The ribosomal protein genes and Minute loci of Drosophila melanogaster

Abstract

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.

Figure 1

Evolution of D. melanogaster CRP gene duplicates and CRP-like genes. The likely pattern of emergence of CRP duplicate genes with restricted expression (blue), CRP-like genes (green) and CRP pseudogenic fragments (brown) in the lineage leading to D. melanogaster is shown. RpL34b is shown in black text: this is the only case where the newly emerged duplicate gene (RpL34b), rather than precursor gene (RpL34a), acts as the principal gene copy. The relative placement of CG11386 and CG33222 is consistent with the model presented by Stewart and Denell [86]. The dendrogram is based on that given in reference [140], in which the relationships among the Drosophilidae are taken from [149]; note that the branch lengths do not accurately reflect evolutionary time.

Figure 2

Chromosomal map of the RP genes of D. melanogaster. RP genes are depicted on a physical map of the genome (Release 5) [60]. Genes encoded on the positive and negative strands are shown above and below the chromosome, respectively. (The orientation of RpL15 is not known and its position below the chromosome is arbitrary.) Chromosomes are divided into cytological bands as determined from sequence-to-cytogenetic band correspondence tables [150]. Minute genes are boxed as described in the key.

Figure 3

The Minute bristle phenotype. Minute flies have shorter and thinner bristles than wild type flies. This is most clearly seen by comparing the scutellar bristles, indicated here by the arrows and pseudocoloring. (a, a') Wild type. (b, b') RpS13¹ heterozygotes. (c, c') RpL14¹ heterozygotes.

Figure 4

Summary of Minute locus - CRP gene correspondences. This figure shows the relationship between Minute loci defined by genetic criteria and CRP genes identified using bioinformatics. '=' indicates definite correspondence, '~' indicates probable correspondence. Daggers mark Minute loci that we know or strongly suspect correspond to two CRP genes (as detailed in Table 4 and Additional data file 4).