cDNA genes formed after infection with retroviral vector particles lack the hallmarks of natural processed pseudogenes

LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling

Two major classes of retrotransposons have invaded eukaryotic genomes: the LTR retrotransposons closely resembling the proviral integrated form of infectious retroviruses, and the non-LTR retrotransposons including the widespread, autonomous LINE elements. Here, we review the modeling effects of the latter class of elements, which are the most active in humans, and whose enzymatic machinery is subverted to generate a large series of "secondary" retroelements. These include the processed pseudogenes, naturally present in all eukaryotic genomes possessing non-LTR retroelements, and the very successful SINE elements such as the human Alu sequences which have evolved refined parasitic strategies to efficiently bypass the original "protectionist" cis-preference of LINEs for their own retrotransposition.

Characterization of the intragenomic spread of the human endogenous retrovirus family HERV-W

This study examines the intragenomic spread of the human endogenous retrovirus family HERV-W from insertions present within the draft sequence of the human genome. Identification of shared diagnostic differences and phylogenetic analyses revealed the existence of three main subfamilies. The average divergence between sequences for each of the subfamilies suggests that most of the HERV-W elements were inserted within the genome during a short period of evolutionary time. Each one of the subfamilies consists of two types of insertions, the expected proviral sequences and other sequences resembling the structure of processed retrogenes. These HERV-W retrosequences extend from the R region of the 5' long-terminal repeat (LTR) to the R region of the 3' LTR (as viral genomic RNAs), end in poly(A) 3' tails, and are flanked by direct repeats longer than the proviral integrations. Furthermore, several of the HERV-W retrosequences are 5'-truncated at different sites. I suggest the involvement of the L1 machinery in these integrations and discuss the characteristic features of the evolutionary history of HERV-W, with emphasis on the putative impact of HERV-W retrosequence integrations on the mammalian genome.

The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana

We have characterized the two families of SINE retroposons present in Arabidopsis thaliana. The origin, distribution, organization, and evolutionary history of RAthE1 and RAthE2 elements were studied and compared to the well-characterized SINE S1 element from Brassica. Our studies show that RAthE1, RAthE2, and S1 retroposons were generated independently from three different tRNAs. The RAthE1 and RAthE2 families are older than the S1 family and are present in all tested Cruciferae species. The evolutionary history of the RAthE1 family is unusual for SINEs. The 144 RAthE1 elements of the Arabidopsis genome cannot be classified in distinct subfamilies of different evolutionary ages as is the case for S1, RAthE2, and mammalian SINEs. Instead, most RAthE1 elements were probably derived steadily from a single source gene that was maintained intact and active for at least 12-20 Myr, a result suggesting that the RAthE1 source gene was under selection. The distribution of RAthE1 and RAthE2 elements on the Arabidopsis physical map was studied. We observed that, in contrast to other Arabidopsis transposable elements, SINEs are not concentrated in the heterochromatic regions. Instead, SINEs are grouped in the euchromatic chromosome territories several hundred kilobase pairs long. In these territories, SINE elements are closely associated with genes. A retroposition partnership between Arabidopsis SINEs and LINEs is proposed.

Transduction of the human gene FAM8A1 by endogenous retrovirus during primate evolution

Capture of cellular mRNA by mobile elements has been an evolutionary catalyst for the spread of genes and a cause of cancer development. Here we present evidence that an orphan gene, FAM8A1 (family with sequence similarity 8), was captured by a retrovirus, followed by multiple retrotransposition events, during primate evolution between 45 and 58 million years ago. This represents the first record of cellular mRNA transduction in humans. The human gene is localized on chromosome 6p23 with five related pseudogenes (FAM8A2P-A6P), each inserted within a human endogenous retrovirus (HERV). Only the functional FAM8A1 gene is expressed and displays a ubiquitous mRNA and a testis-specific transcript present in the haploid phase of spermatogenesis. The structural features of the FAM8A1 pseudogenes include two short sequences of similarity between the FAM8A1 mRNA and the HERV sequences at both the 5' and 3' integration sites. These hallmarks suggest an alternative model to account for the capture of FAM8A1 cellular mRNA by HERV-K, involving illegitimate recombination events at the two sites of sequence similarity during reverse transcription. Unlike previous models, which assume at least one step of retroviral integration in the genome, our model is consistent with in vitro observations showing that multiple template switches occur among packaged viral transcripts. This leads to the speculation that, in some cases, cellular mRNAs may have been captured through similar processes involved in the retroviral life cycle.

Human LINE retrotransposons generate processed pseudogenes

Long interspersed elements (LINEs) are endogenous mobile genetic elements that have dispersed and accumulated in the genomes of higher eukaryotes via germline transposition, with up to 100,000 copies in mammalian genomes. In humans, LINEs are the major source of insertional mutagenesis, being involved in both germinal and somatic mutant phenotypes. Here we show that the human LINE retrotransposons, which transpose through the reverse transcription of their own transcript, can also mobilize transcribed DNA not associated with a LINE sequence by a process involving the diversion of the LINE enzymatic machinery by the corresponding mRNA transcripts. This results in the 'retroposition' of the transcribed gene and the formation of new copies that disclose features characteristic of the widespread and naturally occurring processed pseudogenes: loss of intron and promoter, acquisition of a poly(A) 3' end and presence of target-site duplications of varying length. We further show-by introducing deletions within either coding sequence of the human LINE-that both ORFs are necessary for the formation of the processed pseudogenes, and that retroviral-like elements are not able to produce similar structures in the same assay. Our results strengthen the unique versatility of LINEs as genome modellers.

Capture of a recombination activating sequence from mammalian cells

We have developed a genetic trap for identifying sequences that promote homologous DNA recombination. The trap employs a retroviral vector that normally disables itself after one round of replication. Insertion of defined DNA sequences into the vector induced the repair of a 300 base pair deletion, which restored its ability to replicate. Tests of random sequence libraries made in the vector revealed a putative recombination signal (CCCACCC). When this heptamer or an abbreviated form (CCCACC) were reinserted into the vector, they stimulated vector repair and other DNA rearrangements. Mutant forms of these oligomers (eg CCCAACC or CCWACWS) did not. Our data suggest that the recombination events occurred within 48 h after transfection.

Selectively infective phages (SIP)

We review here advances in the selectively infective phage (SIP) technology, a novel method for the in vivo selection of interacting protein-ligand pairs. A 'selectively infective phage' consists of two components, a filamentous phage particle made non-infective by replacing its N-terminal domains of gene3 protein (g3p) with a ligand-binding protein, and an 'adapter' molecule in which the ligand is linked to those N-terminal domains of g3p which are missing from the phage particle. Infectivity is restored when the displayed protein binds the ligand and thereby attaches the missing N-terminal domains of g3p to the phage particle. Phage propagation becomes strictly dependent on the protein-ligand interaction. This method shows promise both in the area of library screening and in the optimization of peptides or proteins.

Molecular analysis of bovine actin gene and pseudogene sequences: expression of nonmuscle and striated muscle isoforms in adult tissues

Most studies on the tissue distribution of actin isoform transcripts have been done in small mammals such as rat and mouse. We have begun a characterization of the actin gene family in a large mammal, the bovine. The alpha skeletal gene was isolated, and an isoform-specific probe to the 3' untranslated region of the transcript identified. This probe, in combination with isoform specific probes for alpha cardiac, beta nonmuscle, and gamma nonmuscle actins, was used to examine expression of nonmuscle and striated muscle actin gene transcription in different tissues. In contrast to other species so far examined, striated muscle isoforms were more strictly tissue specific, with virtually no alpha cardiac isoform transcripts detected in skeletal muscle and almost no alpha skeletal transcripts in cardiac tissue. The distribution of the beta and gamma nonmuscle actins was also unique in bovine compared to other species. A partial beta-actin pseudogene, and the chromosomal DNA flanking one end of it, were also cloned and sequenced. This chromosomal site was found to be homologous to a viral integration site previously identified in simian virus 40 (SV40)-transformed rat cells, suggesting that this region of the chromosome may be a preferred target for insertion events.

Retrotransposition and herpesvirus evolution

One of the more interesting developments in herpesvirus evolution concerns the acquisition of novel, non-ubiquitous herpesvirus genes. A number of these are related to known cellular genes. How did herpesviruses acquire such genes? Our recent demonstration of retrovirus integration into herpesviruses suggests a potentially important role for retrotransposition in herpesvirus evolution and in the acquisition of novel genes, cellular in origin. Herpesvirus genome development has been characterized by a number of structural and evolutionary properties that support this proposal. We first discuss the evidence for retroviral integration into herpesviruses. The functional significance of this phenomenon is presently unclear. However, in the broader context of retrotransposition, a number of attractive features serve to explain the capture of structural and regulatory elements throughout herpesvirus evolution. These possibilities are discussed in detail.

Generation of a pseudogene during retroviral infection

During evolution, up to 10% of the mammalian genome may have arisen by rare retroposition events. This process involves reverse transcription of RNA intermediates that originate from retroviral and retroviral-like sequences, highly and middle repetitive DNA elements, and processed pseudogenes. The mechanism, and contemporary nature, for retrotransposition of the viral family and long interspersed elements has been well studied; however, it has proven difficult to demonstrate that the process by which pseudogenes retropose is continuing. In this report a mutation in the murine hypoxanthine-guanosine phosphoribosyl transferase (hprt) gene, which was previously isolated following retroviral infection of ES cells, is shown to result from a de novo retroposition of an alpha-tubulin pseudogene. Repair of this insertion by homologous recombination restores the activity of the hprt locus, thus confirming the site of mutation. This retroposon bears all the hallmarks of a naturally processed pseudogene [intron loss, presence of a poly(A) tail, and target site duplication] while the retroposition event took place at a known time in well-defined conditions, during retroviral infection of ES cells. The study of this mutation demonstrates that under appropriate conditions pseudogenes of protein-coding genes can still retropose in the mammalian genome. The coincidence of this mutagenic event with retroviral infection suggests that in this situation the reverse transcriptase may have had a retroviral origin, which would implicate a retroviral role in facilitating pseudogene formation.

Overview of biological effects of addition of DNA molecules to cells

Injected DNA proceeds with certain probabilities through the following steps: degradation by serum nucleases, adsorption to cells, uptake into cells, ligation to other DNA, mutation, expression of unintegrated DNA, integration, expression of integrated DNA, and activation of or inactivation of cellular genes. The maximal probability per DNA molecule of each of these steps is estimated based on experimental results in cell culture with transfection of DNA and with infection by retroviruses. A maximum cumulative probability of having a harmful effect is calculated to be less than 10(-16) to 10(-19) per DNA molecule from a cell without activated proto-oncogenes or active viral oncogenes. The most frequent harmful effects considered are inactivation of a tumor suppressor gene and activation of a proto-oncogene. Such inactivation and activation in a cell that could give rise to cancer would increase the age-standardized incidence of cancer by a small amount. The amount of increase would differ among individuals depending upon their genotypes and their environments. Thus, the magnitude of the increase will depend upon the frequency of more sensitive individuals. The probability of an increased incidence of cancer as a possible effect of the vaccination should be compared to the number of DNA molecules to be injected per person and to the protective effects of a successful HBV vaccine.