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The molecular domestication of amphibian retroviruses – do they play a physiological role?

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ResearchBlogging.orgWe mostly think of viruses of being ‘bad’ and ‘dangerous’ yet there are countless examples of viruses playing a positive role in their host’s life. These symbiotic agents have been co-opted by the host to do something good; some viruses have even been inserted into our genomes and thus are forever tied to our germline and our descendants – sometimes even these viruses can do good. This is the kind of game evolution plays with our viral parasites and us – its generally pretty cruel and inconsiderate but every so often we get something good out of it.

Xenopus tropicalis - do recently identified ERVs play a functional role?

One example of these endogenous viruses is the endogenous retroviruses or ERVs, which are somewhat related to the non-endogenous – ‘exogenous’ – retroviruses that can cause disease in us and other animals (HIV XMRV?). Just to put it into perspective, 8% of our genome is made up of these ERVs and they also make up a large chunk of other vertebrate genomes. The majority of these inserted retroviral genomes have been destroyed by the forces of evolution and thus bear little resemblance to their ‘wild’ cousins; they are not expressed and their sequence shows little homology to other retroviruses. However, some ERVs have changed very little, suggesting an important function may be conserving them – these are expressed and do sort of resemble the exogenous ones. The insertion of a novel ERV sequence into a host’s genome acts as evolutionary raw material allowing significant adaptive functions to arise and a great deal of evidence suggests they can these can even play a physiological role in host biology – this is known as molecular domestication. One interesting example is the ERV role in the mammalian placenta.

Chromosomal location of the Xenopus ERV-like sequences

A recent paper reports the discovery and characterisation of an amphibian ERV whose genomic organisation is highly conserved making it a good candidate to have a novel physiological function. Investigating the genome of Xenopus tropicalis – an ‘African clawed frog‘, the group discovered a unique DNA sequence that was highly related to a previously characterised Xenopus protein with frost-resistant functions – allowing winter survival in woodland frogs. This 9,551 base-pair DNA sequence not only contained the intact frost-resistant gene but also a full-length retroviral genome with the general organisation of many common ERVs – 5’ LTR-GAG-POL-ENV-3’LTR.

ABSTRACT: We report on the identification and characterization of XTERV1, a full-length endogenous retrovirus (ERV) within the genome of the western clawed frog (Xenopus tropicalis). XTERV1 contains all the basic genetic elements common to ERVs, including the classical 5′-long terminal repeat (LTR)-gag-pol-env-3′-LTR archi- tecture, as well as conserved functional motifs inherent to each retroviral protein. Using phylogenetic analysis, we show that XTERV1 is related to the Epsilonretrovirus genus. The X. tropicalis genome harbors a single full-length copy with intact gag and pol open reading frames that localizes to the centromeric region of chromosome 5. About 10 full-length defective copies of XTERV1 are found interspersed in the genome, and 2 of them could be assigned to chromosomes 1 and 3. We find that XTERV1 genes are zygotically transcribed in a regulated spatiotemporal manner during frog development, including metamorphosis. Moreover, XTERV1 transcription is upregulated under certain cellular stress conditions, including cytotoxic and metabolic stresses. Interestingly, XTERV1 Env is found to be homologous to FR47, a protein upregulated following cold exposure in the freeze-tolerant wood frog (Rana sylvatica). In addition, we find that R. sylvatica FR47 mRNA originated from a retroviral element. We discuss the potential role(s) of ERVs in physiological processes in vertebrates.

Following the characterisation of the genome sequence, the group looked whether there any more ERVs like this one in Xenopus genomes  to see if  this a rare example of a highly conserved ERV and were there any other examples of these sequences present? There turned out to be 59 genomic loci with some sort of homology to the newly found ERV however all had significant mutations present rendering them functionally inactive – at least where gene expression is concerned. These sequences were mapped onto Xenopus chromosomes, showing that the intact ERV was present on chromosome and the ‘damaged’ ones were found throughout the genome. This ERV is after all a lone agent in the Xenopus genome – confirmed by these experiments. Phylogenetic studies were also carried out which suggested that primary retroviral integration occurred roughly 41 million years ago and from then on multiple rounds of movement around the genome or reinfection generated the many mutated copies around the genome. Their results also suggest that this ERV is actively replicating and inserting itself into the genome up to the present day. A cousin of this retrovirus was also found in the closely related X.laevis genome showing that integration occurred prior to the evolutionary separation of these two lineages.

Expression of ERV sequences throughout Xenopus development and time

They next turned their attention to whether this ERV had a functionally active role (is it transcribed; in what tissues and at what points in frog development?) in host biology as observed in other host/ERVs. Using real-time PCR and in situ hybridisaton techniques, the group were able to follow ERV expression throughout X. tropicalis development and assess the level of transcription and tissue localisation and possible infer a physiological function. They noted a highly regulated yet dynamic expression of gag, pol and env expression from fertilisation through metamorphosis (curiously a peak of activity was seen during metamorphosis) and adult life but does this control of expression actually mean something functional or is it merely physiological neutral? This ERV may just be replicating within the host genome without contributing something to host life. In order to understand this, they subjected X. tropicalis tadpoles or cell lines to a number of biological ‘stresses’ e.g. metabolic, temperature and UV stresses. An upregulation of ERV expression was seen upon metabolic and UV stresses and not in temperature – suggesting a fine tuning of its expression in response to a number of stresses. Whether this actually achieved something functionally was not investigated.

A recently discovered retrovirus derived gene in another frog species was found to play a role in protecting frog cells from the effects of freezing conditions. This study, on the backs of that investigation determined that frost-tolerant gene was derived from a highly conserved ERV present within Xenopus genomes. A distinct physiological role for these ERV-derived genes was not validated in this study yet in the future, further characterisation of its expression in vivo under temperature stress should be undertaken. This work underlines the importance that retroviruses and their endogenised cousins play in host cell functioning and evolution. Viruses are not all bad news – sometimes they can help you.

Roossinck, M. (2011). The good viruses: viral mutualistic symbioses Nature Reviews Microbiology, 9 (2), 99-108 DOI: 10.1038/nrmicro2491

Sinzelle, L., Carradec, Q., Paillard, E., Bronchain, O., & Pollet, N. (2010). Characterization of a Xenopus tropicalis Endogenous Retrovirus with Developmental and Stress-Dependent Expression Journal of Virology, 85 (5), 2167-2179 DOI: 10.1128/JVI.01979-10

Written by Connor

February 10, 2011 at 11:39 am

Seeing the big picture of RNA virus evolution

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This post was chosen as an Editor's Selection for

From both a medical and a scientific viewpoint, the evolution of viruses is extremely important to us;  viral adaptation to their ever changing environment is responsible for major morbidity and mortality worldwide so maybe studying this  may allow us to predict virus evolution in the future and may help prevent pandemics occuring?

We kind of know a lot about how viruses evolve at the small-scale; we know how viruses generally create genetic diversity – mutations – and how processes such as natural selection and genetic drift act on these genetic changes and influence the way viral genomes change over time. What we don’t know however, is how viruses change at the larger-scale – how these above processes influence viral genomes over thousands of years, including: how and why viruses speciate, how their genome structure evolves and how and when do new viruses originate.

An example phylogenetic tree - The paramyxoviridae containing a number of important human and animal pathogens. Notice the host/viral species distribution.

A recent study, investigating the evolution of a number of RNA viruses has sought to reconcile this lack of understanding by attempting to assess virus ‘macroevolution’- specifically viral speciation. By generating large and highly robust phylogenetic trees (using significantly highly conserved amino-acid sequences of a single viral protein) for 5 genera of RNA virus including: the Alphaviruses, Caliciviruses, Paramyxoviruses, Rhabdoviruses and the Flaviviruses, the team were able to map the host species of each virus species onto the trees and this allowed them to infer the mode of speciation of each virus genus.

More specifically they asked: Do closely related viral species infect the same host and are therefore believed to have speciated in that host or do they infect completely different hosts which are believed to have speciated following host jumping?

What is a virus species?

General modes of speciation - we may think of viruses speciating by either allopatric (host shift) or sympatric (intra-host divergence).

The concept of the viral species has been a hard one to determine becuase viruses don’t reproduce sexually. It is generally thought to be rather a arbitrary classification, however, most virus ‘species’ tend to be phylogenetically and often phenotypically stable genetic lineages and hence may be thought of as ‘biological relevant’. We may think of viral speciation much like we think of speciation in the classic sense: allopatric or ‘geographical speciation’ (virus adaptation to a new host species) and sympatric – that not requiring the forces of georgaphic isolation (generation of viral speciation within a single host). Virus sympatric speciation requires the adapation to a new infectious niche within a host, for example a new lineage may infect new cell types within that host. Virus allopatric speciation requires host-jumping or adaptation to a new host altogether but may result from co-divergence follwoing host speciation. Both processes may result in two or more ‘stable, phylogenetic and phenotypic genetic lineages. But what does the data say about it – how do viruses evolve in the real world?

What the data says

The results were split – at leats 50% were found to have ‘speciated’ via sympatric-like processes and half from allopatric-like processes. The group stress, however, that a major caveat of this study is that it highlights our limited understanding of what specific host speces particular viruses infect; in this study most hosts were classified as ‘birds’ or ‘plants’ or ‘Carnivores’ which limits the resolution of phylogenetic studies and leads to the overestimation of sympatric speciation events which would otherwise not exist if exact hosts were known. This leads us to put little confidence on our earlier 50/50 estimate and most likely the role of sympatric speciation would be a lot less important than allopatric modes of speciation in reality.

Why do RNA viruses evolve this way – What controls viral speciation?

So, we may say that most RNA virus speciation is caused by allopatric modes – or host jumping, but this may seem counterintuitive as there are some major barriers to viral emergence. The group argue, however, that it may take a lot more – genetically speaking – for a virus to speciate within a host than it does for a virus to jump species – eg. replicate in a new cell type/alter antigenic epitopes. The apparant preference for allopatric speciation may be controlled by intrinsic biological factors of these RNA viruses, namely: their extremely small genome size which effectively constrains evolutionary innovation. Those changes required for host jumping (change in receptor binding sites for instance) may be relatively minor when compared to those and the more closely related the host species are then the more easily host-jumping will occur – which is what we see here.

This study highlights the key role that viral ‘allopatric’ speciation or host – jumping plays in the evolution of RNA viruses yet further emphasizes the need to better study and understand viral biodiversity and host range in the wild – not only focusing on those medically important human viruses. Further research may be carried out on the molecular barriers to both cellular and host switching for these RNA viruses. This study will act as a model system that may be applied to other viral lineages – what about the RNA viruses with segmented genomes? What about the DNA viruses? Retroviruses?
Kitchen A, Shackelton LA, & Holmes EC (2011). Family level phylogenies reveal modes of macroevolution in RNA viruses. Proceedings of the National Academy of Sciences of the United States of America, 108 (1), 238-43 PMID: 21173251

Written by Connor

January 17, 2011 at 1:25 pm