Dipartimento di Genetica, Biologia Generale e Molecolare, Università di Napoli Federico II, I-80134 Napoli, Italy
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Abstract |
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We report here the genetic, molecular, and functional characterization of the Drosophila melanogaster minifly (mfl) gene. Genetic analysis shows that mfl is essential for Drosophila viability and fertility. While P-element induced total loss-of-function mutations cause lethality, mfl partial loss-of-function mutations cause pleiotropic defects, such as extreme reduction of body size, developmental delay, hatched abdominal cuticle, and reduced female fertility. Morphological abnormalities characteristic of apoptosis are found in the ovaries, and a proportion of eggs laid by mfl mutant females degenerates during embryogenesis. We show that mfl encodes an ubiquitous nucleolar protein that plays a central role in ribosomal RNA processing and pseudouridylation, whose known eukaryotic homologues are yeast Cfb5p, rat NAP57 and human dyskerin, encoded by the gene responsible for the X-linked dyskeratosis congenita disease. mfl genetic analysis represents the first in vivo functional characterization of a member of this highly conserved gene family from higher eukaryotes. In addition, we report that mfl hosts an intron encoded box H/ACA snoRNA gene, the first member of this class of snoRNAs identified so far from Drosophila.
Key words: Drosophila; rRNA; ribosome; nucleolus; snoRNA ![]() |
Introduction |
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IN eukaryotic cells, synthesis, maturation and modification of rRNA take place in the nucleolus, and RNP
composed of a variety of nucleolar proteins and small
nucleolar RNAs (snoRNAs)1 are known to be responsible
for these essential cellular processes (reviewed by Melese
and Xue, 1995). Almost 100 different snoRNAs species
have been identified so far in yeast and mammalian cells. Recently, it became evident that most of these snoRNAs
can be classified into two major distinct families, each defined by common associated proteins and by the presence of conserved sequences, designated as either C/D or
H/ACA boxes (reviewed by Balakin et al., 1996
; Smith
and Steitz, 1997
). The C and D box-containing snoRNAs
display extensive sequence complementarity to conserved rRNA regions and are associated with a conserved nucleolar protein, fibrillarin or, in yeast, with the fibrillarin homologue Nop1p (reviewed by Bachellerie and Cavaille,
1997
). Some fibrillarin-associated snoRNAs are required
for rRNA processing, but most of them function as a guide
in site-specific ribose methylation of rRNA (Kiss-Laszlo et
al., 1996
; Nicoloso et al., 1996
).
Members of the other large class of snoRNAs share H
and ACA elements and have only short rRNA complementary motifs, brought together by a conserved stem-loop secondary structure (Ganot et al., 1997b). This structure, composed of two hairpins connected and followed by
short single-stranded regions containing the H and ACA
elements, directs the site-specific pseudouridylation event
with the short (5-9 nucleotide [nt]) regions of snoRNA/ rRNA complementarity flanking both sides of the target
site (Ganot et al., 1997a
; Ni et al., 1997
).
In yeast, members of the box H/ACA class of snoRNAs
are specifically associated with two essential nucleolar proteins, Gar1p and Cbf5p (Balakin et al., 1996; Ganot et al.,
1997b
; Lafontaine et al., 1998
). Gar1p, a glycine-arginine-rich protein required for accumulation of mature 18S rRNA
(Balakin et al., 1996
; Girard et al., 1992
) and for rRNA
pseudouridylation (Bousquet-Antonelli et al., 1997
), is
thought to play a crucial role in structuring box H/ACA
sno-RNPs and favoring association of H/ACA snoRNAs
to the pre-rRNA. In a two hybrid yeast assay, Gar1p
interacts with Cbf5p which, in turn, coprecipitates with
box H/ACA snoRNAs and is required for their stability
(Lafontaine et al., 1998
). Interestingly, Cbf5p is the yeast
member of a highly conserved protein family that includes
homologues from at least 18 organisms. Among eukaryotes, genetic analysis has so far been restricted to two
members of this family: the yeast Cbf5 (Jiang et al., 1993
)
and the DKC1 human gene, whose mutations cause the
X-linked dyskeratosis congenita disease (Heiss et al., 1998
).
Whereas little information is available on human dyskerin,
Cbf5p and its rat homologue, NAP57, are known to be
proteins with prevalent nucleolar localization (Cadwell et al.,
1997
; Meier and Blobel, 1994
). However, whereas it has been proposed that NAP57 may be involved in nucleo-cytoplasmatic shuttling (Meier and Blobel, 1994
), the yeast
protein has been shown to be required for transcription,
processing and efficient rRNA pseudouridylation (Cadwell et al., 1997
; Lafontaine et al., 1998
). This last finding
raises the possibility that Cbf5p might act as eukaryotic
rRNA pseudouridine synthase, a role originally suggested
(Cadwell et al., 1997
) by its homology with E. coli TruB/
P35 synthase. Considering the multiple, essential functions played by Cbf5p in yeast cells, the definition of the roles
played by members of this family in multicellular organisms appears to be a relevant issue that deserves extensive investigation.
Here we describe the cloning of the Drosophila member of the Cbf5/Nap57/DKC1 gene family, that we called minifly (mfl), and report a detailed genetic, molecular, and functional analysis of its expression. With the isolation and the characterization of mfl mutants reported in this paper, we provide the first animal model system for the study of the molecular basis of the DKC human disease. Our data also reveal that mfl has an intriguing molecular organization, hosting an intron-encoded box H/ACA snoRNA that represents the first member of this class thus far described in Drosophila. We named this RNA snoH1 and suggest that it may be functionally equivalent to the human U70 snoRNA.
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Materials and Methods |
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P-Element Mutagenesis/Enhancer-Trap Schemes, P-Cytogenetic Mapping, Construction of Transformed Lines, and Lethal Phase Analysis
The genetic markers and chromosomes used for mutagenesis and mapping are described in Lindsley and Zimm (1992). Most stocks were from
the Bloomington Drosophila Stock Center, while the l(2)k06308 and
l(2)k05318 strains were provided by the Berkeley Drosophila Genome
Project Stock Center. The mfl1 allele was isolated in a small-scale P-element mutagenesis screen performed essentially according to the "reversion jumping" scheme (Tower et al., 1993
). In our experiments, tocl(2)01361,
a lethal P[LacZ, ry+] (O'Kane and Gehring, 1987
) insertion at the toucan
locus, was mobilized by the P[ry+,
(2-3)99B] element (Laski et al., 1986
;
Robertson et al., 1988
) as a source of transposase. Males carrying both the
(2-3) and tocl(2)01361 elements were crossed to females carrying a lethal
toc allele that lost the ry+ marker. This allele, named toc
01361, was generated in our laboratory from tocl(2)01361 by P imprecise excision. In the next
generation, flies lacking the CyO chromosome balancer (reversion event
of the tocl(2)01361 allele) but marked with ry+ were recovered, and second
chromosomes carrying these new insertions were balanced and retained
for further study. Single P-element insertions were verified by genomic
Southern blot analyses with PZ-derived probes. Wild-type P-element excised revertants were generated by crossing homozygous mfl1 males to
w1118; CyO/L2; Sb, P[ry+,(
2-3)99B]/TM6B,Tb virgin females and by individual mating of disgenic F1 males to 5-10 CyO/Sp; ry506 virgin females. Individual non-Stubble males that lost the ry+ marker were collected from
the F2 progeny and balanced over the CyO chromosome. The resulting
stocks were checked for the presence of homozygous revertant flies in
which P-element excision was verified by PCR amplification and DNA sequence analysis. In situ hybridization to salivary gland polytene chromosomes was performed with a DIG-labeled probe derived from the PZ element, essentially as described in Ashburner (1989)
.
The P-element hsp70:mfl construct (P[hs:mfl]) used for P-element-
mediated transformation (Rubin and Spradling, 1982) was prepared by inserting a 1833 bp cDNA sequence containing the complete mfl ORF into
the EcoRI site of the pCaSpeR-hs-act vector (Thummel et al., 1988
).
Transgenic flies carrying the P[hs:mfl] on the X or third chromosome were
used to introduce the transposon in mfl mutant background. Lethal phase
analysis was performed according to Fletcher et al. (1995)
. As control, lethal phases of mfl/Df(2R)Px4 transheterozygous were also determined.
To identify homozygotes carrying mfl lethal alleles we generated y w; mfl/
CyO y+ and y w P[hs:mfl]; mfl/CyO y+ stocks in which homozygous mutant larvae were distinguished from their mfl/CyO y+ heterozygous siblings by the yellow phenotype of mouth hooks and denticle belts.
Cloning Techniques
Basic cloning techniques, DNA and RNA extraction, manipulation and
labeling, screening and sequencing techniques were carried out according
to Sambrook et al. (1989).
RNA and Protein Analysis
For Northern blot analysis, 5 µg of poly(A)+ or 10 µg of total RNA were
electrophoresed and transferred to Hybond-NX (Amersham) filters for
hybridization. The 5' end of SnoH1 RNA was determined by primer extension analyses, using 50 µg of total RNA together with primers complementary to nucleotides 96-135 and 149-189 of the fourth mfl intron.
rRNA processing was studied by [3H]uridine (1 mCi/ml, 22.4 Ci/nmol) incorporation in Drosophila larvae. After 48 h, total RNA was extracted
and analyzed by agarose electrophoresis followed by fluorography, as described by Tollervey (1987).
In rRNA northern blot analyses, probe I corresponds to oligonucleotide 5'-GTTAAAATCTTTTTATGAGGTTGCCAAGCCCCACAC-3';
probe II to oligonucleotide 5'-CACCATTTTACTGGCATATATCAATTCCTTCAATAAATG-3'; probe III to oligonucleotide 5'-CTATTTCCGAATCATTAATAAGAGACAATTCTAGATG-3'. Mapping of Drosophila ribosomal pseudouridines was performed essentially as described
by Bakin and Ofengand (1993) using as primer the oligonucleotides: 5'-AATCAAGTTCGGTCAACTTTTGCGAAACAACCGTAACAC-3' for
18S U1820, U1821, and U1822; 5'-GCGTCGTAATACTAATGCCCCCAAACTGCTTC-3' for 18S U830/U831, U840, U841, and U885; 5'-CCATTCATGCGCGTCACTAATTAGATGACGAG-3' for 28S U2442,
U2444, and U2499. Western blots were analyzed with a 1:1,000 dilution of
an affinity-purified rabbit anti-MFL antibody, kindly provided by S. Poole
(University of California, Santa Barbara, CA).
In Situ Analysis
Whole mount ovaries in situ hybridization, using single-stranded DIG-labeled probes, obtained by PCR, and immunohistochemical staining of
ovaries were performed essentially as described in Ashburner (1989). The
rabbit primary anti-MFL antibody, kindly provided by S. Poole, was diluted 1:400 and detected with a biotin-conjugated secondary antibody and
a horseradish peroxidase-biotin-avidin complex (ABC Elite Kit; Vector Labs).
Computer Analysis
Sequence comparisons were performed using the BLAST search algorithms available at the National Center for Biotechnology Information Web pages; multiple alignments were performed using the CLUSTAL and BOXSHADE programs. The snoH1 RNA putative secondary structure was established using the MFOLD program.
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Results |
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Isolation, Genetic, and Phenotypical Analysis of mfl Mutants
The first minifly allele, mfl1, was isolated in our laboratory
in the course of a PZ-element mutagenesis screen on the
second chromosome (see Materials and Methods) as a viable, recessive mutation causing a variety of phenotypic abnormalities. The mfl1 pleiotropic phenotype included an
extreme reduction of body size (Fig. 1, a and b), developmental delay, essentially due to a 4-5-d prolongation of
the larval life, defects in the abdominal cuticle (Fig. 1 c),
strong reduction in the length and thickness of abdominal bristles, and reduced female fertility. Most traits of the
mfl1 phenotype largely overlapped those caused by the
Drosophila Minute (Kay and Jacobs-Lorena, 1985), mini
(Procunier and Tartof, 1975
) or bobbed mutations (Boncinelli et al., 1972
) that affect, respectively, the synthesis of
ribosomal proteins, 5S, or 18S and 28S rRNAs. This similarity suggested for mfl a possible role in ribosome biogenesis, encouraging us to attempt the molecular cloning of the gene.
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mfl1 mutation was caused by a single P-element insertion, which, by in situ hybridization of a P-specific probe to
salivary gland polytene chromosomes of mfl1 heterozygous larvae (Fig. 1 d), was mapped on the chromosome arm 2R, at the 60B-60C polytene subdivisions boundary.
Given that wild-type revertants could be recovered from
dysgenic crosses after precise excision of the element (see
Materials and Methods), mfl1 mutation appeared to be directly caused by this single PZ insertion. Complementation analysis assigned the gene to the region covered by
the Df(2R)Px4 deficiency. Among a number of P-induced
lethal mutations recovered by Török et al. (1993) and subsequently deposited as part of the Berkeley Drosophila
Genome Project, five mapped at the 60B-60C polytene
subdivisions boundary. These mutations were all tested
in a complementation analysis, by crossing each of them
to mfl1 heterozygous flies. Two lines, l(2)k05318 and
l(2)k06308, yielded transheterozygous flies with a strong
mfl phenotype at the expected ratio, leading us to conclude that they belonged to the mfl complementation group and represented lethal mfl alleles. Accordingly,
these lines were renamed, respectively, mfl05 and mfl06.
Previous cytological mapping by the Berkeley Drosophila
Genome Project assigned these two mfl alleles to the polytene interval 60B11-C2, in good agreement with our results. By lethal phase analysis (Fletcher et al., 1995; see below) we observed that mfl05 homozygotes die mainly as
first instar larvae, while most of the mfl06 animals die later,
either as second or mainly as young third-instar larvae.
Both mfl05 and mfl06 animals fail to increase their size as
compared with their wild-type heterozygous siblings and
survive for an additional 4-5 d as first or third instar larvae, respectively.
Since a feature of the mfl1 pleiotropic phenotype was
represented by reduced female fertility, we looked at the
structure of mutant ovaries. Morphological abnormalities
were often observed, with some of the egg chambers beginning to degenerate beyond approximately stage 7 (according to King, 1970) of oogenesis (Fig. 2 c, see brackets).
In the degenerating egg chambers, fragmented or condensed nurse cell nuclei with irregular shape are frequently found (Fig. 2 c, boxed). These observations raise
the possibility that apoptotic cell death may occur in
mfl1 abnormal ovaries. This possibility was investigated by
staining egg chambers with acridine orange (AO). AO is a
vital dye that is known to selectively stain apoptotic cells
in insects (Spreij, 1971; Abrams et al., 1993
) and has successfully been used to study the distribution of apoptosis
in Drosophila ovaries (Foley and Cooley, 1998
). In our
experiments, wild-type ovaries exhibit a diffuse green
fluorescence (Fig. 2 b), whereas highly fluorescent yellow
spots are detected in mfl1 degenerating egg chambers (Fig.
2 d). These yellow spots are known to correspond to apoptotic, AO highly positive nuclei (Foley and Cooley, 1998
),
thus confirming the occurrence of apoptosis in mfl1 ovaries.
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As a consequence of the gonadic abnormalities observed, mfl1 homozygous females lay a reduced number of
mature eggs, and ~15% of the embryos produced failed to
hatch. Such degenerating embryos show asynchronous and
atypical development, invariantly accompanied by diffuse
apoptotic cell death (data not shown). Many mutations causing partial loss-of-function of vital genes interfere
with the proper development of the egg, causing female
sterility. Inadequate rate of protein synthesis is also known
to affect Drosophila oogenesis, by slowing the level of yolk
production and retarding egg chamber progression into vitellogenesis, beginning at stage 8 (reviewed by Spradling,
1993). This effect is common to mutants unable to produce
large amount of proteins, having reduced levels of either ribosomal proteins, 18S, 28S, or 5S rRNAs.
Molecular Organization, Coding Properties, and Developmental Expression Profile of the Minifly Gene
The genomic region adjacent to the PZ transposon was cloned from the mfl1 stock by plasmid rescue (Wilson et al., 1989) and used to isolate the sequences encompassing the PZ insertion site. Genomic probes spanning a region of ~4 kb surrounding PZ insertion identified on Northern blots of poly(A)+ RNA two main transcripts of 1.8 and 2.0 kb in length, whose expression was affected in each mfl mutant line (see next section). While the 1.8-kb species was constitutively expressed throughout the life cycle, the 2.0-kb RNA was specifically found in adult female and embryonic RNA preparations, in which a further transcript of ~4.0 kb was also occasionally detected (Fig. 3 b). However, no cDNA representative of this mRNA subform was isolated after extensive screening of an adult female cDNA library, so that it remains unclear whether it actually derives from the mfl gene. In contrast, several cDNAs representative of the 1.8 and 2.0 kb were isolated from adult female and larval libraries. The longest cDNAs of each class, respectively, of 1,833 and 2,034 bp, including the poly(A) tail, represented almost full-length transcripts and allowed us to define the mfl gene structure by Southern blot hybridization and alignment with nucleotide sequence of the genomic region. In each mfl mutant line, a copy of P was inserted at the 5' common end of 1.8- and 2.0-kb transcription units: in mfl06, the insertion site was mapped 18 nt upstream from the 5' end of the longest cDNAs obtained, in mfl1 18 nt downstream, within the 5' leader sequence, while in mfl05 the insertion occurred within the first intron of the gene (see Fig. 3 a). The 1.8- and 2.0-kb mfl mRNA subforms share a common coding region and differ from each other only at their alternatively spliced 3' untranslated region, where two additional exons (7 and 8) are specifically included in the 2.0-kb mRNA. When used on northern blots, a probe derived from these two exons (probe 2, depicted below the genomic map) detects exclusively the 2.0-kb subform, specifically present in embryos and adult female RNAs (Fig. 3 c). Hybridization of this probe to whole mount preparations of wild-type ovaries reveals that the female transcript accumulates in germ line cells from the early germarial till last oogenesis stages (Fig. 3 d). We then followed the accumulation profile of both mfl mRNAs during embryogenesis by developmental northern blot analysis of carefully synchronized embryos. As depicted in Fig. 3 e, both mfl mRNAs are detected in very early, 0-2 h embryos. However, while the zygotic 1.8-kb mRNA persists at later stages, the level of female transcript drops subsequently, and becomes very low in 4-6 h embryos. This developmental pattern is very similar to that of other stable maternally supplied RNAs, which persist from early stages up to gastrulation.
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The mfl open reading frame (ORF), identically present
in both mRNA subforms, encodes a predicted protein of
508 amino acids with a calculated molecular mass of 56 kD. Database searches revealed that this protein belongs
to the Cbf5p/NAP57/dyskerin family (Fig. 3 f). The MFL
polypeptide shows a significant degree of conservation to
other members of the family, particularly with the two
very similar rat and human proteins (66% identity, 79%
similarity to human dyskerin). The conservation increases
remarkably within several specific domains, strongly underlining that their function has been preserved during
evolution. As depicted in Fig. 3 f, total identity exists
among Drosophila and human proteins within the two
TruB motifs which have homology with bacterial and
yeast tRNA pseudouridine synthases (Heiss et al., 1998).
A repeated hydrophobic domain, possibly involved in the
nucleo-cytoplasmatic shuttling postulated for the rat protein is also highly conserved. This domain is immediately
followed by a block of >20 amino acids having a central
tyr that is identical in Drosophila, rat, and human proteins.
Although no function has been suggested so far for this
domain, its conservation suggests that it might play a relevant role in protein activity. Within the tyr domain, we noticed a RX-x(2,3)-DE-x(2,3)-Y central core motif highly
conserved among uracil-DNA glycosylases from different
organisms as part of the rigid uracil-binding pocket (Up)
present in these repair enzymes. Within the pocket, the
tyrosine residue has been shown to be directly involved
in uracil recognition (Kavli et al., 1996
; Slupphaug et al.,
1996
). By analogy, it is reasonable to suggest that the
highly conserved tyr motif might play a similar role in
uracil recognition. A highly charged lysin-rich COOH-terminal region containing a nuclear localization signal is
found in MFL, as in NAP57 and dyskerin, and the NH2-terminal nuclear localization signal observed in rat and human proteins is also preserved. Finally, it is interesting to
note that all five missense mutations thus far identified in
DKC patients fall into regions that are conserved between
the human and the Drosophila gene (see positions of asterisks in Fig. 3 f).
mfl Is an Essential Drosophila Gene Playing a Key Role in rRNA Processing
When mfl mutants were checked for gene expression, we
found that they were all characterized by reduced levels of
mfl mRNAs. While the viable, hypomorphic mfl1 allele
showed only a modest reduction, mfl expression was
strongly disrupted in mfl05 and mfl06 (Fig. 4 a), the two alleles causing larval lethality. MFL protein accumulation
strictly paralleled the level of mfl mRNAs, so that it was
strongly reduced in mfl06 and nearly null in mfl05 (Fig. 4 b).
Remarkably, the developmental time at which lethality is
achieved in these two mutants correlates well with MFL
level since, as mentioned above, mfl05 homozygotes die
mainly as first instar larvae, while mfl06 animals as second
or early third-instar larvae (see Fig. 4 c). Note that, considering the timing of persistence of maternal rRNA (Winkles et al., 1985), mortality at the first instar is that which
may be expected for mutations causing severe loss of function of a gene essential for rRNA processing. Taken together, all these data indicated that MFL level may be critical for Drosophila viability. We then attempted to rescue
mfl lethal phenotype by ectopically expressing MFL from
the heat-inducible hsp70 promoter. mfl05 and mfl06 transgenic animals were then obtained and daily treated at 37°C for 30 min. These heat-shock conditions usually produce
amounts of the ectopically expressed protein that largely
exceed the wild-type level. However, in our experiments
they produced a MFL level just comparable to that present in wild-type flies, even though the induced protein remains quite stable from 6 h to as long as 24 h from the
heat-shock pulse (Fig. 4 b). Nevertheless, the level of induced MFL is sufficient to allow mfl05 and mfl06 transformed animals to developed synchronously with their
wild-type siblings and to show a normal increase in their
size. Moreover, 30% of the mfl05 and 80% of the mfl06
transgenic animals develop up to the pupal stage, although
these transgenic pupae all failed to eclose adult flies (see
Fig. 4 c). A possible explanation for this partial rescue of
the mfl mortality is that the level of ectopically expressed
MFL may be inadequate with respect to the rate of protein
synthesis required in specific cell types during metamorphosis. An alternative possibility is suggested by the observation that, in yeast, Cbf5p is required for the stability
of other components of the H/ACA class of RNPs, such
as Gar1p and box H/ACA snoRNAs (Lafontaine et al.,
1998
). It is thus possible that the MFL level reached under
heat-shock conditions may not be constant and this affects
the stability of other essential RNP components. However, since no member of the H/ACA class of RNPs has
yet been described in Drosophila, this hypothesis cannot
be tested at present.
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Given the similarity existing between the mfl phenotype and that caused by mutations affecting the synthesis of ribosomal components, we checked the role of the gene on rRNA processing. Electrophoresis of larval rRNA labeled by [3H]uridine incorporation showed that pre-rRNA processing is inefficient in mfl mutants. In fact, with respect to wild-type flies, increased levels of the pre-rRNA and 28S rRNA and reduced amounts of the 18S, 28Sa, and 28Sb mature species were observed (Fig. 5 a; compare the level of the newly synthesized larval rRNA, labeled by [3H]uridine, with the amount of total rRNA composed of both newly synthesized and maternally inherited rRNA, shown by ethidium bromide staining at the bottom). MFL over-expression in mfl transgenic flies is sufficient to reduce rRNA precursor accumulation and to increase the level of the newly synthesized 18S and 28S species (Fig. 5 a).
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Northern blot analysis with three different probes derived from the rDNA internal transcribed spacer (ITS) led
us to define in greater detail the abnormal rRNA processing occurring in mfl mutants. In Drosophila the rRNA
primary transcript (pre-rRNA) undergoes two alternative
types of initial cleavages (Long and Dawid, 1980). The
most predominant type occurs in the external transcribed
spacer, at site 1, and generates the large type a molecule,
from which both 18S and 28S are derived (see pathway
,
Fig. 5 b). An alternative cleavage occurs within ITS, at site 3, generating the intermediate d and b forms which are, respectively, 18S and 28S rRNA precursors (see pathway
,
Fig. 5 b). Hybridization to a probe derived from the ITS 5'
end (probe I) revealed that the accumulation of the pre-rRNA observed in mfl mutants is accompanied by a reduction of the type a precursor and by an increase of the d
form; both effects become more evident with progression
of the larval development (Fig. 5 c). Thus, mfl mutations
specifically affect site 1 cleavage, inhibiting the formation
of type a molecules and the processing of the d intermediate. With pathway blocked, pre-rRNA processing proceeds mainly through pathway
, generating equimolar
amounts of d and b intermediate molecules. This is confirmed by hybridization to probe II, which shows that,
while in wild-type animals the amount of form b largely
exceeds that of d (as expected, being that the b molecule is
actively produced by both
and
pathways), in mfl mutants these two forms are detected in similar amounts (Fig.
5 d). However, since the processing of form d is inhibited,
this species accumulates progressively along larval development (Fig. 5 d). Conversely, hybridization to probe III indicated that mfl genetic depletion does not impair site 4 cleavage of type b molecule, since the amount of form c
observed in the mutants exceeds even that of the control
(Fig 5 e). We concluded that form c is generated properly,
but its further processing is inhibited by mfl mutations. In
mfl transgenic flies, MFL over-expression leads to a reversal of all of the effects observed, although the efficiency
of pre-rRNA processing is not fully restored. In heat-shocked transformed animals, in fact, MFL expression
causes a decrease of pre-rRNA accumulation and an increase in the production of the type a molecule (Fig. 5 c).
Processing of the type a precursor also occurs properly,
since, as depicted in Fig. 5 d, these larvae show an excess
in form b versus form d, although the amount of the b molecule does not reach that observed in wild-type animals. Finally, the amount of form c appears reduced after the
heat-shock (Fig. 5 e), indicating that its processing is at
least partially restored.
In yeast, lack of Cbf5 gene activity affects not only
rRNA processing, but also rRNA pseudouridylation. Thus,
we checked the level of modification in wild-type and mfl
mutants at several 28S and 18S specific sites. With this
aim, we used oligonucleotide primers complementary to
selected 28S or 18S regions to perform primer extension
analyses on CMC-treated Drosophila rRNA. CMC blocks
reverse transcription, resulting in a gel band terminating in
one residue 3' of the
site (Bakin and Ofengand, 1993
).
In planning these experiments, we took advantage of the
location of Drosophila 28S rRNA pseudouridines recently
reported by Ofengand and Bakin (1997)
. Instead, none of
the 18S
sites checked in our experiments was previously
known. In spite of the persistence of maternal rRNA,
pseudouridylation appears reduced in mfl05 larvae at several 28S sites, such as the U2442, U2444, and U2499 residues (Fig. 5 f). Similar reduction was observed at various 18S rRNA sites, such as U830/U831, U840, U841, and
U885 (Fig. 5 g), indicating that, as Cbf5, mfl is required for
efficient rRNA pseudouridylation.
Minifly Hosts an Intron-encoded Box H/ACA snoRNA
An unexpected feature of the mfl gene structure was revealed by the finding that a small RNA species, ~0.1 kb in
length, hybridized specifically with the genomic sequences
of the fourth mfl intron, while it was not detected by any
cDNA probe. This small RNA was detected in total RNA
preparations from all developmental stages and was specifically enriched in the poly(A) RNA fraction. The
length of the small RNA species was accurately determined on denaturing 6% polyacrylamide gels and its 5'
end precisely mapped by primer extension analysis of total
larval RNA using two different oligonucleotides (Fig. 6, b
and c). These experiments pointed out that this transcript
was ~140 nt long and derived from position +37 to about
+176 of the 235-nt-long fourth mfl intron (Fig. 6 a). Since
a large number of small nucleolar RNAs are intron encoded (Smith and Steitz, 1997
), we checked for the presence of conserved snoRNA elements within the 0.14-kb
RNA sequence. Two H boxes (consensus ANANNA) and
a 3' terminal ACA element were found (Fig. 6 a); in addition, the predicted secondary structure of the mfl intron-encoded RNA (Fig. 6 d) conformed well to the hairpin-hinge-hairpin-tail architecture common to most yeast and
vertebrate box H/ACA snoRNAs (Ganot et al., 1997b
). Two short regions of complementarity between the mfl intron encoded RNA and Drosophila 18S rRNA were also
found (Fig. 6 e). As noticed by Ganot et al. (1997a)
, short
regions of pairing with rRNA flank the site of pseudouridylation, allowing the positioning of the residue to be
isomerized at the base of the stem, at the first unpaired position before the 3' snoRNA helical segment. The pseudouridine selected is found to be separated from the H or
ACA box by 14 or, in a few cases, by 15 nucleotides. On
the basis of these observations, the rRNA pairing properties of the mfl intron-encoded RNA predicted it may
direct pseudouridylation of Drosophila 18S rRNA at position U1820 (Fig. 6 e). Primer extension analysis on CMC-treated Drosophila rRNA shows that the potentially selected residue is actually pseudouridylated (Fig. 6 f). The
selected U1820 residue is equivalent to U1698 of human
18S rRNA, whose pseudouridylation has recently been related to the U70 snoRNA (Ganot et al., 1997a
). As for
U1698 in human rRNA, the Drosophila U1820 residue is
the first of three consecutive uridines, all of which are
pseudouridylated (Fig. 6 f, lane 2).
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In yeast, genetic depletion of most of the box H/ACA
snoRNAs has been reported to inhibit pseudouridylation
of the specifically selected sites (Ganot et al., 1997a).
When we checked modification of the U1820 residue in
rRNA preparations obtained from mfl05 first instar larvae,
we found that pseudouridylation was reduced not only at
U1820, but also at U1821 and U1822 residues (Fig. 6 f,
lane 3). This result may be explained by the widespread inhibition of rRNA pseudouridylation observed in mfl mutants. Further experiments are thus required to define the
specific functional role, if any, played by the mfl intron-encoded RNA.
Finally, we checked the localization of the mfl intron encoded RNA by in situ hybridization experiments to whole
mount ovary preparations. This analysis showed that a
0.14-kb RNA-specific antisense probe exclusively labeled
the nucleoli (Fig. 7, a and b) as it occurs in each tested embryonic or larval tissue (not shown). Specific nucleolar localization may also be observed for MFL (Fig. 7 c), whose
ubiquitous expression resulted from both immunolocalization data and histochemical staining of lacZ activity in mfl1
flies (data not shown). In ovarian tissue preparations we
noticed that the protein occasionally diffuses into the cytoplasm in several patches of follicle cells. As judged by the
presence of well defined, round-shaped nuclei having morphologically well distinguishable nucleoli (Fig. 7 c), these
cells should not be in or around mitosis. Moreover, cytoplasmic diffusion can be observed also after stage 10b of
oogenesis, when follicular cells endocycles are reported to
be terminated (Calvi et al., 1998). It is thus plausible that occasional MFL cytoplasmic localization may be related to
ability to carry out nucleolus-cytoplasmic shuttling, as proposed for NAP57 in rat cells (Meier and Blobel, 1994
).
|
Taken together, the experiments reported indicate that mfl hosts, in its fourth intron, a box H/ACA snoRNA gene, the first member of this class to be identified so far in Drosophila. We have called this gene snoH1 and suggest that it is functionally equivalent to the human U70 snoRNA gene.
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Discussion |
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---|
We reported the cloning of the D. melanogaster mfl gene
and established that it encodes an ubiquitous nucleolar
protein essential for Drosophila viability and female fertility. Our data also showed that mfl is closely related to the
other members of the Cbf5 family so far characterized
from higher eukaryotes, the rat Nap57 and the human
gene responsible for the X-linked dyskeratosis congenita disease. As cogently predicted (Luzzatto and Karadimitris, 1998), flies carrying mutations in the Drosophila
DKC1 orthologue show a pleiotropic phenotype very similar to that caused by mutations that affect the synthesis of
ribosomal RNA. In fact, we found that mfl loss-of-function mutations impair rRNA processing and lead to accumulation of rRNA precursors. Although these effects are
very similar to those caused by Cbf5 genetic depletion,
yeast mutations preferentially affect the production of mature 18S rRNA (Lafontaine et al., 1998
), while mfl mutations cause similar reduction of 18S and 28S rRNA species. It would be of interest to know whether this is due to
a distinctive feature of Drosophila rRNA processing pathways, or whether it reflects a general property of rRNA
processing in higher eukaryotes.
In addition to affecting rRNA maturation, mfl loss-of-function causes reduced levels of pseudouridylation at several 28S and 18S sites, suggesting that gene activity
might be required for fully efficient rRNA pseudouridylation. Again, these results are reminiscent of those obtained in yeast (Lafontaine et al., 1998
), and outline the
existence of a link between rRNA processing and rRNA
pseudouridylation in eukaryotes. By mapping the protein
domains conserved among members of the Cbf5p family
and investigating the definition of their functional roles,
significant information should be generated about the functional role played by rRNA pseudouridylation, which still
remains elusive. Although pseudouridylation of eukaryotic rRNAs occurs predominantly on the primary rRNA
transcripts before nucleolytic processing, this type of modification is not required for efficient processing of 25S
yeast rRNA (Bousquet-Antonelli et al., 1997
). It has been
suggested that pseudouridylation can contribute to rRNA
folding, rRNPs assembly, and ribosomal subunit assembly
(Lane et al., 1995
; Maden, 1990
; Ofengand et al., 1995
). Other hypotheses, such as subtle enhancing of ribosomal
functions or influencing fidelity of codon recognition, have
also been proposed (Ofengand and Bakin, 1997
).
An additional role that could be suggested for MFL is based on the observation that it can occasionally diffuse within the cytoplasm. As previously suggested for NAP57 in rat cells, it is tempting to speculate that this may possibly reflect the ability of MFL to structure and export pre-ribosomal RNP particles into the cytoplasm. If confirmed, this would strongly support the view that members of this family are multifunctional proteins involved in different aspects of ribosome biogenesis. It is possible that these proteins may constitute essential components of a single multifunctional complex or, alternatively, they represent common components of structurally and functionally different RNP particles. The definition of the functional interactions required to carry out such a variety of functions will help to clarify this point.
Remarkably, the identification and the characterization
of mutations disrupting mfl gene expression has led to establishing the first animal model system for the study of
the X-linked dyskeratosis congenita human disease. Some
of the results reported here may immediately provide useful information for the comprehension of the molecular
basis of the DKC disease. A first relevant point concerns
the observation that none of the mfl mutations so far isolated disrupts the gene coding region. Thus, each Drosophila mutant line has certainly quantitative and not
qualitative alterations of the gene product which causes
the pleiotropic abnormalities observed. The level of MFL
protein was found to be critical, and a simple dose-effect
rule may be derived: when the protein level is below a crucial threshold, mortality ensues. Instead, while the protein
level is lowered but still stands above a critical threshold,
the viable, hypomorphic mfl1 phenotype is reached. By
analogy, it can be suggested that in man the level of dyskerin activity may be one of the critical parameters able to
trigger the DKC disease. The finding that DKC mutations
mapped so far all affect the dyskerin coding region (Heiss
et al., 1998) is in only apparent contrast with that found in
Drosophila. In fact, it is reasonable to suppose that, as
observed in Drosophila, total or severe loss-of-function
mutations should not be compatible with life. Mutations
recovered in patients might be those causing partial loss-of-function, so that the level of dyskerin activity is still
compatible with survival. Accordingly, DKC patients might
carry hypomorphic mutations, the human counterparts of
the viable mfl1 phenotype. Whether these hypomorphic
phenotypes are simply a consequence of the inadequate
mature rRNA level or are, at least partially, caused by abnormal accumulation of intermediate rRNA species is an
important point which deserves further investigation. A
further issue concerns the observation that, although MFL
and dyskerin are ubiquitous proteins, phenotypic abnormalities are, in Drosophila as in man, restricted to only
certain tissues. Since the gene product is presumed to be
critically important for protein synthesis in every cell of
the body, the finding that abnormalities are developed
only by selected cell types is quite surprising. However, if
it is accepted that the level of protein activity may be a
critical parameter, then it is reasonable to suppose that the
amount of properly processed rRNA may be sufficient in cells having a slow growth rate, while in highly proliferating tissues or in cells sustaining a high rate of protein synthesis this would not the case, and degenerative cell defects could progressively be accumulated. Interestingly,
inhibition of protein synthesis is known to be one of the
stimuli capable of inducing apoptotic cell death, probably
by decreasing the levels of essential proteins or by inhibiting the synthesis of proteins that normally suppress the
spontaneous activation of apoptosis (reviewed by Wertz
and Hanley, 1996
). In mfl1 ovary, one of the Drosophila
tissues where morphological abnormalities can be observed, we found that degeneration is specifically accompanied by apoptotic cell death. This observation might
also suggest a role for apoptosis in the progressive clinical
manifestations of the DKC disease.
Finally, we showed that mfl gene organization is intriguing, and leads to the identification of the first member of
the box H/ACA class of snoRNAs described so far in
Drosophila. As in the case of the snoH1 gene described
here, most of the snoRNAs are intron encoded, and
snoRNA host genes often encode proteins involved in
translation or ribosome biogenesis (reviewed by Smith and
Steitz, 1997). These intron-encoded snoRNAs are cotranscribed with their host pre-mRNA and their accumulation
is splicing-dependent, since they are released from the excised intron by exonucleolytic processing. Our observation
that snoH1 RNA and mfl mRNAs levels are reduced in
parallel in each mfl mutant line strongly suggests that
snoH1 RNA processing is linked to the splicing of the mfl
primary transcript. This feature, which allows coordinated
regulation of the host protein and the intron encoded
snoRNA, may hinder a precise definition of the specific
functional role played by each product. With regard to
snoH1, it cannot be excluded, in principle, that it may be required for Drosophila viability and that its depletion
might contribute to the generation of mfl phenotype.
However, we have observed that snoH1 has little, if any,
effect on mfl phenotypic rescue when over-expressed in
mfl transgenic flies, either in the presence or in the absence of MFL overexpression (Giordano, E., and M. Furia, unpublished data). This is not surprising, given that all
box H/ACA snoRNAs found in yeast, with the exception of snR30 (Morrissey and Tollervey, 1993
) and snR10 (Tollervey, 1987
; Tollervey and Guthrie, 1985
), are dispensable for viability. It will now be interesting to determine
whether this type of gene organization is restricted to mfl
or is shared by other members of this conserved gene family.
![]() |
Footnotes |
---|
Received for publication 12 November 1998 and in revised form 16 February 1999.
Address correspondence to Maria Furia, Dipartimento di Genetica,
Biologia Generale e Molecolare, via Mezzocannone 8, I-80134, Napoli,
Italy. Tel.: 39 081 7903413 or 39 081 7903419. Fax: 39 081 5527950. E-mail:
furia{at}biol.dgbm.unina.it
S. Senger was supported by a Ph.D. fellowship from European Union.
This work was supported by funds of MURST PRIN Project Molecular
regulation of Development to M. Furia.
We are grateful to S. Poole for the generous gift of the affinity-purified anti-MFL antibody and to D. Bopp and T. Laverty for sending Drosophila stocks. We thank J. Guardiola, L. Luzzatto, S. Banfi, and P. Delli Bovi for encouragement during the course of this work, R. Calogero and G. Iazzetti for friendly and helpful computational assistance, and G. Falcone for excellent photographic assistance.
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Abbreviations used in this paper |
---|
AO, acridine orange; ITS, internal transcribed spacer; nt, nucleotide; ORF, open reading frame; snoRNA, small nucleolar RNA; Up, uracil-binding pocket.
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