Isolation and characterization of cloned DNA sequences containing ribosomal protein genes of Drosophila melanogaster

Picking Winners and Losers: Cell Competition in Tissue Development and Homeostasis

Viable cells with reduced fitness are often eliminated by neighboring cells with greater fitness. This phenomenon, called cell competition, is an important mechanism for maintaining a high-quality population of cells in tissues. Foundational studies characterizing cellular competition and its molecular underpinnings were first carried out utilizing Drosophila as a model system. More recently, competitive behavior studies have extended into mammalian cell types. In this review, we highlight recent advances in the field, focusing on new insights into the molecular mechanisms regulating competitive behavior in various cellular contexts and in cancer. Throughout the review, we highlight new avenues to expand our understanding of the molecular underpinnings of cell competition and its role in tissue development and homeostasis.

The ribosomal protein genes and Minute loci of Drosophila melanogaster

BACKGROUND

Mutations in genes encoding ribosomal proteins (RPs) have been shown to cause an array of cellular and developmental defects in a variety of organisms. In Drosophila melanogaster, disruption of RP genes can result in the 'Minute' syndrome of dominant, haploinsufficient phenotypes, which include prolonged development, short and thin bristles, and poor fertility and viability. While more than 50 Minute loci have been defined genetically, only 15 have so far been characterized molecularly and shown to correspond to RP genes.

RESULTS

We combined bioinformatic and genetic approaches to conduct a systematic analysis of the relationship between RP genes and Minute loci. First, we identified 88 genes encoding 79 different cytoplasmic RPs (CRPs) and 75 genes encoding distinct mitochondrial RPs (MRPs). Interestingly, nine CRP genes are present as duplicates and, while all appear to be functional, one member of each gene pair has relatively limited expression. Next, we defined 65 discrete Minute loci by genetic criteria. Of these, 64 correspond to, or very likely correspond to, CRP genes; the single non-CRP-encoding Minute gene encodes a translation initiation factor subunit. Significantly, MRP genes and more than 20 CRP genes do not correspond to Minute loci.

CONCLUSION

This work answers a longstanding question about the molecular nature of Minute loci and suggests that Minute phenotypes arise from suboptimal protein synthesis resulting from reduced levels of cytoribosomes. Furthermore, by identifying the majority of haplolethal and haplosterile loci at the molecular level, our data will directly benefit efforts to attain complete deletion coverage of the D. melanogaster genome.

A newly identified Minute locus, M(2)32D, encodes the ribosomal protein L9 in Drosophila melanogaster

A gene encoding a ubiquitously expressed mRNA in Drosophila melanogaster was isolated and identified as the gene for ribosomal protein L9 (rpL9) by its extensive sequence homology to the corresponding gene from rat. The rpL9 gene is localized in polytene region 32D where two independent P element insertions flanking the locus are available. Remobilization of either P element generated lines with a typical Minute phenotype, e.g. thin and short bristles, prolonged development, and female semisterility in heterozygotes as well as homozygous lethality. All these characteristics can be rescued when a 3.9 kb restriction fragment containing the rpL9 gene is reintroduced by P element-mediated germline transformation. This result confirms that M(2)32D codes for ribosomal protein L9.

A small gene family in barley encodes ribosomal proteins homologous to yeast YL17 and L22 from archaebacteria, eubacteria, and chloroplasts

The amino acid sequences of two barley ribosomal proteins, termed HvL17-1 and HvL17-2, were decoded from green leaf cDNA clones. The N-terminal sequences of the derived barley proteins are 48% identical to the N-terminal amino acid sequence of protein YL17 from the large subunit of yeast cytoplasmic ribosomes. Via archaebacterial ribosomal proteins this homology extends to ribosomal protein L22 from eubacteria and chloroplast. Barley L17, and ribosomal proteins L22 and L23 from the archaebacteria Halobacterium halobium and H. marismortui, are 25-33% identical. Interestingly, the barley and archaebacterial proteins share a long, central stretch of amino acids, which is absent in the corresponding proteins from eubacteria and chloroplasts. Barley L17 proteins are encoded by a small gene family with probably only two members, represented by the cDNA clones encoding HvL17-1 and HvL17-2. Both these genes are active in green leaf cells. The expression of the L17 genes in different parts of the 7-day old barley seedlings was analyzed by semiquantitative hybridization. The level of L17 mRNA is high in meristematic and young cells found in the leaf base and root tip. In the leaf, the L17 mRNA level rapidly decreases with increasing cell age, and in older root cells this mRNA is undetectable.

Ribosomal protein S14 is encoded by a pair of highly conserved, adjacent genes on the X chromosome of Drosophila melanogaster

We describe a Drosophila DNA clone of tandemly duplicated genes encoding an amino acid sequence nearly identical to human ribosomal protein S14 and yeast rp59. Despite their remarkably similar exons, the locations and sizes of introns differ radically among the Drosophila, human, and yeast (Saccharomyces cerevisiae) ribosomal protein genes. Transcripts of both Drosophila RPS14 genes were detected in embryonic and adult tissues and are the same length as mammalian S14 message. Drosophila RPS14 was mapped to region 7C5-9 on the X chromosome. This interval also encodes a previously characterized Minute locus, M(1)7C.

Antisense ribosomal protein gene expression specifically disrupts oogenesis in Drosophila melanogaster

To assess the functional importance of ribosomal protein rpA1 gene expression during development of Drosophila melanogaster, we have transformed into the fly's genome an antisense rpA1 gene driven by a heat shock promoter. Antisense rpA1 expression severely disrupted oogenesis and produced a "small egg" female-sterile phenotype. The severities of these defects were proportional to the level of antisense rpA1 expression. Anti-rpA1 expression did not affect larval or pupal development. Quantitative RNA analysis suggested that high anti-rpA1 expression results in a general decrease of mRNA in the ovary.

Ribosomal protein S14 is encoded by a pair of highly conserved, adjacent genes on the X chromosome of Drosophila melanogaster

We describe a Drosophila DNA clone of tandemly duplicated genes encoding an amino acid sequence nearly identical to human ribosomal protein S14 and yeast rp59. Despite their remarkably similar exons, the locations and sizes of introns differ radically among the Drosophila, human, and yeast (Saccharomyces cerevisiae) ribosomal protein genes. Transcripts of both Drosophila RPS14 genes were detected in embryonic and adult tissues and are the same length as mammalian S14 message. Drosophila RPS14 was mapped to region 7C5-9 on the X chromosome. This interval also encodes a previously characterized Minute locus, M(1)7C.

Primary structure of human ribosomal protein S14 and the gene that encodes it

Chinese hamster ribosomal protein S14 cDNA was used to recognize homologous human cDNA and genomic clones. Human and Chinese hamster S14 protein sequences deduced from the cDNAs are identical. Two overlapping human genomic S14 DNA clones were isolated from a Charon 28 placental DNA library. A fragment of single-copy DNA derived from an intron region of one clone was mapped to the functional RPS14 locus on human chromosome 5q by using a panel of human X Chinese hamster hybrid cell DNAs. The human S14 gene consists of five exons and four introns spanning 5.9 kilobase pairs of DNA. Polyadenylated S14 transcripts purified from HeLa cell cytoplasma display heterogeneous 5' ends that map within noncoding RPS14 exon 1. This precludes assignment of a unique 5' boundary of RPS14 transcripts with respect to the cloned human genomic DNA. Apparently HeLa cells either initiate transcription at multiple sites within RPS14 exon 1, or capped 5' oligonucleotides are removed from most S14 mRNAs posttranscription. In contrast to the few murine ribosomal protein and several other mammalian housekeeping genes whose structures are known, human RPS14 contains a TATA sequence (TATACTT) upstream from exon 1. Three related short sequence motifs, also observed in murine and yeast ribosomal protein genes, occur in this region of the RPS14 gene. RPS14 introns 3 and 4 both contain Alu sequences. Interestingly, the Alu sequence in intron 3 is located slightly downstream from a chromosome 5 deletion breakpoint in one human X hamster hybrid clone analyzed.

Stable repression of ribosomal protein L1 synthesis in Xenopus oocytes by microinjection of antisense RNA

The synthesis of an endogenous ribosomal protein, L1, is selectively and efficiently inhibited by microinjection of antisense L1 RNAs into Xenopus oocytes. Repression of L1 synthesis is achieved within 12 hr and is maintained for 48 hr. RNase-protection assays reveal the formation of RNA X RNA duplexes in vivo between the endogenous L1 mRNA and injected antisense transcripts. Partial-length antisense RNAs, complementary to only the 3'-terminal region of L1 mRNA, repress translation as effectively as a full-length antisense RNA, indicating that complementarity to the 5' region of L1 mRNA is not required for efficient inhibition. The use of antisense RNA to repress synthesis of an endogenous ribosomal protein provides a functional basis for determining mechanisms that integrate ribosomal protein synthesis with ribosome assembly during oogenesis.

Sequences coding for the ribosomal protein L14 in Xenopus laevis and Xenopus tropicalis; homologies in the 5' untranslated region are shared with other r-protein mRNAs

In the haploid genome of Xenopus laevis there are two genes coding for the r-protein L14. It is not known if they are located on the same chromosome. cDNA clones deriving from the transcripts of the two genes have been isolated from an oocyte messenger cDNA bank showing that they are both expressed. We have studied the structure of one of the L14 genes by Electron Microscopy, restriction mapping and sequencing. An allelic form of the L14 gene was also isolated. It contains a large deletion covering the 5' end region up to the middle of the third intron. The 5' end of the X. laevis L14 gene was compared to that of the corresponding gene in the closely related species X. tropicalis and found to be highly conserved. The L14 gene has multiple initiation sites, but the large majority of the transcripts start in the middle of a pyrimidine tract not preceded by a canonical TATA box as in other eukaryotic housekeeping genes. The X. laevis L1 and L14 genes have a common decanucleotide in the first exon in the same position with regard to the initiator ATG which just precedes the first intron. The decanucleotide shows homology with the X. laevis 18S rRNA.

Homologous ribosomal proteins in bacteria, yeast, and humans

We describe sequences of two human ribosomal proteins, S14 and S17, and messenger RNAs that encode them. cDNAs were used as molecular hybridization probes to recognize complementary genes in rodent, Drosophila, and yeast chromosomal DNAs. Human ribosomal protein sequences are compared to analogous Chinese hamster, yeast, and bacterial genes. Our observations suggest that some ribosomal protein genes have been conserved stringently in the several phylogenetic lines examined. These genes apparently were established early in evolution and encode products that are fundamental to the translational apparatus. Other ribosomal protein genes examined, although similar enough to heterologous DNA sequences to indicate their structural relationships, appear to have diverged substantially during evolution, probably reflecting adaptations to different genetic environments.

Primary structure of human ribosomal protein S14 and the gene that encodes it

Chinese hamster ribosomal protein S14 cDNA was used to recognize homologous human cDNA and genomic clones. Human and Chinese hamster S14 protein sequences deduced from the cDNAs are identical. Two overlapping human genomic S14 DNA clones were isolated from a Charon 28 placental DNA library. A fragment of single-copy DNA derived from an intron region of one clone was mapped to the functional RPS14 locus on human chromosome 5q by using a panel of human X Chinese hamster hybrid cell DNAs. The human S14 gene consists of five exons and four introns spanning 5.9 kilobase pairs of DNA. Polyadenylated S14 transcripts purified from HeLa cell cytoplasma display heterogeneous 5' ends that map within noncoding RPS14 exon 1. This precludes assignment of a unique 5' boundary of RPS14 transcripts with respect to the cloned human genomic DNA. Apparently HeLa cells either initiate transcription at multiple sites within RPS14 exon 1, or capped 5' oligonucleotides are removed from most S14 mRNAs posttranscription. In contrast to the few murine ribosomal protein and several other mammalian housekeeping genes whose structures are known, human RPS14 contains a TATA sequence (TATACTT) upstream from exon 1. Three related short sequence motifs, also observed in murine and yeast ribosomal protein genes, occur in this region of the RPS14 gene. RPS14 introns 3 and 4 both contain Alu sequences. Interestingly, the Alu sequence in intron 3 is located slightly downstream from a chromosome 5 deletion breakpoint in one human X hamster hybrid clone analyzed.