Pseudogene

A Matter of Taste: Lineage-Specific Loss of Function of Taste Receptor Genes in Vertebrates

Vertebrates can perceive at least five different taste qualities, each of which is thought to have a specific role in the evolution of different species. The avoidance of potentially poisonous foods, which are generally bitter or sour tasting, and the search for more nutritious ones, those with high-fat and high-sugar content, are two of the most well-known examples. The study of taste genes encoding receptors that recognize ligands triggering taste sensations has helped to reconstruct several evolutionary adaptations to dietary changes. In addition, an increasing number of studies have focused on pseudogenes, genomic DNA sequences that have traditionally been considered defunct relatives of functional genes mostly because of the presence of deleterious mutations interrupting their open reading frames. The study of taste receptor pseudogenes has helped to shed light on how the evolutionary history of taste in vertebrates has been the result of a succession of gene gain and loss processes. This dynamic role in evolution has been explained by the "less-is-more" hypothesis, suggesting gene loss as a mechanism of evolutionary change in response to a dietary shift. This mini-review aims at depicting the major lineage-specific loss of function of taste receptor genes in vertebrates, stressing their evolutionary importance and recapitulating signatures of natural selection and their correlations with food habits.

Identification and analysis of a processed cytochrome P450 pseudogene of the disease vector Aedes aegypti

OBJECTIVE

To clone cytochrome P450 from Aedes aegypti (Ae. aegypti) and determine the characteristics using bioinformatics tools.

METHODS

Cytochrome P450 of Ae. aegypti was amplified using polymerase chain reaction, cloned and sequenced. Evolutionary relationship of the sequence was inferred and bioinformatics tools were used to predict subcellular localisation, signal peptide, transmembrane helix, phosphorylation, O-glycosylation, secondary and tertiary structures of the deduced protein.

RESULTS

Polymerase chain reaction rather amplified a cytochrome P450 pseudogene which was named CYP4H44P (GenBank accession number KF779932). The pseudogene has 1537 nucleotides and an open reading frame of 335 amino acids containing cytochrome P450 motifs except the WxxxR motif. It is highly homologous to CYP4H28 and CYP4H28v2. Phylogenetic analysis and evolutionary divergence showed strong clustering with CYP4H28 alleles and least divergence from the alleles respectively. The deduced protein was predicted to be found in the cytoplasm and likely to be phosphorylated but devoid of signal peptide, transmembrane helix and O-glycosylated sites. The secondary and tertiary structures were also generated.

CONCLUSIONS

A cytochrome P450 pseudogene, CYP4H44P was cloned from Ae. aegypti. The pseudogene is homologous with CYP4H28 alleles and seems to have recently diverged from this group. Isolating this pseudogene is an important step for evaluating its biological role in the mosquito and for the evolutionary analysis of Ae. aegypti CYPs.

Pseudogenes are not pseudo any more

Recent significant progress toward understanding the function of pseudogenes in protozoa (Trypanosoma brucei), metazoa (mouse) and plants, make it pertinent to provide a brief overview on what has been learned about this fascinating subject. We discuss the regulatory mechanisms of pseudogenes at the post-transcriptional level and advance new ideas toward understanding the evolution of these, sometimes called "garbage genes" or "junk DNA," seeking to stimulate the interest of scientists and additional research on the subject. We hope this point-of-view can be helpful to scientists working or seeking to work on these and related issues.

Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei

Pseudogenes have been shown to acquire unique regulatory roles from more and more organisms. We report the observation of a cluster of siRNAs derived from pseudogenes of African Trypanosoma brucei using high through-put analysis. We show that these pseudogene-derived siRNAs suppress gene expression through RNA interference. The discovery that siRNAs may originate from pseudogenes and regulate gene expression in a unicellular eukaryote provides insights into the functional roles of pseudogenes and into the origin of noncoding small RNAs.

Characterization of a putative hsp70 pseudogene transcribed in protoscoleces and adult worms of Echinococcus granulosus

Searching for hsp70 genes in Echinococcus granulosus, a divergent cytoplasmic hsp70-like sequence (EgpsiHsp70) was isolated, possessing a small truncation in the region coding for the C-terminal glycine-rich linker and EEVD-Ct motif. Southern Blot analyses of E. granulosus, and in silico analyses of E. multilocularis indicate that this truncated sequence is repeated several times in both genomes, in some cases containing clear cut features of pseudogenization. Phylogenetic analyses and comparison of surrounding regions indicate that all these copies originated by successive genomic duplications of one originally truncated copy. These copies are diverging at an increased rate compared to functional cytoplasmic hsp70 genes, and ratios of non-synonymous over synonymous substitutions rates (dN/dS) point to a relaxation of sequence constraint, suggesting that these sequences are pseudogenes. Interestingly, RT-PCR demonstrates that EgpsiHsp70 is transcribed in protoscoleces and adult individuals of E. granulosus. We suggest that this sequence does not code for a functional polypeptide, although some features are unexpected for a sequence evolving under a strictly neutral mode. Transcription could either be vestigial or have a specific, non-coding function.

Genes coding for tryptophan-rich proteins are transcribed throughout the asexual cycle of Plasmodium falciparum

Multigene families are a common feature in Plasmodia spp. and constitute a substantial content of the parasite genome. Here, we analyse the structural organisation and sequence diversity of two further members of the Trp-rich multigene family of P. falciparum. The complete DNA sequence of both genes was determined from a series of laboratory adapted and field isolates. Based on the amino acid sequences, we have termed them tryptophan-rich antigen-3 (TrpA-3) and lysine-tryptophan-rich antigen (LysTrpA). Analysis of the genes using reverse transcriptase-polymerase chain reaction (RT-PCR), showed that both genes are transcribed and that introns are spliced out at predicted positions. Gene expression profiles obtained from microarray analysis indicate that both genes are expressed in the mid-stages of the asexual cycle. In-frame stop codons were detected which interrupted the reading frame of LysTrpA. Whereas the number of the Trp-rich proteins is rather low in P. falciparum, P. chabaudi, P. berghei and P. yoelii, this family seems to have 15 or more members in P. knowlesi and P. vivax.

Pseudogenes: are they "junk" or functional DNA?

Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes.

DNA polymorphism in the beta-Esterase gene cluster of Drosophila melanogaster

We have analyzed nucleotide polymorphism within a 5.3-kb region encompassing the functional Est-6 gene and the psiEst-6 putative pseudogene in 28 strains of Drosophila melanogaster and one of D. simulans. Two divergent sequence types were detected, which are not perfectly associated with Est-6 allozyme variation. The level of variation (pi) is very close in the 5'-flanking region (0.0059) and Est-6 gene (0.0057), but significantly higher in the intergenic region (0.0141) and putative pseudogene (0.0122). The variation in the 3'-flanking region is intermediate (0.0083). These observations may reflect different levels of purifying selection in the different regions. Strong linkage disequilibrium occurs within the region studied, with the largest values revealed in the putative pseudogene and 3'-flanking region. Moreover, recombination is restricted within psiEst-6. Gene conversion is detected both within and (to a lesser extent) between Est-6 and psiEst-6. The data indicate that psiEst-6 exhibits some characteristics that are typical of nonfunctional genes, while other characteristics are typically attributed to functional genes; the same situation has been observed in other pseudogenes (including Drosophila). The results of structural entropy analysis demonstrate higher structural ordering in Est-6 than in psiEst-6, in accordance with expectations if psiEst-6 is indeed a pseudogene. Taking into account that the function of psiEst-6 is not known (but could exist) and following the terminology of J. Brosius and S. J. Gould, we suggest that the term "potogene" may be appropriate for psiEst-6, indicating that it is a potential gene that may have acquired some distinctive but unknown function.

Cytochromes P450 of insects: the tip of the iceberg

The cytochrome P450-dependent monooxygenases are an extremely important metabolic system involved in the metabolism of endogenous compounds and xenobiotics. Collectively, P450 monooxygenases can metabolize numerous substrates and carry out multiple oxidative reactions. The large number of substrates metabolized is due to the plethora of P450 isoforms and to the broad substrate specificity of some isoforms. Monooxygenases of insects have several functional roles, including growth, development, feeding and protection against xenobiotics, including resistance to pesticides and tolerance to plant toxins. This review begins with background information about P450s and their evolution, followed by a discussion of the extraordinary diversity of insect P450s. Given the enormous interest in studying individual P450s, we then provide a synopsis of the different methods that have been used in their isolation and the substrates that are known to be metabolized. We conclude by summarizing the lessons we have learned from the study of individual insect P450s, including their roles in insecticide resistance, plant-insect interactions and insect physiology. However, these studies are just the 'tip of the iceberg'. Our knowledge continues to expand at a rapid pace, suggesting that the next decade will outpace the last in terms of improving our understanding of the cytochromes P450 of insects.

CYP9E2, CYP4C21 and related pseudogenes from German cockroaches, Blattella germanica: implications for molecular evolution, expression studies and nomenclature of P450s

The cDNAs of two novel P450s (CYP9E2 and CYP4C21) were isolated from German cockroaches, Blattella germanica. Both CYP9E2 and CYP4C21 are typical microsomal P450s and their deduced amino acid sequences share a number of common characteristics with other members of the P450 superfamily. Northern blot analyses using a CYP9E2 or CYP4C21 probe showed that 'CYP9E2' and 'CYP4C21' were expressed at all life stages. Two pseudogenes related to CYP9E2 and three pseudogenes related to CYP4C21 were also isolated. These represent the first P450 pseudogenes from an insect other than Drosophila melanogaster. The relative number of P450 pseudogenes in B. germanica is apparently higher than in D. melanogaster. The implications of these results for the molecular evolution, expression studies and nomenclature of P450s are discussed.

The complete human olfactory subgenome

Olfactory receptors likely constitute the largest gene superfamily in the vertebrate genome. Here we present the nearly complete human olfactory subgenome elucidated by mining the genome draft with gene discovery algorithms. Over 900 olfactory receptor genes and pseudogenes (ORs) were identified, two-thirds of which were not annotated previously. The number of extrapolated ORs is in good agreement with previous theoretical predictions. The sequence of at least 63% of the ORs is disrupted by what appears to be a random process of pseudogene formation. ORs constitute 17 gene families, 4 of which contain more than 100 members each. "Fish-like" Class I ORs, previously considered a relic in higher tetrapods, constitute as much as 10% of the human repertoire, all in one large cluster on chromosome 11. Their lower pseudogene fraction suggests a functional significance. ORs are disposed on all human chromosomes except 20 and Y, and nearly 80% are found in clusters of 6-138 genes. A novel comparative cluster analysis was used to trace the evolutionary path that may have led to OR proliferation and diversification throughout the genome. The results of this analysis suggest the following genome expansion history: first, the generation of a "tetrapod-specific" Class II OR cluster on chromosome 11 by local duplication, then a single-step duplication of this cluster to chromosome 1, and finally an avalanche of duplication events out of chromosome 1 to most other chromosomes. The results of the data mining and characterization of ORs can be accessed at the Human Olfactory Receptor Data Exploratorium Web site (http://bioinfo.weizmann.ac.il/HORDE).

Human mouse mast cell protease 7-like tryptase genes are pseudogenes

BACKGROUND

Alpha-tryptase and beta-tryptase are important clinical markers for mast cell-dependent disorders. A third family of tryptase genes on human chromosome 16 has been identified and called human mouse mast cell protease 7 (hmMCP-7)-like tryptase.

OBJECTIVE

This study was designed to determine whether these tryptase genes are expressed by human mast cells.

METHODS

A 2842-bp hmMCP-7-like tryptase gene was cloned and sequenced from a human placental genomic library. PCR and RT-PCR procedures, respectively, were used to determine whether this tryptase gene family was present in most genomes and whether it was expressed.

RESULTS

The tryptase clone was almost identical to the hmMCP-7-like tryptase II and I genes, and therefore it was called hmMCP-7-like tryptase III. All such genes encode a Gln(-3) like alpha-tryptase. They also terminate translation after amino acid 235, whereas alpha- and beta-tryptase genes each encode a 275-amino acid protein. In this study, cell lines HMC-1, KU812, and Mono-Mac-6; mast cells derived in vitro from cord blood and fetal liver progenitors; and mast cell-enriched preparations of dispersed skin and lung cells contained hmMCP-7-like tryptases in their genomes by PCR with gene-specific primers. To identify whether such genes were transcriptionally active, RT-PCR revealed alpha- or beta-tryptase products in all mast cell preparations and cell lines and in activated skin-derived mast cells, but no hmMCP-7-like tryptase products.

CONCLUSION

These results indicate hmMCP-7-like tryptase (I, II, III) genes are pseudogenes and unlikely to affect measurements of alpha- and beta-tryptases.

New world, but not Old World, monkeys carry several genes encoding beta-microseminoprotein

It was shown by Southern hybridization that cotton-top tamarin and common marmoset, New World monkeys, carry three or more genes encoding beta-microseminoprotein, also known as PSP94. In contrast, the genomes of Old World monkeys, as represented by rhesus macaque and sacred baboon, contain a single gene. Clones containing three different genes encoding beta-microseminoprotein were isolated from a cotton-top tamarin genomic library. They carry two complete genes of four exons and a third gene lacking the first exon. The structure suggests that the three genes are functionally active and give rise to transcripts that are approximately 86% similar in sequence. By sequencing one gene in full, it was shown that the introns carry an excess of interspersed repeats, on average 29% of the introns consist of Alu repeats. A phylogenetic analysis demonstrated that the genes probably arose in New World monkeys after the separation from Old World primates.

A set of highly conserved RNA-binding proteins, alphaCP-1 and alphaCP-2, implicated in mRNA stabilization, are coexpressed from an intronless gene and its intron-containing paralog

Gene families normally expand by segmental genomic duplication and subsequent sequence divergence. Although copies of partially or fully processed mRNA transcripts are occasionally retrotransposed into the genome, they are usually nonfunctional ("processed pseudogenes"). The two major cytoplasmic poly(C)-binding proteins in mammalian cells, alphaCP-1 and alphaCP-2, are implicated in a spectrum of post-transcriptional controls. These proteins are highly similar in structure and are encoded by closely related mRNAs. Based on this close relationship, we were surprised to find that one of these proteins, alphaCP-2, was encoded by a multiexon gene, whereas the second gene, alphaCP-1, was identical to and colinear with its mRNA. The alphaCP-1 and alphaCP-2 genes were shown to be single copy and were mapped to separate chromosomes. The linkage groups encompassing each of the two loci were concordant between mice and humans. These data suggested that the alphaCP-1 gene was generated by retrotransposition of a fully processed alphaCP-2 mRNA and that this event occurred well before the mammalian radiation. The stringent structural conservation of alphaCP-1 and its ubiquitous tissue distribution suggested that the retrotransposed alphaCP-1 gene was rapidly recruited to a function critical to the cell and distinct from that of its alphaCP-2 progenitor.

Characterization and localization to chromosome 7 of psihGABPalpha, a human processed pseudogene related to the ets transcription factor, hGABPalpha

GABP is a heteromeric transcription factor complex which consists of the ets related protein, GABPalpha, and the Notch-related protein, GABPbeta. We isolated a human genomic DNA fragment which is highly homologous and colinear with human GABPalpha cDNA, but which lacks introns. This processed pseudogene, psihGABPalpha, is expressed as RNA in U937 human myeloid cells, but a mutation at the site that corresponds to the ATG start methionine codon prevents its translation into protein. The pseudogene was localized to chromosome 7 using a somatic cell hybrid mapping panel and it is not syntenic with authentic GABPalpha, which was localized to chromosome 21. We have identified psihGABPalpha, a novel, GABPalpha-related processed pseudogene which is expressed as a RNA transcript in human myeloid cells.

Transcriptional analysis of the PTEN/MMAC1 pseudogene, psiPTEN

PTEN/MMAC1 is a recently characterized tumor suppressor. A pseudogene derived from the human PTEN/MMAC1 phosphatase, psiPTEN, has been reported. Recent analysis of the pseudogene revealed conflicting results about the expression of psiPTEN. In this study, we show that the PTEN/MMAC1 pseudogene is actively transcribed in all cells and tissues examined. In some cases, pseudogene transcripts were found to represent as much as 70% of the total PTEN/MMAC1 RNA. As psiPTEN is transcribed, there is a potential for misinterpretation of PTEN/MMAC1 mutations when RT-PCR techniques are used, as well as potential for a psiPTEN-encoded translation product. Although we were unable to detect a pseudogene protein product in the cell lines examined, a baculovirus produced GST pseudogene fusion protein exhibited phosphatase activity comparable to wild type. The results of this study, taken together, indicate the potential complication of PTEN/MMAC1 molecular analysis caused by the expression of psiPTEN.

Cloning, mRNA localization and evolutionary conservation of a human 5-HT7 receptor pseudogene

Initial experiments designed to clone novel serotonin receptor subtypes in the substantia nigra have led to the discovery of a transcribed human 5-HT7 receptor pseudogene that is expressed in a wide range of tissues. The original clone (S771) possessed greater than 90% homology to the 5-HT7 receptor sequence and was identified by a degenerate PCR approach. Expression of the pseudogene transcript was detected throughout the brain and peripheral tissues in general agreement with 5-HT7 mRNA localization. Interestingly, the transcript was detected in tissues not known to express the 5-HT7 receptor (i.e. liver and kidney). Analysis of genomic DNA explained the genesis of the human pseudogene via a processed parental transcript (retrotransposition) and led to the discovery of a species homologue in the rhesus monkey.

cDNA cloning of two splice variants of a human copper-containing monoamine oxidase pseudogene containing a dimeric Alu repeat sequence

Two alternatively spliced transcripts, psiHLAO1 and psiHLAO2, of a copper-containing monoamine oxidase pseudogene have been isolated from a human-liver cDNA library. The larger psiHLAO1 cDNA (2073bp) contains a 5'-flanking segment of 134bp, followed by an apparent open reading frame (ORF) of 1725bp. The deduced amino acid sequence of this ORF (574 residues) shares 81.0% similarity with the 763-residue monoamine oxidase from human placenta (HPAO) (the N-terminal 533 residues of psiHLAO1 share 86.7% similarity with HPAO). The psiHLAO1 ORF is interrupted by an in-frame stop codon corresponding to amino acid 225 and terminates within a type S(a) dimeric Alu repeat sequence. psiHLAO2 appears to be an alternatively spliced variant of psiHLAO1 that has 413 bases of psiHLAO1 excised according to the 'GT-AG' rule. The slightly longer 3' end of the psiHLAO2 transcript shows that the Alu repeat is followed by an 11-bp poly(A) tract that, in turn, is followed by an AT-rich (81%) sequence of 105bp. A reverse transcriptase-polymerase chain reaction (RT-PCR) protocol was used to confirm that both psiHLAO1 and psiHLAO2 are transcribed in human liver and placenta. A search of the expressed sequence tag (EST) database indicates that, like HPAO, psiHLAO derives also from the region 17q21 of the human genome.

A phosphoglycerate mutase brain isoform (PGAM 1) pseudogene is localized within the human Menkes disease gene (ATP7 A)

We have identified a phosphoglycerate mutase brain isoform (PGAM 1, PGAM B) cDNA that is localized between exons 1 and 2 of the Menkes disease gene (ATP7 A, MNK) at Xq13.3. The cDNA shows 98% identity to the previously identified PGAM 1 cDNA (Sakoda et al., J. Biol. Chem. 263 (1988) 16899-16905) and probably represents a recent retroposition of this parent PGAM 1 mRNA. Although the typical features of a processed pseudogene are present, the open reading frame (ORF) of this PGAM cDNA is potentially expressed. There are 11 bp changes in the 765 bp ORF, none of which are nonsense mutations or deletions. The region upstream from the ORF shows some features of a possible promoter region, although it lacks a CpG island often associated with functional promoters. We analyzed the expression of this PGAM 1 cDNA using RT-PCR followed by restriction enzyme digestion based on a 1 bp missmatch in this cDNA to distinguish it from normal PGAM 1 gene expression. With this sensitive method, we could not find expression in any of the tissues examined. Taken together, we conclude that the PGAM 1 cDNA upstream from exon 2 of the Menkes gene is likely to be a processed pseudogene originating from a very recent retroposition of a PGAM 1 transcript. To our knowledge this is the first report of a pseudogene located within a gene.

An unprocessed pseudogene of inducible nitric oxide synthase gene in human

Inducible nitric oxide synthase (iNOS or NOSII) is one of three distinct NOS isoforms in human. The NOSII isoform is expressed in a variety of cells and tissues in response to endotoxins and cytokines. The human genome contains at least two loci for the NOSII gene, one of which (NOSII-1) has previously been assigned to proximal region of the long arm (cen-q11.2 or q11.2-q12) or to pericentric (p11-q11) regions of chromosome 17. The present study, carried out using fluorescence in situ hybridization (FISH) method, shows that a pseudogene gene (NOSII-2) is mapped to chromosome 17q11.2 site. The NOSII-2 sequence contains the exon and intron sequences present in NOSII-1 but with several mutations such as single base substitutions, additions, and deletions. Additionally, the NOSII-2 sequence also contains an incomplete reductase domain which corresponds only to the cofactor binding sites without the oxygenase domain that carry heme and substrate binding sites. NOSII-2, therefore, appears to be an unprocessed pseudogene, which cannot be translated to a functional enzyme because of its incomplete sequences and mutations.

Molecular genetic analysis of a human neuropeptide Y receptor. The human homolog of the murine "Y5" receptor may be a pseudogene

Neuropeptide Y is a 36-amino-acid peptide amide with numerous biological activities. These functions are mediated through several pharmacologically distinct receptors. To date five receptor subtypes have been cloned. Here we report the isolation, by low stringency homology cloning from a hypothalamic library, of a cDNA encoding the human homolog of the murine neuropeptide Y receptor subsequently reported (). Translation of the human Y1-like receptor clone suggested that it encoded a receptor which is truncated in the third extracellular loop. Comparison of the human Y1-like sequence to that of the human Y1 receptor suggested that the truncated receptor could have resulted from a frameshift due to a single nucleotide deletion in the sixth transmembrane domain. Southern blot analysis suggested that the gene is single copy in the human genome. The gene is located on chromosome 5q. To test the hypothesis that allelic variation of nucleic acid length within the sixth transmembrane domain of the Y1-like receptor may exist to produce a functional receptor, genomic DNA from 192 individuals of various ages, ethnic backgrounds, and degrees of obesity were analyzed electrophoretically and by direct sequencing. No variation was detected in any of the subjects, indicating that this receptor subtype may be a transcribed pseudogene in humans.

Cloning, sequencing, and chromosomal localization of two tandemly arranged human pseudogenes for the proliferating cell nuclear antigen (PCNA)

We have characterized a human genomic clone carrying two pseudogenes for the proliferating cell nuclear antigen (PCNA), which were tandemly arranged on human Chromosome (Chr) 4. One is a processed pseudogene that showed a 73% nucleotide homology to the human PCNA cDNA and possessed none of the introns existing in the functional PCNA gene. This pseudogene presumably arose by reverse transcription of a PCNA mRNA followed by integration of the cDNA into the genome. The other is a 5' and 3' truncated pseudogene that showed a nucleotide homology to a 3' region of the exon 4 and to a 5' region of the exon 5 of the PCNA gene and did not have the intronic sequence between the exons 4 and 5. Both pseudogenes had the same nucleotide deletion as compared with the human functional PCNA gene. A phylogenetic analysis of PCNA gene family, including the functional PCNA gene and another PCNA pseudogene located on a different chromosome, revealed that the truncated pseudogene exhibits the closest evolutionary relationship with the processed pseudogene, suggesting that the truncated pseudogene was generated by duplication of the processed pseudogene after translocation to Chr 4. Furthermore, fluorescence in situ hybridization revealed that these pseudogenes are located on the long arm of Chr 4, 4q24.

Cloning and sequence of a processed p53 pseudogene from rat: a potential source of false 'mutations' in PCR fragments of tumor DNA

We describe here the nucleotide (nt) sequence of a p53 processed pseudogene (psi-gene) from the normal F344 rat genome. Exon-derived primers were utilized to amplify and clone a 1447-bp polymerase chain reaction (PCR) product corresponding to the coding regions of exons 2-11 of the functional gene. This psi-gene is a cDNA-like sequence possessing 87% homology with the functional rat p53. We have also partially characterized two additional and distinctly different putative rat p53 psi-genes, focussing on the sequences surrounding the reported rat p53 mutational hot spots of codons 202R and 211R within exon 6/7. Each of these three psi-gene sequences contained various single- and/or double-nt substitutions, small deletions and insertions that distinguish them from p53. One substitution, 211R CGG-->CAG, found both in the cloned psi-gene and in one of the partially characterized, putative psi-genes, corresponded precisely with the sequence that has been reported as a mutation at one of the hot spots. Co-amplification of one or more of the p53 psi-genes with portions of the functional p53 is likely, if exon-based primers are utilized for PCR amplification of rat p53. Consequently, psi-gene sequences are potential sources of sequence variations that can be misidentified as somatic cell mutations by direct sequencing of inappropriately generated PCR products.

Characterization of a processed pseudogene of human FAU1 on chromosome 18

A member of the human FAU (Finkel-Biskis-Reilly murine sarcoma virus-associated ubiquitously expressed) gene subfamily, encoding the ribosomal protein S30 fused in frame to an ubiquitin-like protein, was cloned, sequenced and analysed. This clone, FAU1P, is a processed pseudogene with a completely intact, although transcriptionally silent, open reading frame of 137 codons. FAU1P exhibits an amplification of the (AAG) triplet repeat present in the S30 coding part of FAU. FAU1P is integrated in an antisense orientation within a sequence homologous to the promoter of the islet amyloid polypeptide (IAPP or amylin)-encoding gene. By means of PCR hybrid panel mapping, FAU1P was assigned to chromosome 18.

Isolation of the rat F1-ATPase inhibitor gene and its pseudogenes

Multiple mitochondrial ATPase inhibitor genes have been identified in the rat-genome. The sequences of two genomic clones indicate that one encodes the functional gene, and the other is a processed pseudogene. The ATPase inhibitor gene isolated is about 1.5 kb long and the coding region contains three exons and two introns. The presence of multiple pseudogenes in the rat is suggested by this study and this is unique since in the bovine genome only a single gene has been found, which is also confirmed here. The presence of multiple inhibitor transcripts in the rat suggests that the functional gene might have multiple transcriptional start sites.

Characterization of the cDNA and three processed pseudogenes from the murine protein kinase CK2 alpha subunit

Seven protein kinase CK2 alpha clones were isolated from a murine genomic DNA library. They were assigned to four different genomic loci (A,B,C,D). Locus D was previously identified as a processed pseudogene (Boldyreff et al. (1992) Biochem. Biophys. Res. Commun. 186, 723-730). Here we present sequences of genomic loci B and C and the murine CK2 alpha cDNA. Loci B and C are like locus D processed pseudogenes, however, with considerable differences among each other and to the cDNA, especially with respect to the lengths of the putative gene products. Genomic locus D would code for a protein of 82 amino acids, locus B for a protein of 132 amino acids and locus C product for the full length product of 391 amino acids as the murine cDNA.

The mammalian genome shaping activity of reverse transcriptase

Reverse transcriptase catalyses the conversion of RNA into DNA. This operation seems to have largely contributed to the evolution of complex genomes. More than 10% of a mammalian genome is composed of sequences with reverse transcribed origin, most of which consists of repeated sequences (SINEs, LINEs). In spite of their simplicity, these sequences can play a key role in evolution by favoring illegitimate recombination. In addition to this abundant material, retrotransposed sequences include retrotransposons, retroviruses and genes depleted from intervening sequences, known as pseudogenes. Some of these sequences can be functional or involved in the regulation of neighbouring genes. These hallmarks of reverse transcription activity indicate that it has largely contributed to the fluidity of modern genomes.

The human prothymosin alpha gene family contains several processed pseudogenes lacking deleterious lesions

The six members of the human prothymosin alpha gene family have been cloned and sequenced. One gene (PTMA) contains introns and appears to be the source of all isolated prothymosin alpha cDNAs. The remaining five genes are processed pseudogenes. Four of them have consensus TATA elements upstream of sequences nearly identical to the transcriptional start region of the intron-containing gene. Those four genes also contain open reading frames coding for proteins closely related to prothymosin alpha. In two of the pseudogenes, PTMAP2 and 5, the encoded proteins differ from the product of the parental gene at only two and four locations, respectively. The fifth pseudogene (PTMAP1) encodes a different protein owing to an upstream translational initiation start site and multiple deletions and insertions. Because the potential for expression exists in this system, a search for pseudogenomic transcripts was undertaken using the polymerase chain reaction to amplify reverse transcripts of mRNAs from many human tissues and bulk DNA from several human cDNA libraries. Evidence for pseudogenomic transcripts was not obtained. Therefore, we conclude that the human prothymosin alpha gene family contains only one functional gene.

Isolation and characterization of a sheep cysteine-rich cuticle keratin pseudogene

The cysteine-rich keratin proteins of the hair cuticle are derived from a multigene family that has been highly conserved during mammalian evolution. We have recently characterized one cuticle keratin gene isolated from a sheep lambda library, and Southern blot analysis of that clone suggested the presence of a second related gene. In the present paper sequencing of the second gene has now indicated that it is a pseudogene, a finding supported by a lack of expression in vivo. The pseudogene appears to have arisen by gene duplication, possibly from the adjacent functional gene. Key mutations seem to have occurred in the promoter and processing signals of this gene to render it non-functional and two in-frame termination codons are present in the coding region. A possible recombination point between sequences encoding glycine-rich repeats was identified that could have lead to the creation of the in-frame termination codons.

Processed pseudogenes in Drosophila

Two species of Drosophila, D. yakuba and D. teissieri, possess pseudogenes of Adh. These pseudogenes lack introns and map to chromosome arm 3R, rather than to chromosome arm 2L, wherein are located the functional Adh genes. Their structure suggests that the pseudogenes arose from reverse transcripts. Because the pseudogenes map to homologous sites in both species, they presumably arose before these species diverged. Remarkably, the pattern of base substitution in the pseudogenes differs between sites that correspond to degenerate and non-degenerate codon positions in their functional paralogs.

Nucleotide sequences and novel structural features of human and Chinese hamster hsp60 (chaperonin) gene families

A number of clones that specifically hybridize to the human hsp60 cDNA (chaperonin protein; GroEL homolog) were isolated from human and Chinese hamster ovary cell genomic libraries. DNA sequence analysis shows that one of these clones, pGem-10, is completely homologous to the human hsp60 cDNA (in both coding and noncoding regions) with no intervening sequences. The other human clones analyzed were all nonfunctional pseudogenes containing numerous small additions, deletions, and base substitutions, but no introns. On the basis of sequence data, six different hsp60 pseudogenes were identified in human cells. In addition, we also cloned and completely sequenced a genomic clone from CHO cells. This clone, which was also a pseudogene, contained a small 87-nucleotide intron near the 3' end. Southern blot analysis of human, mouse, and Chinese hamster DNA, digested with unique restriction enzymes (no sites in cDNA), indicates the presence of about 8-12 genes for hsp60 in the vertebrate genomes. The sequence data, however, suggest that most of these genes, except one (per haploid genome), are likely to be nonfunctional pseudogenes.

Analysis of the human ornithine aminotransferase gene family

Ornithine aminotransferase is a mitochondrial matrix enzyme that is deficient in patients with gyrate atrophy, an autosomal recessive disease of the eye. Southern blots of human DNA probed with a previously characterized OAT cDNA showed a complex pattern of gene fragments, suggesting a gene family. Hybridization of these blots with 5' and 3' OAT cDNA probes indicated that there are at least three to four copies of the OAT (approximately 22 kbp) and OAT-related gene sequence(s). We have isolated and partially characterized human OAT gene clones from total genomic and X-chromosome DNA libraries. Sequence analysis confirmed the following previously reported findings on the functional OAT gene: 11 exons, ten introns, an atypical TATA box (TTTAA), two CCAAT boxes, several GC-rich binding sites, 5' sequence homologous to SV40 enhancer core sequence (GTGGA/GA/GA/GG) and promoter region of three urea cycle enzymes (GTATCCTGCCCTC). In addition, we extended the OAT gene sequence in both the 5' and 3' directions and found its promoter region also contained a sequence homologous to the progesterone receptor (TGTTCA/TCC/T), several of the glucocorticoid responsive element (AGAACA), a cyclic AMP-responsive element (TGACGTCG), and recognition motifs for transcription factors AP-2, NF1 and Sp1. Partial sequence analyses of X-chromosome clones demonstrated an intron-less pseudogene with 77% identity to the functional OAT gene. These results demonstrate that the OAT gene is a gene family that contains both functional and related OAT gene sequence(s).

Absence of reverse transcriptase activity in human diploid fibroblasts

The reverse flow of genetic information from RNA transcripts to DNA has been postulated to be the mechanism for the generation of pseudogenes, dispersed repetitious DNA families, and small extrachromosomal circular DNAs in eukaryotic cells. We were unable to detect reverse transcriptase-like activity in several strains of cultured human cells, with or without induction by a variety of chemical and physical agents known to induce latent retroviruses.

Subfamily structure and evolution of the human L1 family of repetitive sequences

Comparative analysis of the available 3'-portions of the human L1 (LINE-1) family of repeated sequences indicates that all the sequences can be classified in two major subfamilies. The division is based on patterns of diagnostic bases shared within L1 subfamilies of sequences but differing between them. The overall ratio of replacement to synonymous positions, occupied by the diagnostic bases in the large open reading frame of the L1 sequence, is 1.15. This indicates that both subfamilies were obtained from genes coding for functional proteins. The L1 subfamilies appear to be of different ages and may represent a "fossil record" of the same active gene at different times in the history of primates. The younger subfamily can be split further into at least two closely related branches of sequences. The above facts combined with the recent data for the Alu subfamily structure show that LINE and SINE families of interspersed repeats share discontinuous patterns in their evolution. These data are consistent with the model that both Alu and L1 families, as well as other pseudogene families, contain active genes producing discrete layers of pseudogenes throughout the history of primates. Models of evolutionary processes that could generate these discontinuities are discussed together with the possible biological role of Alu and L1 genes.

A mouse thymidylate synthase pseudogene derived from an aberrantly processed RNA molecule

A DNA fragment containing a mouse-thymidylate-synthase(TS) processed pseudogene was cloned and analyzed. Comparison with the sequences of the mouse TS-encoding gene (ts) and cDNA revealed that the pseudogene started at one of the normal 5' termini of TS mRNA, ended with a poly(A) tail, and was flanked by 16-nucleotide (nt) direct repeats. The region corresponding to the open reading frame was 97.3% identical to that of the cDNA. Two unusual features were observed. First, the poly(A) tail of the pseudogene was located 2 kb downstream from the normal location. Second, the final 10 nt of intron 5 were retained in the 'coding region' of the pseudogene. Therefore, it appears that the pseudogene was derived from a nonfunctional TS 'mRNA' that was aberrantly spliced and polyadenylated. Analysis of the sequence of intron 5 of the ts gene revealed the presence of an alternative 3' splice site 10 nt upstream from the normal splice site. S1-nuclease protection assays showed that about 10% of TS mRNA isolated from mouse cells was spliced at the alternative site.

A capripoxvirus pseudogene whose only intact homologs are in other poxvirus genomes

Equivalent regions from within the inverted terminal repeats (ITRs) of the genomes of two capripoxviruses, KS-1 and InS-1, were sequenced. The sequence from KS-1 DNA covers the major part of three contiguous open reading frames (ORFs), which match three contiguous ORFs from within the genomic ITRs of the leporipoxvirus Shope Fibroma Virus (SFV). The sequenced region of InS-1 DNA contains only two of the three ORFs. The region homologous to the third ORF has no coding potential due to the presence of several stop codons, resulting from small frameshifting deletions and insertions. The significance of a degenerate poxvirus gene, intact homologs of which are only found in other poxvirus genomes, is discussed.

Genomic organization of human 5 S rDNA and sequence of one tandem repeat

An organization of human 5 S rDNA repeats is inferred from Southern analyses of restriction digests of genomic DNA fractionated by pulsed-field and conventional gel electrophoreses. A single unit of 2.2 kb is repeated approximately 90 times within a 200-kb fragment (defined by enzymes that do not cleave within individual units, i.e., EcoR1, BglII, HindIII, and PvuII); a comparable number of 5 S sequences are scattered elsewhere in the genome. A lambda clone containing six complete 5 S repeats was obtained from a human placental DNA library. One repeat contains 2231 bp and includes poly(dG-dT).(dC-dA), tracts of polypyrimidine, and an Alu sequence in the spacer region. Also, 5-S-hybridizing clones, containing DNA inserts with an average size of 250 kb, have been obtained as yeast artificial chromosomes. Thus far, four clones have been partially characterized and shown to be 5 S sequences from loci separate from the tandem repeat units.

The keratin BIIIB gene family: isolation of cDNA clones and structure of a gene and a related pseudogene

The nucleotide sequence of cDNA clones encoding the three major BIIIB high-sulfur wool keratin proteins (BIIIB2, 3, and 4) and the structure of a BIIIB4 gene and a BIIIB3 pseudogene are reported. Although Southern blot analysis indicates that the BIIIB genes comprise a multigene family in the sheep genome, they are poorly represented in genomic DNA libraries. The family sequence homology of the coding region extends into the 5' and 3' untranslated regions and the near 5' flanking region of the BIIIB3 and 4 genes. These homologies suggest that the BIIIB3 and 4 genes represent the latest gene duplication event in the evolution of the BIIIB multigene family. Like the genes coding for other wool keratin matrix protein components, the BIIIB genes have the conserved 18-bp sequence immediately 5' to the initiation codon and also appear to lack introns.

Characterization, evolutionary relationships, and chromosome location of processed mouse HPRT pseudogene

Studies on a cell line with amplified copies of the mouse hypoxanthine-guanine phosphoribosyltransferase (HPRT) gene and HPRT gene transfer experiments revealed the existence of a nonfunctional HPRT-related sequence in the mouse genome. This sequence was isolated and found to be a processed HPRT pseudogene. With the exception of a small internal deletion, the pseudogene is believed to comprise a complete reverse transcript of HPRT mRNA, although the 3' end of the pseudogene was lost in the cloning process. A probe from a region flanking the mouse pseudogene was used to investigate the evolutionary relationships of mammalian HPRT pseudogenes. The pseudogenes in mouse and Chinese hamster appear to have a common origin, but no homology to any of the four known human HPRT pseudogenes was detected. A pseudogene-linked restriction fragment length polymorphism was used to map the pseudogene to the distal end of mouse chromosome 17.

Primary structure of a C-hordein gene from barley

The nucleotide sequence of a 2065 base pair HindIII fragment, containing a gene (lambda hor1-14) belonging to the Hor1 locus in barley, has been determined. The fragment consists of 1044 bp of coding region interrupted by an amber codon at base 481, a 5' non-coding region of 428 bp and a 3' non-coding region with 593 bp. The deduced amino acid sequence of the mature protein (327 amino acids) is characterized by an octapeptide motif PQQPFPQQ which is repeated throughout the peptide chain between a unique 12 amino acid long NH2-terminal and an equally unique 10 amino acid long COOH-terminal end. The proline + glutamine content is 62% and the next three most abundant amino acids are leucine (9%), phenylalanine (8%) and isoleucine (3%). In the 5' non-coding region there is a TATA box at -98 bp from the start methionine. The 3' non-coding region has a polyadenylation signal 76 bp downstream from the TAA stop codon. The deduced amino acid sequences of the NH2- and COOH-terminals of lambda hor1-14 are very similar but not identical to those known from the Edman degradation and carboxypeptidase Y analysis of C-hordein polypeptides. The 3' coding and non-coding region of lambda hor1-14 is closely similar but different in detail to the known C-hordein cDNA clones. One polyadenylation signal is found in lambda hor1-14 whereas two are present in each of the three known C-hordein cDNAs. These differences and the amber codon interrupting the open reading frame indicate that this gene is silent.

Characterization of mouse H3.3-like histone genes

We designed a strategy to select genomic clones of mouse replication-independent H3.3 histone genes. We obtained three clones which met our selection criteria for being H3.3 genes. Upon sequencing two of these clones we found that they were unlike previously isolated chicken H3.3 clones: they code for several unpredicted amino acid substitutions and contain no introns in the coding regions. We showed by S1 nuclease assays that these genes are protected by mRNAs that have expression characteristics of H3.3 mRNA. The protection data and nucleotide sequence analysis show that the H3.3 transcripts can be processed at one of four cleavage/polyadenylation sites. We show that these genes probably evolved through reverse transcription intermediates, and are processed pseudogenes which are no longer under selective pressure. The 5' and 3' transcribed, nontranslated sequences show extensive homology to those of a human cDNA clone, and we suggest that these sequences may be required for appropriate regulation of expression of H3.3 genes.