Monday, June 22, 2009

RAG1: Viral or TE?

Today’s post is another article summary but about something a bit different. This one concerns the origins of adaptive immunity in jawed vertebrates, and more specifically the origin of the RAG1 protein. RAG1 is a gene expressed in T and B-lymphocytes in the immune system which along with RAG2 mediates the creation antibodies. It does this via a process known as V(D)J recombination, after the variable and joining sequence segments that are joined together to create a complete antibody gene. The RAG1/2 complex binds to recognition signal sequences (RSS) between segments and cuts out the intervening DNA. The subsequent double-strand breaks are joined back together via non-homologous end-joining proteins to join the previously separated sequence into a single coding region. This is an oversimplification of the process but basically this occurs several times in a somewhat random manner to create a novel antibody gene. Through a selection process that occurs in the immune system only cells with antibodies which recognize foreign antigens survive to prevent autoimmunity.

Researchers noticed some time ago that the process of V(D)J recombination was very similar to what occurs during the transposition of a Class II TE, also known as a DNA transposon. A transposase protein recognizes and binds to the inverted terminal repeats (ITR) on either end of the element and cuts it out of the sequence it is inserted into. In a similar manner RAG1/2 complexes bind to a pair of RSS’s, cut out the sequence in between and circularize it for degradation by the cell. In 2005 Kapitonov and Jurka published a paper showing that roughly 60 amino acids in the C-terminus of RAG1, within the so-called “RAG core”, were found to be significantly similar to the Transib transposases. As well, the ITRs of Transib elements are very similar to the RSS’s (with a probability of the similarity occurring by chance of 1.0 x 10-3) and both RAG complexes and Transib elements generate 5 bp target site duplications (TSD). It seemed like the origin of RAG1 had been at least partially solved.

Several weeks ago a paper popped up in my iGoogle Reader that has been published in PLoS One contesting the transposon origin of RAG. This seemed odd to me because I thought the conclusions of Kapitonov and Jurka (2005) were pretty sound. The paper by Dreyfus (2009) claimed that there was more evidence that RAG1 was derived from the insertion of a herpes virus-like element long ago in a deuterostome ancestor. You can judge for yourself, the paper is available free to download here, but I’d like to tell you why this new hypothesis doesn’t hold up as well to me as the Transib origin one does.

Dreyfus states that the regulatory sequences of the Epstein-Barr Virus (EBV), a herpes virus, are very similar, identical in some cases, to the regulatory sequences possessed by RAG1. He also cites the fact that EBV infections activate the expression of RAG1/2 and that when the virus excises from host DNA it forms a circle, much in the same way intervening sequences form circular intermediates during V(D)J recombination. And both RAG1 and the ICP-8 protein of EBV have DDE metal ion binding motifs important for cleavage of target DNA despite the fact they do not possess any significant primary sequence identity. Dreyfus says that despite the sequence similarity between the RAG1 core and Transib transposases there is the problem of the RAG1 amino terminus which is not similar. He also states that during the evolution of the proto-RAG1 there would be no selective benefit to the expression of a Transib element in proto-immune cells and that the antigenic effects of some herpes-virus proteins would provide a reason for the selective maintenance of an inserted herpes-like element. Also, no autonomous “RAG transposon” has been found in nature yet and neither has an element been found encoding a RAG2 homolog which is required for V(D)J recombination to occur.

The regulatory similarities between EBV and RAG1 are interesting but I think the answer as to the probable origin of RAG is pretty clear. The fact that both ICP-8 and RAG1 possess the DDE catalytic motif is not evidence of common ancestry as this motif evolved multiple times independently in several DNA transposon superfamilies, including Transib, and in proteins like RNase H and the Argonaute component of RISC. DNA transposons forming circles as intermediates is not unknown and a good example I read of recently are the TEs in ciliates that seem to be involved in the drastic chromosomal rearrangement of those species. Dreyfus did not put any sequence alignment diagrams in his paper because ICP-8 and RAG1 could not be aligned while Kapitonov and Jurka (2005) were able to align the Transib transposase and RAG1 and show their significant similarity. The so-called “ amino terminus problem” really isn’t a problem at all because last year Panchin and Moroz (2008) published a paper where they found a Chapaev superfamily DNA transposon, N-RAG, from the mollusc Aplysia californica whose transposase had significant similarity to the “ problematic” N terminus of RAG1. This paper is not cited by Dreyfus. It turns out RAG1 might actually be derived from two separate DNA transposons, not just one. As for the maintenance problem because TEs are selfish and can proliferate even at a fitness cost to the host there really is no need to explain why the proto-RAG1 transposon could persist.

The story is not over for RAG1 though. I agree with Dreyfus that the issue of where the RAG2 gene came from needs to be addressed as well as trying to flesh exactly how the evolutionary process proceeded from an autonomous DNA transposon to modern day RAG.

Dreyfus, D.H. 2009. Paleo-immunology: evidence consistent with insertion of a primordial herpes virus-like element in the origins of acquired immunity. PLoS One 4: e5778.

Kapitonov, V.V. and J. Jurka. 2005. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biology 3: e181.

Klobutcher, L.A. and G. Herrick. 1997. Developmental Genome Reorganization in Ciliated Protozoa: The Transposon Link. In Progress in Nucleic Acid Research and Molecular Biology (eds. E. Cohn and K. Moldave), pp. 1-62. Academic Press.

Panchin, Y. and L.L. Moroz. 2008. Molluscan mobile elements similar to the vertebrate Recombination-Activating Genes. Biochemical and Biophysical Research Communications 369: 818-823.

Friday, June 12, 2009

TEs and Macroevolution

I'm going to discuss two papers that were recently released electronically by the journal BioEssays, both having to do with TEs and macroevolution. The first, by Oliver and Greene (2009), came to my attention last month when I read a horrible press release that has become the norm in science journalism these days. I recently got my hands on the paper in question and after reading it was relieved to see it wasn't nearly as bad as I thought it was going to be. However, it certainly wasn't the earth-shattering, paradigm-shifting, gift from the heavens for evolutionary biology that the press release made it out to be. It did however elaborate on and articulate some interesting ideas that have only been mentioned briefly, if at all, in the TE literature.

First they detail the effects TE can have on organisms and species by the varied and numerous kinds of mutations they can cause which introduce variability. Next they briefly discuss that the mutagenic potential of TEs might be harmful to the individual but at the population and species level this could actually translate into a higher capacity to evolve via greater variability. Basically they are mentioning a form of multi-level selection. In theory, lineages with TEs which are actively causing new mutations through insertions, ectopic recombination and other mechanisms will have higher genetic variability than those whose TEs are mostly inactive or suppressed.

Examples of this might be things like the tuatara or the coelacanth ,whose genomes are either composed of little TE DNA or their elements have been silenced either through host-level selection or through stochastic events at the level of both the host and the elements. The authors also discuss the activity of TEs in the germline and the regulatory changes that can take place due to this activity through TEs perturbing methylation and chromatin patterns. Stress induced TE activity is also mentioned as well as the fact that one of the few examples of an organism that has almost completely reigned in it's TEs, the fungus Neurospora crassa via repeat-induced point mutation, has also crippled it's ability to evolve new genes by gene duplication because these are recognized in the same manner as TEs and mutated into oblivion.

Overall I found this paper interesting but there were a few notable flaws. In the discussion about N. crassa and its apparent evolutionary disadvantage by mutating multi-copy DNA the authors seem to imply that other species allow TEs to be active because this is selectively beneficial at higher levels. Evolution does not work this way. Selection at the host-level would never favour any mutations which allowed TEs to be active simply because the variation they cause could be beneficial to the lineage or group that species belongs to. TEs and the host genomes they inhabit are locked in a co-evolutionary arms race where selective pressures on the TEs favour elements which can slip free of the suppressive bonds the host imposes on them, while in turn pressure at the level of the host favours individuals who can suppress TEs as effectively and efficiently as is possible. TEs are never allowed to transpose. Any species which allowed TEs to transpose probably does not exist anymore because it went extinct, along with its complement of elements. Similarly, they talk of TEs being permitted to transpose in the germline where they will do the least harm to the organism and contribute to genetic variation. I don't think they did this intentionally but it weakens their overall argument when they lapse into explanations such as these. They also fall into the classic " looks like TEs aren't junk DNA after all" trap and refer to them as "helpful parasites" several times throughout the paper. To repeat again: no species keep TEs around because they are beneficial. While it could be true that lineages which possess active TEs have a greater capacity for evolvability, it is next to impossible that TEs are maintained by host-level selection for their variation inducing qualities. You don't need to invoke that to explain the presence of TEs.

The second paper is along the same lines and expands upon something that was brought up by Oliver and Green. Zeh et al. (2009) deals with punctuated equilibria, TEs and the epigenetic alterations they can cause. Epigenetics is basically gene regulation but in the paper what the authors mean is things like methylation patterns, chromatin remodelling and RNA interference, or the more recently popularized and charismatic forms of gene regulation. The heart of this paper is the “epi-transposon hypothesis” put forth by the authors as an explanation for the punctuated evolutionary events often seen in the fossil record:

1) TEs become active during stressful events such as the colonization of new habitats or climate change etc.
2) TE activity causes mutations via disruptive insertions, chromosomal rearrangements, epigenetic alterations etc.
3) These mutations can push a species out of a local adaptive peak into another higher one in a short period of time

The authors propose that during periods of stasis TEs are kept relatively silent by epigenetic silencing and other control mechanisms of the host. Stress or the invasion of a new habitat perturbs these controls, TEs run wild and muck things up and can cause these punctuated events that can lead to rapid speciation. They cite several examples of bursts of TE activity coinciding with the diversification of various taxa such as haplochromid cichlids, mammals in general and bats.

I think they are right that bursts of TE activity could be contributing to punctuated events, in conjunction with the isolation of populations. The question is the frequency with which punctuated events are generated by TEs and not something like polyploidy. Seeing this paper and writing this blog post also prompted me to actually go read the gigantic Eldredge and Gould paper of 1972 where they explain punctuated equilbria.

These are both important papers in the sense that they are potentially bringing these sorts of issues to the attention of the TE community at large. It would just be nice if they weren’t tied to horrendous press releases and tired and incorrect statements about how because some TE mutations might be beneficial this means they aren’t selfish or junk. Maybe someday.

Oilver, K.R. and W.K. Greene. 2009. Transposable elements: powerful facilitators of evolution. BioEssays: DOI 10.1002/bies.200800219.

Zeh, D.W., J.A. Zeh, and Y. Ishida. 2009. Transposable elements and an epigenetic basis for punctuated equilibria. BioEssays: DOI 10.1002/bies.200900026.

Wednesday, June 10, 2009

Greetings all, and welcome to The Mobilome, my new blog venture. I’ve been musing about creating a TE-devoted blog for a while now because they don’t seem to be well represented in the blogosphere. The goal of this blog is to spread the word about how cool TEs and other parasitic nucleic acids are by talking about interesting elements, papers both old and new and perhaps some educational posts about what TEs in general and why they are important to understand. I’m going to assume most people reading this blog, if any do, will be familiar with TEs so I won’t go into detail off the bat about TE basics.

I am T.E. and I find TEs fascinating. I’m a graduate student at the University of Guelph in Ontario, Canada where I’m doing my Masters. I’m co-supervised by Dr. Teresa Crease and Dr. Ryan Gregory and my project involves a type of TE called Pokey found in freshwater crustaceans called Daphnia, or water fleas. I might say more about my project in the future and I’ll certainly tell you more about Pokey and why I think it is one of the most interesting TEs you could choose to study for a number of reasons.

So what are TEs exactly you ask? TEs are selfish, mobile pieces of DNA that inhabit the genomes of both prokaryotes and eukaryotes like tiny little parasites. I’ll be covering the classic TEs like DNA transposons and retrotransposons but I also plan to write some posts on some more obscure or less popularized types of parasitic nucleic acids as well.

What about the blog title you ask? Mobilome is a word that was coined, I believe and correct me if I am wrong, in a paper by Frost et al. (2005) to describe the collection of mobile genetic elements which inhabit the genomes of eubacteria and archaebacteria. It was further fleshed out in a book chapter by Janet Siefert (2009) where the different constituents of the mobilome were outlined. I’m merely extending it to describe the mobile DNA found in all forms of life.

Check back soon J

Frost, L.S., R. Leplae, A.O. Summers, and A. Toussaint. 2005. Mobile genetic elements: the agents of open source evolution. Nature Reviews Microbiology 3: 722-732.

Siefert, J.L. 2009. Defining the Mobilome. In Horizontal Gene Transfer: Genomes in Flux (eds. M.B. Gogarten J.P. Gogarten J. Peter, and L.C. Olendzenski). Humana Press.

Tuesday, June 2, 2009

In the beginning....

Welcome all to the inaugural post of The Mobilome, the transposable element-related blog of yours truly T.E. With those initials it seems I'm destined to inform the world about the wonderful little pieces of DNA known as transposable elements (TE). What are TEs you might ask? Well, all shall be revealed soon in an up-coming introductory post. Stay tuned.....