Identification of endogenous retroviral sequences based on modular organization: proviral structure at the SSAV1 locus

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

Endogenous retroviral sequences provide a molecular fossil record of ancient infections whose analysis might illuminate mechanisms of viral extinction. A close relative of gammaretroviruses, HERV-T, circulated in primates for ~25 million years (MY) before apparent extinction within the past ~8 MY. Construction of a near-complete catalog of HERV-T fossils in primate genomes allowed us to estimate a ~32 MY old ancestral sequence and reconstruct a functional envelope protein (ancHTenv) that could support infection of a pseudotyped modern gammaretrovirus. Using ancHTenv, we identify monocarboxylate transporter-1 (MCT-1) as a receptor used by HERV-T for attachment and infection. A single HERV-T provirus in hominid genomes includes an env gene (hsaHTenv) that has been uniquely preserved. This apparently exapted HERV-T env could not support virion infection but could block ancHTenv mediated infection, by causing MCT-1 depletion from cell surfaces. Thus, hsaHTenv may have contributed to HERV-T extinction, and could also potentially regulate cellular metabolism.

DOI:http://dx.doi.org/10.7554/eLife.22519.001

Over millions of years, viruses and the animals that they infect have been locked in a battle for survival, where each has needed to evolve ways to counteract the effects of the other. While the evolution of ancient animals can be studied by looking at the fossilized remains of their extinct relatives, studying how ancient viruses have evolved is more difficult as they usually do not leave behind physical traces of their existence. However, a family of viruses called retroviruses is a notable exception to this rule.

Retroviruses have a step in their life cycle in which their genetic material is integrated into the genome (the name for an organism’s complete set of genetic material) of the cell that they have infected. In rare cases, when that cell is a precursor of a sperm or egg cell, then the viral genes may then be passed on to the animal’s offspring, ultimately leaving genetic traces that can be studied in modern animals. This acts as a genetic ‘fossil record’ of extinct viruses.

HERV-T was a retrovirus that spread among our primate ancestors for about 25 million years before its extinction roughly 11 million years ago. Blanco-Melo et al. have now analyzed the genetic remains left by HERV-T in the genomes of humans and related primates, and were able to use this information to recreate a protein that made up the outer envelope that surrounded the virus. Further experiments showed that this viral protein helped HERV-T to infect human cells by interacting with a protein called MCT1 on the cell surface.

Blanco-Melo et al. also found a particular HERV-T gene that was unexpectedly well preserved in the human genome. The gene retained its ability to produce an envelope protein for about 13 to 19 million years. It is likely that ancient primates ‘hijacked’ the viral gene and used the protein it produced to remove the MCT1 protein from the surface of their own cells. Without MCT1 on the surface, HERV-T was unable to infect the cells. Thus, these findings present an example of how viruses themselves can provide the genetic material that animals use to combat them, potentially leading to their extinction.

DOI:http://dx.doi.org/10.7554/eLife.22519.002

Endogenous retroviral pathogenesis in lupus

PURPOSE OF REVIEW

Genetic and environmental factors influence the development of systemic lupus erythematosus (SLE). Endogenous retroviruses (ERVs) are proposed as a molecular link between the human genome and environmental factors, such as viruses, in lupus pathogenesis.

RECENT FINDINGS

The HRES-1 human ERV encodes a 28-kD nuclear autoantigen and a 24-kD small GTP-ase, termed HRES-1/Rab4. HRES-1/p28 is a target of cross-reactive antiviral antibodies, whereas HRES-1/Rab4 regulates the surface expression of CD4 via endosome recycling. The tat gene of HIV-1 induces the expression of HRES-1/Rab4, which in turn downregulates expression of CD4 and susceptibility to reinfection by HIV-1. HRES-1/Rab4 is overexpressed in lupus T cells where it correlates with increased recycling of CD4 and CD3 and contributes to downregulation of CD3/TCRzeta via lysosomal degradation. Chilblain lupus has been linked to the deficiency of 3'-5' repair exonuclease Trex1 that metabolizes DNA reverse-transcribed from ERV. Trex1 deficiency or blocked integration of ERV-encoded DNA also promotes lupus in murine models.

SUMMARY

ERV proteins may trigger lupus through structural and functional molecular mimicry, whereas the accumulation of ERV-derived nucleic acids stimulates interferon and anti-DNA antibody production in SLE.

Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data

Background

Retroviral LTRs, paired or single, influence the transcription of both retroviral and non-retroviral genomic sequences. Vertebrate genomes contain many thousand endogenous retroviruses (ERVs) and their LTRs. Single LTRs are difficult to detect from genomic sequences without recourse to repetitiveness or presence in a proviral structure. Understanding of LTR structure increases understanding of LTR function, and of functional genomics. Here we develop models of orthoretroviral LTRs useful for detection in genomes and for structural analysis.

Principal Findings

Although mutated, ERV LTRs are more numerous and diverse than exogenous retroviral (XRV) LTRs. Hidden Markov models (HMMs), and alignments based on them, were created for HML- (human MMTV-like), general-beta-, gamma- and lentiretroviruslike LTRs, plus a general-vertebrate LTR model. Training sets were XRV LTRs and RepBase LTR consensuses. The HML HMM was most sensitive and detected 87% of the HML LTRs in human chromosome 19 at 96% specificity. By combining all HMMs with a low cutoff, for screening, 71% of all LTRs found by RepeatMasker in chromosome 19 were found. HMM consensus sequences had a conserved modular LTR structure. Target site duplications (TG-CA), TATA (occasionally absent), an AATAAA box and a T-rich region were prominent features. Most of the conservation was located in, or adjacent to, R and U5, with evidence for stem loops. Several of the long HML LTRs contained long ORFs inserted after the second A rich module. HMM consensus alignment allowed comparison of functional features like transcriptional start sites (sense and antisense) between XRVs and ERVs.

Conclusion

The modular conserved and redundant orthoretroviral LTR structure with three A-rich regions is reminiscent of structurally relaxed Giardia promoters. The five HMMs provided a novel broad range, repeat-independent, ab initio LTR detection, with prospects for greater generalisation, and insight into LTR structure, which may aid development of LTR-targeted pharmaceuticals.

Molecular mimicry and immunomodulation by the HRES-1 endogenous retrovirus in SLE

Genetic and environmental factors are believed to influence development of systemic lupus erythematosus (SLE). Endogenous retroviruses (ERV) correspond to the integrated proviral form of infectious retroviruses, which are trapped within the genome due to mutations. ERV represent a key molecular link between the host genome and infectious viral particles. ERV-encoded proteins are recognized by antiviral immune responses and become targets of autoreactivity. Alternatively, ERV protein may influence cellular processes and the life cycle of infectious viruses. As examples, the HRES-1 human ERV encodes a 28-kDa nuclear autoantigen and a 24-kDa small GTP-ase, termed HRES-1/Rab4. HRES-1/p28 is a nuclear autoantigen recognized by cross-reactive antiviral antibodies, while HRES-1/Rab4 regulates surface expression of CD4 and the transferrin receptor (TFR) through endosome recycling. Expression of HRES-1/Rab4 is induced by the tat gene of HIV-1, which in turn down-regulates expression of CD4 and susceptibility to re-infection by HIV-1. CD4 and the TFR play essential roles in formation of the immunological synapse (IS) during normal T-cell activation by a cognate MHC class II peptide complex. The key intracellular transducer of T-cell activation, Lck, is brought to the IS via binding to CD4. T-cell receptorzeta (TCRzeta) chain binds to the TFR. Abnormal T-cell responses in SLE have been associated with reduced lck and TCRzeta chain levels. HRES-1 is centrally located on chromosome 1 at q42 relative to lupus-linked microsatellite markers and polymorphic HRES-1 alleles have been linked to the development of SLE. 1q42 is one of the three most common fragile sites in the human genome, and is inducible by DNA demethylation, a known mechanism of retroviral gene activation. Molecular mimicry and immunomodulation by a ERV, such as HRES-1, may contribute to self-reactivity and abnormal T and B-cell functions in SLE.

Isolation and characterization of RNase LTR sequences of Ty1-copia retrotransposons in common bean (Phaseolus vulgaris L)

Retroelements have proved useful for molecular marker studies and play an important role in genome evolution. Ty1-copia retrotransposons are ubiquitous and heterogeneous in plant genomes, and although many elements have been isolated and characterized, almost no information about them is available in the literature for Phaseolus vulgaris L. We report here the isolation and characterization of new RNase long terminal repeat (LTR) sections of the Ty1-copia group for this crop plant. RNAse sections showed conserved amino acids with the downstream sections corresponding to the polypurine-tract and 5' sections of 3' LTRs. The RNase sections were aligned using ClustalX to find potential relationships between sequences. A comparison with this analysis was made using the partition analysis of quasispecies package (PAQ), which is specific for quasispecies-like populations. The analysis revealed eight distinct groups. To uncover LTR variability and potential conserved promoter motifs, we also designed new primers from the presumed polypurine-tract regions. A similarity search found short stretches similar to upstream and downstream regions of some genes. Conserved motifs, corresponding to transcription factor binding sites, were discovered through MatInspector software and two sequences characterized. From a putative LTR fragment, we then designed a new primer, which, through sequence-specific amplification polymorphism (SSAP), showed numerous polymorphic bands between two distinct P. vulgaris accessions.

A polymerase chain reaction-based protocol for the detection of transmission of pig endogenous retroviruses in pig to human xenotransplantation

BACKGROUND

Xenotransplantation of pig organs and tissues to humans bears the risk of infection of immunosuppressed recipients by porcine endogenous retrovirus (PERV) released from the transplanted tissue. However, when diagnosing potential PERV transmission, it is essential to exclude microchimerism, i.e., persisting pig cells in analyzed bioptic material of xenotransplanted patients, which give rise to false positive PERV signals. Polymerase chain reaction (PCR) is so far the only suitable method to diagnose a cross-species transfer of PERV, but the exclusion of microchimerism might be a serious problem because most of the presently employed primer pairs detect PERV sequences with higher sensitivity than primers used for the detection of contaminating pig sequences.

METHODS

We designed and evaluated a novel and improved primer set for detection of pig sequences as well as complementing positive control primers on the basis of mitochondrial cytochrome B, an approved marker for phylogenetic studies. We further established primer pairs derived from the long terminal repeat/leader region of PERV isolated from a Duroc German Landrace cross-bred pig and tested their sensitivity in comparison with known PERV- and pig-specific PCR markers.

RESULTS

In standard PCR assays, the new cytochrome B-derived primers are at least 10 times more sensitive than the presently used PERV retroviral polymerase gene and mammalian beta-actin primers. When tested in a tissue culture infection model, PERV transmission to human 293 cells can be unambiguously demonstrated, even in the presence of up to 10% pig cells. One of the primer combinations derived from the PERV DuxDL3791 long terminal repeat/leader region amplifies with even lower sensitivity than primers detecting porcine beta-globin, thus permitting the exclusion of microchimerism also via chromosomal loci.

CONCLUSIONS

The availability of the new PCR markers allows the proposal of a rigorous setup for the routine detection of PERV transmission after xenotransplantation.

A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter

Functional promoters are composed of individual modules (e.g. transcription factor binding sites, secondary structure elements, repeats) arranged in distinct patterns. Recognition of such patterns is essential for identification of promoters in non-coding sequences. However, this is difficult due to the absence of overall sequence similarity in promoters even if they are regulated in a similar way. We implemented simple formal representations of general features of regulatory regions into an algorithm capable of developing complex models reflecting both the element composition and the functional organization of individual elements (ModelGenerator). Though ModelGenerator requires a very simple initial model (e.g. two modules and their relative order) it will generate a much more sophisticated model by analysis of the training set of at least ten sequences. We show ModelGenerator to successfully model different retroviral long terminal repeat (LTR) classes (Lentivirus as well as avian and mammalian C-type) which contain functional promoters. Database searches with the program ModelInspector demonstrated the high specificity of these models and no apparent false negatives were detected. We also verified one match from GenBank to the mammalian C-type LTR model experimentally and showed this sequence to contain an active promoter. Thus, the concept of modular organization of functional regulatory DNA regions (e.g. promoters) could be successfully implemented into a set of computer tools which might be flexible and specific enough to be suitable for prospective analysis of new genomic DNA sequences.