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Genetics, Vol. 169, 683-695, February 2005, Copyright © 2005
doi:10.1534/genetics.104.034124
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Growth Regulation Laboratory, Cancer Research UKLondon Research Institute, London WC2A 3PX, United Kingdom
1 Corresponding author: Growth Regulation Laboratory, Cancer Research UKLondon Research Institute, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom.
E-mail: sally.leevers{at}cancer.org.uk
| ABSTRACT |
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Most, if not all, Minute phenotypes are a direct result of suboptimal protein synthesis. For example, bristle production and gametogenesis require maximal protein synthesis and are therefore particularly sensitive to a reduction in the translational capacity of the cell. Indeed, it is now generally accepted that Minute mutations disrupt genes that encode cytosolic ribosomal proteins (RPs). There is both direct and indirect evidence for this conclusion. First, the number of genes encoding (cytosolic) RPs in the D. melanogaster genome (
90; http://flybase.bio.indiana.edu; S. J. MARYGOLD, unpublished results) compares well with the number of described Minutes (>50; LINDSLEY and ZIMM 1992), considering that potentially separable Minute loci may well have been grouped together in the past (see below). Second, reduction in any single RP is expected to result in the same Minute phenotype because ribosome function depends on an equimolar balance of all RPs (together with rRNAs; WARNER 1999). Moreover, the vast majority of D. melanogaster RPs are present in a single copy in the genome (S. J. MARYGOLD, unpublished results). Third, of the historically defined Minute loci, several have since been unambiguously linked to RP genes, and many others map to the same genomic region as cloned RP genes (LAMBERTSSON 1998). More recent work has generated new mutations in RP genes and many of these have also been shown to cause the Minute phenotype. Finally, to date, only mutations in RP genes have been shown to display the full complement of Minute traits (LAMBERTSSON 1998).
Of the
50 well-documented classical Minute loci, only 1015 have been unequivocally assigned to one of the
90 RP genes in the D. melanogaster genome (LAMBERTSSON 1998; http://flybase.bio.indiana.edu; S. J. MARYGOLD, unpublished results). This relatively poor Minute-to-RP gene correspondence is because most classical Minutes have been discovered through the phenotype of a deficiency (i.e., deletion-bearing) heterozygote rather than a point mutation heterozygote (LINDSLEY and ZIMM 1992). Thus, many Minutes have only a crude cytogenetic location on the chromosome that is hard to correlate with a specific RP gene predicted from the physical, sequence-based genome. Furthermore, as deletions often remove many genes, some Minute deficiencies may uncover two or more RP genes located in close proximity, leading to an underestimation of the number of distinct Minute loci in the genome. Two key questions therefore remain: Do all currently described Minutes disrupt RP genes? And does a 50% reduction in the dosage of any RP gene generate the Minute phenotype?
It is evident that molecularly defined, nondeficiency mutations of RP genes will be required to address these questions. Such mutations will also permit specific genetic analyses of the function of individual RPs and interactions between them. Much progress has been made in this direction in recent years, mainly through P-element-mediated mutagenesis, and today discrete, molecularly defined mutations are described for
30 of the
90 RP genes in the D. melanogaster genome (LAMBERTSSON 1998; http://flybase.bio.indiana.edu ; S. J. MARYGOLD, unpublished results).
All Minute/RP mutations described to date reduce the overall rate of organismal growth in a dominant manner, thereby resulting in retarded development (BREHME 1939, 1941a; LAMBERTSSON 1998). Like other Minute traits, these growth defects are likely to be caused by suboptimal cellular protein synthesis, leading to a cell-autonomous lengthening of individual cell cycles (MORATA and RIPOLL 1975). Although many heterozygous Minutes attain a normal final body size, some have been reported to be smaller than wild type (BREHME 1939; LAMBERTSSON 1998; MONTAGNE et al. 1999). Moreover, BREHME (1941a) reported that individual adult wing cells in three different Minutes were abnormally small and that at least in the case of M(3)95A1 (RpS31), this reduction in cell size was sufficient to account for an overall reduction in wing and body size (BREHME 1941a). It should also be noted that the rate of growth and/or the final organ size attained is perturbed by mutations in genes encoding other components or regulators of the translational machinery such as translation initiation and elongation factors, S6 kinase and components of the insulin/phosphatidylinositol 3-kinase (PI3K) pathway, and the cMyc transcription factor (LEHNER 1999; RUGGERO and PANDOLFI 2003). However, unlike RP mutants, the growth defects in these cases are not associated with the dominant Minute phenotype.
Curiously, other work has linked a reduction in RP gene dosage to hyperplasia and overgrowth. For example, mutation of D. melanogaster RpS21 or RpS6 causes overgrowth of the imaginal discs and/or hematopoietic organs (WATSON et al. 1992; STEWART and DENELL 1993; TOROK et al. 1999), while a recent mutagenesis screen in zebrafish embryos revealed that many RP genes behave as tumor suppressors in this organism (AMSTERDAM et al. 2004). Furthermore, certain RPs have been shown to be downregulated in some human cancers or cancer syndromes (KONDOH et al. 1996; LOFTUS et al. 1997; DRAPTCHINSKAIA et al. 1999). Recent studies in D. melanogaster have also challenged earlier reports that cells heterozygous for a Minute/RP mutation are small (BREHME 1941a,b): RpS3Plac92/+ cells in the developing wing disc are wild type in size (NEUFELD et al. 1998), whereas RpS131/+ wing-disc cells are abnormally large (MARTIN-CASTELLANOS and EDGAR 2002). It is unclear at the present time whether these discrepancies reflect different methodologies or gene/allele-specific differences. In summary, differential expression of RPs and modification of the translational apparatus can impinge on growth and size regulation in a number of ways.
Here, we report the isolation and analysis of point mutations in two previously uncharacterized D. melanogaster RP genes located in the centric heterochromatin of the second chromosome, namely RpL38 and RpL5. We find that these mutants display the classic Minute phenotypes of small adult bristles and delayed development. In addition, trans-heterozygous viable combinations of RpL38 mutant alleles generate flies with distinct patterning defects. Compared to wild-type flies, flies with a reduced dosage of either RpL38 or RpL5 have larger wings that contain larger cells.
| MATERIALS AND METHODS |
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Crosses to assess developmental delay, dominant effects on wing size, and notal bristle phenotypes were set up in vials and then transferred to egg-laying cages for 2-hr laying periods. Embryos were then aged for
26 hr and 60 control or [30 Rp/+ and 30 CyO, Kr-Gal4 UAS-GFP/+] first instar larvae were transferred to fresh vials supplemented with wet yeast. An appropriate control cross was set up at the same time and kept under the same conditions as the test crosses for each experiment. To measure the delay in eclosion, vials were checked and the number of eclosed adults counted every 2 hr throughout the day, starting 8 days after egg deposition and continuing until no more flies emerged.
Cuticle preparations:
For wing preparations, adult flies were collected 23 days after eclosion and stored in isopropanol. Wings were subsequently dissected in isopropanol, mounted in Euparal (Agar Scientific), and baked at 65° overnight. Male and female flies were dissected and their wings mounted separately. Only one wing from each fly was analyzed when assessing dominant phenotypes while both wings were taken from RpL38NC21 trans-heterozygous flies, owing to the small number of escapers. For notal preparations, adult female flies were boiled in 5 M KOH for 10 min to dissolve the soft tissues, rinsed and dissected in H2O, mounted in Euparal (Agar Scientific), and baked at 65° overnight. Cuticle preparations were viewed on a Zeiss Axioplan 2 microscope, captured using an AxioCam HRm digital camera and Axiovision 4.1 software, and processed in Adobe Photoshop.
Bioinformatics and mapping strategy:
The mapping strategy and location of single nucleotide polymorphisms (SNPs) will be described in detail elsewhere (our unpublished results). The design of primer pairs and the determination of SNP locations on the physical map were based on the D. melanogaster Genome Release 3.1 and relied entirely on the BDGP GadFly annotation database. The location of deficiency breakpoints is based on the data in MYSTER et al. (2004) at http://flybase.bio.indiana.edu and on our own studies. The CLUSTAL alignment in Figure 5C was achieved by first performing a BLAST search with the D. melanogaster RpL5 protein sequence against the RefSeqP data library; the highest-scoring hits from various species were then aligned using CLUSTALW at Pôle BioInformatique Lyonnais (http://pbil.ibcp.fr) and subsequently were produced using ESPript 2.1 (http://prodes.toulouse.inra.fr/ESPript). Pfam 12.0 was used to identify protein motifs (http://www.sanger.ac.uk/Software/Pfam).
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10 heterozygous adult flies: the RpL382b1, RpL382b2, RpL52d1, and RpL52d2 strains were each isogenized for the mutant and the balancer chromosome. Flies were homogenized in 400 µl of buffer (0.1 M Tris-HCl pH 9, 0.1 M EDTA, 1% SDS) and the homogenate was incubated at 70° for 30 min. Protein was precipitated by adding 56 µl of 8 M potassium acetate and incubating for 30 min on ice. Protein was then pelleted by centrifugation at 4° for 15 min and DNA precipitated from the resulting supernatant by adding 0.6 volumes of isopropanol and incubating for 5 min at room temperature. DNA was pelleted by centrifugation for 5 min, washed with 70% ethanol, and finally resuspended in 200 µl distilled water. Primers were designed using the Primer3 program (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi). The following primers were used to amplify the RpL38 gene: RpL38-FOR, 5'-CAAAGACAGCCCTCGAAAAG-3'; RpL38-REV, 5'-TTTTCCGTACGCGTTAAAGG-3'. PCR conditions for RpL38 amplification were 95° for 5 min, followed by 30 cycles of 95° for 30 sec, 48° for 1 min, and 72° for 55 sec. RpL5 was amplified in two steps using the following primers: RpL5-FOR1, 5'-CGCTGTCTTGCCTTATATTGG-3'; RpL5-REV1, 5'-ATCGGCTAAACTGCCTTTTG-3'; RpL5-FOR2, 5'-TATATTTGGCCAGCACGTTG-3'; and RpL5-REV2, 5'-TTCTGTCACATTTCTCGGCC-3'. RpL5 PCR conditions were the same as above except that an extension time of 1 min 15 sec was used. Primers and PCR conditions for CG12775 are available upon request. All PCRs were performed using 2 µl of genomic DNA as template in a total volume of 25 µl using Taq PCR Master Mix (QIAGEN, Chatsworth, CA).
PCR products were cleaned up using either the QIAquick PCR purification kit or the QIAquick gel extraction kit (QIAGEN). Sequencing reactions were performed using the BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems, Foster City, CA) according to the manufacturer's instructions. Sequencing reactions were cleaned up using the DyeEx spin kit (QIAGEN) and sequencing was performed on an ABI 3730 DNA analyzer (Applied Biosystems). Sequences were analyzed using AutoAssembler (Applied Biosystems), Sequencher (Gene Codes, Ann Arbor, MI), or SeqManII (Lasergene, DNASTAR) software. Mutations were recognized as double peaks on sequence traces as DNA from both the mutant chromosome and the balancer chromosome from heterozygous flies was amplified and sequenced. All RpL38 mutations were verified by sequencing DNA from heterozygote adults on both strands. RpL5 mutations were confirmed by sequencing DNA from hemizygous embryos. The genomic region containing the entire transcript ±100200 bp was sequenced in each case and found to be wild type except for the mutations reported in the text.
Wing and cell density measurements:
Whole-wing area was calculated from a low-magnification image of the wing and measured using the magnetic Lasso tool and histogram function of Adobe Photoshop. Cell density was calculated by drawing a 200 x 200 pixel square (= 40,000 pixel2) on a high-magnification image of the area described in Table 2 and counting the number of wing hair roots within it. Dimensions were converted from pixels to micrometers and the cell area and total cell number were calculated as described in Table 2.
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| RESULTS |
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Flies heterozygous for a mutation at either the E-2b or the E-2d locus also show dominant phenotypes in a wild-type genetic background: they have short, slender bristles (Figure 1, AC) and eclose with a delay of 1224 hr compared to control flies (Figure 1D). In addition, flies with the genotype E-2b1/E-2b2 or E-2d1/E-2d2 are embryonic or larval lethal, respectively (data not shown). Taken together, these phenotypes are characteristic of the Minute class of mutants (LAMBERTSSON 1998). As Minute mutations are thought to disrupt RP genes, we suspected that the E-2b and E-2d genes might also encode RPs.
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Mapping using visible markers showed that both E-2b and E-2d loci are located close to the centromere of the second chromosome (data not shown). SNP-based mapping confirmed these initial findings and placed physical limits on the chromosomal region that contains these genes (Figure 2A). Unfortunately, we were unable to achieve a high mapping resolution by SNP analysis of recombinants, owing to lower rates of both recombination and SNP discovery close to the centromere, a phenomenon that has also been described by other researchers (BERGER et al. 2001; HOSKINS et al. 2001; MARTIN et al. 2001). We therefore performed complementation tests with deficiency strains that lack genomic sequence in the vicinity of the centric region of the second chromosome (Figure 2B and data not shown). Four overlapping deficiencies that failed to complement E-2b mutations placed the E-2b gene within the centric heterochromatin in band h46 on chromosome arm 2R (
41CE on the cytological map; CORRADINI et al. 2003). Similar complementation analyses localized E-2d to a small region near the euchromatin-heterochromatin border on the 2L arm that corresponds to cytological bands 40AB and includes the distal part of heterochromatic band h35 (HOSKINS et al. 2002).
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20 computed genes (CGs) are located in the h46 band (CORRADINI et al. 2003). Peifer and colleagues confirmed and extended these results and also defined several anchor points between the genetic and physical maps in the h46 region to tile the genomic scaffolds correctly (MYSTER et al. 2004; Figure 3B). Of the genes thus calculated to lie within h46, only CG18001 (also known as CG40278) is predicted to encode a RP. Conceptual translation of the CG18001 coding sequence predicts a 70-amino-acid protein that contains a Ribosomal_L38e (eukaryotic ribosomal protein 38 of the large 60S subunit) domain that comprises almost all the protein (from amino acid 2 to 69). The size, sequence, and organization of the CG18001 protein are typical of RpL38 orthologs from other species. For example, human RpL38 is also 70 amino acids long and shares 73% identity with the D. melanogaster version, and RpL38 from Arabidopsis thaliana comprises 69 residues and is 64% identical to CG18001. Importantly, CG18001 is the only gene in the D. melanogaster genome that is predicted to encode a protein with a Ribosomal_L38e domain (S. J. MARYGOLD, unpublished results) and has recently been renamed RpL38 in FlyBase (http://flybase.bio.indiana.edu) to reflect this. The RpL38 protein is found only in eukaryotes, and although no specific function has been ascribed to this RP, its strong evolutionary conservation suggests that it is a critical component of the eukaryotic ribosome (ESPINOSA et al. 1997). DNA sequence analysis revealed independent point mutations in the RpL38 gene in the E-2b1 and E-2b2 mutant strains (Figure 3, D and E, and Table 1). The E-2b1 mutation changes the initiating ATG codon to AGG, so it is likely to be a null allele. The E-2b2 mutation alters the canonical CAG splice acceptor sequence in the single intron immediately before the initiating ATG, so it is predicted to disrupt proper splicing of the pre-mRNA (MOUNT et al. 1992). We therefore conclude that E-2b/M(2)41A corresponds to RpL38 on the physical map and henceforth refer to this gene as RpL38 and to the two mutant alleles isolated in our screen as RpL382b1 and RpL382b2 (Table 1).
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Defining the RpL38 allelic series:
In addition to the four RpL38 point mutations described so far, we acquired two additional P insertion alleles: RpL38P3 and RpL38KPL1 (N. CORRADINI, K. GAZZETTI and P. DIMITRI, unpublished results). The different RpL38 mutants vary in the strength of their Minute phenotype and their behavior in trans with RpL38NC21, and this allowed us to order them into an allelic series that fits well with their molecular descriptions. By these criteria, RpL38NC21 and RpL38KPL1 are weak alleles, RpL38P3 is a medium strength allele, and RpL381, RpL382b1, and RpL382b2 are strong alleles (Figure 4 and Table 1). Note that the RpL381 allele shows a remarkably strong bristle phenotype relative to its other characteristics, perhaps because of additional mutations on this chromosome. Together, the molecular description and genetic characterization of six RpL38 mutant alleles make RpL38 one of the most genetically tractable Minute/RP genes in the D. melanogaster genome.
In addition to the strong Minute bristle phenotype seen on the notum of RpL38NC21 trans-heterozygotes (Table 1 and Figure 4, GJ), these flies also show patterning defects such as large rough eyes, ectopic wing venation, aberrant wing-blade hair polarity, and notches at the wing margin (Figure 4, AF, and data not shown). The wing notching and venation phenotypes are also seen in RpL38/+ flies at low penetrance (data not shown). Similar wing phenotypes have been reported for a number of other Minute/RP mutations either in a wild-type genetic background or in the context of a second mutation. For example, lowering RpL14 levels at the wing margin results in a severe notching phenotype (ENERLY et al. 2003) and several Minutes enhance the venation defects of plexus, net, and Delta mutants (LAMBERTSSON 1998). Wing-notching effects were also seen when flies were made doubly heterozygous for the RpL381 mutation and any of several mutations in genes required for wing development, such as Notch, vestigial, and cut (ROLLINS et al. 1999). One explanation that can account for many of these effects on wing morphology is that the Notch pathway is exquisitely sensitive to the impaired rate of protein synthesis caused by a reduction in RP expression (HART et al. 1993).
E-2d encodes RpL5:
Deficiency-based mapping placed the E-2d gene in a region containing cytological bands 40AB and h35 of the 2L centric heterochromatin (Figure 2B). Previous genetic studies have mapped two Minute loci to this region: M(2)39F at 39F140A4 (http://flybase.bio.indiana.edu ) and a second Minute at 40BF (HOWE et al. 1995). As M(2)39F1 complements both E-2d mutations (data not shown), it is likely that E-2d corresponds to the more proximal Minute.
To identify the physical gene disrupted by E-2d mutations, we searched for RP genes in the 40AB/h35 region using the D. melanogaster Genome Annotation Database (http://flybase.bio.indiana.edu). This search revealed two potential candidates for E-2d: CG12775, which encodes RpL21, and yip6/CG17489, which encodes RpL5 (Figure 5A). Both genes were sequenced in the two E-2d mutant strains and point mutations were discovered only in the yip6 coding sequence (Figure 5, B and C). yip6 is located in the h35 band and encodes the single RpL5 protein in the D. melanogaster genome (HOSKINS et al. 2002; YASUHARA et al. 2003; S. J. MARYGOLD, unpublished results). We therefore refer to this gene as RpL5 and to the mutant alleles as RpL52d1 and RpL52d2.
EST evidence suggests the existence of many alternative RpL5 transcripts that could theoretically encode three different protein products: RpL5-PA/PB, -PC, and -PD/PE (http://flybase.bio.indiana.edu). RpL5-PA/PB is the longest version at 299 amino acids in length and contains a Ribosomal_L5e (eukaryotic ribosomal protein 5 of the large subunit) domain from residues 26 to 173 (Figure 5, B and C). RpL5-PC consists of just the carboxy-terminal half of PA/PB and entirely lacks the Ribosomal_L5e domain, while RpL5-PD/PE comprises the amino-terminal two-thirds of PA/PB and so retains the Ribosomal-L5e motif but lacks the carboxy-terminal third. Of these three, RpL5-PA/PB is supported by the vast majority of EST evidence and is validated by a full-length cDNA clone. A CLUSTAL alignment of RpL5 protein sequences from diverse eukaryotes confirms that PA/PB is the most likely RpL5 protein product (Figure 5C). All of these orthologs are similar in length to the D. melanogaster RpL5-PA/PB and share a high degree of identity with it. For example, both human and Saccharomyces cerevisiae RpL5 are 297 amino acids in length and share 67 and 55% identity with D. melanogaster RpL5, respectively. Furthermore, the RpL52d1 and RpL52d2 mutations are predicted to have deleterious effects only within the RpL5-PA/PB protein (see below). We therefore conclude that RpL5-PA/PB is likely to be the major protein produced from the RpL5 gene in vivo and refer to it henceforth as RpL5.
The RpL52d1 mutation creates a premature termination codon just after the Ribosomal_L5e domain, so it is predicted to produce a truncated protein missing the carboxy-terminal third of the protein (Figure 5, B and C). This carboxy-terminal region contains motifs involved in both 5S rRNA binding and nuclear/nucleolar localization (MICHAEL and DREYFUSS 1996; ROSORIUS et al. 2000; see below). RpL52d2 is a missense mutation that changes an alanine to a threonine within the Ribsomomal_L5e domain (Figure 5, B and C). This alanine residue is conserved within higher eukaryotes and is therefore expected to be important for normal RpL5 folding/function. Although the dominant Minute phenotypes associated with each mutation are similar, RpL52d1 hemizygous larvae die earlier and at a smaller size than RpL52d2 hemizygotes (data not shown), suggesting that RpL52d1 is the stronger mutant allele.
Eukaryotic RpL5 is homologous to prokaryotic RpL18, suggesting that this protein is of ancient origin and has a key function in the ribosome. Indeed, RpL5 has been shown to specifically bind 5S rRNA and transport it from the nucleoplasm to the nucleolus for assembly into the 60S ribosomal subunit (STEITZ et al. 1988; DESHMUKH et al. 1993, 1995; MICHAEL and DREYFUSS 1996; ROSORIUS et al. 2000). Furthermore, RpL5 has a role in anchoring peptidyl-tRNAs to the P-site of the ribosome to prevent frameshifting (MESKAUSKAS and DINMAN 2001).
Reducing RpL38 or RpL5 gene dosage increases final wing size:
Mutations in RpL38 and RpL5 were originally identified as dominant enhancers of a small-wing phenotype generated by inhibiting PI3K signaling in the fly wing (our unpublished results). Rather than representing a genuine genetic interaction, this observation may have resulted from purely additive effects as some Minutes show dominant reductions in wing and/or body size (BREHME 1939, 1941a). To address this point, we examined the size of adult wings heterozygous for a RpL38 or RpL5 mutation but otherwise wild type. Surprisingly, these wings are 511% larger than wild-type control wings (Figure 6, AC, and Table 2). In RpL382b1/+ wings, these increases in wing area are associated with proportional increases in cell size without any detectable effect on the total number of cells in the wing (Figure 6, A' and B'; Table 2). Although RpL382b2/+, RpL52d1/+, and RpL52d2/+ wings also comprise large cells, these wings contain fewer cells than wild-type wings and therefore show relatively smaller increases in total wing area compared to RpL382b1/+ wings (Figure 6 and Table 2). It is not immediately apparent why cell number is reduced in wings heterozygous for the RpL382b2, RpL52d1, or RpL52d2 mutations but not for the RpL382b1 mutation. However, we note that RpL382b1 is the only null mutation and the consequent severe impairment of cellular protein synthesis in RpL382b1/+ wings may have quantitatively different effects on cell proliferation (see DISCUSSION). In summary, mutation of one copy of either RpL38 or RpL5 increases overall wing and individual cell size and either does not affect or reduces wing cell number. The role of RpL38, RpL5, and other RPs in the control of cell and organ growth is discussed below.
| DISCUSSION |
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Linking RPs to Minute loci:
Approximately 50 well-documented Minute loci are identified in the D. melanogaster genome (LAMBERTSSON 1998). Although it is generally agreed that these loci correspond to RP genes, this has been proven molecularly in relatively few cases. Here, we show that the M(2)41A locus corresponds to the RpL38 gene on the basis of three separate observations. First, comparison of the physical and genetic maps in the h46 region shows that the physical location of RpL38 corresponds well with the genetically defined M(2)41A locus (Figure 3, A and B). Second, several deficiency strains that were used to define M(2)41A all fail to complement point mutations in the RpL38 gene (Figure 3B). Third, RpL38 point mutation heterozygotes have a similar Minute bristle phenotype to flies heterozygous for one of the original M(2)41A alleles, Df(2R)M41A2 (data not shown). Hilliker and colleagues have speculated previously that M(2)41A is a repetitive or duplicated locus (COULTHARD et al. 2003). Although our data suggest otherwise, we note that flies heterozygous for the relatively large Df(2R)M41A1 deletion show a more severe Minute phenotype than flies heterozygous for either the small Df(2R)M41A2 deletion or the RpL382b1 null allele (data not shown). Thus, additional genes in the region, perhaps in the unannotated heterochromatin proximal to RpL38, may contribute to the Minute phenotype defined by the larger Df(2R)M41A1 deletion.
M(2)39F, which maps to cytological bands 39F1-40A4, is the only previously defined Minute locus lying in the 40AB region that contains the RpL5 gene. However, M(2)39F and RpL5 are not allelic to one another, and M(2)39F probably corresponds to the RpL21 gene that is located just distal to RpL5 on the physical map (YASUHARA et al. 2003; Figure 5A). HOWE et al. (1995) refer to a second Minute locus proximal to M(2)39F that maps to 40BF and it is probable that this unnamed Minute corresponds to RpL5. The existence of two separable Minute loci in the vicinity of the 40A band would have been overlooked by many deficiency-based studies in the past because of the close proximity of the RpL21 and RpL5 genes. The same is likely to apply to other regions of the genome and, in part, explains why there are almost twice as many RP genes as well-documented Minutes (see Introduction).
Annotation of the centric heterochromatin of chromosome 2:
Heterochromatin is characteristically rich in repetitive sequence elements and transposons and has a lower gene density than euchromatin (HOSKINS et al. 2002). Nevertheless, the heterochromatin portion of the D. melanogaster genome is substantial, comprising
60 megabases (Mb) of the
175-Mb genome of a female fly, and is predicted to include at least 450 genes (HOSKINS et al. 2002). Although the repetitive nature of heterochromatic DNA has hampered its sequencing and annotation, a number of recent studies have made significant advances to rectifying this situation (HOSKINS et al. 2002; CORRADINI et al. 2003; YASUHARA et al. 2003; MYSTER et al. 2004; http://www.dhgp.org).
RpL38 is the most proximal gene within the heterochromatic scaffold AABU01002769 (formerly the "Release 3 whole-genome shotgun centromere extension sequence") on chromosome arm 2R (CELNIKER et al. 2002; CORRADINI et al. 2003; MYSTER et al. 2004; http://flybase.bio.indiana.edu). By demonstrating that RpL38 is allelic to l(2)41Af, we have been able to correctly order the genes proximal to RpL38 on a genetic map (MYSTER et al. 2004; Figure 3C). In doing so, we have also created an overlap between the genetic and physical maps described by MYSTER et al. (2004), thus correlating the two maps at this key region (Figure 3C). RpL38 should therefore be a useful "anchor point" for extending the annotated map of the 2R centric heterochromatin toward the centromere.
RpL5 may be one of the most distal genes in the 2L centric heterochromatin, lying near the transition zone between the heterochromatin and euchromatin (HOSKINS et al. 2002; YASUHARA et al. 2003). Again, the molecular and genetic data provided here should aid sequence assembly and analysis in this chromosomal region.
We were intrigued to find that RpL38 and RpL5 are located in heterochromatin as this region of the genome is generally associated with transcriptional silencing, whereas RPs are required at high levels in the cell and are known to be genetically haplo-insufficient (LAMBERTSSON 1998; WARNER 1999; ELGIN and GREWAL 2003). However, several other vital genes are located in the heterochromatin of D. melanogaster (DIMITRI et al. 2003), some of which also encode ribosomal components, such as Qm (= RpL10; 3h), RpL15 (3h), and the bobbed locus (Xh) that harbors rRNA genes (RITOSSA 1976; CORRADINI et al. 2003; http://flybase.bio.indiana.edu). All essential heterochromatic genes must therefore lie within transcriptionally active domains to be expressed at levels appropriate for their efficient biological function.
Ribosomal proteins and growth regulation:
One explanation for identifying RpL38 and RpL5 mutations as enhancers of the small-wing phenotype in our original screen is that RPs are a direct and critical target of the PI3K pathway in promoting growth (LEHNER 1999; THOMAS 2000). Stimulation of PI3K signaling activates S6 kinase, which in turn leads to the phosphorylation of RpS6 and the selective increase in translation of mRNAs containing an oligopyrimidine tract at their 5' end (5' TOPs; THOMAS 2000). 5' TOPS are principally found in mRNAs that encode components of the translation machinery, including RPs (MEYUHAS 2000). Indeed, the major transcripts of the RpL38 and RpL5 genes contain a 5' TOP: CTTTCCTTCT and CTTTTT, respectively (http://flybase.bio.indiana.edu; J. YASUHARA, personal communication). However, as we find that a small-wing phenotype generated by inhibiting epidermal growth factor receptor signaling is also enhanced by mutation of either RpL38 or RpL5 (data not shown), we favor the idea that optimal RP production and protein synthesis are more generally required to support wing growth rather than being required specifically for PI3K-driven growth.
Most of the data from D. melanogaster and other species suggests that reducing RP expression slows growth rates and, in some cases, leads to smaller cell, organ, or body size (see Introduction). Consistent with this idea, we find that reducing the dosage of RpL38 or RpL5 slows the organismal growth rate and, in most cases, reduces cell number in the adult wing (Figure 1D and Table 2). However, RpL38/+ and RpL5/+ adult wings are significantly larger than wild-type controls as a result of increased cell size (Figure 6 and Table 2). This latter finding provokes new questions regarding the role of RPs in growth regulation. First, how might a reduction in RP gene dosage, and therefore ribosome biogenesis and cellular protein synthesis, lead to increased cell size? Second, why should mutations in RpL38 and RpL5 dominantly enhance, rather than suppress, the PI3K-sensitized small-wing phenotype?
Similar to adult wing cells that are heterozygous for either a RpL38 or a RpL5 mutation, RpS131/+ cells in the D. melanogaster larval wing disc are enlarged compared to wild-type cells (MARTIN-CASTELLANOS and EDGAR 2002). Likewise, RPL3 deficiency increases cell size in tobacco plants (POPESCU and TUMER 2004). Furthermore, overexpression of the fly brain tumor gene, which inhibits rRNA synthesis and therefore ribosome production, also increases the size of wing imaginal-disc cells (FRANK et al. 2002). Perhaps the simplest explanation of this hypertrophic growth is that a reduction in the protein synthetic capacity of the cell slows the cell division cycle to a greater degree than it impairs the cellular growth rate. Thus, reduction in RP expression results in large, slowly dividing cells. Alternatively, the extended larval period of Rp/+ animals may simply allow more time for cell growth to occur in a given cell cycle or for more food to be eaten and/or assimilated. Such mechanisms have been proposed to account for the increased growth seen when flies are raised at a low temperature (FRENCH et al. 1998) and we note that the growth effects of reduced RP gene dosage and decreased rearing temperature are strikingly similar (FRENCH et al. 1998; AZEVEDO et al. 2002). In a third model, impaired ribosome function may lead to a reduction in the levels of a critical growth-inhibitory protein. Future work will investigate how mutations in RpL38, RpL5, and other RP genes may alter cell size, cell proliferation, and cell death at earlier developmental stages to modify tissue growth and final body size.
The finding that mutations in RpL38 or RpL5 dominantly increase wing size in a wild-type genetic background suggests that they should cause dominant suppression, rather than the observed enhancement, of the original small-wing phenotype. This paradox may be explained by considering the different mechanisms by which reduced PI3K activity (by overexpression of the KD-Dp110 transgene) and mutation of RP genes affect wing growth. Wings overexpressing KD-Dp110 are small because they contain fewer cells of smaller size (LEEVERS et al. 1996). Although RpL38/+ and RpL5/+ wings can also contain fewer cells, they are increased in size overall because they contain larger cells (Table 2). When these two genetic manipulations are combined, it is likely that Dp110-KD overexpression prevents the increase in cell size normally caused by lowering RP gene dosage. In this way, the small-wing phenotype may be enhanced by heterozygosity for RP mutations as a result of a further reduction in cell number. Further research will be necessary to elucidate the true mechanism by which the combined perturbation of both PI3K signaling and protein translation impinges on cell growth and division.
| ACKNOWLEDGEMENTS |
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Note added in proof: It has been brought to our attention that the RpL381 allele was induced on a Pin-bearing mutant chromosome (D. SINCLAIR, personal communication; A. J. HILLIKER, 1976, Genetic analysis of the centromeric heterochromatin of chromosome 2 of Drosophila melanogaster: deficiency mapping of EMS-induced lethal complementation groups. Genetics 83: 765782). This explains why RpL381 mutant flies have such a strong bristle phenotype because Pin mutations are dominant mutations that result in shortened thoracic bristles.
| LITERATURE CITED |
|---|
|
|
|---|
AMSTERDAM, A., K. C. SADLER, K. LAI, S. FARRINGTON, R. T. BRONSON et al., 2004 Many ribosomal protein genes are cancer genes in zebrafish. PLoS Biol. 2: E139.[CrossRef][Medline]
AZEVEDO, R. B. R., V. FRENCH and L. PARTRIDGE, 2002 Temperature modulates epidermal cell size in Drosophila melanogaster. J. Insect Physiol. 48: 231237.[CrossRef][Medline]
BERGER, J., T. SUZUKI, K. A. SENTI, J. STUBBS, G. SCHAFFNER et al., 2001 Genetic mapping with SNP markers in Drosophila. Nat. Genet. 29: 475481.[CrossRef][Medline]
BREHME, K. S., 1939 A study of the effect on development of "Minute" mutations in Drosophila melanogaster. Genetics 24: 131161.
BREHME, K. S., 1941a Development of the Minute phenotype in Drosophila melanogaster: a comparative study of the growth of three Minute mutants. J. Exp. Zool. 88: 135160.[CrossRef]
BREHME, K. S., 1941b The growth of transplanted Minute and wild-type optic discs in Drosophila melanogaster. Growth 5: 183195.
BRIDGES, C. B., and T. H. MORGAN, 1923 The Third Chromosome Group of Mutant Characters of Drosophila melanogaster. Carnegie Institution, Washington, DC.
CELNIKER, S. E., D. A. WHEELER, B. KRONMILLER, J. W. CARLSON, A. HALPERN et al., 2002 Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 3: RESEARCH0079.
CORRADINI, N., F. ROSSI, F. VERNI and P. DIMITRI, 2003 FISH analysis of Drosophila melanogaster heterochromatin using BACs and P elements. Chromosoma 112: 2637.[CrossRef][Medline]
COULTHARD, A. B., D. F. EBERL, C. B. SHARP and A. J. HILLIKER, 2003 Genetic analysis of the second chromosome centromeric heterochromatin of Drosophila melanogaster. Genome 46: 343352.[Medline]
DESHMUKH, M., Y. F. TSAY, A. G. PAULOVICH and J. L. WOOLFORD, JR., 1993 Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits. Mol. Cell. Biol. 13: 28352845.
DESHMUKH, M., J. STARK, L. C. YEH, J. C. LEE and J. L. WOOLFORD, JR., 1995 Multiple regions of yeast ribosomal protein L1 are important for its interaction with 5 S rRNA and assembly into ribosomes. J. Biol. Chem. 270: 3014830156.
DIMITRI, P., 1991 Cytogenetic analysis of the second chromosome heterochromatin of Drosophila melanogaster. Genetics 127: 553564.[Abstract]
DIMITRI, P., N. CORRADINI, F. ROSSI, F. VERNI, G. CENCI et al., 2003 Vital genes in the heterochromatin of chromosomes 2 and 3 of Drosophila melanogaster. Genetica 117: 209215.[CrossRef][Medline]
DRAPTCHINSKAIA, N., P. GUSTAVSSON, B. ANDERSSON, M. PETTERSSON, T. N. WILLIG et al., 1999 The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nat. Genet. 21: 169175.[CrossRef][Medline]
ELGIN, S. C. R., and S. I. S. GREWAL, 2003 Heterochromatin: silence is golden. Curr. Biol. 13: R895R898.[CrossRef][Medline]
ENERLY, E., J. LARSSON and A. LAMBERTSSON, 2003 Silencing the Drosophila ribosomal protein L14 gene using targeted RNA interference causes distinct somatic anomalies. Gene 320: 4148.[CrossRef][Medline]
ESPINOSA, L., M. MARTIN, A. NICOLAS, M. FABRE and E. NAVARRO, 1997 Primary sequence of the human, lysine-rich, ribosomal protein RPL38 and detection of an unusual RPL38 processed pseudogene in the promoter region of the type-1 angiotensin II receptor gene. Biochim. Biophys. Acta 1354: 5864.[Medline]
FRANK, D. J., B. A. EDGAR and M. B. ROTH, 2002 The Drosophila melanogaster gene brain tumor negatively regulates cell growth and ribosomal RNA synthesis. Development 129: 399407.
FRENCH, V., M. FEAST and L. PARTRIDGE, 1998 Body size and cell size in Drosophila: the developmental response to temperature. J. Insect Physiol. 44: 10811089.[CrossRef][Medline]
HART, K., T. KLEIN and M. WILCOX, 1993 A Minute encoding a ribosomal protein enhances wing morphogenesis mutants. Mech. Dev. 43: 101110.[CrossRef][Medline]
HILLIKER, A. J., 1976 Genetic analysis of the centromeric heterochromatin of chromosome 2 of Drosophila melanogaster: deficiency mapping of EMS-induced lethal complementation groups. Genetics 83: 765782.
HOSKINS, R. A., A. C. PHAN, M. NAEEMUDDIN, F. A. MAPA, D. A. RUDDY et al., 2001 Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster. Genome Res. 11: 11001113.
HOSKINS, R. A., C. D. SMITH, J. W. CARLSON, A. B. CARVALHO, A. HALPERN et al., 2002 Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 3: RESEARCH0085.
HOWE, M., P. DIMITRI, M. BERLOCO and B. T. WAKIMOTO, 1995 Cis-effects of heterochromatin on heterochromatic and euchromatic gene activity in Drosophila melanogaster. Genetics 140: 10331045.[Abstract]
KONDOH, N., M. NODA, R. J. FISHER, C. W. SCHWEINFEST, T. S. PAPAS et al., 1996 The S29 ribosomal protein increases tumor suppressor activity of K rev-1 gene on v-K ras-transformed NIH3T3 cells. Biochim. Biophys. Acta 1313: 4146.[Medline]
LAMBERTSSON, A., 1998 The Minute genes in Drosophila and their molecular functions. Adv. Genet. 38: 69134.[Medline]
LEEVERS, S. J., D. WEINKOVE, L. K. MACDOUGALL, E. HAFEN and M. D. WATERFIELD, 1996 The Drosophila phosphoinositide 3-kinase Dp110 promotes cell growth. EMBO J. 15: 65846594.[Medline]
LEHNER, C. F., 1999 The beauty of small flies. Nat. Cell Biol. 1: E129E130.[CrossRef][Medline]
LINDSLEY, D. L., and G. G. ZIMM, 1992 The Genome of Drosophila melanogaster. Academic Press, San Diego.
LOFTUS, T. M., Y. H. NGUYEN and E. J. STANBRIDGE, 1997 The QM protein associates with ribosomes in the rough endoplasmic reticulum. Biochemistry 36: 82248230.[CrossRef][Medline]
MARTIN, S. G., K. C. DOBI and D. ST. JOHNSTON, 2001 A rapid method to map mutations in Drosophila. Genome Biol. 2: RESEARCH0036.
MARTIN-CASTELLANOS, C., and B. A. EDGAR, 2002 A characterization of the effects of Dpp signaling on cell growth and proliferation in the Drosophila wing. Development 129: 10031013.
MESKAUSKAS, A., and J. D. DINMAN, 2001 Ribosomal protein L5 helps anchor peptidyl-tRNA to the P-site in Saccharomyces cerevisiae. RNA 7: 10841096.[Abstract]
MEYUHAS, O., 2000 Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267: 63216330.[Medline]
MICHAEL, W. M., and G. DREYFUSS, 1996 Distinct domains in ribosomal protein L5 mediate 5 S rRNA binding and nucleolar localization. J. Biol. Chem. 271: 1157111574.
MONTAGNE, J., M. J. STEWART, H. STOCKER, E. HAFEN, S. C. KOZMA et al., 1999 Drosophila S6 kinase: a regulator of cell size. Science 285: 21262129.
MORATA, G., and P. RIPOLL, 1975 Minutes: mutants of Drosophila autonomously affecting cell division rate. Dev. Biol. 42: 211221.[CrossRef][Medline]
MOUNT, S. M., C. BURKS, G. HERTZ, G. D. STORMO, O. WHITE et al., 1992 Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res. 20: 42554262.
MYSTER, S. H., F. WANG, R. CAVALLO, W. CHRISTIAN, S. BHOTIKA et al., 2004 Genetic and bioinformatic analysis of 41C and the 2R heterochromatin of Drosophila melanogaster: a window on the heterochromatin-euchromatin junction. Genetics 166: 807822.
NEUFELD, T. P., A. F. DE LA CRUZ, L. A. JOHNSTON and B. A. EDGAR, 1998 Coordination of growth and cell division in the Drosophila wing. Cell 93: 11831193.[CrossRef][Medline]
POPESCU, S. C., and N. E. TUMER, 2004 Silencing of ribosomal protein L3 genes in N. tabacum reveals coordinate expression and significant alterations in plant growth, development and ribosome biogenesis. Plant J. 39: 2944.[CrossRef][Medline]
RITOSSA, F., 1976 The bobbed locus, pp. 801846 in Genetics and Biology of Drosophila, Vol. Ib, edited by M. ASHBURNER and E. NOVITSKI. Academic Press, New York.
ROLLINS, R. A., P. MORCILLO and D. DORSETT, 1999 Nipped-B, a Drosophila homologue of chromosomal adherins, participates in activation by remote enhancers in the cut and Ultrabithorax genes. Genetics 152: 577593.
ROSORIUS, O., B. FRIES, R. H. STAUBER, N. HIRSCHMANN, D. BEVEC et al., 2000 Human ribosomal protein L5 contains defined nuclear localization and export signals. J. Biol. Chem. 275: 1206112068.
RUGGERO, D., and P. P. PANDOLFI, 2003 Does the ribosome translate cancer? Nat. Rev. Cancer 3: 179192.[CrossRef][Medline]
SCHULTZ, J., 1929 The Minute reaction in the development of Drosophila melanogaster. Genetics 14: 366419.
STEITZ, J. A., C. BERG, J. P. HENDRICK, H. LA BRANCHE-CHABOT, A. METSPALU et al., 1988 A 5S rRNA/L5 complex is a precursor to ribosome assembly in mammalian cells. J. Cell Biol. 106: 545556.
STEWART, M. J., and R. DENELL, 1993 Mutations in the Drosophila gene encoding ribosomal protein S6 cause tissue overgrowth. Mol. Cell. Biol. 13: 25242535.
THOMAS, G., 2000 An encore for ribosome biogenesis in the control of cell proliferation. Nat. Cell