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Volume 271,
Number 19,
Issue of May 10, 1996 pp. 11383-11391
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
Yeast
Proteins Related to the p40/Laminin Receptor Precursor Are Essential
Components of the 40 S Ribosomal Subunit (*)
(Received for publication, August 22,
1995; and in revised form, January 31, 1996)
Marina
Demianova
,
Timothy
G.
Formosa
(1),
Steven R.
Ellis (§)
From the Department of Biochemistry, University of Louisville,
Louisville, Kentucky 40292 Department of Biochemistry,
University of Utah, Salt Lake City, Utah 84132
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
ABSTRACT
We report here the isolation of two genes from the yeast, Saccharomyces cerevisiae, that encode proteins closely related
to mammalian p40/laminin receptor precursors (LRPs). The yeast genes,
designated YST1 and YST2, encode proteins with over
95% amino acid sequence identity with one another and over 60% identity
with the human p40/laminin receptor precursor. The Yst/p40/37-LRP
proteins are also more distantly related to the S2 family of ribosomal
proteins. Analysis of the distribution of Yst1 tagged with the
c-myc epitope revealed that the Yst proteins are components of
the 40 S ribosomal subunit. Disruption of either YST1 or YST2 causes a significant reduction in growth rate, while
disruption of both genes is lethal. Compared to wild type, polysome
profiles in strains lacking either YST1 or YST2 show
a pronounced shift from larger to smaller polysomes. This shift is
accompanied by a substantial increase in free 60 S subunits and reduced
levels of 40 S subunits. We conclude that the Yst proteins are required
for translation and contribute to the assembly and/or stability of the
40 S ribosomal subunit.
INTRODUCTION
A cDNA originally reported to encode the 67-kDa high affinity
laminin receptor has also been implicated in the production of an
abundant intracellular protein of approximately 37 kDa that is highly
conserved in a wide spectrum of eukaryotic
cells(1, 2, 3) . The relationship between
these two proteins is unclear but it has been proposed that a fraction
of the intracellular pool of the 37-kDa protein may serve as a
precursor for the 67-kDa laminin receptor(4, 5) . The
cDNA encoding the 37-kDa laminin receptor precursor (37-LRP) ( )is virtually identical to a cDNA encoding a mouse protein,
p40, initially identified in a screen for mRNAs under translational
control in ascites tumors(6, 7) . A cDNA encoding p40
was also shown to encode an antigen that shows regional specificity in
developing mice retinas(8) . This antigen appears to be a
conformational isomer of intracellular p40 that has been proposed to
play a role in defining the dorsal/ventral axis in developing
retinas(9) . Finally, a gene encoding a Drosophila homolog of p40 was shown to complement mutations at the stubarista locus(10) . Certain mutant alleles of Drosophila p40 are zygotic lethals that have been shown to
affect oogenesis and imaginal disc development. Together, these data
indicate that the 67-kDa laminin receptor may be derived from an
abundant intracellular protein, p40/37-LRP, and that p40/37-LRP
proteins, apart from their potential role as precursors for laminin
receptors, may play important roles in early stages of metazoan
development. Several lines of evidence suggest that p40/37-LRP
proteins are components of the protein synthetic machinery. Mammalian, Arabidopsis, and Urechis caupo p40 proteins are
polysome associated and appear to be preferentially associated with 40
S ribosomal
subunits(3, 11, 12, 13) . The
distribution of p40 proteins between free and polysome-associated
states has been shown to depend on the age, growth stage, or
developmental state of the cells
examined(3, 11, 13) . In addition to the
physical association of p40 with polysomes, genetic studies in Drosophila suggest that p40 may be a component of the
translational machinery. Phenotypes associated with certain alleles of
the Drosophila p40 locus are similar to minute phenotypes that
are often associated with genes encoding ribosomal
components(10) . Finally, Davis et al. (14) showed that p40/37-LRP proteins are structurally related
to the S2 family of ribosomal proteins. This relationship has been
further strengthened by the identification of an archaebacterial member
of this family whose sequence is approximately equidistant in terms of
similarity between the eubacterial/organellar S2 proteins and the
eukaryotic p40/37-LRP proteins(15) . We report here the
isolation of two genes from the yeast, Saccharomyces
cerevisiae, that encode proteins closely related to the p40/37-LRP
family of proteins. The yeast genes, designated YST1 and YST2, encode proteins that exhibit over 95% sequence identity
with each other, over 60% sequence identity with mammalian p40/37-LRP
proteins, and approximately 30% sequence identity with members of the
S2 family of ribosomal proteins. Epitope-tagged Yst1 cosediments with
40 S ribosomal subunits, 80 S monosomes, and polysomes during sucrose
gradients centrifugation indicating that the Yst proteins are small
subunit ribosomal proteins. Disruption of either YST1 or YST2 shows a reduction in growth rate compared to wild type.
Cells disrupted in both YST1 and YST2 fail to
germinate indicating that Yst function is essential. Relative to wild
type, polysome distributions in cells lacking one or the other of the YST genes show a pronounced shift from larger to smaller
polysomes. This shift to smaller polysomes in mutant extracts is
accompanied by a substantial increase in free 60 S ribosomal subunits
and a reduction in the level of free 40 S subunits. The Yst proteins
are therefore required for translation and contribute to the assembly
and/or stability of 40 S ribosomal subunits.
MATERIALS AND METHODS
Yeast and Bacterial StrainsThe yeast strains
used in this study were W303 (MATa/MAT , ,
ade2-1/ade2-1, can1-100/can1-100, his3-11, 15/his3-11, 15,
ura3-1/ura3-1, leu2-3, 112/leu2-3, 112, trp1-1/trp1-1) and 7208-12 (MATa/MAT , pep4-3/pep4-3, prb1-1122/prb1-1122,
his7/his7, ura3-52/ura3-52, trp1/trp1, can1/can1). Media used in
cultivating yeast were: YPD (1% (w/v) yeast extract, 2% (w/v) peptone,
2% (w/v) dextrose), YM-1(16) , and minimal (0.67% (w/v) yeast
nitrogen base without amino acids, 2% (w/v) dextrose). Where
appropriate, nutrients were added to minimal media in amounts specified
by Sherman(17) . Diploids were sporulated in solid SPO media
(1% (w/v) potassium acetate, 0.1% (w/v) yeast extract, 0.05% (w/v)
dextrose, 2% (w/v) agar), and where appropriate adenine, histidine,
uracil, leucine, and tryptophan were added in 25% the amounts used in
synthetic complete media. The Escherichia coli strain used in
this study was JM101.
Isolation of DNA-binding ProteinsDNA-binding
proteins were isolated from a crude nuclear fraction of the yeast S. cerevisiae and used to prepare antibodies. A 2-liter
culture of strain 7208-12 was grown to log-phase (2
10 /ml) in YM-1, and the cells were collected by
centrifugation (10 min at 6,000 g). The 6.4-g cell
pellet was suspended in 20 ml of Tris-HCl (pH 9.1), 20 mM Na EDTA, 1 M NaCl, 0.1 M 2-mercaptoethanol, and incubated for 10 min at room temperature.
The cells were collected by centrifugation (5 min at 4,000 g), and suspended in 40 ml of 1 M NaCl, 166 mM KH PO , 34 mM sodium citrate (pH
5.8). The cells were collected again, suspended in 40 ml of glusulase
buffer (10% (w/v) glycerol, 1 M sorbitol, 42 mM KH PO , 8 mM sodium citrate (pH
5.8), collected, and suspended in 10 ml of glusulase buffer. 0.3 ml of
glusulase solution (105,000 units/ml glucuronidase, 11,500 units/ml
sulfatase; DuPont NEN) was added to the suspension, and the mixture was
incubated 1 h at 30 °C. The cells were collected by centrifugation
for 5 min at 2,000 g, gently resuspended in 20 ml of
glusulase buffer, then collected again. The washed spheroplasts were
suspended in 20 ml (2 mM MgCl , 0.2% (v/v) Triton
X-100, 40 mM Tris-HCl, pH 7.4, 1 mM 2-mercaptoethanol, 5% (w/v) Ficoll 400, 0.5 µg/ml leupeptin,
0.7 µg/ml pepstatin, 0.5 mM phenylmethylsulfonyl fluoride)
and lysed with five strokes in a Dounce homogenizer on ice. The
suspension was centrifuged for 10 min at 11,000 g; the
pellet contained cellular debris including nuclei and other organelles.
This material was extracted with 10 ml of 50 mM Tris-HCl, pH
7.4, 2 mM Na EDTA, 1 mM 2-mercaptoethanol,
2.5 M NaCl, 0.5 µg/ml leupeptin, 0.7 µg/ml pepstatin,
and 0.5 mM phenylmethylsulfonyl fluoride, then disrupted with
10 strokes in a Dounce homogenizer on ice. The suspension was
centrifuged for 20 min at 16,000 g. 1.75 g of NaCl,
0.66 g of polyethylene glycol 8000, and 0.44 g of dextran 500 were
added to 12.5 ml of the supernatant and mixed gently for 1 h at 4
°C. The mixture was centrifuged for 10 min at 11,000 g to separate the phases containing protein and nucleic acids. The
clear upper phase containing proteins was dialyzed two times against 2
liters each time of DC without glycerol (20 mM Tris-HCl, pH 8.0, 2 mM Na EDTA, 1 mM 2-mercaptoethanol, and 50 mM NaCl; subscripts denote the
molarity of NaCl). A slight precipitate was removed by centrifugation
(10 min at 11,000 g), then glycerol was added to 10%
(w/v), and the fraction was loaded onto a 5-ml single-stranded DNA
cellulose column equilibrated with DC . After washing
with the same buffer, the DNA-binding fraction was eluted with
DC . Protein concentrations in various fractions were
estimated using the method of Bradford(18) . Lysed spheroplasts
contained about 400 mg of soluble protein, the column load contained
about 23.5 mg of protein (5.8% of the total), and the DNA-binding
fraction contained about 4.6 mg (1.1% of total, 19% of the column
load).
Cloning and Sequencing the Yeast YST1 and YST2
GenesThe DNA-binding protein fraction was dialyzed into
DC , then used to inoculate rabbits (two to three
injections with 0.3-0.5 mg each injection). Antisera were
collected and used to screen a library of yeast genomic sequences in
gt11 (provided by M. Snyder, Yale University). The clone
containing the YST1 gene was recovered and used to purify
antibodies from the total serum. The purified antibodies were used to
immunostain immobilized proteins derived from the cytoplasmic or crude
nuclear fractions. The anti-Yst antibodies recognized a 30-kDa protein
that is enriched in the crude nuclear fraction (data not shown). The
insert from this clone was subcloned, and its nucleotide sequence was
determined using the dideoxy chain termination method (19) with
Sequenase enzyme and protocols (U. S. Biochemical Corp.) after creating
nested sets of deletions using the Exo III method(20) . This
sequence has been deposited in GenBank originally under
the name NAB1A and has since been changed to YST1 (accession no. M88277). The original clone was a fusion of lacZ and YST1 at the unique EcoRI site found
downstream of the intron within the YST1 reading frame. We
used this fragment to recover the remainder of YST1 using the
integration/recovery method (21) .The YST2 gene
was isolated using a radiolabeled fragment of the YST1 gene to
probe a yeast genomic library (American Type Culture Collection no.
37323). The YST2 gene was subcloned into Bluescript II KS in
two fragments: a 1,500-bp HindIII/HindIII 5` fragment
and a 2,100-bp HindIII/SalI 3` fragment creating
plasmid pMD12. The junction between these two fragments was sequenced
in the original clone to assure that they were contiguous. The YST2 gene was subcloned for sequencing by creating nested sets of
deletions using an Exo III/mung bean deletion kit from Strategene or by
subcloning through selected restriction enzyme sites. Sequencing was
carried out by the chain termination method of Sanger et
al.(19) . This sequence has been deposited in
GenBank originally under the name NAB1B and has
since been changed to YST2 (accession no. U33756).
Disruption of YST1 and YST2The YST1 gene
located on a 2.7-kb EcoRV fragment of yeast genomic DNA was
inserted into pBluescript KS at the unique EcoRV site. The
plasmid with the 5` end of the YST gene oriented toward the SacI site in Bluescript KS was designated pJM8 and the reverse
orientation, pJM9. The pJM8 plasmid was digested with BsmI and BstEII, liberating a fragment of 951 bp containing 88% of the YST1 open reading frame. This fragment was replaced by a HindIII fragment containing the yeast URA3 gene after
filling in to produce blunt ends on all fragments (designated pJM10).
This construct produces an allele denoted yst1- 1(::URA3).
pJM10 was digested with EcoRI and SnaBI, liberating a
fragment of approximately 3.0 kb. The fragment released contains the URA3 gene flanked by approximately 1,000 bp of YST1 sequence at its 5` end and 413 bp at its 3` end. The EcoRI/SnaBI fragment was used to transform the
diploid strain W303. Transformants were selected by uracil prototrophy
and sporulated, and the resulting tetrads were dissected by
micromanipulation. Spores were germinated on YPD media and analyzed for
the YST1 disruption by Southern and Northern blot
hybridization.The YST2 gene was disrupted by replacing the
bulk of the YST2 open reading frame with the yeast HIS3 gene. The pMD12 plasmid containing YST2 was digested with NruI and HpaI liberating an 849-bp fragment. This
fragment was replaced by an 1,800-bp HincII/SmaI
fragment containing the HIS3 gene (designated pMD13). This
construct produced an allele denoted yst2- 1(::HIS3).
Cleavage of pMD13 with SspI liberates a fragment of
approximately 2,500 bp that contains the HIS3 gene flanked by
sequences derived from YST2 at its 5` and 3` ends. The SspI fragment was used to transform W303 cells to histidine
prototrophy. Transformants were sporulated, and tetrads were dissected
by micromanipulation. Spores were germinated on YPD medium and analyzed
for the YST2 disruption by Northern hybridization. To
examine the effect of the disruption of both YST1 and YST2, the diploid strain heterozygous for yst2- 1(::HIS3) was transformed with the yst1- 1(::URA3) DNA fragment derived from pJM10.
Transformants prototrophic for histidine and uracil were sporulated and
tetrads dissected by micromanipulation. Spores were germinated on YPD
and the segregation of disrupted alleles of YST1 and YST2 was analyzed by prototrophy for uracil or histidine and confirmed
when possible by Northern hybridization.
Mapping YST1 and YST2The YST1 gene was
shown by meiotic mapping to be linked to the ADE3 gene on the
left arm of chromosome VII (56 tetrads; ADE3-3.8
cM-SER2-1.9 cM-YST1). Hybridization of yeast genomic
clone grids confirmed this location and indicated that YST2 is
on chromosome XII near SPT8 (YST1 hybridizes to ATCC
clone 70361, YST2 hybridizes to clone 70582).
Polysome AnalysisPolysomes were prepared from
yeast cell extracts and fractionated on 7-47% sucrose gradients
as described by Baim et al.(22) . Centrifugation was
for either 5 or 12 h. The longer time was necessary to resolve 40 S
ribosomal subunits from soluble components at the top of the gradient.
Conditions used to prepare yeast cell extracts under high salt or low
magnesium conditions were described by Foiani et
al.(23) . Macromolecules in the polysome fractions were
precipitated with 10% trichloroacetic acid and washed once with 5%
trichloroacetic acid and twice with cold (-20 °C) acetone.
The pellets were air dried, suspended in Laemmli sample
buffer(24) , and run on SDS-polyacrylamide gels.
Tagging Yst1 with the c-myc
EpitopeOligonucleotide-directed mutagenesis was used to insert
the c-myc epitope immediately downstream of the YST1 reading frame in plasmid pJM9. The oligonucleotide used was
5`-ATATCACCTTACTTACAAGTCTTCTTCAGAAATAAGCTTTTGTTCCCACTCGACGTTGTC-3`. The
c-myc epitope was the 10-amino acid sequence EQKLISEEDL
recognized by the monoclonal antibody 9E10(25) . A 2.7-kb BamHI/SalI fragment containing the YST/c-myc gene was cloned into the yeast shuttle
vector pRS315(26) . This construct complements phenotypes
linked to the disruption of either YST1, YST2, or
both genes indicating that sufficient 5`- and 3`-flanking regions from YST1 were included for expression in yeast and that the
epitope-tagged Yst1 protein is functional. The epitope-tagged Yst1
protein was detected by enhanced chemiluminescence using a kit from
Amersham Corp. The monoclonal antibody 9E10 was the generous gift of
Dr. William W. Young, Department of Biology and Biophysics, University
of Louisville.
RESULTS
Isolation and Characterization of Yeast YST
GenesIn an effort to identify proteins involved in DNA
metabolism in the yeast S. cerevisiae, a general class of
DNA-binding proteins was isolated and used as a heterogeneous group of
antigens. The antibodies produced were used to screen an expression
library to identify the genes encoding the DNA-binding proteins. One of
these genes, which we originally called NAB1 (Nucleic Acid
Binding protein 1) and subsequently changed to YST1 (Yeast S
Two) was found to encode a 30-kDa protein that was enriched in the low
speed centrifugation pellet after hypotonic lysis of spheroplasts. This
fraction contains large, insoluble portions of cells, including cell
walls, nuclei, and mitochondria. Under the gentle extraction conditions
used for the preparation of nuclei, a substantial number of ribosomes
are detected in the crude nuclear fraction as judged by the presence of
a large number of small basic proteins observed by two-dimensional gel
electrophoresis (data not shown).The nucleotide sequence of YST1 revealed two adjacent open reading frames separated by a
region containing consensus 5`-donor, lariat, and 3`-acceptor
sequences, suggesting a gene interrupted by a single intron (Fig. 1, top). The inferred spliced message encodes a
protein of 252 amino acids with a predicted molecular mass of 28 kDa. A
deletion of the second exon of the YST1 gene was constructed
and introduced into diploid yeast cells. This mutation is marked with
the URA3 gene and should prevent expression of 88% of YST1 open reading frame (Fig. 1, top). A fragment
containing the disrupted YST1 gene was transformed into the
diploid strain W303 and transformants selected by uracil prototrophy.
Transformants were sporulated and the resulting tetrads dissected.
Spores prototrophic for uracil grew more slowly than the uracil
auxotrophs indicating that disruption of the yeast YST1 gene
conferred a modest reduction in growth rate (data not shown, but see Fig. 3and Fig. 5).
Figure 1:
Organization of the YST1 and YST2 genes. Open boxes represent the YST1 and YST2 open reading frames. Putative introns
interrupting the open reading frames are shown with angled lines.
Sequences at the splice sites encoded by YST1 and YST2 genes that conform to the yeast 5`- donor and 3`-acceptor (upper line) and branch point (lower line) consensus
sequences (36) are shown below the intron in each gene. Slashes indicate exon/intron boundaries. Dashed lines represent 5`- and 3`-flanking regions that have either not been
sequenced or were not deposited in the data base. Restriction enzyme
sites used in cloning and gene disruptions are listed below each
gene.
Figure 3:
Tetrad analysis of the effects of the
disruption of the YST1 and YST2 genes. A diploid
strain heterozygous at both YST loci, YST1/yst1- 1(::URA3) and YST2/yst2- 1(::HIS3), was sporulated and tetrads
dissected. Individual spores were grown on YPD medium at 30 °C. Numbers refer to different
tetrads.
Figure 5:
Growth curves of YST-disrupted
strains complemented with plasmid-borne alleles of YST1 and YST2. Panel A, open circles, YST2-disrupted strain transformed with pRS315 vector alone; crosses, YST1-disrupted strain transformed with
pRS315; closed triangles, wild-type strain transformed with
pRS315; open triangles, YST1-strain transformed with
pRS315 containing the YST1 gene; closed circles, YST2-disrupted strain transformed with pRS315 containing the YST1 gene. Panel B, same as panel A except
strains designated by the closed circles and open
triangles were transformed pRS315 containing the YST2 gene. Lines were drawn using a least squares regression fit (Slide
Write Plus).
DNA and RNA hybridization analyses
indicated that YST1 is not unique and suggested that cells
with the disrupted YST1 allele were expressing Yst protein
from a second locus (data not shown, but see Fig. 4). Using a YST1 fragment as a hybridization probe, we cloned a second
gene closely related to YST1. The second gene also has an open
reading frame capable of coding for a protein of 252 amino acids that
appears to be interrupted with a single intron located at the same
relative position as the intron in the YST1 gene (Fig. 1, bottom). The two genes show over 90% sequence
identity at the nucleotide level and 95% identity in deduced amino acid
sequence (Fig. 2). We have named the second locus YST2.
Figure 4:
Northern analysis of YST1/2 mRNA
levels in wild-type and disrupted strains. Total yeast RNA was prepared
and fractionated on formaldehyde gels as described under
``Materials and Methods.'' RNA was transferred to Zetaprobe
(Bio-Rad) membrane and hybridized with a nick-translated probe derived
from the YST1 gene. RNA was derived from strains that were: lane 1, disrupted in YST1; lane 2, disrupted
in YST2; lane 3, wild type for YST1 and YST2.
Figure 2:
Alignment of primary structures deduced
for the Yst1 and Yst2 proteins with human p40/37-LRP and Mrp4. Amino
acids are represented by the one-letter code. Dashes in the
Yst2 sequence indicate identities with Yst1. Dashes in the
p40/37-LRP sequence show identities with both Yst1 and Yst2. Dashes in
Mrp4 indicate identities with Yst1, Yst2, and p40/37-LRP. Asterisks below the alignments indicate identities between Mrp4 and at least
one of the other proteins. Blank spaces represent gaps in the
alignment. Superscripts specify codon numbers relative to the
initiation codon for each gene. The Mrp4 protein has an amino-terminal
extension of 170 amino acids relative to the region of homology with
the other proteins shown here.
A search of the GenBank data base indicated that the
Yst proteins are closely related to the p40/37-LRP family of
proteins(27) . The Yst proteins are also more distantly related
to the S2 family of ribosomal proteins found in eubacteria and
organelles, suggesting that Yst/p40/37-LRP proteins are eukaryotic
members of the S2 family of proteins. Members of the S2 family have
also been identified in archaebacteria, indicating that the S2 family
of proteins evolved prior to the divergence of the three major lines of
descent(15) . Fig. 2shows the alignment of the Yst
proteins with the human p40/37-LRP protein and the yeast mitochondrial
ribosomal protein Mrp4. The Yst proteins show over 60% sequence
identity with human p40/37-LRP over 201 amino acids spanning the bulk
of the three proteins (Fig. 2). The Yst and p40/37-LRP proteins
diverge at their amino and carboxyl termini where the human protein
also has a carboxyl-terminal extension of 42 amino acids. Fig. 2also shows the alignment of the Yst/p40/37-LRP proteins
with Mrp4, a member of the S2 family of ribosomal proteins (14) . The Mrp4 protein has approximately 30% sequence identity
with at least one of the other proteins shown in Fig. 2.
Overall, the four proteins have 23% sequence identity. This level of
identity is similar to comparisons between other homologous ribosomal
proteins found in both eubacteria and eukaryotes(28) . We
have disrupted YST2 alone and in combination with the YST1 disruption. The bulk of the YST2 reading frame was
deleted and replaced by the HIS3 gene. A fragment containing
the disrupted YST2 gene was transformed into the diploid yeast
strain W303 and transformants were selected by histidine prototrophy.
Transformants were sporulated and the resulting tetrads dissected.
Histidine prototrophy segregated with a slow growth phenotype
indicating that just as for YST1, disruption of YST2 is tolerated, but has an impact on growth rate (data not shown,
but see Fig. 3and Fig. 5). The diploid yeast strain
heterozygous for the YST2 disruption was transformed with a
disrupted copy of YST1 to assess the effects of the disruption
of both YST genes. Transformants were sporulated and tetrads
dissected. Representative results from the growth of individual spores
on YPD are shown in Fig. 3. Examination of colony size in spores
from tetrads 2, 5, 6, and 7 suggests four distinct growth rates. The
fastest growing spores were auxotrophic for both uracil and histidine,
suggesting that they contained wild-type YST1/2 alleles. The
two intermediate sized colonies were prototrophic for either uracil or
histidine. The larger colony was prototrophic for uracil and
auxotrophic for histidine, indicating that it was disrupted in YST1 but wild type for YST2. The smaller colony was
prototrophic for histidine and auxotrophic for uracil indicating that
it contained a disrupted allele of YST2 and a wild-type allele
of YST1. The fourth spore in each of these tetrads did not
germinate. The inviable spores were presumably disrupted in both YST1 and YST2, suggesting that disruption of both YST genes is lethal. Tetrad 4, on the other hand, gave two
colonies and two nonviable spores. In this tetrad, the cells that grew
were both auxotrophic for uracil and histidine, indicating they had
wild-type alleles of YST1/2. We assume that the nonviable
spores were disrupted in both YST genes. Tetrads 1 and 3
showed four spores with intermediate growth rates. In tetrad 1 the four
viable spores were auxotrophic for either uracil or histidine,
indicating that they were disrupted in one or the other YST gene. One of the colonies derived from tetrad 3 was prototrophic
for both uracil and histidine, but was eventually shown to be a mixed
population of cells. Overall, the examination of 124 spores revealed no
viable double mutants, whereas, 31 would have been expected by chance. The segregation pattern of the YST1 and YST2 alleles in Fig. 3suggested that the two genes were
unlinked. This was confirmed by mapping the YST1 and YST2 genes either genetically or by hybridization to a genomic clone
grid library. YST1 hybridized to ATCC clone 70361 and maps
near ADE3 on the left arm of chromosome VII, whereas YST2 hybridized to ATCC clone 70582 and maps near SPT8 on
chromosome XII (data not shown). Disruption of the YST genes was confirmed by Northern hybridization analysis. Northern
analysis revealed that the two YST genes encode mRNAs that
differ in size by approximately 150 bases with the YST2 gene
encoding the larger of the two mRNAs (Fig. 4). The observation
that in wild-type cells the hybridization signals for the two mRNAs are
comparable even though the probe was derived from YST1 suggests that the steady-state levels of YST2 mRNAs might
be somewhat higher than for the YST1 mRNA. This might explain
why the disruption of YST2 causes a more severe reduction in
growth rate than does the disruption of YST1; the Yst proteins
are functionally equivalent, but YST2 makes a greater
contribution to the pool of Yst molecules. Alternatively, since the two
Yst proteins differ in primary structure in several positions it is
possible that the two proteins may only partially overlap in function
with one or the other or both proteins also having unique functional
characteristics that contribute differentially to growth rate. To
examine the extent to which the functions of the two Yst proteins
overlap, we asked whether each of the YST genes could
complement phenotypes linked to the disruption of the other. Strains
harboring disrupted alleles of either YST1 or YST2 were transformed with wild-type copies of either YST1 or YST2 cloned into the low copy number vector
pRS315(26) . Fig. 5shows that plasmid-borne copies of YST1 or YST2 are able to complement the growth
defects associated with disruptions in either gene. These data suggest
that the two Yst proteins have largely overlapping functions during
growth on rich media. However, we cannot rule out the possibility that
the two proteins may have distinct functions under growth conditions
that were not examined here.
Distribution of Epitope-tagged Yst1 in Cell Extracts
Fractionated by Sucrose Gradient CentrifugationMammalian, Arabidopsis, and U. caupo p40/37-LRP proteins have
been shown to be polysome-associated and preferentially associated with
40 S ribosomal
subunits(3, 11, 12, 13) . To
determine if the Yst proteins had a similar distribution, we examined
the distribution of epitope-tagged Yst1 in cell extracts fractionated
by sucrose gradient centrifugation. Yst1 was tagged with the human
c-myc epitope, which is recognized by the monoclonal antibody
9E10, as described under ``Materials and Methods.'' The
epitope-tagged Yst1 complements phenotypes linked to the disruption of
either or both YST genes indicating that it is functional
(data not shown). Fig. 6, lane 2, shows that the 9E10
antibody recognizes a protein with an apparent molecular mass of
approximately 30 kDa in YST1-disrupted cells transformed with
epitope-tagged YST1 on a low copy number plasmid. This protein
is of the size predicted for epitope-tagged Yst1. A weaker signal in
this size range is found in extracts from cells transformed with YST1 alone (Fig. 6, lane 1). This weak signal
corresponds to an abundant protein in whole cell extracts that
cross-reacts with either the primary or secondary antibody. When cell
extracts are fractionated by differential centrifugation, virtually all
of the epitope-tagged Yst1 is found in the ribosomal pellet (lane
4), whereas the abundant cross-reacting protein is localized to
the soluble fraction (lane 3).
Figure 6:
Distribution of epitope-tagged Yst1 in
extracts fractionated by differential centrifugation. Cell extracts
were prepared by disrupting cells with glass beads using conditions
outlined by Baim et al.(22) . Lanes 1 and 2 contain equal amounts of cell extracts derived from cells
transformed with pRS315 plasmids harboring either the YST1 gene or the YST1 gene with the c-myc tag.
Extracts from cells transformed with YST1/c-myc fusion were fractionated by centrifugation for 30 min at 75,000
rpm in a TLA100.2 rotor. The ribosomal pellet was suspended in buffer
equal to that of the supernatant. Equal amounts of each fraction were
loaded in lanes 3 and 4. Proteins were fractionated
by SDS-polyacrylamide gel electrophoresis, transferred to
nitrocellulose, and blotted with the monoclonal antibody 9E10. The 9E10
antibody recognizes epitope EQKLISEEDL derived from human c-myc(25) .
To analyze the distribution
of epitope-tagged Yst1 among ribosomal components, extracts were
fractionated by sucrose gradient centrifugation. Fig. 7, panel A, shows that the epitope-tagged Yst1 is found in
several regions of the gradient. The bulk of the epitope-tagged Yst1 is
distributed in a broad peak that coincides with polysomes.
Epitope-tagged Yst1 is also found in a peak that coincides with 80 S
monosomes. Finally, there appears to be a small amount of
epitope-tagged Yst1 in a region of the gradient that coincides with 40
S subunits. In this gradient 40 S subunits appear as a shoulder to the
main absorbance peak which corresponds to the soluble fraction. To
better evaluate the apparent association of epitope-tagged Yst1 with 40
S subunits, gradients were run for a longer time to separate the small
ribosomal subunits from the soluble fraction. Fig. 7, panel
B, shows after the longer centrifugation time 40 S subunits are
clearly resolved from the soluble fraction and that the epitope-tagged
Yst1 protein cosediments with 40 S subunits. Signals found in soluble
fractions appear to be from the abundant cross-reacting proteins
although we cannot rule out a small amount of the epitope-tagged Yst1
protein in this region of the gradient.
Figure 7:
Distribution of epitope-tagged Yst1 in
extracts fractionated by sucrose gradient centrifugation. Except where
noted, extracts were prepared and fractionated by sucrose gradient
centrifugation as described by Baim et al.(22) .
Gradients were fractionated and the absorbance at 254 nm was monitored
using an ISCO model 185 density gradient fractionator and a UA-5
absorbance detector. Fraction 1 represents the top of each gradient.
Aliquots of each fraction were precipitated with trichloroacetic acid,
run on SDS-polyacrylamide gels, transferred to nitrocellulose and
blotted with the monoclonal antibody 9E10. Blots are shown below the
absorbance tracings. Panel A, centrifugation was for 5 h at
22,000 rpm in an SW28.1 rotor. Panel B, same as panel A except that centrifugation was for 12
h.
Loss of Yst Proteins Alter Polysome ProfilesWhile
several studies have reported that p40/37-LRP proteins are associated
with ribosomal components, none of these studies addressed whether they
are necessary for protein synthesis. To determine if the loss of yeast
Yst protein influences translation rates we examined polysome
distributions in strains disrupted in either YST1 or YST2. Fig. 8, panel A, shows that polysome
profiles from the strain disrupted in YST2 differs
substantially from wild type. Relative to wild type, there is a shift
from larger to smaller polysomes. Similar results were obtained for
strains disrupted in YST1 but they were less pronounced than
with YST2 (data not shown). In addition to the shift in
polysomes, extracts from the disrupted strains also have higher
steady-state levels of 60 S ribosomal subunits. Assessment of 40 S
subunit levels in these gradients is complicated since they run as a
shoulder to the major absorbance peak at the top of the gradient.
Therefore, gradients were run for longer periods of time to resolve 40
S subunits. Fig. 8, panel B, shows that the amount of
free 40 S subunits are reduced in extracts from the strain disrupted in YST2 relative to wild type. However, the 60-80 S region
of this gradient shows a rather unusual shape with a shoulder between
the 60 and 80 S peaks. This shoulder may be the consequence of the
sedimentation-induced dissociation of 80 S monosomes(29) .
Foiani et al. (23) have shown that inactive 80 S
couples can be distinguished from 80 S couples engaged in translation
by their sensitivity to dissociation by high salt. Fig. 8, panel C, shows gradients run for extended periods of time in
high salt. Under these conditions, 40 S subunits can be detected in
extracts from disrupted strains but are still reduced in amount
relative to wild-type extracts. To more specifically address the
overall reduction in 40 S subunits in the mutant strains, extracts were
prepared and gradients run under conditions of low magnesium ion
concentration where polysomes and 80 S monosomes dissociate into 40 and
60 S subunits(23) . Fig. 8, panel D, shows that
relative to wild type 40 S subunits in extracts from strains disrupted
in YST2 are reduced by 20 to 35%.
Figure 8:
Polysome
profiles from wild-type and YST2-disrupted strains. Extracts
were prepared and fractionated as described in Fig. 7. Dashed lines, wild-type extracts; solid lines,
extracts from a YST2-disrupted strain. Panel A,
centrifugation was for 5 h at 22,000 rpm. Panel B,
centrifugation was for 12 h at 22,000 rpm. Panel C, extracts
were adjusted to 0.8 M NaCl and layered onto gradients made in
0.7 M NaCl(23) . Centrifugation conditions were as described
for panel B. Panel D, extracts were prepared and fractionated
under low Mg conditions(23) . Centrifugation
conditions were as described for panel
B.
DISCUSSION
We report here the isolation and characterization of two
yeast genes, YST1 and YST2, that encode members of
the S2 family of ribosomal proteins and are homologous to genes
encoding p40/37-LRP proteins in a number of eukaryotic organisms.
Yst/p40/37-LRP proteins are highly conserved, exhibiting over 60%
sequence identity between yeast and humans. The mammalian p40/37-LRP
proteins have been implicated in diverse processes, from playing a role
in defining the dorsal/ventral axis in the developing mouse retina (9) to serving as a precursor for the 67-kDa laminin
receptor(4) . Despite their importance, little is known
regarding the specific function of p40/37-LRP proteins in these
processes. The results reported here demonstrate that the yeast Yst
proteins are essential components of 40 S ribosomal subunits. In
addition, we show that these proteins are required for translation and
contribute to the assembly and/or stability of the 40 S subunit. Based largely on observations that p40/37-LRP proteins cosediment
with ribosomal components during fractionation through sucrose
gradients, several studies suggested that p40/37-LRP proteins from
mammals and plants were components of the translational
machinery(3, 11, 12, 13) . In these
experiments the p40/37-LRP proteins were found in fractions containing
polysomes and in earlier regions of gradients containing monosomes and
individual ribosomal subunits. In addition, a significant amount of the
total p40/37-LRP protein was found in fractions containing soluble
proteins. Treatments that disrupted polysomes in Arabidopsis and mammalian extracts led to somewhat different conclusions
regarding localization of p40/37-LRP protein. The Arabidopsis p40 protein appeared to be preferentially associated with 40 S
subunits after polysome disruption, while the mammalian p40 protein
appeared to be distributed in particles larger and more heterogeneous
than 40 S subunits. While the nature of these larger particles was
unclear, at least a fraction of the mammalian p40 protein appears to be
associated with 40S subunits, since Tohgo et al. (12) showed that purified preparations of mammalian 40 S
subunits contained p40/37-LRP protein. Consistent with the view that
members of the Yst/p40/37-LRP family of proteins are ribosomal
components is the observation that the YST genes share two
properties with genes known to encode ribosomal proteins in yeast.
First, the yeast genome contains two virtually identical YST genes. While redundant genes are generally uncommon in S.
cerevisiae, almost half of the ribosomal proteins are encoded by
duplicated genes(30) . Second, the YST genes each
appear to contain an intron, another phenomenon that is relatively rare
in yeast but prevalent in genes encoding ribosomal proteins. While
these characteristics are not unique to genes encoding ribosomal
proteins, they are consistent with a role in translation(31) . Both physical and functional properties of the Yst proteins also
indicate that they are ribosomal components. Garrels et al. (32) found that Yst proteins are abundant in yeast whole cell
extracts. Moreover, they reported that the Yst proteins were physically
associated with ribosomes. Our data confirm this association and extend
it by showing that the Yst proteins are components of the 40 S
ribosomal subunit. Furthermore, our studies are the first to
demonstrate that the association of a member of the Yst/p40/37-LRP with
ribosomes is of functional importance rather than a fortuitous
association. Disruption of either of the YST genes has a
pronounced effect on polysome profiles. Relative to wild type, strains
lacking one or the other of the Yst proteins have fewer 40 S subunits
and polysomes but show a pronounced increase in the level of free 60 S
subunits. Similar effects on the relative amount and distribution of
ribosomal subunits have been reported for disruptions in genes coding
for other small subunit ribosomal proteins in
yeast(33, 34, 35) . The reduction in 40 S
subunits and polysomes seen in strains disrupted in either YST1 or YST2 is physiologically relevant, since these strains
have decreased growth rates relative to wild type and cells lacking
both YST genes are inviable. Garcia-Hernandez et
al. (3) have pointed out that the Arabidopsis p40/37-LRP protein has certain characteristics in common with the
acidic class of ribosomal proteins. These properties include an acidic
isoelectric point, distribution between ribosome-associated and soluble
states, and physiological and developmental control over the
distribution of p40/37-LRP protein between these two states. Similar
properties have also been reported for the mouse and U. caupo p40 proteins(11, 13) . Like their counterparts,
the Yst proteins have acidic isoelectric points: Yst1 = 4.67,
Yst2 = 4.7(32) . In contrast to the results reported for
mammalian, U. caupo, and Arabidopsis p40/37-LRP
proteins, there did not appear to be a significant fraction of soluble
Yst proteins in yeast cell extracts. However, we examined the
distribution of Yst proteins only in extracts from log phase cells, so
it is possible that, under other growth conditions, the amount of
soluble Yst protein may be different. In this regard it is worth noting
that the distribution of Arabidopsis p40/37-LRP protein
between soluble and ribosome-associated states has been reported to be
influenced by growth parameters; young, actively growing cell cultures
contain relatively low amounts of soluble protein compared with older
cultures(3) . Clearly, more studies are necessary in yeast
cells before a definitive statement can be made regarding the
distribution of Yst proteins between soluble and ribosome-associated
states. Members of the acidic class of ribosomal proteins are widely
distributed in nature and are found in multiple copies in large
ribosomal subunits. These proteins have been linked to the ribosomal
GTPase center and are important for the association of soluble factors
with ribosomes(36, 37) . Some of these proteins, while
not absolutely required for protein synthesis, have been shown to
promote optimal ribosome function both in vivo and in
vitro(37) . The P0 acidic protein, in contrast, is
essential(38) . P0 appears to mediate the interaction of the
other members of the acidic class of ribosomal proteins with subunits
and may also be necessary for other aspects of 60 S function. While
the Yst/p40/37-LRP proteins have certain characteristics in common with
the acidic class of ribosomal proteins, there are also substantial
differences. In contrast to the acidic proteins of the 60 S subunit,
the Yst/p40/37-LRP proteins are components of the 40 S subunit.
Moreover, unlike the acidic proteins of the 60 S subunit that play a
key role in elongation, our results indicate that the Yst proteins
likely influence initiation rather than elongation rates, since we see
a dramatic shift to smaller polysomes in strains disrupted in the YST genes. While part of this decrease in initiation is likely
the result of a reduction in 40 S subunits, 40 S subunits that are not
polysome-associated in the disrupted strains have distinctive
properties that suggest that they may also be defective in initiation.
Extracts from strains disrupted in YST2 have no free 40 S
subunits but instead contain a new peak that migrates between the 60 S
subunits and 80 S monosomes. This new peak, which is not observed in
wild-type extracts, may be a consequence of sedimentation induced
dissociation of 80 S couples(29) . The appearance of the new
peak in disrupted extracts suggests that it may be composed of
ribosomal subunits with distinctive properties. These properties may be
linked to a decreased initiation rate since the new peak can be
dissociated into ribosomal subunits under high salt conditions known to
selectively dissociate inactive 80 S couples that accumulate in cells
blocked in initiation(23) . Whether the 40 S subunits present
in the new peak contain Yst protein is not known. A potential
functional parallel between the Yst/p40/37-LRP proteins and the acidic
proteins of the 60 S subunit is their association with soluble factors.
As noted above, the acidic ribosomal proteins appear to play an
important role in the association of soluble factors such as EF2 with
elongating ribosomes(37) . Interestingly, mammalian p40 protein
is found as a contaminant in purified preparations of eIF-4A,
suggesting that these two proteins may
interact(11, 39) . In this respect there is an
intriguing parallel between p40 and its bacterial homolog, E. coli ribosomal protein S2 (Eco S2). A mutation in the rpsB gene coding for Eco S2 is suppressed in a dosage-dependent manner
by a member of the DEAD-box family of proteins, a family which also
includes eIF-4A(40) . Whether these physical and genetic
linkages with DEAD-box proteins relate to the function of p40 and Eco
S2 proteins in translation must await further studies. In addition
to their role in protein synthesis, mammalian p40/37-LRP proteins also
appear to function as precursors for the 67-kDa high affinity laminin
receptor. The basis for recruiting p40/37-LRP proteins to the cell
surface to function in this capacity has not been established but it
may be linked to their nucleic acid-binding properties. Guo et
al. (41) have shown that the region of p40/37-LRP thought
to bind laminin also binds heparin. They proposed that p40/37-LRP may
contribute to the function of the 67-kDa laminin receptor by
interacting with heparin found tightly associated with laminin
molecules. Furthermore, they proposed that since many components of the
protein synthetic machinery interact with nucleic acids and many
nucleic acid-binding proteins have been shown to interact with heparin,
these binding properties might contribute to the interaction of the
67-kDa laminin receptor with laminin/heparin complexes. The results
reported here showing that the Yst proteins bind to a DNA cellulose
column are consistent with the possibility that they may be nucleic
acid binding proteins, lending support to the hypothesis that members
of the p40/37-LRP family of proteins may contribute to the function of
the 67-kDa laminin receptor via their ability to interact with nucleic
acids. Recent observations indicate that the recruitment of members of
the Yst/p40/37-LRP family to the cell surface to function as laminin
receptors is not restricted to mammals and that this may be an
important route by which pathogenic fungi such as Candida albicans and Pneumocystis carinii interact with basement membranes
in their hosts(42, 43) .
FOOTNOTES
- *
- This
work was supported in part by United States Public Health Service Grant
GM40632, and grants from the University of Louisville Medical Research
Committee and the Jewish Hospital Foundation (to S. R. E.). The costs
of publication of this article were defrayed in part by the payment of
page charges. This article must therefore by 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
GenBank(TM)/EMBL Data Bank with accession number(s) M88277 [GenBank](YST1) and U33756 [GenBank](YST2). - §
- To
whom correspondence should be addressed. Tel.: 502-852-5222; Fax:
502-852-6222; SRELLI01{at}ULKYVM.LOUISVILLE.EDU.
- (
) - The abbreviations used are: 37-LRP, 37-kDa
laminin receptor precursor; bp, base pair(s); kb, kilobase pair(s).
ACKNOWLEDGEMENTS
We thank Jeff Miles for assistance in sequencing and
plasmid constructions, and Lee Hartwell for supporting the initial
stages of the cloning of YST1.
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19301 - 19309.
[Abstract]
[Full Text]
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Copyright © 1996 by the American Society for Biochemistry and Molecular Biology.
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