Frequent Retroviral Gene Co-option during the Evolution of Vertebrates

Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo

Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.

Wildlife endogenous retroviruses: colonization, consequences, and cooption

Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are yielding remarkable perspectives on long-term retrovirus-host interactions. These initial forays into broader taxonomic analysis, including sequencing of multiple individuals per species, show the incredible plasticity and variation of ERVs within and among wildlife species. This demonstrates that stochastic processes govern much of the vertebrate genome. In this review, we elaborate on discoveries pertaining to wildlife ERV origins and evolution, genome colonization, and consequences for host biology.

A co-opted endogenous retroviral envelope promotes cell survival by controlling CTR1-mediated copper transport and homeostasis

Copper is a critical element for eukaryotic life involved in numerous cellular functions, including redox balance, but is toxic in excess. Therefore, tight regulation of copper acquisition and homeostasis is essential for cell physiology and survival. Here, we identify a different regulatory mechanism for cellular copper homeostasis that requires the presence of an endogenous retroviral envelope glycoprotein called Refrex1. We show that cells respond to elevated extracellular copper by increasing the expression of Refrex1, which regulates copper acquisition through interaction with the main copper transporter CTR1. Downmodulation of Refrex1 results in intracellular copper accumulation leading to reactive oxygen species (ROS) production and subsequent apoptosis, which is prevented by copper chelator treatment. Our results show that Refrex1 has been co-opted for its ability to regulate copper entry through CTR1 in order to limit copper excess, redox imbalance, and ensuing cell death, strongly suggesting that other endogenous retroviruses may have similar metabolic functions among vertebrates.

An immune-suppressing protein in human endogenous retroviruses

Motivation

Retroviruses are important contributors to disease and evolution in vertebrates. Sometimes, retrovirus DNA is heritably inserted in a vertebrate genome: an endogenous retrovirus (ERV). Vertebrate genomes have many such virus-derived fragments, usually with mutations disabling their original functions.

Results

Some primate ERVs appear to encode an overlooked protein. This protein is homologous to protein MC132 from Molluscum contagiosum virus, which is a human poxvirus, not a retrovirus. MC132 suppresses the immune system by targeting NF- κ B, and it had no known homologs until now. The ERV homologs of MC132 in the human genome are mostly disrupted by mutations, but there is an intact copy on chromosome 4. We found homologs of MC132 in ERVs of apes, monkeys and bushbaby, but not tarsiers, lemurs or non-primates. This suggests that some primate retroviruses had, or have, an extra immune-suppressing protein, which underwent horizontal genetic transfer between unrelated viruses.

Contact

mcfrith@edu.k.u-tokyo.ac.jp.

Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes

Background

Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation.

Results

In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily.

Conclusions

With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.

Monotreme-Specific Conserved Putative Proteins Derived from Retroviral Reverse Transcriptase

Endogenous retroviruses (ERVs) have played an essential role in the evolution of mammals. ERV-derived genes are reported in the therians, many of which are involved in placental development; however, the contribution of the ERV-derived genes in monotremes, which are oviparous mammals, remains to be uncovered. Here, we conducted a comprehensive search for possible ERV-derived genes in platypus and echidna genomes and identified three reverse transcriptase-like genes named RTOM1, RTOM2, and RTOM3 clustered in the GRIP2 intron. Comparative genomic analyses revealed that RTOM1, RTOM2, and RTOM3 are strongly conserved and are under purifying selection between these species. These could be generated by tandem duplications before the divergence of platypus and echidna. All RTOM transcripts were specifically expressed in the testis, possibly suggesting their physiological importance. This is the first study reporting monotreme-specific de novo gene candidates derived from ERVs, which provides new insights into the unique evolution of monotremes.

Non-canonical nematode endogenous retroviruses resulting from RNA virus glycoprotein gene capture by a metavirus

Reverse-transcribing retroviruses exist as horizontally transmitted infectious agents or vertically transmitted endogenous retroviruses (ERVs) resident in eukaryotic genomes, and they are phylogenetically related to the long terminal repeat (LTR) class of retrotransposons. ERVs and retrotransposons are often distinguished only by the presence or absence of a gene encoding the envelope glycoprotein (env). Endogenous elements of the virus family Metaviridae include the insect-restricted Errantivirus genus of ERVs, for which some members possess env, and the pan-eukaryotic Metavirus genus that lacks an envelope glycoprotein gene. Here we report a novel Nematoda endogenous retrovirus (NERV) clade with core retroviral genes arranged uniquely as a continuous gag-env-pro-pol ORF. Reverse transcriptase sequences were phylogenetically related to metaviruses, but envelope glycoprotein sequences resembled those of the Nyamiviridae and Chrysoviridae RNA virus families, suggesting env gene capture during host cell infection by an RNA virus. NERVs were monophyletic, restricted to the nematode subclass Chromadoria, and included additional ORFs for a small hypothetical protein or a large Upf1-like RNA-dependent AAA-ATPase/helicase indicative of viral transduction of a host gene. Provirus LTR identity, low copy number, ORF integrity and segregation of three loci in Meloidogyne incognita, taken together with detection of NERV transcriptional activity, support potential infectivity of NERVs, along with their recent emergence and integration. Altogether, NERVs constitute a new and distinct Metaviridae lineage demonstrating retroviral evolution through sequential heterologous gene capture events.

The diversity and evolution of retroviruses: perspectives from viral “fossils”

Retroviruses exclusively infect vertebrates, causing a variety of diseases. The replication of retroviruses requires reverse transcription and integration into host genomes. When infecting germline cells, retroviruses become inherited vertically, forming endogenous retroviruses (ERVs). ERVs document past viral infections, providing molecular fossils for studying the evolutionary history of retroviruses. In this review, we summarize the recent advances in understanding the diversity and evolution of retroviruses from the perspectives of viral fossils, and discuss the effects of ERVs on the evolution of host biology.

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Recent advances in understanding the diversity and evolution of retroviruses.

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Methods to analyze ERVs.

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The effects of ERVs on the evolution of host biology.

Segregating Complete Tf2 Elements Are Largely Neutral in Fission Yeast

Transposable elements (TEs) comprise a large proportion of the eukaryote genomes. Yet it remains poorly understood how TEs influence the fitness of the hosts carrying them. Here, we empirically test the impact of TEs on the host fitness in the fission yeast Schizosaccharomyces pombe. We find that two families of TEs (Tf1 and Tf2 elements), both of which belong to long terminal repeat retrotransposons, are highly polymorphic among individual S. pombe strains. Only 13 complete Tf2 elements are identified in S. pombe laboratory strain 972. These 13 Tf2 elements integrated into host genomes in very recent time and are segregating within the S. pombe population. Through knocking out each of the 13 Tf2 elements in S. pombe strain 972, we find Tf2 knockout does not affect the host fitness, and Tf2 elements do not alter the expression of nearby genes. Challenged by diverse forms of stress, the Tf2 knockout strains do not exhibit different growth rates from wild-type strain. Together, we conclude that segregating complete Tf2 elements insertions are largely neutral to host fitness in the fission yeast. Our study provides genome-wide empirical support for the selfish nature of TEs in fission yeast.

Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control

Excessive replication of Saccharomyces cerevisiae Ty1 retrotransposons is regulated by Copy Number Control, a process requiring the p22/p18 protein produced from a sub-genomic transcript initiated within Ty1 GAG. In retrotransposition, Gag performs the capsid functions required for replication and re-integration. To minimize genomic damage, p22/p18 interrupts virus-like particle function by interaction with Gag. Here, we present structural, biophysical and genetic analyses of p18m, a minimal fragment of Gag that restricts transposition. The 2.8 Å crystal structure of p18m reveals an all α-helical protein related to mammalian and insect ARC proteins. p18m retains the capacity to dimerise in solution and the crystal structures reveal two exclusive dimer interfaces. We probe our findings through biophysical analysis of interface mutants as well as Ty1 transposition and p18m restriction in vivo. Our data provide insight into Ty1 Gag structure and suggest how p22/p18 might function in restriction through a blocking-of-assembly mechanism.

In Saccharomyces cerevisiae, unchecked proliferation of Ty1 retrotransposons is controlled by the process of copy number control (CNC), which requires the p22/p18 protein, translated from an internal transcript within the Ty1 GAG gene. Here, the authors present the 2.8 Å crystal structure of a minimal p18 from Ty1-Gag that is able to restrict Ty1 transposition and identify two dimer interfaces in p18, whose roles were probed by mutagenesis both in vitro and in vivo. As p22/p18 contains only one of two conserved domains required for retroelement Gag assembly, they propose that p22/p18-Gag interactions block the Ty1 virus-like particle assembly pathway, resulting in defective particles incapable of supporting retrotransposition.

Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes

LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview

Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.