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PubMed1987

Isolation of tobacco SSU genes: characterization of a transcriptionally active pseudogene.

Genomic clones containing three genes for the small subunit (SSU) of ribulose bisphosphate carboxylase were isolated from tobacco. Detailed analysis was performed on two of these clones to give a clearer picture of this multigene family in tobacco. This analysis demonstrated that one of the clones contained a pseudogene that was unusual in that it was transcriptionally active. This is the first transcriptionally active pseudogene that has been reported in plants. In addition, another clone was found to contain coding sequences which are 100% homologous to a previously-cloned tobacco SSU gene (Mazur, B.J. and Chiu, C-F. [1985] Nuc. Acids Res. 13, 2372-2386), indicating that gene duplication and/or gene conversion may have played a role in the evolution of the tobacco SSU family.

Amino Acid Sequence↗
PubMed1988

Expression of the human amylase genes: recent origin of a salivary amylase promoter from an actin pseudogene.

The human genes encoding salivary amylase (AMY1) and pancreatic amylase (AMY2) are nearly identical in structure and sequence. We have used ribonuclease protection studies to identify the functional gene copies in this multigene family. Riboprobes derived from each gene were hybridized to RNA from human pancreas, parotid and liver. The sizes of the protected fragments demonstrated that both pancreatic genes are expressed in pancreas. One of the pancreatic genes, AMY2B, is also transcribed at a low level in liver, but not from the promoter used in pancreas. AMY1 transcripts were detected in parotid, but not in pancreas or liver. Unexpected fragments protected by liver RNA led to the discovery that the 5' regions of the five human amylase genes contain a processed gamma-actin pseudogene. The promoter and start site for transcription of AMY1 are recently derived from the 3' untranslated region of gamma-actin. In addition, insertion of an endogenous retrovirus has interrupted the gamma-actin pseudogene in four of the five amylase genes.

Actins↗
PubMed1991

RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera.

An intact gene for the ribosomal protein S19 (rps19) is absent from Oenothera mitochondria. The conserved rps19 reading frame found in the mitochondrial genome is interrupted by a termination codon. This rps19 pseudogene is cotranscribed with the downstream rps3 gene and is edited on both sides of the translational stop. Editing, however, changes the amino acid sequence at positions that were well conserved before editing. Other strange editings create translational stops in open reading frames coding for functional proteins. In coxI and rps3 mRNAs CGA codons are edited to UGA stop codons only five and three codons, respectively, downstream to the initiation codon. These aberrant editings in essential open reading frames and in the rps19 pseudogene appear to have been shifted to these positions from other editing sites. These observations suggest a requirement for a continuous evolutionary constraint on the editing specificities in plant mitochondria.

Amino Acid Sequence↗
PubMed1995

Evolution of immunoglobulin VH pseudogenes in chickens.

In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this unique genetic system, we conducted statistical analyses of VH1 and psi VH genes together with functional VH genes from other higher vertebrate species. The results indicate, first, that chicken VH genes are all closely related to one another and were derived relatively recently from an ancestral gene belonging to one of the three major groups of VH genes in higher vertebrates. Second, the rate of nonsynonymous substitution is slightly higher than that of synonymous substitution in the complementarity-determining regions (CDRs), which suggests that diversity-enhancing selection has operated in the CDRs even for pseudogenes. However, both the rates of synonymous and nonsynonymous substitution are higher in the CDRs than in the framework regions (FRs), apparently because of an interaction between positive selection and meiotic gene conversion in the CDRs. Third, a dot matrix analysis of the psi VH genes and genomic diversity (D) genes has indicated that the 3' end of psi VH genes is attached by D-gene-like sequences, and this region of psi VH genes has high similarity with D gene sequences. This suggests that V and D genes were fused at some point of evolutionary time and this fused element multiplied by gene duplication. Finally, two alternative hypotheses of explaining the evolution of the chicken VH gene system are presented.

Animals↗
PubMed1983

Structure and evolution of human and African ape rDNA pseudogenes.

We discuss the evolutionary significance of four aberrant 18S rDNA clones that were obtained from human, chimpanzee, and gorilla DNA libraries. We show that these clones carry representatives of a small 18S rDNA pseudogene family that arose in a common ancestor of these species. Aspects of their structure and phylogenetic distribution suggest that the 18S pseudogenes no longer interact genetically with normal ribosomal genes and therefore may not be linked to nucleolus organizer regions.

Animals↗
PubMed1984

Rabbit globin pseudogene psi beta 2 is a hybrid of delta- and beta-globin gene sequences.

The evolutionary history of the rabbit globin pseudogene psi beta 2 was studied by completing its nucleotide sequence and aligning the sequence with that of the rabbit adult globin gene beta 1 and the human minor adult globin gene delta. The 5' flanking region and exon 1 of psi beta 2 were most similar to rabbit beta 1, but the large intervening sequence and the 3' untranslated region were most similar to human delta. Intron 1 and exon 2 were equally similar to both delta and beta 1. This pattern indicates that psi beta 2 was originally a delta-like gene that acquired the 5' portion of gene beta 1 by intrachromosomal gene conversion. The presence of a delta-globin gene sequence in both rabbits and humans shows that it is an ancient gene, predating the mammalian radiation that occurred over 85 Myr ago. Delta has shown a pronounced tendency to be altered in its 5' end during the course of mammalian evolution. Quantitative divergence analysis shows that the ancestor to rabbit psi beta 2 was active until 20-30 Myr ago, during which time the lagomorph beta-globin gene family apparently functioned without a pseudogene.

Animals↗
PubMed1986

Neighboring base effects on substitution rates in pseudogenes.

Substitution rates in pseudogenes can be used to estimate the frequencies of different types of mutation on the assumption that pseudogenes are not subject to selective constraints. These rates are used here to investigate the effect of neighboring bases on mutation rates. There is a marked increase in the frequency of transitions, though not of transversions, from the doublet CG. There are also some smaller effects of neighboring bases on the frequencies of transitions from adenine and thymine. The results are used to predict dinucleotide frequencies in a stretch of DNA subject to no selective constraints and to investigate the possibility of non-randomness in the usage of stop codons.

Animals↗
PubMed2004

A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage.

The protein tyrosine phosphatases (PTPs) are now recognized as critical regulators of signal transduction under normal and pathophysiological conditions. In this analysis we have explored the sequence of the human genome to define the composition of the PTP family. Using public and proprietary sequence databases, we discovered one novel human PTP gene and defined chromosomal loci and exon structure of the additional 37 genes encoding known PTP transcripts. Direct orthologs were present in the mouse genome for all 38 human PTP genes. In addition, we identified 12 PTP pseudogenes unique to humans that have probably contaminated previous bioinformatics analysis of this gene family. PCR amplification and transcript sequencing indicate that some PTP pseudogenes are expressed, but their function (if any) is unknown. Furthermore, we analyzed the enhanced diversity generated by alternative splicing and provide predicted amino acid sequences for four human PTPs that are currently defined by fragments only. Finally, we correlated each PTP locus with genetic disease markers and identified 4 PTPs that map to known susceptibility loci for type 2 diabetes and 19 PTPs that map to regions frequently deleted in human cancers. We have made our analysis available at http://ptp.cshl.edu or http://science.novonordisk.com/ptp and we hope this resource will facilitate the functional characterization of these key enzymes.

Amino Acid Sequence↗
PubMed2004

Organization and evolution of the flavin-containing monooxygenase genes of human and mouse: identification of novel gene and pseudogene clusters.

OBJECTIVES: To date, six flavin-containing monooxygenase (FMO) genes have been identified in humans, FMOs 1, 2, 3, 4 and 6, which are located within a cluster on chromosome 1, and FMO5, which is located outside the cluster. The objectives were to review and update current knowledge of the structure and expression profiles of these genes and of their mouse counterparts and to determine, via a bioinformatics approach, whether other FMO genes are present in the human and mouse genomes. RESULTS AND CONCLUSIONS: We have identified, for the first time, a mouse Fmo6 gene. In addition, we describe a novel human FMO gene cluster on chromosome 1, located 4 Mb telomeric of the original cluster. The novel cluster contains five genes, all of which exhibit characteristics of pseudogenes. We propose the names FMO 7P, 8P, 9P, 10P and 11P for these genes. We also describe a novel mouse gene cluster, located approximately 3.5 Mb distal of the original gene cluster on Chromosome 1. The novel mouse cluster contains three genes, all of which contain full-length open-reading frames and possess no obvious features characteristic of pseudogenes. One of the genes is apparently a functional orthologue of human FMO9P. We propose the names Fmo9, 12 and 13 for the novel mouse genes. Orthologues of these genes are also present in rat. Sequence comparisons and phylogenetic analyses indicate that the novel human and mouse gene clusters arose, not from duplications of the known gene cluster, but via a series of independent gene duplication events. The mammalian FMO gene family is thus more complex than previously realised.

Amino Acid Sequence↗
PubMed2004

NCF1 (p47phox) and ncf1 pseudogenes are not associated with inflammatory bowel disease.

Crohn's disease (CD) and ulcerative colitis (UC) have a strong genetic component, contributing to a patient's susceptibility for inflammatory bowl disease (IBD). Linkage analysis has detected an IBD susceptibility locus in a region on chromosome 7q that encompasses the p47 (NCF1) gene and p47 (PsiNCF1) pseudogenes. Involvement of the NCF1 locus in IBD was supported by the observation that chronic inflammation of the bowel is a feature of chronic granulomatous disease caused by NCF1 mutation in 25% of cases. The pseudogenes have a dinucleotide deletion (PsiGT) at the beginning of exon 2, resulting in a frameshift and premature stop codon. APsiNCF1 (DeltaGT) to NCF1 (GTGT) ratio of 2:1 has been proposed as the predominant ratio in humans; but variability may occur after DNA exchange by recombination between PsiNCF1 and NCF1 to produce a potentially functional gene hybrid (type IIPsiNCF1). A preliminary study suggested an association between individuals with a 1:1 ratio and susceptibility to IBD. The possible presence of type IIPsiNCF1 was proposed as a susceptibility factor. We have now established the PsiNCF1 to NCF1 ratio for a significant number of IBD patients (n = 488) and control subjects (n = 181) and show that there is no statistically significant difference between the frequency of the 1:1 ratio in CD (11.2%) or UC (12.2%) patients and controls (13.4%). The 2:1 ratio was identified as the most common ratio (83.3%). Our data show there is no association of the 1:1 ratio with IBD and that susceptibility is unlikely to be a consequence of an inherited 1:1, rather than a 2:1 (PsiNCF1:NCF1) ratio.

Case-Control Studies↗
PubMed1995

Comparison of a mitochondrial gene and a corresponding nuclear pseudogene.

Nuclear copies of mitochondrial genes have been reported several times. Presented here is a direct comparison of a fragment of the mitochondrial gene coding for Cytochrome b and its assumed nuclear pseudogene in a phylogenetic context. By studying eight such sets of genes a direct measurement of relative rates of several types of substitutions were made. As expected mitochondrial third position transitions are the fastest accumulating substitutions, here indicated to be at least up to 39 times faster than corresponding positions in the supposed nuclear pseudogene. Translocated mitochondrial genes, evolving much slower than their functional 'counterpart', reflect the ancestral-pre-translocated form of the gene. A warning is given against unwanted inclusion of paralogous sequences in phylogenetic analysis and against the use of versatile primers that can promote such incidents.

Amino Acid Sequence↗
PubMed2004

Polymorphisms in the prion precursor functional gene but not the pseudogene are associated with susceptibility to chronic wasting disease in white-tailed deer.

Chronic wasting disease (CWD) status and PrP genotypes were determined for a group of 133 wild white-tailed deer in a 780 acre enclosure in western Nebraska, USA. Approximately half of the deer tested showed evidence of PrPd in the brainstem or lymphoid tissues. Four PRNP alleles encoding amino acid substitutions were identified, with substitutions at residues 95 (Q-->H), 96 (G-->S) or 116 (A-->G), each with serine (S) at residue 138. In addition, a processed pseudogene with two alleles encoding five or six copies of the octapeptide repeat was identified in 26 % of the deer. Both alleles encoded asparagine (N) at residue 138. The functional gene alleles sorted into five major diploid genotypes and four rare genotypes. Although all five major diploid genotypes were found in deer with CWD, unaffected deer were less likely to have the allele QGAS and more likely to have QSAS compared with CWD-affected deer. Late-stage disease (PrPd in brainstem) was noted in deer less than 1 year of age, although no single genotype was associated with this rapid neuroinvasion. Early-stage disease (PrPd distribution limited to the lymphoid system) was observed in deer estimated to be more than 5 years old, suggesting that they were infected as adults or that the incubation time might be extremely long in some individuals. The pseudogene was found in deer of all major PRNP genotypes and was not correlated with CWD status. The large number of susceptible genotypes and the possibility of adult-to-adult transmission suggest that much of the white-tailed deer population may be at risk for disease following exposure to CWD, despite the association of specific genotypes with CWD noted here.

Age Factors↗
PubMed1989

Antigenic diversity by the recombination of pseudogenes.

During the course of an infection, the hemoflagellate Trypanosoma equiperdum sequentially expresses an extensive repertoire of surface glycoproteins. There is evidence that combinations of silent genes are involved in the generation of this repertoire, but the combination rules are not known. To gain insight into these rules, we determined the fine structure of a composite gene. The gene coding for the variant surface glycoprotein 20 of T. equiperdum is a late gene generated by the partial duplication of three silent pseudogenes. Two closely related but not identical '5' donors' form a mosaic coding for the antigenic portion of the protein. A telomeric '3' donor' provides the last 200 nucleotides of the expressed gene. The sequences of the 5' and 3' donors are not related except for a short segment in which the hybrid junction is formed. These results demonstrate that recombinational processes generate diversity by reassorting sequences and also allow the expression of pseudogenes. Furthermore, the use of a short sequence similarity for the formation of the 5'-3' donor hybrid suggests a mechanism that may act in ordering the expression of the variant surface glycoproteins.

Animals↗
PubMed2004

Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot.

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.

Arabidopsis↗
PubMed1990

Characterization of polymorphic markers in the von Willebrand factor gene and pseudogene.

Three TaqI restriction fragment length polymorphisms (RFLP) detected by the central portion of von Willebrand factor cDNA, which recognizes the true gene and in addition pseudogenic sequences, were characterized and mapped. Small cDNA fragments which hybridized with DNA from families with von Willebrand disease were used. Two of the RFLP, recognized by 1.7 and 0.45 kb cDNA fragments, are not in linkage either with von Willebrand disease or with RFLP located in the von Willebrand factor (vWF) gene, which indicates their pseudogenic location. These markers located in 22q11, near to the bcr gene, provide new tools for the study of several somatic and constitutional alterations affecting this chromosomal region. The third RFLP is recognized by a cDNA fragment corresponding to the N-terminal portion of mature vWF and is localized in the true gene. Since significant linkage disequilibrium with other informative RFLP is not present, this marker contributes to the definition of family haplotypes associated with von Willebrand disease.

Blotting, Southern↗
PubMed1994

Activation of a vmp pseudogene in Borrelia hermsii: an alternate mechanism of antigenic variation during relapsing fever.

The relapsing fever agent, Borrelia hermsii, undergoes multiphasic antigenic variation to evade its host's immune response. A frequently observed switch is serotype 7 to 26. Unlike silent vmp genes previously characterized, the transcriptionally silent vmp26 sequence was a pseudogene in lacking a start codon. In serotype 7 the location of the silent vmp26 sequence just downstream of vmp7 on the expression plasmid, as well as on the silent plasmid, was also unique. The demonstration of a predicted circular recombination product in serotype 7 but not serotype 21 populations indicates that the pseudogene was activated by an intramolecular recombination producing a deletion of DNA between 20-nucleotide direct repeats in vmp7 and psi vmp26.

Amino Acid Sequence↗
PubMed1989

Mouse U3-RNA-processed pseudogenes are nonrandomly integrated into genomic DNA. Implications for the process of retrogene formation.

We have characterized three mouse U3-RNA-processed pseudogenes. Together with previous analyses of mouse functional genes and of rat genes and pseudogenes, these data provide some insights into the processes of U3 retrogene formation during the evolution of rodents. All the mouse retrogenes correspond to a full-length U3B-coding sequence with a 3'-poly(A) tail and are precisely flanked by a pair of direct repeats, in agreement with formation through an RNA intermediate followed by insertion at staggered nicks in the genome. All the rodents U3 retrogenes identified so far are produced from a U3B-RNA form, with two of them (one for each rodent) formed from a 3'-elongated U3-RNA precursor, pointing to the particular susceptibility of RNA precursors forms to serve as templates for retrogene formation. Rodent full-length U3 retrogenes are not inserted randomly in the genome but are systematically found in a context of simple sequences, prone to slipped-strand mispairings and likely to favour the appearance of single-stranded DNA. Moreover their flanking repeats share not only the same size (15 bp) but also common sequence features (which extend to vicinal upstream nucleotides) suggesting that common mechanisms, specific to this class of retrogenes, have been involved in their formation. For the first time, a model accounting for the generation of full-length cDNA copies from nonpolyadenylated RNA templates is proposed. Rodent U3 retrogenes appear to be of rather recent origin (posterior to the mouse/rat divergence) and some of them could have undergone subsequent genetic exchanges with the functional genes.

Animals↗
PubMed1994

Structural analysis of the functional gene and pseudogene encoding the murine granulocyte colony-stimulating-factor receptor.

Granulocyte colony-stimulating factor is a cytokine which specifically regulates the production of neutrophilic granulocytes. The granulocyte colony-stimulating-factor receptor (GCSFR) is mainly expressed in neutrophils and their precursor cells. In this study, we isolated the chromosomal gene for murine GCSFR and determined its structure. Like the human GCSFR gene homolog, it consists of 17 exons. The exon-intron organization of the murine and human GCSFR-encoding genes are very similar, except that exon 14 and exon 15 in the murine gene are interrupted by a larger intron (greater than 10 kbp) than that found in the human gene (128 bp). This GCSFR-encoding functional gene (Csfgr) was localized to the distal region of murine chromosome 4 by interspecific backcross mapping. A comparison of the 5' flanking sequence of murine and human Csfgr revealed that a sequence of approximately 300 bp upstream from the cap site is highly conserved. Within this region, an 18-nucleotide element conserved in the promoter of the genes for neutrophil-specific enzymes, was found approximately 140 bp upstream from the cap site, suggesting an involvement of this element in the specific expression of GCSFR in neutrophilic granulocytes. In addition to the functional GCSFR-encoding gene, we isolated a pseudogene for GCSFR, which is flanked by a 15-bp direct repeat at the 5' and 3' ends, and lacks all introns, exons 1-3 and exons 7-8 of the functional gene. The processed pseudogene has, in its most 5' region, a sequence of approximately 200 bp that is highly related to the DNA sequence approximately 1.2 kbp upstream of the cap site of the functional gene.

Animals↗