Showing papers on "Pseudogene published in 1983"

Structure and organization of the human Ki-ras proto-oncogene and a related processed pseudogene

Abstract: Analysis of the organization and nucleotide sequence of two human loci related to the transforming gene of Kirsten murine sarcoma virus establishes one as a functional gene and the other as a processed pseudogene. The two final coding exons of the functional gene seem to have arisen by duplication. Differentially spliced mRNAs incorporating one or other of the duplicated exons probably served as the intermediates by which the viral transforming gene and the pseudogene were generated. This suggests that the functional gene may specify either of two related polypeptides depending on the pattern of RNA splicing.

A single gene and a pseudogene for the cellular tumour antigen p53

Abstract: The cellular tumour antigen p53 is a protein found in elevated levels in a great variety of transformed cells (reviewed in ref. 1). Overproduction of p53 was observed in cells transformed by a wide spectrum of agents2–7 as well as in embryonal carcinoma cells3,8 and in spontaneous transformants9,10. Although initially described in mice2,3,9, similar p53-like proteins were also observed in cells of other species, including those derived from several human tumours11. In non-transformed cells the protein turns over very rapidly12,13 and its levels appear to correlate with cell proliferation14,15. Thus far, very little has been known about the precise nature of the protein and of the corresponding genes. We now provide evidence for the existence of a single functional gene for murine p53 and a processed pseudogene. The predicted amino acid sequence of murine p53 is also presented.

Identification of two human beta-tubulin isotypes.

Abstract: The sequence of a human beta-tubulin cDNA clone (D beta-1) is described; our data revealed 95.6% homology compared with the sequence of a human beta-tubulin processed pseudogene derived by reverse transcription of a processed mRNA (Wilde et al., Nature [London] 297:83-84, 1982). However, the amino acid sequence encoded by this cDNA showed less homology with pig and chicken beta-tubulin sequences than the latter did to each other, with major divergence within the 15 carboxy-terminal amino acids. On the other hand, an independently isolated, functionally expressed genomic human beta-tubulin sequence (5 beta) possessed a very high degree of homology with chicken and pig beta-tubulins in this region. Thus, human cells appear to contain two distinct beta-tubulin isotypes. Both the intact beta-tubulin cDNA clone and a subclone containing only the 3' untranslated region detected two mRNA species in HeLa cells; these mRNAs were 1.8 and 2.6 kilobases long and were present in about equal amounts. Two independently subcloned probes constructed from the 3' untranslated region of the 5 beta genomic sequence also detected a 2.6-kilobase beta-tubulin mRNA. However, the 3'-untranslated-region probes from the cDNA clone and the genomic sequence did not cross-hybridize. Thus, at least two human beta-tubulin genes, each specifying a distinct isotype, are expressed in HeLa cells, and the 2.6-kilobase mRNA band is a composite of at least two comigrating beta-tubulin mRNAs.

Rearranged mitochondrial genes in the yeast nuclear genome.

Abstract: We have found a contiguous DNA sequence in the yeast nuclear genome with extensive homology to non-contiguous yeast mitochondrial DNA sequences. Closely linked to this nuclear sequence in some, but not all, yeast strains is a tandem pair of transposable (Ty) elements. Certain features of the content and organization of this nuclear DNA sequence suggest that it may have originated from petite mitochondrial DNA which integrated into the nuclear genome.

Conversion of RNA to DNA in mammals: Alu-like elements and pseudogenes

Abstract: Striking similarities between a subclass of mammalian pseudogenes and the Alu family of short repetitive DNA sequences which are dispersed throughout the mammalian genome, suggest that both are created by integration into the genome of DNA copies of RNA transcripts.

Structure of two human beta-actin-related processed genes one of which is located next to a simple repetitive sequence.

Abstract: From a human gene library we have isolated and sequenced a beta-actin-like pseudogene, H beta Ac-psi 2, which lacks intervening sequences and contains several mutations resulting in frame-shifts, stop codons and in a departure from the known beta-actin protein sequence. We have also extended our sequence work on the intronless human beta-actin-related pseudogene H beta Ac-psi 1 described previously and we find that both genes are processed genes ending in a poly(dA) tract and flanked by direct repeats. The gene H beta Ac-psi 2 is preceded by a 230-bp region in which the simple sequence 5'-GAAA-3' is repeated greater than 40 times. This satellite-like sequence is highly repetitive in the human genome.

Molecular basis of length polymorphism in the human zeta-globin gene complex

Abstract: The length polymorphism between the human zeta-globin gene and its pseudogene is caused by an allele-specific variation in the copy number of a tandemly repeating 36-base-pair sequence. This sequence is related to a tandemly repeated 14-base-pair sequence in the 5' flanking region of the human insulin gene, which is known to cause length polymorphism, and to a repetitive sequence in intervening sequence (IVS) 1 of the pseudo-zeta-globin gene. Evidence is presented that the latter is also of variable length, probably because of differences in the copy number of the tandem repeat. The homology between the three length polymorphisms may be an indication of the presence of a more widespread group of related sequences in the human genome, which might be useful for generalized linkage studies.

Rapid evolution of goat and sheep globin genes following gene duplication.

Abstract: Statistical analyses of DNA sequences of globin genes (beta A, beta C, and gamma) from goat and sheep (including new sequence information for the second intron of sheep beta A and gamma, kindly provided by A. Davis and A. W. Nienhuis) indicate that the rates of nonsynonymous substitution in these genes have been greatly accelerated following the gene duplication separating gamma and the ancestor of beta A and beta C and the gene duplication separating beta A and beta C. In both cases the acceleration was apparently due to relaxation of purifying selection (functional constraints) rather than advantageous mutations because acceleration occurred only in less important parts of the beta globin chain. The rates of nonsynonymous substitution in these genes are estimated to be about 2.3 x 10(-9) per site per year, which is three times higher than that for the divergence between human beta and mouse beta major globin genes. Our analyses further suggest that the rate of synonymous substitution in functional genes and the rate of substitution in pseudogenes are approximately equal and are between 2.8 x 10(-9) and 5.0 x 10(-9) and that the rate of substitution in introns is about 3.0 x 10(-9). The divergence time between beta A and beta C and that between gamma and the beta A-beta C pair are about 12 and 30 million years, respectively. The proportion of transition mutations is estimated to be 64%, two times higher than expected under random mutation but considerably lower than the 96% estimated for animal mitochondrial DNA.

Evolutionary aspects of immunoglobulin heavy chain variable region (VH) gene subgroups.

Abstract: We isolated and determined the sequences of two human germ-line heavy chain variable region (VH) genes and compared them with mouse VH genes. The results show that the human VHI subgroup is evolutionarily related to the mouse VHII subgroup. Evolutionary preservation of homologies in VH genes of the same subgroup includes not only the coding region but also intron size and homology in noncoding regions. This suggests that a VH gene subgroup constitutes a multigene family that undergoes concerted evolution. The homology between genes of the same subgroup in different species is greater than that between genes of different subgroups within a species. One of the VHII genes contains, in complementarity-determining region 2 (CDR2), a 13-base-pair previously shown to be in CDR2 of a VHIII gene and in a heavy chain diversity region gene, DH [Wu, T. T. & Kabat, E. A. (1982) Proc. Natl. Acad. Sci. USA 79, 5031-5032], suggesting the insertion of diversity region gene sequences into the VH gene. One of the human VH genes is a pseudogene because of a terminator, which, together with our previous results, shows that the VH gene repertoire contains 40% pseudogenes. In one of the VH genes, direct and inverted repeats at both 5' and 3' ends of the gene suggest a potential transposable element that encompasses the entire VH gene. It is possible that such a structure may facilitate saltatory replication and rapid expansion of VH gene families.

Organization of the SUC gene family in Saccharomyces.

Abstract: The SUC gene family of yeast (Saccharomyces) includes six structural genes for invertase (SUC1 through SUC5 and SUC7) found at unlinked chromosomal loci. A given yeast strain does not usually carry SUC+ alleles at all six loci; the natural negative alleles are called suc0 alleles. Cloned SUC2 DNA probes were used to investigate the physical structure of the SUC gene family in laboratory strains, commercial wine strains, and different Saccharomyces species. The active SUC+ genes are homologous. The suc0 allele at the SUC2 locus (suc2(0) in some strains is a silent gene or pseudogene. Other SUC loci carrying suc0 alleles appear to lack SUC DNA sequences. These findings imply that SUC genes have transposed to different chromosomal locations in closely related Saccharomyces strains.

Unusual sequences in the murine immunoglobulin μ – δ heavy-chain region

Abstract: The δ heavy (H) chain of mouse immunoglobulin D (IgD) is unusual both in its structure and in its differential expression relative to immunoglobulin M (IgM; reviewed in ref. 1). The region of DNA between IgM and IgD H-chain constant-region genes is probably implicated in this control. So far only fragments of the area have been sequenced. Now, however, we present the complete sequence as well as the sequence of the introns of the Cδ gene. We have found several interesting features (Fig. 1), including an open reading frame (ORF) between Cμ and Cδ which encodes 146 amino acids that might represent a previously unsuspected domain-like protein; three blocks of simple repetitive sequences; a 162-base pair (bp) unique-sequence inverted repeat; and a domain-like pseudogene in the large intron of Cδ. We have not found, however, any sequence 5′ of Cδ resembling the switch (S) recombination sequences associated with class switching in other heavy chains2–5. Moreover, we have determined the 3′ deletion end point of an IgD-producing myeloma and find no sequences reminiscent of switch sites nearby.

Isolation and characterization of multiple human genes homologous to the oncogenes of avian erythroblastosis virus.

Abstract: Human DNA sequences complementary to the oncogenes v-erbA and v-erbB of avian erythroblastosis virus have been isolated from a genomic DNA library. Two clones, lambda he-A1 and lambda he-A2, were related to the erbA gene and one to the erbB gene (lambda he-B). The two erbA genes were only distantly related to each other as judged from hybridization analysis. Furthermore, human chromosomal DNA appears to contain one or two additional genes analogous to the lambda he-A2 sequence, whereas the mouse genome contained only two genes complementary to lambda he-A1 and lambda he-A2, respectively. Polyadenylated RNA species, 5.0 kb in size, were found in the human HeLa and the human hematopoietic K562 cell lines, suggesting that at least some of the erb-related genes are active and do not represent pseudogenes. Taken together, the data demonstrate that two distantly related classes of erbA genes exist in human and mouse DNA, and that multiple copies of genes belonging to one of these two classes exist in the human genome.

Somatic cell genetics and gene families

Abstract: The utility of somatic cell genetic analysis for the chromosomal localization of genes in mammals is well established. With the development of recombinant DNA probes and efficient blotting techniques that allow visualization of single-copy cellular genes, somatic cell genetics has been extended from the level of phenotypes expressed by whole cells to the level of the cellular genome itself. This extension has proved invaluable for the analysis of genes not readily expressed in somatic cell hybrids and for the study of multigene families, especially pseudogenes dispersed in different chromosomes throughout the genome.

Tissue-specific expression of a chicken calmodulin pseudogene lacking intervening sequences.

Abstract: An eel calmodulin cDNA probe has been used to isolate a calmodulin gene from a chicken DNA library. Sequence analysis revealed this calmodulin gene (cCM1) to contain the nucleotides that code for 148 amino acids, a termination codon, and 486 residues of 3'-noncoding sequence before an A-A-T-A-A-A poly(A) addition signal. The amino acid sequence derived from these nucleotides is 87% homologous to that of bovine brain calmodulin. cCM1 is one of two calmodulin genes in the chicken genome but is unique in that it does not contain intervening sequences to interrupt the structural segments of the protein. This suggests that cCM1 originated as a processed gene copy derived from the other calmodulin gene, cCL1, a circumstance usually associated with pseudogenes. In contrast, cCM1 appears to be a functional member of a multigene family whose expression is specific for muscle cells.

Chromosomal arrangement of leghemoglobin genes in soybean

Abstract: A cluster of four different leghemoglobin (Lb) genes was isolated from AluI-HaeIII and EcoRI genomic libraries of soybean in a set of overlapping clones which together include 45 kilobases (kb) of contiguous DNA. These four genes, including a pseudogene, are present in the same orientation and are arranged in the order: 5'-Lba-Lbc1-Lb psi-Lbc3-3'. The intergenic regions average 2.5 kb. In addition to this main Lb locus, there are other Lb genes which do not appear to be contiguous to this locus. A sequence probably common to the 3' region of Lb loci was found flanking the Lbc3 gene. The 3' flanking region of the main Lb locus also contains a sequence that appears to be expressed more abundantly in root tissue. Another sequence which is primarily expressed in root and leaf is found 5' to two Lb loci. Overall, the main leghemoglobin locus is similar in structure to the mammalian globin gene loci.

Structural analysis of gene loci for rat Ul small nuclear RNA

Abstract: Four phage clones which hybridize with U1 small nuclear RNA were obtained from a rat gene library. Two clones contain a presumed pseudogene. A third clone includes two gene candidates that are co-linear with the rat U1-RNA, 3.6kb apart and in the opposite orientation. The two genes are surrounded by identical sequences of 491bp upstream and 178bp downstream. The upstream sequences do not contain a TATA box, but share many block homologies with those for the human U1-RNA gene(1-3). A 101bp "identifier (ID) sequence", which was reported to be specifically expressed in rat brain (4), is inserted immediately after the shared sequence downstream of one of the genes. In the fourth clone, there are two putative pseudogenes, which have one or three nucleotide changes, 3kb apart and in the same orientation. Southern blot analysis of total rat DNA reveals about 50 U1-RNA genes/pseudogenes in the genome.

Polymorphism near the rat prolactin gene caused by insertion of an Alu-like element.

Abstract: Primate Alu and rodent Alu- like elements comprise major families of mammalian small dispersed repetitive DNAs These elements are repeated more than 105 times per haploid genome and are found between known genes, in introns and in satellite DNA1–5 Their dispersion throughout the genome and the presence of directly repeated DNA sequences flanking the elements suggest, but do not prove, that they are capable of transposition We describe here an allelic variation in the 5′-flanking region of the rat prolactin gene that offers the opportunity to examine the sequences of matching regions of two homologous chromosomes which differ in the presence of an Alu-like repetitive DNA element Our findings support the hypothesis that these elements are integrated into the genome by generating short direct repeats of host DNA

Genes for tRNAIle and tRNAAla in the spacer between the 16S and 23S rRNA genes of a blue-green alga: strong homology to chloroplast tRNA genes and tRNA genes of the E. coli rrnD gene cluster.

Abstract: A 6.3 kbp Eco RI-Bam HI fragment which carries most of one of the two rRNA gene clusters of the blue-green alga Anacystis nidulans was cloned into plasmid pBR322. Sequence analysis of the spacer region between the 16S and 23S rRNA genes reveals the presence of genes for tRNAIle and tRNAAla. The 16S rRNA gene is separated from the tRNAIle gene by a 162 bp spacer which shows significant homology to the comparable region in Zea mays plastids. The spacer between the two tRNA genes is 33 bp long and can be folded into a 9 bp stem and loop structure. The 5' portion of the tRNAIle gene is 60% homologous to a "pseudogene"-like sequence which maps beyond the 5S rRNA gene.

Nucleotide sequences of H1 histone genes from Xenopus laevis. A recently diverged pair of H1 genes and an unusual H1 pseudogene.

Abstract: Four clones containing H1 histone gene sequences were previously isolated from a Xenopus laevis genomic library (1) and we now present the complete nucleotide sequences of these H1 genes and their flanking regions. Two of these genes code for minor H1 proteins, probably H1C, when expressed in the oocyte transcription/translation system and are present on clones with almost identical overall organization. However, at the nucleotide level these genes differ in showing base insertions and deletions, as well as substitutions. A third gene sequence which is more related to the major X. laevis H1A, corresponds to the 3' two thirds of an H1 gene. This gene has in place of a 5' coding region at least 1800 bp of apparently noncoding sequence, some of which is A-T rich. The junction does not correspond to the consensus sequence of an intron/exon boundary and therefore this H1 sequence is more likely to represent a pseudogene. Comparisons of the coding and flanking regions of these X. laevis H1 genes indicate the kind of differences which can occur among H1 subtypes within a species. A region of homology noted in the 3' noncoding portion of vertebrate histone genes is discussed in relation to the mechanism of termination of transcription.

Polymorphic restriction endonuclease fragment segregates and correlates with the gene for HLA-B8

Abstract: Cellular DNA from HLA-typed individuals was digested with the restriction endonuclease EcoRV. After electrophoresis and transfer to a hybridization membrane, the restriction endonuclease fragments were probed with cDNA carrying the nucleotide sequence encoding a class 1 HLA gene. Polymorphism for presence or absence of various EcoRV fragments was noted in a panel of unrelated HLA-typed individuals. A polymorphic 8.6-kilobase pair EcoRV fragment was found which correlated in the panel with the serologically defined gene HLA-B8. A family study revealed that this fragment segregated with the haplotype carrying the HLA-B8 gene. This fragment may carry the gene for HLA-B8 or it may represent another class 1 gene (or pseudogene) in linkage disequilibrium with HLA-B8.