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Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?

Bovine seminal ribonuclease (RNase) diverged from pancreatic RNase after a gene duplication ca. 35 million years ago. Members of the seminal RNase gene family evidently remained as unexpressed pseudogene for much of its evolutionary history. Between 5 and 10 million years ago, however, after the divergence of kudu but before the divergence of ox, evidence suggests that the pseudogene was repaired and expressed. Intriguingly, detailed analysis of the sequences suggests that the repair may have involved gene conversion, transfer of information from the pancreatic gene to the RNase pseudogene. Further, the ratio of non-silent to silent substitutions suggests that the pancreatic RNases are divergently evolving under functional constraints, the seminal RNase pseudogenes are diverging under no functional constraints, while the genes expressed in the seminal plasma are evolving extremely rapidly in their amino acid sequences, as if to fulfil a new physiological role.

Amino Acid Sequence↗

Seventeen copies of the human 37 kDa laminin receptor precursor/p40 ribosome-associated protein gene are processed pseudogenes arisen from retropositional events.

A cDNA coding for a 37 kDa polypeptide has been identified in several species as both the potential precursor of the 67 kDa laminin receptor (37LRP) and a putative ribosome-associated protein (p40). Interestingly, increased expression of this polypeptide (37LRP/p40) is consistently observed in invasive and metastatic cancer cells and is associated with poor prognosis. Southern-blot analysis of human genomic DNA predicted multiple copies of the 37LRP/p40 gene. In this study, we report that the number of copies of this sequence in the human genome is 26 +/- 2. We have sequenced and analyzed 19 genomic clones corresponding to the 37LRP/p40 gene and found that they were all processed pseudogenes. They all lack intronic sequences and show multiple genetic alterations leading in some cases to the appearance of stop codons. Moreover, they all bear characteristic features of retroposons as the presence of a poly(A)-tail at their 3' end and short direct repeated flanking DNA sequences. None of the pseudogenes analyzed present cis-elements in their 5' flanking region such as TATA or GC boxes. Our date reveal that over 50% of the 37LRP/p40 gene copies are pseudogenes most probably generated by retropositional events. The finding of multiple pseudogenes for the 37LRP/p40 suggests that the accumulation of several copies of this gene might have given a survival advantage to the cell in the course of evolution.

Base Sequence↗

Repetitive nucleotide sequence insertions into a novel calmodulin-related gene and its processed pseudogene.

A gene containing a transposon-like human repeat element, called THE 1, has been isolated and characterized. The gene, termed T+, encodes a polypeptide resembling known calcium-binding proteins. The THE 1 element is present in the 3'-untranslated region of its message. The cDNA clone corresponding to the gene's mRNA product led to the identification of this gene. A processed RNA pseudogene related to the authentic gene has also been isolated. In addition to intron processing, this pseudogene differs from the gene in that it contains an interspersed Alu repeat instead of a THE 1 element in the 3'-untranslated region. Thus, we compare a site containing a THE 1 element to an ancestrally related transposon-less target site. The comparison suggests a retroviral-related mechanism of THE 1 insertion. This system is unusual in that the parent gene is associated with three distinct retrotransposition events: the parent gene was converted to a processed RNA pseudogene, an Alu repeat inserted into the pseudogene, and a THE 1 element inserted into the parent gene.

Amino Acid Sequence↗

Novel use of a chimpanzee pseudogene for chromosomal mapping of human cytochrome c oxidase subunit IV.

We have isolated a chimpanzee processed pseudogene for subunit IV of cytochrome c oxidase (COX; EC 1.9.3.1) by screening a chimpanzee genomic library in lambda Charon 32 with a bovine liver cDNA encoding COX subunit IV (COX IV), and localized it to a 1.9-kb HindIII fragment. Southern-blot analysis of genomic DNA from five primates showed that DNAs from human, gorilla, and chimpanzee each contained the 1.9-kb pseudogene fragment, whereas orangutan and pigtail macaque monkey DNA did not. This result clearly indicates that the pseudogene arose before the divergence of the chimpanzee and gorilla from the primate lineage. By screening Chinese hamster x human hybrid panels with the human COX4 cDNA, we have mapped COX4 genes to two human chromosomes, 14 and 16. The 1.9-kb HindIII fragment containing the pseudogene, COX4P1, can be assigned to chromosome 14, and by means of rearranged chromosomes in somatic cell hybrids, to 14q21-qter. Similarly, the functional gene, COX4, has been mapped to 16q22-qter.

Amino Acid Sequence↗

The ornithine aminotransferase-encoding gene family of rat: cloning, characterization, and evolutionary relationships between a single expressed gene and three pseudogenes.

As a first step towards understanding the molecular mechanisms through which the expression of the gene (OAT) encoding ornithine aminotransferase (OAT) is regulated in a tissue-specific manner, we have used a near full length OAT cDNA to isolate related sequences from a rat genomic DNA library. Twenty-one unique clones representing five contigs and spanning approximately 140 kb of genomic DNA were isolated and characterized. From these clones we have identified a single expressed OAT gene and three processed pseudogenes. The comparison of the EcoRI, BamHI, and HindIII fragments contained within these genomic clones with those detected in total genomic DNA by the cDNA probe suggests that essentially all of the OAT-related sequences in the rat genome have been isolated. Thus, the tissue-specific regulation of OAT gene expression appears to be effected through a single expressed gene. Data are presented which suggest that the OAT-1, OAT-2, and OAT-3 pseudogenes arose approximately 28.5, 7.3, and 25.1 Myr ago, respectively. Mutation rates are presented for each codon position of the expressed rat and human OAT genes. The region of the rat genome flanking the boundary of the OAT-3 pseudogene is of additional interest as it shares considerable identity to sequences contained within expressed genes and flanking other processed pseudogenes.

Animals↗

Characterization of a processed pseudogene derived from the gene encoding bovine adenylate kinase isozyme 2.

We have isolated an intronless processed pseudogene for an isoform of bovine adenylate kinase isozyme 2 (AK2B). The pseudogene which was flanked by 11-nucleotide (nt) direct repeats contained an open reading frame of 519 bp which encodes 173 amino acids (aa), 61 aa shorter than AK2B. In the entire pseudogene sequence, substitutions as well as deletions and insertions were noted in 78 nt positions as compared with the AK2B cDNA (95.1% homology). Northern-blot analysis showed that this pseudogene was not expressed in bovine tissues.

Adenylate Kinase↗

A rabbit AldA pseudogene derived from a partially spliced primary aldolase A transcript.

The entire AldA processed pseudogene of rabbit was isolated and characterized. The pseudogene encodes the C-terminal portion of the protein from amino acids (aa) 126-363. There are deletions, insertions and nucleotide (nt) substitutions distributed throughout the 931 bp of identity shared with the 1.4-kb mRNA. There are 21 replacement codon substitutions, including a clearly deleterious change in the stop codon. This processed pseudogene has several uncommon features: (i) it has a 5'-boundary coincident with an intron/exon junction and does not encode the entire mRNA, (ii) there is a broken direct repeat that overlaps the region of shared identity with the mRNA rather than flanking it, and (iii) there is no poly(A) sequence. This processed pseudogene probably arose by integration of a DNA copy of a partially spliced primary transcript. The structure of this gene has added implications for the timing of posttranscriptional processing events.

Amino Acid Sequence↗

Cloning, sequencing and phylogenetic analysis of a human 5-hydroxytryptamine 1D receptor pseudogene.

A third member of the human 5HT1D gene family has been identified using a combination of homology cloning and DNA sequence analysis. This human gene is most related to the 5HT1D alpha subtype (77% shared identity) and is a pseudogene, based on the lack of an open reading frame (ORF) caused by multiple in-frame stop codons and nucleotide (nt) deletions relative to the functional 5HT1D alpha gene (encoding the 5-hydroxytryptamine 1D alpha receptor). The 5HT1D pseudogene also contained an insertion that shares 87% identity to the Alu consensus sequence. Phylogenetic analysis of the three human genes in this family reveals that although the two functional genes, 5HT1D alpha and 5HT1D beta, are detected in all mammalian species examined, the 5HT1D pseudogene is only detected in a subset of primates (catarrhines) that evolved approximately 35-45 million years (Myr) ago. Alternatively, based on the 23% divergence between the functional 5HT1D alpha gene and the 5HT1D pseudogene, we estimate that these two genes began to diverge approximately 50 Myr ago.

Amino Acid Sequence↗

A novel transcript from a pseudogene for human glucocerebrosidase in non-Gaucher disease cells.

Human glucocerebrosidase (GC)-encoding cDNA clones were isolated from a promyelocytic HL-60 cDNA library and analyzed. A novel cDNA clone was found to originate from a gene referred to as a GC pseudogene. Using the polymerase chain reaction (PCR) with primers specific for the GC pseudogene, we found that all the human cell lines examined, HL-60, K-562, WI-38, HepG2 and HeLa, expressed a pseudogene transcript. In vitro translation of RNA synthesized by transcription of the pseudogene cDNA produced a polypeptide of approximately 30 kDa.

Amino Acid Sequence↗

Conservation of sequences between human and gorilla lineages: ADP-ribosyltransferase (NAD+) pseudogene 1 and neighboring retroposons.

The evolution of ADP-ribosyltransferase (NAD+) pseudogene 1 (ADPRTP1) was studied among higher primates. When the human pseudogene was used to probe genomic DNA from chimpanzee, gorilla, macaque, howler monkey and lemur, a fragment from gorilla produced the most intense hybridization signal. The resultant hybridization pattern indicated a modified pseudogene structure in these primates relative to the human and gorilla loci. Sequence comparison of this new DNA locus (ADPRTP1 and surrounding retroposons) showed a nucleotide (nt) identity of 98.13% (over 5.8 kb) between the genomic regions of human and gorilla. A unique duplicated region of 30 base pairs (bp) was found in gorilla ADPRTP1, separate from the duplicated region (193 bp) responsible for the restriction-fragment length polymorphism (RFLP) previously reported in humans, and which appeared to represent a marker for a predisposition to cancer. An endogenous pol (gene encoding polymerase) related element that flanked the human pseudogene was used as a probe to identify a fragment from this retroviral family in New World monkeys. Altogether, analysis of these retroposons will provide an opportunity for future studies on the molecular phylogenetic relationship of higher primates.

Animals↗

Identification of a human RAD52 pseudogene located on chromosome 2.

A human testis cDNA library was screened with a hybridization probe encoding the mouse RAD52 gene. Two classes of clones were identified, one derived from the human RAD52 homolog (hRAD52), the other derived from a pseudogene. In addition to many point mutations, several of which encode stop codons, the pseudogene contains a number of frame shifts and a 103-bp deletion. We further determined that the pseudogene is processed and is located on human chromosome 2, in contrast to hRAD52 which is found on chromosome 12. Reverse transcription-PCR analysis of cultured human diploid fibroblasts, as well as fibrosarcoma cells, revealed that while hRAD52 is expressed at low, but detectable levels in these cells, the pseudogene is not.

Animals↗

Serial Alu sequence transposition interrupting a human B creatine kinase pseudogene.

We have isolated, sequenced, and characterized a single-copy B creatine kinase pseudogene. The chromosomal assignment of this gene is 16p13 and a unique sequence probe from this locus detects EcoRI restriction fragment length polymorphisms of 7.8 and 5.4 kb. In 26 unrelated individuals, the frequencies for the 7.8- and 5.4-kb B creatine kinase pseudogene alleles were calculated to be 17.3 and 82.7%, respectively. The B creatine kinase pseudogene is interrupted by a 904-bp DNA insertion composed of three Alu repeat sequences in tandem flanked by an 18-bp direct repeat, derived from the pseudogene sequence. Nucleotide sequence analysis of the Alu elements suggests that the Alu sequences were incorporated into this locus in three separate integration events. Several complex clustered Alu repeat sequences without defined integration borders have been previously identified at different genomic loci. This is the first evidence that complex tandem Alu elements can integrate in an apparently serial manner in the human genome and supports the contention that Alu repeats integrate nonrandomly into the human genome.

Animals↗

Characterization of the MCT-1 pseudogene: identification and implication of its location in a highly amplified region of chromosome 20.

The MCT-1 oncogene was initially identified as an amplified gene on chromosome Xq22-24 in a T-cell lymphoma. MCT-1 is over-expressed in a subset of diffuse large B-cell lymphoma (DLBCL), a common form of Non-Hodgkin's Lymphoma (NHL). We have identified a pseudogene for MCT-1 (PsiMCT-1) that is located on chromosome 20q11.2, a region within an amplicon containing several important genes frequently amplified in certain breast and ovarian cancers. Genomic analysis revealed that PsiMCT-1 is a processed pseudogene. Interestingly, both MCT-1 and its pseudogene are located on regions of the genome that are frequently amplified in several different human malignancies. MCT-1 is the oldest known oncogene and its insertion as a pseudogene occurred at a later time point in evolution. Existence of PsiMCT-1 should be considered when analyzing genomic amplification and or expression of MCT-1. Analysis of MCT-1 and PsiMCT-1 might provide clues to cancer genes and their evolution across species.

Amino Acid Sequence↗

Glucocerebrosidase recombinant allele: molecular evolution of the glucocerebrosidase gene and pseudogene in primates.

Glucocerebrosidase is a lysosomal enzyme that hydrolyses the beta-glycosidic linkage of glucocerebroside, a ubiquitous sphingolipid present in the plasma membrane of mammalian cells. Deleterious mutations in the glucocerebrosidase gene result in Gaucher disease, the most prevalent lysosomal storage disease. Humans have one glucocerebrosidase functional gene and pseudogene that were located 16 kb apart on chromosome 1q21 and share 96% overall sequence similarity. Recombination between the two genes creates a 'complex allele' that renders glucocerebrosidase non-functional and accounts for >20% of the total Gaucher disease mutations in some population. The glucocerebrosidase pseudogene is absent in all other mammalian species surveyed so far. In order to learn more about the molecular evolution of the glucocerebrosidase functional gene and pseudogene, we have sequenced approximately 1.1 kb of the C-terminal region of these genes that encodes the enzyme catalytic site, from PCR-amplified genomic DNA of gorilla, chimpanzee, orangutan (the great apes), and squirrel monkey (a new-world monkey). In gorilla, chimpanzee, and orangutan, there are two copies of the glucocerebrosidase gene while the squirrel monkey possesses only a single copy. Similar to human, the second copy of glucocerebrosidase gene in gorilla and chimpanzee is non-functional because of a 55-bp deletion in exon 9, while that in orangutan appears to be unaffected and may still be functional. These data suggest that the glucocerebrosidase gene duplication event occurred after squirrel monkey divergence from the great apes, and that the exon 9 deletion that rendered the second copy of the glucocerebrosidase gene non-functional occurred prior to the divergence of gorilla and chimpanzee but after the divergence of orangutan from their common ancestor to human. The two genes in each species are least similar in gorilla and chimpanzee (97.8%) and most similar in orangutan (99.5%). None of the nucleotide variations in the GBA gene among the primates correspond to known mutations in Gaucher disease. Phylogenetic tree analysis using DNAstar and PAUP4.0 software indicates that gene conversion caused the evolution of glucocerebrosidase functional gene and pseudogene to be concerted.

Alleles↗

mRNA surveillance of expressed pseudogenes in C. elegans.

Messenger RNAs (mRNAs) that contain premature translation termination codons (PTCs) are targeted for rapid degradation in all eukaryotes tested. The mechanisms of nonsense-mediated mRNA decay (NMD) have been described in considerable detail, but the biological roles of NMD in wild-type organisms are poorly understood. mRNAs of wild-type organisms known to be degraded by NMD ("natural targets" of NMD) include by-products of regulated alternative splicing, out-of-frame mRNAs derived from unproductive gene rearrangements, cytoplasmic pre-mRNAs, endogenous retroviral and transposon RNAs, and mRNAs having upstream open reading frames or other unusual sequence features. NMD may function to eliminate aberrant PTC-containing mRNAs in order to protect cells from expression of potentially deleterious truncated proteins. Pseudogenes are nonfunctional genes or gene fragments that accumulate mutations through genetic drift. Such mutations will often introduce shifts of reading frame and/or PTCs, and mRNAs of expressed pseudogenes may thus be substrates of NMD. We demonstrate that mRNAs expressed from C. elegans pseudogenes are degraded by NMD and discuss possible implications for both mRNA surveillance and protein evolution. We describe an expressed pseudogene that encodes a small nucleolar RNA (snoRNA) within an intron and suggest this represents an evolutionary intermediate between snoRNA-encoding host genes that do or do not encode proteins.

Animals↗

A processed pseudogene contributes to apparent mule deer prion gene heterogeneity.

Pathogenesis and transmission of the prion disorders (transmissible spongiform encephalopathies, TSEs) are mediated by a modified isoform of the prion protein (PrP). Prion protein gene (PRNP) alleles associated with relative susceptibility to TSE have been identified in sheep, humans and possibly elk. Comparable data have not been derived for mule deer, a species susceptible to the TSE chronic wasting disease (CWD). Initial analysis of the open reading frame (ORF) in exon 3 of the mule deer PRNP gene revealed polymorphisms in all 145 samples analyzed, with 10 potential polymorphic sites. Because 144/145 (99.3%) of the samples were heterozygous for a coding change (N/S) at codon 138 (bp 412) and a non-coding polymorphism at bp 418, and individual deer with three or four different alleles were identified a possible gene duplication was indicated. Analysis of BAC clones containing mule deer PRNP genes revealed a full length functional gene and a processed pseudogene. The pseudogene was characteristic of previously described retroelements, in that it lacks introns and is flanked by repeat sequences. Three alleles of the functional gene were identified, with coding changes only at codons 20 (D/G) and 225 (S/F). Determination of PRNP functional gene alleles from 47 CWD-positive mule deer showed the predominant allele encoded 20D225S (frequency 0.85). When alleles were grouped by coding changes in the functional gene, four of the six possible peptide combinations were identified in infected deer. Three pseudogene alleles with coding changes in exon 3 were identified in the mule deer samples examined. Because the TSEs appear to be "protein only" disorders, the presence of an untranslated pseudogene is not expected to affect disease resistance. Therefore, selection of a genotyping method specific for the functional gene is critical for large-scale studies to identify the role of the PRNP gene in susceptibility to CWD in mule deer.

Alleles↗

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.

Base Sequence↗

Isolation of novel olfactory receptor genes in marmosets (Callithrix): insights into pseudogene formation and evidence for functional degeneracy in non-human primates.

Nineteen olfactory receptor (OR) genes were isolated from three OR subfamilies in two species of marmoset (Callithrix). Olfactory receptor 912-93 has high sequence similarity among marmosets and between marmosets and humans, suggesting strong conservation of function. All of the remaining seventeen OR genes identified from subfamilies 3A and 1E were pseudogenes. Following pseudogene formation, marmoset OR genes in both 1E and 3A subfamilies underwent duplications, indel events and a high rate of nucleotide substitution. These results provide a contrast to previous studies, and show that in spite of the keen olfactory sense of marmosets, they harbour many OR pseudogenes. A high rate of in vitro recombination using Pfu polymerase but not Taq polymerase was confirmed. The rapid molecular evolution of OR pseudogenes suggests that they do not provide a useful source of sequence variation for conversion to intact OR genes over evolutionary timescales. The overall pattern of OR evolution in marmosets is comparable to the 'birth-and-death' model of gene family evolution. An unbiased view on the evolutionary timing of the reduction of the functional olfactory repertoire in humans must await more data.

Animals↗