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Query: UNIPROT:P06889 (Mol)
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We have isolated and analysed a 2 kb region of the mitochondrial genome of Arabidopsis thaliana (Columbia) showing a high level of nucleotide identity with the mitochondrial (mt) rps14 small-subunit ribosomal protein gene from Oenothera berteriana and Vicia faba, as well as with an open reading frame (ORF) located upstream of the nad3 locus in O. berteriana. The rps14 locus is present as a single copy in the A. thaliana mt genome and has a translational stop codon located near the initiation codon, as well as a deletion of one nucleotide that disturbs the coding sequence. The cloning and sequencing of nine amplified mt rps14 cDNAs clearly demonstrated that this gene is transcribed and that the mRNA precursors are edited at three positions, all involving C-to-U conversions. No editing events changing the stop codon and restoring the correct coding sequence were witnessed within the 9 individual cDNA clones. Therefore, we conclude that the single rps14 sequence of the mitochondrial genome from A. thaliana is in fact a pseudogene that is transcribed and edited but not translated.
Plant Mol Biol 1992 Dec
PMID:Mitochondrial rps14 is a transcribed and edited pseudogene in Arabidopsis thaliana. 146 50

The vitopine Ti plasmid pTiS4 of Agrobacterium vitis has an unusual T-DNA organization. The pTiS4 oncogenes, localized by screening selected pTiS4 clones for growth-inducing activity, are localized on three T-DNAs, whereas in all other characterized Ti plasmids one or two T-DNAs are found. The nucleotide sequences and predicted amino acid sequences of the pTiS4 oncogenes set them apart from the corresponding genes from other Ti or Ri plasmids. The oncogenes induce the same type of reaction on various test plants as the well-known pTiAch5 oncogenes but the pTiS4 ipt gene induces considerably more shoots than its Ach5 homologue. We have also identified the gene coding for vitopine synthase as well as a vitopine synthase pseudogene. Both sequences show homology to the octopine synthase gene. In terms of both nucleotide sequence and overall organization, the pTiS4 T-DNAs appear to be only distantly related to previously characterized T-DNAs.
Mol Gen Genet 1992 Nov
PMID:Organization and functional analysis of three T-DNAs from the vitopine Ti plasmid pTiS4. 146 4

A genomic clone, pTt21, containing DNA apparently transcribed specifically in Trypanosoma cruzi trypomastigotes, was obtained by differentially screening a genomic library with trypomastigote and epimastigote cDNA. This 3444-bp clone contained open reading frames at each end, separated by a 1.8-kb non-coding region. The translated polypeptide from the 3' open reading frame (ORF2) of 1037 bp had 25-30% identity with 5 recently published T. cruzi gp85/sialidase sequences, and 20-25% identity with bacterial sialidases. Rabbit antiserum raised against an Escherichia coli fusion protein derived from the 5' open reading frame (ORF1) identified a surface antigen of 160 kDa, specifically expressed in trypomastigotes. A probe containing the first 211 bp from ORF1 was used to obtain a complete copy (c1821) of a gene that was closely related to ORF1, and encoded another member of the gp85/sialidase family. c1821 encodes a protein of 897 amino acids, but assignment of the N-terminus of the polypeptide was not possible. The 5'-most start codon is an unfavourable context to act as a translation initiator, it does not align with the initiator methionines of other gp85/sialidase sequences, nor is it followed by a signal peptide sequence characteristically found in other gp85/sialidase sequences. Although homology with the 5' ends of other gp85/sialidase sequences decays towards the 5' end of c1821, alignment of c1821 with 4 other gp85/sialidases indicated that the coding sequence should extend upstream at least 160 amino acids. In this region of c1821 there are multiple stop codons in each frame. The presence of the stop codons, the alignment data and our inability to amplify reverse transcribed mRNA using four internal primers, suggest that c1821 may not be present as a mature mRNA and is a pseudogene. Comparison of the apparently non-repetitive 3' coding domain of c1821 with the corresponding repetitive domains of two other members of the gp85/sialidase family revealed a high degree of similarity in nucleotide but not in amino acid sequence, and c1821 may thus represent an evolutionary intermediate between sub-families of the gp85/sialidase superfamily.
Mol Biochem Parasitol 1992 Nov
PMID:Sequence homology and absence of mRNA defines a possible pseudogene member of the Trypanosoma cruzi gp85/sialidase multigene family. 147 90

Patterns of nucleotide substitutions in human major histocompatibility complex (MHC) class I genes were estimated by using phylogenetic trees of DNA sequences. The pattern is defined as a set of 12 parameters, each of which represents the relative frequency of substitutions from a particular nucleotide to another. The pattern at the antigen recognition sites (ARS) in functional MHC genes was remarkably different from that at the remaining coding region (non-ARS). In particular, the proportion of transitions among all the nucleotide substitutions (Ps) was extremely low at the third codon positions of ARS. In the HLA-A genes, Ps at the third codon positions was only 6% in ARS, whereas it was 69% in non-ARS. In HLA-B, the corresponding values were 30% in ARS and 80% in non-ARS, respectively. On the other hand, Ps in a class I pseudogene (HLA-H) was 57%, which was in good agreement with Ps in other pseudogenes. Because pseudogenes are selectively neutral, the pattern in pseudogenes is regarded as the pattern of spontaneous substitution mutations. In general, the pattern in functional genes that are subject to selective forces deviates from the pattern in pseudogenes. At the third codon positions in coding regions, transitions scarcely cause amino acid replacements, whereas about half of transversions do cause replacements. Accordingly, Ps at the third codon positions decreases if amino acid replacements are accelerated by natural selection but increases if amino acids are conserved by functional constraint. Our observations imply that the ARS region is subject to natural selection favoring amino acid replacements, whereas the non-ARS region is subject to functional constraint.
J Mol Evol 1992 Sep
PMID:Patterns of nucleotide substitutions inferred from the phylogenies of the class I major histocompatibility complex genes. 151 87

Inactivating point mutations and small deletions in the p53 tumor suppressor gene have been found in human liver and lung tumor--derived cell lines and tumors. However, little evidence has been reported concerning inactivation or mutation of the p53 gene in mouse primary tumors. To examine CD-1 mouse liver and lung tumors for mutations in the p53 gene, we first sequenced p53 introns 5-8 so that polymerase chain reaction amplification and sequencing primers located within the introns could be prepared. Use of these primers prevented amplification of the mouse p53 pseudogene and allowed sequencing of exons 5-8 in their entirety as well as their intron-exon junctions. DNA isolated from CD-1 mouse tumors was amplified and directly sequenced using nested primers. Nine spontaneous hepatocellular carcinomas (HCCs) and 34 chemically induced HCCs (induced by single intraperitoneal injections of N-nitrosodiethylamine [DEN] [8 HCCs], 7,12-dimethylbenz[a]anthracene [DMBA] [8 HCCs], 4-aminoazobenzene [8 HCCs], and N-OH-2-acetylaminofluorene [10 HCCs]) were examined for mutations in exons 5-8 of the p53 gene. In addition, 12 spontaneous, 10 DMBA-induced, and 13 DEN-induced lung adenocarcinomas or adenomas were analyzed for mutations. No mutations were found in any of the tumors examined. However, a mutation was demonstrated at codon 135 in the positive-control plasmid LTRp53cG(val). The results of this study suggest that inactivation of p53 is unlikely to play a major role in murine lung or liver carcinogenesis. However, inactivation of p53 may occur at a very low frequency, or it may occur as a late event and therefore be present in only a very small number of the tumor cells, rendering it undetectable by this method. Lastly, although few p53-inactivating mutations are found outside of exons 5-8 in human tumors, it is possible that these murine tumors contained mutations outside of this region and were therefore missed by our approach.
Mol Carcinog 1992
PMID:Murine p53 intron sequences 5-8 and their use in polymerase chain reaction/direct sequencing analysis of p53 mutations in CD-1 mouse liver and lung tumors. 154 44

A cDNA from human placenta and liver tissues that contained both sequence for the lysosomal glycosidase di-N-acetylchitobiase and sequence homologous to the gamma subunit of GTP-binding proteins was previously isolated. Here we have shown that the gamma-subunit-homologous portion of this unusual cDNA is derived from a member of the gamma-subunit multigene family. The partial human gamma-subunit sequence was used to isolate the corresponding full-length cDNA clones from bovine and rat livers. The two cDNAs encode identical 68-amino-acid proteins (7.3 kDa) homologous to previously cloned G protein gamma subunits. The bovine gene sequence encoding this new gamma-subunit isoform (gamma 5) was determined and found to have an intron-exon structure consistent with the original human chitobiase-gamma 5-subunit hybrid mRNA being a product of alternative splicing. Genomic cloning also resulted in the isolation of a human gamma 5 pseudogene.
Mol Cell Biol 1992 Apr
PMID:Characterization of the cDNA and genomic sequence of a G protein gamma subunit (gamma 5). 154 14

The Class V zygote-specific gene from Chlamydomonas reinhardtii has been cloned and sequenced. This gene encodes a polypeptide of 86 amino acids, which contains a signal peptide and 6 cysteine residues arranged in an inverted symmetrical repeat. The Class V gene product is postulated to be a component of the zygote cell wall. Southern analysis revealed two tandemly oriented and closely linked copies of the Class V gene, designated A and B. The A gene appears to be a pseudogene, based on analysis of Class V cDNAs, primer extension with gene-specific primers, and Northern analysis which failed to detect an A gene transcript. Genetic analysis using a related Chlamydomonas species that lacks the A gene, but which produces normal zygotic progeny, further indicates that the A gene is not required for zygote development.
Mol Gen Genet 1992 Mar
PMID:A gene/pseudogene tandem duplication encodes a cysteine-rich protein expressed during zygote development in Chlamydomonas reinhardtii. 155 7

We have determined the nucleotide sequence of a 7343 bp zein genomic clone (gZ22.8H3) from the maize inbred W64A. Computer-aided analysis of the DNA sequence revealed two contiguous 22 kDa alpha-zein genes. The 5' gene (gZ22.8) encodes a complete polypeptide and contains putative regulatory sequences in both the 5' and 3' flanking regions that are typical of zein genes. In contrast, the 3' gene (psi gZ22.8) appears to be a pseudogene, because it contains numerous insertions and deletions that would prevent translation of the mRNA. Alignment of the 5' and 3' flanking sequences of both genes indicated that they resulted from a 3.3 kb DNA duplication event.
Plant Mol Biol 1992 Feb
PMID:Sequence analysis of linked maize 22 kDa alpha-zein genes. 155 57

The chimpanzee and African green monkey insulin genes have been cloned and sequenced. These two sequences together with the previously reported sequences for the human and owl monkey insulin genes provide additional support for the hominoid-rate-slowdown hypothesis, i.e., a slower rate of nucleotide substitution in humans and apes than in monkeys. When these sequences and other primate sequences available for the relative-rate test were considered together, the substitution rate in the Old World monkey lineage was shown to be significantly higher than the rates in the human and chimpanzee lineages. This was true regardless of whether the eta-globin pseudogene was included in the analysis. Therefore, in contrast to the claim by Easteal, the hominoid-rate-slowdown is not unique to the eta-globin pseudogene but appears to be a rather general phenomenon. On average, the substitution rate at silent sites is about 1.5 times higher in the Old World monkey lineage than in the human and chimpanzee lineages.
Mol Biol Evol 1992 Mar
PMID:Sequences of primate insulin genes support the hypothesis of a slower rate of molecular evolution in humans and apes than in monkeys. 156 Jul 57

We determined the nucleotide sequence of a 2.5 kb DNA fragment (1 kb is 10(3) base-pairs) that includes exon 1, intron 1 and about 1.4 kb of 5'-flanking DNA of the spider monkey gamma 1-globin pseudogene locus and compared this sequence to its homologous from other primates and rabbit. This region of the gamma 1 locus of spider monkey still retains conserved regulatory elements, suggesting that it became a pseudogene late in New World monkey phylogeny. In the 250 base-pair region immediately 5' from the transcription start site where many known regulatory elements are located, a higher rate of nucleotide substitutions occurred in the ancestral anthropoid (human, ape and monkey) lineage than in the prosimian (galago) lineage, as was also the case for non-synonymous substitutions in the coding region. The opposite pattern was observed for most other non-coding regions and for synonymous substitutions. These substitution patterns correlate with the embryonic-to-fetal transformation of the gamma-globin genes of the ancestral anthropoids. Analysis of the 5'-flanking sequences suggests that 11 gene conversion events have occurred in the anthropoid gamma-gene lineages. In the parts of the 5'-flanking region where no gene conversions have been detected, gamma 2-gene sequences have accumulated more nucleotide changes than gamma 1, which suggests that the gamma 2 gene was the more redundant duplicate that may have accumulated first the nucleotide changes responsible for the anthropoid fetal pattern of gamma-globin gene expression.
J Mol Biol 1992 Apr 05
PMID:Fetal recruitment of anthropoid gamma-globin genes. Findings from phylogenetic analyses involving the 5'-flanking sequences of the psi gamma 1 globin gene of spider monkey Ateles geoffroyi. 156 63


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