Lampreys not as weird as once thought.

[Petrel]

Zhang, G.; Miyamoto, M.; Cohn, M. "Lamprey type II collagen and Sox9 reveal an ancient origin of the vertebrate collagenous skeleton." Proceedings of the National Academy of Sciences of the United States of America, 2006, 103, 3180-3185.

Gnathostomes (jawed vertebrates) all possess cartilege with type II collagen the major matrix protein. Previously it has been thought that the lampreys and hagfish, jawless fish that branched off the vertebrate lineage before the evolution of the jaw, did not possess type II collagen, instead using mainly lamprin or myxinin respectively. This conclusion was at odds with 19th century comparative anatomy findings which showed lampreys have hyaline cartilege. The authors of this paper decided to examine this by looking for the Col2a1 gene (that's Col2-alpha-1) that codes for type II collagen and the Sox transcription factor that controls type II collagen expression.

A PCR screening turned up not one, but two type II collagen genes which produced proteins 80% identical in sequence to mouse type II collagen. These were named Col2a1a (Col2-alpha-1a) and Col2a1b (Col2-alpha-1b). They next used whole-mount in situ hybridization to detect gene transcription during embryo development. This complicated technique uses a probe to bind to RNA of the desired sequence, an antibody to bind to the probe, and a dye to bind to the antibody. At the end the lamprey embryo is dyed blue where the Col2a1a or Col2a1b is being expressed. They discovered that these genes are expressed regionally in the embryo.

Histological sections showed that Col2a1a transcripts in the somites were localized ventromedially to the sclerotome, which gives rise to the axial skeleton, and dorsolaterally to the dermatome, which gives rise to the dermis (Fig. 2B). In the midline, lamprey Col2a1a expression was observed in the floor plate of the neural tube and in the hypochord, but not in the notochord (Fig. 2B). This pattern represents a subset of the zebrafish Col2a1 expression pattern, which occurs along the midline in three domains, the floor plate, notochord, and hypochord (24). The second lamprey orthologue, Col2a1b, was expressed in a pattern similar to Col2a1a along the anteroposterior axis and in the midline; however, Col2a1b transcripts also localized to the notochord and to endoderm immediately ventral to the hypochord (Fig. 2 C and D).

Wish you could see the pictures. . .

Next they used anti-Col2a1 antibody to determine that Col2a1 is widespread in the cartilagenous skeleton of adult lampreys.

Having confirmed that type II collagen is produced in lampreys, they next checked to see if the transcription factor Sox9 was present. PCR tests showed that it was, and transcription studies showed that Sox9 mimicked Col2a1 in expression during development.

In addition to demonstrating that type II collagen is probably a distinguishing characteristic of vertebrates, this study also demonstrates how gene duplication and modification of the genes can result in protein specialization for various tasks.

Our molecular phylogenetic analyses of fibril A collagens lead us to conclude that Col1 to Col5 duplicated before the speciation of lampreys and jawed vertebrates. Thus, one prediction of our phylogenetic results is that future studies will recover lamprey orthologues of Col1, Col3, and/or Col5, which should join at the bases of their respective gnathostome clades in the fibril A collagen tree (Fig. 1). An independent duplication of the Col2a1 gene then occurred in the lamprey lineage. The expression patterns of Col2a1a and Col2a1b suggest that subfunctionalization followed this duplication of the ancestral Col2a1 gene, with the ancestral expression pattern being partitioned between Col2a1a and Col2a1b. Force and colleagues (28, 29) proposed a mechanism by which duplicated genes are preserved during evolution by subfunctionalization, in which the combined expression patterns of both duplicated genes equal that of their single ancestral gene. Our finding that the expression domains of Col2a1a and Col2a1b in lampreys correspond to that of the single Col2a1 gene in jawed vertebrates is consistent with their duplication-degeneration-complementation model.

It is also noteworthy that collagen genes are physically linked to the Hox clusters in gnathostomes (6, 30). In lampreys, there are at least three Hox clusters (31–33). Our identification of two Col2a1 genes supports the suggestion that one of their three Hox clusters may have arisen by an independent duplication in the lamprey lineage (31–33). If type A fibril collagens are linked with Hox clusters in all chordates, then based on the presence of a single Hox cluster in amphioxus, we predict that (barring tandem duplications) cephalochordates may possess a single type A fibril collagen gene.

If anyone can tell me a way to make Greek characters appear in my posts I would be grateful. Perhaps I should ask the pastors on the board, I believe I saw someone posting Greek before. . .

 

[Deacon]

Originally posted by Petrel:
If anyone can tell me a way to make Greek characters appear in my posts I would be grateful. Perhaps I should ask the pastors on the board, I believe I saw someone posting Greek before. . .

Often it's a problem of not having the necessary fonts installed.
Basic Greek for scientific notation can be located by finding "insert; then tabbing symbols" in some word processing programs.

Google up "Greek fonts"
Here's a good site to download a few (you don't need to pay money for the basic ones).
http://www.ntgateway.com/greek/fonts.htm

Typing in Greek is a bit more problematic---
I've found that the easiest way is to cut and paste what you need into the message realizing that computers without the fonts will not be able to decipher the message.

Rob

 

[npc]

A couple of questions:
Why was it thought that lampreys had no type II collagen despite the anatomy findings (they lacked a recognizable gene for it?)
Also, regarding the gene specialization: is there any particular reason not to just deactivate one of the duplicate genes?

As for Greek letters, I disagree that it is a font issue; most fonts include Greek letters. As Deacon said, you could copy and paste from a word processor or your sources.
If you often want to use Greek letters, you could turn on the language bar to switch between American and Greek keyboard layouts. ( Windows XP instructions)

 

[Petrel]

I think this was not realized because when scientists analyzed lamprey and hagfish cartilage before they found the primary ingredients were lamprin and myxinin. They probably just did not go looking for the collagen.

It hasn't been very long that we've been able to do genetic analysis, so this is probably the first time we've gotten around to poking around in the lamprey and hagfish genome.

Regarding gene duplication, I don't think it can really be thought of like that. The lamprey doesn't think to itself, "Now I have this extra copy of my collagen gene, maybe I should turn it off." When a gene is duplicated the duplicate's fate depends largely upon chance. If one copy is hit by a mutation deactivating it early enough, that copy may persist as a pseudogene while the other copy carries on with the work. If both copies persist then a mutation may tone down gene transcription, which could be beneficial if down-regulation of the extra transcription is necessary. It may be that having multiple copies of the gene (such as for histones or rRNA) is beneficial because so much of that product is needed, and in this case selection might work against down-regulation. Or we can see what happened in this case (as with the original hemoglobin gene)--copying followed by mutation causes multiple variations of the protein to arise, and selection pressures can cause specialization of the new proteins for various chores.

 

[Petrel]

I found a way for you to see the pictures! This page discusses this article in more length and also provides the key photograph and figures.

 

[Daisy]

Well, they may not be unique, but I still find them weird.

Are you a Peez fan?

 

[Petrel]

Peez?? I might be, but if I am I don't know!

 

[Daisy]

P.Z.Meyers, commonly known as Peez - pharyngula, the science website you linked to, is his.

 

[Petrel]

I'm just a little late responding!

I'd actually never read it before. I was just searching for some background on lampreys and ran across it.