Isolation of a mouse pseudo tRNA gene encoding CCA--a possible example of reverse flow of genetic information

Deletions in processed pseudogenes accumulate faster in rodents than in humans

The relative rates of point nucleotide substitution and accumulation of gap events (deletions and insertions) were calculated for 22 human and 30 rodent processed pseudogenes. Deletion events not only outnumbered insertions (the ratio being 7:1 and 3:1 for human and rodent pseudogenes, respectively), but also the total length of deletions was greater than that of insertions. Compared with their functional homologs, human processed pseudogenes were found to be shorter by about 1.2%, and rodent pseudogenes by about 2.3%. DNA loss from processed pseudogenes through deletion is estimated to be at least seven times faster in rodents than in humans. In comparison with the rate of point substitutions, the abridgment of pseudogenes during evolutionary times is a slow process that probably does not retard the rate of growth of the genome due to the proliferation of processed pseudogenes.

Fragments of rDNA within the Chinese hamster genome

We report the isolation and partial characterization of distinct EcoRI fragments of the Chinese hamster genome which contain regions complementary to a 1-kb portion of the mature 18 S ribosomal RNA molecule. This previously undescribed 18 S rDNA-like region, which we have termed a "fragment of ribosomal DNA" (frDNA), has been shown by sequence analysis to correspond to a region extending 1 kb upstream from the 3' terminus of the mature 18 S rRNA. Within the five frDNA-containing clones described here, no other region of the ribosomal RNA cistron was detected, making it unlikely that these are polymorphic forms of the ribosomal DNA repeat. The 18 S rDNA-complementary region appears to be flanked by an imperfect direct repeat, which could have been the result of the retroinsertion of a fragment of ribosomal RNA. Directly adjacent to the 18 S rDNA-like region we have identified nonribosomal sequences which appear common to all of the frDNA-containing clones we examined. At least eight different-sized EcoRI fragments contain frDNAs and the abundance of the frDNAs appears to be of the order of 30 per genome. The occurrence of multiple copies of this ribosomal-nonribosomal chimera suggests that, once formed, the chimera was duplicated within the genome.

Identification and sequence analysis of a silent gene (ushA0) in Salmonella typhimurium

The evolution of new or improved enzyme specificities in prokaryotes has been proposed to involve gene duplication, followed by silencing of one of the duplicates at the transcriptional or translational level. Such "silent gene intermediates" are distinct from "cryptic" genes, which are proposed to have a different role in evolution. We describe the identification in Salmonella typhimurium of a silent gene (ushA0) using the active (homologous) ushA gene (encoding UDP-sugar hydrolase) from Escherichia coli as a probe. The ushA0 gene has been cloned and, in the multicopy state, very weak expression can be detected; the gene product was shown to be immunologically and functionally related to the enzyme from E. coli. The sequence of the ushA0 gene was found to be highly homologous to the previously determined sequence of the ushA gene, and the respective promoter and ribosomal-binding sites are also very similar. However, a presumed strong rho-independent terminator in the ushA gene is absent from ushA0; although a weak stem-and-loop structure is present in the 3' region of ushA0, its structure is atypical of rho-independent terminators. The sequence analysis also revealed an insertion-sequence like sequence at the 3' end of ushA0 with a convergent open reading frame terminating 116 base-pairs from the ushA0 stop codon. A deletion of the 5' region of the open reading frame results in increased expression of ushA0, indicating that convergent transcription plays some role in the silencing of ushA0. S. typhimurium contains a UDP-sugar hydrolase, biochemically and genetically distinct from that in E. coli, encoded by the ushB gene. Our results indicate that ushB is not strongly sequence-related to ushA0, and its gene product is not immunologically related to the ushA gene product. ushB is hence a functional duplicate of ushA and provides a rationale for the silencing of ushA0. This situation, and the DNA sequence comparison of ushA and ushA0, strongly suggests that rather than being a cryptic gene, ushA0 has been silenced recently during the evolution of S. typhimurium.

Molecular organization of the class I genes of human major histocompatibility complex

In this brief review, our main emphasis has been on the analysis of the sequence diversity among various class I genes and their functional implications. The availability of complete nucleotide sequences of 7 different genes representing different loci allowed us to derive a consensus sequence. One mouse MHC Class I gene was included in these comparisons as a representative of H2 genes Evolutionary patterns can be seen on the basis of divergence of various genes from the derived consensus sequence. At least 1 human gene which has a promoter similar to that of H2 genes and which contains a single initiation codon following this promoter (unlike all other human genes and like all the H2 genes) has been identified. Both variable and homology regions can be identified in the entire length of the gene. While exons show relatively strong conservation of sequences, the introns have many variable regions, introns 6 and 7 being the most heterogeneous. Stretches of conserved nucleotide sequences are noticed at the 3' regions of most introns. Estimation of total number of class I genes is presented on the basis of cloning experiments, and the abundance of 1 particular pseudogene is discussed.

Structure and transcription of eukaryotic tRNA genes

The availability of cloned tRNA genes and a variety of eukaryotic in vitro transcription systems allowed rapid progress during the past few years in the characterization of signals in the DNA-controlling gene transcription and in the processing of the precurser RNAs formed. This will be the subject matter discussed in this review.

Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp

We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al., 1981, Nucleic Acids Res. 9, 2239-2250). The mouse and rat tRNAAsp and tRNAGly coding regions are identical. The tRNAGlu coding regions differ at two positions. The flanking sequences contain 3 non-homologous areas: a c. 100 bp insertion in the first mouse spacer, short tandemly repeated sequences in the second spacers and unrelated sequences at the 3' ends of the clusters. In contrast, most of the flanking regions are homologous, consisting of strings of consecutive, identical residues (5-17 bp) separated by single base differences and short insertions/deletions. The latter are often associated with short repeats. The homology of the flanking regions is c. 75%, similar to other murine genes. The second lambda clone contains a solitary mouse tRNAAsp gene. The coding region is identical to that of the clustered tRNAAsp gene. The 5' flanking regions of the two genes contain homologous areas (10-25 bp) separated by unrelated sequences. Overall, the flanking regions of the two mouse tRNAAsp genes are less homologous than those of the mouse and rat clusters.