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PubMedDate not supplied

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

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 agents as well as in embryonal carcinoma cells, and in spontaneous transformants. Although initially described in mice, similar p53-like proteins were also observed in cells of other species, including those derived from several human tumours. In non-transformed cells the protein turns over very rapidly and its levels appear to correlate with cell proliferation. 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.

Amino Acid Sequence↗
PubMedDate not supplied

Unusual abundance of vertebrate 3-phosphate dehydrogenase pseudogenes.

Only one gene coding for glyceraldehyde 3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12), a key enzyme in the control of glycolysis, is known to be functional in man, mouse, rat and chicken. The gene has been localized to chromosome 12 in human and chromosome 6 in mouse. Only a single mRNA species has been found in chicken and rat. However, analysis of genomic DNA blots of various species with a cloned GAPDH cDNA probe has revealed large differences in the level of reiteration, ranging from one to over 200 copies. On this basis, we have grouped these organisms into three classes according to the number of GAPDH-related sequences they contain; one class with a unique representation (chicken), another class of relatively low reiteration (10-30 copies in man, hare, guinea-pig and hamster) and a third class of high reiteration (greater than 200 copies in mouse and rat). The third class represents the first reported occurrence of such an extreme number of pseudogenes related to an enzyme-coding gene and suggests that a dramatic amplification event took place between 15 and 25 million years ago.

Animals↗
PubMed1983

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

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.

Amino Acid Sequence↗
PubMed1984

Rearranged immunoglobulin heavy chain variable region (VH) pseudogene that deletes the second complementarity-determining region.

We have cloned two rearranged heavy chain variable region (VH) genes from the IgG-producing human cell line CESS. The VH gene, which is linked to the mu chain constant region (C mu) gene, has two deletions at residues 45-62 and 82A-90, the former of which corresponds closely to the second complementarity-determining region (CDR2). These results could indicate that translocation of CDR2 occurred and could give support to the argument that reassortment of the V mini-genes is involved in the generation of hypervariability during evolution. However, the rearranged pseudogene could have also arisen by fortuitous deletion. The other VH gene of CESS is an expressed form and is probably linked to the C gamma gene. The diversity region (D) segments used in these rearranged V genes are less than 38% homologous to known human germline D segments, indicating the presence of more unknown germline D segments.

Amino Acid Sequence↗
PubMed1984

Human dihydrofolate reductase gene is located in chromosome 5 and is unlinked to the related pseudogenes.

The chromosomal location of the human dihydrofolate reductase (DHFR; EC 1.5.1.3) gene that is amplified in a methotrexate-resistant human cell line has been investigated by screening a large number of human-mouse cell hybrids containing overlapping subsets of human chromosomes. A correlation of genomic blotting data with the chromosome constitution of the individual cell hybrids has allowed the assignment of the human DHFR gene to chromosome 5. This chromosome assignment has been confirmed by the observation of a concomitant loss of the human DHFR gene and of sensitivity to diphtheria toxin, a marker associated with chromosome 5, in two human-mouse cell hybrids selected for resistance to the toxin. Six EcoRI fragments of human DNA containing DHFR pseudogenes or other DHFR-related sequences have been assigned to chromosomes other than chromosome 5.

Animals↗
PubMed1984

Evidence for a human histone gene cluster containing H2B and H2A pseudogenes.

Not all members of the human histone gene family are functional. We have isolated a human H2B pseudogene that contains alterations in the protein-coding sequences as well as in the 3' and 5' flanking sequences that preclude expression of a functional H2B histone protein. There are three modifications in the amino acid-coding region: a single-base deletion producing a frame shift, a single-base substitution resulting in a codon change from serine to tryptophan (an amino acid not present in histones), and the absence of a stop codon. Analysis of nucleotide sequences upstream from the AUG start signal indicates the absence of a "TATA" box and other putative consensus regulatory sequences. In the 3' flanking region, a highly conserved block of 22 nucleotides that exhibits hyphenated dyad symmetry is displaced downstream. Within the same genomic segment, the adjacent H2A histone gene is missing 12 nucleotides, resulting in a deletion of four amino acids in a highly conserved region of the protein.

Amino Acid Sequence↗
PubMed1985

Evolutionary amplification of a pseudogene.

The family of mouse major urinary protein (MUP) genes has about 35 members, clustered together on chromosome 4. Most of the genes belong to two major subfamilies (group 1 and group 2) each with 12-15 members. Recently we showed that most of the group 1 and group 2 genes are arranged in pairs, each containing a group 1 and a group 2 gene in divergent transcriptional orientation, with 15 kilobases of DNA between the two cap sites. Here we present the nucleotide sequence of the first exon of six group 1 genes and four group 2 genes. The data confirm the close relationship of the genes within each group and the considerable divergence of the two groups from each other. The four group 2 genes all carry the same nonsense mutation in codon 7 of the sequence that specifies the mature protein. Thus, not only do these genes have a common ancestor, but also it seems that their amplification followed the mutation of the ancestor to a pseudogene. Taking into account the 3' flanking regions of the two genes, the overall size of each gene-pair is about 45 kilobases. The sequencing data supports our earlier suggestion that this 45 kilobase domain is the unit of Mup amplification.

Animals↗
PubMed1985

A 78-kilobase region of mouse chromosome 3 contains salivary and pancreatic amylase genes and a pseudogene.

Genetic studies have demonstrated that salivary and pancreatic amylase genes are closely linked in human and mouse. To analyze the arrangement of genes within the amylase cluster, a library of YBR mouse genomic DNA was cloned in the cosmid vector pJB8. Clones containing amylase genes were identified by hybridization with amylase cDNA probes. Salivary and pancreatic amylase genes were isolated on separate cosmid clones, but no overlapping clones were evident from the initial screening. A strategy for the rapid isolation of terminal noncoding fragments from the cosmid clones was developed. By using these terminal fragments for chromosome "walking," a map of 78 kilobases of the amylase gene region was constructed. The salivary and pancreatic amylase genes are present within this region in the same 5'-to-3' orientation, separated by 22 kilobases of genomic DNA. A truncated amylase pseudogene is located 10 kilobases downstream from the pancreatic amylase gene.

Amylases↗
PubMed1985

The I region of the C57BL/10 mouse: characterization and physical linkage to H-2K of an SB beta-like class II pseudogene, psi A beta 3.

In the C57BL/10 mouse, 140 kilobases (kb) of the I region (I-Ab, I-Eb) were isolated as recombinant cosmids. The class II genes A beta 2, A beta 1, A alpha,E beta 1, E beta 2, and E alpha are located from centromere to telomere in a region of approximately equal to 110 kb, which shows that the I region in the b haplotype has a similar overall organization to those described for the d, k, and wr7 haplotypes. In addition to these genes, we have also isolated a class II gene, psi A beta 3, which is physically linked to the class I H-2K region, 75 kb telomeric to the H-2Kb gene. This orients the H-2K region on the genetic map with the H-2Kb gene being located toward the I region. The sequence of the beta 2 domain of psi A beta 3 is similar to the immunoglobulin-like domain of other class II genes. Interestingly, it shows 83% nucleotide homology to the human SB beta gene, the same homology that was seen previously between the immunoglobulin-like exons of A beta 1 and DC beta and between E beta 1 and DR beta, respectively. It is likely, therefore, that psi A beta 3 represents a member of a third SB-like class II gene family present in addition to I-A and I-E genes and that the divergence of the SB family predates the speciation of rodents and primates. Comparison of the DNA sequence of the exon encoding the beta 2 domain of psi A beta 3 in the b or k haplotypes with functional class II genes shows that a deletion of eight nucleotides has occurred, such that the psi A beta 3 sequence cannot be translated into a functional class II protein. This suggests that psi A beta 3 is a pseudogene.

Alleles↗
PubMed1985

One gene and one pseudogene for the cytokeratin endo A.

The recombinant cDNA RecXVI, which hybridizes to the endo A mRNA, detects two specific bands on a Southern blot of EcoRI-digested genomic mouse DNA. We have screened a mouse genomic library with this cDNA and isolated these two sequences. Endo A is encoded by a 7.5-kilobase gene and by a 1.6-kilobase pseudogene devoid of introns. A repetitive sequence belonging to the B2 family is located in the third intron of the gene. We have observed that transcription of B2 sequences and of the endo A gene are mutually exclusive.

Animals↗
PubMed1986

Human Cu/Zn superoxide dismutase gene family: molecular structure and characterization of four Cu/Zn superoxide dismutase-related pseudogenes.

Four distinct human Cu/Zn superoxide dismutase (SOD1; EC 1.15.1.1)-related sequences were isolated from genomic DNA libraries. Genomic blots, heteroduplex analyses, and DNA sequencing showed that they are processed pseudogenes not residing on chromosome 21. Three of them originated from the 0.7-kilobase SOD1 mRNA, while the fourth was derived from the 0.9-kilobase mRNA species. Comparison between the coding sequences of the functional gene and two of the processed genes suggested that they integrated into the genome about 25 million years ago.

Animals↗
PubMed1986

Determinator-inhibitor pairs as a mechanism for threshold setting in development: a possible function for pseudogenes.

Thresholds are frequently thought to be involved in the development of discrete structures in response to a shallow, monotonic gradient of morphogenetic information. We propose a mechanism for threshold setting that incorporates two essential components: (i) determinator genes that produce intracellular "determinators" that control cellular differentiation during development and (ii) intracellular "inhibitors" that bind tightly and specifically to the determinators to form "determinator-inhibitor pairs" that are inactive with respect to determinator function. The interaction of these components amplifies the intracellular response to an extra-cellular morphogen, thus producing a sharp transition in determinator gene activity. This system could operate at either the RNA level with the determinator-inhibitor pairs taking the form of sense-antisense RNAs or at the protein level via a competitive inhibition mechanism. In either case this model suggests a possible role for pseudogenes in development as a source of the intracellular inhibitors.

Animals↗
PubMed1983

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

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.

Amino Acid Sequence↗
PubMed1983

Transcriptional activity of the human pseudogene psi alpha globin compared with alpha globin, its functional gene counterpart.

Transcriptional analysis of the human pseudogene psi alpha globin has revealed the following features: (1) The promoter with a 23 bp deletion between the CCAAT and ATA boxes is functional both in vitro and in vivo, 3 fold and 10 fold less efficient, respectively, than alpha. (2) Both the psi alpha and alpha globin gene promoters are active in the absence of transcriptional enhancers, either a gene-encoded or viral enhancer. (3) The mutated poly(A) addition signal in psi alpha (AATGAA) appears to be completely nonfunctional. This result provides an explanation for the absence of psi alpha transcripts in human erythroid cells.

Base Sequence↗
PubMed1984

The human c-Ha-ras2 is a processed pseudogene inactivated by numerous base substitutions.

The human c-Ha-ras2 gene, one of two known members of the Harvey ras family, is reportedly located on the X-chromosome and has lost introns (1, 2). There has heretofore been no information on its precise gene structure and oncogenic potential. We have determined the nucleotide sequence of the c-Ha-ras2 and demonstrate that it is a processed pseudogene surrounded by several direct repeats and contains numerous base substitutions as well as a notable mutation (AGT at codon 12 of the p21 protein) responsible for oncogenic conversion of the known ras genes (3-8).

Base Composition↗
PubMed1985

Sequence of a pseudogene in the legumin gene family of pea (Pisum sativum L.).

A second legumin gene, denoted psi Leg D, has been located on the pea genomic clone lambda Leg 1, approx. 1.3 Kbases 3' of Leg A, in the same orientation. The complete sequence of psi Leg D shows that it is a pseudogene, having two stop codons near the 5' end of its predicted coding sequence, as well as deletions and frame shift errors when compared to Leg A. No transcripts from this gene could be detected in developing pea seeds. Leg A and psi Leg D are homologous over their coding sequences, and partially homologous in the intron sequences and the immediate 5' flanking sequences. Other flanking sequences of the two genes show no significant homology, apart from the presence of polyadenylation signals 3' to both coding sequences. The introns in the two genes occur in corresponding positions in the sequences, but a deletion in psi Leg D affects the 3' boundary of IVS-2. Hybridisation of psi Leg D to pea genomic DNA suggests that it does not represent a hitherto undetected sub-family of legumin genes.

Amino Acid Sequence↗
PubMed1985

Characterization of a mouse somatic cytochrome c gene and three cytochrome c pseudogenes.

Mouse contains two functional, but differentially expressed, cytochrome c genes. One of these genes is expressed in all somatic tissues so far examined. The other gene is expressed only in testis and is assumed to be spermatogenesis-specific. The nucleotide sequence of four mouse cytochrome c-like genes has been determined. One of these genes (MC1) contains an intron and encodes a polypeptide sequence identical to the published mouse somatic cytochrome c amino acid sequence. The other three genes can not properly encode a mouse cytochrome c protein and appear to be pseudogenes which have arisen via an insertion into the mouse genome of a cDNA copy of a cytochrome c mRNA molecule.

Amino Acid Sequence↗