Comments on: Sea urchin immune systems

By: Science letter roundup | Mystery Rays from Outer Space

Science letter roundup | Mystery Rays from Outer Space — Fri, 24 Jul 2009 16:27:58 +0000

[...] Sea urchin immune systems [...]

By: Mystery Rays from Outer Space - Meddling with things mankind is not meant to understand. Also, pictures of my kids » Same trip, different routes: Lamprey immunity

Sun, 02 Dec 2007 17:12:06 +0000

[...] there. Sea urchins (which have a common ancestor with lampreys) have molecules that are much like RAG. Lampreys have cells that are very lymphocyte-like.2 These cells accumulate in a region that looks [...]

By: Mystery Rays from Outer Space - Meddling with things mankind is not meant to understand. Also, pictures of my kids » Invertebrate memory, or wishful thinking?

Thu, 25 Oct 2007 13:30:22 +0000

[...] adaptive immune system have been pushed back further back in time (e.g. the identification of RAG in sea urchins); and on the other, invertebrate immune systems are looking much more complex than previously [...]

By: Suicyte

Suicyte — Tue, 04 Sep 2007 22:28:48 +0000

I like to re-analyze topics like these, and I am a pathological skeptic when it comes to claims of non-obvious sequence similarity (unless they are my own…). I must say that I liked the Kapitonov paper a lot, very neat work. By the way, the similarity between the transib transposons and the Rag1 family is relatively easy to spot if you start from the transposons, but next to impossible if you start with Rag1.

It is also interesting to note that the significance of similarity between the insect transposons and the sea urchin sequence is seven (!) orders of magnitude higher than that between the transposons and vertebrate Rag1. While this – by itself – doesn’t tell nothing about the evolutionary branching pattern, I am nevertheless quite certain that the sea urchin “Rag1″ would behave more like a transposon than like a true vertebrate style Rag1/2 system.

Nevertheless, a very interesting topic.

By: iayork

iayork — Tue, 04 Sep 2007 11:45:58 +0000

First, there is no doubt that sea urchins have something that looks a lot like Rag1. … To me, they look like remnants of transposons.

I have to admit that I didn’t spend a lot of time running comparisons on Fugmann’s lineups. The transposon problem was just too much for me. Of course, RAGs are believed to be derived from transposons, so as you found there’s a huge amount of “noise” in searches – not real noise, because they’re genuine matches, but I’m not good enough to separate out things that are “just” transposons from things that are RAG-like transposons. I ran a quick look, and said to myself, Well, they know more than I do. But maybe it was as much an inspired guess as it was advanced knowledge!

By: Kay

Kay — Mon, 03 Sep 2007 15:24:33 +0000

I think that Fugmann et al were extremely optimistic and also very lucky. I had a look at the bioinformatical situation, and must say that on the basis of that alone, I never would have started experiments to see if SpRag1 binds to SpRag2. In their description of the bioinformatical situation, it all looks rather straightforward, but I am not at all convinced. Here is why:
First, there is no doubt that sea urchins have something that looks a lot like Rag1. But so does Nematostella, which is a sea anemone and VERY distant from vertebrates, and probably also other cnidarians. The N-terminal domain of Rag1 seems even older, I have seen ESTs from sponges and other very distant invertebrates. SpRag1 looks more closely related to the nematostella sequences than to the vertebrates. What’s more: there are many pseudogenized copies in the sea urchin and the nematostella genomes. To me, they look like remnants of transposons.
With regard to SpRag2, I see even more problems. I agree with the authors, that this protein has some vaguely KELCH-like repeats and also some vaguely PHD-like finger at the C-terminus. However, neither the KELCH-like propeller region nor the PHD-like region look anything like vertebrate Rag2. If SpRag2 and vertebrate Rag2 are really distant orthologs, I would have expected so see at least some similarity that would go beyond the similarity to any other Kelch or PHD protein. This is not the case. Thus, I would never have guessed that SpRag2 really is a Rag2 and would do something together with Rag1. But, apparently, this seems to be the case. Congratulations! Fugmann 1, me 0.