Binding Motifs

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Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs

Karen W. Shannon and Christine Guthrie Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143 USA

U4 and U6 small nuclear RNAs are associated by an extensive base-pairing interaction that must be disrupted and reformed with each round of splicing. U4 mutations within the U4/U6 interaction domain destabilize the complex in vitro and cause a cold-sensitive phenotype in vivo. Restabilization of the U4/U6 helix by dominant (gain-of-function), compensatory mutations in U6 results in wild-type growth. Cold-insensitive growth can also be restored by two classes of recessive (loss-of-function) suppressors: (1) mutations in PRP24, which we show to be a U6-specific binding protein of the RNP-consensus family; and (2) mutations in U6, which lie outside the interaction domain and identify putative PRP24-binding sites. Destabilization of the U4/U6 helix causes the accumulation of a PRP24/U4/U6 complex, which is undetectable in wild-type cells. The loss-of-function suppressor mutations inhibit the binding of PRP24 to U6, and thus presumably promote the release of PRP24 from the PRP24/U4/U6 complex and the reformation of the base-paired U4/U6 snRNP. We propose that the PRP24/U4/U6 complex is normally a highly transient intermediate in the spliceosome cycle and that PRP24 promotes the reannealing of U6 with U4. [Key Words: Saccharomyces cerevisiae; splicing; snRNP; U6 snRNA; PRP24; RNP motif] Received January 18, 1991; revised version accepted February 28, 1991.

The removal of intervening sequences from pre-mRNA events suggests that destabilization of the U4/U6 inter- occurs in a large complex called the spliceosome. Essen- action may be involved in the catalytic activation of the tial components of the spliceosome include five evolu- spliceosome (Brow and Guthrie 1989). Once splicing has tionarily conserved small nuclear RNAs (snRNAs), U1, occurred, the U4/U6 interaction must presumably be re- U2, U4, U5, and U6 (for review, see Sharp 1987; Guthrie formed prior to the next round of splicing. Thus, the and Patterson 1988). U1, U2, and U5 are found in sepa- spliceosome cycle appears to involve the dynamic inter- rate small ribonucleoprotein particles (snRNPs), each conversion between the base-paired and the destabilized containing a set of common proteins (known as Sm pro- forms of the U4/U6 snRNP. teins) and a number of snRNP-specific proteins (for re- It has been proposed on phylogenetic grounds (Brow view, see L~hrmann 1988). In contrast, U4 and U6 are and Guthrie 1988) that U4 and U6 interact via base-pair- found base-paired together within a single particle ing to form two intermolecular helices (stem I and stem (Bringmann et al. 1984; Hashimoto and Steitz 1984). II), which are separated by an intramolecular stem in U4 The formation of the spliceosome is a highly ordered (see Fig. 1, below). The existence of stem I has been es- process that involves the stepwise assembly of the tablished by psoralen cross-linking experiments (Rinke snRNPs onto the pre-mRNA. Following binding of U1 et al. 1985). In vitro reconstitution studies have shown and U2 snRNPs to the 5' splice site and branchpoint re- that both stem I and stem II are required for the forma- gions, respectively (Mount et al. 1983; Black et al. 1985), tion of the U4/U6 snRNP (Hamm and Mattaj 1989; Pik- the U4/U6 snRNP is incorporated into the spliceosome, ielny et al. 1989; Bindereif et al. 1990; Vankan et al. probably in association with the U5 snRNP (Pikielny et 1990). The extensive base-pairing interaction between al. 1986; Bindereif and Green 1987; Cheng and Abelson U4 and U6 is consistent with the observation that the 1987; Konarska and Sharp 1987). Subsequently, the U4/ U4/U6 snRNP is very stable in vitro (T m ~53°C} [Brow U6 snRNP undergoes a dramatic conformational change, and Guthrie 1988); this has prompted speculation that such that U4 is no longer associated with the spliceo- an ATP-dependent RNA helicase may mediate the un- some upon electrophoresis in nondenaturing conditions winding event. Because the U4/U6 helix is energetically (Pikielny et al. 1986; Cheng and Abelson 1987; Lamond favorable compared to the unwound state, an RNA-bind- et al. 1988). This conformational rearrangement is ac- ing protein may additionally be required to stabilize U4 companied by the appearance of splicing intermediates and/or U6. Finally, in that the reformation of hydrogen and products. The temporal correlation between these bonds between the complementary bases in U4 and U6

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Shannon and Guthrie requires the two RNAs to be closely and specifically Results aligned, the reannealing event may also be an active pro- U4 mutations that destabilize the U4/U6 interaction cess. However, there is as yet little information about cause a cold-sensitive phenotype the role of such putative factors in splicing. Here, we describe a genetic approach to identify trans- In initial experiments we used a genetic approach to acting factors required for the destabilization and/or re- identify nucleotides required for the stability of the U4/ stabilization of the U4/U6 complex during the spliceo- U6 complex in vivo. In yeast, U4 and U6 are encoded by some cycle. Our strategy involved (1) the generation of single-copy genes that are essential for growth (Siliciano mutations in U4 that destabilize the U4/U6 complex in et al. 1987; Brow and Guthrie 1988). We used site-di- vitro and cause conditional lethal phenotypes in vivo, rected mutagenesis to make each of the single-base and (2) the isolation of extragenic suppressor mutations changes in U4 at positions 14, 13, 10, and 9 from the 5' that restore wild-type growth. This has led us to identify end of U4 (Fig. 1). The mutations were introduced into a a new member of the RNP-consensus family of RNA- strain carrying a deletion of the gene encoding U4 binding proteins (Bandziulis et al. 1989; Query et al. (SNR14) using the plasmid shuffle technique (Boeke et 1989), PRP24. We show that PRP24 is a novel U6- al. 1987). Strains containing both wild-type and mutant snRNP protein and that the growth defect resulting from U4 alleles showed no growth defect, indicating that the the destabilization of U4/U6 is suppressed by mutations mutations are recessive (data not shown). However, in the RNP-consensus motifs of PRP24 and by muta- most of the strains containing only the mutant alleles tions in putative-binding sites for this protein in U6. The showed a cold-sensitive phenotype (Table 1). The snrl4- genetic and biochemical properties of these mutants sug- G14C mutant, which contains a G ~ C change at posi- gest that PRP24, shown previously to be an essential tion 14, had the most dramatic cold-sensitive phenotype; splicing factor (Vijayraghavan et al. 1989), mediates the it failed to grow at 18°C, 22°C, or 25°C but grew well at reformation of the U4/U6 snRNP. Another member of 30°C and 37°C. The secondary structure model predicts the RNP-consensus family, hnRNP A1, has recently that this mutation would disrupt a stack of three G : C been reported to promote RNA annealing in vitro (Pon- base pairs between U4 and U6. The snrl 4--C10T mutant, tius and Berg 1990). which contains the C ~ T change at position 10, was the

A A C U C log- C A- U G91 A- U G-C 9o~ 100 110 C - G2o B0 GAACCGUU UUACAAAGAGAUUUAUUUCGUUUU O~ G-U U, C-G yeast U6 A ~ ApppO G, U U" G C38 G43 U-A Ahc C A G- C 30 f,o f so • U Xppp AU U UGGUCAA UU UGAAACAAUACAGA 72 A U,, U G C ~ A I A ', U G40 U G C u~GkcG 9 160 90 A UUUCCAUAAGGUUUUUAA CUGCCAGACCAAAUAUUAAUUUAAAGU " .,' U 6 7 C A 1 0 fO 150 G • U 80 70 U . C "G C 140G-CG-C G ~,./C U" A G 60~- G U'~UG~'GGI~'A : 3 stem II A - U stem I 60 C GJ~A o A UG-C U A U-A U U A - U UU U - A20 yeast U4 U-G G-C C-G U-G A - U100 50G-C 13OAG.CA U -A A A U -A U U A-U C GC u G-C UU" A A G3O C-G G A-U C U UoGl10 C G A-U U A A - U 4o G G C G lZ0G-C U U A U G U C U U Figure 1. Secondarystructure of the yeast U4/U6 complex, as proposed by Brow and Guthrie (1988). The position of the snrl4 and snr6 mutations generated by site-directed mutagenesis are indicated in boldface type. The position and sequence of the spontaneous recessive suppressor mutations in U6 are indicated with arrows.

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Novel U6 snRNP protein

Table 1. Phenotype of snrl4 mutants Two classes of mutations in U6 suppress the cold-sensitive phenotype of the snrl4-G14C mutation Temperature (°C) The finding that mutations that destabilize the U4/U6 snrl 4 strain 18 22 25 30 37 base-pairing interaction cause a cold-sensitive pheno- Wild-type + + + + + type was unexpected, because cold sensitivity is gener- G14A - + + + + ally thought to reflect the hyperstabilization of a com- G14C - - - + + plex. One possible explanation is that the U4/U6 com- G14T - - + + + plex is in equilibrium with an alternative, competing G13A - + + + + complex; mutations that destabilize the U4/U6 complex G13C - + + + + would drive this equilibrium toward the formation of the G13T - + + + + alternative complex. If true, we would expect mutations C10A - + + + + C10G - + + + + that destabilize the competing complex to suppress the C10T + + + + + cold-sensitive phenotype of the U4 mutant strains. To G9A - + + + + pursue this possibility, we isolated five spontaneous in- G9C - + + + + dependent revertants that grew at 18°C. Each revertant G9T - + + + +

only mutant strain of the 12 tested that did not show a Temperature (°C) cold-sensitive phenotype. This mutation would allow A 20 35 40 45 50 55 60 20 the formation a G : U base pair, which would presumably maintain a stable U4/U6 interaction. U4/U6 To test whether these mutations in fact destabilize the U4/U6 complex, we prepared snRNP-enriched fractions from several mutant strains and determined the Tm (temperature at which 50% dissociation is observed) of U4 "-~ the U4/U6 complex in these fractions after treatment with proteinase-K and SDS (Fig. 2). The Tm of the U4/U6 complex in the snrl4--ClOT strain was ~51°C, which is 20 35 40 45 50 55 60 20 similar to the Tm of ~53°C measured in wild-type strains (Brow and Guthrie 1988). The Tm of U4/U6 in the snrl4- G14C strain was ~37°C, indicating that the U4/U6 com- U4/U:6 plex is significantly less stable in this mutant. These data may suggest that destabilizing the U4/U6 complex causes the cold-sensitive phenotype observed in vivo. To provide more direct evidence for this hypothesis, U4"-~ we used the strategy of making compensatory base-pair changes. Using site-directed mutagenesis, we made each single-base change in U6 at positions 67 and 72; posi- C 20 35 40 45 50 55 60 20 tions 67 and 72 of U6 are predicted to base-pair with positions 14 and 9 of U4, respectively (Fig. 1). We intro- U4/U6 duced the U6 mutant alleles into strains containing the U4 mutations and looked for suppression of the cold- sensitive phenotype (Fig. 3). Each of these strains also o contained a wild-type copy of the gene encoding U6 (SNR6). Strains carrying mutant U6 alleles in combina- tion with wild-type U4 alleles showed no growth defect, indicating that the U6 mutations did not have a dominant negative effect. Transforming the U4 mutant Figure 2. Tm determinations of the U4/U6 complex in snrl4 strains with the wild-type U6 allele or the predicted non- mutant strains. Aliquots of proteinase-K/SDS-treated fraction I compensatory U6 alleles did not alleviate the cold-sen- prepared from a wild-type strain (MA Ta trp l his3 ura3 ade2 lys2 sitive growth defect. However, when we restored the po- snr14::TRPI pUN90-SNR14) (A), the snr14-G14C strain tential for base-pairing between U4 and U6 by introduc- (MATa trpl his3 ura3 ade2 lys2 snrl4::TRP1 pUN90-snrl4- G14C) (B), or the snrl 4-Cl OT strain (MA Ta trp l his3 ura3 ade2 ing the compensatory U6 alleles, wild-type growth was lys2 snrl4::TRP1 pUNgO-snrl4-ClOT) (C) were incubated at restored. These results demonstrate that U4 (positions the temperatures indicated for 5 rain and then subjected to elec- 14 and 9) and U6 (positions 67 and 72, respectively) in- trophoresis on a native gel. RNA was transferred to a nylon teract via Watson-Crick base-pairing. Moreover, these membrane and probed with a 32p-labeled oligonucleotide spe- results argue that the cold-sensitive phenotype is due to cific for U4. The bands corresponding to free U4 and its complex the disruption of base-pairing between U4/U6. with U6 are indicated with arrows.

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Shannon and Guthrie

Temperature ( o C) Temperature (Oc)

U4, U6 allele 18 25 30 37 U4, U6 allele 18 25 30 37

SNR14, SNR6 ÷ ÷ + + SNR14, SNR6 + + ÷ +

SNR14, snr6-C67A + + + + SNR14, snr6-C72A + + + +

SNR14, snr6-C67G + + + ÷ SNR14, snr6-C72G + + + +

SNR14, snr6-C67T + + + + SNR14, snr6-C72T + + + +

snr14-G14A, SNR6 - + + + snr14-G9A, SNR6 - + + +

snr14-G14A, snr6-C67A - + -I- + snr14-G9A, snr6-C72A - + + +

snr14-G14A, snr6-C67G - + + + snr14-G9A, snr6-C72G - + ÷ +

snr14-G14A, snr6-C67T + + + + snr14-G9A, snr6-C72T + + + -I-

snr14-G14C, SNR6 - + + snr14-G9C, SNR6 - + + +

Figure 3. Growth of snrl4 snr6 double snr14-G14C, snr6-C67A - + + snr14-G9C, snr6-C72A - + + -I- mutants, snrI4 mutant strains (MATa trpl his3 ura3 ade2 lys2 SNR6 snrl4::TRP1 snr14-G14C, snr6-C67G -I- + + + snr14-G9C, snr6-C72G + + + + pUN90-snrl4) were generated as described snr14-G14C, snr6-C67T - + + snr14-G9C, snr6-C72T - + + + in Materials and methods. YCp50 plasmids carrying the snr6 mutations were introduced into these strains by transformation. snr14-G14T, SNR6 - + + + snr14-G9T, SNR6 - + + +

Transformants were selected, plated onto snr14-G14T, snr6-C67A + + + + snr14-G9T, snr6-C72A + + + + SD medium lacking histidine and uracil, and incubated at the temperatures indi- snr14-G14T, snr6-C67G + + + + snr14-G9T, snr6-C72G + + + + cated. Strains were scored for growth ( + ) or snr14-G14T, snr6-C67T - + + + snr14-G9T, snr6-C72T + + + no growth (-).

was crossed to a parent strain of the opposite mating type To determine whether these suppressors act by resta- to generate diploid strains homozygous for snrl4-G14C bilizing the U4/U6 complex, we determined the Tm of and heterozygous for the suppressor alleles. One diploid the U4/U6 complex in proteinase-K/SDS-treated frac- strain grew at 18°C, indicating that this suppressor mu- tions prepared from several strains. As expected, the Tm tation was dominant. Four diploid strains did not grow at of the U4/U6 complex in the dominant suppressor con- 18°C, indicating that these suppressor mutations were taining the compensatory change in U6 (SNR6-C67G) recessive. We expected the compensatory U6 mutation was -53°C (Fig. 4A), the same as that measured in the to confer a dominant phenotype since the SNR6--C67G wild-type strain. In contrast, the T m of the complex in mutation suppressed the snrl4-G14C mutation in the one of the recessive suppressor strains (snr6-A91 G) was presence of wild type U6 (Fig. 3). We partially sequenced -37°C (Fig. 4B), the same as that measured in the snrl4- U6 from total RNA prepared from the dominant suppres- G14C strain. Thus, it appears there are at least two sor and found a C--* G change at position 67. We had mechanisms by which mutations in U6 can suppress the shown that this single-base change, when generated by snrl4-G14C mutation, one of which does not restore site-directed mutagenesis, is sufficient to confer suppres- wild-type stability to the U4/U6 complex in vitro. sion (Fig. 3). In an attempt to determine the identity of the reces- Mutations in PRP24 suppress the cold-sensitive sive suppressors, we first transformed these strains with phenotype of the snrl4--G14C mutation plasmids carrying wild-type alleles of genes encoding the U snRNAs. When a plasmid carrying SNR6 was intro- The fact that we isolated recessive suppressor mutations duced into any of the recessive suppressor strains, the in U6 suggested to us that U6 may be involved in an cells again became cold-sensitive (data not shown). Plas- interaction that competes with the U4/U6 base-pairing mids carrying genes encoding U1, U2, U4, and U5 had no interaction. If true, we would expect to recover addi- effect. These data suggest that the recessive suppressor tional recessive suppressor mutations in genes encoding mutations are alleles of SNR6. We then sequenced either factors that are associated with U6. Thus, we attempted the U6 snRNA or the U6 gene from each of the recessive to isolate suppressors by a second strategy, in which we suppressors. In each case, we identified a single-nucle- selected against recessive suppressors in the U6 gene. To otide change. Each of these mutations maps outside the accomplish this, an additional copy of the wild-type U6 U4/U6 interaction domain: Three are found in a short gene was introduced into the snr14--G14C strain by stretch 5' of the interaction domain (snr6-T38C, snr6- transformation with a plasmid carrying SNR6 and A4OG, and snr6-C43G), and one is found 3' of the inter- URA3. We plated these cells at 18°C and picked rever- action domain (snr6-A91 G) (Fig. 1). tants. Cells that lost the URA3-marked plasmid were

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Novel U6 snRNP protein

Temperature (°C) regated with the temperature-sensitive growth defect,

20 35 40 45 50 55 60 20 indicating that a single mutation caused both pheno- A types. Standard complementation and allelism tests showed that all three suppressors were due to mutations in the same gene. U4/U6---~ In an attempt to identify the suppressor gene, we took advantage of the temperature-sensitive suppressor allele and performed complementation analysis with a set of u4 --..~ temperature-sensitive mutants defective in pre-mRNA splicing (Hartwell 1967; Vijayraghavan et al. 1989). This analysis demonstrated that the suppressors were muta- 20 35 40 45 50 55 60 20 tions in PRP24. The prp24-1 allele was originally iden- B tified as a temperature-sensitive mutation that accumu-

u4/u6..-.~ lates pre-mRNA at the nonpermissive temperature (Vi- jayraghavan et al. 1989). We cloned the wild-type PRP24 gene on the basis of its ability to complement the temperature-sensitive growth defect of the U4 suppressor. This temperature-sensitive strain was transformed with u4--~ a yeast genomic library constructed in a centromere plasmid (Rose 1987) and plated on selective medium at 3 7°C. Two related plasmids containing 19- to 20-kb inserts Figure 4. Tm determinations of the U4/U6 complex in suppres- were recovered. We isolated a 3.5-kb XbaI fragment that sor strains. Aliquots of proteinase-K/SDS-treated fraction I pre- conferred temperature resistance. We partially se- pared from the suppressor containing the SNR6--C67G muta- quenced this clone and found an open reading frame that tion (MATa trpl his3 ura3 ade2 lys2 snrl4::TRP1 pUN90- snrl4--G14C SNR6--C67G) (A) or the snr6-A91G mutation contained sequence motifs conserved among RNA-bind- (MATa trpl his3 ura3 ade2 lys2 snrl4::TRP1 pUN90-snrl4-- ing proteins of the RNP-consensus family (Fig. 5) (Band- G14C snr6-A91G) (B) were incubated at the temperatures indi- ziulis et al. 1989; Query et al. 1989). Mahshid Company cated for 5 min. The samples were analyzed by native gel elec- and John Abelson have independently cloned and se- trophoresis as described in the legend to Fig. 2. The bands cor- quenced this 3.5-kb genomic fragment and found a single responding to free U4 and the U4/U6 complex are indicated. open reading frame that can encode a 51-kD protein (pets. comm.). We examined this sequence and found that PRP24 contains three tandem regions homologous to the -80 amino acid RNP-consensus domain. then selected by plating the cells on 5-fluoro-orotic acid (5-FOA). Cells that could not grow at 18°C on 5-FOA Changes in the RNP-consensus domain of PRP24 are presumably contain a dominant suppressor mutation in necessary for suppression a gene carried by the plasmid and were discarded. Using this scheme, we recovered 14 independent revertants. As a first step toward understanding how prp24 muta- Each revertant was crossed to a parent strain of the op- tions act to suppress the snrt4--G14C mutation, we posite mating type to generate diploids homozygous for cloned and partially sequenced the prp24 gene from each the snrl4-G14C allele and heterozygous for the suppres- of the suppressors containing the prp24 alleles. We used sor allele. These diploids were tested for their ability to the gap repair method (Orr-Weaver et al. 1981) to isolate grow at 18°C. Diploid strains generated from 11 of the the mutant prp24 genes. A yeast centromere plasmid car- revertants did grow at 18°C, indicating that these sup- rying the wild-type PRP24 gene was linearized at an in- pressor mutations were either dominant or intragenic ternal ClaI site and introduced into each of the three revertants. Diploid strains generated from three of the suppressors. Transformants were selected and screened suppressors did not grow at 18°C, indicating that these for their ability to grow at 18°C. Approximately 80% of mutations were recessive. Only the recessive revertants the transformants grew at 18°C, suggesting that the plas- were considered further. mid-linked allele of PRP24 was efficiently repaired to the Two of the recessive revertants grew at all tempera- mutant allele. In each case, we recovered the plasmids tures tested. The third recessive revertant showed a re- from three independent 18°C + transformants and se- cessive temperature-sensitive growth defect; these hap- quenced -275 nucleotides on either side of the ClaI site. loid cells grew at 18°C and 25°C but failed to grow at We compared these sequences to the wild-type PRP24 30°C and 37°C. The diploid strains generated from the sequence and found single nucleotide changes in regions recessive revertants were sporulated. In each case, tetrad corresponding to highly conserved elements within the analysis showed that the cold-resistant phenotype segre- carboxyoterminal RNP-consensus domain (Fig. 5). Two gated 2 : 2, indicating that each suppressor is caused by a of the suppressors (prp24-2 and prp24-3) contained a mu- mutation in a single nuclear gene. Tetrad analysis of the tation in the conserved element, called RNP 1. This 8- diploid strain generated from the temperature-sensitive amino-acid motif is the region of highest conservation revertant showed that the suppressor phenotype coseg- within the -80-amino-acid RNP-consensus domain

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Shannon and Guthrie

Domain RNP 2 RNP 1

PRP24 3 TDSATLEGRE IMIRNL STELLDENLLRESFEG-FGSIEKINI--PAG-QKEHSFN NCCAFMVF ENKDSAERAL-QMNRS-LLGNREISVSLAD prp24-2 3 ...... R ...... prp24-3 3 ...... S ......

prp24-4 3 ...... P ......

PABP Human 4 DRITRYQGVN LYVKNL DDG-IDDERLRKEFSP-FGTITSAKVM-MEG-GRS .... KGFGFVCF SSPEEATKAVTEMNGRIVATKPLYVALAQR

hnRNP A1 Fly 2 PNAGA-TVKK LFVGAL KDD-HDEQSIRDYFQH-FGNIVDINIVIDKETGKK .... RGFAFVEFIDDYDPVDKWLQKQHQ-LNGKMVDVKKALP

UIA Human 1 AVPETRPNHT IYINNL NEKIKKDE-LKKSLYAIFSQFGQILDILVSRSLKM .... RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKT

U1 70K Human PNAQGDAFKT LFVARV N-YDTTESKLRREFEV-YGPIKRIHMVYSKRSGKP .... RGYAFIEY EHERDMHSAYKHADGKKIDGRRVLVDVERG

elav Fly 3 LASGPGGAYP IFIYNL -APETEEAALWQLFGP-FGAVQSVKIVKDPTTN-QC .... KGYGFVSM TNYDEAAMAIR ..... ALNGYTMGNRVLQV

RNP consensus LFVGNL E L F FG I K KGFGFVXF A L G IYIKG D Y V R R YA Y I Figure 5. Sequence of PRP24 in suppressor strains. Amino acid sequences of PRP24 (amino acids 202-288) in a wild-type strain and the suppressor strains containing the prp24-2, prp24-3, and prp24-4 mutations are aligned with sequences containing the RNP- consensus domain: human polyadenylate-binding protein (PABP) domain 4 tGrange et al. 1987), Drosophila hnRNP A1 domain 2 {Haynes et al. 1987), human U1 A (Sillekens et al. 1987), human U1 70K (Theissen et al. 1986), and Drosophila elav domain 3 (Robinow et al. 1988). Residues of PRP24 from the suppressor strains that are identical to PRP24 from the wild-type strain are indicated by dots. Gaps introduced to maximize homology are marked by hyphens. Sequence elements RNP 2 and RNP 1 are boxed. RNP-consensus sequences were identified previously by Bandziulis et al. {1989).

{Bandziulis et al. 1989}. The temperature-sensitive sup- prepared from the wild-type strain at various ionic pressor {prp24-4) contains a mutation in a region called strengths. Coprecipitated RNA species were visualized RNP 2 that changes a highly conserved leucine residue by Northem blot analysis using labeled oligonucleotide to a proline. Previous work has shown that mutations in probes {Fig. 6A). Anti-PRP24 antiserum immunoprecip- RNP 2 or RNP 1 block the binding of the snRNP protein itated U6 at salt concentrations up to 2.0 M, the highest UIA to U1 snRNA in vitro (Scherly et al. 1989}. salt concentration tested. Antibodies affinity-purified using the trpE/PRP24 fusion protein also immunoprecipitated U6 {data not shownl. U1, U2 {data not shown}, U4, U6 snRNA coimmunoprecipitates with the PRP24 and the two forms of yeast U5 were not detectably im- protein in wild-type extracts munoprecipitated at salt concentrations above 250 mM. The genetic analysis demonstrates that mutations that Under the less stringent conditions (100 and 250 mM}, destabilize the U4/U6 complex can be suppressed by sin- immunoprecipitation of snRNAs was not dependent on gle-nucleotide changes in U6 and single-amino-acid the addition of anti-PRP24 antiserum {data not shown}. changes in regions of PRP24 that correspond to putative We reproducibly found that the immunoprecipitability RNA-binding sites. A parsimonious explanation for of U6 increased with increasing sah concentrations up to these observations is that the U4/U6 complex is in equi- 750 mM. Although this observation may be unexpected, librium with a complex containing PRP24 and U6. To it is not unprecedented; the binding of several hnRNP test this prediction directly we generated antibodies to proteins to poly(G) or poly{U) is more efficient at 0.5 si PRP24. We used the cloned PRP24 gene to construct a salt than at 0.1 M NaC1 {Swanson and Dreyfuss 1988}. trpE/PRP24 fusion, which contained -85% of the PRP24 The higher salt concentrations may expose epitopes on open reading frame. This gene fusion was expressed in PRP24 that are masked at lower ionic strengths. The Escherichia coli, and the fusion protein was gel-purified addition of ATP to the splicing extract prior to addition from insoluble fractions of E. coli lysate. The purified of anti-PRP24 antiserum did not affect the amount of U6 fusion protein was used to immunize rabbits to generate immunoprecipitated nor change the pattem of snRNAs polyclonal antiserum. We cannot detect PRP24 in yeast immunoprecipitated {data not shown}. splicing extracts by Western blot analysis; however, the We also immunoprecipitated PRP24 from splicing ex- anti-PRP24 antiserum recognized an -45-kD protein in tracts prepared from various mutant strains {Fig. 6B}. extracts prepared from strains that overexpress PRP24 Surprisingly, anti-PRP24 antiserum immunoprecipitated under the control of the glucose-6-phosphate dehydroge- both U4 and U6 from extracts prepared from the strain nase promoter (Schena et al. 1991)(data not shown). This containing the snrl4-G14C mutation (lane 2). The asso- is not inconsistent with the molecular mass of 51 kD ciation of PRP24 with U4 and U6 in this mutant extract predicted from the nucleotide sequence of PRP24. was stable at salt concentrations up to at least 2.0 M. In We immunoprecipitated PRP24 from splicing extracts contrast, only U6 was immunoprecipitated with anti-

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Novel U6 snRNP protein

A with U4 migrates on gradients as a U6 snRNP (Hamm 1 2 3 4 5 6 7 8 1 2 3 4 5 and Mattaj 1989; Bordonn4 et al. 1990). Gradient sedi- mentation of splicing extracts also resolves two other U 1 ---I~. U 1 ---I~ particles containing U6:U4/U6 and U4/U5/U6 (Black and Pinto 1989; Bordonn6 et al. 1990). Native gel electrophoresis (Konarska and Sharp 1987)and immunoprecipitation experiments (Bordonn6 et al. 1990)have dem-

USL ~ USL onstrated that the particles separated on glycerol gradi- USS ~ USS ents represent bona fide associations and not fortuitous U 4 ----I~ U 4 ---.1~ comigrations. To determine whether PRP24 is associated with all U6-containing complexes or with specific U6-containing complexes, we fractionated wild-type U 6 ---IP. U 6 ---I~ yeast splicing extract on glycerol gradients, immunoprecipitated PRP24 from gradient fractions, and analyzed Figure 6. Precipitation of snRNAs with anti-PRP24 antiserum. the coprecipitated RNA on Northern blots. A Northern (A) Splicing extract prepared from a wild-type strain (MATa trpl blot of RNA isolated from gradient fractions showed that his3 ura3 ade2 lys2 snrl4::TRP1 pUN90--SNR14J was incu- the gradient separated U4/U5/U6 (fractions 29-25), U4/ bated with anti-PRP24 antiserum at 100 mM (lane 1), 250 mM U6 (fractions 19-15), and free U6 snRNP (fractions 13-9) (lane 2), 500 mM (lane 3), 750 mM (lane 4), 1.00 M (lane 5), 1.25 (Fig. 7A). Anti-PRP24 antiserum immunoprecipitated M (lane 6), 1.50 M (lane 7), or 2.00 M (lane 8) NaC1. RNA recov- U6 only from the region of the gradient containing free ered from the immune complexes was electrophoresed on a 6% U6 snRNP (fractions 14-10) (Fig. 7B). We think it is un- polyacrylamide denaturing gel, transferred to a nylon mem- likely that PRP24 is inaccessible for the binding of anti- brane, and probed with 32p-labeled oligonucleotides specific for U1, U4, U5, and U6. The positions of the bands corresponding PRP24 antibodies in the larger particles because the im- to U1, U4, U5, and U6 are indicated with arrows. {B) Splicing munoprecipitation experiments were performed under extract prepared from a wild-type strain (MATa trpl his3 ura3 conditions (750 mM NaC1) that disrupt the HeLa U4/U6 ade2 lys2 snrl4::TRP1 pUN90--SNRI4) (lane 1), the snrl4- and U4/U5/U6 particles in vitro (R. Lfihrmann, pers. G14C mutant (MATa trpl his3 ura3 ade2 lys2 snrl4::TRP1 comm.). These observations suggest that PRP24 is asso- pUN90-snrI4-G14C) (lane 2), the suppressor strain carrying ciated specifically with free U6 snRNP in wild-type ex- the SNR6-C67G mutation (MATa trpl his3 ura3 ade2 lys2 tracts. However, we cannot rule out the possibility that snrl4::TRP1 pUN90-snrl4-G14C SNR6--C67G) (lane 3), the PRP24 also binds the U4/U6 helix, but it dissociates un- snr6-A91G mutation (MATa trpl his3 ura3 ade2 lys2 der the conditions necessary for immunoprecipitation. snr14::TRP1 pUN90-snrl4--G14C snr6--A91G) (lane 4) or the We repeated these experiments with extract prepared prp24-2 mutation (MATa trpl his3 ura3 ade2 lys2 snrl4::TRP1 pUNgO--snrl 4-G14C prp24-2) (lane 5) was incubated with anti- from the snrl4-GI4C strain. The Northern blot of RNA PRP24 antiserum at 2.0 M NaC1. RNA recovered from the im- isolated from the gradient fractions showed that the ex- mune complexes was treated as in A. tracts prepared from the snrl4-G14C strain contain significantly more U4/U6 snRNP (fractions 19-13} and significantly less free U6 snRNP (fractions 11-9) than the wild-type extracts (Fig. 7C). However, Northern blot PRP24 antiserum in extracts prepared from the domi- analysis also showed that total RNA from this extract nant suppressor SNR6-C67G (lane 3). Thus, it appears contained approximately fivefold more U4 than extracts that U4 coimmunoprecipitates with PRP24 only when prepared from the wild-type strain (data not shown). the U4/U6 base-pairing interaction is disrupted. Anti- Thus, it appears that the excess U4 present in the snrl4-- PRP24 antiserum precipitated neither U4 nor U6 from G14C strain can sequester the excess U6 normally found extracts prepared from recessive suppressors containing in wild-type strains into a U4/U6 snRNP. Anti-PRP24 the snr6-A91G allele (lane 4) or the prp24-2 allele (lane antiserum immunoprecipitated U4 and U6 from the re- 5) at 2.0 M salt or at any salt concentration we tested (250 gion of the gradient containing the U4/U6 snRNP (frac- mM to 2.0 M; data not shown). Although it appears that tions 1.8-14) and free U6 snRNP (fractions 12-10). Thus, the binding of PRP24 to U6 is blocked in these strains, in contrast to wild-type strains, the snrl4-G14C strain our assay cannot detect low-affinity binding because we contains a U4/U6 snRNP population that is tightly as- cannot measure PRP24/U6 binding in wild-type strains sociated with PRP24. at salt concentrations below 500 mM NaC1. Thus, these results suggest that the recessive suppressor mutations in SNR6 and PRP24 either disrupt or destabilize the as- Discussion sociation of PRP24 with the U6 snRNA. Base-pairing, but not specific sequences, is required at two positions in U4/U6 stem H PRP24 is associated with free U6 snRNP, not U4/U6 snRNP or U4/U5/U6 snRNP in wild-type extracts We proposed previously that U4 and U6 are tightly associated via an extensive base-pairing interaction com- In yeast, U6 is present in 5- to 10-fold excess over U4 posed of two intermolecular helices, stem I and stem II (D.A. Brow and C. Guthrie, unpubl.). U6 not associated (Brow and Guthrie 1988). The stem I interaction was

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Shannon and Guthrie

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U4/:U51U6 U4/U6 U6 U4/U5/U6 U41U6 U6 Figure 7. Immunoprecipitation of snRNPs with anti-PRP24 antiserum. Splicing extract prepared from a wild-type strain (MATa trpl his3 ura3 ade2 lys2 snrl4::TRP1 pUN90--SNR14) (A and B) or the snrl4--Gl4C mutant (MATa trpl his3 ura3 ade2 lys2 snr14::TRP1 pUN90--snrl4-G14C) (C and D) was fractionated on a 10-30% glycerol gradient. RNA was recovered from odd-numbered fractions, electrophoresed on a 6% polyacrylamide denaturing gel, transferred to a nylon membrane, and probed with 32p-labeled oligonucleotides specific for U4, U5, and U6 (A and C). Even-numbered fractions were incubated with anti-PRP24 antiserum at 750 m~ NaC1. RNA recovered from the immune complexes was analyzed as described above (B and D). The top of the gradient is at the right. The position of the bands corresponding to U4, US, and U6 are indicated with arrows. The fraction numbers are indicated at the top, and the position of the different snRNPs are shown at the bottom.

previously established by psoralen cross-linking [Rinke principle, the cold-sensitive phenotype could then be et al. 1985). We have now provided genetic evidence for suppressed either by increasing the stability of the mu- the existence of stem II. A U4 point mutation, snr14- tant U4/U6 complex or by decreasing the strength of the G14C, which is predicted to disrupt base-pairing in stem altemative interaction. We isolated spontaneous cold- II of the interaction domain, dramatically destabilizes insensitive suppressors of the G---* C mutation in U4 the U4/U6 complex in an in vitro assay, lowering the Tm (snrl4-G14C), which fell into three classes: (1) a domi- from 53°C to 37°C. This mutation and several nearby nant mutation in the U6 gene, SNR6, which restores mutations in U4 (positions 14, 13, 10, and 9) cause a U4/U6 base-pairing and U4/U6 complex stability; (2) re- recessive, cold-sensitive lethal phenotype in vivo. Wild- cessive mutations in SNR6, which are found in two re- type growth of strains carrying U4 mutations at posi- gions outside the interaction domain and do not restabi- tions 9 and 14 in stem II is restored by introducing U6 lize the U4/U6 complex; and (3) recessive mutations in genes containing mutations predicted to restore base- PRP24. PRP24 was initially identified in a screen for pairing with the U4 snRNA. This suppression is allele- temperature-sensitive lethal mutations that block pre- specific because U6 genes containing noncompensatory mRNA splicing (Vijayraghavan et al. 1989). The prp24-I mutations had no effect. These results demonstrate that mutant accumulates pre-mRNA at the nonpermissive a stable base-pairing interaction between U4 and U6 is temperature, suggesting that PRP24 acts prior to the first essential for growth at low temperature. covalent modification in the splicing reaction. We cloned and partially sequenced the PRP24 gene and noted sequence motifs characteristic of RNA-binding A suppressor of the base-pairing defect encodes a U6-binding protein proteins of the RNP-consensus family. The gene was independently cloned by Mahshid Company and John We took advantage of the conditional lethal phenotype Abelson, who provided us with the complete sequence. of the U4 mutations to understand the consequences of Upon examination, we identified three regions homolo- destabilizing the U4/U6 base-pairing interaction. We gous to the RNP-consensus domain. This -80-amino- reasoned that destabilization of this complex might lead acid motif is shared among a number of proteins that to the hyperstabilization of a competing interaction. In bind RNA, including polyadenylate-binding protein, het-

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Novel U6 snRNP protein erogeneous nuclear RNP (hnRNP) proteins, and proteins U6 snRNP present in the wild-type strain, at least a frac- associated with specific U snRNPs (for review, see Band- tion of the U4/U6 snRNP found in the snrl4-G14C mu- ziulis et al. 1989). We used immunoprecipitation exper- tant contains PRP24. These results suggest that PRP24, iments to show that PRP24 is tightly associated with the U4, and U6 can form a stable complex in the snrl4- U6 snRNA in wild-type extracts. PRP24 remains bound G14C mutant. The accumulation of the PRP24/U4/U6 to U6 at salt concentrations as high as 2 M NaC1. For complex is apparently caused by destabilizing the U4/U6 comparison, yeast poly{A)-binding protein binds poly(A) interaction, since PRP24 bound only U6 in a dominant in vitro up to 1 M NaC1, and hnRNP A1 binds poly(U) in suppressor strain containing the snrl4-Gl4C mutation vitro up to 0.5 M NaC1 (Swanson and Dreyfuss 1988). and the U6 mutation that restores U4/U6 base pairing. Although these experiments do not prove that PRP24 interacts directly with the RNA, analysis of the recessive suppressors demonstrated that the association of PRP24 A model for PRP24-mediated suppression with U6 is weakened by either single-base changes in U6 We have shown that destabilizing the U4/U6 base-pair- or by single-amino-acid changes in regions of PRP24 cor- ing interaction leads to a cold-sensitive phenotype and responding to the RNP 2 and RNP 1 motifs of the car- the accumulation of a novel complex containing PRP24, boxy-terminal RNP-consensus domain. RNP 2 and RNP U4, and U6. In the simplest view, the inability to grow at 1 are the two most highly conserved elements within the low temperature is causally related to the accumulation RNP-consensus domain and are essential for RNA bind- of the PRP24/U4/U6 complex. This is consistent with ing in vitro. UV cross-linking experiments have shown the idea that cold sensitivity is due to the hyperstabili- that residues of RNP 2 and RNP 1 in hnRNP A1 directly zation of a complex. We have not yet tested whether the contact the bound nucleic acid (Merrill et al. 1988). Fur- accumulation of the PRP24/U4/U6 complex is exacer- thermore, mutations in RNP 2 and RNP 1 in the U1A bated in extracts prepared from snr14-G14C cells shifted protein block binding to U1 snRNA in vitro (Scherly et to 18°C; however, this kind of experiment is complicated al. 1989). Together, these results suggest that PRP24 di- by the fact that splicing extracts are prepared at temper- rectly binds the U6 snRNA and that the regions of atures well below the permissive temperature for the PRP24 and U6 defined by the recessive suppressor mu- growth of this mutant strain. If the accumulation of the tations may be good candidates for binding sites. PRP24/U4/U6 complex causes the cold-sensitive phenotype, then mutations that reduce the levels of this com- A complex containing PRP24, U4, and U6 plex would be expected to act as suppressors. Indeed, the accumulates when the U4/U6 interaction is two classes of recessive suppressors appear to inhibit the destabilized binding of PRP24 to U6. This leads us to propose that a reaction exists that interconverts the PRP24/U4/U6 U6 can be found in three particles: free U6, U4/U6, and complex and the U4/U6 complex. Mutations that desta- U4/U5/U6. The formation of the U4/U5/U6 snRNP bilize the U4/U6 complex drive the reaction toward the from the U4/U6 and U5 snRNPs appears to be an obli- formation of the PRP24/U4/U6 complex. The recessive gate step in vivo (Bordonn6 et al. 1990). This multi- suppressors compensate by reducing the affinity of snRNP may function to deliver the U4, U5, and U6 PRP24 for U6, either by partially inactivating the bind- snRNAs to the spliceosome (Konarska and Sharp 1987). ing activity of the protein or the binding site(s) on the The function of the free U6 snRNP is not known. Free RNA. Although we cannot yet rule out the possibility U6 snRNP probably acts as a pool of U6 for the assembly that the PRP24/U4/U6 complex is aberrant and unique of the U4/U6 and U4/U5/U6 snRNPs although it is also to the snrl4--G14C mutant, we favor the interpretation possible that free U6 snRNP represents a distinct popu- that the PRP24/U4/U6 complex is a normal intermedi- lation of U6 not normally recruited for multi-snRNP as- ate in the U4/U6 cycle. sembly. A model that integrates this reaction into the spliceo- In wild-type extracts, PRP24 is tightly associated with some assembly pathway is outlined in Figure 8. Accord- U6 in fractions enriched for the free U6 snRNP but is not ing to this model, the PRP24/U4/U6 complex is nor- detectable in fractions enriched for the U4/U6 snRNP or mally a transient intermediate in the annealing of the U4 the U4/U5/U6 snRNP. Our experiments cannot distin- and U6 snRNAs. After PRP24/U6 binds U4, PRP24 dis- guish whether PRP24 is a component of the entire free sociates from the PRP24/U4/U6 complex concomitant U6 snRNP population or whether PRP24 is associated with a specific subset of the free U6 snRNP. In contrast, both U4 and U6 are tightly associated with PRP24 in a <~ CS defect strain containing the snrl4-G14C mutation, which destabilizes the U4/U6 base-pairing interaction. Because U4 is overproduced approximately fivefold in the snrl4- G14C mutant, the levels of U4 and U6 are comparable to one another in this strain. Glycerol gradient fractionation of extracts prepared from the snrl4-G14C strain showed that most of the U6 is found in a particle that Figure 8. Model outlining the potential function of PRP24 in migrates as a U4/U6 snRNP. However, unlike the U4/ the U4/U6 cycle.

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Shannon and Guthrie with the formation of the U4/U6 helix. This reaction 1989). EcoRI-BamHI fragments carrying the snrl4 genes were may be involved in the initial assembly of the U4/U6 subcloned into pUNg0 (CEN, HIS3) (Elledge and Davis 1988). snRNP during snRNP biogenesis and/or in the reassem- EcoRI-HpaI fragments carrying the snr6 genes were subcloned bly of the U4/U6 complex after the U4/U6 interaction is into YCp50 (CEN, URA3) (Parent et al. 1985). The sequence of each construct was confirmed by dideoxynucleotide sequencing disrupted in the formation of the active spliceosome. In using Sequenase (U.S. Biochemicals). either case, the accumulation of the PRP24/U4/U6 complex in the cold-sensitive mutants would act to sequester U4 and U6 so that the U4/U6 complex cannot efficiently Yeast strains and genetic methods form for the next round of splicing. This model is con- All strains used in this study are derived from Saccharomyces sistent with our data showing that mutations that desta- cerevisiae strain YK82 (MATa trpl his3 ura3 ade2 lys2 bilize the U4/U6 base-pairing interaction lead to the ac- snrl4::TRP1 YCp50--SNR14). YKS2 is a haploid strain carrying cumulation of the PRP24/U4/U6 complex. The recessive a deletion of the chromosomal copy of the SNR14 gene that is suppressor mutations destabilize the binding of PRP24 complemented by the wild-type SNR14 gene carried on YCp50 to U6 and thus promote the release of PRP24 from the (CEN, URA3). The preparation of growth media and the tech- niques used for diploid construction, sporulation, and tetrad PRP24/U4/U6 complex to allow the formation of the dissection have been described (Rose et al. 1989). Intact yeast base-paired U4/U6 complex. This model predicts that cells were transformed using lithium acetate (Ito et al. 1983). the U4/U6 base-pairing interaction is partially or com- The snrl4 mutant strains were generated using the plasmid pletely disrupted in the PRP24/U4/U6 complex. Intri- shuffle technique (Boeke et al. 1987). The strain YKS2 was guingly, Brow and Guthrie (1988) found two forms of the transformed with the plasmids carrying the snrl4 genes. Trans- U4/U6 complex in HeLa cell nuclear extracts: a high-Tm formants were selected on SD medium lacking histidine at 30°C form, with a melting temperature similar to that of the and then plated onto SD medium containing 0.75 mg/ml of yeast U4/U6 complex, and a low-Tin form. It is possible 5-fluoro-orotic acid (5-FOA) to select for cells that have lost the that the PRP24/U4/U6 complex we identified in the U4 YCp50-SNR14 plasmid. mutant strain may represent the low-T~ form of the U4/ Two cold-sensitive haploid strains were used for reversion analysis. The construction of strain snrl4--G14C (MATa trpl U6 complex identified previously in human cells. Bio- his3 ura3 ade2 lys2 snrl4::TRP1 pUN90-snrl4-Gl4C) was de- chemical analysis of the U4/U6 interaction in the scribed above. This strain was plated on SD medium lacking PRP24/U4/U6 complex is currently under way to test histidine and incubated at 18°C to select for spontaneous cold- this hypothesis. insensitive revertants. Revertants arose at a frequency of Although our data indicate a role for PRP24 in the 6 x 10 -8. The suppressor strains containing the SNR6--C67G, annealing of U4 and U6, PRP24 may play additional roles snr6--T38C, snr6--A40G and snr6-C43G, and snr6-A91G muta- in the U4/U6 cycle. For example, once the U4/U6 base- tions were isolated from this selection. The strain snrl4--G14C pairing interaction is disrupted in the spliceosome, the YCp50-SNR6 was generated by transforming snrl4--G14C with tight binding of PRP24 to U6 could act to stabilize the YCpSO-SNR6, which contains the 1.8-kb EcoRI-PstI fragment unwound form. Interestingly, another member of the carrying the wild-type SNR6 gene. This strain was plated on SD medium lacking histidine and uracil and incubated at 18°C. RNP-consensus family, hnRNP A1, can either promote Revertants arose at a frequency of 4 x 10- 8. Before further anal- the renaturation of complementary single-stranded nu- ysis, these revertants were plated on medium containing 0.75 cleic acids (Pontius and Berg 1990) or inhibit annealing mg/ml 5-FOA to select for cells that lost the YCp50-SNR6 plas- by binding preferentially to single strands (Kumar et al. mid. The suppressor strains containing the prp24-2, prp24-3, 1986), depending on the assay conditions. In support of and prp24-4 mutations were isolated using this scheme. To test this hypothesis, we have recently found that a tempera- dominance or recessiveness, each revertant was crossed to the ture-sensitive mutation in PRP24 is inviable in combi- strain YKS3 (MATs trpl his3 ura3 ade2 lys2 snrl4::TRP1 nation with a cold-sensitive mutation in PRP28, which YCpSO-SNR14) and diploids were selected on SD medium lack- encodes a putative ATP-dependent RNA helicase ing histidine and uracil at 30°C. Diploids were plated on me- (Strauss and Guthrie 1991). This synthetic lethality sug- dium containing 0.75 mg/ml 5-FOA to select for cells that lost the YCp50-SNR14 plasmid and then tested for their ability to gests that PRP24 and PRP28 act at a similar point in the grow at 18°C. The Ura- diploids were sporulated and tetrads splicing pathway. Future experiments to determine were dissected to analyze Mendelian segregation of the suppres- whether PRP24 is associated with specific splicing com- sor mutations and to isolate MATa and MATs suppressor plexes will test the idea that PRP24 is involved in two strains for complementation analysis. distinct but related steps of the U4/U6 cycle. Melting temperature determinations Materials and methods Melting temperature of the U4/U6 complex in deproteinized Site-directed mutagenesis of SNR14 and SNR6 splicing extract fraction I (Cheng and Abelson 1986) was determined by the method of Brow and Guthrie (1988). A 0.55-kb EcoRV-EcoRI fragment carrying the SNR14 gene (Si- liciano et al. 1987) was cloned into Bluescript (+) (Stratagene). The plasmid pEP6 contains a 1.8-kb EcoRI-PstI fragment car- Isolation and characterization of the snr6 alleles rying the SNR6 gene in pUC118 (Brow and Guthrie 1988). Prep- A yeast genomic library enriched for the U6 gene was prepared aration of single-stranded DNA from dut-ung- cells carrying from genomic DNA isolated from the suppressor strain contain- these plasmids and oligonucleotide-directed mutagenesis were ing the snr6--A91G mutation (MATa trpl his3 ura3 ade2 lys2 performed, as described (Kunkel et al. 1987; McClary et al. snr14::TRP1 pUN90-snr14--G14C snr14-A91G). Total geno-

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Novel U6 snRNP protein

mic DNA was prepared as described (Denis and Young 1983) tibody Company, Richmond, CA}. Additional protein {250 ~g) and digested with EcoRI. Fragments ranging from 3.7 to 2.3 kb was injected at 3-week intervals. The antiserum used in these were recovered from a 0.7% agarose gel, digested with PstI and studies was obtained from a single rabbit bled 10 days after the ligated into the EcoRI and PstI sites of pUC118. Bacterial colo- third injection. Antibodies were affinity-purified using the nies transformed with the ligation mixture were plated and trpE-PRP24 fusion protein as described {Smith and Fisher 1984). transferred onto nitrocellulose (Ish-Horowicz and Burke 1981). Anti-PRP24 antiserum (10 lal) was coupled to protein-A/Seph- The filters were probed with U6-specific oligonucleotides end- arose (Pharmacia) and washed three times with Ipp500 buffer labeled with [~-a2P]ATP. Plasmid DNA isolated from two (Hamm et al. 1987) and once with Ipp buffer (10 mM Tris-C1 at clones contained a 1.05-kb EcoRI-ClaI fragment characteristic pH 8.0, 0.1% NP-40, 0.1% sodium azide) containing various of SNR6. Dideoxynucleotide sequencing of these plasmids re- concentrations of NaC1 {indicated in the figure legends). vealed a single mutation in the U6-coding region. Twenty-five microliters of yeast splicing extract {Lin et al. 1985) Total RNA was prepared from the suppressor strains contain- or 400 ~1 of gradient fraction and 400 txl Ipp buffer were added ing the SNR6-C67G, snr6-T38C, snr6-A4OG, and snr6-C43G to the washed beads and incubated for 1 hr at 4°C. The beads mutations using the guanidium thiocyanate method (Wise et al. were washed three times with Ipp buffer at the salt concentra- 1983). RNA sequencing was performed as described (Zaug et al. tion used in the incubation with antiserum. The RNA was ex- 1984), by reverse transcription from an end-labeled oligonucle- tracted with phenol-chloroform, precipitated with three vol- otide primer complementary to nucleotides 96-112 of U6. Most umes of ethanol, and analyzed by Northern blot analysis as of the U6 sequence (nucleotides 5-76) was determined for each described previously (Bordonn6 et al. 1990). snr6 allele, and a single-nucleotide change was found in each case. Glycerol gradient fractionation Yeast splicing extract ( 1.0 mg protein) was incubated for 30 min Isolation and characterization of the prp24 alleles at 25°C in 60 ~tM potassium phosphate IpH 7.0), 2.5 mM MgC12, The PRP24 gene was cloned on the basis of its ability to rescue and 2 mM ATP. The mixture was diluted with buffer A (50 mM the temperature-sensitive cold-resistant phenotype of the sup- Tris-C1 at pH 7.4, 25 mM NAG1, 5 mM MgC12) and layered onto pressor strain containing the prp24-4 mutation (MA Ta trpl his3 10-30% glycerol gradients. The preparation and analysis of the ura3 ade2 lys2 snr14::TRP1 pUN90-snr14-G14C prp24-4). glycerol gradients have been described (Bordonn6 et al. 19901. This strain was transformed with a yeast genomic library constructed in YCp50 (Rose 1987), and transformants were selected on SD medium lacking histidine and uracil at 37°C. Two trans- Acknowledgments formants were isolated that showed the temperature-resistant We gratefully acknowledge Mahshid Company and John Abel- cold-sensitive phenotype characteristic of the prp24-4/PRP24 son for sharing the PRP24 sequence prior to publication. We diploid. Each transformant reverted to the temperature-sensi- thank David Brow, Hiten Madhani, Pat O'Farrell, and Paul tive cold-resistant phenotype of the prp24-4 haploid strain when Schedl for the many helpful discussions, and Ira Herskowitz, plated on medium containing 5-FOA. DNA isolated from these John Abelson, and members of the Guthrie laboratory for crit- transformants was used to transform (Dower et al. 1988) E. coli ical reading of the manuscript. Finally, we extend special thanks strain MH5 to ampicillin resistance and uracil prototropy. Plas- to Lucita Esperas who provided excellent technical assistance. mid DNA isolated from these transformants conferred temper- This work was supported by a National Institutes of Health ature resistance and cold sensitivity when transformed into the grant (GM21119) to C.G. and an American Cancer Society post- suppressor strain containing the prp24-4 mutation. One of these doctoral fellowship (PF-3009) awarded to K.W.S. plasmids was digested with XbaI, and a 3.5-kb fragment was The publication costs of this article were defrayed in part by gel-purified and ligated into pUN50 {CEN, URA3) (Elledge and payment of page charges. This article must therefore be hereby Davis 1988). This subclone (YCpXba) was sufficient to comple- marked "advertisement" in accordance with 18 USC section ment the temperature-sensitive and cold-resistant phenotype of 1734 solely to indicate this fact. the suppressor strain containing the prp24-4 mutation. The prp24 suppressor alleles were isolated from the suppressor strains containing the prp24-2, prp24-3, and prp24-4 mutations References by the gap repair method (Orr-Weaver et al. 1981) using the YCpXba plasmid linearized with ClaI. Bandziulis, R.J., M.S. Swanson, and G. Dreyfuss. 1989. RNA- binding proteins as developmental regulators. Genes & Dev. 3: 431-437. Production of anti-PRP24 antiserum and Bindereif, A. and M.R. Green. 1987. An ordered pathway of sn- immunoprecipitation experiments RNP binding during mammalian pre-mRNA splicing com- YCpXba was digested with HaeIII and XbaI, and a 1.59-kb frag- plex assembly. EMBO I. 6: 2415-2424. ment that encodes the carboxy-terminal 378 amino acids of Bindereif, A., T. Wolff, and M.R. Green. 1990. Discrete domains PRP24 was gel-purified and ligated into the Sinai and XbaI sites of human U6 snRNA required for the assembly of U4/U6 of the trpE fusion vector pATH2 (Spindler et al. 1984). Plasmid snRNP and splicing complexes. EMBO J. 9: 251-255. DNA was isolated from E. coli strain DG-98 and then used to Black, D.L. and A.L. Pinto. 1989. U5 small nuclear ribonucle- transform the protease-deficient E. coli strain CAG456 to oprotein" RNA structure analysis and ATP-dependent inter- ampillicin resistance at 30°C. The induction of the gene fusion action with U4/U6. Mol. Cell. Biol. 9: 3350-3359. with indoleacrylic acid and the preparation of insoluble fraction Black, D.L., B. Chabot, and J.A. Steitz. 1985. U2 as well as U1 of E. coli lysate have been described {Snyder et al. 1989). The small nuclear ribonucIeoproteins are involved in premessen- trpE-PRP24 fusion protein was purified from the insoluble frac- ger RNA splicing. 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Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs.

K W Shannon and C Guthrie

Genes Dev. 1991, 5: Access the most recent version at doi:10.1101/gad.5.5.773

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