The genomes of most eukaryotes are composed of genes arranged on the chromosomes without regard to function, with each gene transcribed from a promoter at its 5 end. However, the genome of the free-living nematode Caenorhabditis elegans contains numerous polycistronic clusters similar to bacterial operons in which the genes are transcribed sequentially from a single promoter at the 5 end of the cluster. The resulting polycistronic pre-mRNAs are processed into monocistronic mRNAs by conventional 3 end formation, cleavage, and polyadenylation, accompanied by trans-splicing with a specialized spliced leader (SL), SL2. To determine whether this mode of gene organization and expression, apparently unique among the animals, occurs in other species, we have investigated genes in a distantly related free-living rhabditid nematode in the genus Dolichorhabditis (strain CEW1). We have identified both SL1 and SL2 RNAs in this species. In addition, we have sequenced a Dolichorhabditis genomic region containing a gene cluster with all of the characteristics of the C. elegans operons. We show that the downstream gene is trans-spliced to SL2. We also present evidence that suggests that these two genes are also clustered in the C. elegans and Caenorhabditis briggsae genomes. Thus, it appears that the arrangement of genes in operons pre-dates the divergence of the genus Caenorhabditis from the other genera in the family Rhabditidae, and may be more widespread than is currently appreciated.In bacteria and archaea, the genomes are primarily organized in arrays of genes whose products have related functions. These gene clusters, called operons, are cotranscribed from an upstream promoter and the resulting polycistronic mRNA is translated by ribosomes initiating at or near the 5Ј end of the RNA. These operons serve to efficiently coregulate proteins that function together. In contrast, eukaryotes have genomes composed of genes arranged apparently at random, with each transcribed by a promoter at its 5Ј end. However, in a group of primitive eukaryotic protozoa, the trypanosomes, genes are transcribed polycistronically (1-3). In this case, the polycistronic pre-mRNA is processed by 3Ј end formation and trans-splicing to create conventional eukaryotic monocistronic mRNAs. The trans-splicing reaction that creates the 5Ј ends of the mRNAs is related to the cis-splicing of higher eukaryotes; it proceeds through a 2Ј-5Ј branched intermediate, the splice sites have the same consensus sequences, and it is catalyzed by some of the same small nuclear ribonucleoprotein particles (4, 5).Trans-splicing was first discovered in trypanosomatids (4, 6), and later shown to occur also in Caenorhabditis elegans and other nematodes (ref. 7; reviewed in refs. 8 and 9), in Euglena (10), and in flatworms (11,12). In contrast to trypanosomes, in which only trans-splicing is present, the genes in the other organisms also contain cis-spliced introns. It was presumed that these genes were monocistronic and arranged randomly on the chromosomes as in other...

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Three vitellogenin genes from the free-living nematode Caenorhabditis elegans have previously been characterized at the molecular level. In order to study evolutionary relationships within this poorly understood taxon, we have cloned a vitellogenin gene, CEW1-vit-6, from a distantly related species belonging to the same family as C. elegans. Screening of a genomic library with a probe to total poly(A+) RNA yielded three clones that hybridized more intensely than all others, and all three corresponded to a single gene homologous to C. elegans vit-6. Comparison of CEW1-vit-6 with Ce-vit-6 reveals both strong similarities and surprising differences. Life Ce-vit-6, the gene is about 5 kb long and contains four unusually small introns (38-41 nt), but only one interrupts the gene at the same location as a Ce-vit-6 intron. The promoter region contains five matches to Vitellogenin Promoter Element 1 (VPE1) and no matches to VPE2, both previously shown to be required for vit gene transcription in C. elegans. Codon usage is in general similar to that of the Ce-vit genes, but a few codon biases are quite different. Alignment of the CEW1-vit-6 protein with Ce-vit-6 and Ce-vit-2 products suggests the existence of two domains which have evolved at different rates. Sequence comparison shows that nematode vitellogenins are much more closely related to vertebrate than to insect vitellogenins.

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